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CLAS – Chem109C – Ch 22 – Key
1. Answer the following:
a. Which amino acid(s) is achiral? glycine
b. Are naturally occurring amino acids D or L? L
2. Draw the following amino acids at pH = 0, 5, and 13.
a. Valine
+
O
O
+
H3N
OH
H3N
O
O
-
O
-
pH = 13
pH = 5
pH = 0
H2N
b. Glutamate
+
O
O
+
H3N
OH
HO
H3N
O
-
O
-
O
O
H2N
-
O
O
O
pH = 13
pH = 5
pH = 0
-
O
c. Lysine
+
H3N
O
+
OH
+
H3N
O
O
O
-
H2N
O
-
+
NH3
NH3
NH2
pH = 0
pH = 5
pH = 13
3. Calculate the pI of the following amino acids.
2.16+9.18
a. Phenylalanine ⇒
pI =
= 5.67
b. Histidine ⇒
pI =
c. Aspartic Acid ⇒
pI =
2
6.04+9.17
2
2.09+3.86
2
= 7.6
= 2.98
4. What is the net charge of the following amino acids at the designated pHs?
2.21+9.15
a. Serine at pH = 4 ⇒
pI =
= 5.68
since the pH < pI there is a net positive
2
b. Arginine at pH = 9 ⇒
pI =
c. Glutamic acid at pH = 5⇒
pI =
9.04+12.48
2
2.19+4.25
2
= 10.76
= 3.22
since the pH > pI there is a net negative
since the pH > pI there is a net negative
5. Which amino acids are the most polar and nonpolar? Most polar amino acids have a charge on their side chain such
as asp, glu, his, lys and arg. However the most nonpolar amino acids have a long saturated hydrocarbon as their
side chain such as leu and ile.
6. Thin layer chromatography of a solution of threonine, valine, lysine, alanine and serine yielded the following;
determine which amino acid goes with each spot?
from top (most nonpolar to bottom (most polar)
⇒ val, ala, thr, ser, lys
7. 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
c
a
from left (most negative or lowest pI) to right (most positive or highest pI)
8. Show how valine can be synthesized via…
a. HVZ
O
O
1. Br2, PBr3
OH
2. H2O
O
Br
O
3. xs NH3
OH
Br
+
NH3
Br
O
-
b. Reductive amination
O
1. xs NH3
O
OH
O
O
O
2. H2, Pd/C
-
+
NH
O
-
NH3
c. N-Phthalimidomalonic ester synthesis
O
O
EtO
OEt
+
OEt
N
O
N
EtO
O
O
4. H2O, HCl
O
OEt
N
2. - OEt
EtO
O
O
O
-
C
N
3. (CH3)2CHBr
OEt
O
O
EtO
O
O
-
Br
O
O
O

O
+
OH
NH3
d. Strecker Sythesis
2. -CN, HCl
1. NH3, trace acid
O
NH
N
+
NH3
2. H2O, HCl

O
+
NH3
O
-
9. Explain kinetic resolution ⇒ When you synthesize amino acids you’ll get a mixture of D and L – enantiomers have
identical physical properties making it challenging to separate them – in kinetic resolution you can take
advantage of the fact that certain enzymes (which are also chiral) will catalyze L faster than D (hence
kinetic) in particular reactions – this alteration on the L amino acid makes it have different physical
properties than the D and therefore can be separated by physical means such as chromatography or
distillation
10. Draw the met-ile-tyr-asn-his at pH = 7
H
N
+
H3N
O
N
O
NH
NH
NH
NH2 O
O
O
-
O
11. Provide 2 ways the following peptide can be synthesized:
p. 1077-1080
ala-gly-ser
12. Distinguish between primary, secondary, tertiary and quaternary structures of peptides and proteins.
primary ⇒ the sequence of the amino acids and the location of the disulfide bridges
secondary ⇒ regular conformations assumed by segments of the protein’s backbone when it folds (in order
to maximize H-bonds in the backbone)
tertiary ⇒ the 3D structure of the entire protein
quaternary ⇒ if a protein has more than one polypeptide chain (aka subunit) the quaternary structure is
the way the individual subunits arrange themselves with respect to one another
13. Descibe denaturation and give examples of possible causes for denaturation.
denaturation is destroying the highly organized tertiary structure of a protein – this may be caused by 1)
changing pH 2) chemical reagents (ex: ox agent) 3) change the solvent or 4) heat or agitation
14. 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