Exam 3 review

Chapters included: 4, 5 and most of 6.

Multiple choice, written, rearrange the order, g

This is only a approximate guide. Do not study only based on the review. Go back
to your class notes, and other sources to study everything thoroughly

Chapter 4 Protein structure and folding

What are the weak/non-covalent interactions within a protein structure.

two major factors that influence protein conformation
Peptide bond properties, flexibility, rotation, backbone
Which bonds are flexible psi & phi; Ramachandran plot
Alpha helix structure amino acids per turn, stabilizing factors, etc.

Chapter 4 Protein structure and folding

Beta sheet structure.

Beta turn common residues found
Features of oligomeric proteins
Domain vs motifs
Results and inferences from RNAse denaturation experiment.
Concept of chaperone proteins

Chapter 5 Protein function

Holoenzyme, apoenzyme, prosthetic groups, etc.

Coordination bonds of Fe2+ in heme binding.
Concept of protein-ligand binding ka versus kd
Similarities and differences between myoglobin and hemoglobin - significance of
hyperbola vs sigmoidal curve.

Chapter 5 Protein function

Factors affecting Hb T/R state transition

Cooperativity concept example, what type of curve would you see?
Val-glu mutation consequences
BPG binding and effect
Bohr effect

Chapter 6 Enzymes

Classification of enzymes based on function

Why are enzymes such great catalysts?
Enzyme-substrate interactions
Binding energy from where does it come, significance, etc.
Induced-fit model
Michaelis-Menton kinetics
what can you conclude from a V0 vs [S] graph.
What does steady-state mean?

Chapter 6 Enzymes

Effects of inhibitors on Km and Vmax.

Enzyme regulation: types of regulation reversible and irreversible.

Chymotrypsin

Serine protease that cleaves peptide bonds at Phe, Tyr and Trp
Active site is a hydrophobic pocket
Asp102, His57 and Serine195 forms the catalytic triad.
Catalysis involves two phases:
1. Acylation: peptide bond cleaved & ester linkage formed between peptidyl carbonyl
carbon and enzyme.
2. Deacylation: ester linkage hydrolysed and non-acylated enzyme regenerated.
Steps 1 and 2
Binding of the substrate changes conformation
shorter H-bond between His57-Asp102
- stronger interaction; lower barrier
- His pKa changes from 7 to 12 making it s general base
His57 removes a proton from Ser195 hydroxyl group
Unstable charge on Ser195 strong nucleophile
Ser195 attacks carbonyl group of substrate
Tetrahedral acyl intermediate formed; H-bonds stabilize the negative charge

Chymotrypsin
Step 3
First intermediate broken down
Exiting amino group protonated by His57
Double bond re-formed by displacing C-N bond in acyl-enzyme intermediate
Peptide bond broken
Step 4
Water comes in; deprotonated
-OH ion strong nuclephile
Attacks the ester bond; forming 2nd intermediate

Steps 5-8
acyl-enzyme intermediate undergoes deacylation
Oxygen takes on a negative charge
2nd intermediate broken down
Product released; enzyme regenerated.

Chymotrypsin catalysis

Histidine acts as strong base, and

takes the H+ from Ser
The remaining O- is a strong
nucleophile; attacks C of the
carbonyl gp of substrate peptide
bond

Acylation

Deacylation

Strong nucleophile

Histidine acts as strong base, and

takes the H+ from water

Uncompetitive inhibition
Competitive:
Km decreases.
Km increases
Vmax remain the same. Vmax decrease.
Compete with the
substrate for the active does not affect
substrate binding.
site of the enzyme.

Binds only to the ES

complex.

Inhibits catalytic
function

Mixed Inhibition
Km increases
Vmax decreases
Inhibits both substrate
binding and catalysis

binds either to E or ES
complex.

Non-competitive Inhibition
Km same
Vmax decreases

Which of the following best represents the backbone

arrangement of two peptide bonds?
A)CaNCaCCaNCaC
B) CaNCCNCa
C) CNCaCaCN
D)CaCNCaCN
E) CaCaCNCaCaC

Amino acid residues commonly found in the middle of b turn

are:
A)Ala and Gly.
B) hydrophobic.
C)Pro and Gly.
D)those with ionized R-groups.
E) two Cys.

Protein S will fold into its native conformation only when protein Q is also present
in the solution. However, protein Q can fold into its native conformation without
protein S. Protein Q, therefore, may function as a ____________ for protein S.
A)proteasome
B) molecular chaperone
C) protein precursor
D)structural motif
E) supersecondary structural unit

In the binding of oxygen to myoglobin, the relationship between the

concentration of oxygen and the fraction of binding sites occupied can best be
described as:
A)hyperbolic.
B) linear with a negative slope.
C) linear with a positive slope.
D)random.
E) sigmoidal.

Which of the following statements about protein-ligand binding is correct?

A)The Ka is equal to the concentration of ligand when all of the binding sites are
occupied.
B) The Ka is independent of such conditions as salt concentration and pH.
C) The larger the Ka (association constant), the weaker the affinity.
D)The larger the Ka, the faster is the binding.
E) The larger the Ka, the smaller the Kd (dissociation constant).

Patients with chronic hypoxia (low O2 levels) due to decreased lung function may
adapt by increasing their circulating BPG levels. Predict which of the following will
be true for such a patient.

A)
B)
C)
D)
E)

p50 for O2 will be decreased.

p50 for O2 will be increased.
The R-state of hemoglobin will be favored.
O2 binding to hemoglobin will be hyperbolic.
None of the above

Identify the correct statements regarding the Bohr effect in hemoglobin.

a) The Bohr effect shifts the fractional O2 saturation curve to the right as pH decreases.
b) The Bohr effect shifts the fractional O2 saturation curve to the right as the pH increases.
c) The Bohr effect favors O2 release in respiring tissues.
d) O2 and H+ compete for binding to Hb.
A) a and c
B) a and d
C) b and c
D) b and d
E) b, c, and d

The role of an enzyme in an enzyme-catalyzed reaction is to:

A)bind a transition state intermediate, such that it cannot be converted back to substrate.
B) ensure that all of the substrate is converted to product.
C) ensure that the product is more stable than the substrate.
D)increase the rate at which substrate is converted into product.
E) make the free-energy change for the reaction more favorable.

The steady state assumption, as applied to enzyme kinetics, implies:

A) Km = Ks.
B) the enzyme is regulated.
C)the ES complex is formed and broken down at equivalent rates.
D)the Km is equivalent to the cellular substrate concentration.
E) the maximum velocity occurs when the enzyme is saturated.

An enzyme-catalyzed reaction was carried out with the substrate concentration initially 1,000
times greater than the Km for that substrate.
After 9 minutes, 1% of the substrate had been converted to product, and the amount of
product formed in the reaction mixture was 12 mol.
If, in a separate experiment, one-third as much enzyme and twice as much substrate had been
combined, how long would it take for the same amount (12mol) of product to be formed?

A. 1.5 min
B. 3 min
C. 6 min
D. 13.5 min
E. 27 min

Ibuprofen is an inhibitor of prostaglandin endoperoxide synthase. By inhibiting the synthesis

of prostaglandins, ibuprofen reduces inflammation and pain.

A) How would you proceed to graph a lineweaver plot?

[S]
(M)
0.5
1
1.5
2.5
3.5

Vo w/o IB
(nmol/min)
23
33
37
44
45

Vo with IB
(nmol/min)
17
26
31
38
40

B) Plot the Lineweaver graph?

C) What type of inhibitor is ibuprofen? Why?

[1/S]

1/Vo w/o IB

(M)

(nmol/min)

Take reciprocal

1/Vo + IB
(nmol/min)