Secondary, Tertiary And Quaternary Structure

Question 1

What is the approximate net charge of the pentapeptide Ala-Arg-Ser-Glu-Asn at pH 7?
A)-2
B)-1
C)0
D)+1
E)+2

Answer 1

C)0
At this pH, the charged groups will consist of the N-terminal amino group (+), the guanidium side chain of Arg (+), the Glu carboxyl side chain (-), and the C- terminal carboxyl group (-). Note that the peptide bonds are not charged. Thus, the net charge of the peptide is zero, all these cancel out. Know the amino acid side chain structures and thus which are negative, neutral and positive at pH 7.

Question 2

What is the approximate isoelectric point of the following he a peptide. Consult your notes to obtain relevant pka values.
Asp-Leu-Ile-Glu-Lys-Gly
A)3.7
B)4.0
C)6.55
D)9.75

Answer 2

B) 4.0
There are 5 protons that can be dissociated from this functional group (the side chains of Asp, Glu, Lys, as well as the N- and C- terminus.
The isoeletric point point of this peptide is enclosed by two pka values (3.9 and 4.1). The average of these two values is 4.0, which is the isoelectric point.

Question 3

If you wanted to best visualize the potential role of a specific amino acid residue in the interaction of a proteins with a small molecule, you would likely ……
A) carry out gel filtration chromatography
B)examine a ribbon model of an x-ray crystal structure of the protein
C)examine wireframe model of an x-ray crystal structure of the protein
D)calculate the amount of beta-sheet secondary structure of the enzyme
E)determine the amino acid sequence of the protein.

Answer 3

C) examine a wireframe model of an x-ray crystal structure of the protein
The wireframe representation of all atoms (except hydrogens) provides the most detailed view to examine potential chemical and binding processes.

Question 4

The formation of a alpha helix by a protein always involves?
A) arrangement of multiple peptide chains to form the alpha helix
B)peptide bond isomerization
C)arrangement of the peptide chain so that R groups are pointed from the helix
D)phosphorylation of side chains
E)hydrogen bonding between neighboring amino acid residues

Answer 4

C)arrangement of the peptide chain so that R groups are pointed away from the helix
An alpha helix consists of one peptide chain arranged between amino acid residues that are 4 residues apart. Phosphorylation or peptide bond isomerization is not required for an alpha helix to form.