Biochemistry: Chapter 18

The mitochondrial form of carbamoyl phosphate synthetase is allosterically activated by N-acetylglutamate. Briefly describe a rationale for this effect. Drag the terms on the left to the appropriate blanks on the right to complete the sentences.

1. N-Acetylglutamate is AN INTERMEDIATE in ornithine biosynthesis. Activity of the urea cycle requires both ornithine and carbamoyl phosphate. 2. If insufficient carbomoyl phosphate is available, ornithine WILL accumulate, and this could cause ACCUMULATION of the precursor, N-acetylglutamate. 3. This ACCUMULATION acts as a signal to stimulate carbamoyl phosphate synthesis to INCREASE urea cycle flux.

Ammonia is a toxic byproduct of protein metabolism. To get rid of it, the body converts it to water-soluble urea through a process called the urea cycle. Put the enzymes in the urea cycle in the correct order, from first to last. Rank from first to last in the urea cycle.

1. ornithine transcarbamolyase 2. argininosuccinate synthetase 3. argininosuccinase 4. arginase

If oxidation of acetyl-CoA yields 10 ATPs per mole through the citric acid cycle, how many ATPs will be derived from the complete metabolic oxidation of 1 mole of alanine in a mammal?

12.5 ATPs

Place the following sequence of events for a transamination reaction that requires pyridoxal phosphate in the correct order: 1) deprotonation by lysine at the α-carbon of the amino acid tethered to pyridoxal phosphate 2) exchange of the amino acid that makes the Schiff base, releasing free lysine 3) hydrolysis via a cabinolamine intermediate, yielding an α-ketoacid and pyridoxamine phosphate 4) reprotonation at the α-carbon, resulting in tautomerization of the imine carbon atom 5) a second α-ketoacid reacting with pyridoxamine to provide a new amino acid

2-1-4-3-5

Methyl-labeled [14C]methionine at a specific activity of 2.0 millicuries per millimole was injected into rats. Six hours later the rats were killed. Phosphatidylcholine was isolated from the liver and found to have a specific activity of 1.5 millicuries per millimole. Calculate the proportions of phosphatidylcholine synthesized by the phosphatidylserine pathway. Express your answer as an integer.

25%

How much energy would be derived from the metabolic oxidation of 1 mole of isoleucine to CO2, H2O, AND NH3?

33.5 ATPs

How much energy would be derived from the metabolic oxidation of 1 mole of tyrosine to CO2, H2O, and NH3?

35.5 ATPs

Starting with carbamoyl phosphate, place the sequence of events for the urea cycle in the correct order: 1) Argininosuccinase hydrolyzes its substrate to arginine and fumarate. 2) Ornithine and urea are the products of the reaction catalyzed by arginase. 3) Citrulline is combined with aspartate in the presence of argininosuccinate synthetase to provide argininosuccinate. 4) Ornithine transcarbamoylase catalyzes the transfer of a carbamoyl group to ornithine.

4-3-1-2

Use numbers 1 to 5 to identify each carbon atom in the product of this reaction. Drag the appropriate labels to their respective targets.

5 4 2 1 3

The following diagram shows the biosynthesis of B12 coenzymes, starting with the vitamin. DMB is dimethylbenzimidazole. What one additional substrate or cofactor is required by enzyme B?

5-Methyltetrahydrofolate

Antimetabolites are clinically useful for which of the following reasons? 1) They interfere with the utilization of the natural substrate (the metabolite) because they are mimics of it. 2) They can interfere with the biosynthesis of thymidine and then DNA synthesis. 3) They can block proliferation of cells, especially cancer cells. 4) They can allosterically alter the function of dihydrofolate reductase.

Statements 1, 2, and 3 are correct.

Most bacterial mutants that require isoleucine for growth also require valine. A. Why? B. Which enzyme or reaction would be defective in a mutant requiring only isoleucine (not valine) for growth?

A. Because the same enzymes are involved in comparable steps of both isoleucine and valine biosynthesis. B. Threonine dehydratase

Which folate structure (from the list below) Has the most highly oxidized one-carbon substituent?

C

Which folate structure (from the list below) Is used in purine nucelotide synthesis?

C

Draw the amino acid product that results from a transamination reaction involving pyruvate and glutamate, shown in the image below. Draw the product as it would occur at the pH of most body fluids, including all charges. You do not need to draw the other product of the reaction. (insert reaction) Draw the molecule on the canvas by choosing buttons from the Tools (for bonds), Atoms, and Advanced Template toolbars. The single bond is active by default. Include all hydrogen atoms and charges.

CH(COO-)(CH3)(NH3+)

Draw the product of the oxidative deamination of alanine. (insert reaction) Draw the molecule on the canvas by choosing buttons from the Tools (for bonds), Atoms, and Advanced Template toolbars. The single bond is active by default. Include all hydrogen atoms and charges.

CH3--CO--CO--O^-

Psilocybin is a hallucinogenic compound found in some mushrooms. Complete a straightforward pathway for its biosynthesis from one of the aromatic amino acids. Drag the appropriate labels to their respective targets.

CO2 PLP --> ahydrobiopt O,hydrobione --> 2AdoMet 2AdoHcy --> ATP ADP

Consider the following questions about glutamate dehydrogenase. Draw the structure of intermediate for this reaction. Draw the molecule on the canvas by choosing buttons from the Tools (for bonds and charges), Atoms, and Templates toolbars, including charges where needed.

COO^- --CH2--CH2--C=NH2+--COO^-

Which folate structure (from the list below) Is used in the conversion of serine to glycine?

D

Nitrogen-fixing bacteria is(are) indicated by the letter(s) _____.

D and E

The following diagram shows the biosynthesis of B12 coenzymes, starting with the vitamin. DMB is dimethylbenzimidazole. Some forms of the condition described in Part B can be successfully treated by injection of rather massive doses of vitamin B12. What kind of genetic alteration in the enzyme would be consistent with this result?

Decreased affinity of enzyme C for B12 coenzyme (KM mutant)

Which of the following statements about the ubiquitination of proteins are true? 1) Ubiquitin is a relatively small protein that is widely expressed in eukaryotic cells. 2) It is covalently attached to target proteins in an ATP-dependent reaction. 3) A carboxyl group of ubiquitin forms amide bonds with free amines found on the target protein. 4) Target selection is determined by ubiquitin-protein ligases.

Only statements 1, 2, and 4 are correct.

The effects of folate deficiencies are manifested in which of the following ways? 1) elevated levels of homocysteine that are correlated with an increased incidence of heart attack 2) the presence of reduced amounts of erythrocytes that are immature and enlarged, a condition known as megaloblastic anemia 3) a decrease in the synthesis of vitamin B12 4) neural tube defects in early stages of pregnancy

Statements 1, 2, and 4 are correct.

The precise mechanism of ammonia toxicity to the brain is not known. Speculate on a possible mechanism, based on possible effects of ammonia on levels of key intermediates in energy generation. Drag the appropriate labels to their respective targets. Note: not all labels will be used.

Succinyl-CoA -> Oxaloacetate -> Citrate -> α-Ketoglutarate -> NH3 -> Glu -> NH3 -> Gln

Which of the following statements about glutamate dehydrogenase is NOT true?

The enzyme is under allosteric control in that ATP stimulates its activity, whereas ADP inhibits its function.

Transamination reactions have equilibrium constants close to unity. What does this mean? 1) In the absence of any other forces, the ratio of products to starting materials is nearly one. 2) Intracellular conditions can dictate the direction the equilibrium favors. 3) The forward reaction is not favored in cells. 4) Aminotransferases can alter the position of the equilibrium.

Statements 1 and 2 are accurate.

N2 gas can be converted to NH3 by:

legumes.

Which folate structure (from the list below) What amino acid is synthesized as the end result of reaction mentioned in the part D? Spell out the full name of amino acid.

methionine

What coenzyme is involved?

methylcobalamin

Denitrifying bacteria convert ________ to ________.

nitrates ... nitrogen gas

Draw the structure of the next intermediate formed in this reaction. Draw the molecule on the canvas by choosing buttons from the Tools (for bonds and charges), Atoms, and Templates toolbars, including charges where needed.

same as molecule at the top but without the COO^-

All amino acids can be synthesized from intermediates of the:

the glycolytic pathway, the pentose phosphate pathway and citric acid cycle.

In bacteria much of the putrescine is synthesized, not from ornithine but from arginine, which decarboxylates to yield agmatine. Formulate a plausible pathway from arginine to putrescine, using this intermediate.

the one with PLP

The proteasome is a large multisubunit ATP-dependent protease that degrades proteins that have been modified by the attachment of ________.

ubiquitin

Which of the following amino acids is both glucogenic and ketogenic?

Tryptophan

Suppose that you wanted to determine the metabolic half-life of glutamine synthetase in HeLa cells (a line of human tumor cells) growing in tissue culture. Describe how this could be done experimentally. Check all stages of the the experiment. Check all that apply.

- At intervals following removal of the labeled amino acid (a pulse-chase experiment), prepare a cell-free protein extract, treat an aliquot with antiserum, and count the radioactivity in the immunoprecipitate. - Purify the enzyme from HeLa cells or another human tissue and prepare antiserum against the enzyme. - Label HeLa cell cultures by growth in a radioactive amino acid.

Choose necessary reactants for getting this intermediate. Check all that apply.

- H2O - H+

Essential amino acids must be obtained from the diet, whereas nonessential amino acids can be synthesized in the body. Which of the following statements about essential and nonessential amino acids are true? Check all that apply.

- Humans obtain phenylalanine from their diet. - Nonessential amino acids are synthesized by the human body. - About half of the 20 amino acids must be acquired from food. - Many of the nonessential amino acids are derived from other amino acids.

Methyl-labeled [14C]methionine at a specific activity of 2.0 millicuries per millimole was injected into rats. Six hours later the rats were killed. Phosphatidylcholine was isolated from the liver and found to have a specific activity of 1.5 millicuries per millimole. What further information would you need for your calculated values to reflect the true rates of these processes? Check all that apply.

- The specific radioactivity of the final intermediate in each pathway. - The rate of degradation of the product.

Show the fate of the carbon atoms in the metabolism of glutamate (shown below) by dragging the appropriate molecule names onto the flowchart. (insert molecule) Drag the appropriate labels to their respective targets.

- glutamate - α-ketoglutarate - succinyl-SCoA - succinate - fumarate - malate - oxaloacetate - glucose

Formaldehyde reacts nonenzymatically with tetrahydrofolate to generate 5,10-methylenetetrahydrofolate. [14C]Formaldehyde can be used to prepare serine labeled in the β-carbon. What else would be needed? Check all that apply.

- glycine - serine hydroxymethyltransferase - tetrahydrofolate

Which of the following molecules make up naturally occurring folates? 1) p-aminobenzoic acid 2) a tail of aspartate residues ranging from 3 to 8 residues 3) a bicyclic, heterocyclic pteridine ring 4) a tail of glutamate residues ranging from 3 to 8 residues

1, 3, and 4

Complete a series of balanced equations and a summary equation for the reactions of the glucose-alanine cycle. Drag the terms on the left to the appropriate blanks on the right to complete the sentences.

1. . NH+4(muscle) + α-ketoglutarate + NADH + H+ -> glutamate + NAD+ + H2O 2. Glutamate + pyruvate -> alanine + α-ketoglutarate 3. Alanine + α-ketoglutarate -> glutamate + pyruvate 4. Glutamate + H2O + NAD+ -> NH+4(liver) + NADH + H+ + α-ketoglutarate 5. Sum: NH+4(muscle) -> NH+4(liver)

Identify the most likely additional substrates, products, and coenzymes for each reaction in the following imaginary pathway. Drag the terms on the left to the appropriate blanks on the right to complete the sentences. Not all terms will be used.

1. Additional substrate / product / coenzyme for reaction A is 5'-Deoxyadenosyl-B12 2. Additional substrate / product / coenzyme for reaction B is tetrahydrofolate. 3. Additional substrate / product / coenzyme for reaction C is ATP + glutamine 4. Additional substrate / product / coenzyme for reaction D is α-ketoglutarate + pyridoxal phosphate 5. Additional substrate / product / coenzyme for reaction E is S-adenosylmethionine.

Mutants of Neurospora crassa that lack carbamoyl phosphate synthetase I (CPSI) require arginine in the medium in order to grow, whereas mutants that lack carbamoyl-phosphate synthetase II (CPSII) require a pyrimidine, such as uracil. A priori, one would expect the active CPSII in the arginine mutants to provide sufficient carbamoyl phosphate for arginine synthesis, and the active CPSI in the pyrimidine mutants to "feed" the pyrimidine pathway. Explain these observations. Match the words in the left column to the appropriate blanks in the sentences on the right. Make certain each sentence is complete before submitting your answer.

1. CPS I is in MITOCHONDRIA, and CPS II is in CYTOSOL. 2. Carbamoyl phosphate CANNOT cross the mitochondrial membrane. 3. So the carbamoyl phosphate formed in mitochondria can be used only for ARGININE synthesis, and that formed in cytosol is used only for PYRIMIDINE synthesis.

Using the principles described in the text regarding pyridoxal phosphate mechanisms, propose a schema for the reaction catalyzed by serine hydroxymethyltransferase. Drag the stages on the left to the appropriate blanks on the right to complete the schema.

1. Displacement -> 2. Deprotonation -> 3. Reprotonation -> 4. Hydrolysis -> 5. Second reaction

Methyl-labeled [14C]methionine at a specific activity of 2.0 millicuries per millimole was injected into rats. Six hours later the rats were killed. Phosphatidylcholine was isolated from the liver and found to have a specific activity of 1.5 millicuries per millimole. Calculate the proportions of phosphatidylcholine synthesized by the pathway starting from free choline. Express your answer as an integer.

75%

Assimilation is indicated by the letter(s) _____.

A

Which folate structure (from the list below) Is the coenzyme for the thymidylate synthase reaction?

A

One can identify phenylketonurics and PKU carriers (heterozygotes) by means of a phenylalanine tolerance test. One injects a large dose of phenylalanine into the bloodstream and measures its clearance from the blood by measuring serum phenylalanine levels at regular intervals. Choose corresponding curve showing relative blood phenylalanine concentration versus time that you would expect to be displayed by A. a normal individual B. PKU patient C. a heterozygote D. What kind of tolerance test could you devise to distinguish between PKU resulting from either phenylalanine hydroxylase deficiency or dihydropteridine reductase deficiency?

A. III B. I C. II D. A tryptophan tolerance test

Indicate whether each of the following statements is true or false, and briefly explain your answer. A. In general, the metabolic oxidation of protein in mammals is less efficient, in terms of energy conserved, than the metabolic oxidation of carbohydrate or fat. B. Given that the nitrogen of glutamate can be redistributed by transamination, glutamate should be a good supplement for nutritionally poor proteins. C. Arginine is a nonessential amino acid for mammals because the enzymes of arginine synthesis are abundant in liver. D. Alanine is an essential amino acid because it is a constituent of every protein.

A. True.The complete catabolism of amino acids yields CO2, H2O, and ammonia. However, the ammonia must be converted to urea for detoxification and excretion, and this requires ATP, which decreases the net ATP yield. B. False. Glutamate can be used to synthesize essential amino acids only if the carbon skeletons are available as keto acids. C. False. Arginine is used catalytically in the urea cycle in liver, and thus most of the arginine that is formed is cleaved to urea and ornithine. Little arginine is left over to meet the needs of other tissues. D. False. Although it is present in all proteins, alanine can be synthesized by mammalian cells and is not required in the diet.

Proline betaine is a putative osmoprotectant in plants and bacteria, helping to prevent dehydration of cells. Propose a plausible pathway for biosynthesis of this compound.

AdoMet -> AdoMet

Would the corresponding energy yield in a fish be higher or lower? Why?

All of these pathways would generate a little more energy in a fish because it is not necessary to consume ATP in converting ammonia to urea for excretion.

Nitrification is indicated by the letter(s) ________.

B

Which folate structure (from the list below) Is the substrate for the enzyme that is inhibited by methotrexate and trimethoprim?

B

Why is phenylketonuria resulting from dihydropteridine reductase deficiency a more serious disorder than PKU resulting from phenylalanine hydroxylase deficiency?

Because a pteridine reductase deficiency would impair all tetrahydrobiopterin-dependent reactions.

Some nonessential amino acids are synthesized in the body by a simple transamination. The transamination between oxaloacetate, an αα-keto acid, and glutamate, an amino acid with the side chain −CH2CH2COO−, proceeds according to the following reaction: (insert reaction) Predict the structure of the amino acid product, indicated by amino acid 2, for the reaction. Draw the molecule on the canvas by choosing buttons from the Tools (for bonds), Atoms, and Advanced Template toolbars. The single bond is active by default. Include all hydrogen atoms and formal charges.

COO^- --CHNH3+--CH2--COO^-

Folic acid is synthesized in bacteria as dihydrofolate, in a pathway starting from guanosine triphosphate. In this pathway, C−8 is lost as formate. From the structural similarities between guanine and pterin, predict which carbon and nitrogen atoms of GTP are the precursors to N−1, C−2, C−4, N−5, C−7, N−8, and C−9 of dihydrofolate. Drag the appropriate labels to their respective targets.

Dihydrofolate: GTP: N-1 N-3 C-2 C-2 C-4 C-6 N-5 N-7 C-7 C-1' N-8 N-9 C-9 C-3'

Which folate structure (from the list below) Transfers its one-carbon substituent to a B12 coenzyme? What amino acid is synthesized as the end result of this reaction?

E

Which folate structure (from the list below) Is not known to exist in nature?

F

Nitrate can be reduced to ammonia by virtually all organisms.

False

Nitrogen fixation requires the hydrolysis of 8 ATPs to produce 2 NH3 molecules from 1 N2.

False

The H2S produced by metabolism of cysteine is a waste product with no physiological or biochemical function.

False

The Krebs-Henseleit urea cycle takes place in liver cells entirely within the mitochondrion.

False

Tyrosine is the precursor of serotonin which has a number of roles in the nervous system.

False

A clinical test sometimes used to diagnose folate deficiency or B12 deficiency is a histidine tolerance test, where one injects a large dose of histidine into the bloodstream and then carries out a series of biochemical determinations. What histidine metabolite would you expect to accumulate in a folate- or B12- deficient patient, and why?

Formiminoglutamate, because the next reaction in its catabolism requires tetrahydrofolate.

Sort each of the following amino acids based on whether it is glucogenic, ketogenic, or both glucogenic and ketogenic. Drag the appropriate amino acids to their respective bins.

Glucogenic: - proline - asparagine - glutamine - serine Ketogenic: - leucine Both glucogenic and ketogenic: - phenylalanine - isoleucine - tyrosine

Which of the following enzymes is NOT involved in the conversion of NH3 to an organic nitrogen-containing compound?

Glutamate-oxaloacetate transaminase

The structure shown above is an intermediate in the synthesis of which biogenic amine? Spell out the full name of the compound.

Histamine

Which of the following amino acids cannot be used to provide an intermediate of the citric acid cycle?

Lysine

The following diagram shows the biosynthesis of B12 coenzymes, starting with the vitamin. DMB is dimethylbenzimidazole. Genetic deficiency in animals of enzyme C would result in excessive urinary excretion of what compound?

Methylmalonate

Since all organs degrade amino acids, which leads to the production of ammonia, which of the following statements regarding the fate of ammonia is NOT correct?

Most tissues convert ammonia directly to urea.

Consider the following questions about glutamate dehydrogenase. The reaction above has NH3 as a reactant, instead of NH4+, which is far more abundant at physiological pH. Why is NH3 preferred?

NH3 has an unshared electron pair that can initiate nucleophilic attack on the electron-poor carbonyl carbon atom.

Which one of these is a nitrite?

NO2-

Which one of these is a nitrate?

NO3-

_____ removes nitrogen from the atmosphere.

Nitrogen fixation

Explain the basis for the following statement: As a coenzyme, pyridoxal phosphate is covalently bound to enzymes with which it functions, yet during catalysis the coenzyme is not covalently bound.

PLP forms a covalent Schiff base between the aldehyde carbon of the coenzyme and an ϵ-amino group of a lysine residue in the active site of the enzyme. This bond must be broken for the coenzyme to form a Schiff base with an amino acid substrate.

[14C]Serine, prepared as described above, is useful for many things, but you would probably not want to use it for studies on protein synthesis because it would label nucleic acids, carbohydrates, and lipids, as well as proteins. Indicate how each of these classes of compounds could become labeled by this precursor. Drag the appropriate labels to their respective targets.

Pyruvate Oxaloacetate Phosphoenol-pyruvate Glucose Serine Phosphatidyl-serine Phosphatidylethanol-amine Phosphatidylcholine Thymine nucleotides Nuclelic acids

Nitrogen is a limited resource, despite the presence of strong demand. Which of the following is NOT a metabolic consequence of the inability to store nitrogen?

Proteolysis is a non-selective, exergonic process.

Ammonia is a toxic byproduct of protein metabolism. To get rid of it, the body converts it to water-soluble urea through a process called the urea cycle. Identify the reactants and the products of the preparation step to the urea cycle. Drag the appropriate items to their respective bins.

Reactants: NH4+, 2ATP, CO2, H2 Products: H2N(CO)OPO3^2- (carbomoyl phosphate), 2ADP, Pi

Pyridoxal phosphate is a versatile coenzyme as it is capable of forming a stable ________ base between an amino acid substrate and the coenzyme.

Schiff

Consider the following questions about glutamate dehydrogenase. The thermodynamic equilibrium for the reaction greatly favors α-ketoglutarate reduction, yet in mitochondria the enzyme acts primarily to oxidize glutamate to α-ketoglutarate. Explain.

The direction of a reaction depends both on the equilibrium constant and the concentrations of reactants and products. The intramitochondrial [NAD+]/[NADH] ratio is high, and this drives the reaction toward α-ketoglutarate.

Determine whether each reaction represents a transamination or an oxidative deamination. Drag the appropriate items to their respective bins.

Transamination: - Aspartic acid is transferred from an amino acid to a keto acid. - Glutamate aminotransferase catalyzes a reaction. Oxidative deamination: - Alanine dehydrogenase, which requires a coenzyme, catalyzes a reaction. - The ammonium ion is converted to urea.

Arginine and methionine can be synthesized by mammals but are generally classed as essential amino acids.

True

The oxidation of branched chain amino acids shares a similar chemical strategy with β-oxidation of fatty acids.

True

With appropriate nutrition, animals maintain nitrogen intake and excretion at equivalent rates.

True

Consider the following questions about glutamate dehydrogenase. Glutamate dehydrogenase has a KM for ammonia (NH3) of ~1 mM. However, at physiological pH the dominant ionic species is ammonium ion, NH4+ (pKa=9.2). Calculate the velocity (as a fraction of Vmax) that would be achieved by glutamate dehydrogenase if the total intracellular ammonia concentration (NH3+NH4+) is 100 μM (approximate physiological concentration). Assume a mitochondrial matrix pH of 8.0. Express your answer using three significant figures.

V/Vmax = 5.90*10^-3

Tetrahydrofolate is a coenzyme involved in the mobilization and utilization of single carbon functional units in the: - metabolism of serine, glycine, methionine, and histidine. - biosynthesis of thymine. - biosynthesis of purine nucleotides. - biosynthesis of formylmethionyl-tRNA - all of the above

all of the above

A transamination can be summarized as an amino group (−NH3+) of an amino acid and the keto group (C=O) of an α-keto acid changing places and forming different amino acid and α-keto acid products, as in the generic reaction below: amino acid 1 + α−keto acid 1 ⟶ α−keto acid 2 + amino acid 2 Draw the α-keto acid product of the transamination of an αα-keto acid with an amino acid that has the side chain X. (insert reaction) Draw the molecule on the canvas by choosing buttons from the Tools (for bonds), Atoms, and Advanced Template toolbars. The single bond is active by default. Show formal charges on all atoms.

X--CO--COO^-

In the degradation of amino acids in muscle NH4+ is carried to the liver for conversion into urea by:

alanine.

Nitrifying bacteria convert _____ to _____.

ammonium ... nitrites

The following diagram shows the biosynthesis of B12 coenzymes, starting with the vitamin. DMB is dimethylbenzimidazole. Genetic deficiency in animals of enzyme B will result in excessive urinary excretion of what amino acid? Spell out the full name of the amino acid.

homocysteine