Organic Chemistry : Help with Organic Proteins
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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?
Lysine
Alanine
Aspartic acid
Leucine
Tyrosine
Lysine
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 #1 : Sulfide Chemistry
Which of the following amino acids can participate in the formation of a disulfide bridge?
Alanine
Tyrosine
Aspartic acid
Phenylalanine
Cysteine
Cysteine
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 #3 : 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?
Lysine
Aspartic acid
Alanine
Glycene
Glycene
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 #2 : Help With Organic Proteins
How many essential amino acids are there?
Ten
Zero
Twelve
Twenty
Nine
Nine
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 #1 : Help With Organic Proteins
What is the D/L configuration and the absolute (R/S) configuration of the following amino acid (cysteine)?
L, R
D, S
L, S
Cysteine is achiral
D, R
L, R
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:
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 #1 : Help With Organic Proteins
Consider L-glutamate, which is shown below.
Using the pKa information provided, what is the isoelectric point (pI) of the given molecule?
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 #1 : Help With Organic Proteins
Consider the amino acid L-lysine, shown below.
Given the pKa values shown, calculate the pI of lysine.
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 #1 : Help With Organic Proteins
Treatment of a peptide with Edman's reagent yielded the following phenylthiohydantoin (PTH) derivative:
What is the side chain of the amino acid at the N-terminus of the peptide?
Hydrogen
Isobutyl
Benzyl
Amide
sec-Butyl
sec-Butyl
Treatment of a peptide with Edman's reagent (
In the molecule in the question, a sec-butyl replaces the R group. This is the amino acid isoleucine.
Example Question #2 : Help With Organic Proteins
What is the amino acid that is synthesized from the malonic ester synthesis shown?
Lysine
Leucine
Isoleucine
Valine
Alanine
Valine
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.
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