BioChem Exam 3 PP

What reaction serves to link glycolysis and the citric acid cycle, and what is the enzyme that catalyzes the reaction?

The pyruvate dehydrogenase complex links glycolysis and the citric acid cycle by converting pyruvate into acetyl-CoA.

(Textbook Answer)The pyruvate dehydrogenase complex catalyzes the following reaction, linking glycolysis and citric acid cycle:
Pyruvate+CoA+NAD+ → acetyl CoA + NADH + H+ + CO2

The conversion of pyruvate into acetyl CoA consists of three steps. What are these steps?

Decarboxylation, oxidation, and transfer of the resultant acetyl group to CoA.

The conversion of pyruvate into acetyl CoA commits the carbon atoms to either of two principal fates. What are the fates?

Oxidation to CO2 by the citric acid cycle or incorporation into lipids.

What coenzymes are required by the pyruvate dehydrogenase complex, and what are their roles? 6

Thiamine pyrophosphate plays a role in the decarboxylation of pyruvate. Lipoic acid (as lipoamide) transfers the acetyl group. Coenzyme A accepts the acetyl group from lipoic acid to form acetyl CoA. FAD accepts the electrons and hydrogen ions when oxidized lipoic acid is reduced. NAD+ accepts electrons and a proton from FADH2

Distinguish between catalytic coenzymes and stoichiometric coenzymes in the pyruvate dehydrogenase complex.7

Catalytic coenzymes (TPP, lipoic acid, and FAD) are modified but regenerated in each reaction cycle. Thus, they can play a catalytic role in the processing of many molecules of pyruvate. Stoichiometric coenzymes (coenzyme A and NAD+) are used in only one reaction because they are the components of products of the reaction.

Which of the following is not a component of the citric acid cycle?

propionyl CoA

Distinguish between an oxidizing agent and a reducing agent.

An oxidizing agent, or oxidant, accepts electrons in oxidation–reduction reactions. A reducing reagent, or reductant, donates electrons in such reactions.

Explain why coenzyme Q is an effective mobile electron carrier in the electron-transport chain.

Coenzyme Q is an effective mobile electron carrier because its long tail makes it dissolve well in the inner mitochondrial membrane, which is fatty. It can also carry two electrons and two protons by switching between two forms—quinone (empty) and quinol (loaded)

(Textbook Answer): The 10 isoprene units render coenzyme Q soluble in the hydrophobic environment of the inner mitochondrial membrane. The two oxygen atoms can reversibly bind two electrons and two protons as the molecule transitions between the quinone form and the quinol form.

What is the yield of ATP when each of the following substrates is completely oxidized to CO2 by a mammalian cell homogenate (p. 77)? Assume that glycolysis, the citric acid cycle, and oxidative phosphorylation are fully active.

a. Pyruvate

b. Lactate

c. Fructose 1,6-bisphosphate

d. Phosphoenolpyruvate

e. Galactose

f. Dihydroxyacetone phosphate

a. 12.5;

b. 14;

c. 32;

d. 13.5;

e. 30;

f. 16

What is the effect of each of the following inhibitors on electron transport and ATP formation by the respiratory chain?

a. Azide

b. Atractyloside

c. Rotenone

d. DNP

e. Carbon monoxide

f. Antimycin A

a. Azide blocks electron transport and proton pumping at Complex IV.

b. Atractyloside blocks electron transport and ATP synthesis by inhibiting the exchange of ATP and ADP across the inner mitochondrial membrane.

c. Rotenone blocks electron transport and proton pumping at Complex I.

d. DNP blocks ATP synthesis without inhibiting electron transport by dissipating the proton gradient.

e. Carbon monoxide blocks electron transport and proton pumping at Complex IV.

f. Antimycin A blocks electron transport and proton pumping at Complex III.

Which of the following is not a component of the pentose phosphate pathway?

Phosphoenolpyruvate

Which of the following enzymes is the regulatory enzyme in the pentose phosphate pathway?

Glucose 6-phosphate dehydrogenase

a. Identify ‐‐6-phosphglucono‐𝛿‐lactone. 3

b. Which reactions produce NADPH?

c. Identify ribulose 5-phosphate.

d. What reaction generates CO2?

e. Identify 6-phosphogluconate.
f. Which reaction is catalyzed by phosphopentose isomerase?

g. Identify ribose 5-phosphate.

h. Which reaction is catalyzed by lactonase?

i. Identify glucose 6-phosphate.

j. Which reaction is catalyzed by 6-phosphogluconate dehydrogenase?

k. Which reaction is catalyzed by glucose 6-phosphate dehydrogenase?

a. C
b. B and F
c. G
d. F
e. E
f. H
g. I
h. D
i. A
j. F
k. B

The pentose phosphate pathway is composed of two distinct phases. What are the two phases, and what are their roles?

The oxidative phase generates NADPH and is irreversible. The nonoxidative phase allows for the interconversion of phosphorylated sugars.

What is the key regulatory enzyme in the pentose phosphate pathway, and what is its most prominent regulatory signal?

Glucose 6-phosphate dehydrogenase; NADP+ concentration.

Glucose is normally completely oxidized to CO2 in the mitochondria. Under what circumstance can glucose be completely oxidized to CO2 in the cytoplasm?

When much NADPH is required. The oxidative phase of the pentose phosphate pathway is followed by the nonoxidative phase. The resulting fructose 6-phosphate and glyceraldehyde 3-phosphate are used to generate glucose 6-phosphate through gluconeogenesis, and the cycle is repeated until the equivalent of one glucose molecule is oxidized to CO2

A “t” instead of an “s”? Differentiate between a nucleoside and a nucleotide.

A nucleoside is a base attached to a ribose sugar. A nucleotide is a nucleoside with one or more phosphoryl groups attached to the ribose.

What is a Watson–Crick base pair?

Hydrogen-bond pairing between the base A and the base T as well as hydrogen-bond pairing between the base G and the base C in DNA.

Why are GC and AT the only base pairs permissible in the double helix?

Two purines are too large to fit inside the double helix, and two pyrimidines are too small to form base pairs with each other.

Write the complementary sequence (in the standard

5′ →3′ notation) for (a) GATCAA, (b) TCGAAC, (c) ACGCGT, and (d) TACCAT.

a. TTGATC;

b. GTTCGA;

c. ACGCGT;

d. ATGGTA

Define template and primer as they relate to DNA synthesis. 1

A template is the sequence of DNA or RNA that directs the synthesis of a complementary sequence. A primer is the initial segment of a polymer that is to be extended on which elongation depends.

Explain why DNA synthesis depends on RNA synthesis.

DNA polymerase cannot initiate primer synthesis. Consequently, an RNA polymerase, called primase, synthesizes a short sequence of RNA that is used as a primer by the DNA polymerase.

What are Okazaki fragments?

Okazaki fragments are short segments of DNA that are synthesized on the lagging stand of DNA. These fragments are subsequently joined by DNA ligase to form a continuous segment of DNA.

Distinguish between the leading and the lagging strands in DNA synthesis.

When DNA is being synthesized at the replication fork, the leading strand is synthesized continuously in the 5-to-3′ direction as the template is read in the 3′-to-5′ direction. The lagging strand is synthesized as short Okazaki fragments.

Explain, on the basis of nucleotide structure, why DNA synthesis proceeds in the 5-to-3 direction 6

The nucleotides used for DNA synthesis have the triphosphate attached to the 5′-hydroxyl group with free 3′-hydroxylgroups. Such nucleotides can be utilized only for 5-to-3′ DNA synthesis.

For long double-stranded DNA molecules, the rate of spontaneous strand separation is negligibly low under physiological conditions despite the fact that only weak reversible bonds hold the strands together. Explain.

The rate of strand separation is low owing to the hydrogen bonds of the helix and the stacking forces between bases. Although individually weak, the thousands or millions of such bonds that hold a helix together make spontaneous separation of the strands unlikely.