Biochemistry

Reginald H. Garrett, Charles M. Grisham

Chapter 25

Nitrogen Acquisition and Amino Acid Metabolism - all with Video Answers

Educators

Chapter Questions

Problem 1

What is the oxidation number of $\mathrm{N}$ in nitrate, nitrite, $\mathrm{NO}, \mathrm{N}_{2} \mathrm{O},$ and $\mathrm{N}_{2} ?$

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Problem 2

How many ATP equivalents are consumed per N atom of ammonium formed by (a) the nitrate assimilation pathway and (b) the nitrogen fixation pathway? (Assume for this problem NADH, NADPH, and reduced ferredoxin are each worth 3 ATPs.

Carlene Jimenez

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Problem 3

Suppose at certain specific metabolite concentrations in vivo the cyclic cascade regulating $E$ coli glutamine synthetase has reached a dynamic equilibrium where the average state of GS adenylylation is poised at $n=6 .$ Predict what change in $n$ will occur if:
a. $[\mathrm{ATP}]$ increases
b. $P_{11} / P_{110}$ increases
c. $[\alpha-\mathrm{KG}] / \mathrm{Gln}]$ increases
d. $\left[P_{i}\right]$ decreases.

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Problem 4

How many ATP equivalents are consumed in the production of 1 equivalent of urea by the urea cycle?

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Problem 5

Why are persons on a high-protein diet (such as the Atkins diet) advised to drink lots of water?

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Problem 6

How many ATP equivalents are consumed in the biosynthesis of lysine from aspartate by the pathway shown in Figure $25.27 ?$

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Problem 7

If PEP labeled with $^{14} \mathrm{C}$ in the 2 -position serves as the precursor to chorismate synthesis, which $C$ atom in chorismate is radioactive?

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Problem 8

(Integrates with Chapter $22 .$ ) Write a balanced equation for the synthesis of glucose (by gluconeogenesis) from aspartate.

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Problem 9

For each of the 20 common amino acids, give the name of the enzyme that catalyzes the reaction providing its $\alpha$ -amino group.

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Problem 10

Which vitamin is central in amino acid metabolism? Why?

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Problem 11

Vitamins $\mathrm{B}_{6}, \mathrm{B}_{12},$ and folate may be recommended for individuals with high blood serum levels of homocysteine (a condition called hyperhomocysteinemia). How might these vitamins ameliorate hyperhomocysteinemia?

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Problem 12

(Integrates with Chapter $19 .$ ) On the basis of the following information, predict a reaction mechanism for the mammalian branched-chain $\alpha$ -keto acid dehydrogenase complex (the BCKAD complex - This complex carrics out the oxidative decarboxylation of the $\alpha$ -keto acids derived from valine, leucine, and isoleucine.
a. One form of maple syrup urine disease responds well to administration of thiamine.
b. Lipoic acid is an essential coenzyme.
c. The enzyme complex contains a flavoprotein.

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Problem 13

People with phenylketonuria must avoid foods containing the low-calorie sweetener Aspartame also known as NutraSweet. Find the structure of $A$spartame in the Merck Index (or other scientific source), and state why these people must avoid this substance.

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Problem 14

Glyphosate (otherwise known as RoundUp ) is an analog of PEP. It acts as a noncompetitive inhibitor of 3 -enolpyruvylshikimate- 5 -P synthase; it has the following structure in its fully protonated state:
\[
\mathrm{HOOC}-\mathrm{CH}_{2}-\mathrm{NH}-\mathrm{CH}_{2}-\mathrm{PO}_{3} \mathrm{H}_{2}
\]
Consult Figures 25.35 and $25.36,$ and construct a list of the diverse metabolic consequences that might be experienced by a plant cell exposed to glyphosate.

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Problem 15

(Integrates with Chapter 18 .) When cells convert glucose to glycine, which carbon atoms of glucose are represented in glycine?

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Problem 16

Although serine is a nonessential amino acid, serine deficiency syndrome has been observed in humans One such form of the syndrome is traceable to a deficiency in 3-phosphoglycerate dehydrogenase (see Figure 25.31). Individuals with this syndrome not only are serine-deficient but also are impaired in their ability to synthesize another common amino acid, as well as a class of lipids. Describe why.

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Problem 17

Go to www.pdb,org, and examine the pdb file 1 LM 1 for glutamate synthase. Find its iron-sulfur cluster and FMN prosthetic group. Discover how this enzyme is organized into an N-terminal domain that functions in ammonia removal from glutamine (the glutaminase domain) and the $\alpha$ -ketoglutarate-binding site near the Fe/S and flavin prosthetic groups, Consult van den Heuvel, R. H. H., et al., 2002. Structural studies on the synchronization of catalytic centers in glutamate synthase. Journal of Biological Chemistry $277: 24579-24583,$ to see how these two sites are connected by a tunnel for passage of ammonia from glutamine to $\alpha$ -ketoglutarate.

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Problem 18

The thermic effect of food is a term used to describe the energy cost of processing the food we eat, digesting it, and either turning it into precursors for needed biosynthesis, usable energy in the form of ATP, or storing the excess intake as fat. The thermic effect is usually approximated at $10 \%$ of the total calories consumed, but the thermic effect of fat is only $2 \%$ to $3 \%$ of total fat calories and the thermic effect of protein is $30 \%$ or more of calories consumed as protein. Why do you suppose dietary protein has a much higher thermic effect than either dietary carbohydrate or fat?

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Problem 19

From the dodecameric $\left(\alpha_{12}\right)$ structure of glutamine synthetase shown in Figure 25.14 , predict the relative enzymatic activity of GS monomers (isolated $\alpha$ -subunits).

Carlene Jimenez

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Problem 20

Consider the synthesis and degradation of tyrosine as shown in Figures $25.37,25.38,$ and 25.48 to determine where the carbon atoms in PEP and erythrose- 4 -P would end up in acetoacetate and fumarate.

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Problem 21

Examine the ActiveModel for glutamine synthetase, and describe the formation of the GS dodecamer.

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Problem 22

Using the ActiveModel for glutamate oxaloacetate transaminase 1 explain how this enzyme accomplishes a "ping-pong" mechanism for its catalyzed reaction.

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Carlene Jimenez

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