Dr. Amin F.

Majdalawieh NAME:

Biochemistry (CHM 350)

ASSIGNMENT 2 (DUE: 15 March 2021)
Max. (80 Points)
Definitions (be as specific and precise as you can) (10 Points)
1. Prions

Prions are infectious misfolded proteins that lead to pathogenic diseases in the host. Moreover, prions carry
out the wrong function (because it is misfolded) and can also cause autoimmune conditions because the
immune system would consider them as foreign substances, initiating an immune attack against it. An example
of a disease caused by prions is mad cow disease.

2. Essential Amino Acids

Essential amino acids are the amino acids that the body is incapable of synthesizing on its own. Instead, these
amino acids are supplied through the diet (by eating animal and plant proteins). The 8 essential amino acids
are isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine.

3. Ramachandran Plots

A Ramachandran plot is a map with phi and psi angles as the x and y coordinates of the plot. This plot
demonstrates the sterically allowed (favored) secondary conformations. Each point on this plot demonstrates
a specific secondary structure for a certain segment of a protein.

4. Turnover Number (Kcat)

The turnover number (Kcat) is a direct measure of the rate of the catalytic synthesis of the product under
optimal conditions as it represents the time frame required by an enzyme to “turnover” one substrate molecule.
Kcat also measures the number of substrate molecules turned over per enzyme per second.

5. Zymogens

Zymogens are slightly long, catalytically inactive molecules that are cleaved proteolytically in the intestine to
yield active enzymes. In other words, zymogens are inactive enzymes that are converted into their active
forms through proteolytic cleavage. Examples include trypsinogen, chymotrypsinogen, proelastase, and
procarboxypeptidase.

True (A) OR False (B) Questions (12 Points)

1. ( B ) Local folding within an amino acid sequence forces quaternary structure formation of a protein.

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 Dr. Amin F. Majdalawieh NAME:

2. ( A ) Like DNA, protein structure was primarily revealed through x-ray diffraction experiments.

3. ( A ) In an  helix, hydrogen bonds are almost parallel to the helix axis.

4. ( A ) The ψ bond links the -carbon of an amino acid and the carbon atom within its carboxyl group.

5. ( B ) In 310 helix, there are 10 residues per single H-bonding loop.

6. ( A ) Fibrous proteins are elongated, filamentous molecules with well-defined secondary structures.

7. ( B ) A protein that functions as an enzyme in the stomach will most likely be a fibrous protein.

8. ( B ) All regions of a globular protein can be classified as either  helices,  sheets, or turns.

9. ( B ) All naturally occurring catalysts are proteins.

10. ( A ) A particular enzyme inhibitor can inhibit a catalytic reaction either reversibly or irreversibly.

11. ( A ) Many essential vitamins are constituents of coenzymes.

12. ( B ) All enzymes require sufficient amounts of Mg++ ions (a form of metal ions) to function at their
optimal efficiency.

Multiple-Choice Questions (18 Points)

1. All amino acids share the following entities EXCEPT
A. Amino group
B. H-atom
C. -carbon
D. Aromatic ring
E. Carboxyl group

2. Glycine is unique compared to the other 19 amino acids in that

A. It contains two side chains (R groups)
B. It contains two H atoms associated with the -carbon
C. It is non-polar
D. It is polar
E. It cannot be titrated by a base

3. Proteins found in the human body are made of

A. L-amino acids only
B. D-amino acids only
C. Mostly L-amino acids with a few D-amino acids
D. Mostly D-amino acids with a few L-amino acids
E. None of the above

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 Dr. Amin F. Majdalawieh NAME:
4. Amino acids at a pH that is almost equal to their isoelectric points (pI) are called
A. Enantiomers
B. Stereoisomers
C. Zwitterions
D. Macroions
E. Oligopeptides

5. A protein that is made of two identical polypeptide chains is called a

A. Heterodimer
B. Heterotrimer
C. Homodimer
D. Homotrimer
E. Oligopeptide

6. Which of the following secondary structures have the highest number of residues per turn?
A.  helix
B.  helix
C. 310 helix
D. Parallel  sheet
E. Anti-parallel  sheet

7. Ramachandran plots enable biochemists to predict the

A. Number of amino acids in a protein
B. Number of H bonds in a protein
C. Possible conformations of a protein
D. Melting temperature of nucleic acids (DNA and RNA)
E. Number of monosaccharide residues in a homopolysaccharide

8. Keratins, fibroin, collagen, and elastin are examples of

A. Globular proteins
B. Fibrous proteins
C. Non-catalytic proteins
D. Two of the above
E. All of the above

9. Which of the following is found in animals but NOT in plants?

A. Globular proteins
B. Fibrous proteins
C. Digestive proteins
D. None of the above
E. All of the above

10. Which of the following families of cytoskeletal forms do keratins belong to?
A. Microtubules
B. Intermediate filaments
C. Microfilaments
D. None of the above
E. All of the above

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Dr. Amin F. Majdalawieh NAME:

11. Fibroin is a protein found in silkworms and spiders, and it is composed of

A.  helices
B. Parallel  sheets
C. Anti-parallel  sheets
D.  helices
E. 310 helices

12. Collagen is a fibrous protein that is primarily found in

A. Ligaments
B. Nails
C. Bone & cartilage
D. Beesweb & spiders
E. None of the above
13. Which of the following amino acid residues create “kinks” or “turns” in protein structure?
A. Glycine
B. Methionine
C. Proline
D. Two of the above
E. All of the above

14. Proteins that assist in proper folding of proteins are called

A. Immunoglobulins
B. Topoisomerases
C. Mutarotases
D. Keratins
E. Chaperonins

15. 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

16. Which of the following factors can affect enzyme activity?

A. pH
B. Temperature
C. The presence of certain metal ions
D. The addition or removal of phosphate
E. All of the above

17. 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

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Dr. Amin F. Majdalawieh NAME:

18. Kinase-Phosphatase reactions

A. Inhibit ATP breakdown
B. Involve the addition or removal of a phosphate group
C. Involve the addition or removal of a ketone group
D. Involve the addition or removal of an amino acid to a polypeptide chain
E. Involve the transfer of hydrogen atoms

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 Dr. Amin F. Majdalawieh NAME:
Short-Answer Questions (40 Points)
1. Using structures and equations, illustrate how a tripeptide made of alanine, tyrosine, and glycine forms.
Make sure you include proper labeling of all structural components of the tripeptide. (10 Points)

2. What are the four criteria (or principles) that were postulated by Linus Pauling and his colleagues that
protein structures should obey? (6 Points)

- The bond lengths and bond angles should be distorted as little as possible from those found by X-ray
diffraction studies.
- No two atoms can come close to each other more than their Van der Waals radii allow
- The peptide bond should remain planar and in the trans configuration
- Non-covalent bonding is necessary to stabilize protein folding

3. There are two main families of proteins. Name these two families and briefly describe their
characteristics/functions. (6 Points)

The two main families of proteins are fibrous and globular proteins.
- Fibrous proteins are the class of proteins that are elongated, filamentous molecules with well-defined
secondary structures in the cell. They mostly have a structural role and hold things together in the
cell. Examples include alpha and beta keratins, collagen, fibroins, and elastin.
- Globular proteins are a class of protein with more compact 3D folding (high-level compact folding) with
well-defined tertiary and/or quaternary structures. This compact folding allows globular proteins to
possess pockets that can fit prosthetic groups. These proteins play a vital role in biochemical
processes and chemical work at the cellular level, such as synthesis, transport, metabolism, catalysis,
etc. Examples of globular proteins include hemoglobin, histones, immunoglobulin, and prealbumin.

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 Dr. Amin F. Majdalawieh NAME:
4. Folded proteins can be denatured and converted into random coils by different means. Simply indicate
three ways by which such proteins can be denatured. (6 Points)

Proteins can be denatured by

o High temperatures
o Highly acidic/basic environments
o Addition of some organic compounds (ex: urea, alcohol)

5. Nine reaction mixtures containing 1.0x10-8 M of an enzyme are made up with five different substrate
concentrations and the initial rates of the reactions were measured: (12 Points)

[Substrate] (M) Initial Reaction Velocity (mol/min)

2 7
5 17
10 29
20 44
50 67
100 80
200 89
500 95
1000 98

(a) Given the following kinetic data, estimate Km and Vmax for the enzyme. Make sure you include
a sketch representing the Lineweaver-Burke plot of this catalysis.

Lineweaver-Burke Plot y = 0.2641x + 0.0093

R² = 0.9989
0.16
0.14
0.12
1/V (min/μmol)

0.1
0.08
0.06
0.04
0.02
0
0 0.1 0.2 0.3 0.4 0.5 0.6
1/S (1/μM)
Equation of the line: y = 0.2641x + 0.0093
y intercept = = 0.0093
Therefore, Vmax = .
= 107.5 μmol/min
Slope = = 0.2641
Therefore, Km = 0.2641 ∗ 107.5 = 28.4 𝜇𝑀

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Dr. Amin F. Majdalawieh NAME:
(b) What would be the effect on the initial reaction velocities if [Enzyme] was reduced to 10% of the
amount used above?

Because the reaction is a first order reaction with respect to the [enzyme], reducing the enzyme
concentration to 10% will decrease the initial reaction velocities to 10% of the rate previously
(decreases by 10 folds).

(c) How would this change in [Enzyme] affect the observed KM and Vmax?

The observed Km value will not change because the affinity between the enzyme and substrate has
not changed and because Km is independent of enzyme concentration. However, the Vmax value will
decrease by 10 folds.

(d) A poison is added to the reaction mixture that is known to bind the enzyme at a site different from
where the substrate binds. The poison and the substrate can bind the enzyme simultaneously but
the poison prevents the formation of product. Qualitatively, how does the poison affect Km and
Vmax? What kind of inhibition is caused by such a poison?

The poison is a non-competitive inhibitor because it does not bind directly to the active site yet it still
affects enzyme activity and prevents product formation. This poison will not affect the Km value
because the affinity between the enzyme and substrate was not affected by the poison. However, the
Vmax value will decrease because there are less enzymes available to from ES complexes that will
later form products (so less substrate required to reach maximum velocity).