Chemistry 255
Sample exam I-- section 1
Multiple choice :
1. When considering th
mixtureMpuret
e,
-,-'
J
1. If the
enthalpy change for a reaction under standard conditions is zero, AGO is equal
to:
@ b.AHO
d. + TASO
c. +RT ln Ke,
e. none of these
2. In the figure below, part of a polypeptide sequence is shown. What is the amino acid
sequence of residues 94 - 96? (This question may also designate the amino acids using
the 3 letter term -gly, phe etc)
b. YVS
a. SAY
c. YATd. TGY
0.
Are any portions of this protein segment capable of forming hydrogen bonds? If yes,
which?
5
-
~ q sA
pkv
I K - I ~
3. Consider the following amino acids: K, A, I, F. What is the correct order of increasing
hydrophobicity for the side chains?
a.FIKA
b.IFAK
c.AKIF
e.FIAK
4. Which one of the following is not occurring during protein denaturation?
a. Increase of disorder and of fluctuating conformations.
b. Loss of tertiary structure.
m h a n g e in primary structure.
d. Loss of quaternary structure.
e. Loss of secondary structure.
5 . Below is shown the oxygen binding curves for myoglobin and hemoglobin. Which one
of the following statements is correct?
@he
shape of curve I1 is characteristic of a cooperative binding process.
b. Curve I is sigmoidal in shape.
c. Curve I1 is hyperbolic in shape.
d. Curve I is the binding curve for hemoglobin.
e. Curve I1 is the binding curve for myoglobin
6. Draw the dipeptide Ala-Asp at pH 6
7. Peptide bonds exist in the 'trans' configuration. Depict a trans peptide bond and
explain; (I) why is this bond 'locked' into the trans state-why no free rotation?
2) how does this bond effects the secondary structure of a peptide.
) - p l ~ ~ d c_=/J - ~
r t ~ o n n n c r -S ? J ~ C . ~ ~ ~ C
~
&,JS
~
b
k
bLLL
8. Draw the tripeptide phe-Asn-His at pH 5.5. Point an arrow to the bond(s) that rotate
to form torsional angles within the backbone of the peptide. ::
-h)hp
9. Albumin is a protein in the blood to help buffer the pH of the blood. Which amino
acid side chain would you most expect to contribute the most it its capacity to buffer at
pH 7.4
Glu, Cys, Tyr Ala
lo. Hemoblogin binds oxygen better at relatively lower P co2. Explain this phenomena
referencing pH values, T states and R states. Also depict this comparison using a
fractional saturationlbinding vs oxygen partial pressure graph-show the curves for
Q
~ ~ B ~ cb-bv-tl
C O ~
high vs low C02.
0 3+ 0
3
I
' ace,
/,ow Pea,
~ . c ~ w ( H ?HlqhpH
~
*
11. Which Amino acid
residue binds directly to iron in myoglobin. Draw the structure
and show the specific atom of this amino acid that binds to iron.
12. To which hemoglobin form does BPG bind with? Briefly describe the location of this
T dat,tin
,,. r a u h /ceof,b/ r $ ..
-
8'
2
13. What would be the effect buffering range of an ammonia/ammonium ion buffer.
The pKa of ammionium ion is 9.25
14. A reaction (A + B 3 C) has a AG of + 15 kJ.
The temperature is 298K and R = 8.3 J/Kmol
Is this reaction
/,'---l
~6 z - LTL~PI
51
exergonic? What is the v lue of K for the reaction?
J
Is the value of AS positive, negative or 'o'?
A 6 =LnK
Y=<
-
-A%+
+
15. In a protein, which types of bonds listed below would be influenced by pH changes:
/-\
\
Disulfide bond, 6 i d g e (sah bridge)
( G o g e n bond)
C
nst
,,,CI-CP-
\,-
-
16. Draw a reaction coordinate diagram (AG plots) of the enzyme-catalyzed
k~3228 4 o o e r
reaction:
in which the overall AGrxn = - 20 kJ/mol. Use E, S and P to stand for enzyme, substrate
and product, respectively. Use the
symbol to represent the transition state.
"*"
a. (5 points) Draw a curve representing the uncatalyzed reaction that has an activation
energy of 20 kJ/mol. Make sure to label your axes with quantities and units, and label
this curve (a).
b. (5 points) Given a hydrogen bond energy of 7 kJ/mol, draw a curve representing
the binding of the enzyme to the transition state with 1 H bond. Label this curve (b).
to the transition state
---
c. (5 points) Draw a curve
with 2 H bonds. Label this
.r
- I N
bmd
z ,-bods
7
iGf
b
4
__.--.
s --3
p
d. (6 points) Label the AG*for each curve. Which curve (a) or (b) or (c) would have the
greatest rate constant? Explain your choice.
PY PJ
c l n a r q . u a + ~ d t / / ~ v d ~ 4 t ~t ~ n S S h n i - '
17. The protein myoglobin is found in numerous organisms, and the amino acid residue
sequence of the protein from a wide variety of organisms has been determined. The
word "conserved"is applied to a particular region of the protein if the sequence of that
region is regular between several organisms. If the sequence is altered slightly in this
region but the protein still functions, the changes are said to be "conservative
substitutions".
a Which substitution would be considered conservative: Val replaced by Ala or Val
replaced by Phe? Briefly explain your choice. n
b. Explain why replacing a Val by a I,ys might result in a defective protein-(one that
couldn't carry out its regular functions).
ygen dissociation constant K,
c. For the defective protein above, describe how
might change in regards to regular myoglobin. arge , smaller, the same).
the fractional saturation Y o2 change from that o regular myoglobin (larger
same
iafcer or urn\& d 1 5 5 0 c l ~ b 4 r h l J ---[ O W <
yo_
K