Organic Chemistry : Help with Organic Proteins

Study concepts, example questions & explanations for Organic Chemistry

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Example Questions

Example Question #1 : Help With Organic Proteins

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

Possible Answers:

Tyrosine

Alanine

Lysine

Leucine

Aspartic acid

Correct answer:

Lysine

Explanation:

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

Example Question #25 : Organic Chemistry

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

Possible Answers:

Tyrosine

Alanine

Cysteine

Phenylalanine

Aspartic acid

Correct answer:

Cysteine

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.

Example Question #2 : Help With Organic Proteins

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

Possible Answers:

Alanine

Lysine

Glycene

Aspartic acid

Correct answer:

Glycene

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.

Example Question #3 : Help With Organic Proteins

How many essential amino acids are there?

Possible Answers:

Twenty

Ten

Nine

Zero

Twelve

Correct answer:

Nine

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.

Example Question #4 : Help With Organic Proteins

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

Possible Answers:

L, R

D, R

L, S

D, S

Cysteine is achiral

Correct answer:

L, R

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.

Example Question #5 : Help With Organic Proteins

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?

Possible Answers:

Correct answer:

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.

Example Question #6 : Help With Organic Proteins

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.

Possible Answers:

Correct answer:

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.

Example Question #7 : Help With Organic Proteins

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?

Possible Answers:

Amide

Isobutyl

sec-Butyl

Benzyl

Hydrogen

Correct answer:

sec-Butyl

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.

Example Question #8 : Help With Organic Proteins

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

Screen shot 2015 11 18 at 9.28.04 pm

Possible Answers:

Isoleucine

Leucine

Valine

Alanine

Lysine

Correct answer:

Valine

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

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