Lecture 1

Life has a Hierarchical Order, that is each level of biological structure builds on the level below it.

Atoms (carbon)

Complex Biological Molecules (hemoglobin)

Subcellular Organelles (mitochondria)

Cells (neurons)

Tissues (nervous tissue)

Organs (brain)

Organ systems (nervous system)

Complex Organisms (insects, birds, mammals)


Emergent properties = Properties that emerge as a result of interactions between components.

Holism = The principle that a higher level of order cannot be completely explained by examining component parts in isolation.

Reductionism = The principle that a complex system can be understood by studying its component parts.

Cell Biology

The cell is an organism’s basic unit of structure and function.

Prokaryotic cells are cell that lack membrane-bound organelles and a membrane-enclosed nucleus

e.g. bacteria

Eukaryotic cells are cells with a membrane-enclosed nucleus and membrane-enclosed organelles.

e.g. Pants and animals


The Scientific Process

Hypothesis = educated guess proposed as a possible answer to a specific question or problem.

A hypothesis is often formulated by inductive reasoning, that is making an inference from a set of specific observations to formulate a general conclusion.

Use deductive reasoning to make predictions from the hypothesis and then test the validity of those predictions. Deductive reasoning is making an inference from general premises to specific consequences which logically follow if the premises are true.

Usually involves If...then logic.


Variable = condition of an experiment that is subject to change.

Control Group = the group in which all variables are held constant.

Experimental Group = the group in which one factor is varied.



Lecture 2 Chapter 2

Chemical Elements and Compounds

Matter consists of chemical elements in pure form and in combinations called compounds.

Matter = anything that takes up space and has mass.

Mass = a measure of the amount of matter an object contains.

Weight vs. Mass---weight takes into account the effects of gravity.

Element = a substance that cannot be broken down into other substances by chemical reactions.

All matter is made of elements.

92 naturally occurring

25 are essential to life

C = Carbon

O = oxygen

H = hydrogen

N = nitrogen

Trace element = element required by an organism in very small amounts

Compound = a pure substance composed of 2 or more elements combined in a fixed ratio, i.e. NaCl


Atoms and Molecules

Atomic structure determines the behavior of an element.

Atom = smallest possible unit of matter that retains the physical and chemical properties of its element.

Atoms are made up of subatomic particles

Subatomic particles

Neutrons = no charge 1.009 Dalton

Protons = +1 1.007 Dalton

Electrons = -1 1/2000 Dalton

Dalton = 1.67 X 10-24 grams

Atomic number = number of protons in an atom of a particular element.

All atoms of an element have the same atomic number

Written as subscript e.g. 11Na

In electrically neutral atoms the number of protons = the number of electrons.

Mass number = number of protons and neutrons in an atom.

Written as superscript e.g. 23Na

Approximately equal to the mass of the whole atom.

Number of neutrons = mass number-atomic number

Can be different than the atomic weight which is the weighted mean of the masses of all of the element’s isotopes.

Isotopes = atoms of an element that have the same atomic number but different mass numbers

They have the same number of protons but different number of neutrons.

Different isotopes of the same element react chemically in the same way.

Some isotopes are radioactive.

Radioactive isotopes = unstable, the nucleus spontaneously decays emitting subatomic particles and/or energy as radioactivity.

Radioactive decay can change one element into another if it results in a change in the number of protons.

N---> P + e-

Half life = time for 50% of radioactive atoms in a sample to decay.

Radioactive decay occurs at a fixed rate.

Carbon dating can determine the age of fossils by comparing the ratio of 14C to 12C.

Radioactive tracers

Radiation damage

Cancer treatment

Electrons = Very low mass negatively charged particles that orbit the nucleus.

Electrons are the only subatomic particles that participate in chemical reactions.

Electrons have potential energy because of their position relative to the nucleus.

Energy = ability to do work

Potential energy = energy stored because of its position.

potential energy of electrons exists in discrete amounts called quanta. This is because electrons reside in discrete energy levels or electron shells.

The closer to the nucleus the less energy.

Orbitals = three-dimensional space where an electron will most likely be found.

No more than two electrons can occupy the same orbital.

Electron configuration = distribution of electrons in an atom’s electron shells. This determines the chemical behavior.

Chemical properties of an atom depend on the number of valence electrons = electrons in the outermost energy shell (valence shell).

Octet rule = is that a valence shell is full when it has 8 electrons.

An atom with a complete valence shell is unreactive or inert, e.g. noble elements.

Atoms with incomplete valence shells are chemically reactive, and atoms with the same number of valence electrons tend to show similar chemical characteristics.



Chemical Bonds

Covalent bonds = chemical bond between atoms formed by sharing a pair of valence electrons.

Polar and nonpolar covalent bonds

Electronegativity = atom’s ability to attract and hold electrons.

Nonpolar covalent bond = bond formed by equal sharing of electrons between atoms.

Polar covalent bond = bond formed by an unequal sharing of electrons.

Ionic bond = bond formed by the electrostatic attraction after the complete transfer of an electron from a donor atom to an acceptor atom.

Ion = Charged atom or molecule

Anion = negatively charged ion, has more electrons than protons.

Cation = positively charged ion, has more protons than electrons.

Weak Chemical Bonds

Hydrogen bonds = bond formed by the charge attraction when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom.

1/20 the strength of covalent bonds

Van der Waals interactions are weak interactions that occur between atoms or molecules that are very close together and are due to charge asymmetry in electron clouds.

The biological function of molecules depend on their molecular shape.

Chemical reactions = process of making and breaking chemical bonds leading to changes in the composition of matter.

Reactants undergo changes into products

Matter is conserved

Most reactions are reversible

Reaction rate is dependent on the concentration of reactants and products (the higher the concentration the faster the rate)

Chemical equilibrium = when the rate of forward reaction equals the rate of the reverse reaction. That is the concentration of reactants and products stops changing (doesn’t mean that the concentration of products and reactants are equal).

Lecture 3 Chapter 3


Life on earth probably evolved in water.

Living cells are 70-95% H2O.

Water covers 3/4 of the earth.

Water naturally exists in all three physical states of matter--solid, liquid, and gas.

The polarity of water molecules results in hydrogen bonding.

Polar bonds and asymmetrical shape give water molecules opposite chares on opposite sides.

Hydrogen bonding imparts a higher level of structural organization to water.

Each water molecule can form a maximum of 4 hydrogen bonds with neighboring water molecules.

Fig 3.1

Polarity and hydrogen-bonding impart special properties to water.


Resists changes in temperature

High heat of vaporization and cools surfaces as it evaporates

Expands when it freezes

Versatile solvent

Cohesion = phenomenon of a substance being held together by hydrogen bonds---gives water more structure than other liquids.

Surface tension = measure of how difficult it is to stretch or break the surface of a liquid.

Air/water interface

Causes water to bead

Heat and Temperature

Kinetic energy = the energy of motion

Heat = total kinetic energy due to molecular motion in a body of matter.

Temperature = measure of heat intensity due to the average kinetic energy of molecules in a body of matter.

Calorie (cal)= amount of heat it takes to raise the temperature of one gram of water one degree Celsius, also the amount of heat that one gram of water releases when it cools by one degree Celsius.

Kilocalorie (Kcal or Cal) =1000 cal

Water has a high specific heat, that is it resists temperature changes when it absorbs or releases heat.

Specific heat = amount of heat that must be absorbed or lost for one gram of a substance to change its temperature by one degree Celsius.

Specific heat of water = 1 cal per gram per degree Celsius (1 cal/g/oC

Evaporative cooling

Vaporization (evaporation) = transformation from liquid to gas.

Heat of vaporization = quantity of heat a liquid must absorb for 1 gram to be converted to the gaseous state.

Water has a high heat of vaporization at the boiling point due to hydrogen bonding.

(540 cal/g or 2260 J/g; Joule = 0.239 cal)

Evaporative cooling = cooling of a liquid’s surface when a liquid evaporates.

Water density

Water is most dense at 4oC

Water contracts as it cools to 4oC

As water cools from 4oC to freezing 0oC, it expands and become less dense due to hydrogen bonding--therefore ice floats

Fig 3.5

Water as a solvent

Solution = a liquid that is a completely homogenous mixture of 2 or more substances

Solvent= dissolving agent of a solution

Solute = substance dissolved in a solution

Aqueous solution = solution in which water is the solvent

Water is a versatile solvent because of the polarity of the water molecule.

Ionic and most polar compounds dissolve in water.

Non-polar compounds are not water soluble

Ionic and polar substances are hydrophilic, but nonpolar compounds are hydrophobic.

Hydrophilic = water loving (some large hydrophilic molecules can absorb water without dissolving).

Hydrophobic = water fearing, not water soluble.

Fig 3.7

Fig 3.8

There are 2 important quantitative properties of aqueous solutions: solute concentration and pH.

Molecular weight = sum of the weight of all atoms in a molecule (expressed in daltons)

Mole = amount of a substance that has mass in grams numerically equivalent to its molecular weight in daltons. All substances have the same number of molecules in a mole = 6.02 X 1023 (Avogadro’s number).

Molarity = number of moles of a solute per liter of solution.

Dissociation of water

Occasionally, the hydrogen atom that is shared in a hydrogen bond with 2 water molecules can be transferred.

Only a hydrogen ion (proton +1 charge) is transferred, the electron stays behind.

Creates a hydronium ion (H3O+) and a hydroxide ion (OH-).

H2O + H2O H3O+ + OH-

Fig 3.UN1

By convention, ionization of H2O is expressed as the dissociation into H+ and OH-. H2O H+ + OH-

This reaction is reversible, and at equilibrium most H2O is not ionized.

Acid and Bases

At equilibrium in pure water at 25 oC

The number of H+ = the number of OH-

[H+] =[OH-] = 1/10,000,000 or M= 10-7 M

Therefore very few molecules are dissociated (only 1 of 554,000,000).

Acid = substance that increases the relative concentration of H+ of a solution.

Base = substance that reduces the relative concentration of H+ of a solution.

A solution in which:

[H+] = [OH-] is neutral

[H+] > [OH-] is acidic

[H+] < [OH-] is basic

Strong acids and bases dissociate completely in water

e.g. HCl and NaOH.

i.e. HCl H+ + Cl-

Weak acids and bases dissociate on partially and reversibly

e.g. NH3 (ammonia) and H2CO3 (carbonic acid)

pH Scale

In any aqueous solution [H+]X[OH-] = 1.0 X 10-14

In a neutral solution both = 10-7 M

In a basic solution where [H+] = 10-9 M, the [OH-] = 10-5

In a acidic solution where [H+] = 10-5 M, the [OH-] = 10-9

pH scale = scale used to measure degree of acidity (ranges from 0 to 14)

pH = negative log10 of the [H+] expressed in moles per liter.

pH of 7 is neutral

pH < 7 is an acid solution

pH > 7 is a basic solution

Most biological fluids are within the pH range of 6 to 8 (some exceptions e.g. stomach acid with a pH of 1.5)

Each pH unit represents a tenfold difference (scale is logarithmic), so a small change in pH represents a large change in actual [H+].

Fig 3.9


Buffer = substance that minimizes large sudden changes in pH---helps organisms maintain the pH of body fluids within a narrow range.

Buffers are combinations of H+ donor and H+ acceptor forms in a solution of weak acids or bases.

They work by accepting H+ ions from a solution when they are in excess and by donating H+ ions to the solution when they have been depleted.

e.g. Bicarbonate buffer

H2CO3 HCO3- + H+

H+ donor H+ acceptor Hydrogen ion

(weak acid) (weak base)

Lecture 4 Chapter 4


Organic chemistry is the branch of chemistry that specializes in the study of carbon compounds.

Organic molecules are molecules that contain carbon.

The carbon atom

Has an atomic number of 6; therefore has 4 valence electrons.

4 valence electrons means that carbon completes its outer energy shell by forming 4 covalent bonds.

The tetravalent electron configuration makes large, complex molecules possible, with the carbon atom at a central point from which the molecule brances off in 4 directions.

This electron configuration also gives carbon covalent compatibility with many different elements.

The 4 major atomic components of organic molecules are:

Hydrogen Valence of 1

Oxygen Valence of 2

Nitrogen Valence of 3

Carbon Valence of 4

Fig 4.2

The electron configuration of carbon determines the molecule’s three-dimensional shape. Three-dimensional shapes are important to function.

Fig 4.3

Variations in carbon skeletons contribute to the diversity of organic molecules.

Covalent bonds link carbon atoms together in long chanins that form the skeletal framework for organic molecules. These vary in:


Shape (straight chain, branched, rings)

Number and location of double bonds

Other elements covalently bonded to available sites

Fig 4.4

Hydrocarbons = molecules containing only carbon and hydrogen

Fossil fuels

Diverse in lengths and shapes

Hydrocarbons are hydrophobic because of nonpolar bonds, C-C and C-H

Isomers are compounds with the same molecular formula but with different structures and hence different properties.

There are 3 types of isomers:

Structural isomers = isomers that differ in the covalent arrangement of their atoms. Number of possible isomers increases as the carbon skeleton size increases.

Geometric isomers = isomers which share the same covalent partnerships but differ in their spatial arrangements. This is due to the fact that double bonds will not allow the atoms they join to rotate about the axis of the bonds.

Enantiomers = isomers that are mirror images of each other. Can occur when four different atoms or groups of atoms are bonded to the same carbon (asymmetric carbon). There are 2 different spatial arrangements. Often one form is biologically active and the other is not.

Fig 4.6

Fig 4.7

Functional groups

Functional groups also contribute to the molecular diversity of life.

Small characteristic groups of atoms (functional groups) are frequently bonded to the carbon skeleton of organic molecules. These functional groups:

Have specific chemical and physical properties

Are the regions of organic molecules that are chemically reactive.

Behave consistantly from one organic molecule to another.

Determine the unique chemical properties of organic molecules in which they occur.

These molecules can be viewed as hydrocarbon derivatives with functional groups in place of H, bonded to carbon at various sites along the molecule.

Hydroxyl group = a functional roup that consists of a hydrogen atom bonded to an oxygen atom, which in turn is bonded to carbon (-OH).

It is a polar group, the bond between the oxygen and hydrogen is a polar convalent bond.

Polarity makes the molecule to which it is attached water soluble.

Organic compounds with hydroxly groups are called alcohols.

Carbonyl group = functional group that consists of a carbon atom double-bonded to oxygen (-CO)

It is a polar group, water soluble

Is a functional group found in sugars

If the carbonyl is at the end of the carbon skeleton, the compound is an aldehyde--if in another region of the skeleton it is a ketone.

Carboxyl group = functional group that consists of a carbon atom which is both double-bonded to an oxygen and single-bonded to the oxygen of a hydroxyl group (-COOH)

Polar and water soluble. The convalent bond between oxygen and hydrogen is so polar that the hydrogen reversibly dissociates as H+. The polarity results from the combined effect of the 2 electronegative oxygen atoms bonded to the same carbon.

Since it can donate protons (H+ ions), this group is acidic, and these compounds are called carboxylic acids.

Amino group = functional group that consists of a nitrogen atom bonded to two hydrogens and to the carbon skeleton (-NH2)

Polar and water soluble

Acts as a weak base because the nitrogen can accept a proton (H+).

These compounds are called amines

Sulfhydryl group = functional group that consists of an atom of sulfur bonded to an atom of hydrogen (-SH).

Helps stabilize the structure of proteins (disulfide bridges)

These compounds are called thiols.

Phosphate group = functional group which is the dissociated form of phosphoric acid (H3PO4)

Loss of 2 protons (H+) by dissociation leaves the phosphate group with a negative charge.

Has acid properties since it donates protons

Polar and water soluble

Organic phosphates are important in cellular energy storage and transfer (e.g. ATP).

Methy group = functional group that consists of a carbon bonded to 3 hydrogen atoms.

Nonpolar and not water soluble



Lecture 5 Chapter 5

Polymer Principles

Most macromolecules are polymers

Polymer = (Poly = many; mer = part); large molecule consisting of many identical or similar subunits connected together.

Monomer = Subunit or building block molecule of a polymer

Macromolecule = (Macro = large); large organic polymer

Formation of macromolecules from smaller building block molecules represents another level in the hierarchy of biological organization.

There are four classes of macromolecules in living organisms:




Nucleic acids

Most polymerization reactions in living organisms are condensation reactions.

Polymerization reactions = Chemical reactions that link two or more small molecules to form larger molecules with repeating structural units.

Condensation reactions = Polymerization reactions during which monomers are convalently linked, producing net removal of a water molecule for each covalent linkage.

One monomer loses a hydroxyl (-OH), and the other monomer loses a hydrogen (-H)

Removal of water is actually indirect, involving the formation of "activated" monomers (discussed in Chapter 6, Introduction toMetabolism).

Process requires energy.

Process requires biological catalysts or enzymes.

Fig 5.2

Hydrolysis = (Hydro = water; lysis = break); a reaction that breaks covalent bonds between monomers by the addition of water molecules.

A hydrogen from water bonds to one monomer, and the hydroxyl bonds to the adjacent monomer.

Fig 5.2

Example: Digestive enzymes catalyze hydrolytic reactions which break apart large food molecules into monomers that can be absorbed into the bloodstream.

An immense variety of polymers can be built from a small set of monomers

Structural variation of macromolecules in the basis for the enormous diversity of life.

There is unity in life as there are only about 40 to 50 common monomers used to construct macromolecules.

There is diversity in life as new properties emerge when these universal monomers are arranged in different ways.


Carbohydrates: Fuel and Building Material

Sugars, the smallest carbohydrates, serve as fuel and carbon sources

Carbohydrates = Organic molecules made of sugars and their polymers

Monomers or building block molecules of carbohydrates are simple sugars called monosaccharides.

Polymers are formed by condensation reactions.

Carbohydrates are classified by the number of simple sugars.

Monosaccharides = (Mono = single; sacchar = sugar); simple sugar in which C, H, and O occur in the ratio of (CH2O).

Fig 5.3

Are major nutrients for cells; glucose is the most common

Can be produced (glucose) by photosynthetic organisms from CO2, H2O, and sunlight

Store energy in their chemical bonds which is harvested by cellular respiration

Their carbon skeletons are raw material for other organic molecules

Can be incorporated as monomers into disaccharides and polysaccharides

Characteristics of a sugar:

An —OH group is attached to each carbon except one, which is double bonded to an oxygen (carbonyl).

Aldoses (aldehydes) and Ketoses (ketones)

Size of the carbon skeleton varies from three to seven carbons. The most common monosaccharides are: Triose (3), Pentose (5), Hexose (6) sugars

Spatial arrangement around asymmetric carbons may vary. For example, glucose and galactose are enantiomers.

The small difference between isomers affects molecular shape which gives these molecules distinctive biochemical properties.

In aqueous solutions, many monosaccharides form rings. Chemical equilibrium favors the ring structure.

Fig 5.4



Disaccharide = (Di = two; sacchar = sugar); a double sugar that consists of two monosaccharides joined by a glycosidic linkage.

Glycosidic linkage = Covalent bond formed by a condensation reaction between two sugar monomers; for example, maltose from 2 glucose molecules.

Fig 5.5

Polysaccharides, the polymers of sugars, have storage and structural roles

Polysaccharides = Macromolecules that are polymers of a few hundred or thousand monosaccharides.

Are formed by linking monomers in enzyme-mediated condensation reactions

Have two important biological functions:

1) Energy storage (starch and glycogen)

2) Structural support (cellulose and chitin)

Storage polysaccharides

Cells hydrolyze storage polysaccharides into sugars as needed. Two most common storage polysaccharides are starch and glycogen.

Starch = Glucose polymer that is a storage polysaccharide in plants.

Helical glucose polymer with a 1-4 linkages (see Campbell, Fig. 5,6)

Stored as granules within plant organelles called plastids.

Amylose, the simplest form, is an unbranched polymer.

Amylopectin is branched polymer.

Most animals have digestive enzymes to hydrolyze starch.

Major sources in the human diet are potato tubers and grains (e.g., wheat, corn, rice, and fruits of other grasses).

Glycogen = Glucose polymer that is a storage polysaccharide in animals.

Large glucose polymer that is more highly branched (a 1-4 and 4-6 linkages) than amylopectin

Stored in the muscle and liver of humans and other vertebrates.

Structural polysaccharides

Structural polysaccharides include cellulose and chitin.

Cellulose = Linear unbranched polymer of D-glucose in (b 1-4, b 4-6) linkages. A major structural component of plant cell walls

Fig 5.7

Differs from starch (also a glucose polymer) in its glycosidic linkages (b vs. a glucose)

Cellulose and starch have different three-dimensional shapes and properties as a result of differences in glycosidic linkages.

Cellulose reinforces plant cell walls, hydrogen bonds hold together parallel cellulose molecules in bundles of microfibrils (see Campbell, Fig 5.8).

Cellulose cannot be digested by most organisms, including humans, because they lack an enzyme that can hydrolyze the b 1-4 linkage.

(Exceptions are some symbiotic bacteria, other microorganisms and some fungi.)

Chitin = A structural polysaccharide that is a polymer of an amino sugar (see Campbell, Fig 5.9).

Forms exoskeletons of arthropods

Found as a building material in the cell walls of some fungi

Monomer is an amino sugar, which is similar to beta-glucose with a nitrogen-containing group replacing the hydroxyl on carbon 2.

Lipids: Diverse Hydrophobic Molecules

Lipids = Diverse group of organic compounds that are insoluble in water, but will dissolve in nonpolar solvents (e.g., ether chloroform, benzene). Important groups are fats, phospholipids, and steroids.

Fats store large amounts of energy

Fig 5.10

Fats = Macromolecules are constructed from:

Glycerol, a three-carbon alcohol

Fatty acid (carboxylic acid) = Composed of a carboxyl group at one end and an attached hydrocarbon chain ("tail")

Carboxyl functional group ("head") has properties of an acid

Hydrocarbon chain has a long carbon skeleton usually with an even number of carbon atoms (most have 16-18 carbons).

Nonpolar C-H bonds make the chain hydrophobic and not water soluble

During the formation of a fat, enzyme-catalyzed condensation reactions link glycerol to fatty acids by an ester linkage.

Ester linkage = Bond formed between a hydroxyl group and a carboxyl group.

Each of glycerol’s three hydroxyl groups can bond to a fatty acid by an ester linkage producing a fat.

Triacylglycerol = A fat composed of three fatty acids bonded to one glycerol by ester linkages (triglyceride).

Some characteristics of fat include:

Fats are insoluble in water. The long fatty acid chains are hydrophobic because of the many nonpolar C-H bonds.

The source of variation among fat molecules is the fatty acid composition.

Fatty acids in a fat may all be the same, or some (or all) may differ.

Fatty acids may vary in length.

Fatty acids may vary in the number and location of carbon-to-carbon double bonds.



Saturated Fats

No double bonds between carbons in the tail

Saturated with hydrogen

Solid at room temperature

Most animal fats, e.g. bacon grease, lard, butter

Unsaturated Fats

One or more double bonds between carbons in tail

Tail kinks at each carbon-carbon double bond, so cannot pack together closely enough to solidify at room temperature, so liquid at room temperature

Most plant fats

In many commercially prepared food products, unsaturated fats are artificially hydrogenated to prevent them from separating out as oil (e.g., peanut butter and margarine).

Fat serves many useful functions:

Energy storage. One gram of fat stores twice as much energy as a gram of polysaccharide. (Fat has a higher proportion of energy rich C-H bonds.)

More compact fuel reservoir than carbohydrate. Animals store more energy with less weight than plants which use starch, a bulky form of energy storage.

Cushions vital organs in mammals (e.g, kidney).

Insulates against heat loss (e.g., in mammals such as whales and seals).


Phospholipids = Compounds with molecular building blocks of glycerol, two fatty acids, a phosphate group, and usually, an additional small chemical group attached to the phosphate.

Fig 5.12

Differs from fat in that the third carbon of glycerol is joined to a negatively charged phosphate group

Can have small variable molecules (usually charged or polar) attached to phosphate

Are diverse depending upon differences in fatty acids and in phosphate attachments

Show ambivalent behavior toward water. Hydrocarbon tails are hydrophobic and the polar head (phosphate group with attachments) is hydrophilic.

Cluster in water as their hydrophobic portions turn away from water. One such cluster, a micelle, assembles so the hydrophobic tails turn toward the water-free interior and the hydrophilic phosphate heads arrange facing outward in contact with water.

Fig 5.13

Are major constituents of cell membranes. At the cell surface, phospholipids form a bilayer held together by hydrophobic interactions among the hydrocarbon tails. Phospholipids in water will spontaneously form such a bilayer.


Steroids = Lipids which have four fused carbon rings with various functional groups attached.

Cholesterol is an important steroid

Fig 5.14

Is the precursor to many other steroids including vertebrate sex hormones and bile acids.

Is a common component of animal cell membranes.

Can contribute to atherosclerosis.


Lecture 6 Chapter 5 continued

Proteins: The Molecular Tools of the Cell

Polypeptide chains = Polymers of amino acids that are arranged in a specific linear sequence and are linked by peptide bonds.

Fig 5.15

Protein = A macromolecule that consists of one or more polypeptide chains folded and coiled into specific conformations.

Are abundant, making up 50% or more of cellular dry weight

Have important and varied functions in the cell:

Structural support

Storage (of amino acids)

Transport (e.g., hemoglobin)

Signaling (chemical messengers)

Cellular response to chemical stimuli (receptor proteins)

Movement (contractile proteins)

Defense against foreign substances and disease-causing organisms (antibodies)

Catalysis of biochemical reactions (enzymes)

Vary extensively in structure; each type has a unique three-dimensional shape (conformation)

Though they vary in structure and function, they are commonly made of only 20 amino acid monomers.

A polypeptide is a polymer of amino acids connected in a specific sequence

Fig 5.16

Amino acid = Building block molecule of a protein; most consist of an asymmetric carbon, termed the alpha carbon, which is covalently bonded to a(n):

Hydrogen atom

Carboxyl group

Amino group

Variable R group (side chain) specific to each amino acid. Physical and chemical properties of the side chain determine the uniqueness of each amino acid.

(At pH’s normally found in the cell, both the carboxyl and amino groups are ionized.)

Amino acids contain both carboxyl and amino functional groups. Since one group acts as a weak acid and the other group acts as a weak base, an amino acid can exist in three ionic states. The pH of the solution determines which ionic state predominates.

Fig 5.15

The twenty common amino acids can be grouped by properties of side chains:

Nonpolar side groups (hydrophobic). Amino acids with nonpolar groups are less soluble in water.

Polar side groups (hydrophilic). Amino acids with polar side groups are soluble in water. Polar amino acids can be grouped further into:

Uncharged polar

Charged polar

Acidic side groups. Dissociated carboxyl group gives these side groups a negative charge.

Basic side groups. An amino group with an extra proton gives these side groups a net positive charge.

Polypeptide chains are polymers that are formed when amino acid monomers are linked by peptide bonds Fig 5.16

Peptide bond = Covalent bond formed by a condensation reaction that links the carboxyl group of one amino acid to the amino group of another.

Has polarity with an amino group on one end (N-terminus) and a carboxyl group on the other (C-terminus).

Has a backbone of the repeating sequence —N-C-C-N-C-C

Polypeptide chains:

Range in length from a few monomers to more than a thousand

Have unique linear sequences of amino acids

Fig 5.18

A protein’s function depends on its specific conformation

Protein conformation = Three-dimensional shape of a protein.

Native conformation = Functional conformation of a protein found under normal biological conditions

Enables a protein to recognize and bind specifically to another molecule

(e.g., hormone/receptor, enzyme/substrate, and antibody/antigen)

Is a consequence of a specific linear sequence of amino acids in the polypeptide

Is produced when a newly formed polypeptide chain coils and folds spontaneously, mostly in response to hydrophobic interactions

Is stabilized by chemical bonds and weak interactions between neighboring regions of the folded protein

Four levels of protein structure

The correlation between form and function in proteins is an emergent property resulting from superimposed levels of protein structure (see

Campbell, Figure 5.24):

Primary structure Fig 5.18

Secondary structure Fig 5.20

Tertiary structure Fig 5.22

When a protein has two or more polypeptide chains, it also has quaternary structure

Fig 5.24

Primary structure

Fig 5.18

Primary structure = Unique sequence of amino acids in a protein.

Determined by genes

Slight change can affect a protein’s conformation and function (e.g., sickle-cell hemoglobulin; see Campbell, Figure 5.19).

Can be sequenced in the laboratory.

Secondary structure

Secondary structure = Regular, repeated coiling and folding of a protein’s polypeptide backbone

Fig 5.20

Contributes to a protein’s overall conformation.

Stabilized by hydrogen bonds between peptide linkages in the protein’s backbone (carbonyl and amino groups).

The major types of secondary structure are alpha (a) helix and beta (b) pleated sheet.

Alpha (a) helix

Alpha (a) helix = Secondary structure of a polypeptide that is a helical coil stabilized by hydrogen bonding between every fourth peptide bond (3.6 amino acids per turn).

Described by Linus Pauling and Robert Corey, 1951

Found in fibrous proteins (e.g., a -keratin and collagen) for most of their length and in some portions of globular proteins.

Beta (b) pleated sheet

Beta (b) pleated sheet = Secondary protein structure which is a sheet of antiparallel chains folded into accordion pleats.

Parallel regions are held together by either intrachain or interchain hydrogen bonds (between adjacent polypeptides).

Make up the dense core of many globular proteins (e.g., lysozyme) and the major portion of some fibrous proteins (e.g., fibroin, the structural protein of silk).

Tertiary structure

Tertiary structure = The three-dimensional shape of a protein.

The irregular contortions of a protein are due to bonding between and among side chains (R groups) and to interaction between R groups and the aqueous environment.

Figure 5.22

Types of bonds contributing to tertiary structure are weak interactions and covalent linkage (both may occur in the same protein).

Weak interactions

Protein shape is stabilized by the cumulative effect of weak interactions. These weak interactions include:

Hydrogen bonding between polar side chains

Ionic bonds between charged side chains

Hydrophobic interactions between nonpolar side chains in protein’s interior.

Hydrophobic interactions = (Hydro=water; phobos = fear); the clustering of hydrophobic molecules as a result of their mutual exclusion from water.

Covalent linkage

Disulfide bridges form between two cysteine monomers brought together by folding of the protein. This is a strong bond that reinforces conformation.

Quaternary structure

Quaternary structure = Structure that results from the interactions between and among several polypeptides chains (subunits).

Fig 5.23

Example: Collagen, a fibrous protein with three helical polypeptides supercoiled into a triple helix; found in animal connective tissue, collagen’s supercoiled quaternary structure gives it strength.

Some globular proteins have subunits that fit tightly. Example: Hemoglobulin, a globular protein that has four subunits (two a chains and two b chains).

Fig 5.24

What determines protein conformation?

A protein’s three-dimensional shape is a consequence of the interactions responsible for secondary and tertiary structure.

This conformation is influenced by physical and chemical environmental conditions

If a protein’s environment is altered, it may become denatured and lose its native conformation.

Denaturation = A process that alters a protein’s native conformation and biological activity. Proteins can be denatured by:

Transfer to an organic solvent. Hydrophobic side chains, normally inside the protein’s core, move towards the outside. Hydrophilic side chains turn away from the solvent towards the molecule’s interior.

Chemical agents that disrupt hydrogen bonds, ionic bonds and disulfide bridges.

Excessive heat. Increased thermal agitation disrupts weak interactions

Fig 5.25

The protein-folding problem

Nucleic Acids: Informational Polymers

Nucleic acids store and transmit hereditary information

Protein conformation is determined by primary structure. Primary structure, in turn, is determined by genes; hereditary units that consist of DNA, a type of nucleic acid.

There are two types of nucleic acids.

Deoxyribonucleic acid (DNA)

Contains coded information that programs all cell activity

Contains directions for its own replication

Is copied and passed from one generation of cells to another

In eukaryotic cells, is found primarily in the nucleus

Makes up genes that contain instructions for protein synthesis. Genes do not directly make proteins, but direct the synthesis of mRNA.

Ribonucleic acid (RNA)

Functions in the actual synthesis of proteins coded for by DNA

Sites of protein synthesis are on ribosomes in the cytoplasm

Messenger RNA (mRNA) carries encoded genetic message from the nucleus to the cytoplasm

The flow of genetic information goes from DNA to RNA to protein

Fig 5.26

A nucleic acid strand is a polymer of nucleotides

Nucleic acid = Polymer of nucleotides linked together by condensation reactions.

Nucleotide = Building block molecule of a nucleic acid; made of (1) a five-carbon sugar covalently bonded to (2) a phosphate group and (3) a nitrogenous base.

Pentose (5-carbon sugar)

There are two pentoses found in nucleic acids: ribose and deoxyribose.


The phosphate group is attached to the number 5 carbon of the sugar.

Nitrogenous base

There are two families of nitrogenous bases:

Pyrimidine = Nitrogenous base characterized by a six-membered ring made up of carbon and nitrogen atoms. For example:

Cytosine C

Thymine (T); found only in DNA

Uracil (U); found only in RNA

Purine = Nitrogenous base characterized by a five-membered ring fused to a six-membered ring. For example:

Adenine (A)

Guanine (G)

Nucleotides have various functions:

Are monomers for nucleic acids.

Transfer chemical energy from one molecule to another (e.g., ATP).

Are electron acceptors in enzyme-controlled redox reactions of the cell (e.g., NAD).

A nucleic-acid polymer or polynucleotise, results from joining nucleotides together by covalent bonds called phosphodiester linkages. The bond is formed between the phosphate of one nucleotide and the sugar of the next.

Results in a backbone with a repeating pattern of sugar-phosphate-sugar-phosphate.

Variable nitrogenous bases are attached to the sugar-phosphate backbone.

Each gene contains a unique linear sequence of nitrogenous bases which codes for a unique linear sequence of amino acids in a protein.

Inheritance is based on precise replication of the DNA double helix

In 1953, James Watson and Francis Crick proposed the double helix as the three-dimensional structure of DNA.

Consists of two nucleotide chains wound in a double helix

Sugar-phosphate backbones are on the outside of the helix

The two polynucleotide strands of DNA are held together by hydrogen bonds

Between the paired nitrogenous bases and by van der Waals attraction between the stacked bases

Fig 5.28

Base-pairing rules are that adenine (A) always pairs with thymine (T); guanine (G) always pairs with cytosine C.

Two strands of DNA are complimentary and thus can serve as templates to make new complementary strands. It is this mechanism of precise copying that makes inheritance possible.

Most DNA molecules are long, containing thousands or millions of base pairs.

We can use DNA and proteins as tape measures of evolution.

Closely related species have more similar sequences of DNA and amino acids, than more distantly related species. Using this type of molecular evidence, biologists can deduce evolutionary relationships among species.


Lecture 7 Chapter 6

Metabolism, Energy and Life

A. The chemistry of life is organized into metabolic pathways

Metabolism = Totality of an organism's chemical processes.

Property emerging from specific molecular interactions within the cell.

Concerned with managing cellular resources: material and energy.

Metabolic pathways are generally of two types:

Catabolic pathways = Metabolic pathways that release energy by breaking down complex molecules to simpler compounds (e.g., cellular respiration which degrades glucose to carbon dioxide and water; provides energy for cellular work).

Anabolic pathways = Metabolic pathways that consume energy to build complicated molecules from simpler ones (e.g., photosynthesis which synthesizes glucose from C02 and H20; any synthesis of a macromolecule from its monomers).

Metabolic reactions may be coupled, so that energy released from a catabolic reaction can be used to drive an anabolic one.

B. Organisms transform energy

Energy = Capacity to do work

Kinetic energy = Energy in the process of doing work (energy of motion). For example:

Heat (thermal energy) is kinetic energy expressed in random movement of molecules.

Light energy from the sun is kinetic energy which powers photosynthesis.

Potential energy = Energy that matter possesses because of its location or arrangement (energy of position). For example:

• In the earth's gravitational field, an object on a hill or water behind a dam has potential energy.

• Chemical energy is potential energy stored in molecules because of the arrangement of nuclei and electrons in its atoms.

Energy can be transformed from one form to another. For example:

• Kinetic energy of sunlight can be transformed into the potential energy of chemical bonds during photosynthesis.

• Potential energy in the chemical bonds of gasoline can be transformed into kinetic mechanical energy which pushes the pistons of an engine.

C. The energy transformations of life are subject to two laws of thermodynamics

Thermodynamics = Study of energy transformations

First Law of Thermodynamics = Energy can be transferred and transformed, but it cannot be created or destroyed (energy of the universe is constant).

Second Law of Thermodynamics = Every energy transfer or transformation makes the universe more disordered (every process increases the entropy of the universe).

Entropy = Quantitative measure of disorder that is proportional to randomness (designated by the letter S).

Closed system = Collection of matter under study which is isolated from its surroundings.

Open system = System in which energy can be transferred between the system and its surroundings.

The entropy of a system may decrease, but the entropy of the system plus its surroundings must always increase. Highly ordered living organisms do not violate the second law because they are open systems. For example, animals:

· Maintain highly ordered structure at the expense of increased entropy of their surroundings.

· Take in complex high energy molecules as food and extract chemical energy to create and maintain order.

· Return to the surroundings simpler low energy molecules (CO2 and water) and heat.

Combining the first and second laws; the quantity of energy in the universe is constant, but its quality is not.

D. Organisms live at the expense of free energy

1. Free energy: a criterion for spontaneous change

Not all of a system's energy is available to do work. The amount of energy that is available to do work is described by the concept of free energy. Free energy (G) is related to the system's total energy (H) and its entropy (S) in the following way:

G = H - TS


G = Gibbs free energy (energy available to do work)

H = enthalpy or total energy

T = temperature in oK

S = entropy

Free energy (G) = Portion of a system's energy available to do work; is the difference between the total energy (enthalpy) and the energy not available for doing work (TS).

The maximum amount of usable energy that can be harvested from a particular reaction is the system's free energy change from the initial to the final state. This change in free energy (ÆG) is given by the Gibbs-Helmholtz equation at constant temperature and pressure:



ÆG = change in free energy

ÆH = change in total energy (enthalpy)

ÆS = change in entropy

T = absolute temperature in 0K (which is OC + 273)

Significance of free energy:

a. Indicates the maximum amount of a system's energy which is available to do work.

b. Indicates whether a reaction will occur spontaneously or not.

· A spontaneous reaction is one that will occur without additional energy.

· In a spontaneous process, ÆG or free energy of a system decreases (ÆG<O).

• A decrease in enthalpy (-ÆH) and an increase in entropy (+ÆS) reduce the free energy of a system and contribute to the spontaneity of a process.

• A higher temperature enhances the effect of an entropy change. Greater kinetic energy of molecules tends to disrupt order as the chances for random collisions increase.

• When enthalpy and entropy changes in a system and have an opposite effect on free energy, temperature may determine whether the reaction will be spontaneous or not (e.g., protein denaturation by increased temperature).

• High energy systems, including high energy chemical systems, are unstable and tend to change to a more stable state with a lower free energy.

Fig 6.4

2. Free energy and equilibrium

There is a relationship between chemical equilibrium and the free energy change (ÆG) of a reaction:

• As a reaction approaches equilibrium, the free energy of the system decreases (spontaneous and exergonic reaction).

• When a reaction is pushed away from equilibrium, the free energy of system increases (non-spontaneous and endergonic reaction).

• When a reaction reaches equilibrium, ÆG = 0, because there is no net change in the system.

3. Free energy and metabolism

a. Reactions can be classified based upon their free energy changes:

Exergonic reaction = A reaction that proceeds with a net loss of free energy.

Endergonic reaction = An energy-requiring reaction that proceeds with a net gain of free energy; a reaction that absorbs free energy from its surroundings.

Exergonic Reaction

  1. Chemical products have less free energy than the reactant molecules.

Endergonic Reaction

If a chemical process is exergonic, the reverse process must be endergonic. For example:

· For each mole of glucose oxidized in the exergonic process of cellular respiration, 2870 kJ are released (ÆG = -2870 kJ/mol or -686 kcal/mol).

· To produce a mole of glucose, the endergonic process of photosynthesis requires an energy input of 2870 kJ (ÆG = +2870 kJ/mol or +686 kcal/mol).

The text uses joules and kilojoules as energy units and puts the caloric equivalent in parentheses. The joule (J) is the metric unit of energy; some handy conversions:

joule (J) = 0.239 cal

Kilojoule (J) = 1000 J or 0.239 kcal

calorie (cal) = 4.184 J

In cellular metabolism, endergonic reactions are driven by coupling them to reactions with a greater negative free energy (exergonic). ATP plays a critical role in this energy coupling.

b. Metabolic disequilibrium

Since many metabolic reactions are reversible, they have the potential to reach equilibrium.

• At equilibrium, ÆG = 0, so the system can do no work.

• Metabolic disequilibrium is a necessity of life; a cell at equilibrium is dead.

• In the cell, these potentially reversible reactions are pulled forward away from equilibrium, because the products of some reactions become reactants for the next reaction in the metabolic pathway.

• For example, during cellular respiration a steady supply of high energy reactants such as glucose, and removal of low energy products such as C02 and H20, maintain the disequilibrium necessary for respiration to proceed.

Fig 6.5

E. ATP powers cellular work by coupling exergonic to endergonic reactions

ATP is the immediate source of energy that drives most cellular work, which includes:

Mechanical work such as beating of cilia, muscle contraction, cytoplasmic flow, and chromosome movement during mitosis and meiosis.

Transport work such as pumping substances across membranes.

Chemical work such as the endergonic process of polymerization.

  1. The structure and hydrolysis of ATP

ATP (adenosine triphosphate) = Nucleotide with unstable phosphate bonds that the cell hydrolyzes for energy to drive endergonic reactions. ATP consists of:

Fig 6.6

Unstable bonds between the phosphate groups can be hydrolyzed in an exergonic reaction that releases energy.

• When the terminal phosphate bond is hydrolyzed, a phosphate group is removed producing ADP (adenosinediphosphate).

• In a living cell, this reaction releases -55 kJ/mol (-13 kcal/mol).

The terminal phosphate bonds of ATP are unstable, so:

• The products of the hydrolysis reaction are more stable than the reactant.

• Hydrolysis of the phosphate bonds is thus exergonic as the system shifts to a more stable state.

How ATP performs work

Exergonic hydrolysis of ATP is coupled with endergonic processes by transferring a phosphate group to another molecule.

• Phosphate transfer is enzymatically controlled.

• The molecule acquiring the phosphate (phosphorylated or activated intermediate) becomes more reactive.

Fig 6.7

3. The regeneration of ATP

ATP is continually regenerated by the cell.

Fig 6.8

H. Enzymes

A. Enzymes speed up metabolic reactions by lowering energy barriers Free energy change indicates whether a reaction will occur spontaneously, but does not give infromation about the speed of reaction.

• A chemical reaction will occur spontaneously if it releases free energy (-ÆG), but it may occur too slowly to be effective in living cells.

• Biochemical reactions require enzymes to speed up and control reaction rates.

Catalyst = Chemical agent that accelerates a reaction without being permanently changed in the process, so it can be used over and over.

Enzymes = Biological catalysts are made of protein.

Before a reaction can occur, the reactants must absorb energy to break chemical bonds.

This initial energy investment is the activation energy.

Free energy of activation (activation energy) = Amount of energy that reactant molecules must absorb to start a reaction (EA).

Transition state = Unstable condition of reactant molecules that have absorbed sufficient free energy to react.

Fig 6.9

Even though a reaction is energetically favorable, there must be an initial investment of activation energy (EA ).

The breakdown of biological macromolecules is exergonic. However, these molecules react very slowly at cellular temperatures because they cannot absorb enough thermal energy to reach transition state.

In order to make these molecules reactive when necessary, cells use biological catalysts called enzymes, which:

Are proteins.

• Lower EA, so the transition state can be reached at cellular temperatures.

• Do not change the nature of a reaction (ÆG), but only speed up a reaction that would have occurred anyway.

• Are very selective for which reaction they will catalyze.

Fig 6.10

B. Enzymes are substrate-specific

Enzymes are specific for a particular substrate, and that specificity depends upon the enzyme's three-dimensional shape.

Substrate = The substance an enzyme acts on and makes more reactive.

• An enzyme binds to its substrate and catalyzes its conversion to product. The enzyme is released in original form.

Substrate + enzyme-->enzyme-substrate complex--> product + enzyme

• The substrate binds to the enzyme's active site.

Active site = Restricted region of an enzyme molecule which binds to the substrate.

• Is usually a pocket or groove on the protein's surface.

• Formed with only a few of the enzyme's amino acids.

• Determines enzyme specificity which is based upon a compatible fit between the shape of an enzyme's active site and the shape of the substrate.

• Changes its shape in response to the substrate.

• As substrate binds to the active site, it induces the enzyme to change its shape.

• This brings its chemical groups into positions that enhance their ability to interact with the substrate and catalyze the reaction.

Induced fit = Change in the shape of an enzyme's active site, which is induced by the substrate

Figs 6.11,12

C. The active site is an enzyme's catalytic center The entire enzymatic cycle is quite rapid

Steps in the catalytic cycle of enzymes:

I . Substrate binds to the active site forming an enzyme-substrate complex. Substrate is held in the active site by weak interactions (e.g., hydrogen bonds and ionic bonds).

2. Induced fit of the active site around the substrate. Side chains of a few amino acids in the active site catalyze the conversion of substrate to product.

3 . Product departs active site and the enzyme emerges in its original form. Since enzymes are used over and over, they can be effective in very small amounts.

Enzymes lower activation energy and speed up reactions by several mechanisms:

• Active site can hold two or more reactants in the proper position so they may react.

• Induced fit of the enzyme's active site may distort the substrate's chemical bonds, so less thermal energy (lower ÆG) is needed to break them during the reaction.

• Active site might provide a micro-environment conducive to a particular type of reaction (e.g., localized regions of low pH caused by acidic side chains on amino acids at the active site).

• Side chains of amino acids in the active site may participate directly in the reaction.

The initial substrate concentration partly determines the rate of an enzyme controlled reaction.

• The higher the substrate concentration, the faster the reaction - up to a limit.

• If substrate concentration is high enough, the enzyme becomes saturated with substrate. (The active sites of all enzymes molecules are engaged.)

• When an enzyme is saturated, the reaction rate depends upon how fast the active sites can convert substrate to product.

• When enzyme is saturated, reaction rate may be increased by adding more enzyme.

D. A cell's physical and chemical environment affects enzyme activity Each enzyme has optimal environmental conditions that favor the most active enzyme conformation.

1. Effects of temperature and pH

Optimal temperature allows the greatest number of molecular collisions without denaturing the enzyme.

• Enzyme reaction rate increases with increasing temperature. Kinetic energy of reactant molecules increases with rising temperature, which increases substrate collisions with active sites.

• Beyond the optimal temperature, reaction rate slows. The enzyme denatures when increased thermal agitation of molecules disrupts weak bonds that stabilize the active conformation.

• Optimal temperature range of most human enzymes is 35- 40oC.

Fig 6.13

Optimal pH range for most enzymes is pH 6 - 8.

• Some enzymes operate best at more extremes of pH.

• For example, the digestive enzyme, pepsin, found in the acid environment of the stomach has an optimal pH of 2.

2. Cofactors

Cofactors = Small nonprotein molecules that are required for proper enzyme catalysis.

• May bind tightly to active site.

• May bind loosely to both active site and substrate.

• Some are inorganic (e.g., metal atoms of zinc, iron or copper).

• Some are organic and are called coenzymes (e.g., most vitamins).

3. Enzyme inhibitors

Certain chemicals can selectively inhibit enzyme activity

• Inhibition may be irreversible if the inhibitor attaches by covalent bonds.

• Inhibition may be reversible if the inhibitor attaches by weak bonds.

Competitive inhibitors = Chemicals that resemble an enzyme's normal substrate and compete with it for the active site.

• Block active site from the substrate.

• If reversible, the effect of these inhibitors can be overcome by increased substrate concentration.

Noncompetitive inhibitors = Enzyme inhibitors that do not enter the enzyme's active site, but bind to another part of the enzyme molecule.

• Causes enzyme to change its shape so the active site cannot bind substrate.

• May act as metabolic poisons (e.g., DDT, many antibiotics).

• Selective enzyme inhibition is an essential mechanism in the cell for regulating metabolic reactions.

Fig 6.14

III. The Control of Metabolism

A. Metabolic pathways are regulated by controlling enzyme activity. Metabolic control often depends on allosteric regulation

1. Allosteric regulation

Allosteric site = Specific receptor site on some part of the enzyme molecule other than the active site.

• Most enzymes with allosteric sites have two or more polypeptide chains, each with its own active site. Allosteric sites are often located where the subunits join.

• Allosteric enzymes have two conformations, one catalytically active and the other inactive

• Binding of an activator to an allosteric site stabilizes the active conformation.

Binding of an inhibitor (noncompetitive inhibitor) to an allosteric site stabilizes the inactive conformation.

• Enzyme activity changes continually in response to changes in the relative proportions of activators and inhibitors (e.g., ATP/ADP).

• Subunits may interact so that a single activator or inhibitor at one allosteric site will affect the active sites of the other subunits.

Fig 6.15

2. Feedback inhibition

Feedback inhibition = Regulation of a metabolic pathway by its end product, which inhibits an enzyme within the pathway.

Prevents the cell from wasting chemical resources by synthesizing more product than is necessary.

Fig 6.16

3. Cooperativity

Substrate molecules themselves may enhance enzyme activity.

Cooperativity = The phenomenon where substrate binding to the active site of one subunit induces a confonnational change that enhances substrate binding at the active sites of the other subunits.

Fig 6.17

B. The localization of enzymes within the cell helps order metabolism Cellular structure orders and compartmentalizes metabolic pathways.

• Some enzymes and enzyme complexes have fixed locations in the cell because they are incorporated into a membrane.

• Other enzymes and their substrates may be localized within membrane-enclosed eukaryotic organelles (e.g., chloroplasts and mitochondria).


Lecture 8, Chapter 7

All organisms are made of cells, the organism's basic unit of structure and function.

How We Study Cells

A. Microscopes provide windows to the world of the cell

Two important concepts in microscopy are magnification and resolving power.

Magnification = How much larger an object is made to appear compared to its real size.

Resolving power = Minimum distance between two points that can still be distinguished as two separate points.

• Resolution of a light microscope is limited by the wavelength of visible light. Maximum possible resolution of a light microscope is 0.2 Ám.

• Highest magnification in a light microscope with maximum resolution is about I000 times.

In the 1950s, researchers began to use the electron microscope which far surpassed the resolving power of the light microscope.

• Resolving power is inversely related to wavelength. Instead of light, electron microscopes use electron beams which have much shorter wavelengths than visible light.

• Modem electron microscopes have a practical resolving power of about 2 nm.

• Enhanced resolution and magnification allowed researchers to clearly identify subcellular organelles and to study cell ultrastructure.

Two types of electron microscopes are the transmission electron microscope (TEM) and the scanning electron microscope.

The transmission electron microscope (TEM) aims an electron beam at a thin section of specimen which may be stained with metals to absorb electrons and enhance contrast.

• Electrons transmitted through the specimen are focused and the image magnified by using electromagnetic lenses (rather than glass lenses) to bend the trajectories of the charged electrons.

• Image is focused onto a viewing screen or film.

• Used to study internal cellular ultrastructure.

The scanning electron microscope (SEM) is useful for studying the surface of a specimen.

• Electron beam scans the surface of the specimen usually coated with a thin film of gold.

• Scanning beam excites secondary electrons on the sample's surface.

• Secondary electrons are collected and focused onto a viewing screen.

• SEM has a great depth of field and produces a three-dimensional image.

Fig 7.1

B. Cell biologists can isolate organelles to study their function

Cell fractionation is a technique that enables researchers to isolate organelles without destroying their function.

Figure 7.3

Cell fractionation = Technique which involves centrifuging disrupted cells at various speeds and durations to isolate components of different sizes, densities, and shapes.

II. A Panoramic View of the Cell

A. Prokaryotic and eukaryotic cells differ in size and complexity Living organisms are made of either prokaryotic or eukaryotic cells-two major kinds of cells, which can be distinguished by structural organization.


(pro = before; karyon = kernel)

Figure 7.4


(Eu = true; karyon = kernel)

Found in the Kingdoms Protista, Fungi, Plantae, and Animalia

Cytoplasm = Entire region between the nucleus and cell membrane

Cytosol = Semi-fluid medium found in the cytoplasm

1. Cell size

Cell Type Diameter

Mycoplasmas 0.1 - 1.0 ÁM

Most bacteria 1.0 - 10.0 Ám

Most eukaryotic cells 10.0 - 100.0 Ám

Range of cell size is limited by metabolic requirements. The lower limits are probably determined by the smallest size with enough:

The upper limits of size are imposed by the surface area to volume ratio. As a cell increases in size, its volume grows proportionately more than its surface area.

Figure 7.5

The surface area of the plasma membrane must be large enough for the cell volume, in order to provide an adequate exchange surface for oxygen, nutrients and wastes.

B. Internal membranes compartmentalize the functions of a eukaryotic cell The average eukaryotic cell has a thousand times the volume of the average prokaryotic cell, but only a hundred times the surface area. Eukaryotic cells compensate for the small surface area to volume ratio by having internal membranes


Figure 7.6

III. The Nucleus and Ribosomes

A. The nucleus contains a eukaryotic cell's genetic library

Nucleus = A generally conspicuous membrane-bound cellular organelle in a eukaryotic cell; contains most of the genes that control the entire cell.

Figure 7.9

• Averages about 5 Ám diameter.

• Enclosed by a nuclear envelope.

Nuclear envelope = A double membrane which encloses the nucleus in a eukaryotic cell.

• Is two lipid bilayer membranes separated by a space of about 20 to 40 nm. Each lipid bilayer has its own specific proteins.

• Attached to proteins on the envelope's nuclear side is a network of protein filaments, the nuclear lamina, which stabilizes nuclear shape.

• Is perforated by pores (100 nm diameter), which are ordered by an octagonal array of protein granules.

The envelope's inner and outer membranes are fused at the lip of each pore.

Pore complex regulates molecular traffic into and out of the nucleus.

There is new evidence of an intranuclear framework of fibers, the nuclear matrix.

The nucleus contains most of the cell's DNA which is organized with proteins into a complex called chromatin.

Chromatin = Complex of DNA and histone proteins, which makes up chromosomes in eukaryotic cells; appears as a mass of stained material in nondividing cells.

Chromosomes = Long threadlike association of genes, composed of chromatin and found in the nucleus of eukaryotic cells.

• Each species has a characteristic chromosome number.

• Human cells have 46 chromosomes, except egg and sperm cells, which have half or 23.

The most visible structure within the nondividing nucleus is the nucleolus

Nucleolus = Roughly spherical region in the nucleus of nondividing cells, which consists of nucleolar organizers and ribosomes in various stages of production.

• May be two or more per cell.

• Packages ribosomal subunits from:

• rRNA transcribed in the nucleolus.

• RNA produced elsewhere in the nucleus.

• Ribosomal proteins produced and imported from the cytoplasm.

• Ribosomal subunits pass through nuclear pores to the cytoplasm, where their assembly is completed.

Nucleolar organizers = Specialized regions of some chromosomes, with multiple copies of genes for rRNA (ribosomal RNA) synthesis.

The nucleus controls protein synthesis in the cytoplasm:

from DNA instructions.

is translated into primary protein structure.


B. Ribosomes build a cell's proteins

Ribosome = A cytoplasmic organelle that is the site for protein synthesis.

Figure 7.10

Ribosomes function either free in the cytosol or bound to endoplasmic reticulum.

Bound and free ribosomes are structurally identical and interchangeable.

Free ribosomes = Ribosomes suspended in the cytosol.

Bound ribosomes = Ribosomes attached to the outside of the endoplasmic reticulum.

IV. The Endomembrane System

Biologists consider many membranes of the eukaryotic cell to be part of an endomembrane system.

• Membranes may be interrelated directly through physical contact.

• Membranes may be related indirectly through vesicles.

Vesicles = Membrane-enclosed sacs that are pinched off portions of membranes moving from the site of one membrane to another.

Membranes of the endomembrane system vary in structure and function, and the membranes themselves are dynamic structures changing in composition, thickness and behavior.

The endomembrane system includes:

• Nuclear envelope

• Endoplasmic reticulum

• Golgi apparatus

• Lysosomes

• Vacuoles

Plasma membrane (not actually an endomembrane, but related to endomembrane system)

A. The endoplasmic reticulum manufactures membranes and performs many other biosynthetic functions

Endoplasmic reticulum (ER) = (Endoplasmic = within the cytoplasm; reticulum = network); extensive membranous network of tubules and sacs (cisternae) which sequesters its internal lumen (cisternal space) from the cytosol.

• Most extensive portion of endomembrane system.

• Continuous with the outer membrane of the nuclear envelope; therefore, the space between the membranes of the nuclear envelope is continuous with cistenal space.

There are two distinct regions of ER that differ in structure and function: smooth ER and rough ER.

Figure 7.11

1. Functions of smooth ER

Appears smooth in the electron microscope because its cytoplasmic surface lacks ribosomes. Smooth ER functions in diverse metabolic processes:

a. Participates in the synthesis of lipids, phospholipids and steroids

For example, vertebrate, particularly mammalian sex hormones and steroids secreted by the adrenal gland.

• Cells that produce and secrete these products are rich in smooth ER (e.g., testes, ovaries, skin oil glands).

b. Participates in carbohydrate metabolism

Smooth ER in liver contains an embedded enzyme that catalyzes the final step in the conversion of glycogen to glucose (removes the phosphate from glucose-phosphate).

c. Detoxifies drugs and poisons

Smooth ER, especially in the liver, contains enzymes which detoxify drugs and poisons.

• Enzymes catalyze the addition of hydroxyl groups to drugs and poisons. This makes them soluble in the cytosol, so they may be excreted from the body.

• Smooth ER in liver cells proliferates in response to barbiturates, alcohol and other drugs. This, in turn, may increase drug tolerance.

d. Stores calcium ions necessary for muscle contraction

In a muscle cell, the ER membrane pumps Ca++ from the cytosol into the cistenal space.

In response to a nerve impulse, Ca++ leaks from the ER back into the cytosol, which triggers muscle cell contraction.

2. Rough ER and protein synthesis

Rough ER:

• Appears rough under an electron microscope because the cytoplasmic side is studded with ribosomes.

• Is continuous with outer membrane of the nuclear envelope (which may also be studded with ribosomes on the cytoplasmic side).

• Manufactures secretary proteins and membrane.

Proteins destined for secretion are synthesized by ribosomes attached to rough ER:

Ribosomes attached to rough ER synthesize

secretary proteins.

Growing polypeptide is threaded through ER

membrane into the lumen or cisternal space.

Protein folds into its native conformation.

If destined to be a glycoprotein, enzymes

localized in the ER membrane catalyze the

covalent bonding of an oligosaccharide to the

secretory protein.

Protein departs in a transport vesicle pinched off

from transitional ER adjacent to the rough ER site of


Glycoprotein = Protein covalently bonded to carbohydrate.

Oligosaccharide = Small polymer of sugar units.

Transport vesicle = Membrane vesicle in transit from one part of the cell to another.

3. Rough ER and membrane production

Membranes of rough ER grow in place as newly formed proteins and phospholipids are assembled:

materials in the cytosol.

B. The Golgi apparatus finishes, sorts, and ships cell products Many transport vesicles leave the ER and travel to the Golgi apparatus.

Golgi apparatus = Organelle made of stacked, flattened membranous sacs (cisternae), that modifies, stores and routes products of the endoplasmic reticulum.

Figure 7.12

Two poles are called the cis face (forming face) and the trans face (maturing face).

Cis face, which is closely associated with transitional ER, receives products by accepting transport vesicles from the ER. A vesicle fuses its membrane to the cis face of the Golgi and empties its soluble contents into the Golgi's cistenal space.

Trans face pinches off vesicles from the Golgi and transports molecules to other sites.

Enzymes in the Golgi modify products of the ER in stages as they move through the Golgi stack from the cis to the trans face:

• Each cistenae between the cis and trans face contains unique combinations of enzymes.

• Golgi products in transit from one cisternae to the next, are carried in transport vesicles.

During this process, the Golgi:

• Alters some membrane phospholipids.

• Modifies the oligosaccharide portion of glycoproteins.

• Manufactures certain macromolecules itself

• Targets products for various parts of the cell.

• Phosphate groups or oligosaccharides may be added to Golgi products as molecular identification tags.

• Membranous vesicles budded from the Golgi may have external molecules that recognize docking sites on the surface of certain other organelles.

• Sorts products for secretion. Products destined for secretion leave the trans face in vesicles which eventually fuse with the plasma membrane.

C. Lysosomes are digestive compartments

Lysosome = An organelle which is a membrane-enclosed bag of hydrolytic enzymes that digest all major classes of macromolecules.

Figure 7.13

• Enzymes include lipases, carbohydrases, proteases, and nucleases.

• Optimal pH for lysosomal enzymes is about pH 5.

• Lysosomal membrane performs two important functions:

• Sequesters potentially destructive hydrolytic enzymes from the cytosol.

• Maintains the optimal acidic environment for enzyme activity by pumping H+ ions inward from the cytosol to the lumen.

• Hydrolytic enzymes and lysosomal membrane are synthesized in the rough ER and processed further in the Golgi apparatus.

• Lysosomes probably pinch off from the trans face of the Golgi apparatus.

Figure 7.14

1. Functions of lysosomes

a. Intracellular digestion

Phagocytosis = (Phago = to eat; cyte = cell); cellular process of ingestion, in which the plasma membrane engulfs particulate substances and pinches off to form a particle-containing vacuole.

• Lysosomes may fuse with food-filled vacuoles, and their hydrolytic enzymes digest the food.

• Examples are Amoeba and other protists which eat smaller organisms or food particles.

• Human cells called macrophages phagocytize bacteria and other invaders.

b. Recycle cell's own organic material

Lysosomes may engulf other cellular organelles or part of the cytosol and digest them with hydrolytic enzymes (autophagy).

• Resulting monomers are released into the cytosol where they can be recycled into new macromolecules.

c. Programmed cell destruction

Destruction of cells by their own lysosomes is important during metamorphosis and development.

2. Lysosomes and human disease

Symptoms of inherited storage diseases result from impaired lysosomal function. Lack of a specific lysosomal enzyme causes substrate accumulation which interferes with lysosomal metabolism and other cellular functions.

• In Pompe's disease, the missing enzyme is a carbohydrase that breaks down glycogen. The resulting glycogen accumulation damages the liver.

• Lysosomal lipase is missing or inactive in Tay-Sachs disease, which causes lipid accumulation in the brain.

D. Vacuoles have diverse functions in cell maintenance

Vacuole = Organelle which is a membrane-enclosed sac that is larger than a vesicle (transport vesicle, lysosome, or microbody).

Vacuole types and functions:

Food vacuole = Vacuole formed by phagocytosis which is the site of intracellular digestion in some protists and macrophages.

Figure 7.14

Contractile vacuole = Vacuole that pumps excess water from the cell; found in some freshwater protozoa.

Central vacuole = Large vacuole found in most mature plant cells.

Figure 7.15.

• Is enclosed by a membrane called the tonoplast which is part of the endomembrane system

• Develops by the coalescence of smaller vacuoles derived from the ER and Golgi apparatus

• Is a versatile compartment with many functions:

• Stores organic compounds (e.g., protein storage in seeds)

• Stores inorganic ions (e.g., K+ and CI-)

• Sequesters dangerous metabolic by-products from the cytoplasm

• Contains soluble pigments in some cells (e.g., red and blue pigments in flowers)

• May protect the plant from predators by containing poisonous or unpalatable compounds

• Plays a role in plant growth by absorbing water and elongating the cell

Contributes to the large ratio of membrane surface area to cytoplasmic volume. (There is only a thin layer of cytoplasm between the tonoplast and plasma membrane.)

F. A summary of relationships among endomembranes

Components of the endomembrane system are related through direct contact or through vesicles

Figure 7.16


Lecture 9 Chapter 7 Continued

V. Other Membranous Organelles

A. Peroxisomes consume oxygen in various metabolic functions Peroxisomes = Membrane-bound organelles that contain specialized teams of enzymes for specific metabolic pathways; all contain peroxide-producing oxidases.


RH2 + O2 ------> R + H2O2

Figure 7.19

Contain catalase, an enzyme that converts toxic hydrogen peroxide to water


2H2O2 --------> 2H20 + O2

Peroxisomal reactions have many functions, some of which are:

• Breakdown of fatty acids into smaller molecules (acetyl CoA). The products are carried to the mitochondria as fuel for cellular respiration.

• Detoxification of alcohol and other harmful compounds. In the liver, peroxisomes enzymatically transfer H from poisons to 02-

Specialized peroxisomes (glyoxysomes) are found in heterotrophic fat-storing tissue of germinating seeds.

• Contain enzymes that convert lipid to carbohydrate.

• These biochemical pathways make energy stored in seed oils available for the germinating seedling.

Current thought is that peroxisome biogenesis occurs by pinching off from preexisting peroxisomes. Necessary lipids and enzymes are imported from the cytosol.

B. Mitochondria and chloroplasts are the main energy transformers of cells Mitochondria and chloroplasts are organelles that transduce energy acquired from the surroundings into forms useable for cellular work.

• Enclosed by double membranes.

• Membranes are not part of endomembrane system. Rather than being made in the ER, their membrane proteins are synthesized by free ribosomes in the cytosol and by ribosomes located within these organelles themselves.

• Contain ribosomes and some DNA that programs a small portion of their own protein synthesis, though most of their proteins are synthesized in the cytosol programmed by nuclear DNA.

• Are semiautonomous organelles that grow and reproduce within the cell.

Figure 7.17

1. Mitochondria

Mitochondria = Organelles which are the sites of cellular respiration, a catabolic oxygen-requiring process that uses energy extracted from organic macromolecules to produce ATP.

Found in nearly all eukaryotic cells

Number of mitochondria per cell varies and directly correlates with the cell's metabolic activity

Are about I Ám in diameter and 1-10 Ám in length

Are dynamic structures that move, change their shape and divide

Structure of the mitochondrion:

• Enclosed by two membranes that have their own unique combination of proteins embedded in phospholipid bilayers

• Smooth outer membrane is highly permeable to small solutes, but it blocks passage of proteins and other macromolecules

• Convoluted inner membrane contains embedded enzymes that are involved in cellular respiration. The membrane's many infoldings or cristae increase the surface area available for these reactions to occur.

• The inner and outer membranes divide the mitochondrion into two internal compartments:

a. Intermembrane space

Narrow region between the inner and outer mitochondrial membranes

Reflects the solute composition of the cytosol, because the outer membrane is permeable to small solute molecules.

b. Mitochondrial matrix

Compartment enclosed by the inner mitochondrial membrane

• Contains enzymes that catalyze many metabolic steps of cellular respiration

• Some enzymes of respiration and ATP production are actually embedded in the inner membrane.

2. Chloroplasts

Plastids = A group of plant and algal membrane-bound organelles that include amyloplasts, chromoplasts and chloroplasts.

Amyloplasts = (Amylo = starch); colorless plastids that store starch; found in roots and tubers.

Chromoplasts = (Chromo = color); plastids containing pigments other than

chlorophyll; responsible for the color of fruits, flowers and autumn leaves.

Chloroplasts = (Chloro = green); chlorophyll-containing plastids which are the sites of photosynthesis.

Structure of the chloroplast:

Chloroplasts are divided into three functional compartments by a system of membranes:

Figure 7.18

a. Intermembrane space

The chloroplast is bound by a double membrane which partitions its contents from the cytosol. A narrow intermembrane space separates the two membranes.

b. Thylakoid space Thylakoids form another membranous system within the chloroplast.

The thylakoid membrane segregates the interior of the chloroplast into two compartments: thylakoid space and stroma.

Thylakoid space = Space inside the thylakoid

Thylakoids = Flattened membranous sacs inside the chloroplast

Chlorophyll is found in the thylakoid membranes.

Thylakoids function in the steps of photosynthesis that initially convert light energy to chemical energy.

Some thylakoids are stacked into grana.

Grana = (Singular, granum); stacks of thylakoids in a chloroplast.

c. Stroma

Photosynthetic reactions that use chemical energy to convert carbon dioxide to sugar occur in the stroma.

Stroma = Viscous fluid outside the thylakoids

VI. The Cytoskeleton

A. Provides structural support to the cells for cell motility and regulation

Cytoskeleton = A network of fibers throughout the cytoplasm that forms a dynamic framework for support and movement and regulation.

Figure 7.20

• Gives mechanical support to the cell and helps maintain its shape

• Enables a cell to change shape in an adaptive manner

• Associated with motility by interacting with specialized proteins called motor molecules (e.g., organelle movement, muscle contraction, and locomotor organelles)

• Play a regulatory role by mechanically transmitting signals from cell's surface to its interior

• Constructed from at least three types of fibers: microtubules (thickest), microfilaments (thinnest), and intermediate filaments (intermediate in diameter)

Table 7.2

1. Microtubules Found in cytoplasm of all eukaryotic cells, microtubules:

• Are straight hollow fibers about 25 nm in diameter and 200 nm - 25 Ám in length

• Are constructed from globular proteins called tubulin that consists of one alpha-tubulin and one beta-tubulin molecule

Functions of microtubules include:

• Cellular support; these microtubule function as compression-resistant girders to reinforce cell shape

• Tracks for organelle movement

Figure 7.21

Protein motor molecules (e.g., kinesin) interact with microtubules to translocate organelles (e.g., vesicles from the Golgi to the plasma membrane).

• Separation of chromosomes during cell division

a. Centrosomes and centrioles

Centriole = Pair of cylindrical structures located in the centrosome of animal cells, composed of nine sets of triplet microtubules arranged in a ring

Figure 7.22

• Are about 150 nm in diameter and are arranged at right angles to each other.

• Pair of centrioles located within the centrosome, replicate during cell division.

• May organize microtubule assembly during cell division, but must not be mandatory for this function since plants lack centrioles.

b. Cilia and flagella

Cilia and flagella = Locomotor organelles found in eukaryotes that are formed from a specialized arrangement of microtubules.

 Cilia (singular, cilium)

Flagella (singular, flagellum)

Figure 7.23

Ultrastructure of cilia and flagella:

Are extensions of plasma membrane with a core of microtubules

Figure 7.24

Microtubular core is made of nine doublets of microtubuies arranged in a ring with two single microtubules in the center

(9 + 2 pattern)

Each doublet is a pair of attached microtubules.

One of the pair shares a portion of the other's wall.

Each doublet is connected

to the center of the ring

by radial spokes that end near the central microtubules.

Each doublet is attached to the neighboring doublet by a pair of side arms. Many pairs of side arms are evenly spaced along the doublet's length.

Structurally identical to centrioles, basal bodies anchor the microtubular assemblies.

Basal body = A cellular structure, identical to a centriole, that anchors the microtubular assembly of cilia and flagella.

• Can convert into a centriole and vice versa

• May be a template for ordering tubulin into the microtubules of newly forming cilia or flagella. As cilia and flagella continue to grow, new tubulin subunits are added to the tips, rather than to the bases.

The unique ultrastructure of cilia and flagella is necessary for them to function:

• Sidearms are made of dynein, a large protein motor molecule that changes its conformation in the presence of ATP as an energy source.

• A complex cycle of movements caused by dynein's conformational changes, makes the cilium or flagellum bend

Figure 7.25

• In cilia and flagella, linear displacement of dynein sidearms is translated into a bending by the resistance of the radial spokes. Working against this resistance, the "dynein-walking" distorts the microtubules, causing them to bend.


2. Microfilaments (actin filaments)

Structure of microfilaments

Figure 7.26:

Function of microfilaments:

a. Provide cellular support

Bear tension (pulling forces)

• In combination with other proteins, they form a three-dimensional network just inside plasma membrane that helps support cell shape.

• In animal cells specialized for transport, bundles of microfilaments make up the core of microvilli (e.g., intestinal epithelial wall).

b. Participate in muscle contraction

Figure 7.27a.

With ATP as the energy source, a muscle cell shortens as the thin actin filaments slide across the myosin filaments. Sliding results from the swinging of myosin cross-bridges intermittently attached to actin.

c. Responsible for localized contraction of cells

Small actin-myosin aggregates exist in some parts of the cell and cause localized contractions. Examples include:

Cytoplasmic streaming (cyclosis) = Flowing of the entire cytoplasm around the space between the vacuole and plasma membrane in a plant cell

Figure 7.27c.

3. Intermediate filaments Structure of intermediate filaments:

Filaments that are intermediate in diameter (8-12 nm) between microtubules and microfilaments

Figure 7.26

Diverse class of cytoskeletal elements that differ in diameter and composition depending upon cell type

Constructed from keratin subunits

More permanent than microftiaments and microtubules

Function of intermediate filaments:

I. Specialized for bearing tension; may function as the framework for the cytoskeleton

2. Reinforce cell shape (e.g., nerve axons)

3. Probably fix organelle position (e.g., nucleus)

4. Compose the nuclear lamina, lining the nuclear envelope's interior

VII. Cell Surfaces and Junctions

A. Plant cells are encased by cell walls Most cells produce coats that are external to the plasma membrane.

1. Cell walls Plant cells can be distinguished from animal cells by the presence of a cell wall:

• Thicker than the plasma membrane (0.1-2 Ám)

• Chemical composition varies from cell to cell and species to species.

• Basic design includes strong cellulose fibers embedded in a matrix of other polysaccharides and proteins.

• Functions to protect plant cells, maintain their shape, and prevent excess water uptake

• Has membrane-lined channels, plasmodesmata, that connect the cytoplasm of neighboring cells

Plant cells develop as follows:

• Young plant cell secretes a thin, flexible primary cell wall. Between primary cell walls of adjacent cells is a middle lamella made of pectins, a sticky polysaccharide that cements cells together.

• Cell stops growing and strengthens its wall. Some cells:

1. secrete hardening substances into primary wall.

2. add a secondary cell wall between plasma membrane and primary wall.

Secondary cell wall is often deposited in layers with a durable matrix that supports and protects the cell

Figure 7.28.

B. The extracellular matrix (ECM) of animal cells functions in support, adhesion, movement, and development

Figure 7.29

Animal cells lack walls, but they do have an elaborate extracellular matrix (ECM).

Extracellular matrix (ECM) = Meshwork of macromolecules outside the plasma membrane of animal cells. This ECM is:

• locally secreted by cells.

• composed mostly of glycoproteins, the most abundant of which is collagen that:

• accounts for about half of the total protein in the vertebrate body.

• forms strong extracellular fibers embedded in a meshwork of carbohydrate-rich glycoproteins called proteoglycans.

Some cells are attached:

Fibronectins bind to transmembrane receptor proteins called integrins that:

• bond on their cytoplasmic side to microfilaments of the cytoskeleton.

• integrate cytoskeletal responses to ECM changes and vice versa. The extracellular matrix:

• provides support and anchorage for cells.

• functions in a cell's dynamic behavior. For example, some embryonic cells migrate along specific pathways by orienting their intracellular microfilaments to the pattern of extracellular fibers in the ECM

• helps control gene activity in the cell's nucleus. Perhaps the transcription of specific genes is a response to chemical signals triggered by communication of mechanical stimuli across the plasma membrane from the ECM through integrins to the cytoskeleton.

C Intercellular junctions help integrate cells into higher levels of structure and function

Neighboring cells often adhere and interact through special patches of direct physical contact.

Intercellular junctions in plants:

Plasmodesmata (singular, plasmodesma) = Channels that perforate plant cell walls, through which cytoplasmic strands communicate between adjacent cells.

Figure 7.28

• Lined by plasma membrane. Plasma membranes of adjacent cells are continuous through a plasmodesma.

• Allows free passage of water and small solutes. This transport is enhanced by cytoplasmic streaming.

Intercellular junctions in animals

Figure 7.30

Tight junctions = Intercellular junctions that hold cells together tightly enough to block transport of substances through the intercellular space.

• Specialized membrane proteins in adjacent cells bond directly to each other allowing no space between membranes.

• Usually occur as belts all the way around each cell, that block intercellular transport.

• Frequently found in epithelial layers that separate two kinds of solutions.

Desmosomes = Intercellular junctions that rivet cells together into strong sheets, but still permit substances to pass freely through intracellular spaces. The desmosome is made of:

Gap junctions = Intercellular junctions specialized for material transport between the cytoplasm of adjacent cells.

• Formed by two connecting protein rings (connexon), each embedded in the plasma membrane of adjacent cells. The proteins protrude from the membranes enough to leave an intercellular gap of 2-4 nm.

• Have pores with diameters (1.5 nm) large enough to allow cells to share smaller molecules (e.g., inorganic ions, sugars, amino acids, vitamins), but not macromolecules such as proteins.

• Common in animal embryos and cardiac muscle where chemical communication between cells is essential.


Lecture 10 Chapter 8

A. Membrane Structure

The plasma membrane is the boundary that separates the living cell from its nonliving surroundings. This membrane:

• Is about 8 nm thick

• Surrounds the cell and controls chemical traffic into and out of the cell

Is selectively permeable; it allows some substances to cross more easily than others

• Has a unique structure which determines its function and solubility characteristics

Amphipathic = Condition where a molecule has both a hydrophilic region and a hydrophobic region.

Figure 8.1a

Figure 8.1b

Figure 8.2a


I . Not all membranes are identical or symmetrical.

· Membranes with different functions also differ in chemical composition and structure.

· Membranes have distinct inside and outside faces.

2. A membrane with an outside layer of proteins would be an unstable structure.

· Membrane proteins are not soluble in water, and, like phospholipid, they are amphipathic.

· Protein layer not likely because its hydrophobic regions would be in an aqueous environment, and it would also separate the hydrophilic phospholipid heads from water.

thefluid mosaic model accounts for the amphipathic character of proteins

Figure 8.2b

• Proteins are individually embedded in the phospholipid bilayer, rather than forming a solid coat spread upon the surface.

• Hydrophilic portions of both proteins and phospholipids are maximally exposed to water resulting in a stable membrane structure.

• Hydrophobic portions of proteins and phospholipids are in the nonaqueous environment inside the bilayer.

• Membrane is a mosaic of proteins bobbing in a fluid bilayer of phospholipids.

• Evidence from freeze fracture techniques have confirmed that proteins are embedded in the membrane. Using these techniques, biologists can delaminate membranes along the middle of the bilayer. When viewed with an electron microscope, proteins appear to penetrate into the hydrophobic interior of the membrane

B. A membrane is a fluid mosaic of lipids, proteins and carbohydrates

1. The fluid quality of membranes

Membranes are held together by hydrophobic interactions, which are weak attractions

Figure 8.3)

Most membrane lipids and some proteins can drift laterally within the membrane.

Molecules rarely flip transversely across the membrane because hydrophilic parts would have to cross the membrane's hydrophobic core.

Phospholipids move quickly along the membrane's plane averaging 2 Ám per second.

Membrane proteins drift more slowly than lipids. The fact that proteins drift laterally was established experimentally by fusing a human and mouse cell.

Figure 8.4

Some membrane proteins are tethered to the cytoskeleton and cannot move far.

Membranes must be fluid to work properly. Solidification may result in permeability changes and enzyme deactivation.

• Unsaturated hydrocarbon tails enhance membrane fluidity, because kinks at the carbon-to-carbon double bonds hinder close packing of phospholipids.

• Membranes solidify if the temperature decreases to a critical point. Critical temperature is lower in membranes with a greater concentration of unsaturated phospholipids.

• Cholesterol, found in plasma membranes of eukaryotes, modulates membrane fluidity by making the membrane:

• Cells may alter membrane lipid concentration in response to changes in temperature. Many cold tolerant plants (e.g., winter wheat) increase the unsaturated phospholipid concentration in autumn, which prevents the plasma membranes from solidifying in winter.

2. Membranes as mosaics of structure and function

A membrane is a mosaic of different proteins embedded and dispersed in the phospholipid bilayer. These proteins vary in both structure and function, and they occur in two spatial arrangements:

Figure 8.5

a. Integral proteins are generally transmembrane protein with hydrophobic regions that completely span the hydrophobic interior of the membrane

Figure 8.6

b. Peripheral proteins, which are not embedded but attached to the membrane's surface.

• May be attached to integral proteins or held by fibers of the ECM

• On cytoplasmic side, may be held by filaments of cytoskeleton

Membranes are bifacial. The membrane's synthesis and modification by the ER and Golgi determines this asymmetric distribution of lipids, proteins and carbohydrates:

• Two lipid layers may differ in lipid composition.

• Membrane proteins have distinct directional orientation.

• When present, carbohydrates are restricted to the membrane's exterior.

• Side of the membrane facing the lumen of the ER, Golgi and vesicles is topologically the same as the plasma membrane's outside face

Figure 8.7

• Side of the membrane facing the cytoplasm has always faced the cytoplasm, from the time of its formation by the endomembrane system to its addition to the plasma membrane by the fusion of a vesicle.

Figure 8.8, provides an overview of the six major kinds of function exhibited by proteins of the plasma membrane.

3. Membrane carbohydrates and cell-cell recognition

Cell-cell recognition = The ability of a cell to determine if other cells it encounters are alike or different from itself

Cell-cell recognition is crucial in the functioning of an organism. It is the basis for:

• Sorting of an animal embryo's cells into tissues and organs

• Rejection of foreign cells by the immune system

The way cells recognize other cells is probably by keying on cell markers found on

the external surface of the plasma membrane. Because of their diversity and location, likely candidates for such cell markers are membrane carbohydrates:

• Usually branched oligosaccharides (< 15 monomers)

• Some covalently bonded to lipids (glycolipids)

• Most covalently bonded to proteins (glycoproteins)

• Vary from species to species, between individuals of the same species and among cells in the same individual

II. Traffic Across Membranes

A. A membrane's molecular organization results in selective permeability The selectively permeable plasma membrane regulates the type and rate of molecular traffic into and out of the cell.

Selective permeability = Property of biological membranes which allows some substances to cross more easily than others. The selective permeability of a membrane depends upon:

I. Permeability of the lipid bilayer

The ability of substances to cross the hydrophobic core of the plasma membrane can be measured as the rate of transport through an artificial phospholipid bilayer:

a. Nonpolar (hydrophobic) molecules

Dissolve in the membrane and cross it with ease (e.g., hydrocarbons, 02, C02)

• If two molecules are equally lipid soluble, the smaller of the two will cross the membrane faster.

b. Polar (hydrophilic) molecules

Small, polar uncharged molecules (e.g., H20, ethanol) that are small enough to pass between membrane lipids, will easily pass through synthetic membranes.

• Larger, polar uncharged molecules (e.g., glucose) will not easily pass through synthetic membranes.

• All ions, even small ones (e.g., Na', H') have difficulty penetrating the hydrophobic layer.

2. Transport proteins

Small polar molecules and nonpolar molecules rapidly pass through the plasma membrane as they do an artificial membrane.

Unlike artificial membranes, however, biological membranes are pen-neable to specific ions and certain polar molecules of moderate size. These hydrophilic substances avoid the hydrophobic core of the bilayer by passing through transport proteins.

Transport proteins = Integral membrane proteins that transport specific molecules or ions across biological membranes

Figure 8.8a

• May provide a hydrophilic tunnel through the membrane.

• May bind to a substance and physically move it across the membrane.

• Are specific for the substance they translocate.



B. Passive transport is diffusion across a membrane

Concentration gradient = Regular, graded concentration change over a distance in a particular direction.

Net directional movement = Overall movement away from the center of concentration, which results from random molecular movement in all directions.

Diffusion = The net movement of a substance down a concentration gradient

Figure 8.9

• Results from the intrinsic kinetic energy of molecules (also called thermal motion, or heat)

• Results from random molecular motion, even though the net movement may be directional

• Diffusion continues until a dynamic equilibrium is reached-the molecules continue to move, but there is no net directional movement.

In the absence of other forces (e.g., pressure) a substance will diffuse from where it is more concentrated to where it is less concentrated.

• A substance diffuses down its concentration gradient.

• Because it decreases free energy, diffusion is a spontaneous process (-ÆG). It increases entropy of a system by producing a more random mixture of molecules.

• A substance diffuses down its own concentration gradient and is not affected by the gradients of other substances.

Much of the traffic across cell membranes occurs by diffusion and is thus a form of passive transport.

Passive transport = Diffusion of a substance across a biological membrane.

• Spontaneous process which is a function of a concentration gradient when a substance is more concentrated on one side of the membrane.

• Passive process which does not require the cell to expend energy. It is the potential energy stored in a concentration gradient that drives diffusion.

• Rate of diffusion is regulated by the permeability of the membrane, so some molecules diffuse more freely than others.

• Water diffuses freely across most cell membranes.

C Osmosis is the passive transport of water

Hypertonic solution A solution with a greater solute concentration than that inside a cell.

Hypotonic solution A solution with a lower solute concentration compared to that inside a cell.

Isotonic solution = A solution with an equal solute concentration compared to that inside a cell.

Osmosis = Diffusion of water across a selectively permeable membrane Figure 8.10

Water diffuses down its concentration gradient.

Some solute molecules can reduce the proportion of water molecules that can freely diffuse. Water molecules form a hydration shell around hydrophilic solute molecules and this bound water cannot freely diffuse across a membrane.

In dilute solutions including most biological fluids, it is the different in the proportion of the unbound water that causes osmosis, rather than the actual difference in water concentration.

Direction of osmosis is determined by the difference in total solute concentration, regardless of the type or diversity of solutes in the solutions.

If two isotonic solutions are separated by a selectively permeable membrane, water molecules diffuse across the membrane in both directions at an equal rate. There is no net movement of water.

Osmotic concentration = Total solute concentration of a solution

Osmotic pressure = Measure of the tendency for a solution to take up water when separated from pure water by a selectively permeable membrane.

· Osmotic pressure of pure water is zero.

· Osmotic pressure of a solution is proportional to its osmotic concentration. (The greater the solute concentration, the greater the osmotic pressure.)

Osmotic pressure can be measured by an osmometer:

D. Cell survival depends on balancing water uptake and loss

1. Water balance of cells without walls

Since animal cells lack cell walls, they are not tolerant of excessive osmotic uptake or loss of water

Figure 8.11

Organisms without cell walls prevent excessive loss or uptake of water by:

• Living in an isotonic environment (e.g., many marine invertebrates are isosmotic with sea water).

• Osmoregulating in a hypo- or hypertonic environment. Organisms can regulate water balance (osmoregulation) by removing water in a hypotonic environment (e.g., Paramecium with contractile vacuoles in fresh water) or conserving water and pumping out salts in a hypertonic environment (e.g., bony fish in seawater)

Figure 8.12

2. Water balance of cells with walls

Cells of prokaryotes, some protists, fungi and plants have cell walls outside the plasma membrane.

• In a hypotonic environment, water moves by osmosis into the plant cell, causing it to swell until internal pressure against the cell wall equals the osmotic pressure of the cytoplasm. A dynamic equilibrium is established (water enters and leaves the cell at the same rate and the cell becomes turgid).

Turgid = Firmness or tension such as found in walled cells that are in a hypoosmotic environment where water enters the cell by osmosis.

• Ideal state for most plant cells.

• Turgid cells provide mechanical support for plants.

• Requires cells to be hyperosmotic to their environment.

• In an isotonic environment, there is no net movement of water into or out of the cell.

• Plant cells become flaccid or limp.

• Loss of structural support from turgor pressure causes plants to wilt.

• In a hypertonic environment, walled cells will lose water by osmosis and will plasmolyze, which is usually lethal.

Plasmolysis = Phenomenon where a walled cell shrivels and the plasma membrane pulls away from the cell wall as the cell loses water to a hypertonic environment.

E Specific proteins facilitate the passive transport of selected solutes

Facilitated diffusion = Diffusion of solutes across a membrane, with the help of transport proteins.

• Is passive transport because solute is transported down its concentration gradient.

• Helps the diffusion of many polar molecules and ions that are impeded by the membrane's phospholipid bilayer.

Transport proteins share some properties of enzymes:

• Transport proteins are specific for the solutes they transport. There is probably a specific binding site analogous to an enzyme's active site.

• Transport proteins can be saturated with solute, so the maximum transport rate occurs when all binding sites are occupied with solute.

Transport proteins can be inhibited by molecules that resemble the solute normally carried by the protein (similar to competitive inhibition in enzymes).

Transport proteins differ from enzymes in they do not usually catalyze chemical reactions.

One model for facilitated diffusion

Figure 8.13

Transport protein most likely remains in place in the membrane and translocates solute by alternating between two conformations.

• In one conformation, transport protein binds solute; as it changes to another conformation, transport protein deposits solute on the other side of the membrane.

• The solute's binding and release may trigger the transport protein's conformational change.

Other transport proteins are selective channels across the membrane.

• The membrane is thus permeable to specific solutes that can pass through these channels.

• Some selective channels (gated channels) only open in response to electrical or chemical stimuli. For example, binding of some types of neurotransmitters to nerve cells opens gated channels that allow sodium ions to diffuse into the cell.

F. Active transport is the pumping of solutes against their gradients

Active transport = Energy-requiring process during which a transport protein pumps a molecule across a membrane, against its concentration gradient.

• Is energetically uphill (+AG) and requires the cell to expend energy.

• Helps cells maintain steep ionic gradients across the cell membrane (e.g., Na+, K+, Mg++, Ca++ and CI-).

• Transport proteins involved in active transport harness energy from ATP to pump molecules against their concentration gradients.

An example of an active transport system that translocates ions against steep concentration gradients is the sodium-potassium pump. Major features of the pump are:

I .The transport protein oscillates between two conformations:

a. High affinity for Na+ with binding sites oriented towards the cytoplasm.

b. High affinity for K' with binding sites oriented towards the cell's exterior.

2 . ATP phosphorylates the transport protein and powers the conformational change from Na+ receptive to K+ receptive.

3 . As the transport protein changes conformation, it translocates bound solutes across the membrane.

4. Na+/K+ pump translocates three Na+ ions out of the cell for every two K' ions pumped into the cell.

Figure 8.14

G. Some ion pumps generate voltage across membranes

Because anions and cations are unequally distributed across the plasma membrane, all cells have voltages across their plasma membranes.

Membrane potential = Voltage across membranes

• Ranges from -50 to -200 mV. As indicated by the negative sign, the cell's inside is negatively charged with respect to the outside.

• Affects traffic of charged substances across the membrane

• Favors diffusion of cations into cell and anions out of the cell (because of electrostatic attractions)

Two forces drive passive transport of ions across membranes:

1. Concentration gradient of the ion

2. Effect of membrane potential on the ion

Figure 8.15

Electrochemical gradient = Diffusion gradient resulting from the combined effects of membrane potential and concentration gradient.

• Ions may not always diffuse down their concentration gradients, but they always diffuse down their electrochemical gradients.

• At equilibrium, the distribution of ions on either side of the membrane may be different from the expected distribution when charge is not a factor.

• Uncharged solutes diffuse down concentration gradients because they are unaffected by membrane potential.

Factors which contribute to a cell's membrane potential (net negative charge on the inside):

I. Negatively charged proteins in the cell's interior.

2. Plasma membrane's selective permeability to various ions. For example, there is a net loss of positive charges as K' leaks out of the cell faster than Na+ diffuses in.

3 . The sodium-potassium pump. This electrogenic pump translocates 3 Na' out for every 2 K+ in - a net loss of one positive charge per cycle.

Electrogenic pump = A transport protein that generates voltage across a membrane

Figure 8.16

• Na+/K+ ATPase is the major electrogenic pump in animal cells.

A proton pump is the major electrogenic pump in plants, bacteria, and fungi. Also, mitochondria and chloroplasts use a proton pump to drive ATP synthesis.

• Voltages created by electrogenic pumps are sources of potential energy available to do cellular work.

H. In cotransport, a membrane protein couples the transport of one solute to another

Cotransport = Process where a single ATP-powered pump actively transports one solute and indirectly drives the transport of other solutes against their concentration gradients.

One mechanism of cotransport involves two transport proteins:

1. ATP-powered pump actively transports one solute and creates potential energy in the gradient it creates.

2. Another transport protein couples the solute's downhill diffusion as it leaks back across the membrane with a second solute's uphill transport against its concentration gradient.

For example, plants use a proton pump coupled with sucrose-H+ symport to load sucrose into specialized cells of vascular tissue. Both solutes, H+ and sucrose, must bind to the transport protein for cotransport to take place

Figure 8.17

I. Exocytosis and endocytosis transport large molecules

Water and small molecules cross membranes by:

1. Passing through the phospholipid bilayer.

2. Being translocated by a transport protein.

Large molecules (e.g., proteins and polysaccharides) cross membranes by the processes of exocytosis and endocytosis.




There are three types of endocytosis: (1) phagocytosis, (2) pinocytosis and (3) receptor-mediated endocytosis

Figure 8.18

Phagocytosis = (cell eating); endocytosis of solid particles

• Cell engulfs particle with pseudopodia and pinches off a food vacuole.

• Vacuole fuses with a lysosome containing hydrolytic enzymes that will digest the particle.

Pinocytosis = (cell drinking); endocytosis of fluid droplets

• Droplets of extracellular fluid are taken into small vesicles.

• The process is not discriminating. The cell takes in all solutes dissolved in the droplet.

Receptor-mediated endocytosis = The process of importing specific macromolecules into the cell by the inward budding of vesicles formed from coated pits; occurs in response to the binding of specific ligands to receptors on the cell's surface.

• More discriminating process than pinocytosis.

• A molecule that binds to a specific receptor site of another molecule is called a ligand.

• Membrane-embedded proteins with specific receptor sites exposed to the cell's exterior, cluster in regions called coated pits.

• A layer of clathrin, a fibrous protein, lines and reinforces the coated pit on the cytoplasmic side and probably helps deepen the pit to form a vesicle.

Receptor-mediated endocytosis enables cells to acquire bulk quantities of specific substances, even if they are in low concentration in extracellular fluid. For example, cholesterol enters cells by receptor-mediated endocytosis.

In the blood, cholesterol is bound to lipid and protein complexes called lowdensity lipoproteins (LDLs).

These LDLs bind to LDL receptors on cell membranes, initiating endocytosis.

An inherited disease call familial hypercholesterolemia is characterized by high cholesterol levels in the blood. The LDL receptors are defective, so cholesterol cannot enter the cells by endocytosis and thus accumulates in the blood, contributing to the development of atherosclerosis.

In a nongrowing cell, the amount of plasma membrane remains relatively constant.

• Vesicle fusion with the plasma membrane offsets membrane loss through endocytosis.

• Vesicles provide a mechanism to rejuvenate or remodel the plasma membrane.


Lecture 11 Chapter 9

1. Principles of Energy Conservation

As open systems, cells require outside energy sources to perform cellular work (e.g.,

chemical, transport, and mechanical).

Photosynthetic organisms trap a portion of the light energy and transform it into chemical bond energy of organic molecules. 02 is released as a byproduct.

Cells use some of the chemical bond energy in organic molecules to make ATP-the energy source for cellular work.

Energy leaves living organisms as it dissipates as heat.

The products of respiration (CO2 and H20) are the raw materials for photosynthesis. Photosynthesis produces glucose and oxygen, the raw materials for respiration.


A. Cellular respiration and fermentation are catabolic (energy-yielding) pathways

Fermentation = An ATP-producing catabolic pathway in which both electron donors and acceptors are organic compounds.

Cellular respiration = An ATP-producing catabolic process in which the ultimate electron acceptor is an inorganic molecule, such as oxygen.

Is an exergonic process (ÆG = - 2870 kJ/mol or - 686 kcal/mol)

Can be summarized as:


C6HI206 + 6 02---> 6 C02 + 6 H20 + Energy (ATP + Heat)

B. Cells recycle the ATP they use for work

The catabolic process of cellular respiration transfers the energy stored in food molecules to ATP.

ATP (adenosine triphosphate) = Nucleotide with high energy phosphate bonds that the cell hydrolyzes for energy to drive endergonic reactions.

• The cell taps energy stored in ATP by enzymatically transferring terminal phosphate groups from ATP to other compounds.

• The compound receiving the phosphate group from ATP is said to be phosphorylated and becomes more reactive in the process.

• The phosphorylated compound loses its phosphate group as cellular work is performed; inorganic phosphate and ADP are formed in the process

Figure 9.2

• Cells must replenish the ATP supply to continue cellular work. Cellular respiration provides the energy to regenerate ATP from ADP and inorganic phosphate.

C. Redox reactions release energy when electrons move closer to electronegative atoms

1. An introduction to redox reactions

Oxidation-reduction reactions = Chemical reactions which involve a partial or complete transfer of electrons from one reactant to another; called redox reactions for short.

Oxidation = Partial or complete loss of electrons

Reduction = Partial or complete gain of electrons

Generalized redox reaction:

Electron transfer requires both a donor and acceptor, so when one reactant is oxidized the other is reduced.

Xe- + Y ---> X + Ye-


X = Substance being oxidized; acts as a reducing agent because it reduces Y.

Y = Substance being reduced; acts as an oxidizing agent because it oxidizes X.

Not all redox reactions involve a complete transfer of electrons, but, instead, may.just change the degree of sharing in covalent bonds

Figure 9.3

Oxygen is a powerful oxidizing agent because it is so electronegative.

D. Electrons "fall" from organic molecules to oxygen during cellular respiration

Cellular respiration is a redox process that transfers hydrogen, including electrons with high potential energy, from sugar to oxygen.


C6H1206 + 6 02----> 6 C02 + 6 H20 + energy (used to make ATP)

• Valence electrons of carbon and hydrogen lose potential energy as they shift toward electronegative oxygen.

• Released energy is used by cells to produce ATP.

• Carbohydrates and fats are excellent energy stores because they are rich in C to H bonds.

Without the activation barrier, glucose would combine spontaneously with oxygen.

• Igniting glucose provides the activation energy for the reaction to proceed; a mole of glucose yields 686 kcal (2870 kJ) of heat when burned in air.

• Cellular respiration does not oxidize glucose in one explosive step, as the energy could not be efficiently harnessed in a form available to perform cellular work.

• Enzymes lower the activation energy in cells, so glucose can be slowly oxidized in a stepwise fashion during glycolysis and Krebs cycle.

E The "fall" of electrons during respiration is stepwise, via NAD+ and an electron transport chain

Hydrogens stripped from glucose are not transferred directly to oxygen, but are first passed to a special electron acceptor-NAD+.

Nicotinamide adenine dinucleotide (NAD+) = A dinucleotide that functions as a coenzyme in the redox reactions of metabolism

Figure 9.4

• Found in all cells

• Assists enzymes in electron transfer during redox reactions of metabolism

Coenzyme = Small nonprotein organic molecule that is required for certain enzymes to function.

Dinucleotide = A molecule consisting of two nucleotides.

During the oxidation of glucose, NAD+ functions as an oxidizing agent by trapping energy-rich electrons from glucose or food. These reactions are catalyzed by enzymes called dehydrogenases, which:

· Remove a pair of hydrogen atoms (two electrons and two protons) from substrate

· Deliver the two electrons and one proton to NAD+

· Release the remaining proton into the surrounding solution


NAD+ = Oxidized coenzyme (net positive charge)

NADH = Reduced coenzyme (electrically neutral)

The high energy electrons transferred from substrate to NAD+ are then passed down the electron transport chain to oxygen, powering ATP synthesis (oxidative phosphorylation).


Electron transport chains convert some of the chemical energy extracted from food to a form that can be used to make ATP

Figure 9.5.

These transport chains:

Electron transfer from NADH to oxygen is exergonic, having a free energy change of -222 kJ/mole (-53 kcal/mol).

II. The Process of Cellular Respiration

A. Respiration involves glycolysis, the Krebs cycle, and electron transport: an overview

There are three metabolic stages of cellular respiration

Figure 9.6

1. Glycolysis

2. Krebs cycle

3. Electron transport chain (ETC) and oxidative phosphorylation

GIycolysis is a catabolic pathway that:

• Occurs in the cytosol

• Partially oxidizes glucose (6C) into two pyruvate (3C) molecules

The Krebs cycle is a catabolic pathway that:

• Occurs in the mitochondrial matrix

• Completes glucose oxidation by breaking down a pyruvate derivative (acetyl CoA) into carbon dioxide

Glycolysis and the Krebs cycle produce:

• A small amount of ATP by substrate-level phosphorylation

• NADH by transferring electrons from substrate to NAD+ (Krebs cycle also produces FADH2 by transferring electrons to FAD)

The electron transport chain:

• Is located at the inner membrane of the mitochondrion

• Accepts energized electrons from reduced coenzymes (NADH and FADH2) that are harvested during glycolysis and Krebs cycle. Oxygen pulls these electrons down the electron transport chain to a lower energy state.

• Couples this exergonic slide of electrons to ATP synthesis or oxidative phosphorylation. This process produces most (90%) of the ATP.

Oxidative phosphorylation = ATP production that is coupled to the exergonic transfer of electrons from food to oxygen.

A small amount of ATP is produced directly by the reactions of glycolysis and Krebs cycle. This mechanism of producing ATP is called substrate-level phosphorylation.

Substrate-level phosphorylation = ATP production by direct enzymatic transfer of phosphate from an intermediate substrate in catabolism to ADP.

B. Glycolysis harvests chemical energy by oxidizing glucose to pyruvate

Glycolysis = (Glyco = sweet, sugar; lysis = to split); catabolic pathway during which six-carbon glucose is split into two three-carbon sugars, which are then oxidized and rearranged by a step-wise process that produces two pyruvate molecules.

• Each reaction is catalyzed by specific enzymes dissolved in the cytosol.

• No C02 is released as glucose is oxidized to pyruvate; all carbon in glucose can be accounted for in the two molecules of pyruvate.

• Occurs whether or not oxygen is present.

The reactions of glycolysis occur in two phases:

Energy-investment phase. The cell uses ATP to phosphorylate the intermediates of glycolysis.

Energy-yielding phase. Two three-carbon intermediates are oxidized. For each glucose molecule entering glycolysis:

1. A net gain of two ATPs is produced by substrate-level phosphorylation.

2. Two molecules of NAD+ are reduced to NADH. Energy conserved in the high energy electrons of NADH can be used to make ATP by oxidative phosphorylation.


Energy-investment phase:

The energy investment phase includes five preparatory steps that split glucose in two.

This process actually consumes ATP.

Energy-yielding phase:

The energy-yielding phase occurs after glucose is split into two three-carbon sugars.

During these reactions, sugar is oxidized, and ATP

and NADH are produced.



Summary equation for glycolysis:

C6H1206-------------->2 C3H403 (Pyruvate)

+ 2 NAD+------------->+ 2 NADH + 2 H+

+ 2 ADP + 2 (P)----->+ 2 ATP

+ 2 H20

Glucose has been oxidized into two pyruvate molecules.

The process is exergonic (ÆG = -140 kcal/mol or -586 kJ/mol); most of the energy harnessed is conserved in the high-energy electrons of NADH and in the phosphate bonds of ATP.


Lecture 12 Chapter 9 continued

C. The Krebs cycle completes the energy-yielding oxidation of organic molecules:

Most of the chemical energy originally stored in glucose still resides in the two pyruvate molecules produced by glycolysis. The fate of pyruvate depends upon the presence or absence of oxygen. If oxygen is present, pyruvate enters the mitochondrion where it is completely oxidized by a series of enzyme-controlled reactions.

1. Formation of acetyl CoA

• Pyruvate molecules are translocated from the cytosol into the mitochondrion by a carrier protein in the mitochondrial membrane.

• This step is catalyzed by a multienzyme complex which:

1. Removes C02 from the carboxyl group of pyruvate, changing it from a three-carbon to a two-carbon compound. This is the first step where C02 is released.

2. Oxidizes the two-carbon fragment to acetate, while reducing NAD+ to NADH. Since glycolysis produces two pyruvate molecules per glucose, there are two NADH molecules produced.

3 . Attaches coenzyme A to the acetyl group, forming acetyl CoA. This bond is unstable, making the acetyl group very reactive.

Figure 9.10

2. Krebs cycle

The Krebs cycle reactions oxidize the remaining acetyl fragments of acetyl CoA to C02.

Energy released from this exergonic process is used to reduce coenzyme (NAD+ and FAD) and to phosphorylate ATP (substrate-level phosphorylation).

NOTE: The FAD dinucleotide upon reduction accepts two electrons and two protons.

For every turn of Krebs cycle:

• Two carbons enter in the acetyl fragment of acetyl CoA.

• Two different carbons are oxidized and leave as C02

• Coenzymes are reduced; three NADH and one FADH2 are produced.

• One ATP molecule is produced by substrate-level phosphorylation.

• Oxaloacetate is regenerated.

Figure 9.11

For every glucose molecule split during glycolysis two acetyl fragments are produced.

Therefore, it takes two turns of Krebs cycle to complete the oxidation of glucose.

Two turns of the Krebs cycle produce two ATPs by substrate-level phosphorylation. However, most ATP output of respiration results from oxidative phosphorylation.

Figure 9.12

D. The innermitochondrial membrane couples electron transport to ATP synthesis:

Only a few molecules of ATP are produced by substrate-level phosphorylation:

• Two net ATPs per glucose from glycolysis

• Two ATPs per glucose from the Krebs cycle

Most molecules of ATP are produced by oxidative phosphorylation.

• At the end of the Krebs cycle, most of the energy extracted from glucose is in molecules of NADH and FADH2

• These reduced coenzymes link glycolysis and the Krebs cycle to oxidative phosphorylation by passing their electrons down the electron transport chain to oxygen. (Though the Krebs cycle occurs only under aerobic conditions, it does not use oxygen directly. The ETC and oxidative phosphorylation require oxygen as the final electron acceptor.)

• This exergonic transfer of electrons down the ETC to oxygen is coupled to ATP synthesis.

1. The pathway of electron transport

The electron transport chain is made of electron carrier molecules embedded in the inner mitochondrial membrane.

Protein Electron Carriers Prosthetic Group

flavoproteins flavin mononucleotide (FNTN)

iron-sulfur proteins iron and sulfur

cytochromes heme group

Heme group = Prosthetic group composed of four organic rings surrounding a single iron atom

Cytochrome = Type of protein molecule that contains a heme prosthetic group and that functions as an electron carrier in the electron transport chains of mitochondria and chloroplasts

• There are several cytochromes, each a slightly different protein with a heme group.

• It is the iron of cytochromes that transfers electrons.

Sequence of electron transfers along the electron transport chain

Figure 9.13

NADH is oxidized and flavoprotein is reduced as high energy electrons from NADH are transferred to FMN

Flavoprotein is oxidized as it passes electrons to an iron-sulfur protein, Fe•S.

Iron-sutfur protein is oxidized as it passes electrons to ubiquinone (Q)

Ubiquinone passes electrons on to a succession of electron carriers, most of which are cytochromes.

Cyt a3, the last cytochrome passes electrons to molecular oxygen, 02.

As molecular oxygen is reduced it also picks up two protons from the medium to form water. For every two NADH, one 02 is reduced to two H20 molecules.

• FADH2 also donates electrons to the electron transport chain, but those electrons are added at a lower energy level than NADH.

• The electron transport chain does not make ATP directly. It generates a proton gradient across the inner mitochondrial membrane, which stores potential energy that can be used to phosphorylate ADP.

2. Chemiosmosis: the energy-coupling mechanism

The mechanism for coupling exergonic electron flow from the oxidation of food to the endergonic process of oxidative phosphorylation is chemiosmosis.

Chemiosmosis = The coupling of exergonic electron flow down an electron transport chain to endergonic ATP production by the creation of a proton gradient across a membrane. The proton gradient drives ATP synthesis as protons diffuse back across the membrane.

The term chemiosmosis emphasizes a coupling between (1) chemical

reactions (phosphorylation) and (2) transport processes (proton transport).

Process involved in oxidative phosphorylation and photophosphorylation.

The site of oxidative phosphorylation is the inner mitochondrial membrane, which has many copies of a protein complex, ATP synthase. This complex:

• Is an enzyme that makes ATP

• Uses an existing proton gradient across the inner mitochondrial membrane to power ATP synthesis

Figure 9.14

Cristae, or infoldings of the inner mitochondrial membrane, increase the surface area available for chemiosmosis to occur.

Membrane structure correlates with the prominent functional role membranes play in chemiosmosis:

• Using energy from exergonic electron flow, the electron transport chain creates the proton gradient by pumping H+s from the mitochondrial matrix, across the inner membrane to the intermembrane space.

• This proton gradient is maintained, because the inner membrane's phospholipid bilayer is impermeable to H+ and prevents them from leaking back across the membrane by diffusion.

ATP synthases use the potential energy stored in a proton gradient to make ATP by allowing H+ to diffuse down the gradient, back across the membrane. Protons diffuse through the ATP synthase complex, which causes the phosphorylation of ADP

How does the electron transport chain pump hydrogen ions ftom the matrix to the intermembrane space? The process is based on spatial organization of the electron transport chain in the membrane. Note that:

• Some electron carriers of the transport chain transport only electrons.

• Some electron carriers accept and release protons along with electrons. These carriers are spatially arranged so that protons are picked up from the matrix and are released into the intermembrane space.

Most of the electron carriers are organized into three complexes:

  1. NADH dehydrogenase complex
  2. cytochrome b-c1 complex; and
  3. cytochrome oxidase complex

Figure 9.15.

Each complex is an asymmetric particle that has a specific orientation in the membrane.

As complexes transport electrons, they also harness energy from this exergonic process to pump protons across the inner mitochondrial membrane.

Mobile carriers transfer electrons between complexes. These mobile carriers are:

I . Ubiquinone (Q). Near the matrix, Q accepts electrons from the NADH dehydrogenase complex, diffuses across the lipid bilayer, and passes electrons to the cytochrome b-c1 complex.

2. Cytochrome c (Cyt c). Cyt c accepts electrons from the cytochrome b-c1 complex and conveys them to the cytochrome oxidase complex.

When the transport chain is operating:

• The pH in the intermembrane space is one or two pH units lower than in the matrix.

• The pH in the intermembrane space is the same as the pH of the cytosol because the outer mitochondrial membrane is permeable to protons.

The H+ gradient that results is called a proton-motive force to emphasize that the gradient represents potential energy.

Proton motive force = Potential energy stored in the proton gradient created across biological membranes that are involved in chemiosmosis

• This force is an electrochemical gradient with two components:

1. Concentration gradient of protons (chemical gradient)

2. Voltage across the membrane because of a higher concentration of positively charged protons on one side (electrical gradient)

It tends to drive protons across the membrane back into the matrix.

Chemiosmosis couples exergonic chemical reactions to endergonic H+ transport, which creates the proton-motive force used to drive cellular work, such as:

• ATP synthesis in mitochondria (oxidative phosphorylation). The energy to create the proton gradient comes from the oxidation of glucose and the ETC.

• ATP synthesis in chloroplasts (photophosphorylation). The energy to create the proton gradient comes from light trapped during the energycapturing reactions of photosynthesis.

• ATP synthesis, transport processes, and rotation of flagella in bacteria. The proton gradient is created across the plasma membrane.

3. Biological themes and oxidative phosphorylation

The working model of how mitochondria harvest the energy of food illustrates many of the text's integrative themes in the study of life:

• Energy conversion and utilization

• Emergent properties - Oxidative phosphorylation is an emergent property of the intact mitochondrion that uses a precise interaction of molecules.

• Correlation of structure and function - The chemiosmotic model is based upon the spatial arrangement of membrane proteins.

• Evolution - In an effort to reconstruct the origin of oxidative phosphorylation and the evolution of cells, biologists compare similarities in the chemiosmotic machinery of mitochondria to that of chloroplasts and bacteria.

E Cellular respiration generates many ATP molecules for each sugar molecule it oxidizes: a review

During cellular respiration, most energy flows in this sequence:

Glucose ==> NADH => electron transport chain => proton motive force => ATP.

The net ATP yield from the oxidation of one glucose molecule to six carbon dioxide molecules can be estimated by adding:

1. ATP produced directly by substrate-level phosphorylation during glycolysis and the Krebs cycle.

A net of two ATPs is produced during glycolysis. The debit of two ATPs used during the investment phase is subtracted from the four ATPs produced during the energy-yielding phase.

2. ATP produced when chemiosmosis couples electron transport to oxidative phosphorylation.

• The electron transport chain creates enough proton-motive force to produce a maximum of three ATPs for each electron pair that travels from NADH to oxygen. The average yield is actually between two and three ATPs per NADH (2.7).

• FADH2 produced during the Krebs cycle is worth a maximum of only two ATPS, since it donates electrons at a lower energy level to the electron transport chain.

• In most eukaryotic cells, the ATP yield is lower due to a NADH produced during glycolysis. The mitochondrial membrane is impermeable to NADH, so its electrons must be carried across the membrane in by one of several "shuttle" reactions. Depending on which shuttle is operating, electrons can be transferred to either NAD+ or FAD+ . A pair of electrons passed to FAD+ yields about two ATP, whereas a pair of electrons passed to NAD+ yields about 13 ATP.

See Figure 9.16

This tally only estimates the ATP yield from respiration

Some variables that affect ATP yield include:

• The proton-motive force may be used to drive other kinds of cellular work such as active transport.

• The total ATP yield is inflated (-10%) by rounding off the number of ATPs produced per NADH to three.

Cellular respiration is remarkably efficient in the transfer of chemical energy from glucose to ATP.

• Estimated efficiency in eukaryotic cells is about 40%.

• Energy lost in the process is released as heat.



Calculated by 7.3 kcal/mol ATP x 38 mol ATP/mol glucose x 100

686 kcal/mol glucose



III. Related Metabolic Processes

A. Fermentation enables some cells to produce ATP without the help of oxygen Food can be oxidized under anaerobic conditions.

Aerobic = (Aer = air; bios = life); existing in the presence of oxygen

Anaerobic = (An = without; aer = air); existing in the absence of free oxygen

Fermentation = Anaerobic catabolism of organic nutrients

Glycolysis oxidizes glucose to two pyruvate molecules, and the oxidizing agent for this process is NAD+, not oxygen.

• Some energy released from the exergonic process of glycolysis drives the production of two net ATPs by substrate-level phosphorylation.

• Glycolysis produces a net of two ATPs whether conditions are aerobic or anaerobic.

Aerobic conditions: Pyruvate is oxidized further by substrate-level

phosphorylation and by oxidative phosphorylation and more ATP is made as NADH passes electrons to the electron transport chain. NAD+ is regenerated in the process.

Anaerobic conditions: Pyruvate is reduced, and NAD+ is regenerated. This prevents the cell from depleting the pool of NAD+, which is the oxidizing agent necessary for glycolysis to continue. No additional ATP is produced.

Fermentation recycles NAD+ from NADH. This process consists of anaerobic glycolysis plus subsequent reactions that regenerate NAD+ by reducing pyruvate. Two of the most common types of fermentation are (1) alcohol fermentation and (2) lactic acid fermentation

Figure 9.17


Pyruvate is converted to ethanol in two steps:

Many bacteria and yeast carry out alcohol fermentation under anaerobic conditions.

Lactic acid fermentation:

Commercially important products of lactic acid fermentation include cheese and yogurt.

When oxygen is scarce, human muscle cells switch from aerobic respiration to lactic acid fermentation. Lactate accumulates, but it is gradually carried to the liver where it is converted back to pyruvate when oxygen becomes available.

1. Fermentation and respiration compared

The anaerobic process of fermentation and aerobic process of cellular respiration are similar in that both metabolic pathways:

• Use glycolysis to oxidize glucose and other substrates to pyruvate, producing a net of two ATPs by substrate phosphorylation

• Use NAD+ as the oxidizing agent that accepts electrons from food during glycolysis

Fermentation and cellular respiration differ in:

• How NADH is oxidized back to NAD+. Recall that the oxidized form, NAD+, is necessary for glycolysis to continue.

• During fermentation, NADH passes electrons to pyruvate or some

derivative. As pyruvate is reduced, NADH is oxidized to NAD+. Electrons transferred from NADH to pyruvate or other substrates are not used to power ATP production.

• During cellular respiration, the stepwise electron transport from NADH to oxygen not only drives oxidative phosphorylation, but regenerates NAD+ in the process.

• Final electron acceptor

• In fermentation, the final electron acceptor is pyruvate (lactic acid fermentation), acetaldehyde (alcohol fermentation), or some other organic molecule.

• In cellular respiration, the final electron acceptor is oxygen.

Amount of energy harvested

• During fermentation, energy stored in pyruvate is unavailable to the cell.

• Cellular respiration yields 18 times more ATP per glucose molecule than does fermentation. The higher energy yield is a consequence of the Krebs cycle which completes the oxidation of glucose and thus taps the chemical bond energy still stored in pyruvate at the end of glycolysis.

Requirement for oxygen

• Fermentation does not require oxygen.

• Cellular respiration occurs only in the presence of oxygen. Organisms can be classified based upon the effect oxygen has on growth and metabolism.

Strict (obligate) aerobes = Organisms that require oxygen for growth and as the final electron acceptor for aerobic respiration.

Strict (obligate) anaerobes = Microorganisms that only grow in the absence of oxygen and are, in fact, poisoned by it.

Facultative anaerobes = Organisms capable of growth in either aerobic or anaerobic environments.

• Yeasts, many bacteria, and mammalian muscle cells are facultative anaerobes.

• Can make ATP by fermentation in the absence of oxygen or by respiration in the presence of oxygen.

• Glycolysis is common to both fermentation and respiration, so pyruvate is a key juncture in catabolism

Figure 9.18

3. The evolutionary significance of glycolysis

The first prokaryotes probably produced ATP by glycolysis. Evidence includes the following:

• Glycolysis does not require oxygen, and the oldest known bacterial fossils date back to 3.5 billion years ago when oxygen was not present in the atmosphere.

• Glycolysis is the most widespread metabolic pathway, so it probably evolved early.

• Glycolysis occurs in the cytosol and does not require membrane-bound organelles. Eukaryotic cells with organelles probably evolved about two billion years after prokaryotic cells.

B. Glycolysis and the Krebs cycle connect to many other metabolic pathways

1. The versatility of catabolism

Respiration can oxidize organic molecules other than glucose to make ATP. Organisms obtain most calories from fats, proteins, disaccharides and polysaccharides. These complex molecules must be enzymatically hydrolyzed into simpler molecules or monomers that can enter an intermediate reaction of glycolysis or the Krebs cycle.

Figure 9.19

Glycolysis can accept a wide range of carbohydrates for catabolism.

• Starch is hydrolyzed to glucose in the digestive tract of animals.

• In-between meals, the liver hydrolyzes glycogen to glucose.

• Enzymes in the small intestine break down disaccharides to glucose or other monosaccharides.

Proteins are hydrolyzed to amino acids.

• Organisms synthesize new proteins from some of these amino acids.

• Excess amino acids are enzymatically converted to intermediates of glycolysis and the Krebs cycle. Common intermediates are pyruvate, acetyl CoA, and (alpha-ketoglutarate.

• This conversion process deaminates amino acids, and the resulting nitrogenous wastes are excreted and the carbon skeleton can be oxidized.

Fats are excellent fuels because they are rich in hydrogens with high energy electrons. Oxidation of one gram of fat produces twice as much ATP as a gram of carbohydrate.

• Fat sources may be from the diet or from storage cells in the body.

• Fats are digested into glycerol and fatty acids.

• Glycerol can be converted to glyceraldehyde phosphate, an intermediate of glycolysis.

Most energy in fats is in fatty acids, which are converted into acetyl CoA by beta oxidation. The resulting two-carbon fragments can enter the Krebs cycle.

2. Biosynthesis (anabolic pathways)

Some organic molecules of food provide the carbon skeletons or raw materials for the synthesis of new macromolecules.

• Some organic monomers from digestion can be used directly in anabolic pathways.

• Some precursors for biosynthesis do not come directly from digested food, but instead come from glycolysis or Krebs cycle intermediates which are diverted into anabolic pathways.

These anabolic pathways require energy (ATP) produced by catabolic pathways of glycolysis and respiration.

Glycolysis and the Krebs cycle are metabolic interchanges that can convert one type of macromolecule to another in response to the cell's metabolic demands.

C. Feedbackmechanisms control cellular respiration

Cells respond to changing metabolic needs by controlling reaction rates.

• Anabolic pathways are switched off when their products are in ample supply. The most common mechanism of control is feedback inhibition.

• Catabolic pathways, such as glycolysis and Krebs cycle, are controlled by regulating enzyme activity at strategic points.

A key control point of catabolism is the third step of glycolysis, which is catalyzed by an allosteric enzyme, phosphoftuctokinase

Figure 9.20

• The ratio of ATP to ADP and AMP reflects the energy status of the cell, and phosphofructokinase is sensitive to changes in this ratio.

• Citrate (produced in Krebs cycle) and ATP are allosteric inhibitors of phosphofructokinase, so when their concentrations rise, the enzyme slows glycolysis. As the rate of glycolysis slows, Krebs cycle also slows since the supply of acetyl CoA is reduced. This synchronizes the rates of glycolysis and Krebs cycle.

• ADP and AMP are allosteric activators for phosphofructokinase, so when their concentrations relative to ATP rise, the enzyme speeds up glycolysis which speeds up the Krebs cycle.

• There are other allosteric enzymes that also control the rates of glycolysis and the Krebs cycle.


Chapter 10


1. Photosynthesis in Nature

Photosynthesis transforms solar light energy trapped by chloroplasts into chemical bond energy stored in sugar and other organic molecules. This process:

• Synthesizes energy-rich organic molecules from the energy-poor molecules, C02 and H20

• Uses C02 as a carbon source and light energy as the energy source.

A. Plants and other autotrophs are the producers of the biosphere

Organisms acquire organic molecules used for energy and carbon skeletons by one of two nutritional modes: 1) autotrophic nutrition or 2) heterotrophic nutrition.

Autotrophic nutrition = (Auto = self-, trophos = feed); nutritional mode of synthesizing organic molecules from inorganic raw materials

• Examples of autotrophic organisms are plants, which require only C02, H20 and minerals as nutrients.

• Because autotrophic organisms produce organic molecules that enter an ecosystem's food store, autotrophs are also known as producers.

Autotrophic organisms require an energy source to synthesize organic molecules. That energy source may be from light (photoautotrophic) or from

the oxidation of inorganic substances (chemoautotrophic).

Photoautotrophs = Autotrophic organisms that use light as an energy source to synthesize organic molecules. Examples are photosynthetic organisms such as plants, algae, and some prokaryotes.

Chemoautotrophs = Autotrophic organisms that use the oxidation of inorganic substances, such as sulfur or ammonia, as an energy source to synthesize organic molecules. Unique to some bacteria, this is a rarer form of autotrophic nutrition.

Heterotrophic nutrition = (Heteros = other; trophos = feed); nutritional mode of acquiring organic molecules from compounds produced by other organisms. Heterotrophs are unable to synthesize organic molecules from inorganic raw materials.

B. Chloroplasts are the sites of photosynthesis in plants Although all green plant parts have chloroplasts, leaves are the major sites of photosynthesis in most plants.

Figure 10.2

Chloroplasts are primarily in cells of mesophyll, green tissue in the leaf's interior.

· C02 enters and 02 exits the leaf through microscopic pores called stomata.

· Water absorbed by the roots is transported to leaves through veins or vascular bundles which also export sugar from leaves to nonphotosynthetic parts of the plant.

Chloroplasts are lens-shaped organelles measuring about 2 - 4 Ám by 4 - 7 Ám. These organelles are divided into three functional compartments by a system of membranes:

1. Intermembrane space The chloroplast is bound by a

double membrane which partitions its contents from the

cytosol. A narrow intermembrane space separates

the two membranes.

2. Thylakoid space Thylakoids form another membranous system within the chloroplast. The thylakoid membrane segregates the interior of the chloroplast into two compartments: thylakoid space and stroma.

Thylakoids = Flattened membranous sacs inside the chloroplast

• Chlorophyll is found in the thylakoid membranes.

• Thylakoids function in the steps of photosynthesis that initially convert light energy to chemical energy.

Thylakoid space = Space inside the thylakoid

Grana = (Singular, granum); stacks of thylakoids in a chloroplast

3 Stroma

Reactions that use chemical energy to convert carbon dioxide to sugar occur in the stroma, viscous fluid outside the thylakoids.

Photosynthetic prokaryotes lack chloroplasts, but have chlorophyll built into the plasma membrane or membranes of numerous vesicles within the cell.

• These membranes function in a manner similar to the thylakoid membranes of chloroplasts.

• Photosynthetic membranes of cyanobacteria are usually arranged in parallel stacks of flattened sacs similar to the thylakoids of chloroplasts.

11. The Pathways of Photosynthesis

A. Evidence that chloroplasts split water molecules enabled researchers to track atoms through photosynthesis:

summary equation has been known since the early 1800s:

6 C02 + 12 H20 + light energy --> C6H1206 + 6 02 + 6 H20

• Glucose (C6H1206) is shown in the summary equation, though the main products of photosynthesis are other carbohydrates.

• Water is on both sides of the equation because photosynthesis consumes 12 molecules and forms 6.

Indicating the net consumption of water simplifies the equation:

6 C02 + 6 H20 + light energy --> C6H1206 + 6 02

• In this form, the summary equation for photosynthesis is the reverse of that for cellular respiration.

• Photosynthesis and cellular respiration both occur in plant cells, but plants do not simply reverse the steps of respiration to make food.

The simplest form of the equation is:

C02 + H20 ---> CH20 + 02

• CH20 symbolizes the general formula for a carbohydrate.

• In this form, the summary equation emphasizes the production of a sugar molecule, one carbon at a time. Six repetitions produces a glucose molecule.

1. The splitting of water The discovery that 02 released by plants is derived from H20 and not from C02, was one of the earliest clues to the mechanism of photosynthesis.

• All photosynthetic organisms required hydrogen, but that the source varied:

general: C02 + 2 H2X ---> CH20 + H20 + 2 X

sulfur bacteria: C02 + 2 H2S ---> CH20 + H20 + 2 S

plants: C02 + 2 H20 ---> CH20 + H20 + 02

Plants split water as a source of hydrogen and release oxygen as a by-product.

Scientists later confirmed this hypothesis by using a heavy isotope of oxygen

(180) as a tracer to follow oxygen's fate during photosynthesis.

• If water was labeled with tracer, released oxygen was 180:

Experiment 1: C02 + 2 H20* --> CH20 + H20 + 02*

• If the 180 was introduced to the plant as C02, the tracer did not appear in the released oxygen:

Experiment 2: C02* + 2H20 ---> CH20* + H20* + 02

An important result of photosynthesis is the extraction of hydrogen from water and its incorporation into sugar.

Electrons associated with hydrogen have more potential energy in organic molecules than they do in water, where the electrons are closer to electronegative oxygen.

Energy is stored in sugar and other food molecules in the form of these high-energy electrons.

2. Photosynthesis as a redox process

Respiration is an exergonic redox process; energy is released from the oxidation of sugar.

• Electrons associated with sugar's hydrogens lose potential energy as carriers transport them to oxygen, forming water.

• Electronegative oxygen pulls electrons down the electron transport chain, and the potential energy released is used by the mitochondrion to produce ATP.

Photosynthesis is an endergonic redox process; energy is required to reduce carbon dioxide.

• Light is the energy source that boosts potential energy of electrons as they are moved from water to sugar.

• When water is split, electrons are transferred from the water to carbon dioxide, reducing it to sugar.

B. The light reactions and the Calvin cycle cooperate in transforming light to the chemical energy of food.

Photosynthesis occurs in two stages: the light reactions and the Calvin cycle.

Light reactions = In photosynthesis, the reactions that convert light energy to chemical bond energy in ATP and NADPH. These reactions:

• Occur in the thylakoid membranes of chloroplasts

• Reduce NADP+ to NADPH

• Light absorbed by chlorophyll provides the energy to reduce NADP+ to NADPH, which temporarily stores the energized electrons transferred from water.

• NADP+ (nicotinamide adenine dinucleotide phosphate), a coenzyme similar to NAD+ in respiration, is reduced by adding a pair of electrons along with a hydrogen nucleus, or H+.

•Give Off 02 as a by-product from the splitting of water

•Generate ATP. The light reactions power the addition of a phosphate group to ADP in a process called photophosphorylation.

Calvin cycle = In photosynthesis, the carbon-fixation reactions that assimilate atmospheric C02 and then reduce it to a carbohydrate; named for Melvin Calvin. These reactions:

Carbon fixation = The process of incorporating C02 into organic molecules.

The Calvin cycle reactions do not require light directly, but reduction of C02 to sugar requires the products of the light reactions:

• NADPH provides the reducing power.

• ATP provides the chemical energy.

Chloroplasts thus use light energy to make sugar by coordinating the two stages of photosynthesis.

Figure 10.4

As NADP+ and ADP contact thylakoid membranes, they pick up electrons and phosphate respectively, and then transfer their high-energy cargo to the Calvin cycle.

C The light reactions transform solar energy to the chemical energy of ATP and NADPH.

To understand how the thylakoids of chloroplasts transform light energy into the chemical energy of ATP and NADPH, it is necessary to know some important properties of light.

1. The nature of sunlight

Sunlight is electromagnetic energy. The quantum mechanical model of electromagnetic radiation describes light as having a behavior that is both wavelike and partictelike.

a. Wavelike properties of light

Electromagnetic energy is a form of energy that travels in rhythmic waves which are disturbances of electric and magnetic fields.

A wavelength is the distance between the crests of electromagnetic waves.

• The electromagnetic spectrum ranges from wavelengths that are less than a nanometer (gamma rays) to those that are more than a kilometer (radio waves).

Figure 10.5

Visible light, which is detectable by the human eye, is only a small portion of the electromagnetic spectrum and ranges from about 380 to 750 nm. The wavelengths most important for photosynthesis are within this range of visible light.

b. Particielike properties of light

Light also behaves as if it consists of discrete particles or quanta called photons.

• Each photon has a fixed quantity of energy which is inversely proportional to the wavelength of light. For example, a photon of violet light has nearly twice as much energy as a photon of red light.

The sun radiates the full spectrum of electromagnetic energy.

• The atmosphere acts as a selective window that allows visible light to pass through while screening out a substantial fraction of other radiation.

The visible range of light is the radiation that drives photosynthesis.

Blue and red, the two wavelengths most effectively absorbed by chlorophyll, are the colors most useful as energy for the light reactions.

2. Photosynthetic pigments: the light receptors

Light may be reflected, transmitted, or absorbed when it contacts matter.

Figure 10.6

Pigments = Substances which absorb visible light

• Different pigments absorb different wavelengths of light.

• Wavelengths that are absorbed disappear, so a pigment that absorbs all wavelengths appears black.

• When white light, which contains all the wavelengths of visible light, illuminates a pigment, the color you see is the color most reflected or transmitted by the pigment. For example, a leaf appears green because chlorophyll absorbs red and blue light but transmits and reflects green light.

Each pigment has a characteristic absorption spectrum or pattern of wavelengths that it absorbs. It is expressed as a graph of absorption versus wavelength.

• The absorption spectrum for a pigment in solution can be determined by using a spectrophotometer, an instrument used to measure what proportion of a specific wavelength of light is absorbed or transmitted by the pigment.

• Since chlorophyll a is the light-absorbing pigment that participates directly in the light reactions, the absorption spectrum of chlorophyll a provides clues as to which wavelengths of visible light are most effective for photosynthesis.

Figure 10.7a

A graph of wavelength versus rate of photosynthesis is called an action spectrum and profiles the relative effectiveness of different wavelengths of visible light for driving photosynthesis

Figure 10.7b

• The action spectrum of photosynthesis can be determined by illuminating chloroplasts with different wavelengths of light and measuring some indicator of photosynthetic rate, such as oxygen release or carbon dioxide consumption.

Figure 10.7c

• It is apparent from the action spectrum of photosynthesis that blue and red light are the most effective wavelengths for photosynthesis and green light is the least effective.

The action spectrum for photosynthesis does not exactly match the absorption spectrum for chlorophyll a.

Since chlorophyll a is not the only pigment in chloroplasts that absorb light, the absorption spectrum for chlorophyll a underestimates the effectiveness of some wavelengths.

Even though only special chlorophyll a molecules can participate directly in the light reactions, other pigments, called accessor pigments, can absorb light and transfer the energy to chlorophyll a.

The accessory pigments expand the range of wavelengths available for photosynthesis. These pigments include:

Chlorophyll b, a yellow-green pigment with a structure similar to chlorophyll a. This minor structural difference gives the pigments slightly different absorption spectra.

Figure 10.8

Carotenoids, yellow and orange hydrocarbons that are built into the thylakoid membrane with the two types of chlorophyll.

Figure 10.7a

3. Photoexcitation of chlorophyll

What happens when chlorophyll or accessory pigments absorb photons?

Figure 10.9

• Colors of absorbed wavelengths disappear from the spectrum of transmitted and reflected light.

• The absorbed photon boosts one of the pigment molecule's electrons in its lowest-energy state (ground state) to an orbital of higher potential energy (excited state).

The only photons absorbed by a molecule are those with an energy state equal to the difference in energy between the ground state and excited state.

• This energy difference varies from one molecule to another. Pigments have unique absorption spectra because pigments only absorb photons corresponding to specific wavelengths.

• The photon energy absorbed is converted to potential energy of an electron elevated to the excited state.

The excited state is unstable, so excited electrons quickly fall back to the ground state orbital, releasing excess energy in the process. This released energy may be:

• Dissipated as heat

• Reradiated as a photon of lower energy and longer wavelength than the original light that excited the pigment. This afterglow is called fluorescence.

Pigment molecules do not fluoresce when in the thylakoid membranes, because nearby primary electron acceptor molecules trap excited state electrons that have absorbed photons.

• In this redox reaction, chlorophyll is photo-oxidized by the absorption of light energy and the electron acceptor is reduced.

• Because no primary electron acceptor is present, isolated chlorophyll fluoresces in the red part of the spectrum and dissipates heat.

4. Photosystems: light-harvesting complexes of the thylakoid membrane.

Chlorophyll a, chlorophyll b and the carotenoids are assembled into photosystems located within the thylakoid membrane. Each photosystem is composed of:

a. Antenna complex

Several hundred chlorophyll a, chlorophyll b and carotenoid molecules are light-gathering antennae that absorb photons and pass the energy from molecule to molecule

Figure 10.10

This process of resonance energy transfer is called inductive resonance.

• Different pigments within the antennal complex have slightly different absorption spectra, so collectively they can absorb photons from a wider range of the light spectrum than would be possible with only one type of pigment molecule.

b. Reaction-center chlorophyll

Only one of the many chlorophyll a molecules in each complex can actually transfer an excited electron to initiate the light reactions. This specialized chlorophyll a is located in the reaction center.

c. Primary electron acceptor

Located near the reaction center, a primary electron acceptor molecule traps excited state electrons released from the reaction center chlorophyll.

• The transfer of excited state electrons from chlorophyll to primary electron acceptor molecules is the first step of the light reactions. The energy stored in the trapped electrons powers the synthesis of ATP and NADPH in subsequent steps.

Two types of photosystems are located in the thylakoid membranes, photosystem I and photosystem II.

• The reaction center of photosystem I has a specialized chlorophyll a molecule known as P700, which absorbs best at 700 nm (the far red portion of the spectrum).

• The reaction center of photosystem 11 has a specialized chlorophyll a molecule known as P680, which absorbs best at a wavelength of 680 nm.

P700 and P680 are identical chlorophyll a molecules, but each is associated with a different protein. This affects their electron distribution and results in slightly different absorption spectra.

5. Noncyclic electron flow

There are two possible routes for electron flow during the light reactions: noncyclic flow and cyclicflow.

Both photosystem I and photosystem 11 function and cooperate in noncyclic electron flow, which transforms light energy to chemical energy stored in the bonds of NADPH and ATP.

Figure IO.11

This process:

• Occurs in the thylakoid membrane

• Passes electrons continuously from water to NADP+

• Produces ATP by noncyclic photophosphorylation

• Produces NADPH.

• Produces 02

Light excites electrons from P700, the reaction center chlorophyll in photosystem 1. These excited state electrons do not return to the reaction center chlorophyll, but are ultimately stored in NADPH, which will later be the electron donor in the Calvin cycle.

• Initially, the excited state electrons are transferred from P700 to the primary electron acceptor for photosystem 1.

• The primary electron acceptor passes these excited state electrons to ferredoxin (Fd), an iron-containing protein.

NADP+ reductase catalyzes the redox reaction that transfers these electrons from ferredoxin to NADP+, producing reduced coenzyme - NADPH.

• The oxidized P700 chlorophyll becomes an oxidizing agent as its electron "holes" must be filled; photosystem 11 supplies the electrons to fill these holes.

When the antenna assembly of photosystem 11 absorbs light, the energy is transferred to the P680 reaction center .

• Electrons ejected from P680 are trapped by the photosystem 11 primary electron acceptor.

• The electrons are then transferred from this primary electron acceptor to an electron transport chain embedded in the thylakoid membrane.

• As these electrons pass down the electron transport chain, they lose potential energy until they reach the ground state of P700.

• These electrons then fill the electron vacancies left in photosystem I when NADP+ was reduced.

Electrons from P680 flow to P700 during noncyclic electron flow, restoring the missing electrons in P700. This, however, leaves the P680 reaction center of photosystem 11 with missing electrons; the oxidized P680 chlorophyll thus becomes a strong oxidizing agent.

• A water-splitting enzyme extracts electrons from water and passes them to oxidized P680, which has a high affinity for electrons.

• As water is oxidized, the removal of electrons splits water into two hydrogen ions and an oxygen atom.

• The oxygen atom immediately combines with a second oxygen atom to form 02- It is this water-splitting step of photosynthesis that releases 02.

As excited electrons give up energy along the transport chain to P700, the thylakoid membrane couples the exergonic flow of electrons to the endergonic reactions that phosphorylate ADP to ATP.

• This coupling mechanism is chemiosmosis.

• Some electron carriers can only transport electrons in the company of protons.

• The protons are picked up on one side of the thylakoid membrane and deposited on the opposite side as the electrons move to the next member of the transport chain.

• The electron flow thus stores energy in the form of a proton gradient across the thylakoid membrane - a proton-motive force.

• An ATP synthase enzyme in the thylakoid membrane uses the protonmotive force to make ATP. This process is called photophosphorylation because the energy required is light.

This form of ATP production is called noncyclic photophosphorylation.

6. Cyclic electron flow

Cyclic electron flow is the simplest pathway, but involves only photosystem I and generates ATP without producing NADPH or evolving oxygen.

The function of the cyclic pathway is to produce additional ATP.

• It does so without the production of NADPH or 02-

• Cyclic photophosphorylation supplements the ATP supply required for the Calvin cycle and other metabolic pathways. The noncyclic pathway produces approximately equal amounts of ATP and NADPH, which is not enough ATP to meet demand.

• NADPH concentration might influence whether electrons flow through cyclic or noncyclic pathways.

7. A comparison of chemiosmosis in chloroplasts and mitochondria Chemiosmosis = The coupling of exergonic electron flow down an electron transport chain to endergonic ATP production by the creation of an electrochemical proton gradient across a membrane. The proton gradient drives ATP synthesis as protons diffuse back across the membrane.

Chemiosmosis in chloroplasts and chemiosmosis in mitochondria are similar in several ways:

a. Electron transport chain

b. Spatial organization

The inner mitochondrial membrane pumps protons from the matrix out to the interrnembrane space, which is a reservoir of protons that power ATP synthase.

• The chloroplast's thylakoid membrane pumps protons from the stroma into the thylakoid compartment, which functions as a proton reservoir. ATP is produced as protons diffuse from the thylakoid compartment back to the stroma through ATP synthase complexes that have catalytic heads on the membrane's stroma side. Thus, ATP forms in the stroma where it drives sugar synthesis during the Calvin cycle.

Figure 10.14

There is a large proton or pH gradient across the thylakoid membrane.

• When chloroplasts are illuminated, there is a thousand-fold difference in H+ concentration. The pH in the thylakoid compartment is reduced to about 5 while the pH in the stroma increases to about 8.

• When chloroplasts are in the dark, the pH gradient disappears, but can be reestablished if chloroplasts are illuminated.

A tentative model for the organization of the thylakoid membrane includes the following:

• Proton pumping by the thylakoid membrane depends on an asymmetric placement of electron carriers that accept and release protons (H+).

• There are three steps in the light reactions that contribute to the proton gradient across the thylakoid membrane:

1. Water is split by Photosystem 11 on the thylakoid side, releasing protons in the process.

2. As plastoquinone (Pq), a mobile carrier, transfers electrons to the cytochrome complex, it translocates protons from the stroma to the thylakoid space.

3. Protons in the stroma are removed from solution as NADP+ is reduced to NADPH.

• NADPH and ATP are produced on the side of the membrane facing the stroma where sugar is synthesized by the Calvin cycle.

Figure 10.15

8. Summary of light reactions

During noncyclic electron flow, the photosystems of the thylakoid membrane transform light energy to the chemical energy stored in NADPH and ATP. This


During cyclic electron flow, electrons ejected from P700 reach ferredoxin and flow back to P700. This process:

• Produces ATP

• Unlike noncyclic electron flow, does not produce NADPH or 02

D. The Calvin cycle uses ATP and NADPH to convert C02 to sugar: a closer look ATP and NADPH produced by the light reactions are used in the Calvin cycle to reduce carbon dioxide to sugar.

• The Calvin cycle is similar to the Krebs cycle in that the starting material is regenerated by the end of the cycle.

• Carbon enters the Calvin cycle as C02 and leaves as sugar.

• ATP is the energy source, while NADPH is the reducing agent that adds highenergy electrons to form sugar.

• The Calvin cycle actually produces a three-carbon sugar glyceraldehyde 3phosphate (G3P).

Figure 10.16

For the Calvin cycle to synthesize one molecule of sugar (G3P), three molecules Of C02 must enter the cycle. The cycle may be divided into three phases:

Phase 1: Carbon Fixation. The Calvin cycle begins when each molecule of C02 is attached to a five-carbon sugar, ribulose biphosphate (RuBP).

• This reaction is catalyzed by the enzyme RUBP carboxylase (rubisco) - one of the most abundant proteins on Earth..

• The product of this reaction is an unstable six-carbon intermediate that immediately splits into two molecules of 3-phosphoglycerate.

• For every three C02 molecules that enter the Calvin cycle via rubisco, three RUBP molecules are carboxylated forming six molecules of 3-phosphoglycerate.

Phase 2: Reduction. This endergonic reduction phase is a two-step process that couples ATP hydrolysis with the reduction of 3-phosphoglycerate to glyceraidehyde phosphate.

An enzyme phosphorylates 3-phosphoglycerate by transferring a phosphate group from ATP. This reaction:

Electrons from NADPH reduce the carboxyl group of 1,3-bisphosphoglycerate to the aldehyde group of glyceraidehyde 3-phosphate (G3P).

• The product, G3P, stores more potential energy than the initial reactant, 3-phosphoglycerate.

• G3P is the same three-carbon sugar produced when glycolysis splits glucose.

For every three C02 molecules that enter the Calvin cycle, six G3P molecules are produced, only one of which can be counted as net gain.

• The cycle begins with three five-carbon RUBP molecules - a total of 15 carbons.

• The six G3P molecules produced contain 18 carbons, a net gain of three carbons from C02-

• One G3P molecule exits the cycle; the other five are recycled to regenerate three molecules of RUBP.

Phase 3: Regeneration of C02 acceptor (RuBP). A complex series of reactions rearranges the carbon skeletons of five G3P molecules into three RUBP molecules.

• These reactions require three ATP molecules.

• RUBP is thus regenerated to begin the cycle again.

For the net synthesis of one G3P molecule, the Calvin cycle uses the products of the light reactions:

G3P produced by the Calvin cycle is the raw material used to synthesize glucose and other carbohydrates.

The Calvin cycle uses 18 ATP and 12 NADPH molecules to produce one glucose molecule.

E Alternative mechanisms of carbon fixation have evolved in hot, arid climates

1. Photorespiration: an evolutionary relic?

A metabolic pathway called photorespiration reduces the yield of photosynthesis. Photorespiration = In plants, a metabolic pathway that consumes oxygen, evolves carbon dioxide, produces no ATP and decreases photosynthetic output.

When the 02 concentration in the leaf's air spaces is higher than C02 concentration, rubisco accepts 02 and transfers it to RUBP. (The "photo" in photorespiration refers to the fact that this pathway usually occurs in light when photosynthesis reduces C02 and raises 02 in the leaf spaces.)

(The "respiration" in photorespiration refers to the fact that this process uses 02 and releases C02)

This affinity for oxygen has been retained by rubisco and some photorespiration is bound to occur.

Whether photorespiration is beneficial to plants is not known.

· It is known that some crop plants (e.g., soybeans) lose as much as 50% of the carbon fixed by the Calvin cycle to photorespiration.

· If photorespiration could be reduced in some agricultural plants, crop yields and food supplies would increase.

Photorespiration is fostered by hot, dry, bright days.

* Under these conditions, plants close their stomata to prevent dehydration by reducing water loss from the leaf.

· Photosynthesis then depletes available carbon dioxide and increases oxygen within the leaf air spaces. This condition favors photorespiration.

Certain species of plants, which live in hot and climates, have evolved alternate modes of carbon fixation that minimize photorespiration. C4 and CAM are the two most important of these photosynthetic adaptations.

2. C4 plants

The Calvin cycle occurs in most plants and produces 3-phosphoglycerate, a threecarbon compound, as the first stable intermediate.

These plants are called C3 plants because the first stable intermediate has three carbons.

Agriculturally important C3 plants include rice, wheat, and soybeans.

Many plant species preface the Calvin cycle with reactions that incorporate carbon dioxide into four-carbon compounds.

• These plants are called C4 plants.

• The C4 pathway is used by several thousand species in at least 19 families including corn and sugarcane, important agricultural grasses.

• This pathway is adaptive, because it enhances carbon fixation under conditions that favor photorespiration, such as hot, arid environments.

Leaf anatomy of C4 plants spatially segregates the Calvin cycle from the initial incorporation of C02 into organic compounds. There are two distinct types of photosynthetic cells:

1. Bundle-sheath cells

• Arranged into tightly packed sheaths around the veins of the leaf

• Thylakoids in the chloroplasts of bundle-sheath cells are not stacked into grana.

• The Calvin cycle is confined to the chloroplasts of the bundle sheath.

2. Mesophyll cells are more loosely arranged in the area between the bundle sheath and the leaf surface.

The Calvin cycle of C4 plants is preceded by incorporation of C02 into organic compounds in the mesophyll

Figure 10.18

Step 1: C02 is added to phospboenolpyruvate (PEP) to form oxaloacetate, a four-carbon product.

PEP carboxylase is the enzyme that adds C02 to PEP. Compared to rubisco, it has a much greater affinity for C02 and has no affinity for 02-

Thus, PEP carboxylase can fix C02 efficiently when rubisco cannot under hot, dry conditions that cause stomata to close, C02 concentrations to drop and 02 concentrations to rise.

Step 2: After C02 has been fixed by mesophyll cells, they convert oxaloacetate to another four-carbon compound (usually malate).

Step 3: Mesophyll cells then export the four-carbon products (e.g., malate) through plasmodesmata to bundle-sheath cells.

• In the bundle-sheath cells, the four carbon compounds release C02, which is then fixed by rubisco in the Calvin cycle.

• Mesophyll cells thus pump C02 into bundle-sheath cells, minimizing photorespiration and enhancing sugar production by maintaining a C02 concentration sufficient for rubisco to accept C02 rather than oxygen.

3. CAM plants

A second photosynthetic adaptation exists in succulent plants adapted to very arid conditions. These plants open their stomata primarily at night and close them during the day (opposite of most plants).

This conserves water during the day, but prevents C02 from entering the leaves.

• When stomata are open at night, C02 is taken up and incorporated into a variety of organic acids. This mode of carbon fixation is called crassulacean acid metabolism (CAM).

• The organic acids made at night are stored in vacuoles of mesophyll cells until morning, when the stomata close.

• During daytime, light reactions supply ATP and NADPH for the Calvin cycle. At this time, C02 is released from the organic acids made the previous night and is incorporated into sugar in the chloroplasts.

The CAM and C4 pathways:

• Are similar in that C02 is first incorporated into organic intermediates before it enters the Calvin cycle.

• Differ in that the initial steps of carbon fixation in C4 plants are structurally separate from the Calvin cycle; in CAM plants, the two steps occur at separate times.

Regardless of whether the plant uses a C3, C4 or CAM pathway, all plants use the Calvin cycle to produce sugar from C02-

F. Photosynthesis is the biosphere's metabolic foundation: a review

On a global scale, photosynthesis makes about 160 billion metric tons of carbohydrate per year. No other chemical process on Earth is more productive or is as important to life.

• Light reactions capture solar energy and use it to:

• Produce ATP

• Transfer electrons from water to NADP+ to form NADPH

• The Calvin cycle uses ATP and NADPH to fix C02 and produce sugar.

Photosynthesis transforms light energy to chemical bond energy in sugar molecules.

• Sugars made in chloroplasts supply the entire plant with chemical energy and carbon skeletons to synthesize organic molecules.

• Nonphotosynthetic parts of a plant depend on organic molecules exported from leaves in veins.

• The disaccharide sucrose is the transport form of carbohydrate in most plants.

• Sucrose is the raw material for cellular respiration and many anabolic pathways in nonphotosynthetic cells.

• Much of the sugar is glucose - the monomer linked to form cellulose, the main constituent of plant cell walls.

Most plants make more organic material than needed for respiratory fuel and for precursors of biosynthesis.

• Plants consume about 50% of the photosynthate as fuel for cellular respiration.

• Extra sugars are synthesized into starch and stored in storage cells of roots, tubers, seeds, and fruits.

• Heterotrophs also consume parts of plants as food.

Photorespiration can reduce photosynthetic yield in hot dry climates. Alternate methods of carbon fixation minimize photorespiration.

C4 plants spatially separate carbon fixation from the Calvin cycle.

CAM plants temporally separate carbon fixation from the Calvin cycle.


Chapter 11


Regulation is an essential feature of life. It unifies the various levels of biological organization by embracing the fields of molecular and cell biology, organismal biology, and population biology and ecology. It provides the necessary coordination for all aspects of life, including metabolism, growth, development, and reproduction.

Chemical substances are the principal agents of biological regulation and they exert their effects on cells through signaling systems. Chapter 11 describes the fundamental components of cell signaling systems.

I. An Overview of Cell Signaling

A. Cell signaling evolved early in the history of life

Yeast mating behavior is coordinated by chemical signaling.

Figure 11.1

The steps by which yeast mating signals are converted into yeast cell responses are similar to how chemical signals in prokaryotes (bacteria), plants, and animals are converted to specific cell responses.

In general, the steps by which a chemical signal is converted to a specific cell response is called a signal transduction pathway.

B. Communicating cells may be close together or far apart

A chemical signal that communicates between two nearby cells is called a local regulator. Two types of local signaling have been described in animals: paracrine signaling and synaptic signaling.

In synaptic signaling, a nerve cell releases a signal (e.g., neurotransmitter) into a synapse, the narrow space between the transmitting cell and a target cell, such as another nerve cell or muscle cell.

Figure 11.3

A chemical signal which communicates between cells some distance apart is called a hormone.

Hormones have been described in both plants (e.g., ethylene, a gas which promotes growth and fruit ripening) and animals (e.g., insulin, a protein which controls various aspects of metabolism, including the regulation of blood glucose levels).

The distinction between local regulators and hormones is for convenience. A particular chemical signal may act both as a local regulator and as a hormone.

Insulin, for example, may act in a paracrine fashion on adjacent cells (e.g., other insulin cells in the pancreas, acting to inhibit the further release of insulin in a negative feedback manner) and in a hormonal fashion on distant cells (e.g., liver cells, which store carbohydrate as glycogen).

Cells also may communicate by direct contact. Some plant and animal cell possess junctions (gap junctions) though which signals can travel between adjacent cells.

Figure 11.4

C. The three stages of cell signaling are reception, transduction, and response

For a chemical signal to elicit a specific response, the target cell must possess a signaling system for the signal. Cells which do not possess the appropriate signaling system do not respond to the signal.

The signaling system of a target cell consists of the following elements:

Signal reception. The signal binds to a specific cellular protein called a receptor, which is often located on the surface of the cell.

Signal transduction. The binding of the signal changes the receptor in some way, usually a change in conformation or shape. The change in receptor shape initiates a process of converting the signal into a specific cellular response; this process is called signal transduction. The transduction system may have one or many steps.

Cellular response. The transduction system triggers a specific cellular response. The response can be almost any cellular activity, such as activation of an enzyme or altered gene expression.

Figure 11.5

Epinephrine stimulates glycogen breakdown by stimulating the cytosolic enzyme, glycogen phosphorylase (cellular response).

Epinephrine could only stimulate glycogen phosphorylase activity when presented to intact cells, suggesting that:

The mechanisms of the cell signaling process help ensure that important processes occur in the right cells, at the right time, and in proper coordination with other cells of the organism.

Signal Reception and the Initiation of Transduction

A. A chemical signal binds to a receptor protein, causing the receptor protein to change shape

Binding of the ligand to the receptor can lead to the following events:

B. Most signal receptors are plasma-membrane proteins

Many signal molecules cannot pass freely through the plasma membrane. The receptors for such signal molecules are located on the plasma membrane. Three families of plasma-membrane receptors are:

1. G-protein-linked receptors

The structure of a G-protein-Iinked receptor is characterized by a single polypeptide chain that is threaded back and forth through the plasma membrane in such a way as to possess seven transmembrane domains. An example of a protein-linked receptor is the epinephrine receptor.

Figure 11.7

The receptor propagates the signal by interacting with a variety of proteins on the cytoplasmic side of the membrane called G-proteins, so named because they bind guanine nucleotides, GTP and GDP.

• The function of the G-protein is influenced by the nucleotide to which it is bound:

• G-proteins bound to GDP are inactive.

• G-proteins bound to GTP are active

• When a ligand binds to a G-protein-linked receptor, the receptor changes its conformation and interacts with a G-protein. This interaction causes the GDP bound to the inactive G-protein to be displaced by GTP, thereby activating the G-protein.

• The activated G-protein binds to another protein, usually an enzyme, resulting in the activation of a subsequent target protein.

• The activation state of the G-protein is only temporary, because the active G-protein possesses endogenous GTPase activity, which hydrolyzes the bound GTP to GDP.

Figure 11.6

G-protein-linked receptors and G-proteins mediate a host of critical metabolic and developmental processes (e.g., blood vessel growth and development, signaling between neurons in the brain). Defects in the G-protein signaling system form the bases of many human disease states (e.g., cholera).

2. Tyrosine-kinase receptors

The structure of a tyrosine-kinase receptor is characterized by an extracellular ligand-binding domain and a cytosolic domain possessing tyrosine kinase enzyme activity. Examples of tyrosine-kinase receptors are the receptors for numerous growth factors.

Propagation of the signal involves several steps as follows:

• Ligand binding causes aggregation of two receptor units, forming receptor dimers.

• Aggregation activates the endogenous tyrosine kinase activity on the cytoplasmic domains.

• The endogenous tyrosine kinase catalyzes the transfer of phosphate groups from ATP to the amino acid tyrosine contained in a particular protein. In this case, the tyrosines which are phosphoryled are in the cytoplasmic domain of the tyrosine-kinase receptor itself (thus, this step is an autophosphorylation)

• The phosphoiylated domain of the receptor interacts with other cellular proteins, resulting in the activation of a second, or relay, protein. The relay proteins may or may not be phosphorylated by the tyrosine kinase of the receptor. Many different relay proteins may be activated, each leading to the initiation of many, possibly different, transduction systems.

• One of the activated relay proteins may be protein phosphatase, an enzyme which hydrolyzes phosphate groups off of proteins. The dephosphorylation of the tyrosines on the tyrosine kinase domain of the receptor results in inactivating the receptor and the termination of the signal process.

Figure 11.8

3. Ion-channel receptors

Some chemical signals bind to ligand-gated ion channels. These are protein pores in the membrane that open or close in response to ligand binding, allowing or blocking the flow of specific ions (e.g., Na+, Ca2+). An example of an ion-gated channel would be the binding of a neurotransmitter to a neuron, allowing the inward flow of Na+ that leads to the depolarization of the neuron and the propagation of a nervous impulse to adjacent cells.

Figure 11.9

Not all signal receptors are located on the plasma membrane. Some are proteins located in the cytoplasm or nucleus of target cells.

• For a chemical signal to bind to these intracellular receptors, the signal molecule must be able to pass through plasma membrane. Examples of signals which bind to intracellular receptors include the following:

III. Signal Transduction Pathways

A. Pathways relay signals from receptors to cellular responses

Ligand binding to a receptor triggers the first step in the chain of reactions—the signal transduction pathway— that leads to the conversion of the signal to a specific cellular response.

The transduction system does not physically pass along the signal molecule, rather the information is passed along. At each step of the process, the nature of the information is converted, or transduced, into a different form.

B. Protein phosphorylation, a common mode of regulation in cells, is a major mechanism of signal transduction

The process of phosphorylation, or the transferring a phosphate group from ATP to a protein substrate, which is catalyzed by enzymes called protein kinases, is a common cellular mechanism for regulating the functional activity of proteins.

Protein phosphorylation is commonly used in signal pathways in the cytoplasm of cells. Unlike the case with tyrosine-kinase receptors, protein kinases in the cytoplasm do not act on themselves, but rather on other proteins (sometimes enzymes) and attach the phosphate group to serine or threonine residues.

• Some phosphorylations result in activation of the target protein (increased catalytic activity in the case of an enzyme target). An example of a stimulatory phosphorylation cascade is the pathway involved in the breakdown of glycogen.

Figures 11.10; 11.15

• Some phosphorylations result in inactivation (decreased catalytic activity in the case of an enzyme target).

Cells turn off the signal transduction pathway when the initial signal is no longer present. The effects of protein kinases are reversed by another class of enzymes known as protein phosphatases.

C. Certain small molecules and ions are key components of signaling pathways (second messengers)

Not all of the components of a signal transduction pathways are proteins. Some signaling systems rely on small, nonprotein, water soluble molecules or ions. Such signaling components are called second messengers. Two second messenger systems are:

1. Cyclic AMP

Substance mediating the action of epinephrine on liver glycogen breakdown is cAMP (second messenger).

Figure 11.11

Figure 11.12

Our present understanding of the transduction steps associated with cAMP is as follows:


The pool of cAMP in the cytoplasm is transient because of the breakdown of

cAMP by another enzyme to an inactive form (AMP). This conversion provides a shut-off mechanism to the cell to ensure that the target responses ceases in the absence of ligand.

A number of hormones in addition to epinephrine (e.g., glucagon) use cAMP as a second messenger.

2. Calcium ions and inositol triphosphate

Many signaling molecules induce their specific responses in target cells by

Increasing the cytoplasm’s concentration of Ca++. The Ca++ pool can be affected in two ways:

Figure 11.14

Activation of the IP3 pathway involves the following steps:

Ca++ acts to affect signal transduction in two ways:

IV. Cellular Responses to Signals

A. In response to a signal, a cell may regulate activities in the cytoplasm or transcription in the nucleus

In the cytoplasm, the signaling can affect the function or activity of proteins which carry out various processes, including:

• Rearrangement of the cytoskeleton

• Opening or closing of an ion channel

• Serve at key points in metabolic pathways (e.g., glycogen phosphorylase in the glycogen breakdown scheme.

In the nucleus, the signaling system affects the synthesis of new proteins and enzymes by modulating the expression (turn on or turn off) specific genes. Gene expression involves transcription of DNA into mRNA as well as the translation of mRNA into protein.

• Signal transduction systems can modulate virtually every aspect of gene expression. One example is the regulation of the activity of transcription factors, proteins required for appropriate transcription.

• Dysfunction of signaling pathways that affect gene regulation (e.g., pathways that transduce growth factor action) can have serious consequences and may even lead to cancer.

B. Elaborate pathways amplify and specify the cell’s responses to signals

The elaborate nature of cellular signal transduction systems functions to:

1. Signal amplification

The production of second messengers, such as cAMP, provides a built-in means of signal amplification in that the binding of one ligand (first message) can lead to the production of many second messages. The degree of amplification is heightened when the second messenger system is linked to a phosphorylation cascade as in the case of the process of glycogen breakdown. As a result of this inherent amplification, the binding of very few epinephrine molecules to the surface of a liver cell can result in the release of millions of glucose molecules resulting from glycogen breakdown.

Figure 11.15

2. Signal specificity

Only target cells with the appropriate receptors bind to a particular signaling molecule to initiate the transduction of a signal into a specific cellular response.

A particular signal can bind to different cell types and result in different responses in each of the cell types. This is possible because each of the different cell types can express a unique collection of proteins. As a result, the receptor on (or in) each of the different cell types can be linked to variant signal transduction pathways, each leading to a different response. An example is epinephrine action on vertebrate liver and cardiac muscle cells. In liver cells, the principal response is glycogen breakdown; whereas, in cardiac muscle cells, epinephrine stimulates contraction.

A single cell type may possess divergent and/or convergent ("cross-talk") signal transduction pathways. Such schemes facilitate coordination of cellular responses and economize on the number of required transduction elements.

Figure 11.17

An important feature of cell signaling systems is that there exists mechanisms to both turn-on and turn-off the system. Both mechanisms ensure that cells respond appropriately to changing conditions.


Chapter 16


What is the genetic material?


Proteins -- diverse

DNA -- too uniform??


Griffith experiments provided evidence that genetic material is a specific molecule.


Transformation = The assimilation of external genetic material by a cell, cell takes on new genotype and phenotype.

Hershey Chase experiment -- Protein or DNA?


Bacteriophage (phage) = Virus that infects bacteria

Protein coat with DNA inside (or sometimes RNA)

DNA is the hereditary material in eukaryotes as well.

Erwin Chargaff demonstrated:

DNA composition is species-specific

The number of: adenine residues = thymines

guanines = cytosines


1950’s DNA accepted as the genetic material but the 3D structure remained unknown



Watson and Crick

In part because A=T and G=C, they proposed specific pairing between bases

Double Helix

Uniform width of crystallized DNA and hydrogen bonds between bases dictates paring.

Sugar phosphate backbone-hydrophilic

Antiparallel -- run in opposite directions


The formation of specific pairs between bases provides a mechanism for replication -- one strand complements the other.

Sequence of bases can be highly variable -- suitable for coding genetic information.


DNA Replication I




Meselson and Stahl experiment


DNA Replication II


Is complex

Untwist molecule

copy two antiparallel strands simultaneously

requires more than a dozen enzymes and other proteins

Is rapid -- up to 500 nucleotides per second

Is accurate -- 1 in a billion is incorrectly paired

Replication starts at special sites called origins of replication


Specific proteins required to initiate replication

Replication fork spread creating a replication bubble

Bacteria or viral DNA have only one replication origin

Eukaryotic chromosomes have 100s to 1000s


Elongation of new DNA strand

Strand Separation

Helicases -- unwind double helix to expose template

Single strand binding proteins -- keep stands apart and stable

Synthesis of New Strands

DNA polymerases -- catalyze synthesis of new strand


Strands grow 5’ to 3’ direction

i.e. new nucleotides are added only to the 3’ end

Exergonic hydrolysis of nucleoside triphosphates provides energy for endergonic synthesis of DNA

Antiparallel arrangement prevent continuous synthesis in both directions.



Leading strand -- single polymer

Lagging strand -- discontinuously synthesized

Okazaki fragments

DNA ligase

Primers = Short RNA segment that is complementary to a DNA segment and that is necessary to begin DNA replication.


Primers are polymerized by an enzyme - primase

Primer formation must precede DNA replication because DNA polymerase can add nucleotides only to a polynucleotide that is already correctly base-paired with a complementary strand. It can not initiate synthesis.

Only one primer for leading strand but many for lagging strand.

Single-stranded binding protein holds DNA strands apart while they serve as templates.




Enzymes proofread DNA during replication and repair damage to existing DNA.

DNA replication is accurate but not solely because of base-pairing specificity

Initial error 1 in 10,000, final 1 in 1,000,000,000

Mismatch repair -- during synthesis

In bacteria DNA polymerase proofreads each newly added nucleotide -- removes and replaces errors

In eukaryotes additional proteins involved


Excision repair-- existing DNA

Damage -- X-rays, chemical, radioactivity, UV light

100+ DNA repair enzymes

damaged segment cut out by repair enzymes (nuclease), and the gap filled in by DNA polymerase and DNA ligase


Telomeres and the end-replication problem


Prokaryotes have circular DNA so there is no problem---eukaryotic chromosomes are linear.

Eukaryotic chromosomal DNA has special nucleotide sequenses called telomeres at their ends--these are multiple repetitions of one short nucleotide sequence.



Chapter 17

Transcription and Translation


RNA -- ribose, uracil

DNA -- deoxyribose, thymine

The linear sequence of nucleotides in DNA determines the linear sequence of amino acids in a protein.

Transcription -- The synthesis of RNA using DNA as a template.

A gene’s nucleotide sequence is transcribed from DNA to a complementary sequence in messenger RNA (mRNA)

Translation -- Synthesis of a polypeptide (protein) from mRNA

The sequence of bases in mRNA is translated into the linear sequence of amino acids in a protein.

Occurs on ribosomes

Prokaryotes Transciption and translation are coupled

Eukaryotes pre-mRNA (primary transcript), 2 step process

Fig 17.2

Triplet codes

Codons -- A three nucleotide sequence in mRNA that specifies an amino acid or signals termination of a polypeptide

4 nucleotides = 43 or 64 triplet (codons) possibilities

Fig 17.3

61 of 64 triplets code for amino acids

AUG signals "start" and codes for methionine

Three codons do not code for amino acids but signal

termination (UAA, UAG, and UGA)

Fig 17.4

Reading Frame

Fig 17.5

Redundancy (several codons with variations in the third base can code for the same amino acid)

but no ambiguity (codons code for only one amino acid)

Transcription of mRNA from DNA is catalyzed by RNA polymerases which:

Separates the two DNA strands and link RNA nucleotides

Add nucleotides only to the 3" end

Prokaryotes have only one type of RNA polymerase for mRNA, tRNA, and rRNA

Eukaryotes have three

RNA polymerase II catalyzes mRNA synthesis

Transcription Unit = Initiation sequence, termination sequence, and nucleotides in between.

Eukaryotes -- Transcription unit = one gene, one polypeptide

Prokaryotes -- Transcription unit can = several genes

several proteins

Fig 17.6

Three steps to transcription

1. Binding and initiation

2. Elongation

3. Termination

Binding and Initiation

Promoter = region on DNA where RNA polymerase binds and transcription begins (initiation site)

Start Point = where transcription begins

In eukaryotes, RNA polymerases cannot recognize the promoter without the help of transcription factors - DNA binding proteins that bind to specific DNA nucleotide sequences at the promoter.

Transcription initiation complex-- transcription factors and RNA ploymerase bound to the promoter.

TATA box = A short nucleotide sequence of A’s and T’s located upstream from the initiation site

Fig 17.7

RNA polymerase II recognizes the complex between TATA box, transcription factors, and DNA binding site.

Elongation Fig 17.6

1. RNA polymerase untwists and opens DNA

2. Links incoming RNA nucleotides to the 3" end

3. mRNA peels away from DNA template

4. DNA reseals

5. Several RNA polymerases can act at once


Transcription proceeds until RNA polymerase reaches a termination site on the DNA

Terminator sequence--RNA sequence

In eukaryotes the most common is AAUAAA

Prokaryotes mRNA is ready for translation

Eukaryotes mRNA is processed before it leaves the nucleus


RNA Processing

RNA modifications in eukaryotes

Before eukaryotic mRNA is exported from the nucleus:

1. both ends are covalently altered

2. intervening sequences are removed and the remainder is spliced together

Fig 17.8

5' cap--added to 5' end

Protects the growing mRNA from degradation

functions as "attach here" signal for ribosomes

Poly A tail--added to 3' end

inhibits degradation of mRNA

facilitates export to cytoplasm

mRNA splicing

Fig 17.9

RNA Splicing = removes introns and joins exons

Introns = noncoding sequences in DNA

Exons = Coding sequences in DNA

snRNPs ("Snurps") = small nuclear ribonucleoproteins = small nuclear RNA (snRNA) and protein that are involved in RNA splicing

Spliceosome = large molecular complex that catalyzes RNA splicing

Fig 17.10

Ribozymes-- self-splicing, intron RNA catalyzing its own splicing



Transfer RNA (tRNA)--transfers amino acids from the cytoplasmic pool to a ribosome.

Fig 17.11

Anticodon = triplet in tRNA that base pairs with triplet in mRNA

Fig 17.12

tRNA is about 80 nucleotides long

hydrogen bonded


L shaped

amino acid binding site -- 3’ end

Wobble = relaxation in base-pairing rules, third base in mRNA codon can vary with corresponding base in tRNA (U of tRNA can pair with either A or G in 3rd position of mRNA)

some tRNAs contain inosine (I can pair with U, C or A)

45 distinct types of tRNA

Aminoacyl-tRNA synthetase = type of enzyme that catalyzes the attachment of an amino acid to its tRNA

Fig 17.13

Ribosomes = 60% rRNA and 40% protein


two subunits, large and small

constructed in nucleolus

Passed through nuclear pores to cytoplasm

assemble into functional ribosomes only when attached to an mRNA

P site

A site

E site

Building a polypeptide



Initiation complex

1. Small subunit binds initiator tRNA (with methionine)

Small subunit binds special recognition sequence of mRNA complementary to sequence on rRNA

2. Large subunit binds to small one

initiator tRNA fits into the P site

powered by GTP





Termination codon (stop codon)


When stop codon reaches the A site a protein release factor binds to the codon and initiates:

1. hydrolysis of the bond between tRNA and the polypeptide

2. Subunits, mRNA dissociate

Polyribosome -cluster of ribosomes simultaneously translating an mRNA molecule


Post-translational modifications to polypetides

attachments e.g. sugars, lipids, phosphates groups


quaternary structure


Signal peptides

Free ribosomes in cytosol

Bound ribosomes attached to cytosolic side of ER--proteins for endomembrane system and for secretion

Signal recognition particle


Other signal peptides are used to target polypeptides to mitochondria, chloroplasts, etc.

Prokaryotic protein synthesis

Fig 17.20


Mutations = permanent change in DNA

Point mutations = one or two nucleotides in a single gene

Base pair substitutions = replacement of one base with another

Missense mutation = substitution that alters an amino acid codon to a new codon for a different amino acid

Nonsense mutation = changes amino acid codon to a stop codon or vice versa-protein usually nonfunctional


Insertions or deletions-additions or losses of one or more nucleotide pairs in a gene

Frameshift mutation = insertion or deletion that causes a shift in the reading frame


Spontaneous mutations- errors in DNA replication, repair, recombination

Mutagens- physical (e.g. x-rays) or chemical agents (e.g. base analogues, distortions of the double helix) that cause mutations

Summary fig 17.23


Chapter 18


Very, very small -- 20 nm in diameter

Consist of nucleic acid enclosed by a protein coat

Viral Genomes: Double stranded DNA, Single stranded DNA, Double stranded RNA, or Single stranded RNA

Organized as single nucleic acid molecule, linear or circular

4 to 100s of genes

Capsid = Protein coat that encloses the viral genome

Capsomeres = protein subunits made from only one or a few types of protein

Envelope = Membrane that cloaks some viral capsids

Help viruses infect their host

Derived from host cell membrane, usually modified

Viruses are obligate intracellular parasites, meaning that they can only reproduce within a host cell

Host Range = Limited number or range of host cells that a parasite can infect

Viral replication: 1. Infect host with viral genome. 2.Use host cell resources to replicate viral genome, manufacture capsid protein, and assemble new viruses

Three patterns of viral genome replication

DNA -> DNA (eg. Pox and PapovaViruses)

Use DNA polymerase produced by host

RNA ->RNA (eg. Rabies and influenza)

Use RNA replicase (a viral gene product)


Use reverse transcriptase (a viral gene product)

Viral nucleic acid and capsid proteins assemble spontaneously into new virus particle= self-assembly

Bacteriophages or Phages = Viruses that infect bacteria

Two reproductive cycles: 1. Lytic cycle = A viral replication cycle that results in death or lysis of the host cell

Virulent phages = phages that lyse their host cells

Bacterial defenses

Change receptor sites used for virus recognition

Restriction enzymes cut up foreign DNA

2. Lysogenic Cycle = A viral replication cycle that involves the incorporation of viral genome into host cell genome.

Temperate viruses = Viruses that can integrate their genome into host chromosome and remain latent until they initiate a lytic cycle (eg. Lambda Phage)

Prophage = A phage genome that is incorporated into a specific site on the bacterial "chromosome"

Most prophage genes are inactive. However, one active gene codes for a repressor protein which switches off most other prophage genes

Lysogenic cell = Host cell carrying a prophage in its "chromosome"

Some prophage genes may change host’s phenotype, a process called lysogenic conversion

diphtheria, botulism, scarlet fever -- results from toxins coded for by prophage genes

Animal viruses:

Some have envelopes

1. Attachment: glycoproteins. 2. Entry: receptor mediated endocytosis. 3. Uncoating: Viral RNA and Protein Synthesis. 4. Assembly and Release

Provirus =Viral DNA that inserts into a host chromosome

RNA Viruses

+ and - strands

+ = the strand that corresponds to mRNA

- = strand that is a template for synthesis of a plus strand

RNA viruses are classified by type of nucleic acid (1-6)

Retrovirus = RNA virus that uses reverse transcriptase to transcribe DNA from the viral RNA. (HIV, HTLV-1)

Reverse transcriptase = type of DNA polymerase that transcribes DNA from RNA template

Viral Disease

Vaccines = harmless variants or derivatives of viruses that activate hosts immune mechanisms

antiviral drugs = interfere with viral nucleic acid synthesis


Some viruses can transform infected cells to a cancerous state by permanently inserting viral nucleic acids

into host DNA. (Epstein-Barr Virus, HTLV-1, RSV (chickens)

Oncogenes = genes found in viruses or as part of normal eukaryotic genome, that trigger transformation

of a cell to cancer

Often code for cellular growth factors

Carcinogens probably also act by turning on oncogenes

Plant viruses

Horizontal transmission = receives virus from external source (pruning shears, insects…)

Vertical transmission = inherited from parents (Gametic cells, or through plant clippings)

Viroids = plant pathogen that is smaller and simpler than viruses

(naked RNA molecules)

Prions = pathogenic proteins

may be defective versions of a normal protein

catalyze conversion of normal protein to prion. (Cause CJD, Kuru, Mad Cow Disease, Scrapie)

Bacterial DNA

Bacterial chromosome (genophore) is usually circular

Some bacterial contain plasmids = extrachromosomal genes consisting of a double-stranded ring of DNA

Binary fission = asexual bacterial reproduction that produces clones- genetically identical offspring

Genetic recombination

Transformation =process of gene transfer during which a bacterial cell assimilates foreign DNA from the surroundings

e.g. Insulin

Transduction= gene transfer from one bacterium to another by a bacteriophage

Generalized vs Specialized

Conjugation and Plasmids

Conjugation = The direct transfer of genes between two cell that are temporarily joined

Plasmid = small double stranded ring of extrachromosomal DNA -- only a few genes, replicate independently

Episomes = plasmids that can reversibly incorporate into cell’s chromosome

Resistance plasmids = carry genes that confer resistance to certain antibiotics

Transposons = DNA sequences that can move from one chromosomal site to another

Conservative transposition = movement of preexisting genes from one genomic location to another - genes are not replicated before the move (number of gene copies is conserved)

Replicative transposition = movement of gene copies from original site to another location in the genome - transposon’s genes are inserted in new site w/o being lost from original site

Insertion sequence = simplest transposons which contain only the genes necessary for the process of transposition

sequence coding for transposase, the enzyme that catalyzes insertion of transposons

inverted repeats = short noncoding sequences of DNA that are repeated in reverse order on opposite ends of a transposon

e.g ATCCGGT.............ACCGGAT strand 1

TAGGCCA............TGGCCTA strand 2

DNA polymerase helps form direct repeats

Complex transposons = transposons which include additional genetic material besides that required form transposition

Control of gene expression

Regulation of enzyme activity

Feedback inhibition

Regulation of gene expression

gene repression

Structural gene = gene that codes for a polypeptide

Operon = regulated cluster of adjacent structural genes with related functions

Has a single promoter so RNA polymerase transcribes the whole cluster

polycistronic mRNA = large mRNA molecule that is a transcript of several genes

Operon can be controlled by a single Operator = DNA segment between an operon’s promoter and structural genes, which controls access of RNA polymerase to structural genes

Repressor = specific protein that binds to an operator and blocks transcription of the operon -- blocks attachment of RNA polymerase to the promoter

Regulatory genes = genes that code for repressor or regulators of other genes

Corepressor = a molecule, usually a metabolite, that binds to a repressor protein

Repressible enzymes = enzymes which have their synthesis inhibited by a metabolite

Inducible enzymes = enzyme synthesis stimulated by metabolites

Positive control

catabolite activator protein (CAP)



Chapter 19

Eukaryotic gene regulation is more complex than in prokatyotes, because eukaryotes:

• Have larger, more complex genomes.

• Require cell specialization or differentiation.

I. The Structure of Chromatin

A. Chromatin Structure is Based on Successive Levels of DNA Packing

Prokaryotic and eukaryotic cells both contain double-stranded DNA, but their genomes are organized differently.

Prokaryotic DNA is:

• Usually circular

• Much smaller than eukaryotic DNA

• Associated with only a few protein molecules

• Less elaborately structured and folded than eukaryotic DNA

Eukaryotic DNA is:

• Complexed with a large amount of protein to form chromatin

• Highly extended and tangled during interphase

• Condensed into short, thick, discrete chromosomes during mitosis; when stained, chromosomes are clearly visible with a light microscope

Eukaryotic chromosomes contain an enormous amount of DNA, which requires an elaborate system of DNA packing to fit all of the cell’s DNA into the nucleus.

B. Nucleosomes, or "beads on a string"

Histone proteins associated with DNA are responsible for the first level of DNA packing in eukaryotes.

Histones = Small proteins that are rich in basic amino acids and that bind to DNA, forming chromatin.

• Contain a high proportion of positively charged amino acids (arginine and lysine), which bind tightly to the negatively charged DNA

• Are present in approximately equal amounts to DNA in eukaryotic cells

• Are similar from one eukaryote to another, suggesting that histone genes have been highly conserved during evolution.

Partially unfolded chromatin (DNA and its associated proteins) resembles beads spaced along the DNA string. Each beadlike structure is a nucleosome

Figure 19.la

Nucleosome = The basic unit of DNA packing; it is formed from DNA wound around a protein core that consists of two copies each of four types of histone (H2A, H2B, H3, H4). A fifth histone (Hl) attaches near the bead when the chromatin undergoes the next level of packing.

• Nucleosomes may control gene expression by controlling access of transcription proteins to DNA.

• Nucleosome heterogeneity may also help control gene expression; nucleosomes may differ in the extent of amino acid modification and in the type of nonhistone proteins present.

C. Higher levels of DNA packing

The 30-nm chromatin fiber is the next level of DNA packing

Figure 19.lb).

In the next level of higher-order packing, the 30-nm chromatin fiber forms looped domains, which:

• Are attached to a nonhistone protein scaffold

• Contain 20,000 to 100,000 base pairs

• Coil and fold, further compacting the chromatin into a mitotic chromosome characteristic of metaphase

Interphase chromatin is much less condensed than mitotic chromatin, but it still exhibits higher-order packing.

• Its nucleosome string is usually coiled into a 30-nm fiber, which is folded into looped domains.

• Interphase looped domains attach to a scaffolding inside the nuclear envelope (nuclear lamina); this helps organize areas of active transcription.

• Chromatin fibers of different chromosomes do not become entangled as they occupy restricted areas within the nucleus.

Portions of some chromosomes remain highly condensed throughout the cell cycle, even during interphase. Such heterochromatin is not transcribed. Heterochromatin = Chromatin that remains highly condensed during interphase and that is not actively transcribed

Euchromatin = Chromatin that is less condensed during interphase and is actively transcribed; euchromatin becomes highly condensed during mitosis

What is the function of heterochromatin in Interphase cells?

• Since most heterochromatin is not transcribed, it may be a coarse control of gene expression.

• For example, Barr bodies in mammalian cells are X chromosomes that are mostly condensed into heterochromatin. In female somatic cells, one X chromosome is a Barr body, so the other X chromosome is the only one transcribed.

II. Genome Organization at the DNA Level

An organism's genome is plastic, or changeable, in ways that affect the availability of specific genes for expression.

• Genes may be available for expression in some cells and not others, or at some time in the organism’s development and not others.

• Genes may, under some conditions, be amplified or made more available than usual.

• Changes in the physical arrangement of DNA, such as levels of DNA packing, affect gene expression. For example, genes in heterochromatin and mitotic chromosomes are not expressed.

The structural organization of an organism’s genome is also somewhat plastic; movement of DNA within the genome and chemical modification of DNA influence gene expression.

A. Repetitive DNA and noncoding sequences account for much of a eukaryotic genome

DNA in eukaryotic genomes is organized differently from that in prokaryotes.

1. Tandemly repetitive DNA

About 10–25% of total DNA in higher eukaryotes is satellite DNA that consists of short (5 to 10 nucleotides) sequences that are tandemly repeated thousands of times.

• Called satellite DNA because its unusual nucleotide ratio gives it a density different from the rest of the cell’s DNA. Thus, during ultracentrifugation, satellite DNA separates out in a cesium chloride gradient as a "satellite" band separate from the rest of the DNA.

• Is not transcribed and its function is not known. Since most satellite DNA in chromosomes is located at the tips and the centromere, scientists speculate that it plays a structural role during chromosome replication and chromatid separation in mitosis and meiosis.

It is known that short tandem repeats called telomeres–at the ends of eukaryotic chromosomes–are important in maintaining the integrity of the lagging DNA strand during replication.

Telomere= Series of short tandem repeats at the ends of eukaryotic chromosomes; prevents chromosomes from shortening with each replication cycle

• Before an Okazaki fragment of the lagging DNA strand can be synthesized, RNA primers must be produced on a DNA template ahead of the sequence to be replicated.

• Since such a template is not possible for the end of a linear DNA molecule, there must be a mechanism to prevent DNA strands from becoming shorter with each replication cycle.

• This end-replication problem is solved by the presence of special repeating telomeric sequences on the ends of linear chromosomes.

• To compensate for the loss of telomeric nucleotides that occurs each replication cycle, the enzyme telomerase periodically restores this repetitive sequence to the ends of DNA molecules.

• Telomeric sequences are similar among many organisms and contain a block of G nucleotides. For example, human chromosomes have 250–1500 repetitions of the base sequence TTAGGG (AATCCC on the complementary strand).

There are other highly repetitive sequences in eukaryotic genomes. For example,

• Some are transposons; generally regarded as nonfunctional, they are associated with some diseases (e.g., neurofibromatosis-1 or elephant man’s disease and some cancers).

• Mutations can extend the repetitive sequences normally found within the boundary of genes and cause them to malfunction. (e.g., fragile X syndrome and Huntington’s disease.)

2. Interspersed repetitive DNA

Eukaryotes also possess large amounts (25-40% in mammals) of repeated units, hundreds or thousands of base pairs long, dispersed at random intervals throughout the genome.

B. Gene families have evolved by duplication of ancestral genes

Most eukaryotic genes are unique sequences present as single copies in the genome, but some genes are part of a multigene family.

Multigene family is a collection of genes that are similar or identical in sequence and presumably of common ancestral origin; such genes may be clustered or dispersed in the genome.

Families of identical genes:

Probably arise from a single ancestral gene that has undergone repeated duplication. Such tandem gene duplication results from mistakes made during DNA replication and recombination.

• Are usually clustered and almost exclusively genes for RNA products. (One exception is the gene family coding for histone proteins.)

• Include genes for the major rRNA molecules; huge tandem repeats of these genes enable cells to make millions of ribosomes during active protein synthesis

Families of nonidentical genes:

• Arise over time from mutations that accumulate in duplicated genes.

• Can be clustered on the same chromosome or scattered throughout the genome.

• May include pseudogenes or nonfunctional versions of the duplicated gene. A Pseudogene is a nonfunctional gene that has a DNA sequence similar to a functional gene; but as a consequence of mutation, lacks sites necessary for expression.

A good example of how multigene families can evolve from a single ancestral gene is the globin gene family–actually two related families of genes that encode globins, the alpha and beta polypeptide subunits of hemoglobin.

Based on amino acid homologies, the evolutionary history has been reconstructed as follows:

• The original a and beta genes evolved from duplication of a common ancestral globin gene. Gene duplication was followed by mutation.

• Transposition separated the alpha globin and beta globin families, so they exist on different chromosomes.

• Subsequent episodes of gene duplication and mutation resulted in new genes and pseudogenes in each family.

The consequence is that each globin gene family consists of a group of similar, but not identical genes clustered on a chromosome.

Figure 19.3

• In humans, embryonic and fetal hemoglobins have a higher affinity for oxygen than the adult forms, allowing efficient oxygen exchange between mother and developing fetus.

C. Gene amplification, loss, or rearrangement can alter a cell’s genome

1. Gene amplification and selective gene loss

Gene amplification may temporarily increase the number of gene copies at certain times in development.

Gene amplification = Selective synthesis of DNA, which results in multiple copies of a single gene.,

For example, amphibian rRNA genes are selectively amplified in the oocyte, which:

• Results in a million or more additional copies of the rRNA genes that exist as extrachromosomal circles of DNA in the nucleoli.

• Permits the oocyte to make huge numbers of ribosomes that will produce the vast amounts of proteins needed when the egg is fertilized.

• Gene amplification occurs in cancer cells exposed to high concentrations of chemotherapeutic drugs.

• Some cancer cells survive chemotherapy, because they contain amplified genes conferring drug resistance.

Genes may also be selectively lost in certain tissues by elimination of chromosomes.

Chromosome diminution = Elimination of whole chromosomes or parts of chromosomes from certain cells early in embryonic development.

For example, chromosome diminution occurs in gall midges during early development; all but two cells lose 32 of their 40 chromosomes during the first mitotic division after the 16-cell stage.

The two cells that retain the complete genome are germ cells that will produce gametes in the adult. The other 14 cells become somatic cells with only eight chromosomes.

2. Rearrangements in the genome

Substantial stretches of DNA can be re-shuffled within the genome; these rearrangements are more common that gene amplification or gene loss.

a. Transposons

All organisms probably have transposons that move DNA from one location to another within the genome.

Transposons can rearrange the genome by:

• Inserting into the middle of a coding sequence of another gene; it can prevent the interrupted gene from functioning normally

• Inserting within a sequence that regulates transcription; the transposition may increase or decrease a protein’s production.

• Inserting its own gene just downstream from an active promoter that activates its transcription.

Retrotranposons = Transposable elements that move within a genome by means of an RNA intermediate

Figure 19.5

Retrotransposons insert at another site by utilizing reverse transcriptase to convert back to DNA.

b. Immunoglobulin genes

During cellular differentiation in mammals, permanent rearrangements of DNA segments occur in those genes that encode antibodies, or immunoglobulins. Immunoglobulins = A class of proteins (antibodies) produced by B lymphocytes that specifically recognize and help combat virses, bacteria, and other invaders of the body. Immunoglobulin molecules consist of:

• Four polypeptide chains held together by disulfide bridges Each chain has two major parts:

A constant region, which is the same for all antibodies of a particular class

• A variable region, which gives an antibody the ability to recognize and bind to a specific foreign molecule

B lymphocytes, which produce immunoglobulins, are a type of white blood cell found in the mammalian immune system.

• The human immune system contains millions of subpopulations of B lymphocytes that produce different antibodies.

• B lymphocytes are very specialized; each differentiated cell and its descendants produce only one specific antibody.

Antibody specificity and diversity are properties that emerge from the unique organization of the antibody gene, which is formed by a rearrangement of the genome during B cell development

Figure 19.6

• As an unspecialized cell differentiates into a B lymphocyte, its antibody gene is pieced together randomly from several DNA segments that are physically separated in the genome.

• In the genome of an embryonic cell, there is an intervening DNA sequence between the sequence coding for an antibody’s constant region and the site containing hundreds of coding sequences for the variable regions.

• As a B cell differentiates, the intervening DNA is deleted, and the DNA sequence for a variable region connects with the DNA sequence for a constant region, forming a continuous nucleotide sequence that will be transcribed. The primary RNA transcript is processed to form mRNA that is translated into one of the polypeptides of an antibody molecule.

• Antibody variation results from:

• Different combinations of variable and constant regions in the polypeptides

• Different combinations of polypeptides

lII. The Control of Gene Expression

A. Each cell of a multicellular eukaryote expresses only a small fraction of its genes.

Cellular differentiation = Divergence in structure and function of different cell types, as they become specialized during an organism’s development

• Cell differentiation requires that gene expression must be regulated on a long-term basis.

• Highly specialized cells, such as muscle or nerve, express only a small percentage of their genes, so transcription enzymes must locate the right genes at the right time.

• Uncontrolled or incorrect gene action can cause serious imbalances and disease, including cancer. Thus, eukaryotic gene regulation is of interest in medical as well as basic research.

DNA-binding proteins regulate gene activity in all organisms–prokaryotes as well as eukaryotes.

• Usually, it is DNA transcription that is controlled.

• Eukaryotes have more complex chromosomal structure, gene organization and cell structure than prokaryotes, which offer added opportunities for controlling gene expression.

B. The control of gene expression can occur at any step in the pathway from gene to functional protein:

Complexities in chromosome structure, gene organization and cell structure provide opportunities for the control of gene expression in eukaryotic cells.

Figure 19.7

C. Chromatin modifications affect the availability of genes for transcription

Chromatin organization:

• Packages DNA into a compact form that can be contained by the cell’s nucleus.

• Controls which DNA regions are available for transcription.

• Condensed heterochromatin is not expressed.

• A gene’s location relative to nucleosomes and to scaffold attachment sites influences its expression.

Chemical modifications of chromatin play key roles in both chromatin structure and the regulation of transcription.

1. DNA methylation

DNA methylation = The addition of methyl groups (–CH3) to bases of DNA, after DNA synthesis

• Most plant and animal DNA contains methylated bases (usually cytosine); about 5% of the cytosine residues are methylated.

• May be a cellular mechanism for long-term control of gene expression. When researchers examine the same genes from different types of cells, they find:

• Genes that are not expressed (e.g., Barr bodies) are more heavily methylated than those that are expressed.

• Drugs that inhibit methylation can induce gene reactivation, even in Barr bodies.

• In vertebrates, DNA methylation reinforces earlier developmental decisions made by other mechanisms.

• For example, genes must be selectively turned on or off for normal cell differentiation to occur. DNA methylation ensures that once a gene is turned off, it stays off.

• DNA methylation patterns are inherited and thus perpetuated as cells a cell lineage forming specialized tissues have a chemical record of regulatory events that occurred during early development

2. Histone acetylation

• Acetylation enzymes attach –COCH3 groups to certain amino acids of histone proteins

• Acetylated histone proteins have altered conformation and bind to DNA less tightly; as a result, transcription proteins have easier access to genes in the acetylated region.

D. Transcription initiation is controlled by proteins that interact with DNA and with each other

1. Organization of a typical eukaryotic gene

The following is a brief review of a eukaryotic gene and its transcript Figure 19.8

Eukaryotic genes:

Contain introns, noncoding sequences that intervene within the coding sequence

• Contain a promoter sequence at the 5’ upstream end; a transcription initiation complex, including RNA polymerase, attaches to a promoter sequence and transcribes introns along with the coding sequences, or exons

• May be regulated by control elements, other noncoding control sequences that can be located thousands of nucleotides away from the promoter

Control element = Segments of noncoding DNA that help regulate the transcription of a gene by binding specific proteins (transcription factors)

The primary RNA transcript (pre-mRNA) is processed into mature mRNA by:

• Removal of introns

• Addition of a modified guanosine triphosphate cap at the 5’ end

• Addition of a poly-A tail at the 3’ end

2. The roles of transcription factors

In both prokaiyotes and eukatyotes, transcription requires that RNA polymerase recognize and bind to DNA at the promoter. However, transcription in eukaryotes requires the presence of proteins known as transcription factors; transcription factors augment transcription by binding:

Eukaryotic RNA polymerase cannot recognize the promoter without the help of a specific transcription factor that binds to the TATA box of the promoter.

Associations between transcription factors and control elements (specific segments of DNA) are important transcriptional controls in eukaryotes

• Proximal control elements are close to or within the promoter; distal control elements may be thousands of nucleotides away from the promoter or even downstream from the gene.

• Transcription factors known as activators bind to enhancer control elements to stimulate transcription.

• Transcription factors known as repressors bind to silencer control elements to inhibit transcription

How do activators stimulate transcription?

• One hypothesis is that a hairpin loop forms in DNA, bringing the activator bound to an enhancer into contact with other transcription factors and polymerase at the promoter

Figure 19.9

• Diverse activators may selectively stimulate gene expression at appropriate stages in cell development.

The involvement of transcription factors in eukaryotes offers additional opportunities for transcriptional control. This control depends on selective binding of specific transcription factors to specific DNA sequences and/or other proteins; the highly selective binding depends on molecular structure.

• There must be a complementary fit between the surfaces of a transcription factor and its specific DNA-binding site.

• Hundreds of transcription factors have been discovered; and though each of these proteins is unique, many recognize their DNA-binding sites with only one of a few possible structural motifs or domains containing a helices or beta sheeta

Figure 19.10

F. Posttranscriptional mechanisms play supporting roles in the control of gene expression

Transcription produces a primary transcript, but gene expression–the production of protein, tRNA, or rRNA–may be stopped or enhanced at any posttranscriptional step.

Because eukaryotic cells have a nuclear envelope, translation is segregated from transcription. This offers additional opportunities for controlling gene expression.

1. Regulation of mRNA degradation

Protein synthesis is also controlled by mRNA’s lifespan in the cytoplasm.

• Prokaryotic mRNA molecules are degraded by enzymes after only a few minutes. Thus, bacteria can quickly alter patterns of protein synthesis in response to environmental change.

• Eukaryotic mRNA molecules can exist for several hours or even weeks.

• The longevity of a mRNA affects how much protein synthesis it directs. Those that are viable longer can produce more of their protein.

• For example, long-lived mRNAs for hemoglobin are repeatedly translated in developing vertebrate red blood cells.

2. Control of translation

Gene expression can also be regulated by mechanisms that control translation of mRNA into protein. Most of these translational controls repress initiation of protein synthesis; for example.

• Binding of translation repressor protein to the 5’-end of a particular mRNA can prevent ribosome attachment.

• Translation of all mRNAs can be blocked by the inactivation of certain initiation factors. Such global translational control occurs during early embryonic development of many animals.

• Prior to fertilization, the ovum produces and stores inactive mRNA to be used later during the first embryonic cleavage.

• The inactive mRNA is stored in the ovum’s cytosol until fertilization, when the sudden activation of an initiation factor triggers translation.

• Delayed translation of stockpiled mRNA allows cells to respond quickly with a burst of protein synthesis when it is needed.

3. Protein processing and degradation

Posttranslational control is the last level of control for regulating gene expression.

• Many eukaryotic polypeptides must be modified or transported before becoming biologically active. Such modifications include:

• Adding phosphate groups

• Adding chemical groups, such as sugars

• Dispatching proteins targeted by signal sequences for specific sites

• Selective degradation of particular proteins and regulation of enzyme activity are also control mechanisms of gene expression.

• Cells attach ubiquitin to proteins to mark them for destruction

• Proteasomes recognize the ubiquitin and degrade the tagged protein

Figure 19.11

• Mutated cell-cycle proteins that are impervious to proteasome degradation can lead to cancer

IV. The Molecular Biology of Cancer

A. Cancer results from genetic changes that affect the cell cycle

Cancer is a variety of diseases in which cells escape from the normal controls on growth and division–the cell cycle–and it can result from mutations that alter normal gene expression in somatic cells. These mutations:

• Can be random and spontaneous

• Most likely occur as a result of environmental influences, such as:

• Infection by certain viruses

• Exposure to carcinogens

Carcinogens = Physical agents such as X-rays and chemical agents that cause cancer by mutating DNA

Whether cancer is caused by physical agents, chemicals or viruses, the mechanism is the same–the activation of oncogenes that are either native to the cell or introduced in viral genomes.

Oncogene = Cancer-causing gene

Discovered during the study of tumors induced by specific viruses

• Harold Varmus and Michael Bishop won a Nobel Prize for their discovery of oncogenes in RNA viruses (retroviruses) that cause uncontrolled growth of infected cells in culture.

Researchers later discovered that some animal genomes, including human, contain genes that closely resemble viral oncogenes. These proto-oncogenes normally regulate growth, division and adhesion in cells.

Proto-oncogenes = Gene that normally codes for regulatory proteins controlling cell growth, division and adhesion, and that can be transformed by mutation into an oncogene.

Three types of mutations can convert proto-oncogenes to oncogenes:

1. Movement of DNA within the genome

Malignant cells frequently contain chromosomes that have broken and rejoined, placing pieces of different chromosomes side-by-side and possibly separating the oncogene from its normal control regions. In its new position, an oncogene may be next to activate promoters or other control sequences that enhance transcription.

2. Gene amplification. Sometimes more copies of oncogenes are present in a cell than is normal.

3.Point mutation. A slight change in the nucleotide sequence might produce a growth-stimulating protein that is more active or more resistant to degradation than the normal protein.

Figure 19.12

In addition to mutations affecting growth-stimulating proteins, changes in tumor-suppressor genes coding for proteins that normally inhibit growth can also promote cancer.

The protein products of tumor-supressor genes have several functions:

• Cooperate in DNA repair (helping obviate cancer-causing mutations)

• Control cell anchorage (cell-cell adhesion; cell interaction with extracellular matrix)

• Components of cell-signaling pathways that inhibit the cell-cycle


Chapter 20

DNA Technology



Restriction enzymes = bacterial enzymes that recognize short, specific nucleotide sequences called recognition sequences and cuts DNA at specific points within those sequences

Restriction fragments

Sticky ends


Cloning Vectors = bacterial plasmid or virus used to move DNA into cells

Host Organisms


Bacterial DNA easily isolated and reintroduced

Grow quickly

However, may not be able to make full use of eukaryotic genes because they lack some enzymes and/or regulatory mechanisms during transcription and translation

can’t make the posttranslational modifications

Eukaryotic cells


Cultured plant and animal cells

Often difficult to introduce engineered DNA

Cloning a human gene in a bacterial plasmid


Clone identification

Finding gene of interest

Screen for protein--enzymatic acitivity or with antibodies

Screen for DNA - hybridization

use gene’s nucleotide sequence or infer from protein product

synthesize probe

cDNA, nucleic acid probes

Sources of genes for cloning

DNA isolated directly form an organism

Complementary DNA (cDNA) made in the lab from mRNA



No introns, but lack control sequences

Posttranslational modifications

Insertion of DNA into cells


infection (virus)

Yeast (a eukaryotic cell) can take up plasmids or linear DNA

Other eukaryotic cells

electroportation = brief electric pulses cause temporary holes in the plasma membrane

direct injection with fine needles

metal particles (DNA gun)

Genomic library

Isolate genome from an organism (contains all genes, including gene of interest)

Restriction enzymes cut DNA into 1000s of pieces

Insert all pieces into plasmid or viral DNA

These function as vectors and introduce new DNA into bacteria

This produces a genomic library = thousands of DNA segments from a genome


cDNA library

Polymerase Chain Reaction (PCR)

A segment of DNA is replicated into billion of copies by incubating special primers and DNA polymerase molecules

Requires only very small amounts of DNA

Can be from ancient DNA

Crime scenes

single embryonic cells for prenatal diagnosis

difficult to detect viral DNA e.g. HIV

Gel Electrophoresis

separate either nucleic acids (DNA, RNA) or proteins based on molecular size, charge and other physical properties

viral DNA, plasmid DNA, and segments of chromosomal DNA can be identified by characteristic banding patterns after being cut with restriction enzymes

DNA fragments can be isolated, purified and recovered from the gel with full biological activity

Southern blotting -- DNA

Northern blotting -- mRNA

Western blotting -- protein

RFLP analysis (Rif-lip)

restriction fragment length polymorphisms = differences in restriction fragment length that reflect variation in homologous DNA sequences

individuals have different sets of RFLP markers corresponding to different alleles (different forms of the same gene e.g. eye color)


Gene mapping

in situ hybridization

radioactive probe base-pairs (hybridizes) with complementary sequence (DNA or RNA)

Chromosome Walking


Gene expression


Disease Diagnosis


Gene therapy

recombinant DNA techniques replace or supplement defective genes


adult cells vs undifferentiated cells or germ lines


Vaccines -- trigger immune response (antibodies)

virus particles (chemically or physically inactivated)

active virus of an attenuated strain

cloned proteins

Antisense nucleic acid

base-pairs and blocks translation of components critical to survival of pathogen

Surface receptor drugs

block or mimic surface receptors (HIV docking site)

Other applications of DNA technology

Forensic, DNA fingerprinting

Environmental, degradation of toxic compounds

Animal Husbandry, milk production

Agraculture, pest resistance, nurtrient value

Chapter 41


Animal Nutrition

Animals are heterotrophs, that is they must rely on organic compounds in their diet to supply energy and raw materials for growth

Herbivores eat autotrophs (plants, algae)

Carnivores eat other animals

Omnivores eat other animals and autotrophs

Suspension-feeders sift small food particles from water

e.g. clams, oysters, baleen whales

Substrate-feeders live on or in their food

e.g. leaf miners

Deposit-feeders are a type of substrate feeder that ingest partially decayed organic materials along with their substrate

e.g. earthworms

Fluid-feeders suck nutrient rich fluids from a living host

e.g. mosquitoes, aphids, bees

Bulk-feeders eat relatively large pieces of food

most animals

Food processing involves 4 stages:

1 Ingestion -- the act of eating

2 Digestion-- breaking down food into small molecules

a. macromolecules (fats, proteins, carbohydrates) are too large to enter cells

b. digestion enzymatically cleaves macromolecules into component monomers

c. digestion uses enzymatic hydrolysis to break bonds by adding H2O

d. digestion occurs in specialized compartments where enzymes are contained so they don’t damage the animal’s own cells

3 Absorption -- uptake of small molecules that result from digestion

4 Elimination -- undigested material passes out of the digestive compartment

Intracellular digestion in food vacuoles

41.8 Paramecium

Extracellular digestion occurs within compartments that are continuous with the outside of the body

Gastrovascular cavity = digestive sac with a single opening- found in animals with simple body plan e.g. hydra


Combination of extracellular and intracellular digestion allows consumption of larger prey.

Alimentary canals = digestive tube running between two openings: mouth where food is ingested and anus where wastes are egested

organized into specialized regions for digestion and absorption

more efficient than gastrovascular cavities


Mammalian Digestive System

41.11 1. Physical and chemical digestion begins in the oral cavity

a. chewing breaks down large pieces

b. saliva contains:

1. mucin to lubricate food

2. buffers neutralize acids

3. antibacterial agents

4. salivary amylase - hydrolyzes starch and glycogen

c. tongue --taste, and food manipulation (forms bolus)

2. Pharynx

a. intersection between digestive and respiratory systems

3. Esophagus


a. conducts food from pharynx to stomach

b. peristalsis moves the bolus to the stomach

4. Stomach


a. Food storage (2 liters)

1. permits periodic feeding

b. Churning

a. longitudinal, vertical, and diagonal muscles mix food

b. mixing and stomach acid convert food into a nutrient broth called acid chyme

1. acid chyme passes through the pyloric sphincter at the bottom of the stomach to the small intestine

c. Secretion

1. gastric secretion is controlled by nerve impulses and the hormone gastrin

a. stomach Mucous cells secrete:

1. mucin - protects stomach lining from digestion

2. gastrin - a hormone produced by the stomach, released into the bloodstream, and acts to stimulate HCl and pepsin secretion

b. Chief cells secrete:

1. pepsinogen- an inactive protease or zymogen that is the precursor to pepsin

a. zymogen - inactive form of a protein digesting enzyme

c. Parietal cells secrete:

1. HCl

d. Protein digestion

1. HCl-provides acidity which:

a. kills bacteria

b. denatures proteins

c. aids conversion of pepsinogen to pepsin

2. Pepsin - splits some but not all peptide bonds

5. Small Intestine

a. site of most enzymatic hydrolysis of food and absorption of nutrients

b. pancreas, liver, and gall bladder also contribute to digestion

1. pancreas produces:

a. hydrolytic enzymes that break down all major classes of macromolecules

b. bicarbonate buffer to neutralize acid chyme

2. liver performs many functions including production of bile which:

a. is stored in the gall bladder

b. contains bile salts that emulsify fat

c. contains pigments that are byproducts of destroyed red blood cells

41.13 Enzymatic summary diagram

Hormonal control of digestion

1. Gastrin-- released by stomach in response to food--stimulates HCl and pepsin release

2. Secretin -- released by duodenum in response to acid chyme--signals pancreas to release bicarbonate buffer

3. Cholecystokinin (CCK)-- released by duodenum in response to chyme, signals gall bladder to release bile and the pancreas to release pancreatic enzymes

4. Enterogastrone-- released by duodenum in response to fat, inhibits peristalsis and slows digestion

Carbohydrate digestion

1. Salivary amylase in mouth

2. pancreatic amylases in duodenum (hydrolyze starch and glycogen)

3. disaccharidases attached to duodenal epithelium hydrolyzes disaccharides (maltase, sucrase, lactase) into monosaccharides

Protein digestion

1. pepsin in the stomach

2. pancreatic proteases

a. trypsin

b. carboxypeptidase

c. chymotrypsin

3. intestinal enzymes ( aminopeptidase, dipeptidases)


Fat digestion occurs only in small intestine

a. bile salts emulsify fats - produces small droplets

b. pancreatic lipase hydrolyzes fats into glycerol & fatty acids

Jejunum and ileum of the small intestine are specialized for absorption of nutrients (most absorption occurs here)

41.15 a. villi

b. microvilli

c. lacteal

Nutrients enter the capillaries and veins of the microvilli and converge into the hepatic portal vein which leads to the liver

liver stores or converts organic molecules

Large intestine or colon

a. major function is water reabsorption

b. feces (wastes) are moved through by peristalsis

1. feces stored in rectum and eliminated through anus

Food as fuel

a. excess calories stored as glycogen by liver and muscles

b. further excess is stored in adipose tissue as fat

Food for biosynthesis

a. amino acids supply nitrogen for synthesis of more amino acids

b. fats can be synthesized from carbohydrates

c. liver does most of the conversion

Essential Nutrients = chemicals an animal requires but cannot synthesize

a. amino acids

1. humans can synthesize 12 leaving 8 as essential

The body cannot store amino acids, so need regular supply

b. fatty acids

1. e.g. linoleic acid - required for membrane phospholipds

c. vitamins

1. many serve as coenzymes

2. water soluble - excreted in urine, not stored

1. C, B

3. fat soluble stored in body fat

a. A, D, E, K

d. minerals

1. structural and maintenance roles (calcium, phosphorous), part of enzymes (copper, zinc) or other molecules (iron)


Chapter 42


Circulation and Respiration

The circulatory system is designed to:

transport nutrients and O2 to all body cells

collect waste products and CO2 for excretion

Control blood flow to the skin and extremities for regulation of body heat

distribute hormones

aid in body defenses, antibodies, platelets, leukocytes

The respiratory system:

delivers O2 and removes CO2 from the blood

aid in acid-base balance


Open systems - hemolymph moves through sinuses

Hemolymph = body fluid which acts as both blood and interstitial fluid

Closed systems - blood confined to vessels and separate from interstitial fluid

Fig 42.2

Cardiovascular systems - heart, blood vessels, and blood

atria - chambers that receive blood

ventricles - chambers that pump blood out

Arteries carry blood away from heart

Veins return blood to the heart

Capillaries are the site of chemical exchange between blood and interstitial fluid

Fig 42.3

Fig 42.4

Fig 42.5

Cardiac cycle - complete sequence of contraction and relaxation

Systole - heart muscles contracts and chambers pump blood

Diastole - heart muscles relax and chambers fill with blood

Heart rate = number of beats per minute, normal resting rate is 60 -72

Cardiac output = heart rate times stroke volume (about 5 liters/minute)

Fig 42.6

Cardiac muscle cells are myogenic = self excitable

Fig 42.7

Sinoatrial (SA) node = pacemaker region of the heart located in the right atrium

Atrioventricular (AV) node = located near base of right atrium

Electrocardiogram EKG (ECG) = detection of electrical currents as they pass through the cardiac muscle

Hear rate is influenced by:

nervous system (speed or slow hear rate)


Body temp, exercise

Blood vessels


Blood flow, resistance

Blood pressure = total peripheral resistance times cardiac output

hydrostatic pressure = force exerted by fluids

peripheral resistance = total resistance of blood vessels

mean arterial pressure is about 90 mmHg

venous pressure is near zero

veins have one-way valves

Fig 42.9

Fig 42.10

Precapillary sphincters

Fig 42.11

Capillary exchange

Fig 42.12

Lymphatic system returns fluid back to the blood


Fig 42.13

Plasma - liquid matrix minus cells

electrolytes = inorganic salts (e.g. K+, Na+)

Plasma proteins

buffer pH

osmotic balance

immune proteins

clotting factors (serum is plasma minus clotting factors)


Erythrocytes - red blood cells, transport O2 (hemoglobin)

Leukocytes - white blood cells (5 types), defense and immunity

Platelets - cell fragments that aid clotting

Fig 42.14

Fig 42.15

Cardiovascular Disease

Heart attack (myocardial infarction, MI) = death of cardiac muscle usually from blocked coronary arteries

Stroke = death of brain tissue due to blocked arteries in the brain

Thrombus = blood clot

embolus = moving clot

Atherosclerosis = chronic CV disease from plaques

decreases blood flow, increases risk of clots

Angina pectoris = chest pain from insufficient oxygen to heart

Hypertension = high blood pressure, promotes atherosclerosis

HDL (good cholesterol), LDL (bad cholesterol)

exercise, smoking


Fig 42.17

Gas exchange = movement of O2 and CO2 between animal and environment

Respiratory surface = portion of the animal surface where gas exchange with the environment occurs -skin, gills, tracheae, lungs

Aquatic animals use gills

Fig 42.18, 42.19

Countercurrent exchange - blood flows opposite to the direction in which water passes over gills

Insects use tracheae

Fig 42.20

Most terrestrial vertebrates use lungs




Fig 38.21 (previous text edition)

Vertebrates ventilate lungs by breathing - inhalation and exhalation of air

Some animals (e.g. frogs) ventilate the lungs by positive pressure breathing

Air is pushed into the lungs

Mammals ventilate their lungs by negative pressure breathing

Fig 42.23

During inhalation air is pulled into the lungs by the negative pressure created as the thoracic cavity enlarges by:

contraction of the diaphragm - pushes downward toward the abdomen, and lowers air pressure in the lungs

action of the rib muscles

contraction pulls ribs upward expanding the rib cage and the lungs, which lowers air pressure in the lungs

Exhalation occurs when the diaphragm and/or rib cage relax

Tidal volume - volume of air inhaled and exhaled with each breath -- 500 ml

Vital capacity - maximum air volume that can be inhaled and exhaled during forced breathing -- 4000 ml

Residual volume - the amount of air that remains in the lungs even after forced exhalation

Breathing is automatic - controlled by nerves from the medulla and pons send signals to the rib muscles or diaphragm

medulla also monitors blood and cerebrospinal fluid pH

increases breathing with low pH (high CO2)

there are also O2 sensors in the aorta and carotid arteries

Fig 42.25


Loading and Unloading of O2 and CO2

Partial pressure - the partial pressure of a gas is the proportion of the total atmospheric pressure (760 mmHg) contributed by the gas

e.g. atmosphere is 21% O2 so O2 partial pressure equals

.21 X 760 = 160

Gases always diffuse from areas of high partial pressure to areas of lower partial pressure

Fig 24.26

Hemoglobin is the oxygen transporting pigment in almost all vertebrates

4 subunits each containing a heme group that binds O2

binding of one O2 increases the affinity of the other 3 subunits for oxygen (cooperativity)

Fig 42.27

CO2 transport

Fig 42.28

Chapter 43


Defense Mechanisms

Vertebrates have two classes of mechanisms to protect them from pathogens (viruses, bacteria, etc.)

Nonspecific - don’t distinguish between infective agents

Specific - respond in a very specific manner to a particular type of infective agent

Fig 43. 1


1. Skin and mucous membranes

Physical barriers

Chemical barriers

oil and sweat gland secretions are acidic

Saliva, tears, and mucous secretions wash away microbes and contain antimicrobial proteins

Lysozyme in perspiration, tears, and saliva attack cell walls of bacteria

Respiratory tract

nostril hairs, mucus, cells w/cilia

Digestive tract

stomach acid

2. Phagocytic white blood cells and natural killer cells

Neutrophils become phagocytic and enter infected tissue by amoeboid movement when attracted by chemical signals

Macrophages develop from monocytes and phagocytize microbes

Natural killer cells

Destroy the body’s own infected cells (e.g. infected by viruses, tumors)

are not phagocytic but cause cell lysis



Antimicrobial proteins

complement proteins

at least 20 different proteins that interact with other defense mechanisms

causes lysis of invading microbes

acts as attractants for phagocytes

Interferons - produced by virus infected cells and help other cells resist infection by stimulating production of proteins that inhibit viral replication-most effective against short term infections (colds, flu)

also activate phagocytes

Inflammatory Response


histamine is release from injured basophils and mast cells and causes local vasodilation

prostaglandins are released from white blood cells and damaged tissue - increases blood flow which delivers clotting elements and phagocytes (neutrophils first, then monocytes which become macrophages)

dead cells and fluid from capillaries may accumulate as pus

chemokines --released in response to injury and are chemotatic factors that facillitate phagocyte migration

Lymphatic system --home for macrophages, filtering of mocroorganisms, mocrobial fragments, and foreign molecules

Fig 43.4

Fig 43.5

Systemic inflammatory response vs local response

more white blood cells are produced

fever due to pathogens or by pyrogens released from leukocytes

fever inhibits growth of some organisms

fever facilitates phagocytosis and tissue repair

too high of a fever can denature proteins

Specific defence mechanisms ---The Immune System

Specificity - ability to recognize and eliminate particular microorganisms and foreign molecules

Antigen - foreign substance that elicits an immune response and may be:

molecules exhibited on the surface of, or produced by bacteria, viruses, parasitic worms, pollen, venom, transplanted organs, or worn-out cells

each antigen has a unique molecular shape - produces unique antibody

Antibody- antigen binding protein (immunoglobulin) produced by B cells - specific for particular antigen

Diversity - ability to respond to numerous kinds of invaders

Based on wide variety of lymphocyte populations each of which can be stimulated by a specific antigen to produce specific antibody

Memory - ability to recognize previously encountered antigens and react faster to subsequent exposures (memory cells)

acquired immunity - e.g. to chicken pox

Active Immunity- conferred by recovery from infectious disease

Can be acquired naturally, or artificially by vaccination

vaccines may be inactivated toxin, killed organism

Passive immunity- transferred from one person to another by transfer of antibodies (usually lasts for only a short time)


mother’s milk

artificial transfer of antibodies from immune animal or human (e.g. rabies)

Humoral immunity produces antibodies in response to toxins, free bacteria, and viruses in body fluid

Cell-mediated immunity is the response to intracellular bacteria and viruses, fungi, protozoans, worms, transplanted tissues and cancer cells.

Lymphocytes mediate humoral and cell-mediated immunity

B cells - humoral immunity

Form and mature in bone marrow

Activation gives rise to plasma cells which secrete antibodies (humoral response)

T cells - cell-mediated immunity

Form in bone marrow, mature in thymus

Activation produces:

cytotoxic T cells that destroy infected cells

helper T cells which secrete cytokines

cytokines regulate B and T cell activity

Fig 43.8

Clonal selection = antigenic-specific selection of a lymphocyte (B cell or T cell) that results in the production of clones of effector cells (plasma cells, cytotoxic T cell, helper T cells) dedicated to eliminating the antigen that provoked the initial immune response

Fig 43.6

Fig 43.7

Major histocompatibility complex (MHC) = group of glycoproteins embedded in the plasma membranes of cells

Self/non-self recognition, Self markers - identifies cells as not foreign

Class I MHC - locate on all nucleated cells

Class II MHC - molecules found only on specialized cells (macrophages, B cells, activated T cells) - important in interactions between cells of the immune system

Interactions of T cells with MHC molecules

Fig 43.9

Immune response overview

Fig 43.10

Helper T cells

Fig 43.11

Cytotoxic T cells

Fig 43.12

T-dependent antigens

involve macrophages, helper T cells and B cells--antigens that stimulate antibody production only with help from helper-T cells--most protein antigens are T-dependent

Fig 43.13

T-independent antigens

Only B cells involved--repeated subunits of the antigen provide enough binding and stimulation of B cells to generate antibody-secreting plasma cells w/o IL-2

no memory cells are generated, only plasma cells



Epitope = region of antigen that is chemically recognized by antibodies

Fig 43.14

Antibodies are a class of proteins called immunoglobulins (Igs)

Fig 43.15

Variable regions function as antigen binding sites

Constant regions of heavy chains are responsible for distribution in the body and antigen disposal

Neurtralization-binds and blocks activity of the antigen

Opsonization- bound antibodies enhance macrophage attachment and phagocytosis

Agglutination-clumping of bacteria or viruses, enhances neutralization and opsonization

Complement fixation-activation of complement system by antigen-antibody complexes

Fig 43.16

Fig 43.17

Blood groups


Rh Factors


Mast cells



CD4 Cells--helper T cells, macrophages, some B lymphocytes

AZT, Protease inhibitors

Fig 43.20

Chapter 45

I. An Introduction to Regulatory Systems

Two major systems of internal communication: the nervous system and the endocrine system.

Endocrine glands = Ductless glands that secrete hormones into the body fluids for distribution throughout the body

Exocrine glands = Secrete chemicals, such as sweat, mucus, and digestive enzymes, into ducts which convey the products to the appropriate locations


A. The endocrine system and the nervous system are structurally, chemically, and functionally related

Many endocrine organs and tissues contain specialized nerve cells called neurosecretory cells that secrete hormones.

Several chemicals serve both as hormones of the endocrine system and as signals in the nervous system.

e.g. norepinephrine which functions as both an adrenal hormone and as a neurotransmitter.

Positive and negative feedback regulate mechanisms of both systems

Figure 45.1

II. Chemical Signals and Their Mode of Action
Chemical signals operate at virtually all levels of organization
• Intracellular (includes elements of signal transduction systems)
• Cell to cell
• Tissue to tissue

• Organ to organ

• Organism to organism (includes pheromones, chemical signals that function between organisms of the same species; classified according to function e.g., mate attractant, territorial marker, alarm substance).

Compounds called local regulators operate at the cell to cell and tissue to tissue levels of organization

A. A variety of local regulators affect neighboring target cells

Examples of local regulators include the following:

NO released by endothelial cells of blood vessels makes the adjacent smooth muscle cells relax, dilating the vessel.

NO released by white blood cells kills certain cancer cells and bacteria in the body fluids.

Must be present in the extracellular environment for certain cell types to grow and develop normally.

Often derived from lipids of the plasma membrane

Very subtle differences in their molecular structure profoundly affect how these signals affect target cells.

PGs secreted by the placenta help induce labor during childbirth by causing chemical changes in the nearby uterine muscles.

Other PGs help defend the body by inducing fever and inflammation.

B. Chemical signals bind to specific receptor proteins within target cells or on their surface

A chemical signal can affect different target cells within an animal differently, or it may affect different species differently.

The action of a particular chemical signal depends upon:

Figure 45.3

Binding of a chemical signal to a specific receptor protein triggers chemical events within the target cell that result in a change in the cell's behavior.

The nature of the response to a chemical signal depends on the number and specificity of the receptor proteins

Figure 45.4

C. Most chemical signals bind to plasma-membrane proteins, initiating signal-transduction pathways

Because of their chemical nature, most signal molecules (e.g., peptides, proteins, glycoproteins) are unable to diffuse through the plasma membrane.

• The biological action of these factors begins at the plasma membrane, where the signal molecule binds to a specific plasma membrane receptor.

• Binding of the signal molecule to a plasma membrane receptor initiates a signal transduction pathway, the series of events that converts the signal into a specific cellular response.

D. Steroid hormones, thyroid hormone, and some local regulators enter target cells and bind with intracellular receptors

The chemical nature of some regulators allows them to pass through the plasma membrane (e.g., steroids, thyroid hormones, NO). The receptors for these factors are located within target cells.

In many cases, the signal-receptor complex binds to DNA to modify gene expression.

Figure 45.5

Ill. The Vertebrate Endocrine System

The vertebrate endocrine system, through its production of numerous hormones, coordinates various aspects of metabolism, growth, development, and reproduction.

Figure 45.6 shows where the major endocrine glands in humans are located.

Table 45.1 summarizes the functions of the major vertebrate hormones.

Some of the hormones in vertebrates have a single action while others have multiple actions.

Tropic hormones act on other endocrine glands.

A. The hypothalamus and pituitary integrate many functions of the vertebrate endocrine system

The hypothalamus is a region of the lower brain that receives information from nerves throughout the body and brain and initiates endocrine signals appropriate to the environmental conditions.

• Contains two sets of neurosecretory cells whose secretions are stored in or regulate activity of the pituitary gland.

The pituitary gland is an extension of the brain located at the base of the hypothalamus. It consists of two lobes and has numerous endocrine functions

Figure 45.7

The adenohypophysis, or anterior pituitary, consists of endocrine cells that synthesize and secrete several hormones directly into the blood.

• Controlled by two kinds of hormones secreted by neurosecretory cells in the hypothalamus: releasing hormones and inhibiting hormones.

The neurohypophysis, or posterior pituitary, stores and secretes peptide hormones that are made by the hypothalamus (e.g., oxytocin and antidiuretic hormone).

1. Posterior pituitary hormones

The hypothalamic peptide hormones, oxytocin and antidiuretic hormone (ADH), are stored in and released from the posterior pituitary.

• They are synthesized in neurosecretory cell bodies located in the hypothalamus and are secreted from the neurosecretory cell axons located in the posterior pituitary.

• Oxytocin induces uterine muscle contraction and causes the mammary glands to eject milk during nursing.

ADH acts on the kidneys to increase water retention, which results in a decrease in urine volume.

ADH is part of the feedback mechanism that helps regulate blood osmolarity.

• Osmoreceptors (on specialized nerve cells) in the hypothalamus monitor blood osmolarity.

• When plasma osmolarity increases, the osmoreceptors shrink slightly (lose water by Osmosis) and transmit nerve impulses to certain hypothalamic neurosecretory cells.

• These neurosecretory cells respond by releasing ADH into the general circulation from their tips in the posterior pituitary.

• The target cells for ADH are cells lining the collecting ducts of nephrons in the kidneys and increases water retention in the blood (that is less water is excreted as urine).

• The osmoreceptors also stimulate a thirst drive.

When an individual drinks water it reduces blood osmolarity.

• As more dilute blood (lower osmolarity) arrives at the brain, the hypothalamus responds by reducing ADH secretion and lowering thirst sensations.

This prevents overcompensation by stopping hormone secretion and quenching thirst.

• Note that this negative feedback scheme includes a hormonal action and a behavioral response (drinking).

2. Anterior pituitary hormones

The anterior pituitary produces many different hormones and is regulated by releasing factors and release-inhibiting factors from the hypothalamus.

Four of the hormones (TSH, ACTH, FSH, LH) secreted from the anterior pituitary are tropic hormones that stimulate other endocrine glands to synthesize and release their hormones.

Growth hormone (GH) is a protein hormone that affects a wide variety of tissues.

• It promotes growth directly and stimulates the production of growth factors.

• For example, GH stimulates the liver to secrete insulinlike growth factors (IGFs,) which stimulate bone and cartilage growth.

Prolactin (PRI) is a protein hormone similar in structure to GH, although their physiological roles are very different.

• PRL produces a diversity of effects in different vertebrates, including:

Follicle-stimulating hormone (FSH) is a tropic hormone that affects the gonads (therefore a gonadotropin).

• In males, it is necessary for spermatogenesis.

• In females, it stimulates ovarian follicle growth.

Luteinizing hormone (LH) is another gonadotropin, which stimulates ovulation in females and spermatogenesis in males.

Thyroid-stimulating hormone (TSH) is a tropic hormone that stimulates the thyroid gland to produce and secrete its own hormones.

The remaining hormones from the anterior pituitary are formed by the cleaving of a single large protein, pro-opiomelanocortin, into short fragments.

At least three of these fragments become active peptide hormones:

B. The pineal gland is involved in biorhythms

The pineal gland is a small mass of tissue near the center of the mammalian brain (it is closer to the surface in some other vertebrates).

The pineal contains light-sensitive cells or has nervous connections with the eyes.

It secretes melatonin, a modified amino acid

• Melatonin modulates skin pigmentation.

• Melatonin regulates functions related to light and to seasons marked by changes in day length, such as biological rhythms associated with reproduction.

C. Thyroid hormones function in development, bioenergetics, and homeostasis

The thyroid gland consists of two lobes located on the ventral surface of the trachea in mammals, and on the two sides of the pharynx in other vertebrates.

• Produces two modified amino acid hormones, T3 (triiodothyronine) and T4 (thyroxine or tetraiodothyronine) derived from the amino acid tyrosine.

These differ in structure by only one iodine atom.

Figure 45.8

• Both have the same effects on their target, although T3 is usually more active in mammals than T4.

The thyroid gland plays a major role in vertebrate development and maturation.

• Thyroid hormones control metamorphosis in amphibians.

The thyroid gland is critical for maintaining homeostasis in mammals.

• It helps maintain normal blood pressure, heart rate, muscle tone, digestion, and reproductive functions.

T3 and T4 tend to increase the rate of oxygen consumption and cellular metabolism.

• Serious metabolic disorders can result from a deficiency or excess of thyroid hormones.

Hyperthyroidism, excessive secretion of thyroid hormones, causes high body temperature, sweating, weight loss, irritability, and high blood pressure.

Hypothyroidism, low secretion of thyroid hormones, can cause cretinism in infants and weight gain, lethargy, and cold-intolerance in adults.

Goiter (enlarged thyroid) is caused by a dietary iodine deficiency.

Thyroid hormone secretion is regulated by the hypothalamus and pituitary through a negative feedback system

Figure 45.9.

• The hypothalamus secretes TRH (TSH-releasing hormone), which stimulates TSH (thyroid-stimulating hormone) secretion by the anterior pituitary.

• When TSH binds to receptors in the thyroid, cAMP is generated and triggers release ofT3 and T4.

• High levels of T3, T4, and TSH inhibit TRH secretion.

The thyroid gland in mammals also produces and secretes calcitonin, a peptide hormone that lowers blood calcium levels.

D. Parathyroid hormone and calcitonin balance blood calcium

Four parathyroid glands are embedded in the surface of the thyroid and function in the homeostasis of calcium ions.

• They secrete PTH (parathyroid hormone), which raises blood Ca++ levels (antagonistic to calcitonin) and needs vitamin D to function.

PTH stimulates the kidney to retain Ca++ and induces bone to decompose and release Ca++ into the blood.

PTH and calcitonin (which have opposite affects) work in an antagonistic manner and their balance in the body maintains the proper blood calcium levels

Figure 45.10.

F. Endocrine tissues of the pancreas secrete insulin and glucagon, antagonistic hormones that regulate blood glucose

The pancreas of many vertebrates is a compound gland that performs both exocrine and endocrine functions.

• In addition to secreting two hormones, it produces the pancreatic enzymes associated with digestion, which are carried to the small intestine via ducts (exocrine function).

The endocrine cells are typically clustered together is solid balls called the islets of Langerhans.

• Each islet is composed of alpha cells, which secrete the peptide hormone glucagon, and beta cells which secrete the hormone insulin.

Glucagon and insulin work together in an antagonistic manner to regulate the concentration of glucose in the blood

Figure 45.11

• Blood glucose levels must remain near 90 mg/lO0 mL in humans for proper body function.

• At glucose levels above the set point, insulin is secreted and lowers blood glucose concentration by stimulating body cells to take up glucose from the blood.

It also slows glycogen breakdown in the liver and inhibits the conversion of amino acids and fatty acids to sugar.

• When blood glucose levels drop below the set point, glucagon is secreted and increases blood glucose concentrations by stimulating the liver to increase the hydrolysis of glycogen, convert amino acids and fatty acids to glucose, and to slowly release glucose into the blood.

Glucose homeostasts is critical due to its function as the major fuel for cellular respiration and a key source of carbon for the synthesis of other organic compounds. Serious conditions can result when glucose homeostasis is unbalanced. Diabetes mellitus is caused by a deficiency of insulin or a loss of response to insulin in target tissues. Diabetes occurs in two forms:

Type I diabetes mellitus (insulin-dependent diabetes) is an autoimmune disorder, in which the immune system attacks the cells of the pancreas.

Type II diabetes mellitus (non-insulin-dependent diabetes) occurs most frequently in adults over 40.

Both types of diabetes mellitus will result in high blood sugar concentrations if untreated.

• Kidneys excrete glucose, resulting in higher concentrations in the urine.

• More water is excreted due to the high concentration of glucose (results in the symptoms of copious urine production accompanied by thirst).

• Fat must serve as the major fuel source for cellular respiration since glucose does not enter the cells.

• In severe cases, acidic metabolites formed during fat metabolism may lower the blood pH to a life-threatening level.

F. The adrenal medulla and adrenal cortex help the body manage stress

Adrenal glands are located adjacent to kidneys.

In mammals, each gland has an outer adrenal cortex and inner adrenal medulla, which are composed of different cell types, have different functions, and are of different embryonic origin.

• Different arrangements of these same tissues are found in other vertebrates.

• The adrenal medulla has close developmental and functional ties with the nervous system.

The adrenal medulla synthesizes and secretes catecholamines (epinephrine and norepinephrine)

Figure 45.13.

Catecholamines are secreted in times of stress when nerve cells excited by stressful stimuli release the neurotransmitter acetylcholine in the medulla. Acetylcholine combines with cell receptors, stimulating release of epinephrine.

Norepinephrine is released independently of epinephrine.

• Epinephrine and norepinephrine released into the blood results in rapid and dramatic effects on several targets:

Glucose is mobilized in skeletal muscle and liver cells.

Fatty acid release from fat cells is stimulated (may serve as extra energy sources).

The rate and stroke volume of the heartbeat is increased.

Blood is shunted away from the skin, gut, and kidneys to the heart, brain, and skeletal muscles by stimulation of smooth muscle contraction in some blood vessels and relaxation in others.

Oxygen delivery to the body cells is increased by dilation of bronchioles in the lungs.

The adrenal cortex synthesizes and secretes corticosteroids.

Stressful stimuli cause the hypothalamus to secrete a releasing hormone that stimulates release of ACTH from the anterior pituitary.

• ACTH stimulates release of corticosteroids from the adrenal cortex.

In humans, the two primary types are glucocorticoids (e.g., cortisol) and

mineralocorticoids (e.g., aldosterone).

The liver and kidneys convert the carbon to glucose which is released into the blood to increase the fuel supply.

Also have immunosuppressive effects and are used to treat inflammation.

Mineralocorticoids affect salt and water balance.

• Aldosterone stimulates kidney cells to reabsorb sodium ions and water from the filtrate.

• This raises blood volume and blood pressure.

Current evidence indicates glucocorticoids and mineralocorticoids are important to maintaining body homeostasis during extended periods of stress

Figure 45.15

G. Gonadal steroids regulate growth, development, reproductive cycles, and sexual behavior

The testes of males and ovaries of females produce steroid hormones that affect growth and development as well as regulate reproductive cycles and behaviors.

The gonads of both males and females produce all three categories of gonadal steroids (androgens, estrogens, and progestins), although the proportions differ.

Figure 45.14.

Androgens generally stimulate the development and maintenance of the male reproductive system.

• They are produced in greater quantities in males than females.

• Primary androgen is testosterone.

• Androgens produced during early embryonic development determine whether the fetus will be male or female.

• High androgen concentrations at puberty stimulate development of male secondary sex characteristics.

Estrogens perform the same functions in females as androgens do in males. Estradiol is the primary estrogen produced.

They maintain the female system and stimulate development of female secondary sex characteristics.

Progestins are primarily involved with preparing and maintaining the uterus for reproduction in mammals.

The gonadotropins from the anterior pituitary (FSH and LH) control the synthesis of both androgens and estrogens.

• FSH and LH are in turn controlled by gonadotropin-releasing hormone (GnRH) from the hypothalamus.



Chapter 48


Nervous System

The nervous system has 3 overlapping functions:

1 Sensory input- transmission of signals from sensory receptors to integration centers of the nervous system

2. Integration - interpretation of sensory signals and association with motor responses

3. Motor output - conduction of signals from processing centers to effector cells (muscles, glands, etc)

Fig 48.1

Central nervous system (CNS) - brain and spinal cord

Peripheral nervous system (PNS) - network of nerves that carry sensory input to the CNS and motor output away form the CNS

Synapse - specialized region of contact used for communication between neurons

Neurotransmitter - chemicals that mediate communication between neurons

Glial cells are supporting cells of the CNS

contribute to blood-brain barrier

probably communicate with each other and with neurons

some form myelin sheaths that insulate axons

Schwann cells are the supporting cells of the PNS and form myelin sheaths to insulate axons

Structure and diversity of neurons

Fig 48.2

Fig 48.3

Reflex responses

Fig 48.4

Electrical excitability

Neurons and muscle cells are excitable cells, that is they can change their membrane potential in response to stimuli

membrane potential is a voltage across the plasma membrane

due to the ionic composition of the intracellular and extracellular fluid and the selective permeability of the plasma membrane

resting potential is usually about -70mV

Na+/K+ pump helps to maintain resting potential

Fig 48.5

Ion channel = transmembrane protein that allows a specific ion to cross the membrane

Gated ion channels


ligand-gated (transmitter)

Hyperpolarization - makes the interior more negative, positively charged ions move out of cell or negatively charged ions move into cell

Depolarization - makes the interior more positive (+) ions move into cell or (-) ions move out of cell

Graded potentials

Fig 48.6

If the depolarization reaches threshold the cell will fire an action potential

Fig 44.7

Refractory period

Fig 44.8

Action potentials are all-or-none and strong vs. weak stimuli are encoded by the frequency of APs



Synaptic transmission

Electrical synapses are gap junctions and allow action potentials to spread directly from pre to postsynaptic cells

Chemical synapses use neurotransmitters for communication

Fig 48.10

Excitatory postsynaptic potentials (EPSPs) occur when neurotransmitters open ion channels that result in depolarization (more positive, closer to AP threshold, +ions in or - ions out)

Inhibitory postsynaptic potentials (IPSPs) occur when neurotransmitters open ion channels that result in hyperpolarization (more negative, away from AP threshold, +ions out or -ions in)

Temporal and Spatial Summation

Fig 44.11

Fig 44.12


Glutamate major excitatory transmitter, Na+, Ca++

GABA major inhibitory transmitter, Cl-

Glycine inhibitory, Cl-

Acetylcholine can be either excitatory or inhibitory depending on the receptor it binds to (transmitter used by motor neurons).

Biogenic amines

Epinephrine, norepinephrine, dopamine, serotonin


Substance P, Neuropeptide Y, Endorphins

Gas Transmitters

nitric oxide (NO), Carbon monoxide (CO)


Nervous system diversity

Fig 48.13

Fig 48.14

Peripheral Nervous System (PNS) consists of:

1. Sensory (afferent) nervous system which brings information from sensory receptors to the CNS

2. Motor (efferent) nervous system which carries signals from the CNS to effector cells

a. somatic nervous system signals skeletal muscles

b. autonomic nervous system controls involuntary, automatic, visceral functions of smooth, and cardiac muscle, and organs of the gastrointestinal, excretory, cardiovascular and endocrine systems

Fig 48.15

1. parasympathetic division enhances the conservation of energy, primary transmitter is acetylcholine

2. sympathetic division increases energy expenditures (fight-or-flight responses), primary transmitter is norepinephrine

Fig 48.16

Central Nervous System (CNS) consists of:

1. Spinal cord - receives information from skin and muscles and sends out motor commands

2. Brain - carries out complex integration for homeostasis, perception, movement, intellect, emotion

CNS is covered with meninges, a protective layer of connective tissue

Gray matter consists of nerve cell bodies, White matter consists of axon tracts

Cerebrospinal fluid (CSF) is the extracellular fluid surrounding the brain and spinal cord


Development of the brain

Fig 48.17

1. Forebrain

a. Telencephalon - consists of the cerebral cortex which is the center of complex integration

1. basal ganglia -motor, Parkinson’s disease

2. hemispheres are connected by corpus callosum

b. Diencephalon

1. thalamus - relay for sensory info on way to cortex

2. hypothalamus -hormones, hunger, thirst, sexual responses, pleasure, body’s biological clock (SCN)

3. pituitary gland

2. Brain Stem

a. midbrain

1. superior (visual) and inferior colliculi (hearing)

b. hindbrain

1. pons- breathing

2. medulla- breathing, heart rate, blood pressure

3. cerebellum - coordination of movement

4. spinal cord- receives signals from skin and muscles and sends out motor commands for movement

Functional aspects of the cerebrum

Fig 48.19

Primary motor cortex and somatosensory cortex

Fig 48.20

Motor cortex sends appropriate commands to skeletal muscles in response to sensory stimuli.

Somatosensory cortex receives and integrates signals from the body's touch, pain, pressure, and temperature recetors.

Sleep and Arousal

Characteristic patterns to electroencephalogram (EEG)

the less mental activity, the more synchronous are brain waves

Sleep and arousal are controlled, in part, by the reticular formation and the reticular activating system (RAS)

The RAS selects which information reaches the cortex--the more information the more alert and aware a person is.

Fig 48.22


Left hemishpere-speech, language, calculation

Right hemishpere-overall contex, spatial perception, creative abilities

Split brains

Limbic System-functional center of emotion and memory

Fig 48.23

linked to areas of the cerebral cortex (e.g. prefrontal cortex) involved in complex learning, reasoning, and personality


Learning and Memory



Chapter 49

Sensory and Motor Mechanisms

Sensations = sensory signals (action potentials) sent to the brain and interpreted as perceptions (color, sound, touch, flavor, odor, heat, pain, etc )

Sensory receptors are structures that detect and transmit information about changes in the external and internal environment

they are usually modified neurons

specialized to respond to specific stimuli e.g. light, odor, sound

Reception-each kind of receptor has specific regions which

absorb a particular type of energy

Transduction- conversion of stimulus into action potentials

Amplification is the strengthening of stimulus energy

Integration is the processing of sensory information

Sensory adaptation is a decrease in sensitivity during continued stimulation

Fig 49.1

1. Mechanoreceptors are stimulated by physical deformation caused by pressure, stretch, motion, sound, etc.

bending of the plasma membrane increases its permeability to Na+ and K+ leading to a change in membrane potential

Pacinian corpuscles - strong pressure

Meissner’s corpuscles and Merkel’s disks- light pressure

Muscle spindles - stretch receptors

Hair receptors (touch) and hair cells (motion)

2. Chemoreceptors

osmoregulators-changes in solute concentration in brain

olfactory receptors (smell)

gustatory receptors (taste)

3. Electromagnetic receptors

photoreceptors (vision)

magnetoreceptors (magnetic fields)

4. Thermoreceptors respond to heat or cold

5. Nociceptors are pain receptors

prostaglandins increase pain by lowering thresholds; aspirin and ibuprofen reduce pain by inhibiting prostaglandin synthesis

Structure of Vertebrate Eye

Fig 49.6

Fig 49.7

Signal transduction in the eye

Photoreceptors are rod cells and cone cells in the retina

The light absorbing molecule is retinal (from of vitamin A) bonded to opsin (a protein)

Rods are sensitive to light but do not distinguish color

rod retinal and opsin form rhodopsin which is activated by light

Cones are responsible for daytime color vision

3 types-red, green, and blue cones, each with its own type of opsin (photopsin)

Retinal changes its shape in response to light-affects a G-protein (transducin)- which reduces cGMP levels (converts cGMP to GMP)-closes Na+ channels- hyperpolarizes the photoreceptor- less inhibitory transmitter is released

Figs 49.8, 9, 10

Visual Pathways

Fig 49.11

Human Ear

tympanic membrane (eardrum) transmits vibrations to 3 small bones-malleus, incus, and stapes which transmit vibrations to the oval window

oval window vibrations produce pressure waves in fluid of the cochlea

these pressure waves vibrate the basilar membrane and the organ of Corti, which contains hair cells

the bending of hair cells against the tectorial membrane depolarizes the hair cells which release transmitter onto sensory neurons which transmits info to the brain via the auditory nerve

Fig 49.12

Sound volume is due to amplitude of sound wave, pitch is a function of frequency

Different frequencies affect different areas of the basilar membrane, thus different hair cells

Fig 45.13




opens into 3 semicircular canals

Semicircular canals detect rotation of the head due to endolymph movement against the hair cells

Hair cells in the utricle and saccule respond to changes in head position due to gravitational effects on otoliths (calcium carbonate particles) which land on hairs of receptor cells--tells the brain which way is up and body's position in space

Semicircular canals provide information about rate of rotation.

Fig 45.14

Gustation (taste)

taste buds on tongue and mouth

sweet, sour, salty, and bitter

associated with specific molecular shape and charge

Olfaction (smell)

Olfactory sensory neurons are in the nose

cilia extend into nasal mucus and have receptors for odor molecules

bind odors based on molecular shape, charge

Fig 49.20

Muscle physiology

skeletal muscle = bundle of long fibers running the length of the muscle, attached to and responsible for movement of bones

each fiber is a single cell, consists of myofibrils which have:

thin filaments-actin

thick filaments-myosin

Sarcomere=unit of organization of skeletal muscle

muscle contraction reduces the length of each sarcomere

Fig 49.25

Fig 49.26

thin filaments ratchet across thick filaments to pull the Z lines together

Fig 49.27

Fig 49.28

skeletal muscles contract when stimulated by motor neurons

at rest tropomyosin blocks the myosin binding site on actin

an action potential in the motor neuron releases acetylcholine

the muscle cell depolarizes and transverse tubules carry that depolarization into the cell

Fig 45.30

the depolarization causes the sarcoplasmic reticulum to release Ca++

calcium binds to troponin and causes a shape change in the tropomyosin-troponin complex and exposes the myosin binding sites-the muscle can then contract

contraction is terminated as calcium is pumped out by the sarcoplasmic reticulum

Fig 49.29

Motor Units


a motor unit is a single motor neuron and all of the muscle fibers it controls.

Tension in a muscle can be finely controlled by activating more and more motor neurons in a process called recruitment

Fig 49.32

Fast muscle fibers- fast calcium removal from cytoplasm

Slow muscle- slow calcium removal from cytoplasm

Cardiac muscle--intercalated discs, gap junctions

Smooth muscle--slow contractions but greater range than striated muscle

spiral arrangement of filaments, peristalsis, blood vessels