Biochemistry

Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto, Jr, Lubert Stryer

Chapter 24

The Biosynthesis of Amino Acids - all with Video Answers

Educators

Chapter Questions

Problem 1

Define nitrogen fixation. What organisms are capable of nitrogen fixation?

Madi Sousa

Madi Sousa

Numerade Educator

Problem 2

Match each term with its description.
(a) Nitrogen fixation_____
(b) Nitrogenase complex_____
(c) Glutamate_____
(d) Essential amino acids_____
(e) Nonessential amino acids_____
(f) Aminotransferase_____
(g) Pyridoxal phosphate_____
(h) Tetrahydrofolate_____
(i) S-Adenosylmethionine_____
(j) Homocysteine_____
1. Methylated to form methionine
2. An important methyl donor
3. Coenzyme required by aminotransferases
4. Conversion of $\mathrm{N}_{2}$ into $\mathrm{NH}_{3}$
5. A carrier of various one-carbon units
6. Amino acids that are dietary requirements
7. Amino acids that are readily synthesized
8. Responsible for nitrogen fixation
9. Transfers amino groups between keto acids
10. A common amino group donor

Lottie Adams

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Problem 3

Identify the two components of the nitrogenase complex and describe their specific tasks.

Madi Sousa

Numerade Educator

Problem 4

"The mechanistic complexity of nitrogenase is necessary because nitrogen fixation is a thermodynamically unfavorable process." True or false? Explain.

Madi Sousa

Numerade Educator

Problem 5

Nitrogen-fixing bacteria on the roots of some plants can consume as much as $20 \%$ of the ATP produced by their host - consumption that does not seem very beneficial to the plant. Explain why this loss of valuable resources is tolerated and what the bacteria are doing with the ATP.

Sana Riaz

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Problem 6

What are the seven precursors of the 20 amino acids?

Madi Sousa

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Problem 7

Why are certain amino acids defined as essential for human beings?

Madi Sousa

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Problem 8

Write a balanced equation for the synthesis of alanine from glucose.

Madi Sousa

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Problem 9

What are the intermediates in the flow of nitrogen from $\mathrm{N}_{2}$ to heme?

Madi Sousa

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Problem 10

What cofactor is required by all aminotransferases?

Madi Sousa

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Problem 11

In this chapter, we considered three different cofactors/cosubstrates that act as carriers of onecarbon units. Name them.

Madi Sousa

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Problem 12

Which derivative of folate is a reactant in the conversion of (a) glycine into serine? (b) homocysteine into methionine?

Madi Sousa

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Problem 13

In the reaction catalyzed by glutamine synthetase, an oxygen atom is transferred from the side chain of glutamate to orthophosphate, as shown by the results of $^{18}$ O-labeling studies. Account for this finding.

Madi Sousa

Numerade Educator

Problem 14

In contrast to the production of glutamine by glutamine synthetase (problem 13 ), the generation of asparagine from $^{18}$ O-labeled aspartate does not result in the transfer of an $^{18} \mathrm{O}$ atom to orthophosphate. In what molecule do you expect to find one of the $^{18} \mathrm{O}$ atoms?

Madi Sousa

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Problem 15

Isovaleric acidemia is an inherited disorder of leucine metabolism caused by a deficiency of isovaleryl CoA dehydrogenase. Many infants having this disease die in the first month of life. The administration of large amounts of glycine sometimes leads to marked clinical improvement. Propose a mechanism for the therapeutic action of glycine.

Madi Sousa

Numerade Educator

Problem 16

The atoms from tryptophan shaded below are derived from two other amino acids. Name them. (FIGURE CAN'T COPY)

Madi Sousa

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Problem 17

Blue-green algae (cyanobacteria) form heterocysts when deprived of ammonia and nitrate. In this form, the cyanobacteria lack nuclei and are attached to adjacent vegetative cells. Heterocysts have photosystem I activity but are entirely devoid of photosystem II activity. What is their role?

Madi Sousa

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Problem 18

Most cytoplasmic proteins lack disulfide bonds, whereas extracellular proteins usually contain them. Why?

Madi Sousa

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Problem 19

Suppose that aspartate aminotransferase were chemically synthesized with the use of D-amino acids only. What products would you expect if this mirror-image enzyme were treated with (a) L-aspartate and $\alpha$ -ketoglutarate; (b) D-aspartate and $\alpha$ -ketoglutarate?

Madi Sousa

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Problem 20

The synthesis of $\delta$ -aminolevulinate takes place in the mitochondrial matrix, whereas the formation of porphobilinogen takes place in the cytoplasm. Propose a reason for the mitochondrial location of the first step in heme synthesis.

Madi Sousa

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Problem 21

Which of the 20 amino acids can be synthesized directly from a common metabolic intermediate by a transamination reaction?

Madi Sousa

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Problem 22

Certain species of bacteria possess an enzyme, ornithine cyclodeaminase, that can catalyze the conversion of L-ornithine into L-proline in a single catalytic cycle. (FIGURE CAN'T COPY) The enzyme lysine cyclodeaminase has also been identified. Predict the product of the reaction catalyzed by lysine cyclodeaminase.

Madi Sousa

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Problem 23

For the following example of a branched pathway, propose a feedback inhibition scheme that would result in the production of equal amounts of Y and Z. (FIGURE CAN'T COPY)

Madi Sousa

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Problem 24

Consider the branched pathway in Problem $23 .$ The first common step $(\mathrm{A} \rightarrow \mathrm{B})$ is partly inhibited by both of the final products, each acting independently of the other. Suppose that a high level of Y alone decreased the rate of the $A \rightarrow B$ step from 100 to $60 \mathrm{s}^{-1}$ and that a high level of Z alone decreased the rate from 100 to $40 \mathrm{s}^{-1}$. What would the rate be in the presence of high levels of both Y and Z?

Madi Sousa

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Problem 25

Free sulfhydryl groups can be alkylated with 2 -bromoethylamine to the corresponding thioether. (FIGURE CAN'T COPY) Researchers prepared a mutant form of aspartate aminotransferase in which lysine 258 was replaced by cysteine (Lys258Cys). This mutant protein has no observable catalytic activity. However, treatment of Lys258Cys with 2-bromoethylamine yielded a protein with $\sim 7 \%$ activity relative to the wild-type enzyme. Explain why alkylation recovered some enzyme activity.

Madi Sousa

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Problem 26

Propose a mechanism for the conversion of S-adenosylmethionine into 1 -aminocyclopropane1-carboxylate (ACC) by ACC synthase, a PLP enzyme. What is the other product?

Madi Sousa

Numerade Educator

Problem 27

Brain tissue contains substantial amounts of D-serine, which acts as a neurotransmitter. D-serine is generated from L-serine by serine racemase, a PLP enzyme. Propose a mechanism for the interconversion of L- and D-serine. What is the equilibrium constant for the reaction L-serine $\rightleftharpoons$ D-serine?

Madi Sousa

Numerade Educator

Problem 28

Elongation factor-2 (eEF-2), a protein taking part in translation, contains a histidine residue that is modified posttranslationally in several steps to a complex side chain known as diphthamide. An intermediate along this pathway is referred to as diphthine.
(a) Labeling experiments indicate that the diphthine intermediate is formed by the modification of histidine with four molecules of S-adenosylmethionine (indicated by the four colors). Propose a mechanism for the formation of diphthine.
(b) The final conversion of diphthine into diphthamide is known to be ATP dependent. Propose two possible mechanisms for the final amidation step.
(FIGURE CAN'T COPY)

Madi Sousa

Numerade Educator

Problem 29

In this chapter, we considered three different cofactors/cosubstrates that act as carriers of one-carbon units (problem 11 ). Now, name another carrier of one carbon units that we have encountered previously.

Bobby Barnes

University of North Texas

Problem 30

How might increased synthesis of aspartate and glutamate affect energy production in a cell? How would the cell respond to such an effect?

Madi Sousa

Numerade Educator

Problem 31

Suppose that a mutation in bacteria resulted in the diminished activity of methionine adenosyltransferase, the enzyme responsible for the synthesis of SAM from methionine and ATP. Predict how this diminished activity might affect the stability of the mutated bacteria's DNA.

Madi Sousa

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Problem 32

Shemin and coworkers used acetatelabeling experiments to conclude that succinyl-CoA is a key intermediate in the biosynthesis of heme. Identify the intermediates in the conversion of acetate into succinyl-CoA.

Madi Sousa

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Problem 33

Glutamate dehydrogenase (p. 717 ) and glutamine synthetase (p. 717 ) are present in all organisms. Most prokaryotes also contain another enzyme, glutamate synthase, which catalyzes the reductive amination of $\alpha$ -ketoglutarate with the use of glutamine as the nitrogen donor. $\alpha$ -Ketoglutarate $+$ glutamine $+\mathrm{NADPH}+\mathrm{H}^{+}$ $$\rightleftharpoons2 \text { glutamate }+\mathrm{NADP}^{+}$$
The side-chain amide of glutamine is hydrolyzed to generate ammonia within the enzyme. When $\mathrm{NH}_{4}^{+}$ is limiting, most of the glutamate is made by the sequential action of glutamine synthetase and glutamate synthase. The sum of these reactions is $$\begin{array}{r}
\mathrm{NH}_{4}^{+}+\alpha \text { -ketoglutarate }+\mathrm{NADPH}+\mathrm{ATP} \longrightarrow \\
\text { glutamate }+\mathrm{NADP}^{+}+\mathrm{ADP}+\mathrm{P}_{\mathrm{i}}
\end{array}$$ Note that this stoichiometry differs from that of the glutamate dehydrogenase reaction in that ATP is hydrolyzed. Why do prokaryotes sometimes use this more-expensive pathway? (Hint: The $K_{\mathrm{M}}$ value for $\mathrm{NH}_{4}^{+}$ of glutamate dehydrogenase is higher than that of glutamine synthase.)

Carlene Jimenez

Carlene Jimenez

Numerade Educator

Problem 34

The adjoining graph shows the concentration of several free amino acids in light- and dark-adapted plants.
(FIGURE CAN'T COPY)
(a) Of the amino acids shown, which are most affected by light-dark adaptation?
(b) Suggest a plausible biochemical explanation for the difference observed.
(c) White asparagus, a culinary delicacy, is the result of growing asparagus plants in the dark. What chemical might you think enhances the taste of white asparagus?

Ramesh Singh

Numerade Educator