Biochemistry : Identifying Amino Acids

Study concepts, example questions & explanations for Biochemistry

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Example Questions

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Example Question #1 : Identifying Amino Acids

The conversion of tetrahydrofulate to methylene tetrahydrofulate is coupled to which amino acid conversion?

Possible Answers:

Serine to glycine

Glycine to alanine

Glutamate to glutamine

Serine to alanine

Serine to threonine

Correct answer:

Serine to glycine

Explanation:

The conversion of tetrahydrofulate to methylene tetrahydrofulate is coupled with the amino acid conversion of serine to glycine. Serine converts to form glycine and formaldehyde. The same components are factored in with the conversion of tetrahydrofulate to methylene tetrahydrofulate.

Example Question #2 : Identifying Amino Acids

An unknown amino acid has been isolated from a solution. It has a  charge at a pH of 12. It shows 3 equivalent points on its titration curve, and is found to have amphipathic properties. Which amino acid is this? 

Possible Answers:

Tyrosine

Threonine

Histidine

Glutamic acid

Tryptophan

Correct answer:

Tyrosine

Explanation:

At a pH of 12, the amino group for all of the amino acids would be deprotonated, resulting in at least a  charge from the acid group. Another negative charge comes from the carboxyl group on the backbone. Tyrosine is amphipathic, and the pKa of its sidechain is 10.8, meaning it is a deprotonated  at a pH of 12. This gives it a  charge at a pH of 12. Tryptophan has no side-chain pKa so 3 equivalence points would not be seen. Threonine would also not have 3 equivalence points. Glutamic acid doesn't have amphipathic properties. Histidine is amphipathic, but it is a basic amino acid.

Example Question #3 : Identifying Amino Acids

Glycine

Which amino acid is shown above?

Possible Answers:

Tyrosine

Leucine

Glycine

Valine

Phenylalanine

Correct answer:

Glycine

Explanation:

All amino acids have an amino group, a carboxyl group, a hydrogen, and an R-group that is unique to the amino acid. In this structure, the R-group is a hydrogen, which corresponds to the amino acid glycine.

Example Question #2 : Identifying Amino Acids

A protein in aqueous solution is run through a column containing negatively charged beads. A small amount of protein is found to be inside the column after the mobile phase has finished running. Which of the following amino acids is probably found in higher concentration within this small amount of protein? 

Possible Answers:

Tyrosine

Glutamic acid

Alanine

Lysine

Correct answer:

Lysine

Explanation:

Since this is an ion-exchange chromatography method, we expect that the protein found in the column has the opposite charge of the beads. Since the beads were negatively charged, we expect the amino acid to be positively charged. Lysine has a basic side chain that can easily pick up a hydrogen from solution and become positively charged.

Example Question #3 : Identifying Amino Acids

Suppose that a mutation occurred in the DNA region coding for a very important amino acid in the active site of an enzyme. If the original amino acid at this site before the mutation was a lysine, which of the following amino acid substitutions would likely be the least detrimental?

Possible Answers:

Tryptophan

Arginine

Glycine

Glutamate

Valine

Correct answer:

Arginine

Explanation:

We're told in the question stem that a mutation is causing a single amino acid substitution. Originally, the amino acid encoded by this region was a lysine residue. To find the amino acid that would cause the least detriment to the organism, we need to recognize which amino acid is the most similar to lysine. Since lysine is a basic amino acid under physiological conditions, it will tend to carry a positive charge most of the time. Therefore, we are looking for an amino acid that is also basic and carries a positive charge under physiological conditions. Arginine is one such amino acid that meets this criteria, and thus it is the correct answer. Glutamate is incorrect because it is acidic under physiological conditions, and thus will carry a negative charge. Glycine, valine, and tryptophan are also all incorrect because each of these amino acids are neutral under physiological conditions.

Example Question #4 : Identifying Amino Acids

Which of the following amino acids have side chains capable of hydrogen bonding interactions?

I. Alanine

II. Aspartate

III. Threonine

IV. Methionine

Possible Answers:

II only

II, III, and IV

III only

I, II, and III

II and III

Correct answer:

II and III

Explanation:

Only aspartate and threonine have side chains capable of hydrogen bonding interactions. Aspartate has a terminal carboxylate which can act as a hydrogen bond acceptor and as a hydrogen bond donor when protonated. Threonine has a terminal hydroxyl group which can also act as a hydrogen bond donor. Alanine has an entirely aliphatic side chain which is unable to participate in hydrogen bonding, and methionine has a sulfhydryl group, that cannot participate in hydrogen bonding.

Example Question #7 : Identifying Amino Acids

Which of the following is true regarding sequencing methods?

Possible Answers:

Agarose gel electrophoresis is used to separate out individual amino acid molecules

High performance liquid chromatography (HPLC) can be used to separate peptides

Edman degradation allows the sequencing of an unlimited number of amino acids

None of these

Correct answer:

High performance liquid chromatography (HPLC) can be used to separate peptides

Explanation:

Agarose gel electrophoresis is typically used for large molecules, not small ones like individual amino acids. Isoelectric focusing separates molecules by isoelectric point. Edman degradation only permits sequencing of about 30 amino acids, not an unlimited amount. High-performance liquid chromatography separates proteins which are peptide sequences.

Example Question #8 : Identifying Amino Acids

Suppose that an amino acid with pI = 10.4 in acidic solution is titrated with a strong base, . What will the net charge of this amino acid be at a pH of 2, 8, and 12?

Possible Answers:

Positive, negative, negative

Positive, positive, neutral

Positive, neutral, negative

Positive, positive, negative

Positive, neutral, neutral

Correct answer:

Positive, positive, negative

Explanation:

We're told in the question that this amino acid has a pI = 10.4. Therefore, we expect this to be a basic amino acid. This means that one carboxyl group, one amino group, and one basic R-group will be present.

At the start of the titration, the solution starts out acidic at a very low pH. At a pH of 2, since so many protons are in solution at this pH, all of the important functional groups under consideration will be protonated. Thus, the amino acid will have a positive charge on each of its basic functional groups, and a neutral charge on its carboxyl group, giving the amino acid a net charge of +2.

Once the pH has climbed to a value of 8, we would expect that only the carboxyl group will be deprotonated. As a result, the carboxyl group will have a negative charge, while each of the other two basic functional groups will still retain their positive charge. Thus, the amino acid at this pH will have a net charge of +1.

And finally, once the pH climbs all the way up to a value of 12, we can expect the two basic functional groups to be deprotonated. Consequently, each of the basic functional groups will be neutral, while the carboxyl group will still be negative. Thus, the overall charge of the amino acid will be negative at this pH.

So overall, the amino acid will be positive, then positive, followed by negative.

Example Question #5 : Identifying Amino Acids

Most naturally occurring amino acids exist as the L-isomer. However, there is one exception to this trend. Which amino acid defies this trend?

Possible Answers:

Glutamate

Glycine

Histidine

Tyrosine

Valine

Correct answer:

Glycine

Explanation:

Most amino acids that exist in living organisms contain an alpha-carbon that is a stereocenter (or chiral center). This means that this central carbon is bonded to four different substituents, thus allowing the amino acid to have two possible isomers. Although practically all amino acids in nature occur as the L-isomer, glycine is an exception. The reason for this is that glycine's alpha-carbon is bonded to two hydrogen atoms. As a result, this alpha-carbon is not a stereocenter, which means that glycine only has one possible conformation with no isomers.

Example Question #10 : Identifying Amino Acids

Which of the following amino acids does not contain a ring structure?

Possible Answers:

Tyrosine

Phenylalanine

Histidine

Threonine

Tryptophan

Correct answer:

Threonine

Explanation:

Tryptophan contains a five membered ring and a six membered ring on its side group. Tyrosine and phenylalanine both contain one six membered ring. Histidine contains a five membered ring on its side chain. Threonine's R-group is , and does not have a ring structure.

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