Unit 4 Amino acids, peptides, and proteins

1. Absolute Configuration of Citrulline The citrulline isolated from watermelons has the
structure shown below. Is it a D- or L-amino acid? Explain.

- This structure is the L configuration because the amino group exists in the right of alpha
carbon
2. Relationship between the Titration Curve and the Acid-Base Properties of Glycine
A 100 mL solution of 0.1 M glycine at pH 1.72 was titrated with 2 M NaOH solution. The
pH was monitored and the results were plotted as shown in the graph. The key points in the
titration are designated I to V. For each of the statements (a) to (o), identify the appropriate
key point in the titration, and justify your choice.

(a) Glycine is present predominantly as the species +H3N—CH2—COOH.

- (I): Fully protein
(b) The average net charge of glycine is +1/2.
- (II): At the first pKa, half of the protons are removed from the α – carboxyl group
(c) Half of the amino groups are ionized.
- (IV): at its pKa (9.60) the amino group is half – deprotonated
(d) The pH is equal to the pKa of the carboxyl group.
- (II):
(e) The pH is equal to the pKa of the protonated amino group.
- (IV):
(f) Glycine has its maximum buffering capacity.
- (II), (IV): Molecules have maximum buffering capacity when pH equals to pKa of
functions group
(g) The average net charge of glycine is zero.
- (III): Molecule is zwitterion because both carboxyl and amino groups will be ionized
(h) The carboxyl group has been completely titrated (first equivalence point).
- (III): Amino groups are still protonated and all molecules have ionized carboxyl group
(i) Glycine is completely titrated (second equivalence point).
- (V): At high pH, the molecule is completely deprotonated
(j) The predominant species is +H3N—CH2—COO—.
- (III):The carboxyl group is fully negatively charged (deprotonated) and the amino group
is fully positively charged (protonated)
(k) The average net charge of glycine is -1.
- (V): Both groups are fully deprotonated
(l) Glycine is present predominantly as a 50:50 mixture of +H3N—CH2—COOH and +H3N
—CH2—COO-.
- (II): the carboxyl group is half ionized at pH=pK1
(m) This is the isoelectric point.
- (III): Both molecule is a zwitterion, both amino and carboxyl group are ionized
(n) This is the end of the titration.
- (V): At high pH, the molecule is completely deprotonated
(o) These are the worst pH regions for buffering power.
- (I), (III), and (V): A small addition of OH- will increase pH dramatically

3. pKa of Histidine The amino acid histidine has three ionizable groups, with pKa values of
1.8, 6.0, and 9.2. (a) Which pKa corresponds to the histidine side chain? (b) In a solution at
pH 5.4, what percentage of the histidine side chains will carry a positive charge?

(a) pKa = 6.0

(b) pH = pKa + log([A-]/[HA])

‹ 5.4 = 6.0 + log([A-]/[HA])

‹ log([A-]/[HA]) = 0.6

‹ ([A-]/[HA]) = 4

‹ 4[HA] = [A-] (4/5)

=> At pH 5.4, histidine has 4/5 (80%) will carry a positive charge

4. Protein structure Name factors (bonds or other forces) that contribute to stabilizing the
native structure of a protein and describe one condition or reagent that interferes with each
type of stabilizing force.

- Among forces that stabilize native protein structures are (a) disulfide bonds, (b) hydrogen
bonds, (c) hydrophobic interactions, and (d) ionic interactions. Agents that interfere with
these forces are (a) mercaptoethanol or dithiothreitol, (b) pH extremes, (c) detergents and
urea, and (d) changes in pH or ionic strength, respectively.

5. Subunit Composition of a Protein A protein has a molecular mass of 400 kDa when
measured by gel filtration. When subjected to gel electrophoresis in the presence of sodium
dodecyl sulfate (SDS), the protein gives three bands with molecular masses of 180, 160,
and 60 kDa. When electrophoresis is carried out in the presence of SDS and dithiothreitol
(DTT), three bands are again formed, this time with molecular masses of 160, 90, and 60
kDa. Determine the subunit composition of the protein.

- 160 + 90 + 60 = 310 kDa

- 400 – 310 = 90 kDa

- This means there has more one 90 → Meaning there are 4 subunits

6. Protein denaturation Why does crab/shrimp turn red when cooked?

- Crabs and shrimps have a pigment called "astaxanthin" which lies hidden, camouflaged
by a protein covering. Astaxanthin is a member of the carotene family of pigments, which
are responsible for coloring many of the yellow and orange (or "carotene") fruits and
vegetables. Because these protein chains are not heat-stable, their protein-wrapping uncoils
as soon as crustaceans are put in boiling water. Red-orange astaxanthin molecules are
released

7. Amino Acid Sequence and Protein Structure Our growing understanding of how
proteins fold allows researchers to make predictions about protein structure based on
primary amino acid sequence data. Consider the following amino acid sequence.

(a) Where might bends or β-turns occur?

- Bends or β-turns occur at residues 7 (Pro) and 19 (Pro) or residues 6 (Gly) and
21 (Gly)
(b) Where might intrachain disulfide cross-linkages be formed?
- Between 13 (Cys) and 24 (Cys)