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.

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

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.

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

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

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.

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.

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).

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.

Cohesive

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

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

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 is most dense at 4^oC

Water contracts as it cools to 4^oC

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

Fig 3.5

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.

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.

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)

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)

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

Organic molecules are molecules that contain carbon.

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:

Length

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 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

Most macromolecules are polymers

Macromolecule = (Macro = large); large organic polymer

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

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.

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.

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

Structural polysaccharides include cellulose and chitin.

Fig 5.7

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).

(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 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.

No double bonds between carbons in the tail

Saturated with hydrogen

Solid at room temperature

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

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.

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

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

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 = 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).

Described by Linus Pauling and Robert Corey, 1951

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 = 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).

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.

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

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.

Fig 5.24

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 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.

Phosphate

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.

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:

Significance of free energy:

Fig 6.4

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

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

• Reaction is energetically downhill.
• Spontaneous reaction.
• ÆG is negative.
• -ÆG is the maximum amount of work the reaction can perform.

• Products store more free energy than reactants.
• Reaction is energetically uphill.
• Non-spontaneous reaction (requires energy input).
• ÆG is positive.
• +ÆG is the minimum amount of work required to drive the reaction.

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

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.

1. The structure and hydrolysis of ATP

• Adenine, a nitrogenous base.
• Ribose, a five-carbon sugar.
• Chain of three phosphate groups.

Fig 6.7

• Process is rapid (10⁷ molecules used and regenerated/sec/cell).
• Reaction is endergonic.
• Energy to drive the endergonic regeneration of ATP comes from the exergonic process of cellular respiration.

Fig 6.8

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 (E_A).

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

Fig 6.9

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

Fig 6.14

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

Fig 6.16

Fig 6.17

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

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.

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

Fig 7.1

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.

Prokaryotic

(pro = before; karyon = kernel)

• Found only in bacteria and archaebacteria
• No true nucleus; lacks nuclear envelope
• Genetic material in nucleoid region
• No membrane-bound organelles

Figure 7.4

Eukaryotic

(Eu = true; karyon = kernel)

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

• True nucleus; bounded by nuclear envelope
• Genetic material within nucleus
• Contains cytoplasm with cytosol and membrane-bound organelles

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 µM

Most bacteria 1.0 - 10.0 µm

Most eukaryotic cells 10.0 - 100.0 µm

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

• DNA to program metabolism.
• ribosomes, enzymes and cellular components to sustain life and reproduce.

• Partition the cell into compartments.
• Have unique lipid and protein compositions depending upon their specific functions.
• May participate in metabolic reactions since many enzymes are incorporated directly into the membrane.
• Provide localized environmental conditions necessary for specific metabolic processes.
• Sequester reactions, so they may occur without interference from incompatible metabolic processes elsewhere in the cell.

Figure 7.6

• Messenger RNA (mRNA) transcribed in the nucleus

• Passes through nuclear pores into cytoplams
• Attaches to ribosomes where the genetic message

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

Figure 7.10

• Are complexes of RNA and protein
• Constructed in the nucleolus in eukaryotic cells
• Cells with high rates of protein synthesis have prominent nucleoli and many ribosomes (e.g., human liver cell has a few million).

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.

• Most proteins made by free ribosomes will function in the cytosol.

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

• Generally make proteins that are destined for membrane inclusion or export.
• Cells specializing in protein secretion often have many bound ribosomes (e.g., pancreatic cells).

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.

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

production.

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.

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

• Membrane proteins are produced by ribosomes. As a polypeptide grows, it is inserted directly into the rough ER membrane where it is anchored by hydrophobic regions of the proteins.
• Enzymes within the ER membrane synthesize phospholipids from raw

materials in the cytosol.

• Newly expanded ER membrane can be transported as a vesicle to other parts of the cell.

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

Figure 7.12

• Membranes of the cisternae sequester cisternal space from the cytosol.
• Vesicles may transport macromolecules between the Golgi and other cellular structures.
• Has a distinct polarity. Membranes of cistenae at opposite ends differ in thickness and composition.

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:

During this process, the Golgi:

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

Figure 7.13

• Bound by a single membrane
• Found in nearly all eukaryotic cells
• Often have a granular or crystalline core which is a dense collection of enzymes
• Contain peroxide-producing oxidases that transfer hydrogen from various substrates to oxygen, producing hydrogen peroxide

Oxidase

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

Figure 7.19

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

catalase

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

Figure 7.17

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

Structure of the mitochondrion:

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.

• Found in eukaryotic algae, leaves and other green plant organs.
• Are lens-shaped and measure about 2 mm by 5 mm.
• Are dynamic structures that change shape, move and divide.

Structure of the chloroplast:

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

Figure 7.18

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

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

Stroma = Viscous fluid outside the thylakoids

• Begin as two-dimensional sheets of tubulin units, which roll into tubes
• Elongate by adding tubulin units to its ends
• May be disassembled and the tubulin units recycled to build microtubules elsewhere in the cell

Functions of microtubules include:

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

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

• Many unicellular eukaryotic organisms are propelled through the water by cilia or flagella and motile sperm cells (animals, algae, some plants) are flagellated.
• May function to draw fluid across the surface of stationary cells (e.g., ciliated cells lining trachea).

 Cilia (singular, cilium)

• Occur in large numbers on cell
• surface.
• Shorter than flagella; 2-20 mm in length.
• Work like oars, alternating power with recovery strokes. Creates force in a direction perpendicular to the axis of the cilium.

Flagella (singular, flagellum)

• One or a few per cell.
• Longer than cilia; 10-200 mm in length.
• Undulating motion that creates force in the same direction as the axis of the flagellum.

Figure 7.23

Ultrastructure of cilia and flagella:

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.

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.

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

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

Structure of microfilaments

Figure 7.26:

• Solid rods about 7 nm in diameter
• Built from globular protein monomers, G-actin, which are linked into long chains
• Two actin chains are wound into a helix

Function of microfilaments:

• Along the length of a muscle cell, parallel actin microfilaments are interdigitated with thicker filaments made of the protein myosin, a motor molecule

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

• Contracting ring of microfilaments pinches an animal cell in two during cell division
• Elongation and contraction of pseudopodia during amoeboid movement
• Involved in cytoplasmic streaming (cyclosis) found in plant cells

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:

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:

• directly to the collagen and proteoglycan of their extracellular matrix.
• or to the ECM by another class of glycoproteins-fibronectins.

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

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:

• Intercellular glycoprotein filaments that penetrate and attach the plasma membrane of both cells.
• A dense disk inside the plasma membrane that is reinforced by intermediate filaments made of keratin (a strong structural protein).

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

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

Figure 8.1a

Figure 8.1b

Figure 8.2a

• 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

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

• Less fluid at warmer temperatures (e.g., 37'C body temperature) by restraining phospholipid movement.
• More fluid at lower temperatures by preventing close packing of phospholipids.

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

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:

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

• Membrane solubility characteristics of the phospholipid bilayer
• Presence of specific integral transport proteins

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:

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

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

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.

C Osmosis is the passive transport of water

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

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 can be measured by an osmometer:

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

Membrane potential = Voltage across membranes

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

Figure 8.16

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

Exocytosis:

• Process of exporting macromolecules from a cell by fusion of vesicles with the plasma membrane.
• Vesicle usually budded from the ER or Golgi and migrates to plasma membrane.
• Used by secretary cells to export products (e.g., insulin in pancreas, or neurotransmitter from neuron).

Endocytosis:

• Process of importing macromolecules into a cell by forming vesicles derived from the plasma membrane.
• Vesicle forms from a localized region of plasma membrane that sinks inward; pinches off into the cytoplasm.
• Used by cells to incorporate extracellular substances.

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

Pinocytosis = (cell drinking); endocytosis of fluid droplets

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.

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

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.

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

• Can be an anaerobic process
• Results in a partial degradation of sugars

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

• Most prevalent and efficient catabolic pathway

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

Can be summarized as:

• Organic compounds + Oxygen---> Carbon dioxide + Water+ Energy

(food)

• Carbohydrates, proteins, and fats can all be metabolized as fuel, but cellular respiration is most often described as the oxidation of glucose:

C₆H_I20₆ + 6 0₂---> 6 C0₂ + 6 H₂0 + Energy (ATP + Heat)

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.

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

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

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

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

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

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:

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:

• Are composed of electron-carrier molecules built into the inner mitochondrial membrane.
• Accept energy-rich electrons from reduced coenzymes (NADH and FADH2); and during a series of redox reactions, pass these electrons down the chain to oxygen, the final electron acceptor. The electronegative oxygen accepts these electrons, along with hydrogen nuclei, to form water.
• Release energy from energy-rich electrons in a controlled stepwise fashion; a form that can be harnessed by the cell to power ATP production. If the reaction between hydrown and oxygen during respiration occurred in a single explosive step, much of the energy released would be lost as heat, a form unavailable to do cellular work.

Electron transfer from NADH to oxygen is exergonic, having a free energy change of -222 kJ/mole (-53 kcal/mol).

• Since electrons lose potential energy when they shift toward a more electronegative atom, this series of redox reactions releases energy.
• Each successive carrier in the chain has a higher electronegativity than the carrier before it, so the electrons are pulled downhill towards oxygen, the final electron acceptor and the molecule with the highest electronegativity.

There are three metabolic stages of cellular respiration

Figure 9.6

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.

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:

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.

For every turn of Krebs cycle:

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.

• Reduced coenzymes produced by the Krebs cycle (six NADH and two FADH2 per glucose) carry high energy electrons to the electron transport chain (ETC).
• The ETC couples electron flow down the chain to ATP synthesis.

Figure 9.12

• Each successive carrier in the chain has a higher electronegativity than the carrier before it, so the electrons are pulled downhill towards oxygen, the final electron acceptor and the molecule with the highest electronegativity.
• Except for ubiquinone (Q), most of the carrier molecules are proteins and are tightly bound to prosthetic groups (nonprotein cofactors).
• Prosthetic groups alternate between reduced and oxidized states as they accept and donate electrons.

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

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.

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:

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:

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:

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:

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:

• Two ATPs are produced during the Krebs cycle.

See Figure 9.16

Cellular respiration is remarkably efficient in the transfer of chemical energy from glucose to ATP.

Calculated by 7.3 kcal/mol ATP x 38 mol ATP/mol glucose x 100

Fermentation = Anaerobic catabolism of organic nutrients

Glycolysis oxidizes glucose to two pyruvate molecules, and the oxidizing agent for this process is NAD+, not oxygen.

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:

• Pyruvate loses carbon dioxide and is converted to the two-carbon compound acetaldehyde.
• NADH is oxidized to NAD+ and acetaldehyde is reduced to ethanol.

Many bacteria and yeast carry out alcohol fermentation under anaerobic conditions.

Lactic acid fermentation:

• NADH is oxidized to NAD+ and pyruvate is reduced to lactate.

The anaerobic process of fermentation and aerobic process of cellular respiration are similar in that both metabolic pathways:

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.

• Directly or indirectly supplies energy to most living organisms

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.

• Heterotrophs are also known as consumers.
• Examples are animals that eat plants or other animals.
• Examples also include decomposers, heterotrophs that decompose and feed on organic litter. Most fungi and many bacteria are decomposers.
• Most heterotrophs depend on photoautotrophs for food and oxygen (a byproduct of photosynthesis).

• Chlorophyll is the green pigment in chloroplasts that gives a leaf its color and that absorbs the light energy used to drive photosynthesis.

Chloroplasts are primarily in cells of mesophyll, green tissue in the leaf's interior.

Chloroplasts are lens-shaped organelles measuring about 2 - 4 µm by 4 - 7 µm. These organelles are divided into three functional compartments by a system of 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.

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.

6 C02 + 12 H20 + light energy --> C6H1206 + 6 02 + 6 H20

Indicating the net consumption of water simplifies the equation:

The simplest form of the equation is:

C02 + H20 ---> CH20 + 02

general: C02 + 2 H2X ---> CH20 + H20 + 2 X

sulfur bacteria: C02 + 2 H2S ---> CH20 + H20 + 2 S

plants: C02 + 2 H20 ---> CH20 + H20 + 02

Scientists later confirmed this hypothesis by using a heavy isotope of oxygen

Respiration is an exergonic redox process; energy is released from the oxidation of sugar.

B. The light reactions and the Calvin cycle cooperate in transforming light to the chemical energy of food.

• 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:

• Occur in the stroma of the chloroplast
• First incorporate atmospheric C02 into existing organic molecules by a process called carbon fixation, and then reduce fixed carbon to carbohydrate

• Light reactions occur in the thylakoids of chloroplasts.
• Calvin cycle reactions occur in the stroma.

Light may be reflected, transmitted, or absorbed when it contacts matter.

Figure 10.6

Pigments = Substances which absorb visible light

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

What happens when chlorophyll or accessory pigments absorb photons?

Figure 10.9

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.

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:

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.

When the antenna assembly of photosystem 11 absorbs light, the energy is transferred to the P680 reaction center .

• The first carrier in the chain, plastoquinone (Pq) receives the electrons from the primary electron acceptor. In a cascade of redox reactions, the electrons travel from Pq to a complex of two cytochromes to plastocyanin (Pc) to P700 of photosystem 1.

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.

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.

Cyclic electron flow is the simplest pathway, but involves only photosystem I and generates ATP without producing NADPH or evolving oxygen.

• It is cyclic because excited electrons that leave from chlorophyll a at the reaction center return to the reaction center.
• As photons are absorbed by Photosystem 1, the P700 reaction center chlorophyll releases excited-state electrons to the primary electron acceptor; which, in turn, passes them to ferredoxin. From there the electrons take an alternate path that sends them tumbling down the electron transport chain to P700. This is the same electron transport chain used in noncyclic electron flow.
• With each redox reaction along the electron transport chain, electrons lose potential energy until they return to their ground-state orbital in the P700 reaction center.
• The exergonic flow of electrons is coupled to ATP production by the process of chemiosmosis. This process of ATP production is called cyclic photophosphorylation.
• Absorption of another two photons of light by the pigments send a second pair of electrons through the cyclic pathway.

The function of the cyclic pathway is to produce additional ATP.

Chemiosmosis in chloroplasts and chemiosmosis in mitochondria are similar in several ways:

• An electron transport chain assembled in a membrane translocates protons across the membrane as electrons pass through a series of carriers that are progressively more electronegative.
• An ATP synthase complex built into the same membrane, couples the diffusion of hydrogen ions down their gradient to the phosphorylation of ADP.
• The ATP synthase complexes and some electron carriers (including quinones and cytochromes) are very similar in both chloroplasts and mitochondria.
• Oxidative phosphorylation in mitochondria and photophosphorylation in chloroplasts differ in the following ways:

• Mitochondria transfer chemical energy from food molecules to ATP. The high-energy electrons that pass down the transport chain are extracted by the oxidation of food molecules.
• Chloroplasts transform light energy into chemical energy. Photosystems capture light energy and use it to drive electrons to the top of the transport chain.

Figure 10.15

• Pushes low energy-state electrons from water to NADPH, where they are stored at a higher state of potential energy. NADPH, in turn, is the electron donor used to reduce carbon dioxide to sugar (Calvin cycle).
• Produces ATP from this light driven electron current
• Produces oxygen as a by-product

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).

An enzyme phosphorylates 3-phosphoglycerate by transferring a phosphate group from ATP. This reaction:

• Produce six molecules of 1,3-bisphosphoglycerate
• Primes 1,3-bisphosphoglycerate for the addition of high-energy electrons from NADPH.

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.

• 9 ATP molecules
• 6 NADPH molecules

G3P produced by the Calvin cycle is the raw material used to synthesize glucose and other carbohydrates.

• Occurs because the active site of rubisco can accept 02 as well as C02
• Produces no ATP molecules
• Decreases photosynthetic output by reducing organic molecules used in the Calvin cycle

(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.

Photorespiration is fostered by hot, dry, bright days.

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.

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).

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.

C4 plants spatially separate carbon fixation from the Calvin cycle.

CAM plants temporally separate carbon fixation from the Calvin cycle.

• Yeast (unicellular eukaryotes) have two mating types: a and alpha.
• Type a cells secrete an a-factor chemical signal; type alpha cells secrete alpha-factor.
• The binding of a-factor to type alpha cells and the binding of alpha-factor to type a cells induces type a and type alpha to move toward one another and fuse.

• In paracrine signaling, one cell secretes the signal into extracellular fluid and the signal acts on a nearby target cell. Examples of signals which act in a paracrine fashion are growth factors, a group of factors which stimulate cells to divide and grow.

• The plasma membrane is critical for transmitting the signal (reception)
• Activation of glycogen phosphorylase required the presence of an intermediate step or steps inside the cell (signal transduction)

• Chemical signals bind to specific receptors.
• The signal molecule is complementary to a specific region of the receptor protein; this interaction is similar to that between a substrate and an enzyme.
• The signal behaves as a ligand, a term for a small molecule that binds to another, larger molecule.

• Alteration in receptor conformation or shape; such alterations may lead to the activation of the receptor which enables it to interact with other cellular molecules.
• Aggregation of receptor complexes.

• G-protein-linked receptors
• tyrosine kinase receptors
• ion channel receptors

Figure 11.7

Figure 11.6

• Nitric oxide (NO)
• Steroid (e.g., estradiol, progesterone, testosterone) and thyroid hormones of animals

• the cyclic AMP (cAMP) system
• the Ca++-inositol triphosphate (IP3 system).

Figure11.15

• Ligand (first message) binds to a receptor.
• Receptor conformation changes; G-protein complex is activated.
• The active G-protein in turn activates the enzyme, adenylyl cyclase, which is associated with the cytoplasmic side of the plasma membrane.
• Adenylyl cyclase converts ATP to cAMP.
• cAMP binds to and activates a cytoplasmic enzyme, protein kinase A.
• Protein kinase A, as was the case for protein kinases mentioned previously, propagates the message by phosphorylating various other proteins that lead to the cellular response (e.g., glycogen breakdown)

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.

• Ligand binding to a Ca⁺⁺-gated ion channel (discussed above).
• Activation of the inositol triphosphate (IP3) signaling pathway.

Figure 11.14

Activation of the IP3 pathway involves the following steps:

• Ligand binding results in a conformation change in the receptor.
• The altered receptor activates an enzyme associated with the cytoplasmic side of the plasma membrane (phospholipase). The activated enzyme hydrolyzes membrane phospholipids, giving rise to two important second messengers: IP3 and diacylglycerol.
• Diacylglycerol is linked to a signaling pathway that involves another protein kinase (protein kinase C).
• IP3 is linked to a Ca++ signaling pathway. IP3 binds to Ca++-gated channels. A large number of such channels are located on the ER, in the lumen of which high amounts of Ca++ are sequestered. IP3 binding to these receptors and increases the cytoplasmic concentration of Ca++ (in this case Ca++ could be considered a tertiary messenger; however, by convention, all post-receptor small molecules in the transduction system are referred to as second messengers).

• Directly by affecting the activity or function of target proteins
• Indirectly by first binding to a relay protein, calmodulin. Calmodulin, in turn, principally affects transduction systems by modulating the activities of protein kinases and protein phosphatases.

• ampliify the signal (and, thus, the response)
• contribute to the specificity of the response.

What is the genetic material?

Chromosomes

Proteins -- diverse

DNA -- too uniform??

Griffith experiments provided evidence that genetic material is a specific molecule.

16.1

Transformation = The assimilation of external genetic material by a cell, cell takes on new genotype and phenotype.

Hershey Chase experiment -- Protein or DNA?

16.2

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

16.3

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

16.5

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

16.6

16.7

16.8

Meselson and Stahl experiment

16.9

DNA Replication II

Replication

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

16.10

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

16.11

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.

16.12

16.13

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.

16.14

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.

16.15

Summary

16.16

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

Cancer

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

16.17

Telomeres and the end-replication problem

16.18

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.

16.9

Chapter 17

DNA and RNA

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

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

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

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 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

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

anticodon

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 3^rd 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

17.14

two subunits, large and small

constructed in nucleolus

Passed through nuclear pores to cytoplasm

assemble into functional ribosomes only when attached to an mRNA

Building a polypeptide

17.15

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

17.16

16.15

Termination codon (stop codon)

UAA, AUG, UGA

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

17.18

attachments e.g. sugars, lipids, phosphates groups

cleaved

quaternary structure

Free ribosomes in cytosol

Bound ribosomes attached to cytosolic side of ER--proteins for endomembrane system and for secretion

Signal recognition particle

17.19

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

17.21

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

17.22

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

• There are five types of histones in eukaryotes.

• This structure consists of a tightly wound coil with six nucleosomes per turn.
• Molecules of histone HI pull the nucleosomes into a cylinder 3Onm in diameter.

• In prokaryotes, most DNA codes for protein (mRNA), tRNA or rRNA, and coding sequences are uninterrupted. Small amounts of noncoding DNA consist mainly of control sequences, such as promoters.
• In eukaryotes, most DNA does not encode protein or RNA, and coding sequences may be interrupted by long stretches of noncoding DNA (introns). Certain DNA sequences may be present in multiple copies.

Figure 19.3

Chromatin organization:

Chemical modifications of chromatin play key roles in both chromatin structure and the regulation of transcription.

The following is a brief review of a eukaryotic gene and its transcript Figure 19.8

• Directly to DNA (protein-DNA interactions)
• To each other and/or to RNA polymerase (protein-protein interactions)

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

Restriction enzymes = bacterial enzymes that recognize short, specific nucleotide sequences called recognition sequences and cuts DNA at specific points within those sequences

20.2

Cloning Vectors = bacterial plasmid or virus used to move DNA into cells

Host Organisms

Bacteria

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

Yeast

Cultured plant and animal cells

Often difficult to introduce engineered DNA

Cloning a human gene in a bacterial plasmid

20.3

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

20.4

20.5

No introns, but lack control sequences

Posttranslational modifications

Insertion of DNA into cells

transformation

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)

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

20.6

cDNA library

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

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)

20.7

radioactive probe base-pairs (hybridizes) with complementary sequence (DNA or RNA)

20.8

20.10

recombinant DNA techniques replace or supplement defective genes

20.11

adult cells vs undifferentiated cells or germ lines

Pathogens

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

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

41.9

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

41.10

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

41.12

a. conducts food from pharynx to stomach

b. peristalsis moves the bolus to the stomach

4. Stomach

41.11

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)

41.14

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

a. excess calories stored as glycogen by liver and muscles

b. further excess is stored in adipose tissue as fat

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)

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)

Hormones

Body temp, exercise

Fig

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

Fig 42.11

Fig 42.12

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)

Cells

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

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

Nonspecific - don’t distinguish between infective agents

Specific - respond in a very specific manner to a particular type of infective agent

Fig 43. 1

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

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

vasodilation

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

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)

placenta

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

Fig 43.9

Fig 43.10

Fig 43.11

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

Mast cells

histamine

CD4 Cells--helper T cells, macrophages, some B lymphocytes

AZT, Protease inhibitors

Fig 43.20

Chapter 45

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

Fig 48.2

Fig 48.3

Fig 48.4

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

voltage-gated

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

Fig 48.6

If the depolarization reaches threshold the cell will fire an action potential

Fig 44.7

Fig 44.8

Action potentials are all-or-none and strong vs. weak stimuli are encoded by the frequency of APs

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)

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

nitric oxide (NO), Carbon monoxide (CO)

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

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

Fig 48.19

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

Lateralization

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

lobotomies

Learning and Memory

hippocampus

LTP and LTD

Chapter 49

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

Fig 49.11

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

utricle

saccule

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

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

tetanus

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