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: