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Faculty of Natural and Agricultural Sciences
Department of Biochemistry, Genetics and Microbiology
Introduction to proteins BCM 251
SEMESTER TEST 1
Time: 1 hour
1 March 2019
Total: 60 marks
Internal examiners: Prof. O. Reva
Instructions:
♦ Answer all the questions.
♦ The question paper consists of 9 pages.
Question Maximum Marks
1 10
2 5
3 15
4 15
5 15
Total: 60 /60
Page 1 of 9
QUESTION 1 (10)
1.1 Which chemical properties are common for all amino acids due to the
presence of carboxyl groups? (4)
1. Salt formation (reaction with metals) - 1
2. Esterification (reaction with alcohols) - 1
……………………………………………………………………………………………
3. Decarboxylation - 1
4. Reaction with amines - peptide bond formation – formation of amide
…………………………………………………………………………….……………..
bonds between carboxyl and amine groups - 1
5. Color reactions with ninhydrin and Sanger’s reagent – 0.5
……………………………………………………………………………………………
TOTAL: 4.5 to allow 0.5 error
……………………………………………………………………………………………
1.2 Complete the general structure of L-amino acids. (4)
? COO-
│
? NH3+ ▬C▬ ? H
│
R
If it is –NH2 and –COOH, or –NH3 and COO without signs, it is not an
error, but amino group must be to the left.
1.3 How many chiral carbon atoms do the following amino acids have? (2)
1 1
……………………………………………………………………………………………………………………………………………….
0 2
……………………………………………………………………………………………………………………………………………….
Page 2 of 9
QUESTION (5)
2.1 Which two amino acids are ambivalent (can be found on surface and
inside of proteins)? (1)
A. Leucine and Isoleucine
B. Alanine and Glycine
C. Phenylalanine and Tryptophan
D. Histidine and Tyrosine
E. Glutamic acid and Lysine
2.2 Which two amino acids can never be found in proteins? (1)
A. L-Cysteine and L-Methionine
B. L-Hydroxyproline and L-Hydroxylysine
C. L-Ornithine and L-Citrulline
D. L-Selenocysteine and L-Selenomethionine
E. α-Alanine and β-Alanine
2.3 Which two amino acids may be encoded in genes by stop codons? (1)
A. L-Methyllysine and L-Methyllysine
B. D-Ornithine and L-Citrulline
C. L-Selenocysteine and L-Pyrrolysine
D. L-Thyroxine and Desmosine
E. L-Hydroxyproline and L-Hydroxylysine
2.4 Which two amino acids can bind to each other by electrostatic (ionic)
forces? (1)
A. L-Leucine and L-Isoleucine
B. L-Histidine and L-Glutamate
C. L-Asparagine and L-Aspartate
D. L-Threonine and L-Glycine
E. L-Phenylalanine and L-Tyrosine
Page 3 of 9
2.5 Which two amino acids can bind to each other by hydrophobic forces?
(1)
A. L-Tryptophane and L-Isoleucine
B. L-Glutamine and L-Glutamate
C. L-Alanine and L-Glycine
D. L-Threonine and L-Serine
E. L-Arginine and L-Lysine
QUESTION 3 (15)
3.1 Write single letter codes of the given amino acids in provided spaces
after question marks. (5)
K Q C
R E
3.2 Write down 3-letter codes of the amino acids shown above, grouping
them by the following categories: (6)
a) Positively charged at neutral pH:
……………………………………………………………………………………………
Lys, Arg
……………………………………………………………………………………………
……………………………………………………………………………………………
Page 4 of 9
b) Negatively charged at neutral pH:
……………………………………………………………………………………………
Glu
……………………………………………………………………………………………
……………………………………………………………………………………………
c) Uncharged at neutral pH:
……………………………………………………………………………………………
Gln, Cys
……………………………………………………………………………………………
……………………………………………………………………………………………
d) Amino acids able to create disulfide bonds:
……………………………………………………………………………………………
Cys
……………………………………………………………………………………………
……………………………………………………………………………………………
3.3 Write down full names of the amino acids, which structures are shown
below, grouping them by the following categories: (4)
a) These amino acids may be found predominantly inside of protein globs:
……………………………………………………………………………………………
Leucine
……………………………………………………………………………………………
……………………………………………………………………………………………
Page 5 of 9
b) These amino acids may be found predominantly outside (on the surface) of
protein globs:
……………………………………………………………………………………………
Serine, Histidine, Lysine
……………………………………………………………………………………………
……………………………………………………………………………………………
QUESTION 4 (total is 16 to allow 1 mark error, but the final mark <= 15)
4.1 Calculate the isoelectric points (pI) of the following amino acids. Refer to
the pKa values in the provided table. (5)
𝟏. 𝟖𝟖 + 𝟑. 𝟔𝟔
Aspartate = = 𝟐. 𝟕𝟕
𝟐
𝟐. 𝟏𝟏 + 𝟒. 𝟐𝟐
Glutamate = = 𝟑. 𝟐𝟐
𝟐
𝟔. 𝟎𝟎 + 𝟗. 𝟏𝟏
Histidine = = 𝟕. 𝟓𝟓
𝟐
Proline = 𝟏. 𝟗𝟗 + 𝟏𝟏. 𝟗𝟗 = 𝟔. 𝟗𝟗
𝟐
𝟐. 𝟐 + 𝟗. 𝟏𝟏
Tyrosine = = 𝟓. 𝟔𝟔
𝟐
pI may be estimated roughly
4.2 Electrophoresis was performed at pH 6.5 with a mixture of amino acids:
aspartate, glutamate, histidine, proline and tyrosine. Identify these amino
acids in the scheme below and write their names into the provided fields.
(Hint: refer to the table in question 4.1).
(5)
1 Asp 2 Pro 3 His
4 Glu 5Tyr
Optionally, either in here or there
Starting well
Aspartate Proline Histidine
1:__________________; 2: __________________; 3: __________________;
Glutamate Tyrosine
4: _________________; 5: __________________;
Page 6 of 9
4.3 Inspect the titration curve of glycine shown below and answer the
following questions:
a) Which species of glycine ─ 1, 2 and/or 3, can be found in the solution at
pH 2.34?
(3)
1.
2.
3.
1 and 2
……………………………………………
b) At which pH does glycine exist only as zwitterion? (1)
pH = 5.97
……………………………………………………………………………………………
c) Write down the range of pH, when glycine can be found in the solution in the
form
: (2)
from pH 0 to pH 5.97 if 0–2.34 – give 1 mark
……………………………………………………………………………………………
Page 7 of 9
QUESTION 5 (15)
5.1 Consider the following peptides. Which of these have a positive charge,
negative charge or no charge at neutral pH? Give a short explanation to
motivate your answer. (6)
Charge at neutral pH:
(▬) (0) (+)
Gly─Ile─Cys─Met─Thr
………………………………………………………
This peptide contains only uncharged Yes
………………………………………………………
amino acids
………………………………………………………
Ala─Phe─Asp─Trp─Glu
This peptide contains two negatively
………………………………………………………
Yes
charged Asp and Glu, and uncharged
………………………………………………………
amino acids
………………………………………………………
Leu─His─Val─Lys─Asn
This peptide contains two positively
………………………………………………………
Yes
charged His and Lys, and uncharged
………………………………………………………
amino acids
………………………………………………………
5.2 Write down the sequence of the given peptide using the one letter code.
Hint: i) identify peptide bonds; ii) identify amino acids by their side chains
(R-groups); iii) consider the direction of the peptide chain. (6)
H G CH3 A
│ │
NH─CO─CH─NH─CO─CH─NH3+
K
│
NH3+─CH2─CH2─CH2─CH2─CH
│
CO─NH─CH─CO─NH─CH─COO-
│ │
A CH3 N CH2─CO
│
NH2
……………………………………………………………………………………………
AGKAN
……………………………………………………………………………………………
Page 8 of 9
5.3 Consider the following peptides. Complete the table by indicating whether
the peptides are hydrophilic or hydrophobic and can form internal
disulphide bonds?
(3)
Properties: Internal
Hydrophobic Hydrophilic ─S─S─
bonding
ACNTSCQRH
Yes Yes
MILGVMAGW
Yes
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Page 9 of 9
