Help with Organic Proteins

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Organic Chemistry › Help with Organic Proteins

Questions 1 - 9
1

Which of the following amino acids can participate in the formation of a disulfide bridge?

Cysteine

Tyrosine

Alanine

Phenylalanine

Aspartic acid

Explanation

Cysteine's R-group contains a sulfhydryl group (-SH), which can participate in the formation of a disulfide bridge in a protein's tertiary and/or quaternary structure. Cysteine is the only amino acid to contain a sulfur atom.

2

Consider L-glutamate, which is shown below.

Screen shot 2015 11 17 at 4.34.19 pm

Using the pKa information provided, what is the isoelectric point (pI) of the given molecule?

Explanation

The isoelectric point is the average of the two pKa values around which the molecule has an overall neutral charge. In the case of glutamate, the amino acid is in its neutral (zwitterion) form in between the lower two pKa values. Taking the average of the two values gives the pI.

3

What is the D/L configuration and the absolute (R/S) configuration of the following amino acid (cysteine)?

Screen shot 2015 11 16 at 1.06.26 pm

L, R

L, S

D, R

D, S

Cysteine is achiral

Explanation

Cysteine is an unusual amino acid. Although each of the normal biological amino acids have the L configuration (with the exception of glycine, which is achiral), meaning they can be drawn with the Fischer projection as shown:

Screen shot 2015 11 16 at 1.10.31 pm

the fact that cysteine contains a sulfur group makes the side chain a higher priority than the carboxylic acid. Therefore, the absolute configuration of cysteine will be R, and not S like the other amino acids.

4

Consider the amino acid L-lysine, shown below.

Screen shot 2015 11 16 at 1.44.03 pm

Given the pKa values shown, calculate the pI of lysine.

Explanation

The isoelectric point is the average of the two pKa values around which the molecule has an overall neutral charge. In the case of lysine, the amino acid is in its neutral (zwitterion) form in between the higher two pKa values. Taking the average of the two values gives the pI.

5

Treatment of a peptide with Edman's reagent yielded the following phenylthiohydantoin (PTH) derivative:

Screen shot 2015 11 18 at 8.23.34 pm

What is the side chain of the amino acid at the N-terminus of the peptide?

sec-Butyl

Benzyl

Isobutyl

Amide

Hydrogen

Explanation

Treatment of a peptide with Edman's reagent () will remove the N-terminal amino acid. The PTH derivative will look as follows:

Screen shot 2015 11 18 at 8.40.08 pm

In the molecule in the question, a sec-butyl replaces the R group. This is the amino acid isoleucine.

6

What is the amino acid that is synthesized from the malonic ester synthesis shown?

Screen shot 2015 11 18 at 9.28.04 pm

Valine

Leucine

Alanine

Isoleucine

Lysine

Explanation

First step: Deprotonation of alpha hydrogen and formation of the malonic ester enolate.

Second step: bimolecular nucleophilic substitution, resulting in addition of the isopropyl group to the alpha carbon.

Third step: hydrolysis of amide and ester bonds, followed by decarboxylation

The synthesis forms valine, because the alkyl halide that is attacked is an isopropyl group (Valine's side chain is an isopropyl group). A more detailed mechanism is shown below.

Screen shot 2015 11 18 at 10.00.44 pm

7

How many essential amino acids are there?

Nine

Twenty

Twelve

Ten

Zero

Explanation

The nine essential amino acids are valine, leucine, isoleucine, histidine, phenylalanine, tryptophan, methionine, threonine, and lysine. These amino acids must be consumed in the diet, since they cannot be synthesized by adult humans.

8

Which of the following amino acids is the only one to contain a side chain that results in an achiral amino acid?

Glycene

Alanine

Aspartic acid

Lysine

Explanation

The only achiral amino acid is Glycene. Glycene's side chain is simply a hydrogen. Because a hydrogen already exists on the fundamental structure of an amino acid backbone, a side chain of a single hydrogen atom causes glycene to be achiral.

9

Which of the following is an example of a basic amino acid?

Lysine

Leucine

Alanine

Aspartic acid

Tyrosine

Explanation

Lysine's R-group includes an amine (-NH2), which can be ionized by picking up a hydrogen. This ability classifies lysine as basic.

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