Welcome to the Exam 2 Review

Session!
With: Kaitlyn, Hannah, and Keelyn
Equations/Values Provided on Exam 2
Vo=Vmax {S}/Km + {S}
∆G'° = - RT ln K
∆G = ∆G'° + RT ln K
∆G = ∆H-T∆S
∆G'° = - nF∆E'°
pH = pKa + log [A-]/[HA]
R = 8.3145 J/K.mol
F = 96,485 J/V.mol
Problem 1
What are the primary amino acids and molecules involved in the chymotrypsin
reaction? Select all that apply.

A. Arg
B. His
C. Ser
D. Asn
E. H20
F. CH3OH
Problem 1
What are the primary amino acids and molecules involved in the chymotrypsin
reaction? Select all that apply.

A. Arg
B. His
C. Ser
D. Asn
E. H20
F. CH3OH
The chymotrypsin breaks down
proteins by going through these steps
2 times:

-Remove a hydrogen from protein

-Nucleophilic attack
-Donate a proton → peptide bond
cleaved
Problem 2
What type of inhibition is this?

A. Competitive
B. Uncompetitive
C. Mixed
D. Noncompetitive
Problem 2
What type of inhibition is this?
Mixed!
-Vmax decreases and Km increases
(Only possible w Mixed inhibition)

Follow up question:
Ki is __(smaller/bigger)__ than Kiʼ, and __(ESI/or EI)__ predominates
Problem 2
What type of inhibition is this?

Mixed!

-Vmax decreases and Km increases

Follow up question:

Ki is __(smaller/bigger)__ than Kiʼ, and __(ESI/or EI)__ predominates

-if Km increases, that means competitive inhibition predominates → predomination of EI → Ki must be smaller than Kiʼ
Problem 3
Under these given reaction conditions, is the reaction catalyzed by aldolase going to be
spontaneous? Calculate G.

ΔG° = 23.8 J/mol

[Conc. of DHAP and Glyceraldehyde-3-P] = 0.0307 mM
[Conc. of Fructose 1,6 Bisphosphate]= 0.031 mM
R = 8.31 J/ K * mol
Temp = 310 K
Problem 3
Under these given reaction conditions, is the
reaction catalyzed by aldolase going to be
spontaneous? Calculate G.

ΔG° = 23.8 J/mol

[Conc. of DHAP and Glyceraldehyde-3-P] = 0.0307

mM

[Conc. of Fructose 1,6 Bisphosphate]= 0.031 mM Yes spontaneous because G is negative!

R = 8.31 J/ K * mol

Temp = 310 K
Problem 4
Which of the following would result if phosphoglycerate kinase were mutated such that
its activation energy was raised? Select all that apply.

A. There would be a buildup of 2- phosphoglycerate

B. There would be a buildup of 1,3 bisphosphoglycerate
C. There would be a lack of Glyceraldehye-3-P
D. Less NADH would be produced
E. Less ATP would be produced
Problem 4
Which of the following would result if phosphoglycerate kinase were
mutated such that its activation energy was raised? Select all that
apply.

A. There would be a buildup of 2- phosphoglycerate

B. There would be a buildup of 1,3 bisphosphoglycerate
C. There would be a lack of Glyceraldehye-3-P
D. Less NADH would be produced ..not true. Glyceraldehyde
dehydrogenase is still functional and can still produce NADH
E. Less ATP would be produced

Mnemonic for memorizing glycolysis order: Hungry Idiotic

Peter And The Growling Panther Must Eat Pies
Problem 5
If 3 glucose molecules go through glycolysis, how much net ATP is produced? How much
NADH is produced? How many cycles are there in the energy investment and the energy
payoff phases?

ATP produced: _________

NADH produced: ________
Cycles of energy investment phase: ________
Cycles of energy payoff phase: ________
Problem 5
If 3 glucose molecules go through glycolysis, how much net ATP is produced? How much
NADH is produced? How many cycles are there in the energy investment and the energy
payoff phases?

ATP produced: _6_

NADH produced: _6_
Cycles of energy investment phase: _3__
Cycles of energy payoff phase: _6__
Problem 6
A patient who is incapable of carrying out prolonged intense exercise had a muscle
biopsy showing that they contained a deficiency in phosphoglycerate mutase. Does this
person suffer from lactic acid buildup in the muscle?

A. Yes. They lack 2,3 BPG meaning the muscles canʼt get oxygen.
B. Yes. The personʼs inability to intensely exercise over a long period must be a result
of their lactic acid buildup.
C. No. Because the person isnʼt producing enough pyruvate, there will not be much
lactate.
D. Can not be determined
Problem 6
A patient who is incapable of carrying out prolonged intense exercise had a muscle biopsy
showing that they contained a deficiency in phosphoglycerate mutase. Does this person suffer
from lactic acid buildup in the muscle?

A. Yes. They lack 2,3 BPG meaning the muscles canʼt get oxygen. ..If mutase is deficient,
there will not be any pyruvate around to do lactic fermentation in the first place.
B. Yes. The personʼs inability to intensely exercise over a long period must be a result of their
lactic acid buildup.
C. No. Because the person isnʼt producing enough pyruvate, there will not be much lactate.
Deficient mutase → deficient pyruvate → deficient lactate
D. Can not be determined
Problem 7
Imagine you are designing two drugs. One is an enzyme that called lactase (itʼs actually
found in Lactaid) that will digest lactate. The other drug is an inhibitor that is used in
immunotolerant therapy that will repress immune cells. The Km for the first drug should
be relatively _______ while the Ki for the second drug should be _______.

A. Small, small
B. Large, large
C. Small, large
D. Large, Small
Problem 7

Imagine you are designing two drugs. One is an enzyme that called lactase (itʼs actually
found in Lactaid) that will digest lactate. The other drug is an inhibitor that is used in
immunotolerant therapy that will repress immune cells. The Km for the first drug should
be relatively _______ while the Ki for the second drug should be _______.

A. Small, small ...small Km → large affinity. Small Ki → low dissociation.

B. Large, large
C. Small, large
D. Large, Small
Problem 8
Which of the following parameters will be affected if you increase the substrate
concentration from 5mM to 15mM at nonsaturating conditions ?

A. Vmax
B. [Enzyme conc]
C. Kcat
D. Km
E. Vo
F. None of the above
Problem 8
Which of the following parameters will be affected if you increase the substrate
concentration from 5mM to 15mM at nonsaturating conditions?

A. Vmax
B. [Enzyme conc]
C. Kcat
D. Km
E. Vo
F. None of the above
Problem 9
Which of the following reactants is part of a reaction that has a large negative delta G
and a large Keq?

A. Glyceraldehyde-3-P
B. 3-Phosphoglycerate
C. Fructose 6 phosphate
D. Fructose 1,6 bisphosphate
Problem 9
Which of the following reactants is part of a
reaction that has a large negative delta G and a
large Keq?

A. Glyceraldehyde-3-P ...reactant of
Glyceraldehyde dehydrogenase
B. 3-Phosphoglycerate...reactant of mutase
C. Fructose 6 phosphate ...reactant of PFK
D. Fructose 1,6 bisphosphate...reactant of
aldolase
Problem 10
Which of the following enzymes is involved in a redox reaction?

A. Hexokinase
B. PFK
C. Mutase
D. Glyceraldehyde dehydrogenase
E. Pyruvate kinase
Problem 10
Which of the following enzymes is involved in a redox reaction?

A. Hexokinase
B. PFK
C. Mutase
D. Glyceraldehyde dehydrogenase ...produces NADH!
E. Pyruvate kinase
Problem 11
Based off of the these slopes, which lines represent pHs at 3.5, 6.5, 8.2?
Problem 11
ANSWER: Non steep slope (C)
ANSWER:that
indicates Nonitsteep
takes slope (C)
a more
indicates
oxygen to that it takes
get 100% a more
saturated
oxygen to get 100% saturated

T state (low pH) requires more O2

T state
to (low
get fully pH) requires
saturated
more O2 to get fully saturated
Problem 12
What would happen to fetus in utero if it had a mutation that significantly lowered the
Hbʼs Km.

A. The babyʼs muscles would receive an abnormal influx of O2

B. The baby would suffer from hypoxia (oxygen deprivation)
C. The mother would have more than the average amount of O2 in a pregnant
womanʼs blood
D. Both A and C
Problem 12
What would happen to fetus in utero if it had a mutation that significantly lowered its
Hbʼs Km?

A. The babyʼs muscles would receive an abnormal influx of O2

B. The baby would suffer from hypoxia (oxygen deprivation)
C. The mother would have more than the average amount of O2 in a pregnant
womanʼs blood
D. Both A and C

Low Km → STRONG affinity. But this is an issue because it the Hb would not let go of
the O2 to feed the muscles (R state too strong)
Problem 13
Which of the following mutations on central cavity of Hb would make it hardest for BPG
to bind and which state would it favor?

A. His → Arg
B. Ser → His
C. Trp → Met
D. Glu → Lys
E. Arg → Asp
Problem 13
Which of the following mutations on Hbʼs central cavity would make it hardest for BPG
to bind and stimulate the T state?

A. His → Arg
B. Ser → His
C. Trp → Met
D. Glu → Lys
E. Arg → Asp (+) → (-)

BPG is (-) and likes a (+) central cavity!

Problem 14
What would happen to the stability of the R state if a glycine in the central cavity was
replaced with an arginine?

A. This mutation would cause the R state to be more stable because 2,3-BPG can bind
to the central cavity better.
B. This mutation would cause the R state to be less stable because it would add
another Bohr position which stabilizes the T state.
C. This mutation would not cause a change to R state stabilization of hemoglobin.
D. This mutation would cause the R state to be less stable because 2,3-BPG can bind
to the central cavity better.
E. None of the above.
Problem 14
What would happen to the stability of the R state if a glycine in the central cavity was
replaced with an arginine?

A. This mutation would cause the R state to be more stable because 2,3-BPG can bind
to the central cavity better.
B. This mutation would cause the R state to be less stable because it would add
another Bohr position which stabilizes the T state.
C. This mutation would not cause a change to R state stabilization of hemoglobin.
D. This mutation would cause the R state to be less stable because 2,3-BPG can bind
to the central cavity better.
E. None of the above. Adding another plus charge in the central
cavity helps 2,3-BPG binding (which stabilizes
T state)
Problem 15
A mutation changed a lysine on the surface of Hemoglobin to an aspartic acid. How was
the pI of the protein changed?

A. The pI increased.
B. The pI decreased.
C. The pI stayed the same.
Problem 15
A mutation changed a lysine on the surface of Hemoglobin to an aspartic acid. How was
the pI of the protein changed?

A. The pI increased.
B. The pI decreased.
C. The pI stayed the same.

Lysine has a much higher pka than aspartic acid. This mutation will shift the pI
calculation to the left and therefore decrease it.
Problem 16
What is the central iron in the heme ring bound to?

A. Oxygen, 4 Nitrogens, and Proximal Histidine

B. Oxygen, 3 Nitrogens, and Argon
C. Oxygen, 3 Nitrogens, and Distal Histidine
D. Oxygen, 4 Nitrogens, and Distal Histidine
Problem 16
What is the central iron in the heme ring bound to?

A. Oxygen, 4 Nitrogens, and Proximal Histidine

B. Oxygen, 3 Nitrogens, and Argon
C. Oxygen, 3 Nitrogens, and Distal Histidine
D. Oxygen, 4 Nitrogens, and Distal Histidine
Problem 17
If a person hyperventilates a lot because they suffer from a mutation that affects
their levels of 2,3 BPG, which enzyme in glycolysis could you presume is mutated?

A. Phosphoglycerate kinase
B. Enolase
C. Pyruvate Kinase
D. Both B and C
Problem 17: Answer
If a person hyperventilates a lot because they suffer from a mutation that affects the
their levels of 2,3 BPG, which enzyme in glycolysis could you presume is mutated?
A. Phosphoglycerate kinase
B. Enolase
C. Pyruvate Kinase
D. Both B and C
Phosphoglycerate kinase provides the reactant which will be used by
phosphoglycerate mutase. Phosphoglycerate mutase’s intermediate is 2,3 BPG.
Thus, if mutase lacks sufficient reactants due to a nonfunctional phosphoglycerate
kinase, the levels of 2,3BPG would be affected. Enolase and pyruvate kinase are
enzymes after the formation of 2,3BPG as an intermediate.
Problem 18:
Ser171 and Arg78 are involved in the formation of a covalent intermediate with the
substrate while Cys111 is involved in substrate binding. A mutation of these residues
would likely affect…

A. Km
B. Vmax
C. Koff
D. Kon
E. Kd
F. Kcat
Problem 18
Ser171 and Arg78 are involved in the formation of a covalent intermediate with the
substrate, while Cys111 is involved in substrate binding. A mutation of the Ser and Arg
residues would likely affect…
A. Km
B. Vmax
C. Koff
D. Kon
E. Kd
F. Kcat
These are catalytic residues that are NOT involved in binding, therefore the only step
affected is the ES → E + P
Problem 19
Hemoglobin is typically found in the __-state when in the lungs, and the __-state
when in tissues?
A. R state, R state
B. R state, T state
C. T state, R state,
D. T state, T state
Problem 19: Answer
Hemoglobin is typically found in the __-state when in the lungs, and the __-state when in
tissues?
A. R state, R state
B. R state, T state
C. T state, R state,
D. T state, T state
In the lungs, there is already a high pressure of oxygen, therefore hemoglobin does not
need to release oxygen. Hemoglobin in the lungs will have oxygen tightly bound to it, in
the R state. However, as hemoglobin travels to tissues, or areas with a low pO2, it must
decrease the strength of oxygen binding to allow for oxygen transfer to occur and for the
oxygen-deprived area to receive more oxygen. This means it must transfer from the R
state (lungs) to the T state when in the tissues and wanting to allow transfer.
Problem 20
What is the function of glucose phosphorylation?

A. Commit the molecule to glycolysis

B. Regenerate NAD+ for use in glycolysis
C. Yield ATP
D. Trap glucose in the cell
Problem 20: Answer
What is the function of glucose phosphorylation?
A. Commit the molecule to glycolysis
B. Regenerate NAD+ for use in glycolysis
C. Yield ATP
D. Trap glucose in the cell
Negative charge on the phosphate that is added during glucose phosphorylation
prevents G6P from crossing the hydrophobic cell membrane
Follow up question: what is the relevance of trapping glucose in the cell? Also, what is
the first committed step in glycolysis, and why is the formation of G6P not even though
it is far from equilibrium?
Problem 20: Answer continued
What is the function of glucose phosphorylation?
A. Commit the molecule to glycolysis
B. Regenerate NAD+ for use in glycolysis
C. Yield ATP
D. Trap glucose in the cell
Negative charge on the phosphate that is added during glucose phosphorylation prevents G6P from crossing the
hydrophobic cell membrane

Follow up question: what is the relevance of trapping glucose in the cell? Also, what is the
first committed step in glycolysis, and why is the formation of G6P not even though it is far
from equilibrium? ** trapping G6P allows cells to “stock up” on glucose to be used for
energy breakdown via glycolysis. Non-phosphorylated glucose can easily leave the cell via
glucose transporters, resulting in less glucose for energy within the cell .
G6P can be used in glycogen metabolism!!!! So it is not a committed step to glycolysis
Problem 21
Which of the following would result in an increase p50?

A. Decreased pH
B. Increased pH
C. Arginine in central cavity mutated to valine
D. Lysine in central cavity mutated to arginine
E. Increased activity of carbonic anhydrase
F. Mutation on his146
G. Valine near proximal histidine -> glycine
Problem 21: Answer
Which of the following would result in an increase p50? Increased p50 = less oxygen offinity =
more t state favored
A. Decreased pH increased [H+] = increased Bohr protonation = T state favored
B. Increased pH decreased [H+] = decreased Bohr protonation = R state favored
C. Arginine in central cavity mutated to valine less positive central cavity = less 23BPG binding = more R state
favored
D. Lysine in central cavity mutated to arginine increased bascicity in central cavity = more positive = more 23BPG
binding = T state favored
E. Increased activity of carbonic anhydrase = increased breakdown of CO2 to HCO3- and H+ = more protonation of
Bohr states = T state favored
F. Mutation on his146 → arginine = more basic therefore more time protonated = increased bohr protonation =
more T state favored
G. Valine near proximal histidine -> glycine glycine smaller than valine = less steric clash with proximal histadine
= less O2 binding = more T state favored
H. Mutation of N terminus = less protonated of Bohr states = R state favored
Problem 22
If enzymatic function of phosphoglycerate mutase is inhibited, which of the
following are potential consequences? More than one answer may be correct.

A. Increased [3PG]
B. T state favored hemoglobin
C. R state favored hemoglobin
D. Increased [PEP]
E. Decreased [PEP]
F. Decreased [3PG]
 Explanation:
Problem 22: Answer Phosphoglycerate mutase is an
enzyme that catalyzes the reaction
If enzymatic function of phosphoglycerate of 3PG → 2PG, reaction 8 of
mutase is inhibited, which of the following are glycolysis. Without this enzyme,
potential consequences during glycolysis? there would be an increased [3PG]
More than one answer may be correct. and decreased [2PG]. All
A. Increased [3PG] intermediates after step 8 would
B. T state favored hemoglobin decrease in [ ], therefore E is true.
C. R state favored hemoglobin 2,3 BPG is also an intermediate in
D. Increased [PEP] this step of glycolysis. Since the
E. Decreased [PEP] step is not occurring, less 2,3BPG is
forming, therefore less binding to
F. Decreased [3PG]
the central cavity of hemoglobin =
more R favored.
Problem 23 : Do fetuses and Adults use the same
Hb form? If not, why and what is the reason for the
mutation?
A. Both mother and fetus have same Hb form
B. Fetuses use HbF while adults use HbA because need to have a lower affinity and
higher p50
C. Fetuses use HbF while adults use HbA because need to have a higher affinity and
lower p50
D. Fetuses use HbA while adults use HbF because need to have a higher affinity and
lower p50
 Problem : Do fetuses and Adults use the same Hb form? If not, why and what
is the reason for the mutation?

A. Both mother and fetus have same Hb form

B. Fetuses use HbF while adults use HbA
ADULTS P50 > fetuses b/c a
lower p50 is associated with a
because need to have a lower affinity and
higher affinity (think R state).
higher p50
Fetuses have greater affinity
C. Fetuses use HbF while adults use HbA
for oxygen because need
because need to have a higher affinity and
nutrients to grow and adults
lower p50
has greater supply of it so
D. Fetuses use HbA while adults use HbF
their affinity is lower.
because need to have a higher affinity and
lower p50
Problem 24: What are the similarities and differences between Mb and
Hb? Identify characterizations below as either Hb , Mb or both...

- Primary structure - Quaternary structure (2 alpha, 2

beta)
- Can only bind 1 O2 - Can bind 4 O2
- Always R- STATE - Two states
- Single state - Cooperativity
- Noncooperative protein - Low (tissues) / High (lungs)
affinity
- High affinity - Effector muscles
- Hyperbolic shape - Secondary (alpha - helical)
- Primary structure - Tertiary: similar O2 binding site
- Heme / Fe2+ / Porphyrin ring
Problem: What are the similarities and differences between Mb and Hb?
Identify characterizations below as either Hb , Mb or both...
Problem 25: Which of the following positions is
involved in preventing CO in binding? How? Why?
A. Proximal His
B. Distal His
C. Central Cavity
D. Bohr Positions
Problem: Which of the following positions is
involved in preventing CO in binding? How? Why?
A. Proximal His The distal histidineʼs primary role is to hydrogen bond with the incoming
diatomic oxygen molecule that is forming the 6th coordinate covalent bond.
B. Distal His Distal histidine thus stabilizes the binding of diatomic oxygen, not carbon
C. Central Cavity monoxide.
D. Bohr Positions
Problem 26 : Mb Mutant (MT raises energy of oxygenated state by
5kj/mol) Val in hydrophobic pocket → Asp

P50?

R state or T state

Shape?
Problem : Mb Mutant (MT raises energy of oxygenated state by 5kj/mol)
Val in hydrophobic pocket → Asp

If mutant type is destabilized in the oxygenated

state, it will favor the deoxygenated (thus, T) state.

Favors T state, P50 increases, hyperbolic

Problem 27: You are working in a lab and discover
a new type of inhibition to the molecule are
working with. The inhibition does not bind at the
active site but rather at a site near by the active
site. The inhibitors decreases Km and Vmax You
ewant to see if you flooded with substrate would
overcome this inhibition. What do you find
happens?
Answer

Reversible , Uncompetitive

Allosteric Interaction: I only binds E when Substrate is already bound ---> 2

binding sites

[E] No flooding with [S] possible

Problem 28: Determine the following values
using the accompanying Lineweaver-Burk plots
for an enzyme in the absence (-I) and in the
presence (+I) of an inhibitor

a) Vmax in the absence of inhibitor

b) Vmax in the presence of inhibitor
c) Km in the absence of inhibitor
d) Km in the presence of inhibitor
e) Type of inhibition (explain)
Answer
a) Vmax in the absence of inhibitor
b) Vmax in the presence of inhibitor
c) Km in the absence of inhibitor
d) Km in the presence of inhibitor
e) Type of inhibition (explain)