Dr. Amin F.

Majdalawieh NAME: Tala Abdulateef (74903)

Biochemistry (CHM 350)

MIDTERM 2 (01 July 2020) (8:00AM-8:50AM) – Version 3
Max. (60
Points)
Definitions (be as specific and precise as you can) (4
Points)

1. Fibroin
an example of a fibrous protein that is specifically made up of beta sheets. moreover, it is
composed of anti parallel beta sheets with almost 50% of their amino acids to be glycine.
Fibroin is very strong as the beta sheets are fitted and packed on top of each other. Also,
fibroin makes up the webs in many insects such as spiders.

2. Chaperonins
are cellular proteins that help and aid proteins in folding as they provide the optimal conditions
for proper folding of proteins. They are also called molecular chaperons as they have a groove
or a central cavity in order to help proteins in folding and prevent misfolding.

True (A) OR False (B) Questions (10

Points)

1. ( B ) π helices are examples of primary structures of proteins in vivo.

2. ( A ) The secondary structure of proteins arises from interactions among the R groups of the
amino acids.

3. ( A ) Some proteins in eukaryotic cells are made of two or more polypeptide chains.

4. ( B ) In α helices, hydrogen bonds are perpendicular to the axis of the helix of the polypeptide
chain.

5. ( B ) In π-helix (4.416 helix), there are 16 residues per single H-bonding loop.

6. ( B ) Ramachandran plot is a map that shows the possible tertiary structures within proteins.

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
7. ( B ) Collagen is a protein that is found in tissues that require a high degree of flexibility
and stretchability (e.g. ligaments).

8. ( A ) For the most part of any catalytic reaction, the enzyme-substrate complex concentration
(i.e. [ES]) exhibits a constant profile.

9. ( B ) Non-competitive inhibitors perform their function via covalent interactions.

10. ( A ) Usually, in vivo, enzyme inhibitors interfere with their target enzymes reversibly.

Multiple-Choice Questions (30

Points)

1. Which of the following amino acids is distinctive in its chemical nature among others listed below?
A. Alanine

B. Aspartic acid
C. Valine

D. Leucine
E. Methionine

2. Lysine is a(an) -------- amino acid.

A. Acidic
B. Basic
C. Polar
D. Two of the above
E. None of the above

3. Which of the following is NOT a post-translational modification of proteins?

A. Glycosylation
B. Ubiquitination

C. Phosphorylation
D. None of the above

E. All of the above

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
4. Which of the following amino acids is/are NOT usually found in the “turns” of polypeptide chains?
A. Tryptophan

B. Glycine
C. Proline

D. All of the above

E. None of the above

5. Both tyrosine and serine are uncharged, polar amino acids with similar structures. A one-amino acid
change from serine to tyrosine is designated as being
A. Non-conservative
B. Conservative

C. Semiconservative
D. Dispersive

E. Spontaneous

6. Amino acids at a pH that is almost equal to their isoelectric points (pI) are called
A. Enantiomers

B. Stereoisomers
C. Oligopeptides

D. Macroions
E. None of the above

7. If a protein is composed of two identical polypeptide chains, it is called a

A. Homodimer
B. Heterodimer

C. Quaternary structure
D. Two of the above

E. None of the above

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
8. If a polypeptide chain is 50 amino acids in length, its mRNA should contain at least
A. 50 α-helices

B. 50 nucleotides
C. 150 codons

D. Two of the above

E. None of the above

9. The first amino acid in all polypeptide chains in eukaryotes is

A. Glycine
B. Adenine

C. Alanine
D. Methionine

E. None of the above

10. Which of the following amino acids does/do NOT create “kinks” or “turns” in protein structure?
A. Glycine

B. Methionine
C. Cysteine

D. Two of the above

E. All of the above

11. The ψ (psi) bond links the α-carbon of an amino acid and the
A. Carbon atom within its carboxyl group
B. Nitrogen atom within its amino group
C. Oxygen atom within its carboxyl group
D. Hydrogen atom within its amino group
E. None of the above

12. Which of the following helical secondary structures have the highest number of residues per turn?
Α. 3.613 helix (α helix)
Β. 4.416 helix (π helix)
C. 310 helix
D. Parallel β sheet
E. Anti-parallel β sheet

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
13. Which of the following proteins is the single most abundant protein in mammals?
A. α-keratin

B. Fibroin
C. Collagen

D. Elastin
E. Immunoglobulin
14. The “closed-ring” conformation of proteins, where φ = 0 and ψ = 0, is NOT favored because it
A. Prevents H bonding between residues
B. Creates steric hindrance between the carbonyl oxygen and amino hydrogen in residues
C. Denatures at very low temperatures
D. Makes the size of a protein very large
E. All of the above

15. Keratins, fibroin, and collagen are examples of

A. Globular proteins
B. Quaternary structure proteins

C. Digestive proteins
D. None of the above

E. All of the above

16. Sometimes, protein refolding can be delayed because of
A. High alanine content

B. High proline content

C. Off-path intermediates

D. H bonding
E. None of the above
17. Mad cow disease (or BSE in humans) is caused by
A. Bacteria
B. Viruses

C. Worms
D. Prions

E. None of the above

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
18. The binding of a ligand (protein A) to its receptor (protein B) is considered
A. Ping-Pong interaction

B. Homotypic interaction
C. Random order binding

D. Ordered substrate binding

E. None of the above
19. Multisubunit proteins with multiple active sites that function as catalysts are called
A. Coenzymes
B. Ribosomes

C. Allosteric enzymes
D. Zymogens

E. Hybrid enzymes
20. Biochemists can accurately determine/predict the
A. Primary structure of proteins
B. Secondary structure of proteins
C. Tertiary structure of proteins
D. Two of the above
E. All of the above
21. All enzymes in animals are
A. Polysaccharides

B. Lipids
C. Prions

D. Glycolipids
E. None of the above
22. Ribozymes comprise a family of ----------- that function as biological catalysts/enzymes.
A. Antibodies
B. Polysaccharides

C. Proteins
D. DNA molecules

E. None of the above

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
23. Which of the following classes of enzymes catalyze intramolecular rearrangement?
A. Ligases

B. Isomerases
C. Hydrolases

D. Lyases
E. Transferases

24. In the Michaelis-Menten equation, Vmax refers to

A. Initial velocity of reaction
B. The velocity at which the rates of forward and reverse reactions are equal

C. Maximum concentration of enzyme

D. A state at which [substrate] is 50% of [enzyme]

E. None of the above

25. Which of the following is NOT true about catalysts/enzymes?

A. They increase the rate of reactions

B. They function by increasing the activation energy

C. They can be recycled and reused

D. They do not affect the equilibrium of reactions

E. None of the above

26. Enzyme efficiency can be measured as being equal to

A. [E]/[S] at the beginning of the catalytic reaction
B. [E]/[S] at the end of the catalytic reaction

C. Vmax/Km
D. Kcat/Km

E. 1/Vmax

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
27. Which of the following enzyme inhibitors do NOT affect the order/sequence of amino acids in their
target enzymes?
A. Non-competitive inhibitors

B. Competitive inhibitors
C. Reversible inhibitors

D. Irreversible inhibitors
E. All of the above
28. Which of the following is TRUE about coenzymes?
A. Coenzymes are relatively small organic molecules
B. Coenzymes enhance the catalytic activity of enzymes

C. Most coenzymes are derivatives of water-soluble vitamins

D. All of the above

E. None of the above

29. Which of the following enzyme inhibitors change Vmax but do NOT affect Km?
A. Non-competitive inhibitors

B. Competitive inhibitors
C. Electron carrier inhibitors

D. G protein inhibitors
E. All of the above

30. Competitive inhibitors

A. Compete with substrate for the active site of enzyme
B. Do not compete with substrate for the active site of enzyme

C. Increase the rate of the catalytic reaction

D. Decrease the Km value of the catalytic reaction

E. Two of the above

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
Short-Answer Questions (16
Points)

1. Fill-in the blanks: (6 Points)

(1) renaturation A process by which a globular protein returns to its folded state after being
denatured.

(2) isoelectric species The form of a molecule that has an equal number of positive and negative
charges, thus it is neutral.

(3) closed ring An unfavored conformation of a polypeptide chain with φ = 0 and ψ = 0.

(4) prions Mis-folded forms of the proteins that can cause diseases in mammals.

(5) random substrate binding A class of multi-substrate reactions in which substrates bind in no
specific order to the enzyme.

(6) catalase The enzyme that catalyzes H2O2 decomposition in cells.

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
2. The kinetics of an enzyme are studied in the absence and presence of 0.5 mM inhibitors
(phenylthiourea and PHBA). The Lineweaver-Burk plot depicting 1/[S] versus 1/V is shown below.
Concentration units are mM and rate (velocity) units are mM/s. Answer the following questions.
(10 Points)

(a) Determine Km and Vmax values in absence and presence of

phenylthiourea.

No inhibitor:
Km =
1/ [S] = -1/Km = -1
Km = -1/-1 = 1 mM

Vmax =
1/Vmax = 5
Vmax = 1/5 = 0.2 mM/sec

Phenylthiourea:
Km =
1/ [S] = -1/Km = -1
Km = -1/-1 = 1 mM

Vmax =
1/Vmax = 10
Vmax = 1/10 = 0.1 mM/sec

(b) Does phenylthiourea act as a competitive or non-competitive inhibitor? Why?

According to the graph, phenylthiorea is a non-competitive inhibitor since the km value is not
changed as the enzyme substrate affinity is not affected meaning that adding/ increasing the
substrate concentration does not affect the km value. Also, the Vmax value is lowered or
decreased, from 0.2 mM/sec to 0.1 mM/sec, indicating that the inhibition type is surely non
competitive (Km is constant with the presence and absence of inhibitor and Vmax is
decreased).

(c) What is the concentration of substrate that is required to reach one-half Vmax in absence of presence
of phenylthiourea?

[S] or the concentration of the substrate is the same in the absence and presence of the inhibitor
since it is a non competitive inhibitor. This means that since Km value defines the concentration of
the substrate to reach half of Vmax (Km is the substrate concentration that allows you to reach
half of Vmax), [S]= 1 mM. (Km= Vmax/2). In conclusion, regardless of the presence or absence of
the inhibitor, the concentration of the substrate is 1 mM since Km remains unchanged in
noncompetitive inhibition.

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Dr. Amin F. Majdalawieh NAME: Tala Abdulateef (74903)
(d) Inhibitor X, which has much higher affinity to the enzyme compared to phenylthiourea and PHBA,
binds to a region about 150 amino acids away from the active site of the enzyme. Draw a dashed line
on the plot (above) depicting the effect of inhibitor X. Briefly explain your answer.

In this case, inhibitor X has a much higher affinity to the enzyme making the rate much faster
than phenylthiourea and PHBA such that it functions as a competitive inhibitor as it mimics
and resembles the substrate having similar physical and chemical characteristics. Meaning
that Vmax remains unchanged but Km is increased. This makes Km= -1/-0.25 = 4 mM in
which the Km is higher than that of phenylthiourea and PHBA (1 mM and 2mM respectively).

(e) If [S] = 120 mM, what fraction of the enzyme molecules have a bound substrate in absence of and
presence of 0.5 mM phenylthiourea?

In the case of absence of the inhibitor, all the enzyme molecules will have a bound substrate since
the enzyme will be fully saturated with substrates making the capacity of the enzyme reaching its
absolute maximum and thus the reaction rate increases until it reaches a plato in which it becomes
constant and cannot increase beyond that point. Furthermore, the maximum capacity of the
enzyme is reached and thus 100% of the enzyme molecules would have a bound substrate in the
absence and presence of the inhibitor. This means that 100% of the enzymes have a bound
substrate since the concentration of the substrate is increased leading to a saturated enzyme that
reaches Vmax.

On the other hand, in the presence of the inhibitor, less than 100% of the enzymes will have a
bound substrate since even though noncompetitive inhibitors bind to other positions than the
active site, they do distort the overall structure of the enzyme and affect the shape of the active site
and thus blocking or preventing the substrates to bind to the active site.

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