NAME:
CH4710 Fall 06
Mid-term II, 15 Nov. 06
Answer each answer in a complete and concise manner. Use structural representations
to support your answer where applicable
--------------------------------------------------------------------------------------------------------------------1) Draw the structure of the tripeptide, gly-ala-glu at pH 7.0.
1b) What is the net charge of the peptide at pH 7.0?
2) The following reagents are often used in protein chemistry. How are they used in
establishing the amino acid sequence of polypeptides?
A) CNBr
B) Performic acid
C) Trypsin
3) A polypeptide is hydrolyzed and it is determined that there are three Lys residues,
two Arg residues and other residues. How many peptide fragments can be expected
when the native polypeptide is incubated with the proteolytic enzyme trypsin? How
would you determine the peptide at the carboxylic acid terminus?
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4) Why do amino acid residues with positively charged side chains occur towards the
C-terminus of the α-helix ? Draw a schematic figure to explain your answer.
5) Consider the following observations: Alkaline phosphatase is a metalloenzyme
which requires Ca2+ ions for activity.
In experiment 1, the enzyme denaturated rapidly in the presence of low concentrations
of urea; upon subjecting the denatured enzyme to dialysis, the enzyme recovered
activity.
In experiment 2, the enzyme was denatured in the presence of urea and EDTA. In this
case, the denatured enzyme did not regain activity upon dialysis. Explain the
experimental observations in experiments 1 and 2. Why was the enzymatic activity not
regained in experiment 2?
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8) Is a transition state analog the same as a competitive inhibitor? Explain your
answer.
9) Name three factors that lead to the destabilization of [E-S] complexes. Explain each
in 2-3 sentences.
10) Write a reasonable mechanism for the hydrolysis of the peptide bond between the
dipeptide ala-val.
Papain is a protease that cleaves peptide bonds. A cysteine residue at the enzyme
active site is essential for catalysis. The cysteine residue acts as a nucleophile and
forms a covalent bond with the substrate. Write a mechanism for the papain-catalyzed
hydrolysis for the peptide above.
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