Name:
BIOCHEMISTRY (CHEM 360)
EXAM 1
September 21, 2012
There are five pages, NINE questions, and a total of 105 points in this exam.
Please read each question carefully and possibly more than once. Good luck…
(11)
1.
The structure of tyrosine is given below (ionization behavior is not illustrated) The pKa
values of tyrosine are as follows: pKa1 (carboxylate) 2.2, pKa2 (ammonium) 9.1,
pKa3 (acidic side chain) 10.1.
Please answer questions 1.1 to 1.2. Show your work
1.1.
1.2.
Calculate the average net charge of tyrosine
(i)
at pH 2.2
(ii)
at pH 9.1
(iii)
at pH 10.1
Calculate the isoelectric point, pI, of tyrosine.
(18)
2.
Write structures for the following amino acids. Give their three-letter as well as one-letter
abbreviations (no credit for this without a structure). The ionization state is not important.
2.1.
asparagine
2.3.
an achiral amino acid
2.2.
methionine
(6)
3.
Show the structure of a diester of carbonic acid (dialkyl carbonate) and benzyl alcohol
(2 equivalents)
O
HO
OH
OH
carbonic acid
benzyl alcohol
(9)
4.
Name the following peptide
3.1.
using three-letter abbreviations
3.2.
using single letter abbreviations
(12)
4.
Characteristic features of tRNA is illustrated below. Draw the full structure of the
nucleotide (only one) in tRNAphe which is linked to the amino acid. Comment, from a
synthetic chemist’s point of view, how and why this amino acid is considered
“activated”.
Page 2
(14)
5.
Complete the following equations. Show all the products formed.
5.1.
pH 8.5
5.2.
(5)
6.
What would you add into a dilute aqueous solution of acetic acid to ensure that the pH of
the solution is equal to the pKa of acetic acid?
Page 3
(15)
7.
Circle the best correct answer for the multiple choice questions given below:
7.1.
Which of the following compounds will yield carbon dioxide upon
catalytic hydrogenation?
O
O
O
H
N
O
O
O
(a)
(b)
(1) only (a)
(2) only (b)
(5) both (b) and (c)
7.2.
(3) only (c)
(c)
(4) both (a) and (b)
A protein which contains more isoleucine, leucine, and phenylalanine than
arginine, asparagine, and lysine is likely to be
(1) hydrophobic
(2) hydrophilic
(4) none of the above (5) all of the above
(3) neutral
7.3.
What is the pH of the solution when 1.0 mL of 0.1M NaOH is added to 99
mL of water?
(1) 3
(2) 7
(3) 14
(4) 11
7.4.
Which of the following compounds can be classified as an acetal?
H
N
O
O
O
O
OCH 3
(1)
7.5.
O
O
(2)
O
(3)
(4)
The "central dogma" of information flow in biochemical systems is
protein
DNA
RNA
DNA
protein
DNA
RNA
protein
DNA
protein
(4)
(3)
DNA
protein
(2)
(1)
RNA
RNA
RNA
(5)
protein
RNA
(6)
Page 4
DNA
(12)
8.
The reaction below is one of the steps in the synthesis of a peptide.
8.1.
Describe (only in words) the function of Reagent A
8.3.
Write down the structure of the missing product (for the step below only)
8.4.
Write down the synthetic target dipeptide using three-letter abbreviations for
amino acid residues.
C6H5
O
H3N
O
C6H5
+
O
O
N
H
O
O
Reagent A
?
(15)
9.
In a solution 75 mmol of histidine exists with its side chain protonated and 100 mmol
with the side chain unprotonated (side chain in free base form). Calculate the pH of the
solution after the addition of 25 mL of 1.0 M NaOH. The pKa of the histidine side chain
is 6.0.
9.1.
Draw the full structure of the major species of histidine as it exists at the pH
calculated above after the addition of 25 mL of 1.0 M NaOH.
Page 5
Page 6

1
2
3
4
5
6
7
8
9
10
11
12
TOT
11
18
6
9
14
5
15
12
15
0
0
0
105
Page 7