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UNIVERSITEIT VAN PRETORIA

UNIVERSITY OF PRETORIA
YUNIBESITHI YA PRETORIA

Faculty of Natural and Agricultural Sciences

Department of Biochemistry, Genetics and Microbiology

BCM 251

EXAMINATION

Time: 90 min

20 June 2019
Total: 90marks

Internal examiners: Prof. O, Reva: Dr. P. Motshwene

Internal moderator: Prof. A. Joubert

" Answer all the questions.

" The question paper consists of 17 pages.

Question Maximum Marks

1 10

2 10
3 25
4 10
5 11
6 8
7 6
8 10
Total: 90 I90

Student name and surname:

Student number:
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QUESTION 1 |/10]

1.1 A) Explain properties of the chiral center. (1)

B) How many chiral centers are there in a molecule that has six
stereoisomers? How many enantiomers does this molecule have?
(2)

C) The molecular formula of a compound with two stereoisomers is

CH,NO,S? Explain, which atom (carbon, hydrogen, nitrogen, oxygen or
sulfur) can be a chiral center in this molecule? (2)

1.2 List the amino acids that exhibit the following characteristics: (5)

A) Contain hydroxyl groups in side chains

B) Contain aromatic rings in side chains

 C) Contain a hydrogen atom as the side chain

D) Contain amide groups in side chains

E) Have the following titration curve

10 pk,

8
759
6.0
6
pH

pk, =
1,82
2

1.0 2.0 3.0

OH (equivalents)

QUESTION 2 L 10]

2.1 Histones are proteins found in eukaryotic cell nuclei, tightly bound to
acidic phosphate groups of DNA. Explain what should be the isoelectric
point (p) of histones toallow such strong binding? What class of amino
acid must be abundant in histone structures? (2)
2.2 Complete hydrolysis of a hexapeptide by 6M HCI at 110°C followed by
amino acid analysis indicated the presence of Cys, Met and Gly in an
equal ratio. Complete digestion of the peptide with cyanogen bromide
after a denaturation step with B-mercaptoethanol yielded two smaller
peptides of the same molecular weight.
A) ldentify amino acids in the scheme below and write their names into
provided boxes: (6)

B) Name the N-terminal and C-terminal amino acids of this peptide:

(2)
N-terminal:

C-terminal:

QUESTION 3 L /25]

3.1 Explain the experiment performed by C. Anfinsen with ribonuclease A and

formulate the Anfinsen dogma concluded from this experiment. What is
the importance of the Anfinsen dogma for genetics and general biology?
(6)
3.2 In the scheme below, a globular structure of a trans-membrane protein
within the cellular membrane is shown. Explain the distribution of amino
acids in the core part and on the surface of the globe. (2)

O00
O00

3.3 Explain the role and functioning of chaperone proteins. Explain, why
several chaperones (chaperonins) possess an ATPase activity? (3)
3,4 Edman degradation of a protein revealed N-terminal Ser and Pro in 2:1
ratio? What is the minimal number of sub-units this protein is built of?
(1)

3.5 What is the problem with the identification of Leu and lle by mass
spectrometry?
(1)

3.6 Give examples of at least two fiber proteins. (2)

3.7 Write down the amino acid sequence of the tripeptide shown below. (4)
CH,
-NH,

NH O
3.8 Which types of non-covalent bonds are involved in creation of the
secondary structure of proteins? (2)

3.9 The structure of the heme prosthetic group is shown. This group is
plugged into the protein moiety of myoglobin as in the scheme below.
Explain, which site of the heme structure, A or B, is this prosthetic group
plugged into the core moiety of the myoglobin globe? (2)

4
O
CH
CH

CHg
ccHs
CH

CH C-CH

H, CH
B CH2
3.10Explain the role of amino acid residues His E7 and His F8 in the
functioning of the heme group in myoglobin. (2)

His E7

Binding site
for oxygen

Heme group

His F8
QUESTION 4 1101

4,4 Name the enzyme that catalyses the proteolytic reaction shown on the
(2)
diagram below.

Trypsinogen
Unactive)
val-Aspl,-ys-ile

va-aspl,-y
Trypsin
(active)
245

4.2 With the aid of the diagram below, explain how the shown zymogen is
activated. (8)

Chymotrypsinogen
245

Arg lle

14
Leu lle TvY A
A
 QUESTION 5 L11]
Write the letter of your choice in the box provided.
5.1 Following several experiments, the data presented on the graph below was
obtained. What can you determine from this graph? (1)

1No

14S1

A) This data may have been collected both in the absence (solid line) and
presence (dashed line) of a competitive inhibitor.
B) This data may have been colected both in the absence (solid line) and
presence (dashed line) of a mixed (noncompetitive) inhibitor.
C) This data may have been collected both in the absence (solid line) and
presence (dashed line) of mechanism based inhibitor.
D)) This data may have been collected both in the absence (solid line) and
presence (dashed line) of an inhibitor which binds the active site.
E) More than one of the above are correct.

5.2 Based on the figures below, which of the following expressions would be
Correct? (1)

1
S
A) Vmax = 1/B
B) C= 1/ Vmax
C) D= Vmax
D) D=1/ Vmax
E) A=1/ Vmax

5.3 A Lineweaver-Burk plot is also referred to as (1)

I) a sigmoidal plot.
Il) a linear plot.
I1) a Michaelis-Menten plot.
IV) a double reciprocal plot.
Select a combination of correct answers as shown below:
 A) I
B) II, II
C) IV
D) II, IV
E) II, IV

5.4 The Michaelis constant (KM) is defined as (1)

I) (k+ k,Mk,

IlI) (S]= [ES].

IV) [ESJ2.
Selecta combination of correct answers as shown below:

A) I
B) I, I|
C) II
D) I, IV
E) II, IV

5.5 Enzyme activity in cells is controlled by which of the following? (1)

I) Covalent modifications
II) Modulation of expression levels
III) Feedback inhibition
IV) Allosteric effectors
Select a combination of correct answers as shown below:

A) I
B) I
C) lII
D) III, IV
E) I, I1, II, IV

5.6 An uncatalyzed reaction has a rate of 4.2x 10- sec1. When an enzyme is
added the rate is 3.2 x 10 sec1. Calculate the rate enhancement caused by
the enzyme. (1)
A) 3.2 x 10
B) 7.4 x 10-3
C) 1.3 x 102
D) 7.6 x 1010
E) The data are not appropriate for the calculation requested.

5.7 Which of the following is TRUE about enzymes? (1)

I) Enzymes typically catalyze reactions at much higher rates than chemical
catalyst.
II) Enzymes are often very specific for their substrates.
III) Enzyme activities can often be regulated.
IV) Enzymes typically act under milder conditions of temperature and pH than
chenical catalysts.
Select a combination of correct answers as shown below:
 A) I, I,
B) I, II, II, IV
C) II, II
D) II, IV
E) II, I, IV

5.8 Alcohol dehydrogenase catalyzes the conversion of methanol to

and is, therefore, classified as a(an) (1)
A) acetic acid; transferase
B) formaldehyde; oxidoreductase
C) acetic acid; oxidoreductase
D) ethanol; lyase
E) formaldehyde; transferase

5.9 Zymnogens are not enzymatically active because (1)

A) the active site amino acids have been mutated.
B) they have not yet bound the proper cofactor.
C) their environment has the wrong pH.
D) they are not yet shaped such that essential proximity and orientation
catalysis can occur.
E) None of the above is correct.

5.10 In the lysozyme reaction the Dring in NAM is in the

conformation providing a contribution of catalytic energy via the
distortion. (1)

A) half-chair; electrostatic
B) chair; strain
C) boat; strain
D) boat; electrostatic
E) half-chair; strain
5.11 Determine the Ky and Vmax from the following graph. (Note: On the x
axis the minor tick mark spacing is 0.005; on the y-axis the minor tick mark
spacing is 0.002) (1)
0.05

0.04

0,03

0.02 +

0.01

-005 -0.025 0.025 0.05 0.075 0.1 0.125 0.15 0.175 o.225
-0.01 1/[ST

A) Ku= [0.006]; Vmax =0.0075/s

B) Kå= [0.196]; Vmax =0.0075/s
C) Ky=[165]; Vma =33/s
D) Ku= (33]; Vmax = 167/s
E) Ky= 270]; Vmax X= 68/s

QUESTION 6 L8
The existence of multiple substrates involved in an enzyme-catalysed reaction
leads to a complexity in the order of events that can occur. One of the events
is random substrate binding. Draw a Cleland notation diagram to illustrate this
mode of substrate binding.
QUESTION 7 /6]
We extensively discussed the findings of the paper published in "Molecular
Cell 21, 711-717,
tyrosine kinase
2006"FGFR1
in our lectures. Briefly, the paper
autophosphorylates
reports
itself and
that that
the
autophosphorylation is mediated by a sequential and precisely ordered
reaction. Adiagram describing the autophosphorylation sites of FGFR1 and a
native gel of different FGFR1 autophosphorylation states are shown.

Tryp1 Tryp2
Tryp3 Tryp4 OP
1P
2P 3P
398 4P
SP
480 576 761 cO,H
458 765
FGFR1K

7.1 Which amino acid was mapped to:

A) OP (1)

B) 1P (1)

7.2 If Y463 were mutated to a threonine

A) how many autophosphorylation sites would there be? (2)

B) which amino acids would be autophosphorylated? (2)

QUESTION 8 110]

8.1 An enzyme catalysed reaction has a Km of 8 mM and a Vmax of 13 nM.s-1.

Use the Michaelis-Menten equation to calculate the reaction velocity when
the substrate concentration is 18 mM. (5)

8.2 Briefly describe how Alexander Fleming, a bacteriologist in London

discovered the enzyme lysozyme in 1922. (4)
8.3 The enzyme N-myristoyltransferase catalyses its substrates resulting in
them having a reversible covalent modification. What is the name of this
modification? (1)