Biochemistry, 4E Christopher K Mathews Test Bank

TEST ITEM FILE Scott Lefler Arizona State University

Biochemistry Fourth Edition Christopher K. Mathews Oregon State University

K. E. van Holde Oregon State University

Dean R. Appling The University of Texas at Austin

Spencer J. Anthony-Cahill Western Washington University

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 1: The Scope of Biochemistry

Multiple Choice Questions 1)

The synthesis of which molecule is considered by many to be the root of biochemistry since it was the first synthesis of a biological molecule from non-biological precursors?

A) B) C) D) E)

DNA urea glucose glycine adenosine triphosphate (ATP)

Answer: B Difficulty: 1

2)

Topic: The Roots of Biochemistry

Prior to 1926, the source of biological catalysis was postulated to be possessed by “ferments” which today are called _______.

A) B) C) D) E)

proteins nucleic acids enzymes polysaccharides membranes

Answer: C Difficulty: 1

3)

Topic: The Roots of Biochemistry

Originally, nucleic acids were thought to serve what role within a cell?

A) B) C) D) E)

catalysts genetic structural buffer none of the above

Answer: C Difficulty: 1

Topic: The Roots of Biochemistry

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 1: The Scope of Biochemistry

4)

Which of the following organelles is found in plant cells, but not in animal cells A) B) C) D) E)

chloroplast Golgi apparatus mitochondrion smooth endoplasmic reticulum rough endoplasmic reticulum

Answer: A Difficulty: 1

5)

Topic: The Roots of Biochemistry

Which of the following elements is considered a second tier biochemical element meaning that it is less abundant than first tier elements but still required for life in all organisms?

A) B) C) D) E)

H N P C O

Answer: C Difficulty: 1

6)

Topic: Biochemistry as a Chemical Science

Which of the following is a polymer derived from glucose?

A) B) C) D) E)

cellulose ribonucleic acid polypeptide deoxyribonucleic acid none of the above

Answer: A Difficulty: 1

Topic: Biochemistry as a Chemical Science

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 1: The Scope of Biochemistry

7)

Which of the following macromolecules is considered a homopolymer?

A) B) C) D) E)

polypeptides ribonucleic acids deoxyribonucleic acids starch all of the above

Answer: D Difficulty: 2

8)

Topic: Biochemistry as a Chemical Science

Which of the following is a role played by proteins?

A) B) C) D) E)

structural transport information signaling catalysts all of the above

Answer: E Difficulty: 2

9)

Topic: Biochemistry as a Chemical Science

Of the following biomolecules, which is found only in a monomeric form as opposed to a polymeric form?

A) B) C) D) E)

amino acids carbohydrates lipids nucleotides none of the above

Answer: C Difficulty: 1

Topic: Biochemistry as a Chemical Science

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 1: The Scope of Biochemistry

10) What functional groups are found in the following molecule?

A) B) C) D) E)

amine, carboxylic acid and ketone amine, carboxylic acid and amide amine, aldehyde and amide amine, aldehyde and ketone none of the above

Answer: B Difficulty: 2

Topic: Biochemistry as a Chemical Science

11) What functional groups are found in the following molecule?

A) B) C) D) E)

carboxylic acid, ether, amine and alcohol carboxylic acid, ester, amine and alcohol carboxylic acid, acetal, amine and alcohol carboxylic acid, ether, amide and alcohol carboxylic acid, hemiacetal, amine and alcohol

Answer: E Difficulty: 3

Topic: Biochemistry as a Chemical Science

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 1: The Scope of Biochemistry

12) Of Koshland’s “pillars of life,” which deals specifically with the structure and function of DNA? A) B) C) D) E)

program compartmentation energy regeneration adaptability

Answer: A Difficulty: 2

Topic: Biochemistry as a Biological Science

13) Which of the following best describes homeostasis?

A) B) C) D) E)

a non-equilibrium, non-steady state a non-equilibrium steady state an equilibrium-controlled, non-steady state an equilibrium-controlled steady state none of the above

Answer: B Difficulty: 2

Topic: Biochemistry as a Biological Science

14) Since the earth is approximately 4.5 billion years old, which of the following is true regarding life on this planet?

A) life forms that arose 3.8 billion years ago were able to synthesize the building blocks of life from non-organic molecules B) the earliest organisms on this planet were anaerobic C) the oxygen in the earth’s atmosphere was originally trapped in ice and thus unavailable for living organisms D) all multi-cellular anaerobic organisms died out as oxygen became more plentiful E) none of the above Answer: B Difficulty: 2

Topic: Biochemistry as a Biological Science

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 1: The Scope of Biochemistry

15) While there are many ways to compare biochemical similarities in organisms, the molecular tree of life is based predominantly on similarities in what biological molecule?

A) B) C) D) E)

DNA proteins ribosomal RNA transfer RNA lipids of cell membranes

Answer: C Difficulty: 1

Topic: Biochemistry as a Biological Science

16) The genetic information of viruses is contained within __________ .

A) B) C) D) E)

DNA DNA or RNA specialized proteins with defined amino acid sequence specialized carbohydrates with defined sequence none of the above

Answer: B Difficulty: 1

Topic: Biochemistry as a Biological Science

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 1: The Scope of Biochemistry

Short Answer Questions 1) The molecule pyruvic acid is found at the crossroads of several biochemical pathways.

Pyruvic acid is also known as 2-oxopropanoic acid. Based upon this name, draw the molecule.

Answer:

Difficulty: 2

Topic: Biochemistry as a Chemical Science

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

Multiple Choice Questions 1) Which of the following represents the breaking of a noncovalent interaction?

A) hydrolysis of an ester B) dissolving of salt crystals C) ionization of water D) decomposition of hydrogen peroxide E) none of the above Answer: B Difficulty: 1

Topic: The Nature of Noncovalent Interactions

2) Which of the following is the most likely noncovalent interaction observed between a carboxylic acid and an alcohol?

A) charge-charge interaction B) charge-dipole interaction C) dipole-dipole interaction D) dipole-induced dipole interaction E) formation of an ester bond Answer: B Difficulty: 1

Topic: The Nature of Noncovalent Interactions

3) Which of the following atoms could interact through a hydrogen bond?

A) the oxygen of a ketone and the hydrogen of an aldehyde B) the oxygen of methanol and a hydrogen on the methyl carbon of methanol C) the hydrogen of an amine and the oxygen of an alcohol D) the hydrogen on an aromatic ring and the oxygen of carbon dioxide E) none of the above Answer: C Difficulty: 2

Topic: The Nature of Noncovalent Interactions

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

4) Which of the following would likely form micelles in an aqueous solution?

A) hexane B) glucose C) glutamic acid D) dodecanoic acid E) none of the above Answer: D Difficulty: 2

Topic: The Role of Water in Biological Processes

5) Which of the following best explains the hydrogen bonding that occurs in water?

A) the average number of H-bonds formed by one water molecule is the same in liquid and solid water, the only difference is the duration of the H-bond B) the number of H-bonds formed by one water molecule is greater in liquid water than in solid water C) the structure of liquid water is best described as flickering clusters of H-bonds due to the relative short duration of individual H-bonds D) each water molecule is capable of forming 8 H-bonds: 2 from each lone pair of electrons and 2 from each hydrogen E) none of the above Answer: C Difficulty: 2

Topic: The Role of Water in Biological Processes

6) Given the structure of a glucose molecule, which of the following explains the hydrogen bonding between glucose and water?

A) H-bonds will form with glucose always being the H-bond donor B) H-bonds will form with water always being the H-bond donor C) each glucose molecule could H-bond with as many as 17 water molecules D) due to the cyclic structure of glucose, H-bonding with water does not occur E) none of the above Answer: C Difficulty: 2

Topic: The Role of Water in Biological Processes 2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

7) Which of the following acids or bases is least likely to be encountered in a biochemical setting?

A) nitric acid B) acetic acid C) ammonia D) citric acid E) phosphoric acid Answer: A Difficulty: 1

Topic: Ionic Equilibria

8) What pH range is generally considered to be the physiological pH range?

A) 1.5-3.0 B) 4.5-7.0 C) 5.5-9.0 D) 6.5-8.0 E) 7.5-10.0 Answer: D Difficulty: 1

Topic: Ionic Equilibria

9) Since pKa = -log Ka, which of the following is a correct statement?

A) acetic acid (pKa = 4.7) is stronger than lactic acid, (pKa = 3.9) B) lactic acid, (pKa = 3.9) is weaker than all forms of phosphoric acid, (pKa = 2.1, 6.9 and 12.4) C) since the pKa for conversion of the ammonium ion to ammonia is 9.25, ammonia is a weaker base then the acetate ion D) for carbonic acid with pKa values of 6.3 and 10.3, the bicarbonate ion is a stronger base than the carbonate ion E) none of the above Answer: E Difficulty: 2

Topic: Ionic Equilibria

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

10) If gastric juice has a pH of about 1.5, which of the following would be predominantly deprotonated in the stomach?

A) phenol (pKa = 9.9) B) acetic acid (pKa = 4.7) C) lactic acid, (pKa = 3.9) D) phosphoric acid (pKa = 2.1) E) hydrochloric acid (pKa = -6) Answer: E Difficulty: 2

Topic: Ionic Equilibria

11) Given the pKa values for phosphoric acid of 2.14, 6.86 and 12.4, what is the ratio of HPO42/H2PO4- in a typical muscle cell where the pH is 7.2?

A) 0.46 B) 2.2 C) 6.3  10-6 D) 1.1  105 E) none of the above Answer: B Difficulty: 2

Topic: Ionic Equilibria

12) You have been asked to determine the pKa of an unknown acid. In a solution at pH 7.0, you find that 24% of the acid is in its deprotonated form. What is the pKa of the acid?

A) 7.9 B) 7.5 C) 6.5 D) 5.6 E) none of the above Answer: B Difficulty: 2

Topic: Ionic Equilibria

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

13) Citric acid is a triprotic acid with three carboxylic acid groups having pKa values of 3.1, 4.8, and 6.4. If a solution of citric acid has a pH of 5.5, what can be said about the predominant protonation state of the citric acid?

A) 1 carboxylic acid group is deprotonated, 2 are protonated B) 2 carboxylic acid groups are deprotonated, 1 is protonated C) all 3 carboxylic acid groups are deprotonated D) all 3 carboxylic acid groups are protonated E) the protonation state cannot be determined Answer: B Difficulty: 2

Topic:

Ionic Equilibria

14) Which of the following is the conjugate acid of hydrogen phosphate, HPO42-?

A) H2PO3B) H2PO4C) H3PO4 D) H2PO42E) none of the above Answer: B Difficulty: 1

Topic: Ionic Equilibria

15) Formic acid is the active agent in an ant bite. What is the ratio of base/acid for formic acid (pKa 3.9) in the blood stream at pH 7.4?

A) 3.16  10-4 B) 3.16  103 C) 3.5 D) 0.54 E) 1.90 Answer: B Difficulty: 1

Topic:

Ionic Equilibria

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

16) If a buffer is made with the pH below the pKa of the weak acid, the ratio of [base]/[acid] will be: A) less than 1 B) greater than 1 C) equal to 1 D) equal to 0 E) cannot be determined Answer: A Difficulty: 1

Topic:

Ionic Equilibria

17) A typical amino acid has a carboxylic acid and an amine with pKa values of 2.3 and 9.6, respectively. In a solution of pH 4.5, which of the following best describes the protonation and charge state of the amino acid?

A) carboxylic acid: protonated and neutral; amine: deprotonated and negative B) carboxylic acid: protonated and neutral; amine: protonated and neutral C) carboxylic acid: deprotonated and negative; amine: protonated and neutral D) carboxylic acid: deprotonated and negative; amine: protonated and positive E) carboxylic acid: deprotonated and negative; amine: deprotonated and neutral Answer: D Difficulty: 2

Topic:

Ionic Equilibria

18) Glutamic acid contains two carboxylic acid groups (pKa values of 2.2 and 4.2) and an amine group (pKa 9.7). What is the pI for glutamic acid?

A) 3.2 B) 6.0 C) 6.5 D) 7.0 E) none of the above Answer: A Difficulty: 2

Topic:

Ionic Equilibria

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

19) Lysine contains two amine groups (pKa values of 9.0 and 10.0) and a carboxylic acid group (pKa 2.2). In a solution of pH 9.5, which of the following would best describe the protonation and charge state of lysine?

A) carboxylic acid: deprotonated and neutral; both amines: protonated and positive B) carboxylic acid: deprotonated and negative; both amines: deprotonated and neutral C) carboxylic acid: deprotonated and negative; amine (pKa 9.0): deprotonated and neutral; amine (pKa 10.0): protonated and positive D) carboxylic acid: deprotonated and negative; amine (pKa 9.0): protonated and positive; amine (pKa 10.0): deprotonated and neutral E) carboxylic acid: deprotonated and neutral; amine (pKa 9.0): deprotonated and neutral; amine (pKa 10.0): protonated and positive Answer: C Difficulty: 3

Topic:

Ionic Equilibria

20) In the following titration curve, what does the inflection point represent?

A) pH of solution equals pKa of weak acid B) concentration of weak acid and conjugate base are equal C) the pH where the solution would function most effectively as a buffer D) the weak acid is 50% protonated, 50% deprotonated E) all of the above Answer: E Difficulty: 2

Topic: Ionic Equilibria

21) What happens to DNA when placed into an aqueous solution at physiological pH? 7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

A) individual DNA molecules attract each other due to presence of positive and negative charges B) individual DNA molecules repel each other due to presence of negative charges C) individual DNA molecules repel each other due to presence of positive charges D) DNA molecules bind to negatively charged proteins E) none of the above Answer: B Difficulty: 2

Topic: Interactions Between Macroions in Solution

22) What solution conditions are required for a protein to be a positively charged macroion?

A) pH of solution is greater than the protein’s pI B) pH of solution is less than the protein’s pI C) pH of solution is greater than the protein’s pI and ionic strength is low D) pH of solution is less than the protein’s pI and ionic strength is low E) none of the above Answer: B Difficulty: 2

Topic: Interactions Between Macroions in Solution

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 2: The Matrix of Life: Weak Interactions in an Aqueous Environment

Short Answer Questions 1) Lactic acid is a common product of actively working muscle. It is transported via the bloodstream to the liver. What percent of lactic acid is ionized in the bloodstream if the pH is 7.40 and the pKa is 3.86?

Answer: 99.97% (100% using correct SF)

pH = pKa + log

[lactate] [lactic acid]

[lactate] = 3467 or [lactate] = 3467  [lactic acid] [lactic acid] [lactate] + [lactic acid] = 100% lactate = 99.97% Difficulty: 2

Topic: Ionic Equilibria

 2) Imidazole is a commonly used buffer in biochemistry labs. With a pKa of 7.0, what would be the ratio of base to acid at pH 7.4?

Answer: 2.5

pH = pKa + log

[base] [acid]

[base] = 10(7.4−7.0) = 2.5 [acid]



Difficulty: 1

Topic: Ionic Equilibria

3) Use the equilibrium equation of the blood buffer to predict what would happen to blood pH if respiration were to slow significantly.

Answer: CO2 + H2O

H2CO3

H+ + HCO3-

Slowing of respiration would cause a decrease in pH since more carbon dioxide would be present in the blood, forcing the equilibrium to the right, thus creating more H+.

Difficulty: 2

Topic: Ionic Equilibria 9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

Multiple Choice Questions 1) In the study of thermodynamics, which of the following could be examined as a system?

A) an isolated mitochondria B) a single muscle cell C) an entire organism D) the entire planet Earth E) all of the above Answer: E Difficulty: 1

Topic: Energy, Heat and Work

2) Which of the following would be considered a closed system?

A) a human living alone on a small island B) the planet Earth C) a fish living in a fish bowl D) a bacteria living in the large intestine E) a bacteria living in a Petri dish Answer: B Difficulty: 1

Topic: Energy, Heat and Work

3) Which of the following best describes biochemical systems with respect to the first law of thermodynamics?

A) most biochemical systems operate at constant volume B) most biochemical systems operate at constant temperature C) most biochemical systems operate at constant pressure D) most biochemical systems operate with a constant number of molecules E) none of the above Answer: C Difficulty: 1

Topic: Energy, Heat and Work

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

4) Which of the following best describes the relationship between the oxidation of glucose in a cell versus the oxidation of glucose in a bomb calorimeter?

A) both the reactions involved and the net enthalpy values are identical B) both the reactions involved and the net enthalpy values are different C) the reactions involved are identical but the net enthalpy values are different D) the reactions involved are different but the net enthalpy values are identical E) none of the above Answer: D Difficulty: 2

Topic: Energy, Heat and Work

5) Which of the following reactions would be a non-spontaneous process?

A) complete oxidation of glucose to carbon dioxide and water B) formation of phosphoenolpyruvate from pyruvate and Pi C) hydrolysis of ATP to ADP and Pi D) the coupled reaction of phosphoenolpyruvate + ADP → pyruvate + ATP E) all of the above Answer: B Difficulty: 2

Topic: Entropy and the Second Law of Thermodynamics

6) Which of the following correctly relates the relative entropies?

A) sodium chloride crystals > sodium chloride dissolved in water B) carbon dioxide in air > dry ice C) carbon in a molecule of glucose > carbon in carbon dioxide gas D) a solution of ATP > the same solution with ATP converted to ADP and Pi E) ice made from pure water > ice made from salt water Answer: B Difficulty: 1

Topic: Entropy and the Second Law of Thermodynamics

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

7) Which of the following represents an apparent violation of the second law of thermodynamics?

A) the organization of free amino acids into a protein B) the tendency for dead cells to break down to smaller molecules C) the hydrolysis of nucleic acids into nucleotides D) the conversion of the polymer cellulose into glucose E) the tendency for a professor’s desk to become cluttered Answer: A Difficulty: 1

Topic: Entropy and the Second Law of Thermodynamics

8) If the change in entropy for a process is much less than the change in enthalpy, why might the entropy change be the dominant factor in determining the overall free energy of the process?

A) biochemical reactions are performed at relatively constant pressure B) biochemical reactions generally occur around 300 K. C) biochemical reactions involve few reactants and products D) biochemical reactions involve mixtures of molecules, never pure substances E) all of the above Answer: B Difficulty: 2

Topic: Free Energy: The Second Law in Open Systems

9) If the G value for a given biochemical reaction is a relatively large, positive value, which of the following is true?

A) the reaction is said to be exergonic B) the reaction is thermodynamically favorable C) the reverse reaction is thermodynamically favorable D) the reaction is freely reversible E) the reaction is at equilibrium Answer: C Difficulty: 2

Topic: Free Energy: The Second Law in Open Systems

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

10) Which of the following is true regarding a spontaneous reaction?

A) H must always be negative B) the sign of S does not matter since the entropy value is relatively small C) if both H and S are positive, TS must be larger than H D) if both H and S are negative, the reaction will only proceed at high temperature E) the only scenario that always produces a spontaneous reaction, regardless of temperature, is when H is positive and S is negative Answer: C Difficulty: 2

Topic: Free Energy: The Second Law in Open Systems

11) Which of the following conditions will produce a non-spontaneous reaction?

A) positive H, positive S, low temperature B) negative H, positive S, high temperature C) negative H, negative S, low temperature D) negative H, positive S, high temperature E) positive H, positive S, high temperature Answer: A Difficulty: 2

Topic: Free Energy: The Second Law in Open Systems

12) The conversion of glucose-6-phosphate to fructose-6-phosphate has a G°´ of +1.7 kJ/mol but within a typical cell, the G is -2.9 kJ/mol. What can be said about the value of Keq and Q? A) under standard conditions, Keq > 1; in the cell, Q < 1 B) under standard conditions, Keq < 1; in the cell, Q > 1 C) under standard conditions, Keq > 1; in the cell, Q > 1 D) under standard conditions, Keq < 1; in the cell, Q < 1 E) none of the above Answer: B Difficulty: 2 Equilibrium

Topic: Free Energy and Chemical Reactions: Chemical

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

13) Which of the following is a result of living cells not being at equilibrium?

A) the G for all reactions will always be negative B) all reactions proceed in only one direction C) if the concentration of products is greater than the concentration of reactants, the reaction will always proceed in the reverse direction D) the entropy of cells is always increasing E) the direction in which most reactions will proceed depends upon concentrations of reactants and products Answer: E Difficulty: 2 Equilibrium

Topic: Free Energy and Chemical Reactions: Chemical

14) Which of the following compounds contains a phosphate ester as its most energetically labile bond?

A) pyrophosphate B) adenosine monophosphate C) creatine phosphate D) 1,3-bisphosphoglycerate E) acetyl phosphate Answer: B Difficulty: 2 in Biological Systems

Topic: High Energy Phosphate Compounds: Free Energy Sources

15) The highly exergonic nature of ATP hydrolysis is explained by which of the following?

A) the resulting orthophosphate is stabilized by resonance B) electrostatic repulsion occurs between phosphate groups and the adenine base of ATP C) the resulting product undergoes tautomerization to the keto form of ADP D) the bond that is hydrolyzed is considered an ester of phosphoric acid, making it highly unstable E) all of the above Answer: A Difficulty: 2 in Biological Systems

Topic: High Energy Phosphate Compounds: Free Energy Sources

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

16) The biochemical standard state differs from standard state conditions in what way?

A) pH = 7.0 B) T = 298.15 K C) activity of water = 0 D) ionic strength = 1 E) all of the above Answer: A Difficulty: 1 in Biological Systems

Topic: High Energy Phosphate Compounds: Free Energy Sources

17) If the G for ATP hydrolysis is –31 kJ/mol and the G for phosphoenolpyruvate hydrolysis is –62 kJ/mol, what is the G for the phosphorylation of ADP by phosphoenolpyruvate?

A) –93 kJ/mol B) –31 kJ/mol C) +31 kJ/mol D) +93 kJ/mol E) none of the above Answer: B Difficulty: 2 in Biological Systems

Topic: High Energy Phosphate Compounds: Free Energy Sources

18) The formation of glucose-1-phosphate from glucose and orthophosphate has a G of + 20.9 kJ/mol. If this reaction were coupled to another reaction in order to produce an exergonic reaction, which of the following would produce an overall endergonic reaction and therefore not be suitable for coupling?

A) creatine phosphate + H2O → creatine + Pi B) AMP + H2O → adenosine + Pi C) ATP + H2O → AMP + PPi D) ATP + H2O → ADP + Pi E) 1,3-bisphosphoglycerate + H2O → 3-phosphoglycerate + Pi Answer: B Difficulty: 2 in Biological Systems

Topic: High Energy Phosphate Compounds: Free Energy Sources 6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

19) Based on the half reactions given below, which of the following reactants is the strongest reducing agent?

A) NADH → NAD+ + H+ + 2e- (E = + 0.32 V) B) dihydrolipoic acid → lipoic acid + 2H+ + 2e- (E = + 0.29 V) C) FADH2 → FAD + 2H+ + 2e- (E = + 0.22 V) D) lactate → pyruvate + 2H+ + 2e- (E = + 0.18 V) E) succinate → fumarate + 2H+ + 2e- (E = - 0.03 V) Answer: A Difficulty: 1

Topic: G for Oxidation/Reduction Reactions

20) Which of the following reactions, if coupled to the reduction of -ketoglutarate, would give the most exergonic overall reaction? -ketoglutarate + CO2 + 2H+ + 2e- → isocitrate (E = - 0.38 V) A) ubiquinol → ubiquinone + 2H+ + 2e- (E = - 0.04 V) B) FADH2 → FAD + 2H+ + 2e- (E = + 0.22 V) C) NADH → NAD+ + H+ + 2e- (E = + 0.32 V) D) H2 → 2H+ + 2e- (E = + 0.42 V) E) pyruvate + CoA → acetyl CoA + CO2 + H+ + 2e- (E = + 0.48 V) Answer: E Difficulty: 2

Topic: G for Oxidation/Reduction Reactions

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Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

21) What is the E for the spontaneous reaction that would result if the following reactions were coupled?

NAD+ + H+ + 2e- → NADH pyruvate + 2H+ + 2e- → lactate

E = -0.32 V E = -0.19 V

A) -0.51 V B) -0.13 V C) +0.13 V D) +0.51 V E) none of the above Answer: C Difficulty: 3

Topic: G for Oxidation/Reduction Reactions

22) In a resting muscle cell at 37 C, what is the G for the phosphorylation of ADP by creatine phosphate (CP) given the following concentrations: CP, 25 mM; ATP, 5 mM; ADP, 0.1 mM and creatine, 1 mM? creatine phosphate + H2O → creatine + Pi ATP + H2O → ADP + Pi

G = -43.1 kJ/mol G = -30.5 kJ/mol

A) +14.4 kJ/mol B) +10.8 kJ/mol C) -10.8 kJ/mol D) -14.4 kJ/mol E) none of the above Answer: C Difficulty: 3 Topic: Calculating Free Energy Changes for Biological Oxidations Under Nonequilibrium Conditions

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

Short Answer Questions 1) The typical concentration of glucose-6-phosphate (G6P) in a cell is 1 mM. What concentration of glucose-1-phosphate (G1P) would be required to make the interconversion of G6P and G1P freely reversible at 37 C? G1P + H2O → glucose + Pi G6P + H2O → glucose + Pi

G = -20.9 kJ/mol G = -13.8 kJ/mol

Answer: G1P → G6P G = -7.1 kJ/mol G = -RT ln Q or Q = [G6P]/[G1P]= e(-G/RT) [G1P] = [G6P] / e(-G/RT) = 0.001 M / e(7100 J/mol/(8.314 J/mol•K)(310 K)) = 6.4  10-5 M [G1P] = 0.064 mM

Difficulty: 3 Equilibrium

Topic: Free Energy and Chemical Reactions: Chemical

2) If acetyl phosphate is made from the combination of ATP and acetate, what is the G? How would this reaction proceed within a typical cell? acetyl phosphate + H2O → acetate + Pi + H+ ATP + H2O → ADP + Pi + H+

G = -43.1 kJ/mol G = -30.5 kJ/mol

Answer: G = +12.6 kJ/mol. If this reaction were to occur within a typical cell, the G for ATP hydrolysis is considerably more exergonic and is thus able to supply the necessary energy for the phosphorylation of acetate.

Difficulty: 2 in Biological Systems

Topic: High Energy Phosphate Compounds: Free Energy Sources

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 3: The Energetics of Life

3) Calculate the G for the oxidation of succinate to fumarate, a step in the citric acid cycle.

FAD + 2H+ + 2e- → FADH2 fumarate + 2H+ + 2e- → succinate

E = - 0.22 V E = + 0.03 V

Answer: E = - 0.25 V G = -nFE = -(2)(96.5 kJ/V/mol)(-0.25 V) = 48.3 kJ/mol

Difficulty: 2

Topic: G for Oxidation/Reduction Reactions

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

Multiple Choice Questions 1) Which of the following bases is found only in DNA? A) adenine B) thymine C) uracil D) cytosine E) guanine Answer: B Difficulty: 1

Topic: The Nature of Nucleic Acids

2) Which of the following is correctly paired?

A) adenine: pyrimidine B) RNA: ribose containing nucleic acid C) thymine: purine D) uracil: purine E) DNA: ribose containing nucleic acid Answer: B Difficulty: 1

Topic: The Nature of Nucleic Acids

3) Which of the following correctly describes the structure of a nucleotide?

A) adenine is bound via a link between N-7 and C-1 of ribose B) phosphates are always bound to C-2 of ribose C) cytosine is bound via a link between the amine on C-4 and C-1 of ribose D) guanine is bound via a link between N-9 and C-1 of ribose E) none of the above Answer: D Difficulty: 2

Topic: The Nature of Nucleic Acids

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

4) Which of the following is correctly paired with the type of tautomerization(s) that occurs?

A) adenine: keto-enol B) cytosine: amino-imino and keto-enol C) guanine: amino-imino D) thymine: keto-enol E) none of the above Answer: D Difficulty: 2

Topic: The Nature of Nucleic Acids

5) Based on the following, what can be said about the synthesis of polynucleotides?

A) polynucleotides are unstable and are rapidly degraded B) polynucleotide formation is made much more exergonic by the hydrolysis of pyrophosphate C) the hydrolysis of nucleoside triphosphates is the only driving force to make an overall irreversible reaction D) polynucleotides are highly resistant to hydrolysis, even in the presence of an acid catalyst E) none of the above Answer: B Difficulty: 2

Topic: The Nature of Nucleic Acids

6) Which of the following describes the directionality seen in nucleic acids?

A) most polynucleotides have an unreacted 5 hydroxyl group B) all polynucleotides have an unreacted 2 hydroxyl group C) most polynucleotides have a phosphate group on the 5 end D) sequences of polynucleotides are generally written from 3 on the left to 5 on the right E) none of the above Answer: C Difficulty: 1

Topic: Primary Structure of Nucleic Acids

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

7) Based on the following, which is true regarding the acid/base properties of guanine?

A) at physiological pH, guanine will be positively charged B) at physiological pH, guanine will be negatively charged C) at physiological pH, guanine will be neutral D) at physiological pH, guanine will be a very effective buffer against base E) at physiological pH, guanine will be a very effective buffer against acid Answer: C Difficulty: 2

Topic: The Nature of Nucleic Acids

8) From the following polynucleotide sequence, one would conclude which of the following?

ACCAGTCG A) the base found at the 3 end of the molecule is adenine B) the base found at the 5 end of the molecule is adenine C) the terminal adenosine contains a free 3 hydroxyl group D) the terminal guanosine contains a free 5 phosphate group E) none of the above Answer: B Difficulty: 2

Topic: Primary Structure of Nucleic Acids

9) Which of the following techniques was used to determine the double helical structure of DNA? A) NMR spectroscopy B) X-ray diffraction C) Raman spectroscopy D) UV/Vis spectroscopy E) IR spectroscopy Answer: B Difficulty: 1

Topic: Secondary and Tertiary Structure of Nucleic Acids

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

10) Which of the following base pairs would have 2 hydrogen bonds and a distance between C-1 of 1.08 nm?

A) A-C B) G-C C) A-T D) G-T E) none of the above Answer: C Difficulty: 1

Topic: Secondary and Tertiary Structure of Nucleic Acids

11) Base stacking, or the “stacking interaction,” is most likely the result of which noncovalent interaction A) charge-dipole interaction B) dipole-dipole interaction C) dipole-induced dipole interaction D) van der Waals interaction E) none of the above Answer: D Difficulty: 2

Topic: Secondary and Tertiary Structure of Nucleic Acids

12) In the Watson-Crick DNA model, how many base pairs are found in one turn of the helix?

A) 4 B) 6 C) 8 D) 10 E) 12 Answer: D Difficulty: 1

Topic: Secondary and Tertiary Structure of Nucleic Acids

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

13) Replication of DNA is best considered __________.

A) conservative B) semiconservative C) dispersive D) complementary E) none of the above Answer: B Difficulty: 1

Topic: Secondary and Tertiary Structure of Nucleic Acids

14) Which of the following best explains why the ratios of A/T and G/C are 0.77 and 1.08, respectively in bacteriophage X174?

A) the base pairing in bacteriophages is not always A-T and C-G B) studies done with most bacteriophages do not use complete genomic DNA due to the inherent instability of phage DNA C) bacteriophage DNA often uses bases other than A, T, C and G D) many viruses often use single stranded DNA E) none of the above Answer: D Difficulty: 2

Topic: Secondary and Tertiary Structure of Nucleic Acids

15) Which of the following is a major difference between B-DNA and A-DNA? A) B-DNA has a right-handed helix, A-DNA has a left-handed helix B) B-DNA has 10 residues per helix turn while A-DNA has 9 C) B-DNA base pairs are stacked almost parallel to one another while A-DNA base pairs are significantly tilted with respect to each other D) the major groove of A-DNA is much larger than that in B-DNA E) none of the above Answer: C Difficulty: 2

Topic: Secondary and Tertiary Structure of Nucleic Acids

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

16) Which of the following types of DNA are often supercoiled?

A) extremely long linear DNA, such as seen in human chromosomes B) very short linear DNA C) circular DNA D) DNA molecules that contain both circular and linear regions E) all of the above Answer: C Difficulty: 1

Topic: Secondary and Tertiary Structure of Nucleic Acids

17) While RNA is often single stranded, transfer RNA (tRNA) is usually found with some double stranded structure. Which of the following explains this?

A) tRNAs contain self-complimentary stem-loop structures B) after synthesis, tRNA molecules are hydrolyzed in specific places to allow double stranded structures to form C) regions of tRNAs become supercoiled, thus forcing formation of double stranded regions D) tRNAs adopt a form much like Z-DNA allowing double stranded regions to form E) none of the above Answer: A Difficulty: 2

Topic: Secondary and Tertiary Structure of Nucleic Acids

18) Which of the following is correct regarding the flow of genetic information?

A) replication uses a DNA template to form RNA which serves as the new template for DNA synthesis B) transcription produces RNA from a DNA template using the enzyme RNA polymerase C) translation uses mRNA as a template, rRNA to carry amino acids, and tRNA to catalyze the synthesis of proteins D) during both replication and transcription, the products are double stranded polynucleotides E) none of the above Answer: B Difficulty: 1

Topic: The Biological Functions of Nucleic Acids

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

19) Which of the following is the most commonly observed nucleic acid form for storing of genomic information?

A) single-stranded DNA B) double-stranded DNA C) single-stranded RNA D) double-stranded RNA E) hybrid molecules of DNA and RNA Answer: B Difficulty: 1

Topic: The Biological Functions of Nucleic Acids

20) In a circular DNA molecule of 126 bp with 10.5 bp/turn, which of the following represents an unstrained circle? (L = linking number, T = twist and W = writhe) A) L = 12, T = 12, W = 0 B) L = 11, T = 11, W = 0 C) L = 11, T = 12, W = -1 D) L = 12, T = 11, W = +1 E) L = 11, T = 10, W = 0 Answer: A Difficulty: 3

Topic: Plasticity of Secondary and Tertiary DNA Structure

21) The following shows deoxyadenosine in the _____ conformation

A) syn B) anti C) cis D) trans E) none of the above Answer: B Difficulty: 1

Topic: Plasticity of Secondary and Tertiary DNA Structure 7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

22) Which of the following represents a palindromic sequence?

A) ACCTTCCA B) ATTCCAAT C) GATTAATC D) GGTAATCC E) none of the above Answer: C Difficulty: 1

Topic: Plasticity of Secondary and Tertiary DNA Structure

23) Which of the following secondary structures is correctly identified?

A) Z-DNA: left-handed DNA with pyrimidines in the syn conformation and purines in the anti conformation B) hairpin structure: self-complimentary single stranded molecules that form a parallel helix C) cruciform: a double hairpin formed in a region of palindromic DNA D) H-DNA: triple helical structure that results when Watson-Crick base pairing does not form and instead, Hoogsteen base pairing occurs E) none of the above Answer: C Difficulty: 2

Topic: Plasticity of Secondary and Tertiary DNA Structure

24) Where are G-quadruplexes most commonly found?

A) transcription termination sites B) origin of replication C) the ends of hairpin loops D) telomeres E) none of the above Answer: D Difficulty: 2

Topic: Plasticity of Secondary and Tertiary DNA Structure

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

25) Which of the following, when paired with its complementary strand, would have the highest Tm? A) AAGTTCCAGT B) GCAGCAGCAT C) ATTACGAGCT D) GCGAAATCAA E) TGACCTTGAA Answer: B Difficulty: 2

Topic: Stability of Secondary and Tertiary Structure

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

Short Answer Questions 1) Draw the structure of cytosine and thymine, then show the most common tautomer of each.

Answer: Cytosine:

Difficulty: 2

Thymine:

Topic: The Nature of Nucleic Acids

2) Show the typical hydrogen bonds that from when adenine pairs with its complimentary base.

Answer:

Difficulty: 2

Topic: Secondary and Tertiary Structure of Nucleic Acids

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 4: Nucleic Acids

3) Draw the two forms of a phosphodiester bond that can occur under physiological pH. If the pKa for this conversion is 6.2, what form predominates in the lysosome where the pH is about 5?

Answer:

The protonated form on the left would predominate in the lysosome Difficulty: 2

Topic: The Nature of Nucleic Acids

11 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

Multiple Choice Questions 1) Which of the following is true regarding the -carbon of an amino acid?

A) there are always four different functional groups attached B) the most commonly occurring form of amino acids are the D-amino acids C) when assigning the R-S stereochemistry, the carboxylic acid is always the highest priority functional group D) for all amino acids except glycine, the -carbon is a stereocenter E) none of the above Answer: D Difficulty: 1

Topic: Amino Acids

2) At physiological pH, most amino acids are _______, meaning that they contain both a positive and negative charge.

A) zwitterions B) amphoteric C) chiral D) amphipathic E) none of the above Answer: A Difficulty: 1

Topic: Amino Acids

3) Which of the following pairs of amino acids contains both an aliphatic and an aromatic amino acid?

A) Thr and Tyr B) Val and Gln C) Phe and Ile D) Ser and Cys E) none of the above Answer: C Difficulty: 1

Topic: Amino Acids

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

4) At a pH of 5, all amino acids have at least ____ charged group(s) and at most, _____ charged group(s).

A) 0; 1 B) 1; 1 C) 1; 2 D) 2; 2 E) 2; 3 Answer: E Difficulty: 1

Topic: Amino Acids

5) Which of the following pairs of amino acids could form a hydrogen bond through their Rgroups?

A) serine and phenylalanine B) aspartic acid and methionine C) histidine and tyrosine D) alanine and glutamine E) leucine and cysteine Answer: C Difficulty: 2

Topic: Amino Acids

6) Which of the following pairs of amino acids could form a charge-charge interaction through their R-groups?

A) methionine and histidine B) glutamine and lysine C) serine and glutamic acid D) aspartic acid and arginine E) threonine and asparagine Answer: D Difficulty: 2

Topic: Amino Acids

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

7) Of the following amino acids, which will have a pI closest to 3?

A) Cys B) His C) Gly D) Asp E) Lys Answer: D Difficulty: 2

Topic: Amino Acids

8) Which of the following undergoes an oxidation reaction to form a disulfide bond?

A) serine B) cysteine C) methionine D) threonine E) tyrosine Answer: B Difficulty: 1

Topic: Amino Acids

9) Which of the following amino acids is derived from another amino acid by the addition of an amine group?

A) lysine B) asparagine C) arginine D) histidine E) none of the above Answer: B Difficulty: 1

Topic: Amino Acids

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

10) Which of the following amino acids is incorporated into proteins during ribosomal protein synthesis?

A) sarcosine B) ornithine C) 4-hydroxyproline D) phosphoserine E) selenocysteine Answer: E Difficulty: 1

Topic: Amino Acids

11) Hydrolysis of a peptide bond produces: A) an alcohol and an amine B) an amine and a carboxylic acid C) a carboxylic acid and an anhydride D) an amide and a carboxylic acid E) an alcohol and an amide Answer: B Difficulty: 1

Topic: Peptides and the Peptide Bond

12) Which of the following bonds has partial double bond character?

A) 1 B) 2 C) 3 D) 4 E) 5 Answer: C Difficulty: 1

Topic: Peptides and the Peptide Bond

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

13) Given the following peptide, what pair of protease enzymes would be able to produce three smaller peptides?

Gly-Ser-Ala-His-Phe-Pro-Asn-Ala-Val-Glu-Cys-Ala-Ser A) chymotrypsin and thrombin B) trypsin and chymotrypsin C) thermolysin and chymotrypsin D) trypsin and thermolysin E) none of the above Answer: C Difficulty: 2

Topic: Peptides and the Peptide Bond

14) What is the sequence of the following peptide?

A) Ile-Ala-Glu B) Val-Ala-Asp C) Leu-Gly-Glu D) Val-Ala-Asn E) Val-Gly-Gln Answer: B Difficulty: 1

Topic: Peptides and the Peptide Bond

15) If a cis peptide bond is found in a protein, the most likely amino acid to contribute the amine to the amide bond is ______.

A) phenylalanine B) leucine C) proline D) glycine E) arginine Answer: C Difficulty: 1

Topic: Peptides and the Peptide Bond 5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

16) Given the following peptide, what would be the overall charge at pH 5?

Met-Glu-Ser-Arg-His-Phe-Pro-Asn-Ala-Glu-Cys-Ala-Ser A) +2 B) +1 C) 0 D) -1 E) -2 Answer: C Difficulty: 2

Topic: Peptides and the Peptide Bond

17) The prevalence of the trans orientation in peptide bonds results in the R-groups of adjacent amino acids being oriented approximately ______ degrees with respect to each other.

A) 30 B) 60 C) 90 D) 120 E) 180 Answer: E Difficulty: 1

Topic: Peptides and the Peptide Bond

18) The conversion of ________ represents a conservative change while the conversion of ________ represents a nonconservative change.

A) Asp to Arg; Ile to Ser B) Tyr to Phe; Lys to Arg C) Gln to Asn; Ser to Thr D) Ile to Leu; Asn to Ala E) Cys to His; Lys to Glu Answer: D Difficulty: 2

Topic: Proteins: Polypeptides of Defined Sequence

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

19) The peptide hormone insulin is composed of two peptide held together primarily by what mechanism?

A) disulfide bonds between cysteine residues B) charge-charge interactions between acidic and basic amino acids C) extensive hydrogen bonding due to the relatively high serine and glutamine content D) hydrophobic interactions E) an amide bond formed from the R-groups of a glutamic acid residue and a lysine residue Answer: A Difficulty: 1

Topic: Proteins: Polypeptides of Defined Sequence

20) Which of the following events occurs after the formation of disulfide bonds during the conversion of preproinsulin to mature insulin?

A) folding of proinsulin into a stable conformation B) transport of the molecule through the membranes C) cleavage of the peptide sequence that joins the A and B chains D) cleavage of the leader sequence E) posttranslational modification of specific proline residues Answer: C Difficulty: 1

Topic: From Gene to Protein

21) Which of the following pairs of amino acids represents a conservation of the type of amino acid when considering the sequence of a protein from different species?

A) Asp and Asn B) Lys and His C) Leu and Val D) Gly and Ile E) Phe and Trp Answer: C Difficulty: 2

Topic: Protein Sequence Homology

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

22) In the sequence of cytochrome c, the presence of cysteine at position 17 in hundreds of different species indicates that this particular amino acid is _________.

A) conserved B) mutated C) homologous D) variable E) none of the above Answer: A Difficulty: 1

Topic: Protein Sequence Homology

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

Short Answer Questions 1) What is the pI for the following peptide: Ala-Glu-Val-Asp-Lys-Leu

Answer: Use R-groups of Glu and Asp: (4.2 + 3.9)/2 = 4.05 (4.1 using correct SF)

Difficulty: 1

Topic: Amino Acids

2) Draw each of the structures of aspartic acid that predominate at pH 1, 3, 7, and 11.

Answer: 1

Difficulty: 2

3

7

Topic: Amino Acids

9 .

11

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 5: Introduction to Proteins: The Primary Level of Protein Structure

3) A peptide was treated with protease enzymes and cyanogen bromide followed by complete hydrolysis of the resulting products. Based upon the following data, determine the sequence of the original peptide.

Chymotrypsin gave two peptides containing the following amino acids: Leu, Pro Asp, Gln, Arg, Met, Tyr, Val Cyanogen bromide gave two peptides containing the following amino acids: Asp, Met Gln, Leu, Arg, Tyr, Pro, Val Trypsin gave two peptides containing the following amino acids: Gln, Leu, Tyr, Pro Asp, Arg, Met, Val

Answer: Chymotrypsin treatment shows the C-term 3 amino acids to be Tyr-Pro-Leu Cyanogen bromide treatment shows that the N-term is Asp-Met Trypsin places Arg giving the overall peptide as Asp-Met-Val-Arg-Gln-Tyr-Pro-Leu

Difficulty: 3

Topic: Peptides and the Peptide Bond

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

Multiple Choice Questions 1) If a peptide was composed entirely of -helical structure and found to contain an integer number of complete turns, which of the following would be a possible number of amino acid residues in the peptide?

A) 12 B) 20 C) 32 D) 36 E) 60 Answer: D Difficulty: 2

Topic: Secondary Structure

2) In an -helix, a hydrogen bond is formed between the carbonyl oxygen of the ith residue and the amide hydrogen _____ residues away A) i + 1 B) i + 2 C) i + 3 D) i + 4 E) i + 5 Answer: D Difficulty: 1

Topic: Secondary Structure

3) Which of the following is true regarding -sheet structures?

A) hydrogen bonds in an parallel sheet are non-linear B) hydrogen bonds in an antiparallel sheet are non-linear C) the rise per residue is greater for a parallel sheet than for an antiparallel sheet D) -sheets are an n=3 helix with each residue rotated 120 with respect to its neighbors E) none of the above Answer: A Difficulty: 2

Topic: Secondary Structure

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

4) Which of the following types of secondary structure has a non-integer value of residues per turn?

A) antiparallel -sheet B) parallel -sheet C) -helix D) 310 helix E) polyproline II helix Answer: C Difficulty: 1

Topic: Secondary Structure

5) The two amino acids most often found in a polyproline II helix are proline and _______.

A) alanine B) glycine C) serine D) lysine E) histidine Answer: B Difficulty: 1

Topic: Secondary Structure

6) Which of the following correctly defines the angles  and ?

A) : N-C; : C-C B) : N-C; : C-Ccarbonyl C) : Ccarbonyl-N(i + 1); : N-C D) : Ccarbonyl-N(i + 1); : C-Ccarbonyl E) : C-C; : N-C Answer: B Difficulty: 2

Topic: Secondary Structure

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

7) In a typical Ramachandran plot, _____ is plotted vs _____ to illustrate _______.

A) ; ; dependence of  upon  B) ; ; dependence of  upon  C) ; ; allowable combinations of  and  D) ; ; allowable combinations of  and  E) none of the above Answer: D Difficulty: 1

Topic: Secondary Structure

8) Which of the following statements regarding structural proteins is true?

A) silk fibroin is made from a repeat of three amino acids where each third amino acid is Gly B) -keratin is composed of peptides that contain mostly –helical structure with the exception of short sequences where the peptide folds back on itself C) collagen has its own helical structure where three individual peptides are wound around each other in a left-handed helix D) generally speaking, structural proteins are soluble in water E) none of the above Answer: C Difficulty: 2

Topic: Fibrous Proteins

9) The presence of a hydrophobic amino acid at every third or fourth residue in -keratin results in which of the following?

A) a random placement of hydrophobic amino acids within the helix B) a strip of hydrophobic surface area that, when combined with another monomer, results in the formation of a dimer through hydrophobic interactions C) a strip of hydrophobic surface area that causes individual -keratin molecules to fold back on themselves through hydrophobic interactions D) represents a deleterious mutation that causes the -keratin molecules to aggregate and form plaques E) none of the above Answer: B Difficulty: 2

Topic: Fibrous Proteins 3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

10) What type of interaction occurs between the -sheets of fibroin?

A) charge-dipole interaction B) dipole-dipole interaction C) dipole-induced dipole interaction D) van der Waals interaction E) hydrogen bonding Answer: D Difficulty: 2

Topic: Fibrous Proteins

11) Which of the following structural proteins is correctly paired with the modified amino acid or cross-link that is an integral part of that protein?

A) collagen: 5-hydroxylysine B) elastin: hydroxyproline C) -keratin: cross link formed by oxidation of lysine, then aldol condensation D) collagen: desmosine E) fibroin: cross-link formed by dehydration of serine residues Answer: A Difficulty: 2

Topic: Fibrous Proteins

12) Which of the following would contribute to tertiary structure?

A) charge-charge interaction between lysine and aspartic acid B) disulfide bond C) hydrogen bond between serine hydroxyl group and amide of glutamine D) hydrophobic interaction between leucine and valine E) all of the above Answer: E Difficulty: 2

Topic: Globular Proteins

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

13) Which of the following elements of secondary structure are observed in the following protein?

A) antiparallel -sheet B) parallel -sheet C) an -helix of at least 20 amino acid residues D) 310 helix E) none of the above Answer: A Difficulty: 2

Topic: Globular Proteins

14) To which domain class would the following protein belong?

A) mainly  B) mainly  C)  +  D) few 2 structures E) / barrel 5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

Answer: A Difficulty: 2

Topic: Globular Proteins

15) Which of the following is a highly compact structure that is very commonly used to transition from one region of secondary structure to another in a globular protein?

A)  bend B)  turn C) / hairpin D) high-glycine loop E) none of the above Answer: B Difficulty: 1

Topic: Globular Proteins

16) Which of the following causes denaturation of a protein when disulfide bonds are present?

A) heat B) pH changes C) reducing agent D) detergent E) all of the above Answer: C Difficulty: 1

Topic: Factors Determining Secondary and Tertiary Structure

17) Which of the following contributes to a positive G for protein folding?

A) conformational entropy B) hydrophobic effect C) charge-charge interactions D) internal hydrogen bonds E) van der Waals interactions Answer: A Difficulty: 1

Topic: Factors Determining Secondary and Tertiary Structure

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

18) A protein with five disulfide bonds was treated with -mercaptoethanol and urea. Once the protein was denatured, the -mercaptoethanol and urea were removed by dialysis. What is the likelihood that all five disulfide bonds will reform correctly?

A) 1/5 or 20% B) 1/10 or 10% C) 1/102 or 4% D) 1/5! = 1/120 or 0.83% E) 1/945 or 0.11% Answer: E Difficulty: 3

Topic: Factors Determining Secondary and Tertiary Structure

19) Of the following proteins that aid in the folding process, which is exclusively involved in the interconversion of cis and trans bonds?

A) prolyl isomerase B) protein disulfide isomerase C) Hsp60 D) Hsp70 E) GroEl-ES complex Answer: A Difficulty: 1

Topic: Dynamics of Globular Protein Structure

20) Which of the following is considered a dead-end complex (and therefore dangerous due to its resistance to proteolytic cleavage) in the protein-folding pathway?

A) disordered aggregate B) molten globule state C) prefibrillar species D) amyloid fibril E) unfolded protein Answer: D Difficulty: 1

Topic: Dynamics of Globular Protein Structure

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

21) Which amino acid is often referred to as a “helix-breaker” due to its absence from -helices but is often found in structures such as -turns?

A) Val B) Met C) Pro D) Phe E) Leu Answer: C Difficulty: 2

Topic: Prediction of Secondary and Tertiary Protein Structure

22) Which of the following could contribute to quaternary structure?

A) charge-charge interaction between arginine and glutamic acid B) disulfide bond C) hydrogen bond between threonine hydroxyl group and imidazole ring of histidine D) hydrophobic interaction between phenylalanine and tryptophan E) all of the above Answer: E Difficulty: 2

Topic: Quaternary Structure of Proteins

23) If two protein subunits produced the following structure, what term would be used to describe the interactions that hold the two peptides together?

A) point-group symmetry interactions B) dyad axis symmetry interactions C) isologous interactions D) dihedral symmetry interactions E) none of the above Answer: C Difficulty: 2

Topic: Quaternary Structure of Proteins

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

Short Answer Questions 1) Draw a section of antiparallel -sheet showing two sheets with three residues in each sheet.

Clearly show the hydrogen bond pattern between the two sheets.

Answer:

Difficulty: 2

Topic: Secondary Structure

2) Show the most likely interaction that would occur between a serine residue and a glutamine residue.

Answer: the structure below shows both amino acids acting as a donor and acceptor

Difficulty: 2

Topic: Factors Determining Secondary and Tertiary Structure

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 6: The Three-Dimensional Structure of Proteins

3) Show the reaction catalyzed by prolyl isomerase. Indicate the configuration of both substrate and product.

Answer:

Difficulty: 2

Topic: Dynamics of Globular Protein Structure

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

Multiple Choice Questions 1) Myoglobin without a heme group would be considered a(n) _______.

A) apoprotein B) holoprotein C) apoenzyme D) holoenzyme E) none of the above Answer: A Difficulty: 1

Topic: The Mechanism of Oxygen Binding by Heme Proteins

2) When oxygen is bound to myoglobin, the amino acid _____ is complexed to the iron ion of the heme group while _______ forms a hydrogen bound to the oxygen.

A) cysteine; serine B) cysteine; histidine C) serine; cysteine D) histidine; histidine E) histidine; cysteine Answer: D Difficulty: 1

Topic: The Mechanism of Oxygen Binding by Heme Proteins

3) Which of the following explains why the ferrous ion is not oxidized to the ferric state in the globin proteins even though free heme in solution is readily oxidized?

A) when bound to globins, the heme is always planar; when free in solution, heme adopts a non-planar configuration which allows the oxidation of the iron B) the globin proteins provide a hydrophobic environment that prevents oxidation C) coordination with the proximal histidine allows any oxidized iron to be rapidly reduced back to the ferrous state D) since the oxygen is hydrogen bound to the distal histidine, if oxidation of iron does occur, the distal histidine allows for rapid reduction E) none of the above Answer: B Difficulty: 2

Topic: The Mechanism of Oxygen Binding by Heme Proteins 1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

4) Recent studies have shown that the H-bond between the distal histidine and oxygen molecule in myoglobin has a strength of ~ 15 kJ/mol, but in hemoglobin, the strength of the bond is only ~8 kJ/mol. What does this suggest about the differences between myoglobin and hemoglobin?

A) myoglobin binds oxygen more strongly than hemoglobin B) hemoglobin binds oxygen more strongly than myoglobin C) the iron in myoglobin is more easily oxidized than in hemoglobin D) the iron in hemoglobin is more easily oxidized than in myoglobin E) none of the above Answer: A Difficulty: 2

Topic: The Mechanism of Oxygen Binding by Heme Proteins

5) Based on the plot of oxygen saturation versus partial pressure of oxygen, which of the following statements is true?

A) at oxygen pressure >100 mm Hg, hemoglobin dissociates into individual subunits so that it is able to bind oxygen similar to myoglobin B) at typical resting capillary oxygen pressure of ~30 mm Hg, hemoglobin has only 1 of its 4 oxygen binding sites filled while myoglobin is nearly saturated with oxygen C) under periods of extreme muscle exertion, capillary oxygen pressure can drop to 10 mm Hg, allowing release of ~90% of oxygen carried by hemoglobin D) the structure of hemoglobin allows for complete release of oxygen in capillary beds at all times E) none of the above Answer: C Difficulty: 2

Topic: Oxygen Transport

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

6) The binding of oxygen to hemoglobin is said to be _______________.

A) high affinity B) low affinity C) sigmoidal D) cooperative E) sequential Answer: D Difficulty: 1

Topic: Oxygen Transport

7) Changes in hemoglobin’s oxygen affinity are primarily the result of changes in the _________ structure of the protein.

A) primary B) secondary C) tertiary D) quaternary E) all of the above Answer: D Difficulty: 1

Topic: Oxygen Transport

8) A typical Hill plot (log [YO2/(1- YO2)] vs log PO2)for hemoglobin-oxygen binding does not yield a straight line as it does for myoglobin. Which of the following is the best explanation for this?

A) at high oxygen pressures, hemoglobin is in a low oxygen affinity state B) at low oxygen pressures, hemoglobin is in a high oxygen affinity state C) hemoglobin undergoes a transition from low affinity state under low oxygen pressure to a high affinity state under high oxygen pressure D) hemoglobin undergoes a transition from high affinity state under low oxygen pressure to a low affinity state under high oxygen pressure E) none of the above Answer: C Difficulty: 2

Topic: Oxygen Transport

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

9) Which of the following models of allosteric transitions best applies to hemoglobin?

A) sequential (KNF) model B) concerted (MWC) model C) tertiary two-state model D) tense versus relaxed model E) none of the above Answer: C Difficulty: 1

Topic: Oxygen Transport

10) Which of the following interactions causes a change from the R state (oxy form) to the T state (deoxy form) of hemoglobin?

A) interactions between heme groups B) protonation of the R-group of His146 on the  subunit to allow formation of a salt bridge with Lys40 on the  subunit C) salt bridge formed by 1-Arg141 to the carboxylate of 2Asp126 D) protonation of the 1 subunit terminal carboxyl group disrupts a salt bridge with 2Lys 127 E) none of the above Answer: C Difficulty: 3

Topic: Oxygen Transport

11) Which of the following occurs when hemoglobin switches from the T (deoxy) state to the R (oxy) state?

A) the heme group goes from a slightly puckered conformation to a flat conformation B) the ferrous ion is pulled into the plane of the heme group C) the F8 (proximal) histidine rotates about 8 to better align with the ferrous ion D) movement of the F8 histidine causes a shift in the F helix, thus weakening interactions with other subunits E) all of the above Answer: E Difficulty: 2

Topic: Oxygen Transport

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

12) Which of the following is a homotropic effector of hemoglobin-oxygen binding?

A) O2 B) H+ C) CO2 D) ClE) 2,3-bisphosphoglycerate (2,3-BPG) Answer: A Difficulty: 1

Topic: Allosteric Effectors of Hemoglobin

13) Which of the following reversible reactions of carbon dioxide explains how hemoglobin serves as a transporter of carbon dioxide?

A) reaction with the imidazole group of the distal histidine where oxygen would normally be bound B) reaction with the carboxyl group of glutamic acid to form a carbonic acid anhydride C) reaction with the N-terminal amino groups to form a carbamate D) reaction with the hydroxyl group of serine to form a carbonate E) none of the above Answer: C Difficulty: 2

Topic: Allosteric Effectors of Hemoglobin

14) Which of the following is true regarding the effectors of hemoglobin-oxygen binding?

A) an increase in blood pH will cause hemoglobin to bind more tightly to oxygen B) increased CO2 from increased muscle activity will result in an increase in the R state of hemoglobin C) increased Cl- will cause the formation of a salt bridge between two Lys residues, one on an  subunit, the other on a  subunit D) the binding site of 2,3-BPG contains several Asp and Glu residues which are repelled by the similar charge, pushing the two  subunits away from each other E) all of the above Answer: A Difficulty: 2

Topic: Allosteric Effectors of Hemoglobin

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

15) The ability of some bacteria to resist the cytotoxic effects of macrophages is most likely due to which of the following?

A) they have high levels of flavohemoglobin that allows for the destruction of nitric oxide, a potent cytotoxic compound produced by macrophages B) they possess a protein called cytoglobin that causes macrophages to undergo apoptosis C) they have high levels of a myoglobin-like protein that tightly binds oxygen, preventing proper activity of the macrophage D) they possess the protein neuroglobin which enables them to specifically target nerve cells and thus evade macrophages E) none of the above Answer: A Difficulty: 2

Topic: Other Functions of the Heme Globins

16) Which of the following mutations is correctly defined?

A) silent: change of a single base in the non-coding intron region of a gene B) missense: substitution of a single base results in a premature stop codon C) nonsense: substitution of a single base results in a complete change of amino acid sequence D) frameshift: deletion of a single base results in a single amino acid change E) permissive: results in a protein that has greater thermodynamic stability Answer: E Difficulty: 2

Topic: Protein Evolution

17) Which of the following mutations in the coding strand of DNA would be the most likely to cause a serious mutation?

A) AGA → CGA B) ATA → TTA C) GAA → AAA D) TAA → TGA E) ACT → AGT Answer: C Difficulty: 2

Topic: Protein Evolution

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

18) In sickle cell hemoglobin, a Glu is mutated to a _______. This causes the formation of _______ between hemoglobin molecules, ultimately forming large aggregates.

A) Arg; salt bridges B) Cys; disulfide bonds C) Val; hydrophobic interactions D) Pro; disrupted -helix, resulting in several H-bonds and salt bridges E) none of the above Answer: C Difficulty: 2

Topic: Hemoglobin Variants

19) Why do individuals who are heterozygous for sickle cell anemia have a resistance to malaria?

A) formation of hemoglobin aggregates makes red blood cells impervious to parasitic infection B) shortened life span of red blood cells does not allow sufficient time for the parasite to mature in the red blood cell C) diminished blood flow to the skin as a result of sickled red blood cells blocking capillaries prevents mosquitoes from actually transferring the malaria parasite to individuals D) sickle cell hemoglobin fibers have both decreased O2 and CO2 carrying capacity; since CO2 is a mosquito attractant, diminished CO2 exhalation does not attract mosquitoes E) none of the above Answer: B Difficulty: 2

Topic: Hemoglobin Variants

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

20) One would expect that defects in the globin genes would be so serious as to cause death in utero. Which of the following explains how some thalassemias are found in living people?

A) in -thalassemia, the use of the  subunit allows individuals to live a normal lifespan B) individuals who completely lack functional  subunits can live if placed in a hypobaric chamber to induce hypoxia C) since humans have 4 copies of the  chain gene, effects are only seen when at least 3 of the genes are nonfunctional D) individuals with nonfunctional  chain genes can make 22 tetramers that function normally E) none of the above Answer: C Difficulty: 2

Topic: Hemoglobin Variants

21) Which immunoglobulin is the only one to occur in a dimeric form?

A) IgA B) IgD C) IgE D) IgG E) IgM Answer: A Difficulty: 1

Topic: Immunoglobulins

22) Which of the following methods could be used to produce a Fab fragment from an IgG? A) treatment with reducing agent, isolation of the light chain, removal of reducing agent B) treatment with reducing agent, isolation of the heavy chain, removal of reducing agent C) treatment with papain, separation of the Fab fragment from the rest of the heavy chain D) treatment with papain, separation of the Fab fragment from the rest of the light chain E) none of the above Answer: C Difficulty: 2

Topic: Immunoglobulins

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

23) Which of the following is responsible for the immense diversity of antibodies?

A) recombination of introns B) recombination of exons C) variable domain recombination D) epitope recombination E) none of the above Answer: B Difficulty: 2

Topic: Immunoglobulins

24) Which of the following is the first step in the clonal selection theory for antibody production?

A) binding of an antigen to an antibody on a B lymphocyte stimulates the cell to replicate B) B stem cells in the bone marrow differentiate to become B lymphocytes C) immunoglobulins are exposed on the outer surfaces of the B lymphocytes D) effector B cells and memory cells are produced E) helper T cells recognize a bound antigen, bind to B lymphocytes and stimulate B cell reproduction Answer: B Difficulty: 2

Topic: Immunoglobulins

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

Short Answer Questions 1) Given the following plot of oxygen binding versus pressure of O2 for myoglobin and hemoglobin, (1) draw a curve that shows what happens when the pH is increased to about 7.6 and (2) draw a curve that shows what happens when the pH is decreased to about 6.8.

Answer:

Difficulty: 2

Topic: Allosteric Effectors of Hemoglobin

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

2) 2,3-Bisphosphoglycerate is known to interact with hemoglobin in the following ways: carboxylate with Lys C-2 phosphate with protonated His C-3 phosphate with N-terminal amino acid Using the structure of 2,3-bisphosphoglycerate, show these interactions and identify what type of interaction occurs.

Answer: All interactions are charge-charge interactions

Difficulty: 2

Topic: Allosteric Effectors of Hemoglobin

11 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 7: Protein Function and Evolution

3) Using the following sequence from the coding strand of DNA, determine the amino acid sequence of the corresponding protein. Make three different mutations: (1) silent, (2) missense with little or no effect upon the protein structure (indicate the amino acid substitution) and (3) nonsense.

CATTTATATGAAAGC Answer: His-Leu-Tyr-Glu-Ser Silent with mutation in 3rd base of codon:

CACTTATATGAAAGC CATTTGTATGAAAGC CATTTATACGAAAGC CATTTATATGAGAGC CATTTATATGAAAGT

Silent with mutation in 1st base of codon:

CATCTATATGAAAGC

Missense:

CATATATATGAAAGC CATGTATATGAAAGC CATTTATATGACAGC CATTTATATGATAGC CATTTATATGAAACC

Leu→Ile Leu→Val Glu→Asp Glu→Asp Ser→Thr

Nonsense:

CATTGATATGAAAGC CATTAATATGAAAGC CATTTATAGGAAAGC CATTTATAAGAAAGC CATTTATATTAAAGC

Difficulty: 3

Topic: Protein Evolution

12 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 8: Contractile Proteins and Molecular Motors

Multiple Choice Questions 1)

Which form of myosin is found in striated muscle?

A) B) C) D) E)

I II IV VI all of the above

Answer: B Difficulty: 1

2)

Topic: Muscles and Other Actin–Myosin Contractile Systems

Which portion of the myosin protein found in muscle is responsible for both ATP and actin binding?

A) B) C) D) E)

heavy-chain coiled-coiled tails heavy-chain stalk heavy-chain globular head essential light chain regulatory light chain

Answer: C Difficulty: 1

3)

Topic: Muscles and Other Actin–Myosin Contractile Systems

What type of secondary structure is most prominent in myosin?

A) B) C) D) E)

antiparallel -sheet parallel -sheet -helix 310 helix polyproline helix

Answer: C Difficulty: 1

Topic: Muscles and Other Actin–Myosin Contractile Systems

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 8: Contractile Proteins and Molecular Motors

4)

Which of the following correctly describes the organization that gives rise to muscle?

A) B) C) D) E)

myofibril → sarcomere → myofiber → muscle sarcomere → myofiber → myofibril → muscle myofibril → myofiber → sarcomere → muscle sarcomere → myofibril → myofiber → muscle myofiber → myofibril → sarcomere → muscle

Answer: D Difficulty: 2

5)

Topic: Muscles and Other Actin–Myosin Contractile Systems

In muscle, thin filaments are made of _______ while thick filaments are made of _______.

A) B) C) D) E)

myosin; actin actin; myosin myofibril; myofiber myofiber; myofibril none of the above

Answer: B Difficulty: 1

6)

Topic: Muscles and Other Actin–Myosin Contractile Systems

Which of the following only occurs when ATP (not ADP) is bound to the myosin head?

A) B) C) D) E)

actin is released from its binding site on myosin weak binding of myosin head to actin strong binding of myosin head to actin power stroke of muscle contraction none of the above

Answer: A Difficulty: 2

Topic: Muscles and Other Actin–Myosin Contractile Systems

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 8: Contractile Proteins and Molecular Motors

7)

Which of the following is the best description of how actin and myosin work in cooperation to allow muscle contraction?

A) B) C) D)

myosin head groups push against actin filaments to lengthen the sarcomere myosin head groups walk along the actin filament to shorten the sarcomere myosin head groups interact with actin only when the sarcomere is fully lengthened all myosin head groups move along the actin filament simultaneously to shorten the sarcomere E) none of the above

Answer: B Difficulty: 2

8)

Topic: Muscles and Other Actin–Myosin Contractile Systems

Which protein of the thin filament is responsible for calcium binding?

A) B) C) D) E)

tropomyosin troponin C troponin T calmodulin actin

Answer: B Difficulty: 1

9)

Topic: Muscles and Other Actin–Myosin Contractile Systems

Which of the following correctly describes the difference between red and white muscle?

A) B) C) D)

red muscle has considerably more mitochondria than white muscle white muscle has a lower concentration of myoglobin than red muscle white muscle receives much less blood flow than red muscle the main source of energy in red muscle is fatty acid oxidation while in white muscle it is glycolysis E) all of the above

Answer: E Difficulty: 1

Topic: Muscles and Other Actin–Myosin Contractile Systems

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 8: Contractile Proteins and Molecular Motors

10) Microtubules are made from which of the following proteins?

A) B) C) D) E)

actin myosin tubulin cytoplasmic dynein kinesin

Answer: C Difficulty: 1

Topic: Microtubule Systems for Motility

11) What is the 9 + 2 array seen in the axoneme?

A) B) C) D) E)

2 central microtubules ringed by 9 microtubule doublets 2 central microtubule doublets ringed by 9 microtubules 9 central microtubules with 2 microtubules attached to each central microtubule 9 central microtubules with 2 microtubule doublets attached to each central microtubule none of the above

Answer: A Difficulty: 2

Topic: Microtubule Systems for Motility

12) Which of the following motor proteins is correctly paired with its primary function?

A) B) C) D) E)

myosin V: muscle contraction myosin II: cargo transport cytoplasmic dynein: bending of cilia or flagella axonemal dynein: cargo transport none of the above

Answer: E Difficulty: 1

Topic: Microtubule Systems for Motility

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 8: Contractile Proteins and Molecular Motors

13) Which of the following motor proteins is correctly paired with both its binding target and its direction of movement?

A) B) C) D) E)

myosin II: actin filament, moves towards (-) end myosin V: actin filament, moves towards (+) end kinesin: actin filament, moves towards (+) end cytoplasmic dynein: microtubule, moves towards (+) end axonemal dynein: microtubule, can move in either direction

Answer: B Difficulty: 2

Topic: Microtubule Systems for Motility

14) Which of the following correctly describes the involvement of myosin V and kinesin in intracellular transport?

A) during transport along microtubules, both myosin V and kinesin form nonspecific interactions with tubulin B) during transport along microfilaments, both myosin V and kinesin form highly specific interactions with actin C) myosin V only joins with kinesin at the end of microtubules while kinesin dissociates from the myosin V-cargo complex at the start of microfilaments D) while myosin V can aid kinesin during microtubule transport, kinesin will often disrupt myosin V during transport along microfilaments E) none of the above Answer: E Difficulty: 2

Topic: Microtubule Systems for Motility

15) Which of the following proteins is found in a bacterial flagellum?

A) B) C) D) E)

actin myosin flagellin dynein all of the above

Answer: C Difficulty: 1

Topic: Bacterial Motility: Rotating Proteins 5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 8: Contractile Proteins and Molecular Motors

16) Which of the following is the energy source for flagellum?

A) B) C) D) E)

ATP hydrolysis GTP hydrolysis proton gradient sodium ion gradient none of the above

Answer: C Difficulty: 1

Topic: Bacterial Motility: Rotating Proteins

17) If a bacteria were found with a protein similar to flagellin but with a left-handed helical structure, how would the bacteria move when all flagella were rotating in a clockwise fashion?

A) B) C) D) E)

the bacteria would tumble and change direction the bacteria would run in a straight line the bacteria would turn in a clockwise direction the bacteria would turn in a counterclockwise direction none of the above

Answer: B Difficulty: 3

Topic: Bacterial Motility: Rotating Proteins

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 8: Contractile Proteins and Molecular Motors Short Answer Questions

1) Under typical conditions within a muscle cell, the G for hydrolysis of ATP is about -51 kJ/mol. If the energy required to move through one power stroke is 1.2  10-20 J, what is the percent utilization of the energy from ATP hydrolysis?

Answer: 51 kJ/mol (1 mol / 6.02  1023 molecules) = 8.47  10-23 kJ/molecule or 8.5  10-20 J/ATP molecule (1.2  10-20 J/power stroke)/( 8.5  10-20 J/ATP molecule) = 14% utilization Difficulty: 2

Topic: Muscles and Other Actin–Myosin Contractile Systems

2) In a typical cell, the use of proton gradient to power ATP synthesis requires about 3 protons for each ATP. Based on this, what is the energy expenditure, in ATP/minute, of a typical flagellum if it is running at 120 revolutions per second and requires 1000 protons to make one revolution?

Answer:

120 Difficulty: 2

revolutions  1000 H+  60 s 1 ATP  6    +  = 2.4  10 ATP/min     s  revolution 1 min 3 H Topic: Bacterial Motility: Rotating Proteins



7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

Multiple Choice Questions 1)

Which of the following formulas would be a carbohydrate A) B) C) D) E)

C5H12O5 C4H8O6 C6H10O6 C3H8O3 C6H12O6

Answer: E Difficulty: 1

2)

Topic: Monosaccharides

How many carbon atoms are found in the smallest molecules that are classified as carbohydrates?

A) B) C) D) E)

1 2 3 4 5

Answer: C Difficulty: 1

3)

Topic: Monosaccharides

Dihydroxyacetone is classified as a(n) _______.

A) B) C) D) E)

aldotriose ketotriose aldotetrose ketotetrose none of the above

Answer: B Difficulty: 1

Topic: Monosaccharides

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

4)

Which stereoisomer of threose is shown below?

A) B) C) D) E)

D L D, L L, D

none of the above

Answer: Difficulty: 1

5)

Topic: Monosaccharides

How many stereoisomers would be expected from a ketohexose?

A) B) C) D) E)

4 8 16 32 64

Answer: B Difficulty: 1

6)

Topic: Monosaccharides

What is the C-4 epimer of glucose?

A) B) C) D) E)

allose mannose gulose galactose fructose

Answer: D Difficulty: 2

Topic: Monosaccharides

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

7)

Which of the following would be the correct Haworth projection for -D-gulose, whose linear form is seen below?

A)

B)

C)

D)

E) None of the above Answer: A Difficulty: 2

Topic: Monosaccharides 3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

8)

Which of the following is a ketose?

A)

B)

C)

D)

E) None of the above Answer: B Difficulty: 2

9)

Topic: Monosaccharides

Which of the following is a diastereomer of D-mannose?

A) B) C) D) E)

D-gulose D-altrose D-idose D-talose

all of the above

Answer: E Difficulty: 1

Topic: Monosaccharides

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

10) Which of the following would be an anomer of -D-galactopyranose?

A)

B)

C)

D)

E) None of the above Answer: D Difficulty: 2

Topic: Monosaccharides

11) Gluconic acid is derived from ________ while glucuronic acid is derived from _______.

A) B) C) D) E)

glucose; gulose gulose; glucose glucose; glucose glucose; galactose galactose; glucose

Answer: C Difficulty: 2

Topic: Derivatives of Monosaccharides 5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

12) Of the following phosphate esters of monosaccharides, which has the most spontaneous G´ of hydrolysis?

A) B) C) D) E)

-D-glucose-6-phosphate -D-glucose-6-phosphate -D-glucose-1-phosphate -D-fructose-6-phosphate D-glyceraldehyde-3-phosphate

Answer: C Difficulty: 2

Topic: Derivatives of Monosaccharides

13) The two most common amino sugars, -D-glucosamine and -D-galactosamine are formed from their respective carbohydrates by substitution of an amine group for the hydroxyl on carbon _____.

A) B) C) D) E)

2 3 4 5 6

Answer: A Difficulty: 1

Topic: Derivatives of Monosaccharides

14) The reaction of a cyclic monosaccharide with an alcohol converts a(n) _________ into a(n) ________.

A) B) C) D) E)

acetal; hemiacetal hemiacetal; acetal acetal; ether hemiacetal; ether alcohol; ether

Answer: B Difficulty: 2

Topic: Derivatives of Monosaccharides

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

15) Which of the following designations best characterizes the following disaccharide?

A) B) C) D) E)

Glc(1→4)Gal Glc(1→4)Gal Gal(1→4)Gal Gal(1→4)Gal none of the above

Answer: D Difficulty: 2

Topic: Oligosaccharides

16) Lactose, the disaccharide of galactose and glucose, is synthesized from which of the following activated monosaccharides?

A) B) C) D) E)

uridine triphosphate glucose uridine triphosphate galactose uridine diphosphate glucose uridine diphosphate galactose none of the above

Answer: D Difficulty: 1

Topic: Oligosaccharides

17) Which of the following explains the importance of sucrose as a disaccharide?

A) B) C) D) E)

the glycosidic bond is much more stable than a typical glycosidic bond the presence of two glucose residues provides a readily available glucose source -glycosidic bonds are much more stable than -glycosidic bonds since both anomeric carbons are involved in the glycosidic bond, oxidation is limited none of the above

Answer: D Difficulty: 2

Topic: Oligosaccharides

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

18) Which of the following polysaccharides contains exclusively glucose in (1→4) glycosidic bonds?

A) B) C) D) E)

amylose amylopectin glycogen cellulose chitin

Answer: D Difficulty: 1

Topic: Polysaccharides

19) The role of collagen in vertebrate bones as a matrix for mineral deposition is most analogous to the role of _________ in ___________.

A) B) C) D) E)

cellulose; plant cell walls chitin; invertebrate exoskeletons xylan; plant cell walls keratan sulfate: mammalian skin amylose: plant cell walls

Answer: B Difficulty: 2

Topic: Polysaccharides

20) All glycosaminoglycans contain which of the following?

A) B) C) D) E)

a sulfate ester a (1→4) glycosidic bond a carboxylate an amine group that is either acetylated or sulfated all of the above

Answer: D Difficulty: 2

Topic: Polysaccharides

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

21) Which of the following correctly identifies key elements present on the exterior of Gramnegative (GN) and Gram-positive (GP) bacteria?

A) B) C) D)

GN: single lipid bilayer; GP: two lipid bilayers GN: single peptidoglycan layer; GP: multiple peptidoglycan layers GN: extensively crosslinked peptidoglycans; GP: uncrosslinked peptidoglycan GN: contains both N-acetylmuramic acid and N-acetylglucosamine; GP: contains only N-acetylmuramic acid E) none of the above

Answer: B Difficulty: 2

Topic: Polysaccharides

22) An N-linked glycan would be attached to ______ while an O-linked glycan would be attached to ________.

A) B) C) D) E)

Asn; Ser Lys; Tyr Gln; Thr Arg; Ser Lys; Ser

Answer: A Difficulty: 2

Topic: Glycoproteins

23) Oseltamivir, also known as Tamiflu, is effective as an antiviral against the influenza virus due to its ability to block the action of which protein associated with the surface of the viral particle?

A) B) C) D) E)

hemagglutinin neuraminidase M1 M2 none of the above

Answer: B Difficulty: 2

Topic: Glycoproteins

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

24) The source of nitrogen for the synthesis of glucosamine-6-phosphate from fructose-6phosphate is the amino acid ___________.

A) B) C) D) E)

aspartate asparagine glutamate glutamine lysine

Answer: D Difficulty: 1

Topic: Biosynthesis of Glycoconjugates—Amino Sugars

25) Antibiotic inhibition of cell wall synthesis can be facilitated by a number of agents. The crosslinking of peptidoglycan strands is inhibited by _________ while polymerization of the growing peptidoglycan is inhibited by __________.

A) B) C) D) E)

penicillin; bacitracin penicillin; vancomycin vancomycin; bacitracin vancomycin; penicillin bacitracin; vancomycin

Answer: B Difficulty: 3

Topic: Glycoconjugates of Interest

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

Short Answer Questions 1) Using the structure of D-altrose, shown below, show a Haworth projection for the  anomer.

Answer:

Difficulty: 2

Topic: Monosaccharides

2) Given the structure of D-galactose, draw the structure of L-galactose in both open chain and Haworth projections ( anomer).

Answer:

Difficulty: 3

Topic: Monosaccharides

11 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 9: Carbohydrates: Sugars, Saccharides, Glycans

3) Draw a -disaccharide composed of glucose linked to its C-2 epimer by an (1→4) glycosidic bond with the anomeric carbon of glucose contributing to the glycosidic bond.

Answer:

Difficulty: 2

Topic: Oligosaccharides

4) Show the interaction that would take place between the R-group of asparagine in a protein and the substituent on C-2 of an N-acetylglucosamine residue of a glycan.

Answer:

Shown are 2 different possible interactions.

Difficulty: 3

Topic: Glycoproteins

12 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport

Multiple Choice Questions 1)

Fatty acids are _______ meaning that they have both a hydrophobic and hydrophilic region of the molecule A) B) C) D) E)

aliphatic amphipathic saturated unsaturated phosphorylated

Answer: B Difficulty: 1

2)

Topic: The Molecular Structure and Behavior of Lipids

The fatty acid designated 18:2c9,12 is best described as a _______ fatty acid.

A) B) C) D) E)

saturated unsaturated polyunsaturated hydrogenated partially hydrogenated

Answer: C Difficulty: 1

3)

Topic: The Molecular Structure and Behavior of Lipids

When fatty acids are added to an aqueous solution, they can either sit on top of the solution, forming a ________ or form spherical ________ throughout the solution.

A) B) C) D) E)

monolayer; micelles bilayer; micelles monolayer; bilayer bilayer; monolayer micelle; bilayer

Answer: A Difficulty: 2

Topic: The Molecular Structure and Behavior of Lipids

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport

4)

In animals, the bulk of energy is stored as __________.

A) B) C) D) E)

fatty acids triacylglycerols glycogen waxes glycerophospholipids

Answer: B Difficulty: 1

Topic: The Molecular Structure and Behavior of Lipids

Which of the following would be considered an -3 fatty acid?

5) A) B) C) D) E)

linoleic acid: 9,12-octadecadieneoic acid (18:2c9,12) eicosapentaenoic acid: 5,8,11,14,17-eicosapentaenoic acid (20:5c5,8,11,14,17) -linolenic acid: 6,9,12-octadecatrieneoic acid (18:3c6,9,12) arachidonic acid: 5,8,11,14-eicosatetraenoic acid (20:4c5,8,11,14) all of the above

Answer: B Difficulty: 2

6)

Topic: Excitable Membranes and Neurotransmission

Partial hydrogenation accomplishes which of the following?

A) prevents oxidative cleavage of carbon-carbon double bonds, thus preventing spoilage of fats B) raises the melting point of fatty acids C) converts cis double bonds to trans double bonds D) converts oils into fats E) all of the above

Answer: E Difficulty: 1

Topic: The Molecular Structure and Behavior of Lipids

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport

7)

Addition of a functional group to the pro-R carbon of glycerol places that group on carbon _____ while addition of a second functional group to the pro-S carbon of glycerol places the second group on carbon _____ of sn-glycerol.

A) B) C) D) E)

1; 2 1; 3 3; 2 3; 1 2; 2

Answer: D Difficulty: 2

8)

Topic: The Lipid Constituents of Biological Membranes

What alcohol containing a quaternary amine is commonly found esterified to glycerophospholipids?

A) B) C) D) E)

ethanolamine choline serine inositol cholesterol

Answer: B Difficulty: 1

9)

Topic: The Lipid Constituents of Biological Membranes

A ceramide is derived from which combination of the following?

A) B) C) D) E)

a molecule of sphingosine and a monosaccharide a molecule of sphingosine and a molecule of phosphocholine a molecule of sphingosine and a fatty acid a molecule of sphingosine and two fatty acids a molecule of sphingosine, a fatty acid and a monosaccharide

Answer: C Difficulty: 2

Topic: The Lipid Constituents of Biological Membranes

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport

10) Which of the following is correctly defined?

A) B) C) D) E)

sphingomyelin: ceramide + choline glycoglycerolipid: glycerol + fatty acid + monosaccharide + phosphate cerebroside: ceramide + monosaccharide ganglioside: sphingomyelin + oligosaccharide none of the above

Answer: C Difficulty: 2

Topic: The Lipid Constituents of Biological Membranes

11) Which of the following does not specifically cause a membrane to be more rigid or fluid, but rather causes the Tm to occur over a greater range?

A) B) C) D)

increasing the content of unsaturated fatty acids raising the temperature increasing the cholesterol content decreasing the phosphatidylcholine content while increasing the phosphatidylethanolamine content E) all of the above

Answer: C Difficulty: 2

Topic: The Structure and Properties of Membranes

12) When comparing the sequences of a peripheral membrane protein with an integral membrane protein, which of the following amino acids would most likely be present in a higher percentage in the integral membrane protein?

A) B) C) D) E)

aspartic acid leucine histidine serine none of the above

Answer: B Difficulty: 2

Topic: The Structure and Properties of Membranes

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport

13) A flippase is an enzyme that moves lipids from one side of a lipid bilayer to another in order to maintain the concentrations of specific lipids on each side of the bilayer. Which of the following can be said regarding the reaction of the flippase enzyme?

A) B) C) D) E)

it works against a concentration gradient and requires ATP it works against a concentration gradient but does not require ATP it works with a concentration gradient and requires ATP it works with a concentration gradient but does not require ATP none of the above

Answer: A Difficulty: 3

Topic: The Structure and Properties of Membranes

14) Which of the following is a common mechanism for the covalent attachment of a lipid to a peripheral membrane protein?

A) B) C) D)

addition of a geranylgeranyl group to the hydroxyl of serine, forming an ether addition of a farnesyl group to the thiol of cysteine, forming a thioether addition of a myristoyl group to the amine of lysine, forming an amide reaction of the amine group of phosphatidylethanolamine with the carboxylate of glutamic acid, forming an amide E) all of the above

Answer: B Difficulty: 2

Topic: The Structure and Properties of Membranes

15) The sequence of glycophorin A displays which of the following?

A) the N-terminal domain contains large amounts of hydrophobic amino acids indicating only the N-terminus is embedded in the membrane B) the C-terminal domain contains a high concentration of Ser and Thr for attachment of O-linked oligosaccharides C) both the N-terminal and C-terminal domains contain high concentrations of Ser and Thr for attachment of O-linked oligosaccharides D) the middle portion contains large amounts of hydrophobic amino acids indicating a transmembrane protein E) none of the above Answer: D Difficulty: 3

Topic: The Structure and Properties of Membranes 5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport

16) The transient association of lipid rafts is thought to play a significant role in which of the following?

A) B) C) D) E)

cell signaling bacterial entry into host cells protein trafficking membrane receptor dimerization all of the above

Answer: E Difficulty: 2

Topic: The Structure and Properties of Membranes

17) Which of the following would most likely move across a membrane by simple diffusion?

A) B) C) D) E)

potassium ions glucose carbon dioxide sodium ions water

Answer: C Difficulty: 1

Topic: Transport Across Membranes

18) The movement of potassium ions across a membrane aided by valinomycin is an example of _______________.

A) B) C) D) E)

facilitated diffusion by transport through a pore facilitated diffusion by transport using a carrier molecule facilitated diffusion by use of a permease primary active transport since valinomycin is a sodium-potassium ATPase secondary active transport since valinomycin only moves with the aid of the sodium ion gradient

Answer: B Difficulty: 2

Topic: Transport Across Membranes

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport

19) Movement of ions across a cell membrane by the Na/K ATPase is best described as ________.

A) B) C) D) E)

sodium moved outside to inside, potassium inside to outside sodium moved inside to outside, potassium outside to inside sodium moved inside to outside, potassium inside to outside sodium moved outside to inside, potassium outside to inside none of the above

Answer: B Difficulty: 2

Topic: Transport Across Membranes

20) Which of the following is used to drive glucose uptake by intestinal epithelial cells?

A) B) C) D) E)

potassium gradient across the blood vessel/epithelial cell membrane potassium gradient across the intestinal lumen/epithelial cell membrane sodium gradient across the blood vessel/epithelial cell membrane sodium gradient across the intestinal lumen/epithelial cell membrane none of the above

Answer: D Difficulty: 2

Topic: Transport Across Membranes

21) Which of the following mechanisms of membrane transport is correctly defined?

A) simple diffusion: uses concentration gradient to move highly polar molecules and ions across membranes B) facilitated diffusion: uses proteins such as ion channels to move substances against their concentration gradient across a membrane C) primary active transport: uses ATP hydrolysis to move ions against their concentration gradient across a membrane D) secondary active transport: uses ATP hydrolysis along with an ion gradient to move polar molecules or ions against their concentration gradient across a membrane E) all of the above Answer: C Difficulty: 2

Topic: Transport Across Membranes

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport

22) Which of the following correctly relates the status of the sodium channel during an action potential cycle? (m-gate = activation gate, h-gate = inactivation gate) A) B) C) D) E)

while resting, both the m-gate and h-gate are closed during depolarization, both the m-gate and h-gate open allowing Na+ to exit the cell during repolarization, only the m-gate is closed during the refractory period, both the m-gate and h-gate are closed none of the above

Answer: D Difficulty: 2

Topic: Excitable Membranes and Neurotransmission

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport Short Answer Questions

1) Draw the following fatty acid: 18:3c9,12,15 as it would appear at physiological pH. With reference to the omega carbon, what type of fatty acid is this? Draw the result if this fatty acid underwent partial hydrogenation to produce 18:1t11

Answer:

Difficulty: 2

this is an -3 fatty acid

Topic: The Molecular Structure and Behavior of Lipids

2) Draw a molecule of phosphatidylserine with palmitic acid (16:0) and oleic acid (18:1c9) present. Make sure to put the saturated and unsaturated fatty acids in their proper location.

Answer:

Difficulty: 3

Topic: The Lipid Constituents of Biological Membranes

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 10: Lipids, Membranes and Cellular Transport

3) Given the following concentrations (in mM) for sodium and potassium ions, a membrane potential of 60 mV (inside negative), a temperature of 37C and a G for ATP hydrolysis of -51 kJ/mol, what is the % efficiency of the Na/K ATPase? +

Na K+

inside 12 140

outside 145 4

Answer: For each ATP hydrolyzed, 3 Na+ and 2 K+ are pumped across the membrane.

Calculating the G for ion transport: For both, Z=1 and T = 310 K ΔG = RT ln (C2/C1) + ZFΔψ Na+ transport: C2/C1 = 145/12 = 12.1, Δψ = +0.06 V ΔG = 12.2 kJ/mol × 3 mol = 36.6 kJ Overall: ΔGt =36.6 + 6.8 = 43.4 kJ

Difficulty: 3

K+ transport: C2/C1 = 140/4 = 35, Δψ = -0.06 V ΔG = 3.4 kJ/mol × 2 mol = 6.8 kJ

43.4/51 × 100% = 85%

Topic: Transport Across Membranes

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

Multiple Choice Questions 1) Since an enzyme is a catalyst, which of the following must be true?

A) an enzyme-catalyzed reaction is always exergonic B) enzymes increase the rate of a reaction by providing a completely alternate mechanism to the uncatalyzed reaction C) over the course of an enzyme-catalyzed reaction, the enzyme is not changed D) in the absence of an enzyme, the reaction that is normally catalyzed by the enzyme will not occur E) enzyme-catalyzed reactions never reach equilibrium Answer: C Difficulty: 1

Topic: The Role of Enzymes

2) Which of the following explains why enzymes are extremely effective catalysts?

A) an enzyme stabilizes the transition state B) enzymes bind very tightly to substrates C) enzymes release products very rapidly D) an enzyme can convert a normally endergonic reaction into an exergonic reaction E) an enzyme lowers the energy of activation only for the forward reaction Answer: A Difficulty: 1

Topic: Chemical Reaction Rates and the Effects of Catalysts

3) Which of the following scenarios would result in a relatively low energy of activation?

A) an enzyme binds to the substrate with greater affinity than the transition state B) an enzyme binds to both substrate and transition state with equal affinity C) an enzyme binds to the transition state with greater affinity than the substrate D) an enzyme binds only to the transition state E) none of the above Answer: C Difficulty: 2

Topic: How Enzymes Act as Catalysts

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

4) If an enzyme gave a rate enhancement of 3.4  107 over the noncatalyzed reaction, what is the G‡ at 37C? A) 5.3 kJ/mol B) 45 kJ/mol C) 9.5 kJ/mol D) 19 kJ/mol E) none of the above Answer: B Difficulty: 2

Topic: How Enzymes Act as Catalysts

5) Which amino acid most commonly serves as a general acid and general base in an enzyme mechanism?

A) serine B) arginine C) aspartic acid D) histidine E) cysteine Answer: D Difficulty: 1

Topic: How Enzymes Act as Catalysts

6) The activity of lysozyme is greater than 50% of maximum between pH 3.8 and 6.1 with peak activity occurring around pH 5. Below 3.8 and above 6.1, the activity drops rapidly. Which of the following provides the best explanation for this?

A) two histidine residues in the active site must be protonated for enzyme activity B) the active site contains an aspartic acid and glutamic acid, both of which must be deprotonated C) the active site contains an aspartic acid that must be deprotonated and a glutamic acid that must be protonated D) the active site contains a histidine that must be protonated and a glutamic acid that must be deprotonated E) none of the above Answer: C Difficulty: 3

Topic: How Enzymes Act as Catalysts 2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

7) In the mechanism of chymotrypsin, which of the following amino acids found in the active site is correctly defined in terms of its role in the reaction?

A) serine: hydrogen bonds with carbonyl oxygen to withdraw electron density from the substrate B) histidine: deprotonates aspartic acid to allow a nucleophilic attack to occur C) aspartic acid: electrostatic stabilization of histidine to make a stronger base D) cysteine: performs a nucleophilic attack on the carbonyl carbon of the substrate E) none of the above Answer: C Difficulty: 3

Topic: How Enzymes Act as Catalysts

8) The steady state assumption in enzyme kinetics: A) insures that the product of an enzymatic reaction will always be formed

B) explains why enzymes are effective catalysts C) states that the formation of ES is equal to its breakdown D) is based upon the fact that the maximum velocity of an enzyme is very high E) none of the above Answer: C Difficulty: 1

Topic: The Kinetics of Enzymatic Catalysis

9) An enzymatic reaction has a Vmax of 100 M/min. At a substrate concentration of 5 M, the velocity is 25 M/min. What is the KM for the reaction?

A) 5 M B) 10 M C) 15 M D) 20 M E) none of the above Answer: C Difficulty: 2

Topic: The Kinetics of Enzymatic Catalysis

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

10) What must be true if KM is truly a measure of the affinity of enzyme and substrate?

A) kcat must be larger than KM B) kcat must be smaller than KM C) kcat must be about equal to k1 D) kcat must be much smaller than k-1 E) kcat must be much larger than k-1 Answer: D Difficulty: 2

Topic: The Kinetics of Enzymatic Catalysis

11) In a Lineweaver-Burke plot, what does the slope represent?

A) KM B) Vmax C) Vmax/KM D) KM/Vmax E) none of the above Answer: D Difficulty: 1

Topic: The Kinetics of Enzymatic Catalysis

12) In the following enzyme reaction scheme, what sort of multi-enzyme kinetics are shown?

A) ordered substrate binding with random product release B) ordered substrate binding with ordered product release C) random substrate binding with ordered product release D) random substrate binding with random product release E) ping-pong mechanism Answer: E Difficulty: 1

Topic:

The Kinetics of Enzymatic Catalysis

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

13) Which of the following is an irreversible form of inhibition?

A) competitive inhibitor B) suicide inhibitor C) noncompetitive inhibitor D) uncompetitive inhibitor E) none of the above Answer: Difficulty: 1

Topic: Enzyme Inhibition

14) What type of inhibitor would give the results seen in the following plot?

A) competitive inhibitor B) mixed inhibitor C) noncompetitive inhibitor D) uncompetitive inhibitor E) none of the above Answer: D Difficulty: 2

Topic: Enzyme Inhibition

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

15) In noncompetitive inhibition, which of the following best explains how the inhibitor binds to the enzyme?

A) the inhibitor binds to the active site only after the substrate binds B) the inhibitor binds to a site other than the active site only before the substrate binds C) the inhibitor binds to a site other than the active site only after the substrate binds D) the inhibitor binds to a site other than the active site either before or after the substrate binds E) none of the above Answer: D Difficulty: 2

Topic: Enzyme Inhibition

16) What are the expected changes in kinetics in the presence of a competitive inhibitor?

A) Vmax decreases, KM appears to decrease B) Vmax does not change, KM appears to decrease C) Vmax decreases, KM appears to increase D) Vmax does not change, KM appears to increase E) Vmax decreases, KM does not change Answer: D Difficulty: 2

Topic: Enzyme Inhibition

17) Which of the following cofactors is used during the activation and transfer of carbon dioxide?

A) nicotinamide adenine dinucleotide (NAD) B) thiamine pyrophosphate C) biotin D) coenzyme A E) tetrahydrofolate Answer: C Difficulty: 1

Topic: Cofactors, Vitamins and Essential Metals

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

18) An enzyme that catalyzes the intramolecular movement of a functional group from one carbon atom to another would be called a(n) ____________.

A) isomerase B) transferase C) oxidoreductase D) kinase E) ligase Answer: A Difficulty: 1

Topic: The Diversity of Enzymatic Function

19) Since the product of the reaction catalyzed by hexokinase, glucose-6-phosphate (G6P), can act as both a competitive and uncompetitive inhibitor, what can be said about the interaction between G6P and hexokinase?

A) G6P binds only to active site of the enzyme B) G6P binds only to a regulatory site of the enzyme C) G6P binds to both the active site and a regulatory site of the enzyme D) G6P binds to one of the substrates, ATP, thus preventing ATP from binding to the active site E) none of the above Answer: C Difficulty: 3

Topic: The Regulation of Enzyme Activity: Allosteric Enzymes

20) Both ATP and CTP are allosteric regulators of the enzyme aspartate transcarbamoylase.

Which of the following correctly identifies the activities of these two regulators?

A) ATP: activator; CTP: activator B) ATP: activator; CTP: inhibitor C) ATP: inhibitor; CTP: activator D) ATP: inhibitor; CTP: inhibitor E) none of the above Answer: B Difficulty: 2

Topic: The Regulation of Enzyme Activity: Allosteric Enzymes

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

21) Which of the following is the most common form of reversible covalent modification for control of enzyme activity?

A) acetylation/deacetylation B) adenylation/deadenylation C) phosphorylation/dephosphorylation D) ADP-ribosylation/de-ADP-ribosylation E) none of the above Answer: C Difficulty: 1

Topic: Covalent Modifications Used to Regulate Enzyme Activity

22) What term describes an inactive precursor of an enzyme such as the precursors to protease enzymes produced by the pancreas?

A) allosteric enzyme B) zymogen C) isozyme D) ribozyme E) hydrolase Answer: B Difficulty: 1

Topic: Covalent Modifications Used to Regulate Enzyme Activity

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

Short Answer Questions 1) Given the chymotrypsin catalytic triad and the peptide substrate, draw the first tetrahedral intermediate of the chymotrypsin mechanism.

Answer:

Difficulty: 3

Topic: How Enzymes Act as Catalysts

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

2) A plot of enzyme activity with and without an inhibitor present gave the following plot.

What type of inhibitor is present? How does this inhibitor function? What changes are seen in Vmax and KM? Draw a line that approximates the result from addition of twice as much inhibitor to the reaction.

Answer: A competitive inhibitor is present which functions by binding to the active site and competing with the substrate. Vmax does not change while KM appears to increase.

Addition of twice the concentration of inhibitor would give the bold line in the plot below.

Difficulty: 2

Topic: Enzyme Inhibition

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 11: Enzymes: Biological Catalysts

3) Below is a curve for the enzyme glycogen phosphorylase without any allosteric effectors present showing velocity as a function of the substrate, orthophosphate (Pi). Draw and label a curve that shows the result of addition of the allosteric activator, AMP. Draw and label a curve that shows the result of addition of the allosteric inhibitor, ATP. Glycogen phosphorylase is activated by phosphorylation. Which of these three curves most resembles what happens when glycogen phosphorylase is phosphorylated?

Answer:

The curve with AMP present would most resemble the phosphorylated state of the enzyme.

Difficulty: 3

Topic: The Regulation of Enzyme Activity: Allosteric Enzymes

11 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism

Multiple Choice Questions 1)

Which of the following eukaryotic organisms is both autotrophic and heterotrophic?

A) B) C) D) E)

yeast humans Venus fly trap redwood trees mushrooms

Answer: C Difficulty: 1

2)

Topic: A First Look at Metabolism

In stage ____ metabolism, a catabolic pathway might produce ________ while the opposing anabolic pathway might produce _________.

A) B) C) D) E)

2; monosaccharides; polysaccharides 3; CO2; glucose 2; acetyl CoA; lipids 1; amino acids; proteins 3; NH3; nucleotides

Answer: D Difficulty: 2

3)

Topic: A First Look at Metabolism

Which of the following statements regarding the general concepts of metabolism is true?

A) once glucose is converted to pyruvate, there is no way to convert pyruvate back to glucose B) when triacylglycerols are used as fuel, only the fatty acids can be metabolized, the glycerol is a waste product C) amino acids serve as substrates for many pathways including glycolysis and the citric acid cycle D) the citric acid cycle is generally considered an anabolic pathway while gluconeogenesis is generally considered a catabolic pathway E) none of the above

Answer: C Difficulty: 2

Topic: Freeways on the Metabolic Road Map 1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism

4)

Which of the following would be considered a biosynthetic pathway?

A) B) C) D) E)

glycolysis glycogen synthesis fatty acid -oxidation citric acid cycle electron transport

Answer: B Difficulty: 1

5)

Topic: Freeways on the Metabolic Road Map

Which of the following pairs of pathways, if active at the same time, would be considered a futile cycle?

A) B) C) D) E)

gluconeogenesis and citric acid cycle fatty acid -oxidation and glycolysis fatty acid synthesis and glycolysis fatty acid synthesis and citric acid cycle glycolysis and gluconeogenesis

Answer: E Difficulty: 2

6)

Topic: Freeways on the Metabolic Road Map

Which of the following functional groups is a commonly seen nucleophile in biochemical reactions?

A) B) C) D) E)

aldehyde deprotonated alcohol amide carbocation iodide ion

Answer: B Difficulty: 1

Topic: Biochemical Reaction Types

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism

7)

Which of the following functional groups is commonly the electrophile in nucleophilic acyl substitutions?

A) B) C) D) E)

ester hydroxide ion amine thiol carboxylate

Answer: A Difficulty: 2

8)

Topic: Biochemical Reaction Types

The formation of a hemiacetal when glucose undergoes cyclization represents what type of reaction?

A) B) C) D) E)

nucleophilic substitution nucleophilic addition carbonyl condensation elimination oxidation

Answer: B Difficulty: 2

9)

Topic: Biochemical Reaction Types

Which of the following types of reactions best describes the formation of a peptide bond?

A) B) C) D) E)

nucleophilic substitution nucleophilic addition nucleophilic acyl substitution elimination carbonyl condensation

Answer: C Difficulty: 2

Topic: Biochemical Reaction Types

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism

10) Which of the following types of reactions best describes the reaction shown below?

A) B) C) D) E)

nucleophilic substitution nucleophilic addition nucleophilic acyl substitution elimination carbonyl condensation

Answer: E Difficulty: 2

Topic: Biochemical Reaction Types

11) What is the oxidant in the following reaction?

A) B) C) D) E)

ethanol NAD+ acetaldehyde NADH H+

Answer: B Difficulty: 2

Topic: Biochemical Reaction Types

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism

12) During the oxidation of glucose within a typical animal cell, reduced electron carrier such as NADH are produced. What is the terminal electron acceptor of the electrons carried by NADH? A) B) C) D) E)

NAD+ FAD O2 H2O none of the above

Answer: C Difficulty: 1

Topic: Some Bioenergetic Considerations

13) Of the following, which would have the most reduced state of carbon, and therefore, would yield the largest amount of energy per gram?

A) B) C) D) E)

glucose glycogen alanine stearic acid all of the above would have identical energy yields

Answer: D Difficulty: 1

Topic: Some Bioenergetic Considerations

14) Based on the following reaction, what is the respiratory quotient for stearic acid?

C18H36O2 + 26 O2 → 18 CO2 + 18 H2O A) 1.44 B) 0.69 C) 1.39 D) 0.72 E) none of the above Answer: B Difficulty: 1

Topic: Some Bioenergetic Considerations

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism

15) ________ is commonly used as an oxidizing agent in catabolic pathways while ________ is commonly used as a reducing agent in anabolic pathways.

A) B) C) D) E)

NAD+; NADH NAD+; FADH2 NADP+; NADH FAD; FADH2 NAD+; NADPH

Answer: E Difficulty: 2

Topic: Some Bioenergetic Considerations

16) The glycolytic reaction fructose-6-phosphate + ATP → fructose-1,6-bisphosphate + ADP has an ATP-coupling coefficient of _____ while the gluconeogenic reaction fructose-1,6-bisphosphate + H2O → fructose-6-phosphate + Pi has an ATP-coupling coefficient of _____.

A) B) C) D) E)

1; 0 -1; 0 1; -1 -1; 1 none of the above

Answer: B Difficulty: 2

Topic: Some Bioenergetic Considerations

17) Which of the following is a property of ATP? A) it contains three phosphoanhydride bonds B) cleavage of the phosphoanhydride bond between the middle and terminal phosphates yields ADP which is rapidly hydrolyzed to AMP, thus pushing reactions to completion C) ATP is a high energy compound that is kinetically unstable D) although ATP has a highly negative G of hydrolysis, most reactions with ATP involve transfer of a phosphate, not hydrolysis E) none of the above Answer: Difficulty: 2

Topic: Some Bioenergetic Considerations 6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism

18) The phosphorylation of creatine (Cr) by ATP forming creatine phosphate (Cr-P) is rather endergonic (G°´ = + 12.6 kJ/mol). Which of the following explains how this reaction proceeds in a typical muscle cell?

A) in the cytosol, [ATP] is high and [Cr] is high allowing the reaction to proceed B) in the mitochondria, [ATP] is high and [Cr-P] is low allowing the reaction to proceed C) Cr-P is rapidly transported across the cellular membrane allowing for high levels of CrP in the cytosol D) in the mitochondria, [ADP] is high allowing phosphorylation of Cr to occur E) none of the above Answer: B Difficulty: 2

Topic: Some Bioenergetic Considerations

19) Which of the following accurately describes the adenylate energy charge?

A) B) C) D) E)

numerator: 2 [ATP] + [ADP]; denominator: [ATP] + [ADP] + [AMP] numerator: [ATP] + [ADP]; denominator: [ATP] + 0.5 [ADP] + 0.25 [AMP] numerator: [ATP] + 0.5 [ADP]; denominator: 2 [ATP] + [ADP] + 0.5 [AMP] numerator: [ATP] + 0.5 [ADP]; denominator: [ATP] + [ADP] + [AMP] none of the above

Answer: D Difficulty: 2

Topic: Some Bioenergetic Considerations

20) The concentration of which of the following ions can make a significant change in the G for reactions that involve ATP? A) B) C) D) E)

Mg2+ Na+ ClK+ Ca2+

Answer: A Difficulty: 1

Topic: Some Bioenergetic Considerations

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism

21) Which of the following represents a correct compartmentation of a biochemical process with its cellular location?

A) B) C) D) E)

fatty acid oxidation: endoplasmic reticulum RNA synthesis: Golgi complex citric acid cycle: mitochondria gluconeogenesis: lysosome none of the above

Answer: C Difficulty: 2

Topic: Major Metabolic Control Mechanisms

22) Molecules that are produced inside a cell in response to a hormone binding to its receptor are called _________.

A) B) C) D) E)

internal messengers second messengers secondary messengers intracellular messengers transduction messengers

Answer: B Difficulty: 2

Topic: Major Metabolic Control Mechanisms

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism Short Answer Questions

1) Show the reduction of pyruvate by NADH. Since NADH reduces molecules by a hydride reduction, what type of reaction is pyruvate undergoing?

Answer:

Since the hydride from NADH acts as a nucleophile, this is a nucleophilic addition reaction

Difficulty: 2

Topic: Biochemical Reaction Types

2) Many enzyme-catalyzed reactions that transfer a phosphate from one molecule to another utilize a histidine residue in the active site of the enzyme. The histidine participates in covalent catalysis by performing a nucleophilic attack on a phosphate, forming an intermediate phosphohistidine (the phosphate covalently attached to the histidine residue).

Using ATP as the phosphate donor, show the reaction to form the phosphohistidine intermediate—you do not have to show arrow pushing.

Answer:

Difficulty: 3

Topic: Biochemical Reaction Types 9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 12: Chemical Logic of Metabolism

3) Complete oxidation of glucose by burning in a calorimeter gives a G°´ of -2870 kJ/mol. If we assume this to be the maximum energy that can be extracted from glucose, what is the percent of energy that is captured in a cell given that about 32 ATP can be made from a single molecule of glucose? G°´ for ATP hydrolysis is -30.5 kJ/mol while G for ATP hydrolysis in a cell is about -51 kJ/mol.

Answer:

32

Difficulty: 2

mol ATP  −51 kJ    mol glucose  mol ATP   100% = 57% −2870 kJ/mol glucose Topic: Some Bioenergetic Considerations

 4) Pyruvic acid has the formula C3H4O3. Write the reaction for its complete combustion. What is its respiratory quotient? Does this mean that it is more oxidized or less oxidized than glucose?

Answer:

C3H4O3 + 2.5 O2 → 3 CO2 + 2 H2O 3 CO2 / 2.5 O2 = 1.2 Glucose has an RQ of 1 so pyruvic acid is more oxidized than glucose.

Difficulty: 2

Topic: Some Bioenergetic Considerations

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

Multiple Choice Questions 1)

Besides two molecules of pyruvate, what are the net products of glycolysis?

A) B) C) D) E)

4 ATP and 2 NADH 2 ATP and 2 NADH 4 ATP and 4 NADH 2 ATP and 4 NADH none of the above

Answer: B Difficulty: 1

2)

Topic: Glycolysis: An Overview

During aerobic glycolysis, pyruvate is most likely oxidized to ________ while in anaerobic glycolysis, pyruvate is converted to _________.

A) B) C) D) E)

acetaldehyde; ethanol acetyl CoA; glyceraldehyde acetyl CoA; lactate acetaldehyde; lactate none of the above

Answer: C Difficulty: 2

3)

Topic: Glycolysis: An Overview

Which of the following pairs of phosphorylated molecules contains an intermediate of glycolysis with high phosphate transfer potential and one with low phosphate transfer potential?

A) B) C) D) E)

fructose-1,6-bisphosphate and fructose-6-phosphate phosphoenolpyruvate and glyceraldehyde-3-phosphate fructose-1,6-bisphosphate and 3-phosphoglycerate 1,3-bisphosphoglycerate and phosphoenolpyruvate 1,3-bisphosphoglycerate and pyruvate

Answer: B Difficulty: 2

Topic: Glycolysis: An Overview

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

4)

During the energy investment phase of glycolysis, _____ reaction(s) use ATP as a substrate while during the energy generation phase, _____ reactions produce ATP as a product.

A) B) C) D) E)

2; 2 2; 4 1; 2 1; 4 0; 2

Answer: A Difficulty: 1

5)

Topic: Reactions of Glycolysis

Which isoform of hexokinase is found in the vertebrate liver?

A) B) C) D) E)

hexokinase I hexokinase II hexokinase III hexokinase IV all of the above

Answer: D Difficulty: 1

6)

Topic: Reactions of Glycolysis

In most bacteria that utilize glucose, what molecule both aids in transport of glucose into the cell and is phosphorylating agent for conversion of glucose to glucose-6-phosphate?

A) B) C) D) E)

ATP GTP fructose-1,6-bisphosphate 1,3-bisphosphoglycerate phosphoenolpyruvate

Answer: E Difficulty: 2

Topic: Reactions of Glycolysis

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

7)

With respect to carbons 1 and 2 of the intermediate in the conversion of glucose-6phosphate to fructose-6-phosphate, which of the following would best describe this intermediate?

A) B) C) D) E)

vicinal diol enediol aldehyde ketone enol

Answer: B Difficulty:

8)

Topic: Reactions of Glycolysis

Which enzyme catalyzes the primary regulation site of glycolysis?

A) B) C) D) E)

hexokinase phosphofructokinase-1 glyceraldehyde-3-phosphate dehydrogenase phosphoglycerate kinase pyruvate kinase

Answer: B Difficulty: 1

9)

Topic: Reactions of Glycolysis

What is the initial step in the mechanism of fructose-1,6-bisphosphate aldolase when the substrate is fructose-1,6-bisphosphate in its open-chain form?

A) B) C) D) E)

attack of C-2 carbonyl group by the amine of lysine deprotonation of C-3 hydroxyl by aspartate protonation of C-2 carbonyl oxygen by histidine attack of C-2 carbonyl group by the thiol of cysteine none of the above

Answer: A Difficulty: 2

Topic: Reactions of Glycolysis

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

10) The reaction catalyzed by triose phosphate isomerase is most similar in mechanism to which of the following glycolytic enzymes?

A) B) C) D) E)

glucose-6-phosphate isomerase fructose-1,6-bisphosphate aldolase phosphoglycerate mutase enolase pyruvate kinase

Answer: A Difficulty: 2

Topic: Reactions of Glycolysis

11) During the oxidation of glyceraldehyde-3-phosphate, what intermediate in the enzymecatalyzed mechanism actually undergoes oxidation?

A) B) C) D) E)

enediol thioester thiohemiacetal carbinolamine Schiff base

Answer: C Difficulty: 3

Topic: Reactions of Glycolysis

12) The conversion of 3-phosphoglycerate to phosphoenolpyruvate requires two reactions.

Which of the following correctly identifies the types of reactions in the proper order of glycolysis?

A) B) C) D) E)

isomerization, hydration hydration, isomerization dehydration, isomerization isomerization, dehydration mutation, dehydration

Answer: D Difficulty: 2

Topic: Reactions of Glycolysis 4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

13) The conversion of phosphoenolpyruvate and ADP to pyruvate and ATP occurs in two distinct steps, first the transfer of the phosphate from PEP to ADP, then the conversion of enolpyruvate to pyruvate. Which of the following describes the reversibility of this process?

A) B) C) D) E)

both steps are freely reversible step 1 is freely reversible, step 2 is irreversible step 1 is irreversible, step 2 is freely reversible both steps are irreversible the reversibility of the reaction depends completely upon the concentrations of products and reactants

Answer: B Difficulty: 2

Topic: Reactions of Glycolysis

14) Which of the following is the fate of pyruvate in a blood cell?

A) B) C) D) E)

acetyl CoA carbon dioxide lactate ethanol none of the above

Answer: C Difficulty: 2

Topic: Metabolic Fates of Pyruvate

15) Conversion of pyruvate to acetaldehyde requires _______ while conversion of acetaldehyde to ethanol requires _______.

A) B) C) D) E)

thiamine pyrophosphate; NAD+ pyridoxal phosphate; FADH2 biotin; NADH biotin; FAD thiamine pyrophosphate; NADH

Answer: E Difficulty: 2

Topic: Metabolic Fates of Pyruvate 5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

16) Which of the following glycolytic reactions is freely reversible?

A) B) C) D) E)

hexokinase phosphofructokinase triose phosphate isomerase pyruvate kinase none of the above

Answer: C Difficulty: 1

Topic: Energy and Electron Balance Sheets

17) Under conditions of strenuous exercise, gluconeogenesis occurs primarily in the _______ using _______ formed in the skeletal muscle A) B) C) D) E)

kidney; alanine muscle; glycerol liver; propionate kidney; acetyl-CoA liver; lactate

Answer: E Difficulty: 2

Topic: Gluconeogenesis

18) Which of the following enzymes is used by the gluconeogenic pathway but not the glycolytic pathway?

A) B) C) D) E)

pyruvate kinase phosphoenolpyruvate carboxykinase glyceraldehyde-3-phosphate dehydrogenase triose phosphate isomerase hexokinase

Answer: B Difficulty: 2

Topic: Gluconeogenesis

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

19) Assuming that gluconeogenesis was active in a mammalian liver, under what conditions would PEPCK have more activity in the mitochondria than in the cytosol?

A) B) C) D) E)

the activity of pyruvate carboxylase was very low high levels of malate were being transported out of the mitochondria lactate was serving as the primary carbon source for gluconeogenesis glycerol was serving as the primary carbon source for gluconeogenesis none of the above

Answer: C Difficulty: 3

Topic: Gluconeogenesis

20) If unregulated, which of the following pairs of enzymes would represent a futile cycle?

A) B) C) D) E)

pyruvate kinase and pyruvate carboxylase pyruvate carboxylase and phosphoenolpyruvate carboxykinase pyruvate kinase and fructose-1,6-bisphosphatase fructose-1,6-bisphosphatase and phosphofructokinase glucose-6-phosphatase and phosphofructokinase

Answer: D Difficulty: 2

Topic: Coordinated Regulation of Glycolysis and Gluconeogenesis

21) Experiments that investigated the Pasteur effect showed that when oxygen is introduced to cells where glycolysis is occurring, all intermediates beginning with ________ become depleted due to inhibition of the enzyme _________.

A) B) C) D) E)

fructose-1,6-bisphosphate; phosphofructokinase glucose-6-phosphate: hexokinase fructose-6-phosphate; phosphofructokinase fructose-1,6-bisphosphate; fructose-1,6-bisphosphate aldolase phosphoenolpyruvate; pyruvate kinase

Answer: A Difficulty: 3

Topic: Coordinated Regulation of Glycolysis and Gluconeogenesis

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

22) Which of the following is correctly paired with the glycolytic intermediate that serves as its precursor?

A) B) C) D) E)

ribulose-5-phosphate: fructose-6-phosphate serine: phosphoenolpyruvate glycogen: glucose-6-phosphate glycerol-3-phosphate: glyceraldehyde-3-phosphate glucosamine: fructose-1,6-bisphosphate

Answer: C Difficulty: 3

Topic: Coordinated Regulation of Glycolysis and Gluconeogenesis

23) Which of the following activators is correctly paired with the glycolytic or gluconeogenic enzyme that it activates?

A) B) C) D) E)

glucose-6-phosphate: hexokinase AMP: fructose-1,6-bisphosphatase ATP: pyruvate kinase fructose-2,6-bisphosphate: phosphofructokinase citrate: fructose-1,6-bisphosphatase

Answer: D Difficulty: 2

Topic: Coordinated Regulation of Glycolysis and Gluconeogenesis

24) When glucagon binds to receptors on mammalian liver cells, which of the following occurs due to enzyme phosphorylation?

A) B) C) D) E)

activation of PFK-2 followed by activation of glycolysis activation of FBPase-2 followed by inhibition of gluconeogenesis activation of PFK-2 followed by activation of gluconeogenesis activation of FBPase-2 followed by activation of gluconeogenesis activation of PFK-2 followed by inhibition of glycolysis

Answer: D Difficulty: 3

Topic: Coordinated Regulation of Glycolysis and Gluconeogenesis

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

25) Which of the following intermediates is a feed-forward activator of pyruvate kinase?

A) B) C) D) E)

glucose-6-phosphate fructose-1,6-bisphosphate fructose-2,6-bisphosphate glyceraldehyde-3-phosphate phosphoenolpyruvate

Answer: B Difficulty: 2

Topic: Coordinated Regulation of Glycolysis and Gluconeogenesis

26) In the mammalian liver, hexokinase IV is sequestered in _______ when glucose concentrations are low. When glucose concentrations are high, it is found in the cytosol bound to the enzyme ________.

A) B) C) D) E)

nucleus; PFK-2 Golgi apparatus; PFK-2 endoplasmic reticulum; PFK-2 nucleus; PFK-1 Golgi apparatus; PFK-1

Answer: A Difficulty: 2

Topic: Coordinated Regulation of Glycolysis and Gluconeogenesis

27) Besides its role in glycogen synthesis, which of the following directly relies on UDPglucose?

A) B) C) D) E)

glycolysis gluconeogenesis fructose metabolism sucrose metabolism galactose metabolism

Answer: E Difficulty: 2

Topic: Entry of Other Sugars into the Glycolytic Pathway

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

28) In the vertebrate liver, which major regulatory point is bypassed during fructose metabolism, often leading to conversion of excess fructose into fat?

A) B) C) D) E)

hexokinase phosphofructokinase glyceraldehyde-3-phosphate dehydrogenase pyruvate kinase none of the above

Answer: B Difficulty: 2

Topic: Entry of Other Sugars into the Glycolytic Pathway

29) If a residue of glucose in glycogen is removed from the glycogen molecule and then allowed to proceed through glycolysis to pyruvate, what is the net production of ATP? A) B) C) D) E)

1 2 3 4 5

Answer: C Difficulty: 2

Topic: Glycogen Metabolism in Muscle and Liver

30) What sequence of enzymes allows for the synthesis of glycogen from glucose-6phosphate?

A) UDP-glucose pyrophosphorylase, phosphoglucomutase, glycogen synthase, amylo(1,4→1,6)-transglycosylase B) phosphoglucomutase, UDP-glucose pyrophosphorylase, amylo-(1,4→1,6)transglycosylase, glycogen synthase C) phosphoglucomutase, amylo-(1,4→1,6)-transglycosylase, UDP-glucose pyrophosphorylase, glycogen synthase D) UDP-glucose pyrophosphorylase, phosphoglucomutase, amylo-(1,4→1,6)transglycosylase, glycogen synthase E) phosphoglucomutase, UDP-glucose pyrophosphorylase, glycogen synthase, amylo(1,4→1,6)-transglycosylase Answer: E Difficulty: 2

Topic: Glycogen Metabolism in Muscle and Liver 10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

31) When glucagon binds to its receptor on a liver cell, which of the following sequence of events occurs to activate protein kinase A? A) B) C) D) E)

activation of adenylate cyclase, activation of G protein, production of cAMP activation of G protein, activation of adenylate cyclase, production of cAMP activation of G protein, production of cAMP, activation of adenylate cyclase production of cAMP, activation of adenylate cyclase, activation of G protein none of the above

Answer: B Difficulty: 2

Topic: Coordinated Regulation of Glycogen Metabolism

32) In its non-phosphorylated state, glycogen phosphorylase can be activated by which of the following molecules?

A) B) C) D) E)

ATP glucose-6-phosphate glucose AMP none of the above

Answer: D Difficulty: 2

Topic: Coordinated Regulation of Glycogen Metabolism

33) Which of the following enzymes is activated when acted on by phosphoprotein phosphatase 1?

A) B) C) D) E)

glycogen synthase glycogen phosphorylase phosphorylase kinase phosphoprotein phosphatase inhibitor 1 protein kinase A

Answer: A Difficulty: 2

Topic: Coordinated Regulation of Glycogen Metabolism

11 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

34) The oxidative phase of the pentose phosphate pathway has _____ oxidation reactions, effectively oxidizing an ___________ to ____________.

A) B) C) D) E)

2; alcohol; a carboxylic acid 2; aldehyde; a carboxylic acid 2; aldehyde; carbon dioxide 3; alcohol; a carboxylic acid 3; alcohol; carbon dioxide

Answer: C Difficulty: 2

Topic: A Biosynthetic Pathway that Oxidizes Glucose

35) A transketolase enzyme transfers a _____ carbon fragment from a(n) ________ to a(n) ________.

A) B) C) D) E)

2; aldose; ketose 2; ketose; aldose 2; ketose; ketose 3; aldose; ketose 3; ketose; aldose

Answer: B Difficulty: 2

Topic: A Biosynthetic Pathway that Oxidizes Glucose

36) The conversion of ribulose-5-phosphate to xylulose-5-phosphate requires what enzyme?

A) B) C) D) E)

phosphopentose isomerase phosphopentose epimerase transketolase transaldolase lactonase

Answer: B Difficulty: 2

Topic: A Biosynthetic Pathway that Oxidizes Glucose

12 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

37) When lipid biosynthesis is active using carbohydrates as a source of carbon, three things are needed: NADPH, ATP and acetyl-CoA (from pyruvate). Which of the following best explains the operation of the pentose phosphate pathway (PPP) under such conditions?

G6P = glucose-6-phosphate, F6P = fructose-6-phosphate, G3P = glyceraldehyde-3phosphate A) 3 G6P → 2 F6P + 1 G3P with the F6P recycled to G6P to re-enter the PPP while G3P continues through glycolysis to make acetyl-CoA and ATP B) 6 G6P → 4 F6P + 2 G3P with 1 G3P converted to DHAP, the other G3P + DHAP giving F6P with all F6P recycled to G6P to re-enter the PPP C) 3 G6P → 2 F6P + 1 G3P with the F6P and G3P continuing through glycolysis to make acetyl-CoA and ATP D) 3 G6P → 2 F6P + 1 G3P with all G3P continuing through glycolysis. Some F6P is recycled to G6P while some continues through glycolysis—the amount dependent upon the requirements for NADPH, ATP and acetyl-CoA E) none of the above Answer: D Difficulty: 3

Topic: A Biosynthetic Pathway that Oxidizes Glucose

38) What is the link between glutathione and the pentose phosphate pathway (PPP)?

A) during the oxidative phase, thiol groups on glucose-6-phosphate dehydrogenase become oxidized and must be reduced by glutathione B) glutathione acts as an inhibitor of glucose-6-phosphate dehydrogenase C) NADPH from the PPP is needed to keep glutathione in its reduced state D) phosphopentose epimerase often produces free radicals that are quenched by glutathione E) none of the above Answer: C Difficulty: 2

Topic: A Biosynthetic Pathway that Oxidizes Glucose

13 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway Short Answer Questions

1) For the interconversion of an aldose and ketose, show the intermediate of the reaction.

Answer:

Difficulty: 2

Topic: Reactions of Glycolysis

2) Fill in the missing two intermediates of glycolysis:

Answer:

Difficulty: 2

Topic: Reactions of Glycolysis

14 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 13: Carbohydrate Metabolism: Glycolysis, Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway

3) Provide the missing names or structures for the following scheme of the fermentation of pyruvate

Answer:

Difficulty: 2

Topic: Metabolic Fates of Pyruvate

15 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

Multiple Choice Questions 1)

The oxidation reactions that convert pyruvate to CO2 are specifically catalyzed by ______ enzymes.

A) B) C) D) E)

oxygenase oxidase decarboxylase dehydrogenase none of the above

Answer: D Difficulty: 1

2)

Topic: Overview of Pyruvate Oxidation and the Citric Acid Cycle

In the citric acid cycle, acetyl-CoA reacts with ________ to produce _________.

A) B) C) D) E)

fumarate; -ketoglutarate oxaloacetate; citrate citrate; isocitrate succinyl-CoA; oxaloacetate malate; cis-aconitate

Answer: B Difficulty: 2

3)

Topic: Overview of Pyruvate Oxidation and the Citric Acid Cycle

For each molecule of acetyl-CoA that enters the citric acid cycle, which of the following best represents the net products of the cycle?

A) B) C) D) E)

2 CO2, 2 NADH, 2 FADH2, 1 GTP, 1 oxaloacetate 1 CO2, 3 NADH, 1 FADH2, 2 GTP, 1 oxaloacetate 2 CO2, 3 NADH, 1 FADH2, 1 GTP, 0 oxaloacetate 1 CO2, 2 NADH, 1 FADH2, 2 GTP, 0 oxaloacetate 2 CO2, 3 NADH, 1 FADH2, 1 GTP, 1 oxaloacetate

Answer: C Difficulty: 2

Topic: Overview of Pyruvate Oxidation and the Citric Acid Cycle

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

4)

Which of the following coenzymes is required for the decarboxylation of pyruvate by the pyruvate dehydrogenase complex?

A) B) C) D) E)

thiamine pyrophosphate coenzyme A lipoic acid NAD+ FAD

Answer: A Difficulty: 1

5)

Topic: Pyruvate Oxidation

Which of the following enzymes of the pyruvate dehydrogenase complex is responsible for the oxidation of the hydroxyethyl group from pyruvate decarboxylation to an acetyl group?

A) B) C) D) E)

pyruvate dehydrogenase dihydrolipoamide transacetylase dihydrolipoamide dehydrogenase pyruvate dehydrogenase kinase pyruvate dehydrogenase phosphatase

Answer: B Difficulty: 2

6)

Topic: Pyruvate Oxidation

Which of the following best explains why thioesters have a greater free energy of hydrolysis than ordinary esters?

A) B) C) D) E)

alcohols are better leaving groups than thiols oxygen is more electronegative than sulfur esters are resonance stabilized while thioesters are not the oxygen of an ester is more easily protonated than the sulfur of a thioester none of the above

Answer: C Difficulty: 2

Topic: Coenzymes Involved in Pyruvate Oxidation

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

7)

Which of the following correctly lists the products of the pyruvate dehydrogenase complex in the correct order of release?

A) B) C) D) E)

acetyl-CoA, CO2, NADH acetyl-CoA, CO2, FADH2 CO2, acetyl-CoA, NADH CO2, acetyl-CoA, FADH2 CO2, acetyl-CoA, FADH2, NADH

Answer: C Difficulty: 2

8)

Topic: Action of the Pyruvate Dehydrogenase Complex

Arsenic poisoning by either arsenite or organic arsenical agents work by binding to dithiol compounds such as _________ meaning that in addition to inactivation of pyruvate dehydrogenase, the citric acid cycle enzyme _________ would be inactivated.

A) B) C) D) E)

cysteine; aconitase coenzyme A; -ketoglutarate dehydrogenase coenzyme A; citrate synthase thiamine pyrophosphate; isocitrate dehydrogenase lipoic acid; -ketoglutarate dehydrogenase

Answer: E Difficulty: 2

9)

Topic: Action of the Pyruvate Dehydrogenase Complex

What role does the coenzyme A portion of acetyl-CoA play in the reaction catalyzed by citrate synthase?

A) the CoA group causes the enzyme to close around the substrates, enabling catalysis B) lack of resonance in the thioester makes the methyl carbon of the acetyl group more acidic, allowing proton abstraction to readily occur C) CoA makes the carbonyl carbon highly susceptible to nucleophilic attack D) hydrolysis of the thioester makes the reaction essentially irreversible E) all of the above

Answer: E Difficulty: 3

Topic: The Citric Acid Cycle

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

10) The conversion of citrate to isocitrate by the enzyme aconitase is best described as ______ reaction consisting of a ________ followed by a ________.

A) B) C) D) E)

isomerization; oxidation; reduction isomerization; hydration; dehydration isomerization; dehydration; hydration group transfer; dehydroxylation; hydroxylation group transfer; hydroxylation; dehydroxylation

Answer: C Difficulty: 2

Topic: The Citric Acid Cycle

11) The two reactions of the citric acid cycle where CO2 is produced are catalyzed by _________ and _________ A) B) C) D) E)

isocitrate dehydrogenase; -ketoglutarate dehydrogenase isocitrate dehydrogenase; malate dehydrogenase -ketoglutarate dehydrogenase; succinate dehydrogenase -ketoglutarate dehydrogenase; malate dehydrogenase succinate dehydrogenase; malate dehydrogenase

Answer: A Difficulty: 2

Topic: The Citric Acid Cycle

12) Which of the following is an enzyme-bound intermediate in the reaction catalyzed by succinyl-CoA synthetase?

A) B) C) D) E)

succinyl phosphate glutamyl-CoA N-phosphohistidine N-ADP-histidine none of the above

Answer: C Difficulty: 2

Topic: The Citric Acid Cycle

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

13) Which oxidation reaction requires the coenzyme FAD because it involves oxidation of a carbon-carbon single bond to a double bond?

A) B) C) D) E)

oxidation of isocitrate to -ketoglutarate oxidation of -ketoglutarate to succinyl-CoA oxidation of succinate to fumarate oxidation of malate to oxaloacetate oxidation of pyruvate to acetyl-CoA

Answer: C Difficulty: 2

Topic: The Citric Acid Cycle

14) The complete oxidation of the acetyl group that enters the citric acid cycle yields _____ electrons from the methyl carbon and ____ electrons from the carbonyl carbon.

A) B) C) D) E)

4; 2 6; 2 6; 4 8; 2 8; 2

Answer: B Difficulty: 2

Topic: Stoichiometry and Energetics of the Citric Acid Cycle

15) Which of the following is an equilibrium-controlled reaction of the citric acid cycle?

A) B) C) D) E)

citrate synthase isocitrate dehydrogenase -ketoglutarate dehydrogenase succinate dehydrogenase all of the above

Answer: D Difficulty: 2

Topic: Stoichiometry and Energetics of the Citric Acid Cycle

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

16) Which of the following is an inhibitor of citrate synthase, isocitrate dehydrogenase, and ketoglutarate dehydrogenase?

A) B) C) D) E)

NADH succinyl-CoA ATP acetyl-CoA none of the above

Answer: A Difficulty: 1

Topic: Regulation of Pyruvate Dehydrogenase and the Citric Acid Cycle

17) __________ activates __________, thereby inhibiting pyruvate dehydrogenase.

A) B) C) D) E)

NADH; pyruvate dehydrogenase phosphatase Ca2+; pyruvate dehydrogenase phosphatase NAD+; pyruvate dehydrogenase kinase ATP; pyruvate dehydrogenase kinase pyruvate; pyruvate dehydrogenase kinase

Answer: D Difficulty: 2

Topic: Regulation of Pyruvate Dehydrogenase and the Citric Acid Cycle

18) Which of the following reactions is commonly used to replenish intermediates of the citric acid cycle?

A) B) C) D) E)

citrate → oxaloacetate + acetyl CoA oxaloacetate → aspartate glutamate → -ketoglutarate malate → pyruvate all of the above

Answer: C Difficulty: 2

Topic: Anaplerotic Sequences

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

19) Which of the following molecules is correctly paired with the enzyme that can convert it to oxaloacetate to replenish the citric acid cycle when other intermediates are removed?

A) B) C) D) E)

aspartate: aspartate deaminase pyruvate: malic enzyme phosphoenolpyruvate: PEP carboxylase glutamate: glutamate transaminase none of the above

Answer: C Difficulty: 3

Topic: Anaplerotic Sequences

20) Which of the following citric acid cycle enzymes is bypassed in the glyoxylate cycle?

A) B) C) D) E)

citrate synthase aconitase isocitrate dehydrogenase succinate dehydrogenase fumarase

Answer: C Difficulty: 2

Topic: Glyoxylate Cycle

21) The reaction catalyzed by malate synthase is shown below. Which citric acid cycle enzyme would have a mechanism most similar to malate synthase?

A) B) C) D) E)

malate dehydrogenase citrate synthase fumarase succinyl-CoA synthetase none of the above

Answer: B Difficulty: 2

Topic: Glyoxylate Cycle

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

22) What is the source of acetyl-CoA for the glyoxylate cycle?

A) B) C) D) E)

pyruvate amino acids fatty acids cholesterol all of the above

Answer: C Difficulty: 1

Topic: Glyoxylate Cycle

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle Short Answer Questions

1) Draw the enzyme-bound intermediate of the following reaction clearly showing proper stereochemistry:

Answer:

Difficulty: 3

Topic: The Citric Acid Cycle

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

2) The most common reactions of acetyl acetyl-CoA are with a nucleophile or with a base. Show the reactions of acetyl CoA with the generic base and the generic nucleophile:

Answer:

Difficulty: 2

Topic: The Citric Acid Cycle

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 14: Citric Acid Cycle and Glyoxylate Cycle

3) The glyoxylate cycle reaction catalyzed by isocitrate lyase is a reversible aldol condensation.

As it is written below, the reaction is an aldol cleavage. Propose a mechanism for this reaction using the acid and base supplied by the enzyme.

Answer:

Difficulty: 3

Topic: Glyoxylate Cycle

11 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

Multiple Choice Questions 1)

Which of the following pathways takes place primarily within the inner mitochondrial membrane?

A) B) C) D) E)

fatty acid -oxidation electron transport glycolysis citric acid cycle pentose phosphate pathway

Answer: B Difficulty: 1

2)

Topic: The Mitochondrion

Within the electron transport chain, complex _____ represents the entry point for electrons from NADH while complex _____ represents the entry point for electrons from FADH2.

A) B) C) D) E)

I; III II; III I; II II; I IV; III

Answer: C Difficulty: 1

3)

Topic: The Mitochondrion

If the following two reactions were coupled, what would be the oxidizing agent for the spontaneous reaction?

NAD+ + H+ + 2eNADH + acetaldehyde + 2H + 2e ethanol A) B) C) D) E)

E = -0.32 V E = -0.20 V

NAD+ acetaldehyde NADH ethanol H+

Answer: B Difficulty: 2

Topic: Oxidations and Energy Generation 1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

4)

Based on the following information, what is the G for the oxidation of malate by NAD+?

NAD+ + H+ + 2eNADH + oxaloacetate + 2H + 2e malate A) B) C) D) E)

E = -0.32 V E = -0.17 V

-29 kJ/mol 29 kJ/mol -95 kJ/mol 95 kJ/mol none of the above

Answer: B Difficulty: 2

5)

Topic: Oxidations and Energy Generation

Which amino acid is complexed to iron-sulfur clusters to enable them to associate with proteins?

A) B) C) D) E)

methionine serine lysine tyrosine cysteine

Answer: E Difficulty: 2

6)

Topic: Electron Transport

The oxidized form of coenzyme Q is considered a _______ while the reduced form is considered a _______.

A) B) C) D) E)

semiquinone; quinone quinone; semiquinone quinone; hydroquinone hydroquinone; quinone semiquinone; hydroquinone

Answer: C Difficulty: 2

Topic: Electron Transport

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

7)

In addition to iron, what metal is found in certain cytochromes?

A) B) C) D) E)

manganese copper chromium cobalt zinc

Answer: B Difficulty: 1

8)

Topic: Electron Transport

The inhibition by an unknown inhibitor of electron transport was found to be removed by a large concentration of phenazine methosulfate. Since phenazine methosulfate is known to accept electrons from cytochrome b of complex III, which of the following is most similar to the unknown inhibitor?

A) B) C) D) E)

amytal antimycin A carbon monoxide cyanide rotenone

Answer: B Difficulty: 3

9)

Topic: Electron Transport

Which of the following describes a correct and complete electron transfer pathway?

A) B) C) D) E)

NADH → complex I → CoQ → complex III → cyt c → complex IV NADH → complex I → complex II → CoQ → complex III → cyt c → complex IV NADH → complex I → cyt c → complex III → CoQ → complex IV FADH2 → CoQ → complex II → complex III → cyt c → complex IV FADH2 → complex II → cyt c → complex III → CoQ → complex IV

Answer: A Difficulty: 2

Topic: Electron Transport

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

10) Which of the following correctly indicates the number of protons pumped into the intermembrane space at each complex of electron transport for each FADH2 that is oxidized by the electron transport pathway?

A) B) C) D) E)

II: 2 II: 0 II: 2 II: 0 II: 0

III: 4 III: 2 III: 2 III: 4 III: 2

IV: 2 IV: 4 IV: 2 IV: 2 IV: 2

Answer: D Difficulty: 2

Topic: Electron Transport

11) Which of the following correctly describes what happens in the first stage of the Q cycle, considering that one cytochrome c is reduced in the process?

A) B) C) D) E)

one QH2 is oxidized to QH• while another QH• is reduced to QH2 one QH2 is reduced to QH• while another QH• is oxidized to Q one QH2 is oxidized to QH• one QH2 is oxidized to Q while another Q is reduced to QH• none of the above

Answer: D Difficulty: 2

Topic: Electron Transport

12) What is the approximate P/O ratio if the source of electrons for the electron transport chain is FADH2?

A) B) C) D) E)

1 1.5 2 2.5 3

Answer: B Difficulty: 1

Topic: Oxidative Phosphorylation

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

13) What is the approximate free energy for transporting a mole of protons from the matrix to the intermembrane space under normal conditions within the mitochondria?

A) B) C) D) E)

+220 kJ/mol +21 kJ/mol -21 kJ/mol -220 kJ/mol none of the above

Answer: B Difficulty: 2

Topic: Oxidative Phosphorylation

14) Which of the following acts as an uncoupler of the mitochondrial proton gradient due to its action as an ionophore?

A) B) C) D) E)

valinomycin nigericin trifluorocarbonylcyanide phenylhydrazone 2,4-dinitrophenol cyanide

Answer: A Difficulty: 2

Topic: Oxidative Phosphorylation

15) The presence of 10 copies of the c subunit of the F0 complex of yeast ATP synthase allows for the synthesis of 1 ATP for every ______ proton(s) that are translocated across the inner mitochondrial membrane.

A) B) C) D) E)

10 4 3.3 2.5 1

Answer: C Difficulty: 2

Topic: Oxidative Phosphorylation

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

16) Which of the following steps in the catalytic cycle of the F1 component is the most energetically unfavorable?

A) B) C) D) E)

binding of ADP binding of Pi formation of ATP from ADP and Pi release of ATP all of the above are equally energetically unfavorable

Answer: D Difficulty: 2

Topic: Oxidative Phosphorylation

17) Rotation of the ____ subunit causes the _____ subunit to change from tight conformation where ATP is produced to open conformation where ATP is released.

A) B) C) D) E)

;  ;  ;  ;  ; 

Answer: B Difficulty: 2

Topic: Oxidative Phosphorylation

18) __________ increases oxygen consumption while decreasing ATP synthesis, but ____________ decreases both oxygen consumption and ATP synthesis.

A) B) C) D) E)

rotenone; valinomycin azide; 2,4-dinitrophenol antimycin A; nigericin 2,4-dinitrophenol; oligomycin cyanide; valinomycin

Answer: D Difficulty: 3

Topic: Oxidative Phosphorylation

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

19) Which of the following uses the energy of the proton gradient to drive transport of its substrates?

A) B) C) D) E)

ADP/ATP carrier phosphate translocase in symport mode phosphate translocase in antiport mode pyruvate transport system all of the above

Answer: E Difficulty: 2

Topic: Mitochondrial Transport Systems

20) In the malate/aspartate shuttle, glutamate is converted to _________ in the mitochondria while aspartate is converted to ___________ in the cytosol.

A) B) C) D) E)

oxaloacetate; malate -ketoglutarate; oxaloacetate oxaloacetate; glutamate aspartate; -ketoglutarate malate; oxaloacetate

Answer: B Difficulty: 2

Topic: Mitochondrial Transport Systems

21) A(n) _______ incorporates oxygen from O2 into its products while a(n) _______ uses another oxidizing agent to accomplish the oxidation of its substrate.

A) B) C) D) E)

oxidase; dioxygenase dehydrogenase; oxygenase oxygenase; oxidase dehydrogenase; oxidase dioxygenase; oxygenase

Answer: C Difficulty: 2

Topic: Oxidases and Oxygenases

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

22) Which of the reactive oxygen species is thought to damage lipid membranes?

A) B) C) D) E)

semiquinone radical superoxide nitric oxide hydrogen peroxide hydroxyl radical

Answer: E Difficulty: 1

Topic: Reactive Oxygen Species

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism Short Answer Questions

1) Use the following half reactions to determine the reaction found in the pyruvate dehydrogenase complex. Calculate the G for the reaction. lipoate + 2H+ + 2eFAD + 2H+ + 2eAnswer:

dihydrolipoate FADH2

dihydrolipoate + FAD

E = -0.29 V E = -0.22 V lipoate + FADH2

E = 0.07 V

G = -nFE = -(2) (96.5 kJ/mol•V) (0.07 V) = -13.5 kJ/mol

Difficulty: 2

Topic: Oxidations and Free Energy

2) Using the structure of coenzyme Q, show one reaction to produce the semiquinone and the subsequent reaction to produce the hydroquinone forms of the molecule. (R represents the isoprenoid tail).

Answer:

Difficulty: 2

Topic: Electron Transport

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 15: Electron Transport, Oxidative Phosphorylation, and Oxygen Metabolism

3) The initial oxidation (known as -oxidation) of a 16 carbon saturated fatty acid produces 8 acetyl-CoA, 7 NADH and 7 FADH2. The process requires an input of 2 equivalents of ATP for the activation of the fatty acid. If the acetyl-CoA is further oxidized to CO2, what is the net ATP production from the complete oxidation of the fatty acid assuming that all electron carriers are re-oxidized by the electron transport chain?

Answer: -oxidation citric acid cycle (8) Total

NADH 7 24 31

FADH2 7 8 15

ATP (or equivalent) -2 8 6

NADH: 31 NADH  2.5 ATP/NADH = 77.5 ATP FADH2: 15  1.5 ATP/ FADH2 = 22.5 ATP Total ATP = 77.5 + 22.5 + 6 = 106 ATP

Difficulty: 3

Topic: Energy Yields from Oxidative Metabolism

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

Multiple Choice Questions 1)

What specific part of the chloroplast is responsible for the light reactions of photosynthesis?

A) B) C) D) E)

thylakoid lumen thylakoid membrane stroma inner membrane of chloroplast outer membrane of chloroplast

Answer: B Difficulty: 1

2)

Topic: The Chloroplast

What range type(s) of electromagnetic radiation are absorbed by photosynthetic pigments to allow the reactions of photosynthesis to occur?

A) B) C) D) E)

UV only visible only infrared only UV and visible visible and infrared

Answer: E Difficulty: 1

3)

Topic: The Light Reactions

Which of the following photosynthetic pigments would give rise to the yellow or red color of leaves seen during autumn?

A) B) C) D) E)

chlorophyll a chlorophyll b -carotene phycocyanin none of the above

Answer: C Difficulty: 1

Topic: The Light Reactions

1 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

4)

Which of the following explains why an electron will eventually travel to a chlorophyll molecule in the reaction center as opposed to just “wandering around” all of the antenna molecules?

A) antenna chlorophyll molecules are associated with proteins and have a higher excited state energy level B) antenna chlorophyll molecules are associated with proteins and have a lower excited state energy level C) reaction center chlorophyll molecules are associated with proteins and have a higher excited state energy level D) reaction center chlorophyll molecules are associated with proteins and have a lower excited state energy level E) none of the above

Answer: D Difficulty: 2

5)

Topic: The Light Reactions

Which of the following depicts the general flow of electrons in the two-photosystem light reactions? (Q = plastoquinone, PC = plastocyanin, Fd = ferredoxin A) B) C) D) E)

PSI → Q → cytochrome b6f complex → PC → PSII → Fd → NADP+ PSI → cytochrome b6f complex → Q → PC → PSII → Fd → NADP+ PSII → Q → cytochrome b6f complex → PC → PSI → Fd → NADP+ PSII → PC → Q → Fd → PSI → cytochrome b6f complex → NADP+ PSII → Fd → PC → cytochrome b6f complex → PSI → Q → NADP+

Answer: C Difficulty: 2

6)

Topic: The Light Reactions

Which of the following correctly identifies the proton pumping in the two-photosystem light reactions?

A) B) C) D) E)

PSII: 4 protons; cytochrome b6f complex: 8 protons cytochrome b6f complex: 8 protons; PSI: 4 protons PSII: 4 protons; ferredoxin-NADP+ oxidoreductase: 4 protons PSII: 4 protons; PSI: 4 protons; ferredoxin-NADP+ oxidoreductase: 4 protons none of the above

Answer: A Difficulty: 2

Topic: The Light Reactions 2 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

7)

What is the minimum number of photons that must be absorbed by PSII to reduce two molecules of water to one molecule of oxygen?

A) B) C) D) E)

1 2 4 8 16

Answer: C Difficulty: 2

8)

Topic: The Light Reactions

Which of the following describes the oxidation reactions for the two manganese ions that undergo oxidation in the oxygen-evolving complex?

A) B) C) D) E)

a Mn2+ is oxidized to a Mn4+ and a Mn3+ is oxidized to a Mn5+ a Mn2+ is oxidized to a Mn5+ and a Mn3+ is oxidized to a Mn4+ a Mn2+ is oxidized to a Mn5+ and a Mn2+ is oxidized to a Mn3+ a Mn2+ is oxidized to a Mn5+ and a Mn4+ is oxidized to a Mn5+ two Mn2+ are oxidized to Mn4+

Answer: B Difficulty: 3

9)

Topic: The Light Reactions

Which of the following shows the overall equation for the light reactions?

A) B) C) D) E)

2 H2O + 1 NADP+ → 1 H+ + O2 + 1 NADPH, requires 4 photons 2 H2O + 1 NADP+ → 1 H+ + O2 + 1 NADPH, requires 8 photons 2 H2O + 2 NADP+ → 2 H+ + O2 + 2 NADPH, requires 4 photons 2 H2O + 2 NADP+ → 2 H+ + O2 + 2 NADPH, requires 8 photons 2 H2O + 2 NADP+ → 2 H+ + O2 + 2 NADPH, requires 16 photons

Answer: D Difficulty: 2

Topic: The Light Reactions

3 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

10) The energy available from the protonmotive force across the thylakoid membrane is about 20 kJ/mol of protons. How much energy per mole of photons absorbed by the two photosystems does this equal?

A) B) C) D) E)

13 kJ/mol 30 kJ/mol 40 kJ/mol 60 kJ/mol none of the above

Answer: B Difficulty: 2

Topic: The Light Reactions

11) Under what conditions does the cyclic electron flow of photosystem I occur?

A) B) C) D) E)

high NADPH, low ATP low NADPH, high ATP low NADPH, low ATP high NADPH, high ATP under conditions when light is not intense enough to excite PSII

Answer: A Difficulty: 2

Topic: The Light Reactions

12) Which of the following best describes photosynthesis in purple photosynthetic bacteria?

A) B) C) D) E)

a reaction center resembling PSI transfers electrons to plastocyanin a reaction center resembling PSII transfers electrons to plastoquinone water is split by the reaction center that resembles PSII NADPH is generated using electrons from a protein resembling ferredoxin the proton gradient is used for both ATP synthesis and NADPH generation

Answer: B Difficulty: 3

Topic: The Light Reactions

4 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

13) In the mechanism of Rubisco, what role does the Mg2+ play?

A) neutralizes negative charges of active site Asp and Glu, enabling ionization of CO2 B) activates water molecule that hydrates the carboxy--keto intermediate C) complexes with the phosphate on C-1 to hold ribulose-1,5-bisphosphate in the active site D) repels the product, 3-phosphoglycerate, allowing it to leave the active site more rapidly E) none of the above Answer: B Difficulty: 2

Topic: The Dark Reactions

14) Which of the following is required for the reaction catalyzed by rubisco in order to drive the reaction to completion?

A) B) C) D) E)

NADH NADPH ATP → ADP + Pi ATP → AMP + PPi none of the above

Answer: E Difficulty: 1

Topic: The Dark Reactions

15) For every 12 molecules of 3-phosphoglycerate produced by rubisco, _____ are converted to hexoses while _____ are recycled to ribulose-1,5-bisphosphate.

A) B) C) D) E)

2; 10 4; 8 6; 6 8; 4 10; 2

Answer: A Difficulty: 2

Topic: The Dark Reactions

5 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

16) For each molecule of CO2 fixed by the Calvin cycle, how many ATP and NADPH are required?

A) B) C) D) E)

3 ATP, 1 NADPH 3 ATP, 2 NADPH 6 ATP, 2 NADPH 6 ATP, 3 NADPH none of the above

Answer: B Difficulty: 2

Topic: The Dark Reactions

17) Which of the following carbohydrates is the most common molecule exported by photosynthetic cells for use in other parts of the plant?

A) B) C) D) E)

amylose amylopectin glucose sucrose fructose

Answer: D Difficulty: 2

Topic: The Dark Reactions

6 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

18) The following reaction would be catalyzed by which of the following enzymes?

A) B) C) D) E)

ribulose-5-phosphate epimerase transaldolase transketolase triose phosphate isomerase pentose phosphate transferase

Answer: C Difficulty: 2

Topic: The Dark Reactions

19) The regeneration phase of the dark reactions are best considered in terms of regenerating 6 molecules of ribulose-1,5-bisphosphate, a process that requires 6 ATP. Considering the number of photons required for production of ATP in the light reactions, on average, how many photons must be absorbed for each molecule of ribulose-1,5-bisphosphate regenerated?

A) B) C) D) E)

1.5 3 4.5 6 9

Answer: A Difficulty: 2

Topic: A Summary of the Light and Dark Reactions

7 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

20) Which of the following would have an inhibitory effect upon rubisco?

A) B) C) D) E)

Mg2+ CO2 H+ reduced thioredoxin none of the above

Answer: C Difficulty: 2

Topic: A Summary of the Light and Dark Reactions

21) Which of the following acts as a corepressor for the transcription of chloroplast genes?

A) B) C) D) E)

3-phosphoglycerate fructose-1,6-bisphosphate CO2 sucrose none of the above

Answer: D Difficulty: 2

Topic: A Summary of the Light and Dark Reactions

22) When photorespiration occurs and phosphoglycolate must be salvaged, which of the following occurs during the salvage reactions?

A) B) C) D) E)

NADP+ is used in the oxidation of glycolate to glyoxylate NADPH is used in the reduction of hydroxypyruvate to glycerate carbon is lost in the form of CO2 ATP is made during the conversion of phosphoglycolate to glycolate none of the above

Answer: C Difficulty: 2

Topic: Photorespiration and the C4 Cycle

8 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

23) In C4 plants, CO2 in the mesophyll cell reacts with _________ to form oxaloacetate while in the bundle sheath cell, _________ undergoes decarboxylation to pyruvate.

A) B) C) D) E)

pyruvate; aspartate phosphoenolpyruvate; oxaloacetate pyruvate; malate phosphoenolpyruvate; malate 3-phosphoglycerate; oxaloacetate

Answer: D Difficulty: 2

Topic:

Photorespiration and the C4 Cycle

9 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis Short Answer Questions

1) If light with an average wavelength of 660 nm is used to power the light reactions of photosynthesis, what is the efficiency in terms of energy captured as NADPH and ATP based upon the following information?

2 H2O + 2 NADP+ → 2 H+ + O2 + 2 NADPH E = -0.50 V the oxidation of 2 water molecules with production of 2 NADPH requires 8 photons 12 protons are transported to the thylakoid lumen for each oxygen produced Answer: Energy of 2 NADPH production: (4)(96.5 kJ/V•mol)(-0.50 V) = 193 kJ/2 NADPH Energy of ATP production: 12 protons (1 ATP/3 protons) = 4 ATP 4 ATP (~50 kJ/mol) = 200 kJ/mol Total energy required = 193 kJ + 200 kJ = 393 kJ Energy of 8 einsteins of 660 nm light and calculation of efficiency:

(6.626  10−34 J • s)(2.998  108 m/s)  6.02  1023 einstein−1 = 181 kJ/einstein −7 6.60  10 m 8 einsteins  181 kJ/einstein = 1448 kJ 393 kJ/1448 kJ 100% = 27% E = hc /  =



Difficulty: 3

Topic: The Light Reactions

10 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

2) If the following 14C labeled molecules served as substrates for rubisco (the labeled carbons are indicated with *), where would the 14C labels end up in the immediate product(s) of the reaction? Draw the product(s), clearly showing which atom(s) would be labeled.

Answer:

Difficulty: 3

Topic: The Dark Reactions

11 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 16: Photosynthesis

3) Reaction of ribulose-1,5-bisphosphate with oxygen and then water results in the following intermediate. Show the resulting products from this reaction:

Answer:

Difficulty: 2

Topic: Photorespiration and the C4 Cycle

12 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

Multiple Choice Questions 1)

When comparing the energy in stored fat (triacylglycerols) versus the energy in stored glycogen, what must be taken into account to determine the actual energy available per gram of metabolite?

A) B) C) D) E)

fats are more highly oxidized than glycogen fats are anhydrous while glycogen binds large amounts of water fats are neutral while glycogen is highly charged fats are attached to protein while glycogen is not all of the above

Answer: B Difficulty: 2

2)

Topic: Utilization and Transport of Fat and Cholesterol

Which of the following lipoproteins distributes dietary lipids?

A) B) C) D) E)

chylomicron very low density lipoprotein intermediate density lipoprotein low density lipoprotein high density lipoprotein

Answer: A Difficulty: 1

3)

Topic: Utilization and Transport of Fat and Cholesterol

A(n) ___________ is converted to a(n) _____________ by loss of triacylglycerols.

A) B) C) D) E)

chylomicron; very low density lipoprotein low density lipoprotein; high density lipoprotein very low density lipoprotein; intermediate density lipoprotein low density lipoprotein; very low density lipoprotein intermediate density lipoprotein; very low density lipoprotein

Answer: C Difficulty: 2

Topic: Utilization and Transport of Fat and Cholesterol

1 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

4)

Which of the following roles does the liver play in lipoprotein metabolism?

A) B) C) D) E)

production of chylomicrons uptake of VLDL production of LDL uptake of HDL none of the above

Answer: D Difficulty: 2

5)

Topic: Utilization and Transport of Fat and Cholesterol

Which of the following events occurs first in the process of transporting an LDL into a cell?

A) B) C) D) E)

formation of a coated pit with the aid of clathrin receptor-mediated endocytosis fusion of the clathrin-lined vesicles to produce an endosome fusion of the cell membrane around the LDL particle interaction of apoprotein B-100 with the LDL receptor

Answer: E Difficulty: 2

6)

Topic: Utilization and Transport of Fat and Cholesterol

Which of the following leads to the formation of atherosclerotic plaques?

A) B) C) D) E)

non-specific interactions between LDL particles oxidation of LDL particles resulting in cross linking with proteins uptake of oxidized LDL particles by macrophages excess uptake of LDL particles converting endothelial cells to foam cells none of the above

Answer: C Difficulty: 2

Topic: Utilization and Transport of Fat and Cholesterol

2 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

7)

The enzymes that are responsible for the hydrolysis of triacylglycerols in adipocytes are _________ esterases.

A) B) C) D) E)

serine cysteine tyrosine histidine aspartate

Answer: A Difficulty: 1

8)

Topic: Utilization and Transport of Fat and Cholesterol

The primary activation of triacylglycerol mobilization in adipocytes is through __________ of the enzyme ____________.

A) B) C) D) E)

phosphorylation; perilipin phosphorylation; hormone sensitive lipase dephosphorylation; hormone sensitive lipase phosphorylation; adipose triglyceride lipase dephosphorylation; adipose triglyceride lipase

Answer: B Difficulty: 2

9)

Topic: Utilization and Transport of Fat and Cholesterol

In the mitochondrion, as a ______________ moves from the intermembrane space to the matrix, ___________ is transported in the opposite direction.

A) B) C) D) E)

fatty acyl-CoA; CoA fatty acyl-carnitine; carnitine fatty acyl-CoA; carnitine fatty acyl-carnitine; CoA fatty acid; acetyl-CoA

Answer: B Difficulty: 2

Topic: Fatty Acid oxidation

3 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

10) Which of the following is the major regulation point for transport of fatty acids into the mitochondria?

A) B) C) D) E)

long chain fatty acid specific acyl-CoA synthetase medium chain fatty acid specific acyl-CoA synthetase short chain fatty acid specific acyl-CoA synthetase carnitine acyltransferase I carnitine acyltransferase II

Answer: D Difficulty: 2

Topic: Fatty Acid oxidation

11) Which of the following represents the correct sequence of events in a cycle of -oxidation beginning with a saturated fatty acyl-CoA? A) B) C) D) E)

hydration, FAD-coupled oxidation, NAD+-coupled oxidation, thiolytic cleavage FAD-coupled oxidation, hydration, NAD+-coupled oxidation, thiolytic cleavage FAD-coupled oxidation, NAD+-coupled oxidation, hydration, thiolytic cleavage NAD+-coupled oxidation, FAD-coupled oxidation, hydration, thiolytic cleavage NAD+-coupled oxidation, hydration, FAD-coupled oxidation, thiolytic cleavage

Answer: B Difficulty: 2

Topic: Fatty Acid oxidation

12) The first three reactions of -oxidation are analogous to which of the following reaction sequences of the citric acid cycle?

A) B) C) D) E)

aconitase, isocitrate dehydrogenase, -ketoglutarate dehydrogenase isocitrate dehydrogenase, -ketoglutarate dehydrogenase, succinyl-CoA synthetase -ketoglutarate dehydrogenase, succinyl-CoA synthetase, succinate dehydrogenase succinate dehydrogenase, fumarase, malate dehydrogenase fumarase, malate dehydrogenase, citrate synthase

Answer: D Difficulty: 3

Topic: Fatty Acid oxidation

4 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

13) What enzyme activities are found in the mitochondrial trifunctional protein that metabolizes long chain (LC) fatty acids?

A) B) C) D)

LC-enoyl-CoA hydratase, LC-hydroxyacyl-CoA dehydrogenase, LC-thiolase LC-acyl-CoA synthetase, LC-acyl-CoA dehydrogenase, LC-enoyl-CoA hydratase LC-carnitine acyltransferase II, LC-acyl-CoA dehydrogenase, LC-enoyl-CoA hydratase LC-acyl-CoA dehydrogenase, LC-enoyl-CoA hydratase, LC-hydroxyacyl-CoA dehydrogenase E) LC-acyl-CoA dehydrogenase, LC-hydroxyacyl-CoA dehydrogenase, LC-thiolase

Answer: A Difficulty: 3

Topic: Fatty Acid oxidation

14) Individuals with diets high in coconut oil consume large amounts of lauric (12:0). What are the -oxidation products of lauric acid?

A) B) C) D) E)

6 acetyl-CoA, 6 NADH, 6 FADH2, 1 ATP used for activation 6 acetyl-CoA, 5 NADH, 5 FADH2, 1 ATP used for activation 6 acetyl-CoA, 6 NADH, 6 FADH2, 2 ATP used for activation 6 acetyl-CoA, 5 NADH, 5 FADH2, 2 ATP used for activation none of the above

Answer: D Difficulty: 2

Topic: Fatty Acid oxidation

15) For the -oxidation of a fatty acid with notation of 18:3c6,9,12, how many NADPH would be required and how many FADH2 would be produced?

A) B) C) D) E)

1 NADPH, 7 FADH2 1 NADPH, 8 FADH2 2 NADPH, 6 FADH2 2 NADPH, 7 FADH2 2 NADPH, 8 FADH2

Answer: D Difficulty: 3

Topic: Fatty Acid oxidation

5 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

16) Low levels of oxaloacetate with high levels of -oxidation cause the production of what metabolites, particularly within the liver?

A) B) C) D) E)

acetate and ethanol acetoacetate and -hydroxybutyrate 3-hydroxy-3-methyglutaryl-CoA and propionyl-CoA D-methylmalonyl-CoA and L-methylmalonyl-CoA all of the above

Answer: B Difficulty: 2

Topic: Fatty Acid oxidation

17) Which of the following is the most important regulatory enzyme in fatty acid synthesis?

A) B) C) D) E)

citrate lyase malic enzyme acetyl-CoA carboxylase acetyl-CoA-ACP transacylase malonyl-CoA-ACP transacylase

Answer: C Difficulty: 1

Topic: Fatty Acid Biosynthesis

18) For each acetyl-CoA that is incorporated into a growing fatty acid, what energy inputs are required, assuming that the growing fatty acid already contains at least 4 carbons?

A) B) C) D) E)

1 NADPH, 1 FADH2, 1 ATP 2 NADPH, 1 ATP 2 NADPH, 1 FADH2, 1 ATP 1 NADPH, 1 FADH2, 2 ATP 2 NADPH, 2 ATP

Answer: B Difficulty: 2

Topic: Fatty Acid Biosynthesis

6 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

19) Which of the following coenzymes is required by acetyl-CoA carboxylase?

A) B) C) D) E)

NAD+ biotin pyridoxal phosphate tetrahydrofolate none of the above

Answer: B Difficulty: 1

Topic: Fatty Acid Biosynthesis

20) Which of the following enzymes of fatty acid synthesis is most analogous to thiolase when considering that fatty acid synthesis is analogous to a reversal of -oxidation?

A) B) C) D) E)

-ketoacyl-ACP synthase -ketoacyl-ACP reductase 3-hydroxyacyl-ACP dehydratase enoyl-ACP reductase thioesterase

Answer: A Difficulty: 2

Topic: Fatty Acid Biosynthesis

21) Which of the following lists the enzymes (in order) required to transport a molecule of acetyl-CoA from the mitochondrion to the cytosol while returning the “acetyl-CoA acceptor” back to the mitochondrion?

A) citrate synthase, citrate lyase, pyruvate carboxylase B) citrate synthase, citrate lyase, malate dehydrogenase, pyruvate carboxylase C) citrate synthase, citrate lyase, malate dehydrogenase, pyruvate carboxylase, malic enzyme D) citrate synthase, citrate lyase, malate dehydrogenase E) citrate synthase, citrate lyase, malate dehydrogenase, malic enzyme Answer: D Difficulty: 2

Topic: Fatty Acid Biosynthesis

7 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

22) In mammalian cells, most fatty acid elongation occurs in _____________. Most desaturation of fatty acids in mammalian cells occurs in _____________.

A) B) C) D) E)

endoplasmic reticulum; mitochondria Golgi apparatus; mitochondria endoplasmic reticulum; Golgi apparatus Golgi apparatus; mitochondria endoplasmic reticulum; endoplasmic reticulum

Answer: E Difficulty: 2

Topic: Fatty Acid Biosynthesis

23) The futile cycle of triacylglycerol synthesis and triacylglycerol hydrolysis is controlled largely by AMP-activated protein kinase. Which of the following enzymes is regulated by AMP-activated protein kinase?

A) B) C) D) E)

glycerol kinase pyruvate carboxylase glycerophosphate acyltransferase glycerol-3-phosphate dehydrogenase phosphoenolpyruvate carboxykinase

Answer: C Difficulty: 2

Topic: Biosynthesis of Triacylglycerols

8 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins Short Answer Questions

1) Fill in the missing structures and any reactants or products for one complete round of oxidation:

9 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

Answer:

Difficulty: 2

Topic: Fatty Acid oxidation

10 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 17: Lipid Metabolism I: Fatty Acids, Triacylglycerols, and Lipoproteins

2) If gadoleic acid (20:1c9) underwent complete mitochondrial oxidation to CO2, how many ATP could be produced assuming that all reduced electron carriers are re-oxidized by the mitochondrial electron transport chain?

Answer: Using 2.5 ATP/NADH and 1.5 ATP/FADH2, the following table shows the reduced electron carriers and ATP equivalents from each pathway and the ultimate ATP yield.

Pathway -oxidation (9 cycles) citric acid cycle (10 cycles) Total Total ATP

NADH 9 30 39  2.5 97.5

FADH2, 8 10 18  1.5 27

ATP -2 10 8 8

Overall total ATP: 132.5

Difficulty: 3

Topic: Fatty Acid oxidation

3) Show the result if the following fatty acid underwent one desaturation using a 9 desaturase followed by one round of elongation.

Answer:

Difficulty: 2

Topic: Fatty Acid Biosynthesis

11 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

Multiple Choice Questions 1)

What process in the brain consumes most of the ATP that is produced?

A) B) C) D) E)

movement of actin/myosin maintenance of membrane potentials active transport of glucose and amino acids cellular growth none of the above

Answer: B Difficulty: 1

2)

Topic: Interdependence of the Major Organs

For skeletal muscle, which of the following correctly pairs the activity state with the source of energy?

A) B) C) D) E)

resting: glucose resting: amino acids exertion: glucose exertion: fatty acids none of the above

Answer: C Difficulty: 2

3)

Topic: Interdependence of the Major Organs

Which of the following types of tissue can use glucose, but not fatty acids, as a source of fuel?

A) B) C) D) E)

skeletal muscle cardiac muscle liver brain adipose

Answer: D Difficulty: 2

Topic: Interdependence of the Major Organs

1 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

4)

Which of the following is commonly stored as an energy reserve by the heart?

A) B) C) D) E)

glycogen creatine phosphate triacylglycerols ketone bodies lactate

Answer: B Difficulty: 1

5)

Topic: Interdependence of the Major Organs

Which of the following molecules is made in the liver solely for export?

A) B) C) D) E)

ketone bodies triacylglycerols glucose-6-phosphate glycogen none of the above

Answer: A Difficulty: 1

6)

Topic: Interdependence of the Major Organs

Which of the following is the ultimate action that causes release of insulin from pancreatic -cells?

A) B) C) D) E)

opening of ATP-gated K+ channels closing of ATP-gated K+ channels catabolism of glucose resulting in increased ATP opening of voltage gated Ca2+ channels leading to decreased cytosolic Ca2+ opening of voltage gated Ca2+ channels leading to increased cytosolic Ca2+

Answer: E Difficulty: 3

Topic: Hormonal Regulation of Fuel Metabolism

2 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

7)

Which of the following transporters is only present on the surface of muscle cells following insulin binding?

A) B) C) D) E)

GLUT1 GLUT2 GLUT3 GLUT4 GLUT5

Answer: D Difficulty: 1

8)

Topic: Hormonal Regulation of Fuel Metabolism

Which of the following is true of glucagon?

A) B) C) D) E)

it is released from the pancreatic -cells when glucose levels are low its synthesis and release are exclusively under the control of epinephrine the primary targets of glucagon are liver, adipose and muscle tissue major pathways promoted by glucagon include glycogenolysis and glycolysis none of the above

Answer: E Difficulty: 3

9)

Topic: Hormonal Regulation of Fuel Metabolism

Which of the following pathways is activated in response to phosphorylation of key enzymes by AMPK? A) B) C) D) E)

glycogenolysis in the heart glycolysis in the heart gluconeogenesis in the liver fatty acid synthesis in the liver triacylglycerol synthesis in the liver

Answer: B Difficulty: 2

Topic: Hormonal Regulation of Fuel Metabolism

3 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

10) Although AMPK and mTOR generally play opposing roles in metabolic control, which of the following pathways is activated by both of these molecules?

A) B) C) D) E)

glucose transport glycolysis gluconeogenesis cholesterol synthesis none of the above

Answer: A Difficulty: 2

Topic: Hormonal Regulation of Fuel Metabolism

11) What is the general reaction type catalyzed by most of the sirtuins?

A) B) C) D) E)

deadenylation deacetylation dehydrogenation deamination dehydration

Answer: B Difficulty: 1

Topic: Hormonal Regulation of Fuel Metabolism

12) The transcription factor PGC-1 is controlled by two forms of covalent modification.

Which of the following correctly identifies a mechanism of control?

A) B) C) D) E)

phosphorylation by AMPK inhibits PGC-1 dephosphorylation by AMPK activates PGC-1 acetylation by SIRT1 activates PGC-1 deacetylation by SIRT1 activates PGC-1 dephosphorylation by AMPK and deacetylation by SIRT1 activates PGC-1

Answer: D Difficulty: 2

Topic: Hormonal Regulation of Fuel Metabolism

4 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

13) If a group of transgenic mice that overexpress SIRT1 was fed as much food as the mice desired to eat, what would be the consequences?

A) shortened lifespan with increased incidence of age-related diseases such as diabetes and cardiovascular disease B) normal lifespan with increased incidence of age-related diseases C) normal lifespan with no increased incidence of age-related diseases D) lengthened lifespan with increased incidence of age-related diseases E) lengthened lifespan with no increased incidence of age-related diseases Answer: E Difficulty: 3

Topic: Hormonal Regulation of Fuel Metabolism

14) Which of the following hormones affects the arcuate nucleus of the hypothalamus and ultimately results in an inhibition of nutrient intake?

A) B) C) D) E)

adiponectin leptin ghrelin glucagon none of the above

Answer: B Difficulty: 1

Topic: Hormonal Regulation of Fuel Metabolism

15) Which of the following hormones is correctly described?

A) B) C) D) E)

ghrelin: produced in pancreas, stimulates appetite adiponectin: produced in adipose tissue, stimulates appetite insulin: produced in pancreas, stimulates appetite leptin: produced in intestines, suppresses appetite none of the above

Answer: B Difficulty: 2

Topic: Hormonal Regulation of Fuel Metabolism

5 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

16) Which of the following pathways would be active between meal when blood glucose is low but inactive after several days of starvation?

A) B) C) D) E)

glycogenolysis lipolysis -oxidation ketogenesis gluconeogenesis

Answer: A Difficulty: 2

Topic: Responses to Metabolic Stress

17) Under starvation conditions, which of the following shows an increase in activity in the first few days, followed by a large decrease in activity after a week?

A) B) C) D) E)

use of ketone bodies by the brain lipolysis glycolysis muscle protein mobilization none of the above

Answer: D Difficulty: 2

Topic: Responses to Metabolic Stress

18) The two hypotheses for insulin resistance are the lipid overload and the inflammation hypotheses. The lipid overload hypothesis primarily involves fat accumulation in __________ tissue while the inflammation hypothesis primarily involves secretion of inflammatory molecules from ___________ tissue.

A) B) C) D) E)

adipose; liver muscle; adipose adipose; adipose muscle; liver adipose; muscle

Answer: B Difficulty: 2

Topic: Responses to Metabolic Stress

6 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

19) Insulin resistance causes an increase in gluconeogenic activity in the liver due to the lack of glucose. What serves as the primary carbon source for gluconeogenesis under these conditions?

A) B) C) D) E)

amino acids glycerol fructose acetyl-CoA ketone bodies

Answer: A Difficulty: 1

Topic: Responses to Metabolic Stress

7 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates Short Answer Questions

1) For each of the following tissue types, list the fuel(s) stored, preferred fuel(s) and exported fuel(s) under normal conditions.

Tissue Brain

fuel(s) stored

preferred fuel(s)

exported fuel(s)

fuel(s) stored none

preferred fuel(s) glucose

exported fuel(s) none

Highly active glycogen skeletal muscle Heart none

glucose

lactate, alanine

fatty acids

none

Adipose

fatty acids

fatty acids, glycerol

Highly active skeletal muscle Heart Adipose

Answer: Tissue Brain

Difficulty: 2

triacylglycerols

Topic: Interdependence of the Major Organs

8 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

2) For each of the following biochemical pathways, give the effect of each hormone as either activated (), inhibited () or no effect (NE).

insulin

glucagon

epinephrine

insulin

glucagon

epinephrine

glycolysis (liver)







gluconeogenesis







glycogen synthesis (muscle)



NE



lipolysis







glycogenolysis







glycolysis (liver) gluconeogenesis glycogen synthesis (muscle) lipolysis glycogenolysis

Answer:

Difficulty: 2

Topic: Hormonal Regulation of Fuel Metabolism

9 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 18: Interorgan and Intracellular Coordination of Energy Metabolism in Vertebrates

3) For each of the following liver enzymes, indicate what happens to the enzyme (i.e., phosphorylated/dephosphorylated…) when the cell is under the influence of glucagon.

Indicate whether the enzyme is activated or inhibited and how that contributes to the overall role of glucagon.

PFK-2:

Pyruvate kinase:

Fruc-1,6-BPase:

Glycogen phosphorylase:

Answer: PFK-2: phosphorylated and thus converted to fructose-2,6-bisphosphatase. This breaks down fructose-2,6-bisphosphate (F26BP). F26BP is an activator of PFK-1 and an inhibitor of fructose-1,6-bisphosphatase so removal of F26BP activates gluconeogenesis and inhibits glycolysis.

Pyruvate kinase: phosphorylated and inhibited. This inhibits glycolysis and activates gluconeogenesis.

Phosphorylase: phosphorylates the enzyme converting to phosphorylase a. This activates the enzyme allowing for the breakdown of glycogen, ultimately to liberate glucose Glycogen synthase: phosphorylates the enzyme converting to glycogen synthase b. This inhibits the enzyme preventing the use of glucose for glycogen synthesis, thereby, allowing glucose to be exported by the liver.

Difficulty: 2

Topic: Hormonal Regulation of Fuel Metabolism

10 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

Multiple Choice Questions 1)

In prokaryotes, _________ is used exclusively as the precursor for phosphatidic acid while in eukaryotes, _________is one of three possible precursors.

A) B) C) D) E)

diacylglycerol; glycerol-3-phosphate glycerol-3-phosphate; dihydroxyacetone phosphate dihydroxyacetone phosphate; glycerol-3-phosphate 3-phosphoglycerate; diacylglycerol dihydroxyacetone phosphate; diacylglycerol

Answer: B Difficulty: 2

2)

Topic: Metabolism of Glycerophospholipids

Phospholipids are synthesized in the ___________, then transferred to the ____________ via transport vesicles.

A) B) C) D) E)

smooth endoplasmic reticulum; Golgi complex rough endoplasmic reticulum; smooth endoplasmic reticulum smooth endoplasmic reticulum; lysosome Golgi complex; smooth endoplasmic reticulum Golgi complex; cell membrane

Answer: A Difficulty:

3)

Topic: Metabolism of Glycerophospholipids

Which of the following phospholipids is produced in eukaryotes but not prokaryotes?

A) B) C) D) E)

phosphatidylglycerol phosphatidylserine phosphatidylethanolamine phosphatidylinositol none of the above

Answer: D Difficulty: 2

Topic: Metabolism of Glycerophospholipids

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

4)

Which of the following is used to activate phosphatidic acid for conversion to various phospholipids?

A) B) C) D) E)

ATP UTP CTP GTP TTP

Answer: C Difficulty: 1

5)

Topic: Metabolism of Glycerophospholipids

The biosynthesis of cardiolipin involves the reaction of phosphatidylglycerol with a molecule of ___________.

A) B) C) D) E)

phosphatidylglycerol phosphatidylserine phosphatidylethanolamine glycerol a fatty acyl-CoA

Answer: A Difficulty: 2

6)

Topic: Metabolism of Glycerophospholipids

The synthesis of phosphatidylethanolamine in prokaryotes involves _________________ while in mammals _______________ occurs.

A) reaction of CDP-diacylglycerol with ethanolamine; decarboxylation of phosphatidylserine B) decarboxylation of phosphatidylserine; reaction of CDP-ethanolamine with diacylglycerol C) reaction of phosphoethanolamine with diacylglycerol; reaction of CDP-ethanolamine with diacylglycerol D) decarboxylation of phosphatidylserine; reaction of CDP-diacylglycerol with ethanolamine E) reaction of CDP-diacylglycerol with ethanolamine; reaction of phosphoethanolamine with diacylglycerol

Answer: B Difficulty: 3

Topic: Metabolism of Glycerophospholipids 2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

7)

Which of the following amino acids is critical for choline and phosphatidylcholine synthesis?

A) B) C) D) E)

serine -alanine homocysteine methionine homoserine

Answer: D Difficulty: 2

8)

Topic: Metabolism of Glycerophospholipids

What is the term for the molecule shown below?

A) B) C) D) E)

platelet-activating factor 1-alkyl-2-acetylglcerophosphoethanolamine serine plasmologen choline plasmologen ethanolamine plasmologen

Answer: E Difficulty: 2

9)

Topic: Metabolism of Glycerophospholipids

The synthesis of the glycosphingolipids begins with the reaction of either UDP-glucose or UDP-galactose with _____________.

A) B) C) D) E)

ceramide sphinganine sphingosine sphingomyelin none of the above

Answer: A Difficulty: 1

Topic: Metabolism of Sphingolipids 3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

10) Tay-Sachs disease is caused by a deficiency of __________ which results in an accumulation of ___________.

A) B) C) D) E)

sphingomyelinase; sphingomyelin ceramidase; ceramide -galactosidase A; GM1 ganglioside lysosomal N-acetylhexosaminidase A; GM2 ganglioside -glucosidase; glucosylceramide

Answer: D Difficulty: 2

Topic: Metabolism of Sphingolipids

11) Which of the following is the regulatory step in cholesterol synthesis?

A) B) C) D) E)

HMG-CoA synthase HMG-CoA lyase HMG-CoA reductase squalene synthase squalene epoxidase

Answer: C Difficulty: 2

Topic: Steroid Metabolism

12) The synthesis of 1 molecule of cholesterol requires _____ molecules of isopentenyl pyrophosphate, with each molecule of isopentenyl pyrophosphate requiring _____ molecules of acetyl-CoA. A) B) C) D) E)

4; 2 5; 2 6; 2 5; 3 6; 3

Answer: E Difficulty: 2

Topic: Steroid Metabolism

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

13) Which of the following correctly identifies the order of carbocations found in the mechanism of squalene synthase?

A) B) C) D) E)

tertiary carbocation; allylic carbocation; tertiary cyclopropylcarbinyl carbocation tertiary carbocation; tertiary cyclopropylcarbinyl carbocation; allylic carbocation allylic carbocation; tertiary cyclopropylcarbinyl carbocation; tertiary carbocation allylic carbocation; tertiary carbocation; tertiary cyclopropylcarbinyl carbocation tertiary cyclopropylcarbinyl carbocation ; allylic carbocation; tertiary carbocation

Answer: D Difficulty: 3

Topic: Steroid Metabolism

14) Squalene epoxidase is an example of a mixed function oxidase, meaning that it uses both _______ and _______ as substrates.

A) B) C) D) E)

ATP; NADPH ATP; O2 NAD+; NADPH O2; NAD+ O2; NADPH

Answer: E Difficulty: 2

Topic: Steroid Metabolism

15) How is the activity of HMG-CoA reductase reduced?

A) B) C) D) E)

allosteric inhibition by cholesterol ubiquitination in response to sterol accumulation resulting in proteolysis serine phosphorylation by an insulin-activated protein kinase tyrosine phosphorylation by AMPK none of the above

Answer: B Difficulty: 2

Topic: Steroid Metabolism

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

16) Which of the following explains why the bile acids are much better suited than cholesterol for use as emulsification agents for fats?

A) cholesterol is oxidized to form the more polar molecule 7-hydroxycholesterol in route to formation of the bile acids B) while cholesterol contains a hydroxyl group as its sole hydrophilic functionality, cholic acid contains 3 hydroxyl groups and a carboxylic acid C) cholate is conjugated with glycine to make glycocholate D) cholate is conjugated with taurine to make taurocholate E) all of the above Answer: E Difficulty: 2

Topic: Steroid Metabolism

17) Which of the following is accomplished in one enzyme catalyzed reaction?

A) B) C) D) E)

progesterone to androstenedione 17-hydroxyprogesterone to cortisol progesterone to aldosterone androstenedione to testosterone androstenedione to estradiol

Answer: D Difficulty: 3

Topic: Steroid Metabolism

18) Which of the following forms of vitamin A is covalently attached to a lysine residue of the protein opsin to form the complex called rhodopsin?

A) B) C) D) E)

all-trans-retinal 11-cis-retinal all-trans-retinoic acid all-trans-retinol -carotene

Answer: B Difficulty: 1

Topic: Other Isoprenoid Compounds

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

19) 7-dehydrocholesterol reacts with _________ to produce cholecalciferol (vitamin D3) A) B) C) D) E)

UV light visible light NADPH NAD+ none of the above

Answer: A Difficulty: 1

Topic: Other Isoprenoid Compounds

20) The enzyme PGH synthase contains two different functionalities, a __________ that uses two molecules of oxygen as substrates and __________ which performs a 2 electron reduction.

A) B) C) D) E)

cyclooxygenase; peroxidase cyclooxygenase; reductase dioxygenase; peroxidase dioxygenase; reductase lipoxygenase; peroxidase

Answer: A Difficulty: 2

Topic: Eicosanoids

21) What classification is given to the following molecule?

A) B) C) D) E)

a prostaglandin G derivative a prostaglandin E derivative a leukotriene a thromboxane none of the above

Answer: C Difficulty: 1

Topic: Eicosanoids

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

22) The synthesis of which of the following molecules would be inhibited by aspirin?

A) B) C) D) E)

prostaglandin F2 prostaglandin D2 prostaglandin E2 prostaglandin H2 all of the above

Answer: E Difficulty: 1

Topic: Eicosanoids

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids Short Answer Questions

1) Show the products of the following reaction and name them:

Answer:

phosphatidylserine Difficulty: 2

cytidine monophosphate (CMP)

Topic: Metabolism of Glycerophospholipids

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 19: Lipid Metabolism II: Membrane Lipids, Steroids, Isoprenoids, and Eicosanoids

2) In eukaryotes, the conversion of DHAP to 1-acylglycerol-3-phosphate is a two-step process.

Show the reactants and products missing in the following scheme.

Answer:

Difficulty: 3

Topic: Metabolism of Glycerophospholipids

3) Show the reaction catalyzed by 3-hydroxy-3-methylglutrayl-CoA reductase.

Answer:

Difficulty: 2

Topic: Steroid Metabolism

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

Multiple Choice Questions 1)

The conversion of nitrogen to ammonia can be accomplished by _________ while the conversion of nitrate to ammonia can be accomplished by _________.

A) B) C) D) E)

plants; diazotrophs diazotrophs; plants diazotrophs; invertebrates denitrifying bacteria; bacteria denitrifying bacteria; plants

Answer: B Difficulty: 1

2)

Topic: Utilization of Inorganic Nitrogen

Which of the following represents a correct flow of electrons for nitrogen fixation?

A) B) C) D) E)

ferredoxin → Fe protein → MoFe protein → N2 Fe protein → MoFe protein → ferredoxin → N2 MoFe protein → Fe protein → ferredoxin → N2 ferredoxin → MoFe protein → Fe protein → N2 none of the above

Answer: A Difficulty: 2

3)

Topic: Utilization of Inorganic Nitrogen

In the nitrogen fixation process, which step of the electron transfer process requires ATP hydrolysis?

A) B) C) D) E)

transfer of electron from ferredoxin to the 4Fe-4S complex transfer of electron from 4Fe-4S complex to the P cluster transfer of electron from P cluster to iron-molybdenum cofactor (FeMo-co) transfer of electron from FeMo-co to nitrogen none of the above

Answer: B Difficulty: 3

Topic: Utilization of Inorganic Nitrogen

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

4)

The reaction catalyzed by nitrite reductase requires _______ electrons and is summarized as _____________.

A) B) C) D) E)

2; NO3- → NO22; NO2- → NO4; NO2- → NO- → NH2OH 4; NO2- → NO- → NH3 6; NO2- → NO- → NH2OH → NH3

Answer: E Difficulty: 2

5)

Topic: Utilization of Inorganic Nitrogen

The reaction of ammonia with -ketoglutarate is catalyzed by _________ and requires _________ as a reactant.

A) B) C) D) E)

glutamate synthetase; ATP glutamate synthetase; NADH or NADPH glutamate dehydrogenase; ATP glutamate dehydrogenase; NADH or NADPH none of the above

Answer: D Difficulty: 2

6)

Topic: Utilization of Ammonia

Which of the following enzymes of ammonia incorporation is the most highly regulated?

A) B) C) D) E)

glutamate dehydrogenase glutamate synthetase glutamine synthetase glutamine synthase none of the above

Answer: C Difficulty: 1

Topic: Utilization of Ammonia

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

7)

Which of the following correctly explains the covalent modification used to control glutamine synthetase?

A) B) C) D) E)

uridylylation activates, deuridylylation inhibits uridylylation inhibits, deuridylylation activates adenylation activates, deadenylation inhibits adenylation inhibits, deadenylation activates phosphorylation inhibits, dephosphorylation activates

Answer: D Difficulty: 2

8)

Topic: Utilization of Ammonia

In the regulation of glutamine synthetase activity, an important regulatory protein, PII exists in two states, one with UMP covalently bound (PII-UMP), the other without (PII).

Which of the following statements regarding -ketoglutarate and PII is correct?

A) B) C) D) E)

-ketoglutarate binds to PII causing inhibition of adenylyltransferase -ketoglutarate binds to PII causing activation of adenylyltransferase -ketoglutarate binds to PII-UMP causing inhibition of adenylyltransferase -ketoglutarate binds to PII-UMP causing activation of adenylyltransferase -ketoglutarate does not bind to either form of PII

Answer: A Difficulty: 3

9)

Topic: Utilization of Ammonia

Which of the following amino acids relies upon the synthesis of carbamoyl phosphate?

A) B) C) D) E)

lysine histidine arginine glutamine asparagine

Answer: C Difficulty: 1

Topic: Utilization of Ammonia

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

10) Which of the following is an essential amino acid for humans?

A) B) C) D) E)

alanine serine tyrosine cysteine histidine

Answer: E Difficulty: 1

Topic: The Nitrogen Economy

11) What are the products of the following transamination?

A) B) C) D) E)

glutamine and pyruvate -ketoglutarate and alanine glutamate and alanine oxaloacetate and alanine aspartate and pyruvate

Answer: B Difficulty: 1

Topic: The Nitrogen Economy

12) What is a PEST sequence in a protein?

A) a sequence where phosphorylation occurs at every serine and tyrosine B) a sequence that confers resistance to cathepsin-mediated proteolysis C) a sequence of phenylalanine-glutamate-serine-threonine that is found in many proteins with half lives less than 2 hours D) a sequence that causes ubiquitination of the protein followed by degradation E) none of the above Answer: D Difficulty: 3

Topic: Protein Turnover 4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

13) Ubiquitin is added to _________ residues of the target protein by reaction with the terminal __________ group of ubiquitin.

A) B) C) D) E)

lysine; carboxyl serine; carboxyl cysteine; carboxyl glutamate; amine glutamine; amine

Answer: A Difficulty: 2

Topic: Protein Turnover

14) Which of the following amino acids is exclusively ketogenic?

A) B) C) D) E)

phenylalanine tyrosine isoleucine arginine leucine

Answer: E Difficulty: 3

Topic: Amino Acid Degradation

15) Assuming that ammonia serves as the source of both nitrogen atoms of urea and that all cycles involved in the production of urea make one full turn, how many ATP equivalents and how many NADH are required to produce one molecule of urea?

A) B) C) D) E)

3 ATP equivalents, 1 NADH 3 ATP equivalents, 0 NADH 4 ATP equivalents, 1 NADH 4 ATP equivalents, 0 NADH none of the above

Answer: D Difficulty: 3

Topic: Amino Acid Degradation

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

16) Which of the following correctly accounts for the regulation of carbamoyl phosphate synthetase I? A) B) C) D) E)

inhibited by N-acetylglutamate, activated by acetylation of a lysine residue inhibited by N-acetylglutamate, activated by phosphorylation of a tyrosine residue activated by N-acetylglutamate, inhibited by acetylation of a lysine residue activated by N-acetylglutamate, activated by phosphorylation of a tyrosine residue none of the above

Answer: C Difficulty: 2

Topic: Amino Acid Degradation

17) Which of the following reactions is highly active in the liver when large amounts of amino acids are moving from extrahepatic tissue to the liver?

A) B) C) D) E)

conversion of glutamate to glutamine oxidation of glutamate by glutamate dehydrogenase reduction of -ketoglutarate by glutamate dehydrogenase transamination of glutamate and pyruvate to -ketoglutarate and alanine none of the above

Answer: B Difficulty: 2

Topic: Amino Acid Degradation

18) Which of the following is seen in the transaminase mechanism?

A) B) C) D) E)

aldimine formed between pyridoxal and lysine residue Schiff base pyridoxamine phosphate that reacts only with an -ketoacid a carbanion that is resonance stabilized as a quinonoid intermediate all of the above

Answer: E Difficulty: 2

Topic: Coenzymes Involved in Nitrogen Metabolism

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

19) Which of the following forms of tetrahydrofolate is correctly paired with the reaction for which it serves as a coenzyme?

A) B) C) D) E)

5,10-methenyl-THF: biosynthesis of purines 5-methyl-THF: dUMP → dTMP 5,10-methylene-THF: glycine → serine 5-methyl-THF: methionine → homocysteine all of the above

Answer: C Difficulty: 2

Topic: Coenzymes Involved in Nitrogen Metabolism

20) Which of the following metabolites is elevated as a result of low folate levels and poses a risk for cardiovascular disease?

A) B) C) D) E)

homocysteine methionine 5-formyl-THF formate none of the above

Answer: A Difficulty: 1

Topic: Coenzymes Involved in Nitrogen Metabolism

21) What is the only reaction of mammalian amino acid metabolism that is dependent upon vitamin B12?

A) B) C) D) E)

conversion of phenylalanine to tyrosine conversion of homocysteine to methionine isomerization of methylmalonyl-CoA to succinyl-CoA methane synthesis none of the above

Answer: B Difficulty: 2

Topic: Coenzymes Involved in Nitrogen Metabolism

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

22) What are the commonly observed oxidation states of cobalt found in the various forms of vitamin B12?

A) B) C) D) E)

+1, +2, +3 +1, +3, +5 +2, +3, +5 +3, +4, +5 +3, +5, +6

Answer: A Difficulty: 2

Topic: Coenzymes Involved in Nitrogen Metabolism

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover Short Answer Questions

1) What would be the energy requirements of the urea cycle if both nitrogens of urea came from glutamine (assuming that any NADH made was re-oxidized via electron transport/oxidative phosphorylation)? Explain how this is possible.

Answer: Glutamine can be converted to glutamate and ammonia via glutaminase with the ammonia being converted to carbamoyl phosphate as 1 nitrogen atom for urea. The glutamate undergoes transamination with oxaloacetate to form aspartate, the other nitrogen atom for urea. Once fumarate is formed by argininosuccinase, it must be converted back to oxaloacetate with the production of 1 NADH (converted to 2.5 ATP via ET/OxPhos). With the 4 ATP required by the urea cycle, the net utilization of ATP in this overall process is 1.5 ATP.

Difficulty: 3

Topic: Amino Acid Degradation

2) For the following transamination reaction, show the products of the first half of the reaction.

Answer:

Difficulty:

Topic: Coenzymes Involved in Nitrogen Metabolism

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 20: Metabolism of Nitrogenous Compounds I: Principles of Biosynthesis, Utilization, and Turnover

3) Show the products of the following reaction.

Answer:

Difficulty: 1

Topic: Coenzymes Involved in Nitrogen Metabolism

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

Multiple Choice Questions 1)

Threonine is converted into acetyl-CoA and pyruvate while proline is converted into ketoglutarate. Classify each of these amino acids.

A) B) C) D) E)

threonine is ketogenic, proline is ketogenic threonine is ketogenic and glucogenic, proline is ketogenic threonine is ketogenic, proline is glucogenic threonine is ketogenic and glucogenic, proline is glucogenic none of the above

Answer: D Difficulty: 2

2)

Topic: Pathways of Amino Acid Degradation

Which pair of amino acids can be degraded to oxaloacetate and -ketoglutarate, respectively?

A) B) C) D) E)

aspartate, alanine asparagine, histidine histidine, serine proline, arginine threonine, glutamine

Answer: B Difficulty: 2

3)

Topic: Pathways of Amino Acid Degradation

The route by which methionine is degraded provides for the synthesis of which amino acid?

A) B) C) D) E)

serine threonine valine isoleucine cysteine

Answer: E Difficulty: 2

Topic: Pathways of Amino Acid Degradation 1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

4)

The catabolism of leucine to acetyl-CoA produces three molecules of acetyl-CoA, one NADH, and one FADH2,while consuming two ATP. What is the net ATP production from the complete oxidation of the leucine carbon skeleton?

A) B) C) D) E)

30 32 34 36 none of the above

Answer: B Difficulty: 3

5)

Topic: Pathways of Amino Acid Degradation

Which amino acids are transaminated by the branched-chain amino acid aminotransferase?

A) B) C) D) E)

valine, isoleucine and leucine proline, valine and alanine leucine, isoleucine and phenylalanine leucine, isoleucine and proline lysine, valine and leucine

Answer: A Difficulty: 2

6)

Topic: Pathways of Amino Acid Degradation

One route for tryptophan degradation leads to the coenzyme _____________.

A) B) C) D) E)

pyridoxal phosphate FAD NAD+ tetrahydrobiopterin none of the above

Answer: C Difficulty: 2

Topic: Pathways of Amino Acid Degradation

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

7)

In the pathway for conversion of phenylalanine to fumarate and acetoacetate, there are two well-known enzyme defects that cause inheritable metabolic diseases. What are the names of these two diseases?

A) B) C) D) E)

homocysteinuria and nonketotic hyperglycinemia phenylketonuria and maple syrup urine disease alkaptonuria and nonketotic hyperglycinemia alkaptonuria and phenylketonuria maple syrup urine disease and homocysteinuria

Answer: D Difficulty: 2

8)

Topic: Pathways of Amino Acid Degradation

The regeneration of methionine from homocysteine relies upon the conversion of _________ to __________ as a source of carbon.

A) B) C) D) E)

alanine; pyruvate phenylalanine; tyrosine cystathionine; cysteine proline; glutamate serine; glycine

Answer: E Difficulty: 2

9)

Topic: Amino Acids as Biosynthetic Precursors

The importance of regenerating methionine can be seen in the multiple methionine regeneration pathways found in the liver, such as the pathway that uses betaine as a methyl group donor. What glycerophospholipid component is the precursor for betaine?

A) B) C) D) E)

ethanolamine glycerol choline serine none of the above

Answer: C Difficulty:

Topic: Amino Acids as Biosynthetic Precursors 3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

10) Which of the following is a role of spermine and spermidine, the polyamines derived from glutamate?

A) B) C) D) E)

stabilization of tRNA duplex structure neutralization of DNA negative charge stabilization of double stranded DNA stabilization of bacterial membranes all of the above

Answer: E Difficulty: 2

Topic: Amino Acids as Biosynthetic Precursors

11) Of the following molecules derived from amino acids, which is used to transport amino acids across the cell membrane?

A) B) C) D) E)

glutathione -aminobutyric acid S-adenosylmethionine nitric oxide thyroxine

Answer: A Difficulty: 1

Topic: Amino Acids as Biosynthetic Precursors

12) Which of the following molecules derived from tyrosine is correctly defined?

A) B) C) D) E)

dopamine: thyroid hormone dopaquinone: precursor for melanins thyroxine: catecholamine norepinephrine: thyroid hormone all of the above

Answer: B Difficulty: 2

Topic: Amino Acids as Biosynthetic Precursors

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

13) In animals, all nitrogen and carbon of heme groups comes from the reaction of the amino acid ________ and _________.

A) B) C) D) E)

glutamate; malonyl-CoA aspartate; acetyl-CoA asparagine; propionyl-CoA glycine; succinyl-CoA alanine; methylmalonyl-CoA

Answer: D Difficulty: 2

Topic: Porphyrin and Heme Metabolism

14) Which of the following explains the unique mechanism by which -aminolevulinic acid is synthesized in most bacteria, archaea and plants?

A) B) C) D) E)

glutamic acid is attached to its tRNA and then reduced to glutamate-1-semialdehyde glutamic acid undergoes reduction and cyclization to 1-pyrroline-5-carboxylate glutamic acid undergoes carboxylation to -carboxyglutamic acid glutamic acid condenses with itself via the -carboxyl and amine group none of the above

Answer: A Difficulty: 2

Topic: Porphyrin and Heme Metabolism

15) Bilirubin is conjugated with _________ to increase its solubility for excretion.

A) B) C) D) E)

phospholipids glycine glucuronic acid taurine all of the above

Answer: C Difficulty: 1

Topic: Porphyrin and Heme Metabolism

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

16) The conversion of tryptophan to 5-hydroxytryptophan in the serotonin synthesis pathway is analogous to the conversion of _________ to _________.

A) B) C) D) E)

glycine; serine phenylalanine; tyrosine tyrosine to thyroxine dopa to dopaquinone all of the above

Answer: B Difficulty: 2

Topic: Amino Acids and Their Metabolites as Neurotransmitters

17) Which of the following amino acids is derived from a glycolytic intermediate?

A) B) C) D) E)

aspartate threonine proline arginine serine

Answer: E Difficulty: 2

Topic: Amino Acid Biosynthesis

18) In bacteria, the biosynthetic routes for proline and arginine diverge when glutamate is Nacetylated for arginine synthesis. Which of the following explains why acetylation is required for arginine synthesis but not proline synthesis?

A) B) C) D) E)

acetylation alters the pKa of the amine group acetylation prevents reduction of the amine group in N-acetylglutamate--semialdehyde acetylation activates the amine group for synthesis of the guanidine group of arginine acetylation prevents the cyclization of N-acetylglutamate--semialdehyde none of the above

Answer: D Difficulty: 3

Topic: Amino Acid Biosynthesis

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

19) Glyphosate, the active molecule in the herbicide Roundup, is an inhibitor of the enzyme 5-enolpuruvylshikimate-3-phosphate synthase in the chorismate synthesis pathway.

Which of the following amino acids would not be produced in a plant treated with Roundup?

A) B) C) D) E)

glycine serine tyrosine valine proline

Answer: C Difficulty: 2

Topic: Amino Acid Biosynthesis

20) Which of the following molecules uses chorismate as a precursor?

A) B) C) D) E)

p-aminobenzoic acid coenzyme Q phenylalanine tryptophan all of the above

Answer: E Difficulty: 1

Topic: Amino Acid Biosynthesis

21) Which amino acid utilizes nitrogen and carbon from adenine in the synthesis of its Rgroup?

A) B) C) D) E)

histidine arginine lysine asparagine all of the above

Answer: A Difficulty: 2

Topic: Amino Acid Biosynthesis 7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

22) The Ames test is used to measure the mutagenicity of molecules by introducing a potential mutagen to a culture of bacteria that cannot synthesize histidine. Which of the following explains the results if the bacteria are able to grow in a medium that lacks histidine?

A) all proteins expressed by the bacteria have mutated to not require histidine B) defective histidine synthesis genes are mutated to forms that allow for histidine synthesis C) the mutagen causes the bacteria to use some other molecule in place of histidine D) the bacteria can convert the potential mutagen into histidine E) none of the above Answer: B Difficulty: 2

Topic: Amino Acid Biosynthesis

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters Short Answer Questions

1) Provide the two missing items in the scheme that shows the metabolism of threonine to glycine.

Answer:

Difficulty: 2

Topic: Pathways of amino acid degradation

2) Give the products of the following reaction in the -glutamyl cycle. One product is an amino acid, the other, 5-oxoproline.

Answer:

Difficulty: 3

Topic: Amino Acids as Biosynthetic Precursors 9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 21: Metabolism of Nitogenous Compounds II: Amino Acids, Porphyrins, and Neurotransmitters

3) Tryptophan is converted to serotonin, also known as 5-hydroxytryptamine. Show the intermediate and the product in the following synthetic pathway.

Answer:

Difficulty: 3

Topic: Amino Acids and Their Metabolites as Neurotransmitters

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

Multiple Choice Questions 1)

While endonucleases cleave nucleic acids into smaller oligonucleotides, __________ are responsible for cleaving the oligonucleotides into nucleotides.

A) B) C) D) E)

phosphodiesterases nucleotidase nucleoside kinases phosphorylases phosphoribosyl transferases

Answer: A Difficulty: 1

2)

Topic: Outlines of Pathways in Nucleotide Metabolism

Which of the following is the correct structure for PRPP? A)

B)

C)

D)

E) none of the above Answer: B Difficulty: 2

Topic: PRPP 1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

3)

What molecule contributes at least two nitrogen atoms to each purine?

A) B) C) D) E)

asparagine 10-formyltetrahydrofolate glycine glutamine carbamoyl phosphate

Answer: D Difficulty: 1

4)

Topic: De Novo Biosynthesis of Purine Nucleotides

Which enzyme of the inosinic acid biosynthesis pathway is the major control point for purine synthesis?

A) B) C) D) E)

phosphoribosyl pyrophosphate amidotransferase glycinamide ribonucleotide transformylase formylglycinamidine ribonucleotide amidotransferase 5-aminoimidazole ribonucleotide synthetase 5-aminoimidazole ribonucleotide carboxylase

Answer: A Difficulty: 1

5)

Topic: De Novo Biosynthesis of Purine Nucleotides

The ten enzyme activities that convert PRPP to inosinic acid are part of a multienzyme complex known as the _________.

A) B) C) D) E)

IMP synthetase complex purine synthetase complex purinosome tetrahydrofolate synthase complex none of the above

Answer: C Difficulty: 1

Topic: De Novo Biosynthesis of Purine Nucleotides

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

6)

During the conversion of IMP to GMP and AMP, __________ serves as the nitrogen source for GMP, while _________ serves as the nitrogen source for AMP. A) B) C) D) E)

glutamate, asparagine glutamate, aspartate glutamine, asparagine glutamine, aspartate none of the above

Answer: D Difficulty: 2

7)

Topic: De Novo Biosynthesis of Purine Nucleotides

Which of the following coenzymes contains an adenylate group?

A) B) C) D) E)

cobalamin tetrahydrofolate thiamine pyrophosphate pyridoxal phosphate coenzyme A

Answer: E Difficulty: 1

8)

Topic: De Novo Biosynthesis of Purine Nucleotides

Which of the following is a product of xanthine dehydrogenase?

A) B) C) D) E)

hypoxanthine uric acid guanine xanthosine allantoin

Answer: B Difficulty: 1

Topic: Purine Degradation and Clinical Disorders of Purine Metabolism

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

9)

The following reaction is catalyzed by what enzyme?

A) B) C) D) E)

xanthine oxidoreductase hypoxanthine hydroxylase urate oxidase guanine oxidase none of the above

Answer: A Difficulty: 2

Topic: Purine Degradation and Clinical Disorders of Purine Metabolism

10) Which of the following correctly explains the relationship between xanthine dehydrogenase (XDH) and xanthine oxidase (XO)?

A) B) C) D) E)

in healthy tissue, XDH is abundant while XO is rarely found conversion of XDH to XO occurs under conditions that damage cells XDH is converted to XO by formation of a disulfide bond XDH is converted to XO by proteolysis all of the above

Answer: E Difficulty: 2

Topic: Purine Degradation and Clinical Disorders of Purine Metabolism

11) What molecule(s) is(are) the source of the two nitrogen atoms for pyrimidine synthesis?

A) B) C) D) E)

asparagine glutamine, glutamate aspartate, carbamoyl phosphate carbamoyl phosphate, glutamine aspartate, glutamate

Answer: C Difficulty: 2

Topic: Pyrimidine Nucleotide Metabolism 4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

12) Which enzyme of the pyrimidine synthesis pathway is the most highly regulated?

A) B) C) D) E)

carbamoyl phosphate synthetase aspartate transcarbamoylase orotate phosphoribosyltransferase UMP kinase nucleoside diphosphate kinase

Answer: B Difficulty: 2

Topic: Pyrimidine Nucleotide Metabolism

13) Which of the following sequence of events best explains the formation of carbamate in the mechanism of carbamoyl phosphate synthetase?

A) Bicarbonate and ATP form carboxyphosphate, then NH3 performs a nucleophilic attack on carboxyphosphate to form carbamate B) Bicarbonate is attacked by NH3 to produce carbamate with ATP hydrolysis occurring solely to drive the reaction to completion C) Bicarbonate reacts with ATP forming carboxy adenylate and pyrophosphate, then NH3 performs a nucleophilic attack on carboxy adenylate to form carbamate D) NH3 reacts with ATP, which then reacts with bicarbonate followed by loss of phosphate to produce carbamate E) none of the above Answer: A Difficulty: 3

Topic: Pyrimidine Nucleotide Metabolism

14) The end products of the pyrimidine catabolic pathway are ammonia, carbon dioxide and __________.

A) B) C) D) E)

asparagine aspartic acid dihydrouracil -alanine glutamate

Answer: D Difficulty: 1

Topic: Pyrimidine Nucleotide Metabolism 5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

15) Which of the following best explains the initial steps for the synthesis of deoxynucleotides?

A) B) C) D) E)

begins with reduction of the ribose residue in PRPP deoxy PRPP is formed from deoxyribose-5-phosphate formed by reduction of ribonucleotide counterparts formed by oxidation of ribonucleotide counterparts none of the above

Answer: C Difficulty: 2

Topic: Deoxyribonucleotide Biosynthesis and Metabolism

16) Which of the following best explains the enzyme(s) involved in ribonucleotide reduction?

A) B) C) D) E)

there is 1 enzyme for each of the 4 different nucleotides 1 enzyme for pyrimidine nucleotides and 1 for purine nucleotides 1 enzyme for pyrimidine nucleotides, 1 for ADP and 1 for GDP 1 enzyme for purine nucleotides, 1 for CDP and 1 for UDP 1 enzyme for all 4 nucleotides

Answer: E Difficulty: 1

Topic: Deoxyribonucleotide Biosynthesis and Metabolism

17) Which of the following correctly describes the activity or regulation of E coli ribonucleotide reductase?

A) B) C) D) E)

the overall activity of the enzyme is controlled by ATP and dATP the specificity of the enzyme is controlled by all four dNTPs a tyrosine free radical participates in the reaction the reduction is not a result of simple hydride transfer all of the above

Answer: E Difficulty: 2

Topic: Deoxyribonucleotide Biosynthesis and Metabolism

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

18) Which of the following shows the correct and complete flow of electrons for ribonucleotide reductase?

A) B) C) D) E)

NADH → FAD → thioredoxin → ribonucleotide reductase NADPH → glutathione → glutaredoxin → ribonucleotide reductase NADPH → thioredoxin → cytochrome-b → ribonucleotide reductase FADH2 → glutathione → glutaredoxin → ribonucleotide reductase none of the above

Answer: B Difficulty: 2

Topic: Deoxyribonucleotide Biosynthesis and Metabolism

19) When ATP is bound in the activity site and ______ is bound in the specificity site, _______ will be reduced by ribonucleotide reductase.

A) B) C) D) E)

ATP; ADP and GDP dATP; GDP, UDP and CDP dTTP; GDP and ADP dGTP; ADP none of the above are correct

Answer: D Difficulty: 3

Topic: Deoxyribonucleotide Biosynthesis and Metabolism

20) Which of the following describes the coenzyme involved with thymidylate synthase?

A) B) C) D) E)

5-methyl-THF serves as the methyl donor 10-methyl-THF serves as the methyl donor 5,10-methylene-THF serves as both methylene donor and reducing agent 5,10-methenyl-THF serves as both methylene donor and reducing agent S-adenosylmethionine serves as the methyl donor

Answer: C Difficulty: 2

Topic: Deoxyribonucleotide Biosynthesis and Metabolism

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

21) The following molecule is an irreversible inhibitor of which enzyme of nucleotide metabolism?

A) B) C) D) E)

ribonucleotide reductase thymidylate synthase thymidine kinase dCMP deaminase CTP synthetase

Answer: B Difficulty: 2

Topic: Thymidylate Synthase

22) The molecule below would be an analog of __________ and therefore an effective _________compound.

A) B) C) D) E)

adenosine; anticancer adenosine; antiviral guanosine; anticancer guanosine; antiviral none of the above

Answer: D Difficulty: 2

Topic: Biological and Medical Importance of Nucleotide Analogs

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism Short Answer Questions

1) Given the structure of GMP, indicate the source for all carbons and nitrogens in the guanine base.

Answer:

Difficulty: 3

Topic: De Novo Biosynthesis of Purine Nucleotides

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

2) Show the reaction of allopurinol with xanthine dehydrogenase and explain how this molecule functions as an inhibitor of the enzyme.

Answer:

The product, alloxanthine, binds extremely tightly to the enzyme. Thus, allopurinol is a suicide substrate since once the enzyme acts upon it, it becomes almost permanently inhibited.

Difficulty: 2

Topic: Purine Degradation and Clinical Disorders of Purine Metabolism

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 22: Nucleotide Metabolism

3) Below is the structure of 3-azido-2,3-dideoxythymidine (also known as AZT). Draw the structure of the metabolite of AZT that serves as the inhibitor of reverse transcriptase.

Answer:

Difficulty: 2

Topic: Biological and Medical Importance of Nucleotide Analogs

11 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 23: Mechanisms of Signal Transduction

Multiple Choice Questions 1)

What is the primary target of releasing factors from the hypothalamus?

A) B) C) D) E)

thyroid adrenal medulla adrenal cortex posterior pituitary anterior pituitary

Answer: E Difficulty: 1

2)

Topic: Hierarchical Nature of Hormone Control

The structures of isoproterenol (left) and epinephrine are shown below. What is isoproterenol?

A) B) C) D) E)

agonist antagonist inverse agonist irreversible agonist non-competitive antagonist

Answer: A Difficulty: 2

3)

Topic: Signal Transduction: Receptors

A G protein is inactive when the _____ subunit is bound to __________.

A) B) C) D) E)

; GMP ; GDP ; GMP ; GDP /; GMP

Answer: B Difficulty: 2

Topic: Transducers: G Proteins 1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 23: Mechanisms of Signal Transduction

4)

What happens when the GTPase activity of a G protein is blocked?

A) B) C) D) E)

the  subunit associates only with the  subunit, not the  subunit GTP cyclizes to cGMP binding to GAP occurs with very high affinity adenylate cyclase remains active none of the above

Answer: D Difficulty: 2

5)

Topic: Transducers: G Proteins

In the visual process, activated rhodopsin causes which of the following events to occur?

A) B) C) D) E)

transducin binding to GTP transducin binding to GDP transducin binding to cGMP transducin binding to GMP none of the above

Answer: A Difficulty: 2

6)

Topic: Transducers: G Proteins

Which second messenger is produced as a result of nitric oxide binding?

A) B) C) D) E)

cAMP cGMP PIP2 InsP3 DAG

Answer: B Difficulty: 2

Topic: Second Messenger Systems

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 23: Mechanisms of Signal Transduction

7)

InsP3 binds to _______ channels in the endoplasmic reticulum while DAG activates ___________.

A) B) C) D) E)

Na+; protein kinase A Na+; protein kinase C Ca2+; protein kinase A Ca2+; protein kinase C none of the above

Answer: D Difficulty: 2

8)

Topic: Second Messenger Systems

Which of the following signaling molecules activate the phosphoinositide second messenger system?

A) B) C) D) E)

platelet-derived growth factor acetylcholine vasopressin thyrotropin-releasing hormone all of the above

Answer: E Difficulty: 1

9)

Topic: Second Messenger Systems

Which of the following hormones binds to a receptor tyrosine kinase?

A) B) C) D) E)

thyroxine epinephrine epidermal growth factor glucagon cortisol

Answer: C Difficulty: 1

Topic: Receptor Tyrosine Kinases

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 23: Mechanisms of Signal Transduction

10) Which of the following pathways correctly shows how glycogen synthase is activated in response to the activation of IRS-1 by insulin binding?

A) IRS-1 causes activation of protein kinase B which phosphorylates glycogen synthase kinase thus preventing phosphorylation of glycogen synthase B) IRS-1 activates a cascade that ultimately phosphorylates ERK which then binds to glycogen synthase C) IRS-1 activates phosphoinositide 3-kinase and the resulting PIP3 is an allosteric activator of glycogen synthase D) IRS-1 activates guanylate cyclase and the resulting cGMP binds to glycogen synthase kinase thus preventing phosphorylation of glycogen synthase E) none of the above Answer: A Difficulty: 3

Topic: Receptor Tyrosine Kinases

11) Most steroid hormones exert their effects by initial binding to which of the following receptors?

A) B) C) D) E)

receptor in cell membrane receptor in cytosol receptor in nuclear membrane receptor in nucleus none of the above

Answer: B Difficulty: 2

Topic: Steroid and Thyroid Hormones

12) The complex of zinc and cysteine residues seen in the structure of steroid hormone receptors is referred to as a(an) ______________ structural motif.

A) B) C) D) E)

zinc loop zinc helix antiparallel zinc sheet zinc finger zinc turn

Answer: D Difficulty: 2

Topic: Steroid and Thyroid Hormones 4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 23: Mechanisms of Signal Transduction

13) Glucocorticoids are thought to function as anti-inflammatory agents since they are able to stimulate the synthesis of what protein?

A) B) C) D) E)

tumor necrosis factor (TNF) platelet-derived growth factor (PDGF) transforming growth factor  (TGF-) nuclear factor-kappa B (NF-B) inhibitor-kappa B (IB)

Answer: E Difficulty: 1

Topic: Steroid and Thyroid Hormones

14) Like G proteins, the Ras protein binds _______ when in its active state which is hydrolyzed to ______ to convert the protein to its inactive state.

A) B) C) D) E)

GTP; GDP GTP; GMP GMP; cGMP cGMP; GMP cGMP; GDP

Answer: A Difficulty: 2

Topic: Signal Transduction, Oncogenes and Cancer

15) What neurotransmitter is involved with cholinergic synapses?

A) B) C) D) E)

serotonin dopamine acetylcholine glutamate -aminobutyric acid

Answer: C Difficulty: 1

Topic: Neurotransmission

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 23: Mechanisms of Signal Transduction

16) In the presynaptic neuron, ______ influx causes neurotransmitter release while in the postsynaptic neuron, ______ enters the cell following opening of ion channels.

A) B) C) D) E)

Na+; K+ K+; Na+ Ca2+; K+ Ca2+; Na+ Na+; Ca2+

Answer: D Difficulty: 2

Topic: Neurotransmission

17) When a nerve cell terminates at a muscle cell, the action potential causes opening of _____ channels that results in muscle contraction.

A) B) C) D) E)

Na+ K+ Ca2+ Clnone of the above

Answer: C Difficulty: 2

Topic: Neurotransmission

18) The principle inhibitory neurotransmitter, __________, works by triggering an influx of ______ causing hyperpolarization of nerve cells.

A) B) C) D) E)

-aminobutyric acid; K+ -aminobutyric acid; Clserotonin; K+ serotonin; Clnone of the above

Answer: B Difficulty: 2

Topic: Neurotransmission

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 23: Mechanisms of Signal Transduction

19) Amphetamine and mescaline are agonists of ____________, the neurotransmitter often considered a “pleasure agent.”

A) B) C) D) E)

serotonin -aminobutyric acid N-methyl-D-aspartate glutamate dopamine

Answer: E Difficulty: 2

Topic: Neurotransmission

20) The enkephalins, along with -endorphin, bind to the opioid receptor, so named because the opiate drugs such as __________ bind to it with high affinity A) B) C) D) E)

morphine fluoxetine (Prozac) phencyclidine methyl phenidylacetate (Ritalin) lysergic acid diethylamide (LSD)

Answer: A Difficulty: 2

Topic: Neurotransmission

21) What amino acid is the source of carbon for the synthesis of ethylene in plants?

A) B) C) D) E)

glycine serine aspartate methionine alanine

Answer: D Difficulty: 1

Topic: Signaling in Bacteria and Plants

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 23: Mechanisms of Signal Transduction Short Answer Questions

1) Show the reaction of phospholipase C upon PIP2 and give the names of the products.

Answer:

Difficulty: 2

diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (InsP3)

Topic: Second Messenger Systems

2) Insulin activates glycogen synthase while glucagon inhibits glycogen synthase. Explain the intracellular mechanisms that are used to bring about this activity.

Answer: Glucagon binds to its receptor causing activation of a G protein. This results in activation of adenylate cyclase, producing cAMP, an activator of protein kinase A. PKA phosphorylates glycogen synthase kinase, which phosphorylates glycogen synthase resulting in its inhibition. Insulin binds to its receptor causing activation of the IRS-1 protein with subsequent activation of phosphoinositide-3-kinase. This results in the production of phosphatidylinositol 3,4,5-trisphosphate, an activator of protein kinase B. PKB phosphorylates glycogen synthase kinase, thus inhibiting it.

The activity of phosphoprotein phosphatases, which are constantly active in the cell, removes the phosphorylation of glycogen synthase allowing activation to occur.

Difficulty: 3

Topic: Receptor Tyrosine Kinases

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 23: Mechanisms of Signal Transduction

3) Inside a cell, glucagon ultimately results in the phosphorylation of a wide variety of enzymes to control their activity. For each of the following enzymes that is phosphorylated in response to glucagon binding, explain what happens to its activity and why that is important (considering the pathway that the enzyme is in and the overall goal of glucagon).

Acetyl-CoA carboxylase:

Pyruvate kinase:

Glycogen phosphorylase:

Phosphofructokinase-2:

Answer: Acetyl-CoA carboxylase: is inhibited. This is important since this is the primary control point for fatty acid biosynthesis. When glucagon is present, fatty acid synthesis should be inhibited and fatty acids should be used as fuel.

Pyruvate kinase: is inhibited. As a step in glycolysis, inhibition of PK results in inhibition of glycolysis and allows for activation of gluconeogenesis.

Glycogen phosphorylase: activated since this is the enzyme that allows for the increase in blood glucose from the breakdown of glycogen.

Phosphofructokinase-2: this is a bifunctional enzyme, so the PFK-2 activity is inhibited while the fructose-2,6-bisphosphatase activity is activated. This removes fructose-2,6-bisphosphate, an activator of PFK-1 and an inhibitor of fructose-1,6-bisphosphatase. Ultimately, fructose1,6-bisphosphatase and thus gluconeogenesis are activated, while PFK-1 and thus glycolysis are inhibited.

Difficulty: 2

Topic: An Overview of Hormone Action

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes

Multiple Choice Questions 1)

A typical size for a viral genome is ______ nucleotides per haploid genome while a typical size for a bacterial genome is ______ nucleotides per haploid genome.

A) B) C) D) E)

2106; 4108 8104; 5107 1103; 9104 5104; 4106 3104; 5109

Answer: D Difficulty: 1

2)

Topic: Prokaryotic and Eukaryotic Genomes

What is present in many eukaryotic genes that drastically increases the size of eukaryotic DNA, but are not present in prokaryotic genes?

A) B) C) D) E)

satellite DNA long interspersed elements Alu sequences exons introns

Answer: E Difficulty: 2

3)

Topic: Prokaryotic and Eukaryotic Genomes

A pseudogene is a ___________.

A) B) C) D) E)

gene that codes for a non-functional protein nonexpressed gene mutated gene gene with multiple promoter regions that causes the start of transcription to be mistaken none of the above

Answer: B Difficulty: 2

Topic: Prokaryotic and Eukaryotic Genomes

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes

4)

Where in the following DNA sequence is the start of a 6-base type II restriction site?

Every fifth nucleotide is indicated with a bold letter using the top strand for numbering.

5’ A C T T C A G A A T T C C T T A C G A A G T T A T C 3’ 3’ T G A A G T C T T A A G G A A T G C T T C A A T A G 5’ A) B) C) D) E)

1 7 10 18 there is no restriction site in this sequence

Answer: B Difficulty: 3

5)

Topic: Restriction and Modification

What chemical modification of host DNA is used to protect it against cleavage by the host’s own restriction enzymes?

A) B) C) D) E)

methylation phosphorylation acetylation conversion of some cytosine to uracil conversion of some guanosine to inosine

Answer: A Difficulty: 1

6)

Topic: Restriction and Modification

BamHI has a restriction site of GGATCC while HpaI has a restriction site of GTTACC. Based upon this, BamHI produces __________ and HpaI produces __________.

A) B) C) D) E)

a 5 overhang; a 3 overhang a 5 overhang; a 5 overhang a 5 overhang; blunt ends a 3 overhang; a 5 overhang a 3 overhang; blunt ends

Answer: C Difficulty: 2

Topic: Restriction and Modification

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes

7)

For a restriction enzyme with a 6-base recognition site, what is the average number of base pairs between occurrences of the site?

A) B) C) D) E)

1296 base pairs 4096 base pairs 46656 base pairs 16777216 base pairs none of the above

Answer: B Difficulty: 2

8)

Topic: Restriction and Modification

What term is used to describe a collection of cloned genomic fragments?

A) B) C) D) E)

sequence repository fragmented genome library none of the above

Answer: D Difficulty: 1

9)

Topic: Determining Genome Nucleotide Sequences

What technique is used to amplify portions of DNA, usually about 500 base pairs in size?

A) B) C) D) E)

DNA sequencing polymerase chain reaction cloning restriction digestion electrophoresis

Answer: B Difficulty: 1

Topic: Determining Genome Nucleotide Sequences

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes

10) What is the term used to describe genetic variation that occurs among individuals of the same species resulting in gain or loss of restriction sites that can be detected by Southern analysis?

A) B) C) D) E)

polymorphism hybridization clone epigenetic variant none of the above

Answer: A Difficulty:

Topic: Determining Genome Nucleotide Sequences

11) Which of the following represents the correct order of steps usually taken in a Southern analysis?

A) B) C) D) E)

electrophoresis → restriction digest → nitrocellulose transfer → hybridization electrophoresis → hybridization → restriction digest → nitrocellulose transfer hybridization → restriction digest → electrophoresis → nitrocellulose transfer restriction digest → electrophoresis → hybridization → nitrocellulose transfer restriction digest → electrophoresis → nitrocellulose transfer → hybridization

Answer: E Difficulty: 2

Topic: Determining Genome Nucleotide Sequences

12) What is a haplotype?

A) B) C) D) E)

a collection of polymorphisms that occur by insertions a collection of polymorphisms that occur by deletions a collection of polymorphisms that occur by repetition of short sequences a collection of polymorphisms that occur by single base changes a collection of polymorphisms that display a distinct pattern that arises from the use of similar modifications to the area of the genome in question

Answer: E Difficulty: 2

Topic: Determining Genome Nucleotide Sequences

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes

13) What does a yeast artificial chromosome (YAC) allow one to do?

A) B) C) D) E)

selective analysis of yeast replication and transcription incorporation of eukaryotic genes into prokaryotic cells sequence analysis of DNA fragments up to 106 base pairs in size analysis of chromosomal-sized DNA in the absence of centromeres and telomeres all of the above

Answer: C Difficulty: 2

Topic: Determining Genome Nucleotide Sequences

14) The argument that mitochondria and chloroplasts originally were self-sufficient bacteria is supported by the presence of what protein-DNA structure?

A) B) C) D) E)

nucleoids chromatin importins chromatids nucleosomes

Answer: A Difficulty: 2

Topic: Physical organization of Genes

15) What is the typical percentage of lysine + arginine in histone proteins?

A) B) C) D) E)

<5% 5-10% 10-20% 20-35% >35%

Answer: D Difficulty: 1

Topic: Physical organization of Genes

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes

16) The combination of histone proteins with DNA gives rise to what structure?

A) B) C) D) E)

cohesins telomeres centromeres nuclear scaffold nucleosomes

Answer: E Difficulty: 1

Topic: Physical organization of Genes

17) Which histone protein is associated with the linker DNA and therefore not actually part of the nucleosome?

A) B) C) D) E)

H1 H2A H2B H3 H4

Answer: A Difficulty: 1

Topic: Physical organization of Genes

18) Which of the following describes a proper organization sequence for DNA in the nucleus?

A) B) C) D) E)

DNA helix → nucleosome → chromatin fiber → condensed fiber DNA helix → chromatin fiber → nucleosome → condensed fiber DNA helix → condensed fiber → nucleosome → chromatin fiber DNA helix → nucleosome → condensed fiber → chromatin fiber none of the above

Answer: D Difficulty: 2

Topic: Physical organization of Genes

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes

19) What structure is responsible for linking the centromeres to the spindle fibers during mitosis?

A) B) C) D) E)

metaphase plate nucleosome kinetochore centromere scaffold none of the above

Answer: C Difficulty:

Topic: The Cell Cycle

20) The alteration in chromatin structure that occurs within the centromere is brought about by the replacement of which histone protein?

A) B) C) D) E)

H1 H2A H2B H3 H4

Answer: D Difficulty: 2

Topic: The Cell Cycle

21) What proteins, responsible for specific protein kinase activation, are major control elements in the cell cycle?

A) B) C) D) E)

Rb proteins cyclins p53 cohesins nonhistone chromosomal proteins

Answer: B Difficulty: 2

Topic: The Cell Cycle

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes

22) In the event of DNA damage during mitosis, p53 is phosphorylated and prevents mitosis from continuing until the damage is corrected. If the damage cannot be corrected, what happens?

A) B) C) D)

cell returns to G1 and mitosis stops with excess DNA being degraded cell repeats S phase cell repeats G2 phase cell proceeds through mitotic division and the daughter cell with the damaged DNA is destroyed E) apoptosis

Answer: E Difficulty: 2

Topic: The Cell Cycle

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes Short Answer Questions

1) Show the product of the following restriction digest. PstI has a restriction site of CTGCAG. P- indicate the 5 phosphate, -OH indicates the 3 hydroxyl.

P-T C A C T G C A G C C T-OH HO-A G T G A C G T C G G A-P

+ PstI

→

Answer: P-T C A C T G C A-OH HO-A G T G-P

Difficulty: 2

P-G C C T-OH HO-A C G T C G G A-P

Topic: Restriction and Modification

2) A linear DNA molecule was treated with PstI and gave two fragments with sizes of 2150 and 3420 base pairs. The same DNA was treated with BamHI and gave three fragments of 1250, 1930 and 2390 base pairs. Finally, the DNA was treated with both enzymes at the same time and gave fragments of 900, 1250, 1490 and 1930 base pairs. Provide a map of the DNA molecule clearly indicating the restriction sites.

Answer:

Difficulty: 2

Topic: Restriction and Modification

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 24: Genes, Genomes and Chromosomes

3) Southern analysis of an individual DNA sample with an overall size of 10.1 kbp using a restriction enzyme that recognized a 6-base restriction site gave the following results. If the same test was performed on a different individual and four bands were seen in the analysis, what would the result look like and why?

Sample

DNA size markers

Answer: The expected results would look something like this:

Rationale: With a restriction enzyme that recognizes a 6-base sequence, you would expect a restriction site to appear once in every 4096 base pairs so the most likely fragment from the first individual to be cut would be the 5.5 kbp fragment. This would be cut about 4.1 kbp away from the other restriction sites giving two fragments as seen in the above figure. Obviously, the restriction site could be anywhere in the 5.5 kbp fragment so as long as two fragments are created that add up to 5.5 kbp, the answer would be correct.

Difficulty: 3

Topic: Determining Genome Nucleotide Sequences

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication

Multiple Choice Questions 1)

Replication of DNA in E. coli occurs in what type of fashion?

A) B) C) D) E)

unidirectional bidirectional multidirectional directionality can change depending upon specific conditions in the cell none of the above

Answer: B Difficulty: 1

2)

Topic: Early Insights into DNA Replication

Which of the following is required for DNA polymerase I activity?

A) B) C) D) E)

3 hydroxyl group ATP, GTP, TTP and CTP Zn2+ an RNA template all of the above

Answer: A Difficulty: 2

3)

Topic: DNA Polymerases

Which of the following exonuclease activities is present in DNA polymerase I? A) B) C) D) E)

3 exonuclease that degrades double stranded DNA 3 exonuclease that degrades hairpin DNA 5 exonuclease that degrades single stranded DNA 5 exonuclease that removes RNA from a DNA-RNA duplex none of the above

Answer: D Difficulty: 2

Topic: DNA Polymerases

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication

4)

Which of the following was evidence that DNA polymerase I was not responsible for the bulk of DNA synthesis in vivo?

A) B) C) D) E)

the requirement for an RNA primer the presence of both polymerase and exonuclease activity in the same enzyme the number of enzyme copies in each cell far exceeded the number of replication forks the requirement for Mg2+ none of the above

Answer: C Difficulty: 2

5)

Topic: DNA Polymerases

A mutation in a gene results in a mutant phenotype. What occurs if the wild-type phenotype is restored by a mutation at another site in the gene?

A) B) C) D) E)

reversion silent mutation conjugation silent conjugation suppression

Answer: E Difficulty: 2

6)

Topic: A Brief Review of Microbial Genetics

Which of the following DNA polymerases is correctly defined?

A) B) C) D) E)

polymerase I: DNA repair polymerase I: RNA primer excision polymerase II: DNA repair polymerase III: nucleotide incorporation during replication all of the above

Answer: E Difficulty: 1

Topic: Multiple DNA Polymerases

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication

7)

In the Klenow fragment of many DNA polymerases, the Mg2+ ions that are required for activity are coordinated to which amino acid R-groups?

A) B) C) D) E)

histidine and aspartate two aspartates aspartate and asparagine aspartate and glutamate glutamate and glutamine

Answer: B Difficulty: 2

8)

Topic: Multiple DNA Polymerases

In DNA synthesis, the _____________ strand is synthesized in a __________ fashion.

A) B) C) D) E)

template; discontinuous template; continuous leading; discontinuous lagging; discontinuous none of the above

Answer: D Difficulty: 1

9)

Topic: Other Proteins at the Replication Fork

Which of the following is the best description for primase?

A) B) C) D) E)

a DNA-dependent DNA polymerase an RNA-dependent DNA polymerase a DNA-dependent RNA polymerase an RNA-dependent RNA polymerase none of the above

Answer: C Difficulty: 2

Topic: Other Proteins at the Replication Fork

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication

10) What is an Okazaki fragment?

A) B) C) D) E)

a small section of DNA bound to the leading strand a small section of DNA bound to the lagging strand a small section of RNA and DNA bound to the leading strand a small section of RNA and DNA bound to the lagging strand none of the above

Answer: D Difficulty: 2

Topic: Other Proteins at the Replication Fork

11) Which of the following describes the correct sequence of enzyme activity upon the lagging strand?

A) B) C) D) E)

primase, DNA ligase, DNA polymerase I, DNA polymerase III primase, DNA polymerase I, DNA polymerase III, DNA ligase DNA polymerase III, primase, DNA polymerase I, DNA ligase primase, DNA ligase, DNA polymerase III, DNA polymerase I primase, DNA polymerase III, DNA polymerase I, DNA ligase

Answer: E Difficulty: 2

Topic: Other Proteins at the Replication Fork

12) What enzyme that is part of the primosome is responsible for unwinding of the DNA ahead of the replication fork?

A) B) C) D) E)

topoisomerase helicase primase clamp loading complex single-stranded binding protein

Answer: B Difficulty: 2

Topic: Other Proteins at the Replication Fork

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication

13) Which of the subunits of DNA polymerase III is responsible for the high processivity of the enzyme?

A) B) C) D) E)

    

Answer: A Difficulty: 2

Topic: Other Proteins at the Replication Fork

14) How does the gp32 protein facilitate both stabilization of single-stranded DNA as well as its renaturation to double-stranded DNA? A) B) C) D)

gp32 is an enzyme and thus its reaction of separating DNA strands is freely reversible gp32 binds only to regions of high A and T content so hydrogen bonding is reversible gp32 displays cooperativity in binding to single stranded DNA the gp32 C-terminal domain acts as a switch between weak and strong single stranded DNA binding E) none of the above

Answer: D Difficulty: 3

Topic: Other Proteins at the Replication Fork

15) Type I topoisomerases break _____ strand(s) of DNA; type II topoisomerases break _____strand(s) of DNA. DNA gyrase is a type ___ topoisomerase.

A) B) C) D) E)

both; 1; I both; 1; I both; 1; III 1; both; I 1; both; II

Answer: E Difficulty: 2

Topic: Other Proteins at the Replication Fork

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication

16) In a type I topoisomerase, the active site amino acid _________ is covalently bound to the free _______ end of the cut in the DNA. A) B) C) D) E)

serine; 3 serine; 5 tyrosine; 3 tyrosine; 5 none of the above

Answer: D Difficulty: 2

Topic: Other Proteins at the Replication Fork

17) Which of the following explains the result of type I topoisomerase activity on underwound DNA, considering that no energy (ATP) is used in the reaction?

A) B) C) D) E)

the linking number is decreased by 1 the linking number is increased by 1 the linking number remains the same but the twist decreases by 1 the linking number remains the same but the twist increases by 1 none of the above

Answer: B Difficulty: 2

Topic: Other Proteins at the Replication Fork

18) In eukaryotic replication, which polymerase is analogous to E. coli primase?

A) B) C) D) E)

pol  pol  pol  pol  pol 

Answer: A Difficulty: 2

Topic: Proteins in Eukaryotic DNA Replication

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication

19) What protein complexes with ATP and cardiolipin to initiate E. coli DNA replication by creating negative superhelical tension in the double stranded DNA? A) B) C) D) E)

DnaA DnaB DnaC DnaJ DnaK

Answer: A Difficulty: 2

Topic: Proteins in Eukaryotic DNA Replication

20) Which of the following is an 11-base consensus sequence that makes up the autonomously replicating sequence present in yeast DNA that is a requirement for the start of replication?

A) B) C) D) E)

5-GTGCGTGCGTG-3 5-CCTCCTGGTGG-3 5-AAGCGCGCGCC-3 5-GGTGGACCTCC-3 5-TTTTATATTTT-3

Answer: E Difficulty: 2

Topic: Initiation of DNA Replication

21) What feature of the telomerase enzyme allows it to synthesize DNA without the use of a DNA or RNA primer?

A) it synthesizes new DNA in a 3 to 5 direction B) it contains an RNA oligonucleotide complementary to the telomeric sequence C) since the telomeric sequence is a 15 base repeat, it is synthesized separately from the replication process and merely sealed in place by the ligase action of telomerase D) telomeric DNA forms a hairpin that is used to create its own complimentary primer E) none of the above Answer: B Difficulty: 2

Topic: Replication of Linear Genomes

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication

22) The fact that the following molecule serves as a substrate for DNA polymerase in place of dTTP proves what issue with regard to DNA replication?

A) B) C) D) E)

DNA polymerase is highly error prone hydrogen bonding to N-3 of thymine is not critical for substrate recognition base stacking is the true driving force for nucleotide placement substrate shape might be as important as hydrogen bonding for DNA polymerase none of the above

Answer: D Difficulty: 2

Topic: Fidelity of DNA Replication

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication Short Answer Questions

RNA primer based upon the following sequence

1) If a segment of a eukaryotic chromosome contained three origins of replication (at the sites indicated with arrows), how would the segment appear when replication was about half completed?

Answer:

Difficulty: 2

Topic: Early Insights into DNA Replication

2) For the following sequence, indicate the RNA primer that would be needed to start synthesis of the Okazaki fragment.

5’-A-A-C-T-A-G-A-C-C-A-G-A-3’ Answer: 3’-U-U-G-A-U-C-U-G-G-U-C-U-5’

Difficulty: 2

Topic: DNA Polymerases

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 25: DNA Replication

3) Show the reaction (with arrow pushing) for addition of the next nucleotide:

Answer:

Difficulty: 2

Topic: DNA Polymerases

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

Multiple Choice Questions 1)

Which of the following is formed by oxidation of a DNA base?

A) B) C) D) E)

uracil 8-oxoguanine 7-methylguanine thymine dimer all of the above

Answer: B Difficulty: 2

2)

Topic: DNA Repair

What is the causative agent in the formation of a cyclobutane thymine dimer?

A) B) C) D) E)

benzo[a]pyrene N-methyl-Nnitro-N-nitrosoguanidine methylnitrosourea ethylmethanesulfonate ultraviolet radiation

Answer: E Difficulty: 2

3)

Topic: DNA Repair

Which of the following coenzymes forms the photochemical reaction center of DNA photolyase?

A) B) C) D) E)

NADH thiamine pyrophosphate biotin FADH5-methyltetrahydrofolate

Answer: D Difficulty:

Topic: DNA Repair

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

4)

Methylation of guanine to produce O6-methylguanine (mG) results in what change to DNA? A) mG frequently pairs with thymine resulting in a GC → AT mutation B) mG loses its methoxy group resulting in hydrogen bonding with adenine and a bulge in the double helix C) mG is prone to deamination and eventually, depurination D) repair of mG adducts uses a radical mechanism that has the potential to further damage adjacent bases, particularly thymine E) none of the above

Answer: A Difficulty: 2

5)

Topic: DNA Repair

What is the correct order of enzyme activities required for nucleotide excision repair?

A) B) C) D) E)

exonuclease, helicase, polymerase, ligase exinuclease, helicase, polymerase, ligase exonuclease, polymerase, ligase, helicase exinuclease, polymerase, ligase, helicase exonuclease, ligase, polymerase, helicase

Answer: B Difficulty: 2

6)

Topic: DNA Repair

Which of the following types of DNA repair is often coupled with transcription?

A) B) C) D) E)

photoreactivation base excision repair replication nucleotide excision repair all of the above

Answer: D Difficulty: 2

Topic: DNA Repair

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

7)

Using the figure below, what is the first bond broken in the base excision repair process?

A) B) C) D) E)

1 2 3 4 5

Answer: E Difficulty: 1

8)

Topic: DNA Repair

Which base or bases is/are methylated to identify the original template strand of replicated DNA? A) B) C) D) E)

A C G A and G C and G

Answer: A Difficulty: 1

Topic: DNA Repair

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

9)

Which is a possible outcome when guanine is oxidized to 8-oxoguanine in the following segment of DNA?

A) is the only possible outcome B) is the only possible outcome C) is the only possible outcome D) both

and

are possible outcomes

both

and

are possible outcomes

E)

Answer: E Difficulty: 3

Topic: DNA Repair

10) In mismatch repair coupled to replication, which of the following relates a correct sequence of events?

A) daughter strand identification, mismatch identification, cleavage of daughter strand, helicase, polymerase, ligase B) daughter strand identification, mismatch identification, helicase, cleavage of daughter strand, polymerase, ligase C) mismatch identification, daughter strand identification, cleavage of daughter strand, helicase, polymerase, ligase D) mismatch identification, daughter strand identification, helicase, cleavage of daughter strand, polymerase, ligase E) mismatch identification, helicase, daughter strand identification, cleavage of daughter strand, polymerase, ligase Answer: C Difficulty: 2

Topic: DNA Repair 4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

11) What is a common trigger for the bacterial SOS response?

A) B) C) D) E)

thymine starvation DNA cross-linking agents such as mitomycin C ultraviolet radiation mutation of DNA replication genes all of the above

Answer: E Difficulty: 1

Topic: DNA Repair

12) The repair of a double-strand break can be accomplished by ______________, which requires the Ku70/80 protein to _______________________.

A) B) C) D) E)

nonhomologous end joining; catalyze blunt end ligation nonhomologous end joining; bind to both ends of the break homologous recombination; catalyze blunt end ligation homologous recombination; bind to both ends of the break none of the above

Answer: B Difficulty: 2

Topic: DNA Repair

13) The introduction of DNA into a bacterial cell by first packaging the DNA into a phage particle is referred to as _____________.

A) B) C) D) E)

transduction transformation transposition conjugation illegitimate recombination

Answer: A Difficulty: 1

Topic: Recombination

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

14) In order for lysogeny to occur, the enzyme ______________ must insert the phage DNA into a specific site in the bacterial chromosome.

A) B) C) D) E)

ligase lysogenase helicase integrase none of the above

Answer: D Difficulty: 1

Topic: Recombination

15) Which of the following the represents the correct sequence of events for the Holiday model of homologous recombination?

A) B) C) D)

nicking, strand invasion, branch migration, ligation, crossed strand breakage, rejoining nicking, strand invasion, branch migration, crossed strand breakage, ligation, rejoining nicking, strand invasion, ligation, branch migration, crossed strand breakage, rejoining nicking, strand invasion, ligation, branch migration, isomerization, crossed strand breakage, rejoining E) nicking, strand invasion, branch migration, isomerization, crossed strand breakage, ligation, rejoining

Answer: C Difficulty: 2

Topic: Recombination

16) How does RecA bring about strand exchange?

A) RecA acts as a helicase, unwinding DNA in localized regions B) RecA monomers bind to ssDNA to form a nucleoprotein filament C) RecA monomers interact only with ssDNA and immediately dissociate when binding to dsDNA D) RecA forms a tetramer that wraps around DNA at specific sites that must be cleaved by a nuclease E) none of the above Answer: B Difficulty: 2

Topic: Recombination

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

17) What role does integration host factor (IHF) play in site-specific recombination during phage  lysogeny?

A) B) C) D) E)

binds host DNA forcing a 90 bend supercoils phage DNA cleaves host and phage DNA at specific sites to create sticky ends ligates host and phage DNA once recombination occurs all of the above

Answer: A Difficulty: 2

Topic: Recombination

18) One mechanism to introduce greater diversity into antibody sequences is somatic hypermutation. What enzyme is responsible for somatic hypermutation in the DNA sequences that code for antibodies?

A) B) C) D) E)

deoxyadenosine deaminase deoxycytidine deaminase deoxyadenosine transaminase purine-pyrimidine transposase none of the above

Answer: B Difficulty: 2

Topic: Gene Rearrangements

19) In antibody light chain production, combination of V and J regions occurs at the _____ level; combination of J and C regions occurs at the _____ level.

A) B) C) D) E)

DNA; DNA DNA; RNA DNA; protein RNA; RNA RNA; protein

Answer: B Difficulty: 2

Topic: Gene Rearrangements

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

20) Which of the following transposable elements is correctly defined?

A) insertion sequence: protein-encoding gene flanked by two insertion sequences B) composite transposon: protein-encoding gene + transposase and resolvase genes flanked by two insertion sequences C) class II transposon: protein-encoding gene + resolvase gene flanked by two insertion sequences D) class III transposon: results from infection of a bacteriophage such as Mu E) none of the above Answer: D Difficulty:

Topic: Gene Rearrangements

21) A transposable element in a eukaryotic cell is called a _____________.

A) B) C) D) E)

retrotransposon long terminal repeat oncogene replicative transposon composite transposon

Answer: A Difficulty: 1

Topic: Gene Rearrangements

22) What is contained within a homogeneously staining region?

A) B) C) D) E)

a series of several replication origins a sequence of genes all under control of one promoter tandem duplicates of a specific gene a region of DNA created by a retrovirus none of the above

Answer: C Difficulty: 2

Topic: Gene Amplification

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification Short Answer Questions

1) Show the common base pair seen between 8-oxoguanine and adenine.

Answer:

Difficulty: 2

Topic: DNA Repair

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

2) Using the following DNA segment, show how microsatellite instability is present through a 2base deletion as a result of loop creation within the A-C repeating sequence. Give the sequence after the first round of replication (with loop) and after the second round of replication.

Template strand:

3’-C-A-C-A-C-A-C-A-C-A-5’

Answer: There are several possible products from the first round of replication; all will contain some sort of loop structure:

After the second round of replication, the segment will be shortened with elimination of the loop in one of the products: 3’-C-A-C-A-C-A-C-A-5’ 5’-G-T-G-T-G-T-G-T-3’

3’-C-A-C-A-C-A-5’ 5’-G-T-G-T-G-T-3’

For the loop-containing strand, it will most likely be replicated normally: 3’-C-A-C-A-C-A-C-A-C-A-5’ 5’-G-T-G-T-G-T-G-T-G-T-3’

Difficulty: 3

3’-C-A-C-A-C-A-C-A-C-A-5’ 5’-G-T-G-T-G-T-G-T-G-T-3’

Topic: DNA Repair

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 26: DNA Restructuring: Repair, Recombination, Rearrangement, Amplification

3) Given the following DNA segments, show the intermediate structure that would be produced following isomerization during homologous recombination.

Answer:

Difficulty: 2

Topic: Recombination

11 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing

Multiple Choice Questions 1)

The concept of the operon was proposed based on the ability of E. coli to metabolize the disaccharide ________ only when present in large excess over glucose.

A) B) C) D) E)

sucrose cellobiose galactose lactose maltose

Answer: D Difficulty: 1

2)

Topic: DNA as the Template for RNA Synthesis

Which subunit of E. coli RNA polymerase is responsible for the RNA polymerization reaction?

A) B) C) D) E)

    

Answer: B Difficulty: 1

3)

Topic: Enzymology of RNA Synthesis

Which subunit of E. coli RNA polymerase is responsible for DNA binding?

A) B) C) D) E)

    

Answer: C Difficulty: 1

Topic: Enzymology of RNA Synthesis

1 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing

4)

The E. coli core polymerase is missing the ____ subunit and binds to DNA with _______ specificity than the holoenzyme.

A) B) C) D) E)

; less ; greater ; less ; greater none of the above

Answer: A Difficulty: 2

5)

Topic: Enzymology of RNA Synthesis

E. coli cells achieve a great deal of gene regulatory expression through the  subunit of RNA polymerase. Which  subunit is present most often since it promotes the production of most of the proteins required under normal conditions within the cell?

A) B) C) D) E)

N S H 30 70

Answer: E Difficulty: 2

6)

Topic: Enzymology of RNA Synthesis

How does the concentration of ribonucleotide triphosphates play a role in the regulation of initiation?

A) a high concentration of ATP is required to form the open-promoter complex B) high concentration of both ATP and GTP are required to form the open-promoter complex C) the single nucleotide binding site of RNA polymerase undergoes a conformational change after the first nucleotide to allow subsequent nucleotides to bind more readily D) binding of the first nucleotide requires a half-saturating concentration of ~100 M while the half-saturating concentration for subsequent nucleotides is only ~10 M E) none of the above

Answer: D 2 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing

Difficulty: 2 Topic: Mechanism of Transcription 7) What is required for conversion from the closed-promoter complex to open-promoter complex?

A) B) C) D) E)

ATP binding ATP hydrolysis GTP binding GTP hydrolysis DNA bending

Answer: E Difficulty: 2

8)

Topic: Mechanism of Transcription

Rifampicin is known to inhibit RNA synthesis in E. coli. Once the first ten nucleotides have been incorporated, rifampicin does not inhibit RNA synthesis. Which of the following best explains how rifampicin functions?

A) rifampicin binds only to the core enzyme when bound to DNA but can bind to the holoenzyme when not bound to DNA B) rifampicin can bind to RNA polymerase when the polymerase is not bound to DNA but cannot bind when the polymerase is bound to DNA C) rifampicin only inhibits when the  subunit is bound to the core enzyme D) rifampicin is able to bind to the nucleotide binding site at any time E) none of the above

Answer: B Difficulty: 2

9)

Topic: Mechanism of Transcription

As RNA polymerase moves along the DNA, it creates a single stranded region of about 18 base pairs that is called a ________________.

A) B) C) D) E)

transcription bubble transcription single-stranded region transcription droplet transcription vesicle transcription bead

Answer: A Difficulty: 1

Topic: Mechanism of Transcription 3 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing

10) The E. coli promoter region contains a -10 consensus sequence of _________ on the sense strand.

A) B) C) D) E)

GAGAGA CTCTCT GAGGAG GACGTC TATAAT

Answer: E Difficulty: 2

Topic: Mechanism of Transcription

11) During factor-independent termination, RNA polymerase pauses upon encountering a _____________ and is then displaced downstream upon encountering a ___________.

A) B) C) D) E)

TATAAT sequence; G-C rich segment G-C rich segment; TATAAT sequence G-C rich segment; string of 4-8 A residues string of 4-8 A residues; TATAAT sequence string of 4-8 A residues; G-C rich segment

Answer: C Difficulty: 2

Topic: Mechanism of Transcription

12) What type of enzyme activity is associated with the termination factor ?

A) B) C) D) E)

topoisomerase endonuclease exonuclease helicase ligase

Answer: D Difficulty: 2

Topic: Mechanism of Transcription

4 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing

13) In eukaryotic cells, RNA polymerase ____ transcribes most of the ribosomal RNA, RNA polymerase ____ transcribes the major structural genes and RNA polymerase ____ transcribes tRNAs. A) B) C) D) E)

I; II; III I; III; II II; I; III II; III; I III; II; I

Answer: A Difficulty: 2

Topic: Transcription and its Control in Eukaryotic Cells

14) Rapid transcription of ribosomal RNA is thought to occur as a result of what unique feature in the DNA that encodes these genes?

A) B) C) D) E)

high A-T content highly repetitive sequence multiple promoter sites that allow high affinity with RNA polymerase presence of hairpin structures in the DNA absence of nucleosomes

Answer: E Difficulty: 2

Topic: Transcription and its Control in Eukaryotic Cells

15) Transcription of the 5S rRNA gene occurs by ________ covering the entire gene so that pol III can ____________.

A) B) C) D) E)

TFIIB; transcribe the gene several times before dissociating TFIIIC; transcribe the gene several times before dissociating TFIIB; transcribe both strands of DNA before dissociating TFIIIC; transcribe both strands of DNA before dissociating none of the above

Answer: B Difficulty: 2

Topic: Transcription and its Control in Eukaryotic Cells

5 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing

16) Which of the following is the most common promoter element for pol II? A) B) C) D) E)

CAAT box (GGCCAATCT) GC box (GGGCGG) TRE (GAGGGACGTACCGCA) TATA box (TATAAAA) Octamer (ATTTGCAT)

Answer: D Difficulty: 2

Topic: Transcription and its Control in Eukaryotic Cells

17) In vivo, which of the following transcription initiation factors is required for binding to a TATA box?

A) B) C) D) E)

TFIID TFIIE TFIIF TFIIH TAF

Answer: A Difficulty: 2

Topic: Transcription and its Control in Eukaryotic Cells

18) What is the mechanism by which enhancers, despite the fact that they are often several kilobase pairs away from the promoter, activate transcription?

A) B) C) D) E)

DNA unwinding DNA looping chromatin remodeling DNA hairpin formation none of the above

Answer: B Difficulty: 2

Topic: Transcription and its Control in Eukaryotic Cells

6 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing

19) Phosphorylation of the Rpb1 subunit of pol II causes what to occur?

A) B) C) D) E)

binding to histone proteins hydrogen bonding with guanine residues near the start of transcription dissociation from the promoter transcription termination none of the above

Answer: C Difficulty: 2

Topic: Transcription and its Control in Eukaryotic Cells

20) Which of the following is the first event in the post-translational processing of an E. coli tRNA? A) B) C) D) E)

ribonuclease P cleavage to create the proper 5 end of the molecule methylation of guanine residues conversion of some uridine residues to pseudouridine endonuclease cleavage of about 170 bases from the 3 end of the molecule removal of 9 nucleotides from the 3 end by ribonuclease D

Answer: D Difficulty: 3

Topic: Posttranscriptional Processing

21) Which of the following events commonly occur in the processing of eukaryotic mRNA? A) B) C) D) E)

addition of a 5 cap RNA editing splicing to remove introns alternative splicing to combine different exons into mature mRNA all of the above

Answer: E Difficulty: 2

Topic: Posttranscriptional Processing

7 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing

22) What type of RNA is found in the spliceosome?

A) B) C) D) E)

snRNA tRNA rRNA triple-stranded RNA all of the above

Answer: A Difficulty: 1

Topic: Posttranscriptional Processing

8 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing Short Answer Questions

1) Give the mRNA sequence that would result from the following sense strand: 5’-A-T-C-T-C-G-A-T-C-G-T-A-C-G-A-T-G-T-C-A-3’ Answer: 5’-A-U-C-U-C-G-A-U-C-G-U-A-C-G-A-U-G-U-C-A-3’

Difficulty: 1

Topic: Mechanism of Transcription

2) Draw a transcription bubble, clearly labeling the proteins and nucleic acids involved in the process.

Answer:

Difficulty: 2

Topic: Mechanism of Transcription

9 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 27: Information Readout: Transcription and Post-transcriptional Processing

3) The figure below shows a newly transcribed mRNA still associated with the template DNA. Draw the stem-loop structure that often forms during termination.

3’-GGTCGGGCGGATTACTCGCCCGAAAAAAAA-5’ 5’-CCAGCCCGCCUAAUGAGCGGGCUUUUUUUU-3’

Answer: AAU U C

G A

C-G G-C C-G C-G C-G G-C 5’-CCA UUUUUUUU-3’ Difficulty: 3

Topic: Mechanism of Transcription

10 Copyright © 2013 Pearson Education, Inc.

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing

Multiple Choice Questions 1)

What enzyme attaches the correct amino acid to its tRNA? A) B) C) D) E)

aminoacyl-tRNA synthase aminoacyl-tRNA synthetase aminoacyl-tRNA transferase aminoacyl-tRNA ligase none of the above

Answer: B Difficulty: 1

2)

Topic: An Overview of Translation

A repetitive mRNA of GAG could produce which of the following?

A) B) C) D) E)

polyglutamate polyleucine polyleucine, polyserine, or polyproline polyarginine, polyglycine or polyglutamate none of the above

Answer: D Difficulty: 2

3)

Topic: The Genetic Code

By saying that the genetic code is degenerate, what does this imply?

A) B) C) D) E)

the code is different for bacteria than for eukaryotes some codons can code for non-standard amino acids most amino acids have more than one codon there is more than one start codon there is more than one stop codon

Answer: C Difficulty: 1

Topic: The Genetic Code

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing

4)

If a mutation in the template strand of DNA occurred in the following manner, which of the possible amino acid changes would occur?

5’-CAT-3’ A) B) C) D) E)

→

5’-TAT-3’

methionine → isoleucine histidine → tyrosine methionine → tyrosine histidine → isoleucine none of the above

Answer: A Difficulty: 3

5)

Topic: The Genetic Code

Which position of the anticodon is called the wobble base and with which base of the codon does it pair?

A) B) C) D) E)

the 3 anticodon base which pairs with the first base of the codon the 3 anticodon base which pairs with the last base of the codon the middle anticodon base which pairs with the middle base of the codon the 5 anticodon base which pairs with the first base of the codon the 5 anticodon base which pairs with the last base of the codon

Answer: E Difficulty: 2

6)

Topic: The Genetic Code

In most cases, the first codon in prokaryotic mRNA codes for ________ while the first codon in eukaryotic mRNA codes for ________.

A) B) C) D) E)

methionine; N-formylmethionine N-formylmethionine; methionine proline; N-formylproline N-formylproline; proline none of the above

Answer: B Difficulty: 1

Topic: The Genetic Code

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing

7)

Which are paired by a Shine-Dalgarno sequence?

A) B) C) D) E)

the mRNA sequence just upstream from the start codon with the ribosome the first codon of the mRNA with its tRNA a termination codon with a release factor the 30S subunit with the 50S subunit of the ribosome none of the above

Answer: A Difficulty: 2

8)

Topic: The Major Participants in Translation

Which of the following is an intermediate in the reaction catalyzed by aminoacyl-tRNA synthetase?

A) B) C) D) E)

pyrophosphorylated 3 hydroxyl on the tRNA aminoacyl phosphate aminoacyl pyrophosphate aminoacyl adenylate none of the above

Answer: D Difficulty: 2

9)

Topic: The Major Participants in Translation

Which of the following explains how an aminoacyl-tRNA synthetase (AARS) recognizes the correct tRNA? A) B) C) D) E)

the AARS always recognizes the anticodon the AARS always recognizes elements of the acceptor stem the AARS always recognizes the size and sequence in the variable loop the AARS always recognizes elements in the D loop and TC loop the mechanism of AARS recognition varies from one enzyme to another

Answer: E Difficulty: 2

Topic: The Major Participants in Translation

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing

10) In an E. coli cell, what protein factor is responsible for attaching the initiator tRNA? A) B) C) D) E)

IF2 eIF2 eIF2B IF3 eIF5

Answer: A Difficulty: 1

Topic: The Major Participants in Translation

11) In a eukaryotic cell, what protein factor is responsible for delivering each aminoacyltRNA to the ribosome?

A) B) C) D) E)

EF-Tu EF-Ts eEF1 eEF1 eEF2

Answer: C Difficulty: 1

Topic: The Major Participants in Translation

12) In an E. coli cell, which of the following is the last item to be added to the 70S initiation complex?

A) B) C) D) E)

mRNA tRNA carrying formylmethionine 30S ribosomal subunit 50S ribosomal subunit initiation factors IF1, IF2 and IF3

Answer: D Difficulty: 2

Topic: Mechanism of Translation

4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing

13) What is the energy requirement for the formation of the 70S initiation complex?

A) B) C) D) E)

1 GTP 1 ATP 1 GTP and 1 ATP 2 GTP (from hydrolysis of 1 GTP to GMP) 2 ATP (from hydrolysis of 1 ATP to AMP)

Answer: A Difficulty: 2

Topic: Mechanism of Translation

14) What site is occupied by the tRNAfMet during intitiation?

A) B) C) D) E)

A site P site E site binds first to A site then moves to P site binds first to P site then moves to E site

Answer: B Difficulty: 2

Topic: Mechanism of Translation

15) EF-Tu binds to ______ then to _______. This complex binds to the _____ site of the ribosome.

A) B) C) D) E)

ATP; charged tRNA; P GTP; charged tRNA; A charged tRNA; ATP; A charged tRNA; GTP; P charged tRNA; GTP; A

Answer: B Difficulty: 2

Topic: Mechanism of Translation

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing

16) Which of the following correctly describes the formation of the peptide bond?

A) bond formation occurs while the tRNA in the P site moves to the E site, transferring the growing peptide chain to the tRNA that is moving from the A site to P site B) the growing peptide is transferred first to the 30S subunit of the ribosome, then to the aminoacyl tRNA in the A site C) bond formation occurs while transferring the growing peptide from the tRNA in the E site to the tRNA in the P site D) bond formation occurs while transferring the growing peptide from the tRNA in the P site to the tRNA in the A site E) none of the above Answer: D Difficulty: 2

Topic: Mechanism of Translation

17) Which of the bases present on the ribosome participates in the peptidyltransferase reaction?

A) B) C) D) E)

A C G T U

Answer: A Difficulty: 2

Topic: Mechanism of Translation

18) In prokaryotes, mRNA is ____________. In eukaryotes, mRNA is _____________.

A) B) C) D) E)

equally monocistronic and polycistronic; mostly monocistronic equally monocistronic and polycistronic; mostly polycistronic mostly monocistronic; equally monocistronic and polycistronic mostly polycistronic; equally monocistronic and polycistronic mostly polycistronic; mostly monocistronic

Answer: E Difficulty: 2

Topic: Translation in Eukaryotes

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing

19) Which of the following is a difference between prokaryotic and eukaryotic translation?

A) the genetic code is different B) prokaryotic ribosomes are free in the cytosol; eukaryotic chromosomes are always membrane bound C) eukaryotic translation requires more protein factors D) the ribosomes in prokaryotes are larger E) none of the above Answer: C Difficulty: 2

Topic: Translation in Eukaryotes

20) What mRNA modification, just 5 to the start codon, is used by the eukaryotic cell to enable location of the first AUG codon?

A) B) C) D) E)

a sequence of UAUAUA a short sequence that forms a hairpin loop a GC “box” that is recognized by eIFI a string of four to five O-methylguanine residues 7-methylguanine cap on the 5 end of the mRNA

Answer: E Difficulty: 2

Topic: Translation in Eukaryotes

21) What is a polyribosome?

A) B) C) D) E)

ribosomes that synthesize different subunits of the same protein several ribosomes all attached to the same mRNA ribosomes that are covalently bonded to each other in a polymer fashion a ribosome that only produces proteins that will be excreted by the cell none of the above

Answer: B Difficulty: 1

Topic: Rates and Energetics of Translation

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing

22) How many ATP equivalents are required to make a protein of 150 amino acids?

A) B) C) D) E)

150 300 450 600 none of the above

Answer: D Difficulty: 2

Topic: Rates and Energetics of Translation

23) Prokaryotic proteins that are destined for secretion often contain a sequence of ________ amino acids at the ___ -terminus of the protein A) B) C) D) E)

hydrophilic; N hydrophobic; N hydrophilic; C hydrophobic; C none of the above

Answer: B Difficulty: 2

Topic: The Final Stages in Protein Synthesis

24) What role do the Hsp70 proteins play in delivering proteins to their site of action such as the mitochondria?

A) B) C) D)

aids in proper folding to allow protein to properly traverse membranes prevents proteolysis of the unfolded protein keeps the protein in an unfolded state to allow transfer across membranes aids in formation of an intermediate folded protein that is present only during membrane transport E) none of the above

Answer: C Difficulty: 2

Topic: Protein Targeting in Eukaryotes

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing

25) Proteins destined for extracellular transport produce an N-terminal signal sequence. What binds to this sequence for endoplasmic reticulum association?

A) B) C) D) E)

signal recognition particle ribosome receptor protein Sec61 docking protein SNARE protein none of the above

Answer: A Difficulty: 2

Topic: Protein Targeting in Eukaryotes

26) During apoptosis, proteolysis is catalyzed by ______________ enzymes.

A) B) C) D) E)

ubiquitin autophagic lysosomal protease phagocytic protease HSP protease caspase

Answer: E Difficulty:

Topic: The Fate of Proteins

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 28: Information Decoding: Translation and Post-translational Protein Processing Short Answer Questions

1) Translate the following mRNA into a peptide using the standard genetic code: 5’-AUGCGGAUCCAUGUACAACUGGACGCAGUACCGUAACGCGAU-3’ Answer: Met-Arg-Ile-His-Val-Gln-Leu-Asp-Ala-Val-Pro

Difficulty: 1

Topic: The Genetic Code

2) Show the first step (of the four-step process) for removal of the intein from the following:

Answer:

Difficulty: 2

Topic: The Final Stages in Protein Synthesis

10 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression

Multiple Choice Questions 1)

What elements are contained within the promoter of the lactose operon?

A) B) C) D) E)

operator and CRP site operator and repressor CRP site and repressor operator, CRP site and repressor none of the above

Answer: A Difficulty: 2

2)

Topic: Regulation of Transcription in Bacteria

Which of the following is the true inducer that binds to the lac repressor in vivo?

A) B) C) D) E)

lactose glucose galactose isopropyl--thiogalactoside allolactose

Answer: E Difficulty: 1

3)

Topic: Regulation of Transcription in Bacteria

If both lactose and glucose are present in large amounts, which of the following scenarios would result?

A) B) C) D) E)

lac repressor bound to promoter, CRP bound to promoter, no lac operon transcription lac repressor bound to inducer, CRP bound to promoter, no lac operon transcription lac repressor bound to inducer, CRP bound to promoter, lac operon transcribed lac repressor bound to inducer, CRP not bound, no lac operon transcription lac repressor bound to inducer, CRP not bound, lac operon transcribed

Answer: D Difficulty: 3

Topic: Regulation of Transcription in Bacteria

1 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression

4)

What is thought to occur when CRP binds to DNA? A) B) C) D) E)

formation of a hairpin that prevents progression of RNA polymerase bending of DNA to facilitate RNA polymerase binding blocking of promoter regions to prevent binding of RNA polymerase forms non-covalent interactions with RNA polymerase to bind it to DNA none of the above

Answer: B Difficulty: 2

5)

Topic: Regulation of Transcription in Bacteria

Which of the following bacteriophage  proteins serves as both an activator and a repressor?

A) B) C) D) E)

cI cII cIII Cro N

Answer: A Difficulty: 1

6)

Topic: Regulation of Transcription in Bacteria

Bacteriophage  establishment of lysogeny in E. coli cells requires a high concentration of _____. This is achieved by the ____ protein binding to the PRE regulatory site.

A) B) C) D) E)

Cro; cI Cro; cII Cro; cIII cI; cII cI; cIII

Answer: D Difficulty: 2

Topic: Regulation of Transcription in Bacteria

2 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression

7)

When bacteriophage  lysogeny terminates and lytic growth in E. coli cells begins, ____ is inactivated leading to unoccupied OR sites. _____ is produced, ultimately resulting in DNA replication.

A) B) C) D) E)

Cro; cI cI; Cro cII; Cro cI; cII none of the above

Answer: B Difficulty: 2

8)

Topic: Regulation of Transcription in Bacteria

Which of the genes in the SOS regulon encodes a DNA polymerase?

A) B) C) D) E)

recA lexA uvrA uvrB dinA

Answer: E Difficulty: 2

9)

Topic: Regulation of Transcription in Bacteria

DNA damage that requires RecA to bind to a DNA gap activates proteolysis of _____, which then activates the transcription of genes within the SOS regulon.

A) B) C) D) E)

cI Cro LexA uvrA uvrB

Answer: C Difficulty: 2

Topic: Regulation of Transcription in Bacteria

3 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression

10) At the transcriptional level, how does tryptophan control the production of genes within the trp operon?

A) the trp repressor contains a high percentage of Trp residues and is thus only produced when Trp levels are high B) without sufficient Trp, the production of the trp repressor is truncated, thus producing a protein that cannot bind to the operon, ultimately resulting in structural gene expression C) high levels of Trp cause the repressor to be proteolytically digested D) the trp repressor binds to the operon only when bound to Trp E) none of the above Answer: D Difficulty: 2

Topic: Regulation of Transcription in Bacteria

11) Which of the following structural features of the trp leader sequence, trpL, explains why transcription of the full trp operon is prevented even when the repressor is not bound to the operon?

A) an A-rich region of the template strand acts as a factor-independent transcription terminator B) there is a stop codon present as the 15th codon of the trpL sequence C) the ribosome is stalled at two adjacent Trp codons under conditions where Trp is low D) a charged tRNATrp binds to one of the adjacent Trp codons to block ribosomal movement E) none of the above Answer: A Difficulty: 3

Topic: Regulation of Transcription in Bacteria

12) Which of the following accounts for the greater complexity in eukaryotic transcriptional control when compared with prokaryotic control?

A) B) C) D) E)

physical separation of transcription from translation the presence of chromatin instead of naked DNA the larger size of the chromosomes the presence of introns none of the above

Answer: B Difficulty: 1

Topic: Transcriptional Regulation in Eukaryotes 4 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression

13) In a histone protein, what modification to lysine marks the nucleosome as a transcription target?

A) B) C) D) E)

phosphorylation methylation ubiquitylation ADP-ribosylation acetylation

Answer: E Difficulty: 2

Topic: Transcriptional Regulation in Eukaryotes

14) Lysine methylation in a histone protein produces a form of chromatin known as ________ with the genes being transcriptionally __________.

A) B) C) D) E)

euchromatin; active euchromatin; inactive heterochromatin; active heterochromatin; inactive none of the above

Answer: D Difficulty: 2

Topic: Transcriptional Regulation in Eukaryotes

15) The bromodomain of nucleosome remodeling complexes binds to ____________ histones while the chromodomain binds to ___________ histones.

A) B) C) D) E)

acetylated; methylated acetylated; phosphorylated methylated; acetylated methylated; phosphorylated none of the above

Answer: A Difficulty: 2

Topic: Transcriptional Regulation in Eukaryotes

5 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression

16) The phosphorylation of several RNA polymerase II serine residues has been identified as a key event in eukaryotic translation initiation. Which of the following is one of the enzymes responsible for this phosphorylation?

A) B) C) D) E)

Mediator complex Rap1 TFIIH TATA box-binding protein ACT

Answer: C Difficulty: 2

Topic: Transcriptional Regulation in Eukaryotes

17) In prokaryotes, DNA methylation occurs on ______ while in eukaryotes, methylation occurs on _______.

A) B) C) D) E)

adenine; thymine adenine; cytosine guanine; adenine guanine; thymine guanine; cytosine

Answer: B Difficulty: 1

Topic: DNA Methylation, Gene Splicing and Epigenetics

18) DNA methylation in eukaryotes plays a role in ____________.

A) B) C) D) E)

methyl-directed mismatch repair protection of restriction sites chromatin remodeling cancerous cell growth gene silencing

Answer: E Difficulty: 2

Topic: DNA Methylation, Gene Splicing and Epigenetics

6 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression

19) On the polycistronic mRNA of bacteriophage MS2, the ability to translate multiple copies of the coat protein but only a single copy of the A protein is accomplished by _________.

A) B) C) D) E)

regulatory RNA molecules translational repression by protein binding to mRNA antisense RNA ribosome binding site occlusion none of the above

Answer: D Difficulty:

Topic: Regulation of Translation

20) A short RNA that is complimentary to a specific mRNA and used for inhibition of translation is called ______________.

A) B) C) D) E)

antisense RNA missense RNA nonsense RNA senseless RNA none of the above

Answer: A Difficulty: 1

Topic: Regulation of Translation

21) If an miRNA is completely complementary to an mRNA, what is the result of the pairing of these two molecules?

A) B) C) D) E)

rapid translation of the mRNA repeated translation as the miRNA prevents destruction of the mRNA slowed translation of the mRNA degradation of the mRNA none of the above

Answer: D Difficulty: 2

Topic: RNA Interference

7 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression

22) An mRNA whose translation is controlled by binding of a metabolic end product such as flavin adenine dinucleotide or adenosylcobalamin is called a____________.

A) B) C) D) E)

ribozyme miRNA riboswitch regulatory RNA none of the above

Answer: C Difficulty: 1

Topic: Riboswitches

8 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression Short Answer Questions

1) Show how glutamine interacts with an A-T base pair as seen in the cI and Cro repressors.

Answer:

Difficulty: 3

Topic: Regulation of Transcription in Bacteria

2) Design an antisense RNA that prevents the start of translation for any mRNA in an E. coli cell.

Answer: In order to prevent the start of translation, the most effective mechanism would be an antisense RNA for the Shine-Dalgarno sequence (which is the sequence found on the 16S ribosomal RNA): 5’-ACCUCCUUA-3’.

Difficulty: 3

Topic: Regulation of Translation

9 .

Mathews, van Holde, Appling, and Anthony-Cahill, Biochemistry 4th edition Chapter 29: Regulation of Gene Expression

3) Give the sequence and draw the first two residues of a morpholino oligo that would serve as an antisense RNA for the following mRNA sequence (you may use the letter A, C, G and U to denote the bases): 5’-CAUGUCC-3’ Answer: 5’-GGACAUG-5’

Difficulty: 3

Topic: Regulation of Translation

10 .