Chap01, Chapter 1: The Molecular Logic of Life

Chapter 1 The Foundations of Biochemistry

Multiple Choice Questions

1. Cellular foundations

Page: 5 Difficulty: 2 Ans: B

The bacterium E. coli requires simple organic molecules for growth and energy—it is therefore a:

A) chemoautotroph.

B) chemoheterotroph.

C) lithotroph.

D) photoautotroph.

E) photoheterotroph.


Page: 10 Difficulty: 2 Ans: A

The three-dimensional structure of macromolecules is formed and maintained primarily through

noncovalent interactions. Which one of the following is not considered a noncovalent interaction?

A) carbon-carbon bonds

B) hydrogen bonds

C) hydrophobic interactions

D) ionic interactions

E) van der Waals interactions

3. Chemical foundations

Page: 11 Difficulty: 2 Ans: E

Which one of the following is not among the four most abundant elements in living organisms?

A) Carbon

B) Hydrogen

C) Nitrogen

D) Oxygen

E) Phosphorus


Page: 14 Difficulty: 1 Ans: D

The macromolecules that serve in the storage and transmission of genetic information are:

A) carbohydrates.

B) lipids.

C) membranes.

D) nucleic acids.

E) proteins.



2

Stereoisomers that are nonsuperimposable mirror images of each other are known as:

A) anomers.

B) cis-trans isomers.

C) diastereoisomers.

D) enantiomers.

E) geometric isomers.

6. Physical foundations

Page: 23 Difficulty: 2 Ans: C The major carrier of chemical energy in all cells is:

A) acetyl triphosphate.

B) adenosine monophosphate.

C) adenosine triphosphate.

D) cytosine tetraphosphate.

E) uridine diphosphate.


Page: 25 Difficulty: 2 Ans: A Enzymes are biological catalysts that enhance the rate of a reaction by:

A) decreasing the activation energy.

B) decreasing the amount of free energy released.

C) increasing the activation energy.

D) increasing the amount of free energy released.

E) increasing the energy of the transition state.



Energy requiring metabolic pathways that yield complex molecules from simpler precursors are:

A) amphibolic.

B) anabolic.

C) autotrophic.

D) catabolic.

E) heterotrophic.

9. Genetic foundations


Hereditary information (with the exception of some viruses) is preserved in:

A) deoxyribonucleic acid.

B) membrane structures.

C) nuclei.

D) polysaccharides.

E) ribonucleic acid.

Short Answer Questions

3


Page: 10 Difficulty: 2

(a) List the types of noncovalent interactions that are important in providing stability to the three-

dimensional structures of macromolecules. (b) Why is it important that these interactions be

noncovalent, rather than covalent, bonds?

Ans: (a) Noncovalent interactions include hydrogen bonds, ionic interactions between charged

groups, van der Waals interactions, and hydrophobic interactions. (b) Because noncovalent

interactions are weak, they can form, break, and re-form more rapidly and with less energy input than

can covalent bonds. This is important to maintain the flexibility needed in macromolecules.



Name two functions of (a) proteins, (b) nucleic acids, (c) polysaccharides, (d) lipids.

Ans: Many answers are possible including: (a) proteins function as enzymes, structural elements,

signal carriers, transporters; (b) nucleic acids store and transmit genetic information and act as both

structural and catalytic elements; (c) polysaccharides serve as energy-yielding fuel stores and cellular

and extracellular structural and recognition elements, (d) lipids function as membrane components,

fuel stores, and cellular signals.

12. Chemical Foundations


What is an asymmetric carbon atom, why it is called a chiral center?

Ans: An asymmetric carbon has four different substituents attached, and cannot be superimposed on

its mirror image—as a right hand cannot fit into a left glove. Thus, a molecule with one chiral carbon

will have two stereoisomers, which may be distinguishable from one another in a biological system.


Pages: 16-17 Difficulty: 3

(a) What is optical activity?

Ans: (a) Optical activity is the capacity of a substance to rotate the plane of plane-polarized light.

4

Chapter 2 Water


1. Weak interactions in aqueous systems

Pages: 43–45 Difficulty: 2 Ans: D Which of these statements about hydrogen bonds is not true?

A) Hydrogen bonds account for the anomalously high boiling point of water.

B) In liquid water, the average water molecule forms hydrogen bonds with three to four other water

molecules.

C) Individual hydrogen bonds are much weaker than covalent bonds.

D) Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes.

E) The strength of a hydrogen bond depends on the linearity of the three atoms involved in the

bond.


Page: 51 Difficulty: 2 Ans: C

What is the approximate strength of hydrogen bonds in water (in kJ . mol-1)?

A) 0.2

B) 2

C) 20

D) 100

E) 200



Pages: 43–51 Difficulty: 2

Name and briefly define four types of noncovalent interactions that occur between biological

molecules.

Ans: (1) Hydrogen bonds: weak electrostatic attractions between one electronegative atom (such as

oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom; (2)

electrostatic interactions: relatively weak charge-charge interactions (attractions of opposite charges,

repulsions of like charges) between two ionized groups; (3) hydrophobic interactions: the forces that

tend to bring two hydrophobic groups together, reducing the total area of the two groups that is

exposed to surrounding molecules of the polar solvent (water); (4) van der Waals interactions: weak

interactions between the electric dipoles that two close-spaced atoms induce in each other.

The fitness of the aqueous environment for living organisms


If ice were denser than water, how would that affect life on earth?

5

Ans: Ice formed at the surface of bodies of water would sink, hence streams, ponds, lakes, and so on

would freeze from the bottom up. With a reservoir of ice at the bottom they would be perpetually

cold, and in the limit they would freeze solid, precluding life as we know it.

6

Nucleotides and Nucleic Acids


1. Some basics

Pages: 271-273 Difficulty: 1 Ans: E The compound that consists of ribose linked by an N-glycosidic bond to N-9 of adenine is:

A) a deoxyribonucleoside.

B) a purine nucleotide.

C) a pyrimidine nucleotide.

D) adenosine monophosphate.

E) adenosine.

2. Some basics

Page: 273 Difficulty: 1 Ans: E A major component of RNA but not of DNA is:

A) adenine.

B) cytosine.

C) guanine.

D) thymine.

E) uracil.

3. Some basics

Page: 273 Difficulty: 1 Ans: A The difference between a ribonucleotide and a deoxyribonucleotide is:

A) a deoxyribonucleotide has an —H instead of an —OH at C-2.

B) a deoxyribonucleotide has configuration; ribonucleotide has the configuration at C-1.

C) a ribonucleotide has an extra —OH at C-4.

D) a ribonucleotide has more structural flexibility than deoxyribonucleotide.

E) a ribonucleotide is a pyranose, deoxyribonucleotide is a furanose.

4. Some basics

Pages: 274-275 Difficulty: 2 Ans: E The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA:

A) always link A with T and G with C.

B) are susceptible to alkaline hydrolysis.

C) are uncharged at neutral pH.

D) form between the planar rings of adjacent bases.

E) join the 3' hydroxyl of one nucleotide to the 5' hydroxyl of the next.

5. Some basics

Page: 276 Difficulty: 2 Ans: B The DNA oligonucleotide abbreviated pATCGAC:

7

A) has 7 phosphate groups.

B) has a hydroxyl at its 3' end.

C) has a phosphate on its 3' end.

D) has an A at its 3' end.

E) violates Chargaff's rules.


6. Some basics


How are a nucleoside and a nucleotide similar and how are they different?

Ans: Both have a nitrogenous base and a pentose; nucleotides also have a phosphate group, which

nucleosides lack.

7. Some basics


Match the type of bond with the role below:

Bond_type Role

(a) phosphodiester ___ links base to pentose in nucleotide

(b) N-glycosidic ___ joins adjacent nucleotides in one strand

(c) phosphate ester ___ joins complementary nucleotides in two

strands

(d) hydrogen ___ difference between a nucleoside and a

nucleotide

Ans: b; a; d; c

DNA strand. This results in a kink in the double helix at that site.

8

Chapter 3 Amino Acids, Peptides, and Proteins


1. Amino acids


The chirality of an amino acid results from the fact that its carbon:

A) has no net charge.

B) is a carboxylic acid.

C) is bonded to four different chemical groups.

D) is in the L absolute configuration in naturally occurring proteins.

E) is symmetric.

2. Amino acids


All of the amino acids that are found in proteins, except for proline, contain a(n):

A) amino group.

B) carbonyl group.

C) carboxyl group.

D) ester group.

E) thiol group.

3. Amino acids

Pages: 78–79 Difficulty: 1 Ans: A

Amino acids are ampholytes because they can function as either a(n):

A) acid or a base.

B) neutral molecule or an ion.

C) polar or a nonpolar molecule.

D) standard or a nonstandard monomer in proteins.

E) transparent or a light-absorbing compound.

4. Amino acids

Pages: 79–80 Difficulty: 1 Ans: B

In a highly basic solution, the dominant form of glycine is:

A) NH2—CH2—COOH.

B) NH2—CH2—COO.

C) NH2—CH3+—COO.

D) NH3+—CH2—COOH.

E) NH3+—CH2—COO.

9

5. Peptides and proteins


The formation of a peptide bond between two amino acids is an example of a(n) ______________

reaction.

A) cleavage

B) condensation

C) group transfer

D) isomerization

E) oxidation reduction


6. Amino acids


What are the structural characteristics common to all amino acids found in naturally occurring

proteins?

Ans: All amino acids found in naturally occurring proteins have an carbon to which are attached a

carboxylic acid, an amine, a hydrogen, and a variable side chain. All the amino acids are also in the L

configuration.

7. Amino acids


Briefly name the five major groups of amino acids.

Ans: Amino acids may be categorized by the chemistry of their R groups: (1) nonpolar aliphatics; (2)

polar, uncharged; (3) aromatic; (4) positively charged; (5) negatively charged.

10

The Three-Dimensional Structure of Proteins


1. Overview of protein structure

Pages: 114115 Difficulty: 1 Ans: D All of the following are considered “weak” interactions in proteins, except:

A) hydrogen bonds.

B) hydrophobic interactions.

C) ionic bonds.

D) peptide bonds.

E) van der Waals forces.


Page: 115 Difficulty: 1 Ans: D In an aqueous solution, protein conformation is determined by two major factors. One is the

formation of the maximum number of hydrogen bonds. The other is the:

A) formation of the maximum number of hydrophilic interactions.

B) maximization of ionic interactions.

C) minimization of entropy by the formation of a water solvent shell around the protein.

D) placement of hydrophobic amino acid residues within the interior of the protein.

E) placement of polar amino acid residues around the exterior of the protein.

3. Protein secondary structure


Roughly how many amino acids are there in one turn of an helix?

A) 1

B) 2.8

C) 3.6

D) 4.2

E) 10


Pages: 117-119 Difficulty: 2 Ans: A

In the helix the hydrogen bonds:

A) are roughly parallel to the axis of the helix.

B) are roughly perpendicular to the axis of the helix.

C) occur mainly between electronegative atoms of the R groups.

D) occur only between some of the amino acids of the helix.

E) occur only near the amino and carboxyl termini of the helix.


Pages: 117-118 Difficulty: 2 Ans: B

In an helix, the R groups on the amino acid residues:

A) alternate between the outside and the inside of the helix.

11

B) are found on the outside of the helix spiral.

C) cause only right-handed helices to form.

D) generate the hydrogen bonds that form the helix.

E) stack within the interior of the helix.


Pages: 120-121 Difficulty: 1 Ans: E

The major reason that antiparallel -stranded protein structures are more stable than parallel -

stranded structures is that the parallel:

A) are in a slightly less extended configuration than antiparallel strands.

B) do not have as many disulfide crosslinks between adjacent strands.

C) do not stack in sheets as well as antiparallel strands.

D) have fewer lateral hydrogen bonds than antiparallel strands.

E) have weaker hydrogen bonds laterally between adjacent strands.




Any given protein is characterized by a unique amino acid sequence (primary structure) and three-

dimensional (tertiary) structure. How are these related?

Ans: The three-dimensional structure is determined by the amino acid sequence. This means that the

amino acid sequence contains all of the information that is required for the polypeptide chain to fold

up into a discrete three-dimensional shape.


Pages: 114-115, 140-141 Difficulty: 2

Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a

protein.

Ans: Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen

bonds, (c) hydrophobic interactions, and (d) ionic interactions.



Why are glycine and proline often found within a turn?

Ans: A turn results in a tight 180° reversal in the direction of the polypeptide chain. Glycine is the

smallest and thus most flexible amino acid, and proline can readily assume the cis configuration,

which facilitates a tight turn.

12

Protein Function


1. Reversible binding of a protein to a ligand: oxygen-binding proteins


The interactions of ligands with proteins:

A) are relatively nonspecific.

B) are relatively rare in biological systems.

C) are usually irreversible.

D) are usually transient.

E) usually result in the inactivation of the proteins.



A prosthetic group of a protein is a non-protein structure that is:

A) a ligand of the protein.

B) a part of the secondary structure of the protein.

C) a substrate of the protein.

D) permanently associated with the protein.

E) transiently bound to the protein.


Pages: 154155 Difficulty: 2 Ans: B

When oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are

occupied by:

A) one O atom and one amino acid atom.

B) one O2 molecule and one amino acid atom.

C) one O2 molecule and one heme atom.

D) two O atoms.

E) two O2 molecules.



Myoglobin and the subunits of hemoglobin have:

A) no obvious structural relationship.

B) very different primary and tertiary structures.

C) very similar primary and tertiary structures.

D) very similar primary structures, but different tertiary structures.

E) very similar tertiary structures, but different primary structures.


Pages: 168-169 Difficulty: 1 Ans: D

13

Carbon monoxide (CO) is toxic to humans because:

A) it binds to myoglobin and causes it to denature.

B) it is rapidly converted to toxic CO2.

C) it binds to the globin portion of hemoglobin and prevents the binding of O2.

D) it binds to the Fe in hemoglobin and prevents the binding of O2.

E) it binds to the heme portion of hemoglobin and causes heme to unbind from hemoglobin.




Describe the concept of “induced fit” in ligand-protein binding.

Ans: Induced fit refers to the structural adaptations that occur when a ligand binds to a protein. This

often involves a conformational change in the protein that alters the binding site to make it more

complementary to the ligand.


Page: 163-164 Difficulty: 1

Why is carbon monoxide (CO) toxic to aerobic organisms?

Ans: It binds to heme with a higher affinity than oxygen, and thus prevents oxygen from binding to

hemoglobin.

14

Carbohydrates and Glycobiology


1. Monosaccharides and disaccharides


To possess optical activity, a compound must be:

A) a carbohydrate.

B) a hexose.

C) asymmetric.

D) colored.

E) D-glucose.



When the linear form of glucose cyclizes, the product is a(n):

A) anhydride.

B) glycoside.

C) hemiacetal.

D) lactone.

E) oligosaccharide.

3. Polysaccharides

Pages: 245-246 Difficulty: 1 Ans: D

Starch and glycogen are both polymers of:

A) fructose.

B) glucose1-phosphate.

C) sucrose.

D) -D-glucose.

E) -D-glucose.

4. Polysaccharides

Pages: 245-246 Difficulty: 2 Ans: C

Which of the following statements about starch and glycogen is false?

A) Amylose is unbranched; amylopectin and glycogen contain many (1 6) branches.

B) Both are homopolymers of glucose.

C) Both serve primarily as structural elements in cell walls.

D) Both starch and glycogen are stored intracellularly as insoluble granules.

E) Glycogen is more extensively branched than starch.


15



Explain why all mono- and disaccharides are soluble in water.

Ans: These compounds have many hydroxyl groups, each of which can hydrogen bond with water.

(See Chapter 4.)

6. Polysaccharides


Match these molecules with their biological roles.

(a) glycogen __ viscosity, lubrication of extracellular secretions

(b) starch __ carbohydrate storage in plants

(c) chitin __ exoskeleton of insects

(d) cellulose __ extracellular matrix of animal tissues

(e) hyaluronate __ structural component of plant cell walls

(f) proteoglycan __ carbohydrate storage in animal liver

Ans: e; b; c; f; d; a

16

Lipids


1. Lipids as signals, cofactors, and pigments


Fatty acids are a component of:

A) carotenes.

B) oils.

C) sterols.

D) vitamin B.

E) vitamin K.



Function of lipids is not a:

A) structural role.

B) storage.

C) signaling.

D) protection.

E) transporting.



Which of the following statements about fatty acids is not true?

A) Most are unbranched

B) the unsaturated are in cis form

C) they have usually odd number of carbons

D) they can be even polysaturated

E) they are compounds of fat


4. Storage lipids


What is the effect of a double bond on fatty acid structure?

Ans: Most double bonds in fatty acids are in the cis configuration. This results in a rigid bend in the

hydrocarbon chain. (See Fig. 10-2, p. 345.)

5. Storage lipids


17

In cells, fatty acids are stored as triacylglycerols for energy reserves. (a) What is the molecule to

which fatty acids are esterified to form triacylglycerols?

Ans: (a) Three fatty acids are esterified to glycerol.

18

Biological Membranes and Transport


6. The composition and architecture of membranes

Page: 375 Difficulty: 2 Ans: A Peripheral membrane proteins:

A) are generally noncovalently bound to membrane lipids.

B) are usually denatured when released from membranes.

C) can be released from membranes only by treatment with detergent(s).

D) may have functional units on both sides of the membrane.

E) penetrate deeply into the lipid bilayer.

7. Membrane dynamics

Page: 382 Difficulty: 2 Ans: A Which of these is a general feature of the lipid bilayer in all biological membranes?

A) Individual lipid molecules are free to diffuse laterally in the surface of the bilayer.

B) Individual lipid molecules in one face (monolayer) of the bilayer readily diffuse (flip-flop) to the

other monolayer.

C) Polar, but uncharged, compounds readily diffuse across the bilayer.

D) The bilayer is stabilized by covalent bonds between neighboring phospholipid molecules.

E) The polar head groups face inward toward the inside of the bilayer.

8. Membrane dynamics

Page: 381 Difficulty: 2 Ans: D The fluidity of a lipid bilayer will be increased by:

A) decreasing the number of unsaturated fatty acids.

B) decreasing the temperature.

C) increasing the length of the alkyl chains.

D) increasing the temperature.

E) substituting 18:0 (stearic acid) in place of 18:2 (linoleic acid).

9. Solute transport across membranes

Page: 390 Difficulty: 2 Ans: A Facilitated diffusion through a biological membrane is:

A) driven by a difference of solute concentration.

B) driven by ATP.

C) endergonic.

D) always irreversible.

E) not specific with respect to the substrate.

10. Solute transport across membranes

19

Pages: 395-396 Difficulty: 2 Ans: D The type of membrane transport that uses ion gradients as the energy source is:

A) facilitated diffusion.

B) passive transport.

C) primary active transport.

D) secondary active transport.

E) simple diffusion.


11. The composition and architecture of membranes


Draw the structure of a biological membrane as proposed by the fluid mosaic model. Indicate the

positions and orientations of phospholipids, cholesterol, integral and peripheral membrane proteins,

and the carbohydrate moieties of glycoproteins and glycolipids.

Ans: Phospholipids and sterols are found in both faces of the lipid bilayer. Integral membrane

proteins penetrate or span the lipid bilayer, but peripheral membrane proteins associate at the

membrane surface with lipid head groups or integral membrane proteins. The carbohydrate moieties

of glycolipids and glycoproteins are invariably on the outside face of the plasma membrane. (See Fig.

11-3, p. 373.)

20

Chapter 13 Principles of Bioenergetics


1. Bioenergetics and thermodynamics


If the G'° of the reaction A B is –40 kJ/mol, under standard conditions the reaction:

A) is at equilibrium.

B) will never reach equilibrium.

C) will not occur spontaneously.

D) will proceed at a rapid rate.

E) will proceed spontaneously from left to right.

2. Bioenergetics and thermodynamics

Page: 493 Difficulty: 1 Ans: A Which of the following compounds has the largest negative value for the standard free-energy change

(G'°) upon hydrolysis?

A) Acetic anhydride

B) Glucose 6-phosphate

C) Glutamine

D) Glycerol 3-phosphate

E) Lactose

3. Phosphoryl group transfers and ATP

Pages: 501-506 Difficulty: 2 Ans: B All of the following contribute to the large, negative, free-energy change upon hydrolysis of “high-

energy” compounds except:

A) electrostatic repulsion in the reactant.

B) low activation energy of forward reaction.

C) stabilization of products by extra resonance forms.

D) stabilization of products by ionization.

E) stabilization of products by solvation.

4. Biological oxidation-reduction reactions

Page: 512 Difficulty: 1 Ans: D Biological oxidation-reduction reactions always involve:

A) direct participation of oxygen.

B) formation of water.

C) mitochondria.

D) transfer of electron(s).

E) transfer of hydrogens.

21


5. Phosphoryl group transfers and ATP

Page: 506 Difficulty: 3 In general, when ATP hydrolysis is coupled to an energy-requiring reaction, the actual reaction often

consists of the transfer of a phosphate group from ATP to another substrate, rather than an actual

hydrolysis of the ATP. Explain.

Ans: Hydrolysis of the ATP would result in the loss of most of the free energy as heat. In a transfer

reaction, the gamma (third) phosphate of ATP is transferred to the reaction substrate to produce a

high-energy phosphorylated intermediate, which can then form the product in an exergonic reaction.


Pages: 512-513 Difficulty: 1 What is an oxidation? What is a reduction? Can an oxidation occur without a simultaneous

reduction? Why or why not?

Ans: Oxidation is the loss of electrons; reduction is the gain of electrons. Free electrons are unstable

(do not occur), so whenever an electron is released by oxidation of some species, an electron must be

accepted by reduction of another species.

22


Page: 514 Difficulty: 3 During transfer of two electrons through the mitochondrial respiratory chain, the overall reaction is:

NADH + 1/2 O2 + H+ NAD+ + H2O

For this reaction, the difference in reduction potentials for the two half-reactions (E'°) is +1.14

V. Show how you would calculate the standard free-energy change,G'°, for the reaction. (The

Faraday constant, , is 96.48 kJ/V·mol.)

Ans:G'° = –n E'°

For reactions involving NADH, two electrons are transferred (n = 2). SoG'° = (–2)(96.48

kJ/V·mol)(1.14 V) = –220 kJ/mol.



IfE'° for an oxidation-reduction reaction is positive, willG'° be positive or negative? What is the

equation that relatesG'° andE'°?

Ans: Negative.G'° = –n E'°.


Pages: 514-515 Difficulty: 2 Glycerol 3-phosphate dehydrogenase catalyzes the following reversible reaction:

Glycerol 3-phosphate + NAD+ NADH + H+ + dihydroxyacetone phosphate

Given the standard reduction potentials below, calculateG'° for the glycerol 3-phosphate

dehydrogenase reaction, proceeding from left to right as shown. Show your work. (The Faraday

constant, , is 96.48 kJ/V·mol.)

Dihydroxyacetone phosphate + 2e– + 2H+ glycerol 3-phosphate E'° = –0.29 V

NAD+ + H+ + 2e– NADH E'° = –0.32 V

Ans:

E'° = E'° (electron acceptor) – E'° (electron donor)

= – 0.32 – (–0.29) = –0.03 V

G'° = –n E'° = (–2)(96.48 kJ/V·mol)(–0.03 V)

G'° = +5.8 kJ/mol


Page: 515 Difficulty: 1 For each pair of ions or compounds below, indicate which is the more highly reduced species.

(a) Co2+/Co+

(b) Glucose/CO2

(c) Fe3+/Fe2+

(d) Acetate/CO2

(e) Ethanol/acetic acid

(f) Acetic acid/acetaldehyde

Ans: (a) Co+; (b) glucose; (c) Fe2+; (d) acetate; (e) ethanol; (f) acetaldehyde

23


Page: 515 Difficulty: 3 Lactate dehydrogenase catalyzes the reversible reaction:

Pyruvate + NADH + H+ Lactate + NAD+

Given the following facts (a) tell in which direction the reaction will tend to go if NAD+, NADH,

pyruvate, and lactate were mixed, all at 1 M concentrations, in the presence of lactate dehydrogenase

at pH 7; (b) calculateG'° for this reaction. Show your work.

NAD+ + H+ + 2e– NADH E'° = –0.32 V

pyruvate + 2H+ + 2e– lactate E'° = –0.19 V

The Faraday constant, , is 96.48 kJ/V·mol.

Ans:G'° = E'°(acceptor) – E'°(donor) = –0.19 V – (–0.32 V) = +0.13 V

G'° = –n E'° = (–2)(96.48 kJ/V·mol)(0.13 V)

G'° = –25.1 kJ/mol


Page: 515 Difficulty: 3 Alcohol dehydrogenase catalyzes the following reversible reaction:

Acetaldehyde + NADH + H+ Ethanol + NAD+

Use the following information to answer the questions below:

Acetaldehyde + 2H+ + 2e– ethanol E'° = –0.20 V

NAD+ + H+ + 2e– NADH E'° = –0.32 V

The Faraday constant, , is 96.48 kJ/V·mol.

(a) CalculateG'° for the reaction as written. Show your work.

(b) Given your answer to (a), what is theG'° for the reaction occurring in the reverse direction?

(c) Which reaction (forward or reverse) will tend to occur spontaneously under standard conditions?

(d) In the cell, the reaction actually proceeds in the direction that has a positiveG'°. Explain how

this could be possible.

Ans:

(a) G'° = E'°(acceptor) – E'°(donor) = –0.20 –(–0.32) = +0.12V

G'° = –nE'° = (–2)(96.48kJ/V·mol)(0.12 V) = –23.2 kJ/mol

(b) For the reverse reaction,G'° = +23.2 kJ/mol.

(c) The forward reaction will occur spontaneously.

(d) A reaction for whichG'° is positive can occur ifG is negative.

From the relationship

G =G'° + RT ln [product]

[reactant]

it is clear that if the concentration of product is kept very low (by its removal in a subsequent

metabolic step), the log term becomes negative andG can have a negative value.

24

Chapter 14 Glycolysis, Gluconeogenesis, and the Pentose

Phosphate Pathway


12. Glycolysis


Glycolysis is the name given to a metabolic pathway occurring in many different cell types. When it

consists of 11 enzymatic steps it converts glucose to lactic acid. It is an example of:

A) aerobic metabolism.

B) anabolic metabolism.

C) a net reductive process.

D) anaerobic metabolism.

E) oxidative phosphorylation.

13. Glycolysis


The anaerobic conversion of 1 mol of glucose to 2 mol of lactate by fermentation is accompanied by a

net gain of:

A) 1 mol of ATP.

B) 1 mol of NADH.

C) 2 mol of ATP.

D) 2 mol of NADH.

E) none of the above.

14. Fates of pyruvate under anaerobic conditions: fermentation


During strenuous exercise, the NADH formed in the glyceraldehyde 3-phosphate dehydrogenase

reaction in skeletal muscle must be reoxidized to NAD+ if glycolysis is to continue. The most

important reaction involved in the reoxidation of NADH is:

A) dihydroxyacetone phosphate glycerol 3-phosphate

B) glucose 6-phosphate fructose 6-phosphate

C) isocitrate -ketoglutarate

D) oxaloacetate malate

E) pyruvate lactate

15. Gluconeogenesis

Pages: 551-552 Difficulty: 2 Ans: A Which of the following compounds cannot serve as the starting material for the synthesis of glucose

via gluconeogenesis?

A) acetate

B) glycerol

C) lactate

25

D) oxaloacetate

E) -ketoglutarate

16. The pentose phosphate pathway of glucose oxidation


The main function of the pentose phosphate pathway is to:

A) give the cell an alternative pathway should glycolysis fail.

B) provide a mechanism for the utilization of the carbon skeletons of excess amino acids.

C) supply energy.

D) supply NADH.

E) supply pentoses and NADPH.

17. Glycolysis


Briefly describe the possible metabolic fates of pyruvate produced by glycolysis in humans, and

explain the circumstances that favor each.

Ans: Under aerobic conditions, pyruvate is oxidized to acetyl-CoA and passes through the citric acid

cycle. Under anaerobic conditions, pyruvate is reduced to lactate to recycle NADH to NAD+,

allowing the continuation of glycolysis.

18. Glycolysis


Show how NADH is recycled to NAD+ under aerobic conditions and under anaerobic conditions.

Why is it important to recycle NADH produced during glycolysis to NAD+?

Ans: Cells contain a limited supply of NAD+ and NADH. The oxidation of glyceraldehyde 3-

phosphate requires NAD+ as an electron acceptor—it converts NAD+ to NADH. Unless this NADH

is recycled to NAD+, oxidative metabolism in this cell will cease for lack of an electron acceptor.

Under aerobic conditions, NADH passes electrons to O2; under anaerobic conditions, NADH reduces

pyruvate to lactate, and is thereby recycled to NAD+.

26

Chapter 16 The Citric Acid Cycle


1. Reactions of the citric acid cycle


Which of the following is not an intermediate of the citric acid cycle?

A) Acetyl-CoA

B) Citrate

C) Oxaloacetate D) Succinyl-CoA

E) -Ketoglutarate



In mammals, each of the following occurs during the citric acid cycle except:

A) formation of -ketoglutarate.

B) generation of NADH and FADH2.

C) metabolism of acetate to carbon dioxide and water.

D) net synthesis of oxaloacetate from acetyl-CoA.

E) oxidation of acetyl-CoA.


Pages: 623-625 Difficulty: 2 Ans: E

The reaction of the citric acid cycle that is most similar to the pyruvate dehydrogenase complex-

catalyzed conversion of pyruvate to acetyl-CoA is the conversion of:

A) citrate to isocitrate.

B) fumarate to malate.

C) malate to oxaloacetate.

D) succinyl-CoA to succinate.

E) -ketoglutarate to succinyl-CoA.



All of the oxidative steps of the citric acid cycle are linked to the reduction of NAD+ except the

reaction catalyzed by:

A) isocitrate dehydrogenase.

B) malate dehydrogenase.

C) pyruvate dehydrogenase.

D) succinate dehydrogenase.

E) the -ketoglutarate dehydrogenase complex.

27


5. Production of acetyl-CoA (activated acetate)

Page: 616 Difficulty: 2 The citric acid cycle begins with the condensation of acetyl-CoA with oxaloacetate. Describe three

possible sources for the acetyl-CoA.

Ans: Acetyl-CoA is produced by (1) the pyruvate dehydrogenase complex, (2) oxidation of fatty

acids, or (3) degradation of certain amino acids.

6. Production of acetyl-CoA (activated acetate)

Page: 616 Difficulty: 1 Briefly describe the relationship of the pyruvate dehydrogenase complex reaction to glycolysis and

the citric acid cycle.

Ans: The pyruvate dehydrogenase complex converts pyruvate, the product of glycolysis, into acetyl-

CoA, the starting material for the citric acid cycle.

28

Chapter 19 Oxidative Phosphorylation and Photophosphorylation


1. Electron-transfer reactions in mitochondria

Page: 707 Difficulty: 1 Ans: E Almost all of the oxygen (O

2) one consumes in breathing is converted to:

A) acetyl-CoA.

B) carbon dioxide (CO2).

C) carbon monoxide and then to carbon dioxide.

D) none of the above.

E) water.

2. ATP synthesis

Pages: 723-725 Difficulty: 3 Ans: E In normal mitochondria, the rate of NADH consumption (oxidation) will:

A) be increased in active muscle, decreased in inactive muscle.

B) be very low if the ATP synthase is inhibited, but increase when an uncoupler is added.

C) decrease if mitochondrial ADP is depleted.

D) decrease when cyanide is used to prevent electron transfer through the cytochrome a + a3

complex.

E) All of the above are true.

3. ATP synthesis

Pages: 722-723 Difficulty: 2 Ans: A Which of the following statements about the chemiosmotic theory is correct?

A) Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one

side of the inner mitochondrial membrane.

B) It predicts that oxidative phosphorylation can occur even in the absence of an intact inner

mitochondrial membrance.

C) The effect of uncoupling reagents is a consequence of their ability to carry electrons through

membranes.

D) The membrane ATP synthase has no significant role in the chemiosmotic theory.

E) All of the above are correct.

4. ATP synthesis

Page: 729 Difficulty: 2 Ans: C During oxidative phosphorylation, the proton motive force that is generated by electron transport is

used to:

A) create a pore in the inner mitochondrial membrane.

B) generate the substrates (ADP and Pi) for the ATP synthase.

C) induce a conformational change in the ATP synthase.

D) oxidize NADH to NAD+.

E) reduce O2 to H

2O.

29


5. Electron-transfer reactions in mitochondria


As you read and answer this question, you are (presumably) consuming oxygen. What single reaction

accounts for most of your oxygen consumption?

Ans: O2 is converted to H2O by electrons from the respiratory chain. The final step is the one

catalyzed by cytochrome oxidase (Complex IV).

6. ATP synthesis

Pages: 725-726 Difficulty: 2 When the F1 portion of the ATP synthetase complex is removed from the mitochondrial membrane

and studied in solution, it functions as an ATPase. Why does it not function as an ATP synthetase?

Ans: Like all enzymes, the F1 subunit of the ATP synthase catalyzes a reaction in both directions:

ADP + Pi ATP + H2O

The standard free-energy change (G'°) for ATP hydrolysis is –30.5 kJ/mol. With no proton motive

force to drive the reaction toward ATP synthesis, the hydrolysis (ATPase activity) occurs

spontaneously.

30

Chapter 17 Fatty Acid Catabolism


1. Digestion, mobilization, and transport of fats

Pages: 650-652 Difficulty: 1 Ans: A

Transport of fatty acids from the cytoplasm to the mitochondrial matrix requires:

A) ATP, carnitine, and coenzyme A.

B) ATP, carnitine, and pyruvate dehydrogenase.

C) ATP, coenzyme A, and hexokinase.

D) ATP, coenzyme A, and pyruvate dehydrogenase.

E) carnitine, coenzyme A, and hexokinase.



Carnitine is:

A) a 15-carbon fatty acid.

B) an essential cofactor for the citric acid cycle.

C) essential for intracellular transport of fatty acids.

D) one of the amino acids commonly found in protein.

E) present only in carnivorous animals.

3. Oxidation of fatty acids


Complete oxidation of 1 mole of which fatty acid would yield the most ATP?

A) 16-carbon saturated fatty acid

B) 18-carbon mono-unsaturated fatty acid

C) 16-carbon mono-unsaturated fatty acid

D) 16-carbon poly-unsaturated fatty acid

E) 14-carbon saturated fatty acid

4. Oxidation of fatty acids


The conversion of palmitoyl-CoA (16:0) to myristoyl-CoA (14:0) and 1 mol of acetyl-CoA by the -

oxidation pathway results in the net formation of:

A) 1 FADH2 and 1 NADH.

B) 1 FADH2 and 1 NADPH.

C) 1 FADH2, 1 NADH, and 1 ATP.

D) 2 FADH2 and 2 NADH.

E) 2 FADH2, 2 NADH, and 1 ATP.

5. Ketone bodies


31

The major site of formation of acetoacetate from fatty acids is the:

A) adipose tissue.

B) intestinal mucosa.

C) kidney.

D) liver.

E) muscle.



Difficulty: 1

Why is it more efficient to store energy as lipid rather than as glycogen?

Ans: First, the energy yield per gram of lipid (about 38 kJ/g) is more than twice that for carbohydrate

(about 17 kJ/g). Second, lipid is stored as anhydrous lipid droplets, but carbohydrates such as

glycogen and starch are stored hydrated, and the water of hydration roughly triples the effective

weight of the carbohydrate, reducing the energy yield to about 6 kJ/g.


Difficulty: 1

The oxidation of acetyl-CoA added to isolated, intact mitochondria is stimulated strongly by

carnitine. Why?

Ans: Carnitine is essential in the transport of fatty acyl groups into the mitochondrial matrix, where

fatty acid oxidation occurs.

Chapter 21 Lipid Biosynthesis


1. Biosynthesis of fatty acids and eicosanoids Pages: 811-812 Difficulty: 2 Ans: D

In comparing fatty acid biosynthesis with -oxidation of fatty acids, which of the following

statements is incorrect?

A) A thioester derivative of crotonic acid (trans-2-butenoic acid) is an intermediate in the synthetic

path, but not in the degradative path.

B) A thioester derivative of D--hydroxybutyrate is an intermediate in the synthetic path, but not in

the degradative path.

C) Fatty acid biosynthesis uses NADPH exclusively, whereas -oxidation uses NAD+ exclusively.

D) Fatty acid degradation is catalyzed by cytosolic enzymes, fatty acid synthesis by mitochondrial

enzymes.

32

E) The condensation of two moles of acetyl-CoA in the presence of a crude extract is more rapid in

bicarbonate buffer than in phosphate buffer at the same pH; the cleavage of acetoacetyl-CoA

proceeds equally well in either buffer.

2. Biosynthesis of fatty acids and eicosanoids Page: 815 Difficulty: 2 Ans: A

Which of these can be synthesized by plants but not by humans?

A) Linoleate [18:2(9,12

)]

B) Palmitate (16:0)

C) Phosphatidylcholine

D) Pyruvate

E) Stearate (18:0)


3. Biosynthesis of fatty acids and eicosanoids

Difficulty: 2 Explain briefly why we require fats in our diets.

Ans: Dietary fats provide the linoleate and linolenate that we need (for eicosanoid synthesis) but

cannot synthesize.

33

Chapter 18 Amino Acid Oxidation and the Production of Urea


1. Metabolic fates of amino groups

Page: 677 Difficulty: 2 Ans: E In amino acid catabolism, the first reaction for many amino acids is a(n):

A) decarboxylation requiring thiamine pyrophosphate (TPP).

B) hydroxylation requiring NADPH and O2.

C) oxidative deamination requiring NAD+.

D) reduction requiring pyridoxal phosphate (PLP).

E) transamination requiring pyridoxal phosphate (PLP).

2. Nitrogen excretion and the urea cycle

Page: 682 Difficulty: 1 Ans: C Urea synthesis in mammals takes place primarily in tissues of the:

A) brain.

B) kidney.

C) liver.

D) skeletal muscle.

E) small intestine.


Page: 683 Difficulty: 1 Ans: B Which of these directly donates a nitrogen atom for the formation of urea during the urea cycle?

A) Adenine

B) Aspartate

C) Creatine

D) Glutamate

E) Ornithine

4. Pathways of amino acid degradation

Page: 688 Difficulty: 2 Ans: A Which of these amino acids can be directly converted into a citric acid cycle intermediate by

transamination?

A) glutamic acid

B) serine

C) threonine

D) tyrosine

E) proline

5. Pathways of amino acid degradation

Page: 692 Difficulty: 2 Ans: C Serine or cysteine may enter the citric acid cycle as acetyl-CoA after conversion to:

34

A) oxaloacetate.

B) propionate.

C) pyruvate.

D) succinate.

E) succinyl-CoA.



Page: 682 Difficulty: 2 Why does a mammal go to all of the trouble of making urea from ammonia rather than simply

excreting ammonia as many bacteria do?

Ans: When bacteria release ammonia into the surrounding medium, it is diluted enormously to

nontoxic levels. The ammonia produced by amino acid catabolism in mammals cannot be sufficiently

diluted in the tissues and the blood to avoid accumulating at toxic levels. Urea is much less toxic than

ammonia.


Page: 682 Difficulty: 1 Describe the three general mechanisms for disposing of excess nitrogen obtained in the diet. Which

organisms use each mechanism?

Ans: (1) Ammonotelic: release into the surrounding medium as NH4+ (bacteria and many marine

organisms); (2) Uricotelic: production of uric acid (birds and reptiles); (3) Ureotelic: production and

excretion of urea (land-dwelling animals).

Chap01, Chapter 1: The Molecular Logic of Life

Documents