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Organic Chemistry 1
Biochemistry
Branched Chain Amino Acids
Reading Frame Of A Gene
Amino Acid Side Chains
Flash cards (95)
Basic; Arginine

Neutral polar; Glutamine, Cysteine, Asparagine

Neutral nonpolar; Alanine
Classify these amino acids as acidic, basic, neutral polar, or neutral nonpolar.
Basic; Lysine

Neutral polar; Serine

Neutral nonpolar; Proline, Methionine, Phenylalanine
Classify these amino acids as acidic, basic, neutral polar, or neutral nonpolar.
Acidic; Glutamic Acid

Neutral polar; Threonine

Neutral nonpolar; Tyrosine, Valine, Tryptophan
Classify these amino acids as acidic, basic, neutral polar, or neutral nonpolar.
The CHNH2 group α to the carboxylic acid is oxidized to a C=O group by the transaminase.
When transaminated, the three branched-chain amino acids (valine, leucine, and isoleucine) form compounds that have the characteristic odor of maple syrup. An enzyme called α-keto acid dehydrogenase converts these compounds into CoA esters. Give the structure of the valine-derived compound that smells like maple syrup.
C.

This ionic state, where the carboxylic acid is negative and the amine group is positive, is known as the zwitterionic state.
Select the generic nonpolar amino acid that is in the correct form at pH=7.0, or at physiological conditions. Pay close attention to the charges on the amino group and the carboxylic acid group.

A, B, C, or D
L-aspartic acid is an amino acid that is frequently used in enzymes to perform chemical reactions.
Draw L-aspartic acid as it would occur at the pH of most body fluids.
a. 1:D;2:C;3:F;4:E;5:B;6:A
Match the amino acid (AA) with its correct side chain category:

1. proline
2. histidine
3. alanine
4. threonine
5. tryptophan
6. aspartic acid

a. negatively charged polar AA
b. nonpolar aromatic AA
c. positively charged polar AA
d. nonpolar AA
e. polar AA
f. nonpolar aliphatic AA

Pick A, B, C, or D
a. Only statement 2 is correct.
[Glycine is small, and proline is rigid.]

Glycine is found at the surface of proteins because its side chain is hydrogen, which is very small. This imparts great flexibility to this amino acid. Proline is the only secondary amino acid and as such is very rigid. The geometrical limitations of this amino acid make it well suited for turns in proteins.
Glycine and proline are both non-polar amino acids, and both are very likely to be found at the surface of proteins. What physical characteristic of each is responsible for this observation?

1) Both glycine and proline are small.
2) Glycine is small, and proline is rigid.
3) The side chains of both these amino acids make favorable interactions with molecules near the surface of proteins.
4) Both amino acids make strong interactions with each other and therefore are likely to be found next to each other in a protein.

a. Only statement 2 is correct
b. Only statements 1 and 2 are correct
c. Only statements 2, 3, and 4 are correct
d. Only statements 1, 2 and 3 are correct
a. Statements 1 and 2 are correct.
[The microenvironment around a residue can impact its pKa value.
A positively charged amino acid must be in close proximity to this residue.]

These two statements most accurately describe this result; the presence of a nearby positive charge is likely to decrease the pKa of the His side chain because two neighboring positive charges will repel each other. There is not enough information to draw any conclusion about the location of this residue within the protein structure.
The side chain of histidine has a typical pKa value in the range of 6.5-7.4. However, when analyzing the pKa values in a particular protein, scientists determined that one particular His residue has an unusually low pKa value of 4.8. Which of the following statements correctly explain this anomaly?

1) The microenvironment around a residue can impact its pKa value.
2) A positively charged amino acid must be in close proximity to this residue.
3) A negatively charged amino acid must be in close proximity to this residue.
4) This residue must be located on the surface of the protein.

a. Statements 1 and 2 are correct.
b. Statements 1 and 4 are correct.
c. Statements 2, 3 and 4 are correct.
d. Statements 1, 2 and 4 are correct.
Arg-Val-Tyr
Identify the amino acids in the following tripeptide.
This is the structure of L-alanine. Only L amino acids are found in proteins.

At physiological pH (7.4), amino acids are zwitterions. That is, the carboxyl group loses its hydrogen atom to become −COO−, and the amino group is protonated to become −NH3+.
In the reaction shown here, two amino acids link together to form a dipeptide. The first amino acid, which becomes the N-terminal amino-acid residue, is glutamine.
Draw the L form of the second amino acid in this reaction that would link with glutamine to form the given dipeptide.
The dipeptide form of glycine is called glycylglycine.
Draw the dipeptide that results when a peptide bond is formed between the two glycine molecules shown. Draw it as it would occur at the pH of most body fluids.
a. Only statements 1 and 3 are correct. [The bond is planar. There is substantial double-bond character to this bond.]
Which of the following characteristics are true about a typical peptide (amide) bond?

1) The bond is planar.
2) There is free rotation about the carbonyl carbon and nitrogen bond.
3) There is substantial double-bond character to this bond.
4) There is a net negative charge on nitrogen and net positive charge on oxygen.

a. Only statements 1 and 3 are correct.
b. Only statements 1, 2 and 4 are correct.
c. Only statements 2 and 3 are correct.
d. All of the listed statements are correct.
b. E is the N-terminal residue; Y is the C-terminal residue.
What are the N-terminal and C-terminal residues for the following peptide sequence?
Peptide sequence: EASY

a. Aspartic acid is the N-terminal residue; tyrosine is the C-terminal residue.
b. E is the N-terminal residue; Y is the C-terminal residue.
c. Glutamic acid is the N-terminal residue; tryptophan is the C-terminal residue.
d. Y is the N-terminal residue; E is the C-terminal residue.
c. The acid with the lower pKa value would increase the pKa value for the other acid.

This is correct because the presence of one negative charge is likely to make the formation of a second negative in close proximity less favorable because of charge-charge repulsion. Nonetheless, it is not impossible to overcome this interaction, but it does affect the pKa value as indicated.
For an amino acid such as aspartic acid, what impact do you expect the two neighboring carboxylic acids to have on the pKa values for each?

a. The acid with the higher pKa value would decrease the pKa value for the other acid.
b. The neighboring acids would have no impact on each other"s pKa values.
c. The acid with the lower pKa value would increase the pKa value for the other acid.
d. The acid with the lower pKa value would decrease the pKa value for the other acid.

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