Biochemistry Practice Problems III with Answers

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A series of biochemistry practice problems with answers about cellular respiration, redox reactions, thermodynamics, glycolysis, gluconeogenic pathways, glycogen, the TCA cycle.

Question 1

Write a complete balanced redox reaction, wherein electron(s) are transferred between Coenzyme Q and lipoic/dihydrolipoic acid, that would occur spontaneously in the forward direction.  Be sure to clearly indicate the states of all species on the reactant and product sides:  ubiquinone or ubiquinol;  lipoic acid or dihydrolipoic acid.

Question 2

For the forward reaction that you’ve written, which species is acting as the oxidizing agent?

  • ubiquinone
  • ubiquinol
  • lipoic acid
  • dihydrolipoic acid

Question 3

For the forward reaction that you’ve written, which species is acting as the reducing agent?

  • ubiquinone
  • ubiquinol
  • lipoic acid
  • dihydrolipoic acid

Question 4

(A)  Write the half-reaction involving ubiquinone.

(B)  For the overall redox reaction you’ve written (Question #1), would this half-reaction occur as an oxidation or a reduction?

(C)  What is the value (in volts) of the standard reduction potential for this half-reaction?

Question 5

(A)  Write the half-reaction involving lipoic acid.

(B)  For the overall redox reaction you’ve written (Question #1), would this half-reaction occur as an oxidation or a reduction?

(C)  What is the value (in volts) of the standard reduction potential for this half-reaction?

Question 6

Calculate ΔE’° for the overall redox reaction (from Question #1).

Question 7

Does your calculated ΔE’° value (Question #6) support your contention that the overall redox reaction (Question #1) would be spontaneous in the forward direction?

Question 8

(A)  Calculate ΔG’° for the overall redox reaction.

(B)  Under standard biochemical conditions, is this reaction endergonic or exergonic?

Question 9

Calculate K’eq for the overall redox reaction. Assume 25°C.

Question 10

Calculate the actual free energy change, ΔG, if this redox reaction occurred within our cells (body temperature of 37°C) and typical cellular concentrations were as follows:
[ubiquinone] = 1.2 mM
[ubiquinol] = 5.3 mM
[lipoic acid] = 7.9 mM
[dihydrolipoic acid] = 2.5 mM

Question 11

Calculate the actual change in potential, ΔE, if this redox reaction occurred within our cells (see conditions in Question #10).

Question 12

(A)  Calculate the enthalpy change (ΔH) associated with this redox reaction, assuming the conditions outlined in Question #10 and an entropy change (ΔS) of +0.8 kJ/mol∙K.

(B)  Is this reaction favored or opposed?

Question 13

When one glucose molecule enters the glycolytic pathway, two molecules of pyruvate are created.  This change in stoichiometry is ultimately due to the actions of:

Question 14

The steps of glycolysis between glyceraldehyde 3-phosphate and 3-phosphoglycerate involve which process?

  • ATP hydrolysis
  • oxidative (respiration-linked) phosphorylation
  • substrate-level phosphorylation
  • biological redox (oxidation/reduction)
  • the harnessing of free energy in the form of universal reducing equivalents

Question 15

The conversion of 2 moles of pyruvate to 1 mole of glucose by the gluconeogenic pathway results in a net consumption of:

  • 2 moles of ATP.
  • 4 moles of ATP.
  • 2 moles of GTP.
  • 2 moles of NADH.
  • 4 moles of NADH.

Question 16

Which causes activation (or upregulation) of glycogen synthase?

  • Binding of glucose-6-phosphate
  • Dephosphorylation of multiple residues by phosphoprotein phosphorylase-1 (PP1)
  • Phosphorylation of specific residues by casein kinase II (CKII)
  • Phosphorylation of specific residues by glycogen synthase kinase-3 (GSK-3)
  • The presence of glucagon

Question 17

Describe Glycogenin.

  • catalyzes the conversion of starch into glycogen.
  • is the enzyme responsible for forming branches in glycogen.
  • is the gene that encodes glycogen synthase.
  • is the primer on which new glycogen chains are initiated.
  • regulates the synthesis of glycogen.

Question 18

The enzyme 6-phosphogluconate dehydrogenase catalyzes:

  • catalyzes one step within the glycolytic pathway.
  • catalyzes one step within the gluconeogenic pathway.
  • catalyzes one step within the pentose phosphate pathway.
  • catalyzes the conversion of 6-phosphogluconate to ribulose 5-phosphate.
  • catalyzes a redox reaction.

Question 19

Which is true of the reaction catalyzed by the PDH (pyruvate dehydrogenase) complex?

  • biotin participates in the decarboxylation
  • the reaction occurs in the intermembrane space of the mitochondria
  • both NAD and flavin nucleotide act as electron carriers
  • two different cofactors containing -SH groups participate
  • pyruvate gets decarboxylated as well as reduced

Question 20

The conversion of 1 mole pyruvate to 3 moles CO2, via the PDH complex and the citric acid cycle, also yields ___________  mole(s) of NADH, ___________mole(s) of FADH2, and ___________mole(s) of ATP (or GTP).

Question 21

In mammals, the following occurs during the citric acid cycle (select any/all answers that apply):

  • metabolism of acetate to carbon dioxide
  • formation of malate
  • “substrate-channeling” through the α-ketoglutarate dehydrogenase complex
  • oxidation of NAD and FAD
  • reduction of acetyl-CoA

 

Question 22

Under typical cellular conditions, Step #8 of the TCA cycle (the malate dehydrogenase reaction) is driven to the right primarily by:

  • low malate concentrations.
  • the highly exergonic reaction catalyzed by malate dehydrogenase.
  • the highly exergonic fumarase reaction which keeps malate concentrations very high.
  • the higher electron affinity of NAD+ as compared to malate.
  • the highly exergonic citrate synthase reaction which keeps oxaloacetate concentrations very low.

Question 23

Citrate synthase and the NAD+-specific isocitrate dehydrogenase are two key regulatory enzymes of the citric acid cycle. These enzymes are inhibited by:

  • AMP and/or NADH
  • ATP and/or NADH
  • ATP and/or NAD+
  • AMP and/or NAD+
  • acetyl-CoA and fructose 6-phosphate

Question 24

Which of the steps of the TCA cycle generates universal reducing equivalent(s) as a product of the reaction?

  • the step catalyzed by citrate synthase
  • at least one of the steps catalyzed by aconitase
  • the step catalyzed by isocitrate dehydrogenase
  • the step catalyzed by the α-ketoglutarate dehydrogenase complex
  • the step catalyzed by succinate dehydrogenase

Question 25

Rank the following redox-active coenzymes and prosthetic groups of the electron-transport chain by relative electron affinity (greatest e- affinity at the top and least e- affinity at the bottom). FMN, cytochrome a3, O2, ubiquinone, cytochrome a

Question 26

Which of the inner mitochondrial membrane complexes directly transforms electron movements into the movement of protons (H+) from the matrix to the intermembrane space?

  • Complex I
  • Complex II
  • Coenzyme Q
  • Complex III
  • Complex IV

Question 27

The final electron acceptor in the mitochondrial electron transport chain is:

  • cytochrome c
  • CO2
  • O2
  • FoF1 ATP synthase
  • water

Question 28

Under normal cellular conditions, the FoF1 complex of the inner mitochondrial membrane functions to create new ATP. Under non-physiologic experimental conditions, isolated FoF1 complex can be driven in reverse as long as [ATP] is high. Which of the following would be true under such conditions? Choose any/all answers that apply.

  • The FoF1 complex would be operating as an ATPase rather than an ATP synthase.
  • The FoF1 complex would be driving net H+ movement from the matrix side to the IMS (intermembrane space) side.
  • The FoF1 complex would create more ATP, per unit time, than it does under physiological conditions.
  • As the experiment continues, we would expect to see higher & higher concentrations of ADP.
  • The FoF1 complex would effectively be operating as a proton pump.