CLAS – Chem 109C – Chapter 21
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1. Answer the following:
a. Which amino acid(s) is achiral?
b. Are naturally occurring amino acids D or L?
2. Draw the following amino acids in their predominant form:
a. valine at pH = 0b. glutamate at pH = 11c. histidine at pH = 5
3. Calculate the pI of phenylalanine, lysine and aspartic acid.
4. What is the net charge of the following amino acids at the designated pHs?
a. Serine at pH = 4 b. Arginine at pH = 9c. Glutamic acid at pH = 5
5. Thin layer chromatography of a solution of threonine, valine,
lysine, alanine and serine yielded the following;
determine which amino acid goes with each spot?
6. Gel electrophoresis of a solution of histidine, tyrosine, lysine, aspartate and glutamic acid yielded the following determine which amino acid goes with each spot?
anode cathode
7. Which separation technique will enable you to know how many of each amino acid is in a peptide?
8. Predict the order of elution if a mixture of Arg, Glu and Ile is separated via cation exchange chromatography?
9. Show how valine can be synthesized via the following methods.
a. HVZ
b. Reductive amination
c. N-Phthalimidomalonic ester synthesis
d. Strecker Sythesis
10. Explain kinetic resolution.
11. Draw the met-arg-tyr-asn-his at pH = 7
12. Provide2 waysala-gly-sercan be synthesized.
13. Determine if the following statements are true or false:
a. Disulfide bridges help hold the tertiary structure of a protein together
b. Proteins high in alpha helices stretch better than proteins high in beta pleated sheets.
c. Hydrogen bonding between side chains is what holds the secondary structure of a protein together
14. Describe denaturation and give examples of possible causes for denaturation.
15. Show the cleavage sites on the following peptide if introduced to each of the following reagents:
a. Carboxypeptidase A ⇒ ala-gly-phe-met-ser-lys-tyr-asn-glu-arg-pro-met-leu-his
b. Edman’s ⇒ ala-gly-phe-met-ser-lys-tyr-asn-glu-arg-pro-met-leu-his
c. Cyanogen bromide ⇒ ala-gly-phe-met-ser-lys-tyr-asn-glu-arg-pro-met-leu-his
d. Trypsin ⇒ ala-gly-phe-met-ser-lys-tyr-asn-glu-arg-pro-met-leu-his
e. Chymotrypsin ⇒ ala-gly-phe-met-ser-lys-tyr-asn-glu-arg-pro-met-leu-his
f. Elastase ⇒ ala-gly-phe-met-ser-lys-tyr-asn-glu-arg-pro-met-leu-his
Isoelectric point (pI) ⇒ the pH at which the net charge on the amino acids is zero
1. There are 13 diprotic acids (ala, asn, gln, gly, ile, leu, met, phe, pro, ser, thr, trp, val)
H2A+ ⇋ HA ⇋ A–
Since the neutral form predominates between pKa1and pKa2⇒ pI =
For example the pI of glutamine = = 5.65
2. There are 7 triprotic acids (arg, asp, cys, glu, his, lys, tyr) ⇒ however we can break these 7 into 2 subcatagories
a. Triprotic acids with a net +1 charge when fully protonated (asp, cys, glu, tyr)
H3A+ ⇋ H2A ⇋ HA– ⇋ A2–
Since the neutral form predominates between pKa1and pKa2⇒ pI =
For example the pI of cysteine = = 5.14
b. Triprotic acids with a net +2 charge when fully protonated (arg, lys, his)
H3A2+ ⇋ H2A+ ⇋ HA ⇋ A–
Since the neutral form predominates between pKa2 and pKa3 ⇒ pI =
For example the pI of his = = 7.60
Why do we care? pH and pI will tell you the net charge which helps us to understand how amino acids separate when subjected to a potential (premiss of electrophoresis)
Condition / Net Charge / ElectrophoresispH = pI / 0 / no migration
pH < pI / + / migrates to the cathode
pH > pI / – / migrates to the anode
pI Scale
lowest pI highest pI
asp (2.98), glu (3.22) < ------most amino acids (~5–6) ------> his (7.61), lys (9.87), arg (10.76)
most negative most positive
(at any one pH) (at any one pH)