Out of thin air. Define nitrogen fixation. What organisms are capable of nitrogen fixation?

Like Trinidad and Tobago. Match each term with its description.

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

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

Siphoning resources. 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.

From few, many. What are the seven precursors of the 20 amino acids?

Vital, in the truest sense. Why are certain amino acids defined as essential for human beings?

From sugar to amino acid. Write a balanced equation for the synthesis of alanine from glucose.

From air to blood. What are the intermediates in the flow of nitrogen from N₂ to heme?

Common component. What cofactor is required by all aminotransferases?

Here, hold this. In this chapter, we considered three different cofactors/cosubstrates that act as carriers of one-carbon units. Name them.

One-carbon transfers. Which derivative of folate is a reactant in the conversion of (a) glycine into serine? (b) homocysteine into methionine?

Telltale tag. 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 ¹⁸O-labeling studies. Account for this finding.

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

Therapeutic glycine. 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.

Lending a hand. The atoms from tryptophan shaded below are derived from two other amino acids. Name them.

Deprived bacteria. 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?

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

Through the looking-glass. 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 α-ketoglutarate; (b) d-aspartate and α-ketoglutarate?

To and fro. The synthesis of δ-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.

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

Alternative route to proline. 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.

The enzyme lysine cyclodeaminase has also been identified. Predict the product of the reaction catalyzed by lysine cyclodeaminase.

Lines of communication. 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.

Cumulative feedback inhibition. Consider the branched pathway in Problem 23. The first common step (A → 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 → B step from 100 to 60 s⁻¹ and that a high level of Z alone decreased the rate from 100 to 40 s⁻¹. What would the rate be in the presence of high levels of both Y and Z?

Recovered activity. Free sulfhydryl groups can be alkylated with 2-bromoethylamine to the corresponding thioether.

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 ∼7% activity relative to the wild-type enzyme. Explain why alkylation recovered some enzyme activity.

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

Mirror-image serine. 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 ?

An unusual amino acid. 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.

Here, hold this again. 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.

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

Protection required. Suppose that a mutation in bacteria resulted in the diminished activity of methionine adenosyl-transferase, 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.

Heme biosynthesis. Shemin and coworkers used acetate-labeling 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.

Comparing K_M. Glutamate dehydrogenase and glutamine synthetase are present in all organisms. Most prokaryotes also contain another enzyme, glutamate synthase, which catalyzes the reductive amination of α-ketoglutarate with the use of glutamine as the nitrogen donor.

The side-chain amide of glutamine is hydrolyzed to generate ammonia within the enzyme. When NH₄⁺ is limiting, most of the glutamate is made by the sequential action of glutamine synthetase and glutamate synthase. The sum of these reactions is

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_M value for NH₄⁺ of glutamate dehydrogenase is higher than that of glutamine synthase.)

Light effects. The adjoining graph shows the concentration of several free amino acids in light- and dark-adapted plants.