ID
BIOMG Net 3310 MIDTERM EXAM 10/21/10
1.
2.
3.
Use these pKa values
unless others are given in a
problem:
terminal COOH
4
terminal NH3+
9
R-GROUPS:
Asp 4
Glu 4
Cys 8
Tyr 10
His 7
Lys 10
Arg 12
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
TOTAL
BE SURE TO WRITE/PRINT LEGIBLY. IF WE CAN'T
READ IT, WE CAN'T GRADE IT! (SERIOUSLY)
PRINT NAME (LAST, FIRST) ON THE BACK TOP
OF THE LAST PAGE AND ONLY THE LAST PAGE
1. (7 pts) Given that the side chain of Ala is -CH3.
a. On the right, draw Ala at pH 7. Show every atom. Use symbols and to label those carbons.
b. Below, draw Ala-Ala at pH 7. Circle the 6 atoms that line in a plane.
2. (10 pts) Hb has a terminal amino and a terminal carboxyl that can form an ion pair.
a. What fraction of these ionizable groups are actually in an ion pair:
______ at pH 7.5
______ at pH 7.0
b. Draw curves of vs pO2 that correspond to pH values in question 2a.
Label curves and axes, and show at least two numerical values on each axis.
c. Which curve(s) in 2b involve BPG that stays bound to the Hb
at all the values of pO2 shown on your graph? Circle answer:
pH 7.5
pH 7.0
both curves
neither curve
3. (2 pts) Circle each pair below that are isozymes:
Hb/Mb
hexose/hexokinase
muscle hexokinase/brain hexokinase
tyrosine kinase/serine kinase
4. (5 pts) We know that O2 binds to the heme Fe++ of Mb. Then why is the polypeptide needed?!
a. Briefly (BRIEFLY) describe two important properties of the Mb polypeptide:
i.
ii.
b. We can refer to the Mb polypeptide as apomyoglobin. What term refers to just the heme group: _____________________
5. (6 pts) 6 categories of forces are important for stabilizing protein structure. Name each one, and state whether the geometry
of the interaction is highly directional, weakly directional, or not directional at all.
a.
, which is
directional
b.
, which is
directional
c.
, which is
directional
d.
, which is
directional
e.
, which is
directional
f.
, which is
directional
6. (8 pts) In the blanks below, write the ONE letter, A, B, or C of the corresponding Ramachandran plot. Use each letter any
number of times. The black dots correspond to observed values of ,
a. ___ myoglobin
b. ___ a typical protein with both -helices and -sheets
c. ___ a completely denatured protein
d. ___ a native protein having loops and turns but without recognizable patterns of secondary structure
7. (6 pts) Write out a short, 7-residue peptide that would correspond to each description below. For simplicity, use just
combinations of Val and Gln for your answers, e.g. Val-Val-Gln-Gln-Val-Gln-Val. Create any such 7-residue peptide consisting
of combinations of Val and Gln. No need for you to create a complex answer: Even a 7-residue peptide consisting of all Val or
of all Gln might be possible answers
a. an amphipathic helix:
b. a helix completely buried in the interior of a water-soluble protein:
c. a helix completely buried in the interior of a membrane-bound protein:
8. (5 pts) Define the terms below. Answer below BRIEFLY in the space provided:
a. I structure
b. II structure
c. Fold
d. III structure
e. IV structure
9. (3 pts) Transient IV structure can be useful to a living cell. Define transient IV structure, and give one example.
Definition:
Example:
10. pts) (6 Mb functions well at pH between 6 - 8, but not at pH 3. Illustrate this
information on a graph of Go vs structural coordinates.
Label axes and label curves.
11. (6 pts) Calculate the value of Go, the change in a transition state free energy caused by a catalyst that speeds up a
reaction by 108 - fold. CIRCLE your answer. If you would like your answer to be considered for partial credit, show the steps of
your calculation. Use R = 0.00832kJ/mol x K and T = 300K
12. (10 pts) a. Using the rate constant kcat, write the simple expression for Vmax:
b. For a reaction having multiple steps after binding of S to E, how much time is needed to complete ALL of these steps, if
kcat = 106 sec-1? Circle your answer.
c. For a case of just two steps k2 and k3 after binding of S to E,
kcat = (k2 x k3)/(k2 + k3)
i. On the right, draw the graph of Go vs Progress of Reaction for the case in
which k3 is the rate-determining step. Label axes.
ii. Below, write the new, simplified expression for kcat for this same case
in which k3 is the rate-determining step.
13. (16 pts) Kinetic studies of an enzyme are made in the absence of inhibitors,
and with inhibitors A and B.
[A] = 4.0M and [B] = 1.0M On the following page, you will find questions about Vm, Km, KI
[S], M
V, Mmin-1
VA, Mmin-1
VB, Mmin-1
0.05
0.020
0.0167
0.0143
0.0143
0.00952
0.0100
0.00833
0.0143
0.0100
0.00833
0.0111
0.0100
0.00909
0.00870
0.00645
0.00588
0.00770
0.00645
0.00556
Formulas for types of inhibition:
I
Vm = (Vm)/(1 + [I]/KI)
-1/{Km x (1 + [I]/KI)} is the intercept at 1/V = 0
Calculation steps MUST be shown
Units MUST be shown
THIS PROBLEM CONTINUES WITH QUESTIONS ON THE FOLLOWING PAGE.
a. What is the value of Km?
b. What is the value of Vm of the uninhibited rxn?
c. What kind of inhibitor is A? ____________________ What kind of inhibitor is B? ________________________
d. What is the value of KI for inhibitor A? __________
e. What is the value of KI for inhibitor B? __________
f. Which inhibitor binds more tightly to the enzyme, and how do you know?
14. (16 pts)
15. (3 pts) Very briefly, describe in words the difference between a reaction intermediate and a reaction transition state.
16. (7 pts) Consider the enzyme aspartate carbamoyltransferase.
a. Given that 1/2Vmax occurs at [aspartate] = 15mM, draw the
sigmoid curve showing V vs [aspartate]. Label axes, and
show three numerical values for the [aspartate] axis.
b. Answer T (true) or F (false) for the following:
_____ CTP binds to a regulatory subunit, promoting the T-state
_____ The substrate aspartate shows cooperative binding
_____ ATP binds to a regulatory subunit, promoting the R-state
_____ CTP binds to the same site where aspartate binds
_____ Regulation of the enzyme ATCase provides an example of
covalent modification of an amino acid residue
_____ The ATCase enzyme exhibits Michaelis-Menten kinetics
17. (8 pts) This question refers to the PyMOL chymotrypsin assignment.
On the figure below:
Label: Gly193, Ser195, His57, and Asp102.
Draw a rectangle around the one residue, and only this residue, that fits in the substrate binding pocket.
Draw a triangle around the oxyanion.
Circle the peptide backbone NH (and only these atoms) of both Gly193 and Ser195.