Name Key A (White) BIS102-001, Spring '15, Page 1 of 8

Last, First C. S. Gasser

May 19, 2015, Second Midterm

BioSci 102-001
TEST FORM A
Instructions:
• There are eight pages in this exam including this cover sheet, please count them
before you start to make sure all are present.
• Write your name on each page of the exam.
• When indicated, write your short answers in the space provided below each
question on this exam. If you need more space use the back of the page and
indicate clearly that you have continued your answer on the back. Do not use
additional paper.
• For calculation problems a clear line of calculation/reasoning must be shown to
obtain full credit.
• When indicated, fill in your answers on your UCD 2000 Scantron form. Note
that you must write in your name as well as bubble in your:
• Student ID number
• Test form identifier (i.e. A, B, or C)
2 points will be subtracted for omission of either of the above pieces of information

On the Scantron form, please bubble in ‘A’ for True, and ‘B’ for False. Choose the one
best answer for all Scantron questions. For the Scantron questions, only the
answer filled in on your Scantron sheet will be considered.

Use the following pKa values for the exam.

Amino Acid α -NH2 α -COOH R-group log 1.0 = 0.00
Ala, Gly, Ile, Leu, Val 9.7 2.3 – log 1.5 = 0.18
Asn, Gln 9.0 2.1 – log 2.0 = 0.30
Met, Ser, Trp 9.3 2.3 – log 2.5 = 0.40
Phe 9.1 1.8 – log 3.0 = 0.48
Pro 10.6 2.0 – log 3.5 = 0.54
Thr 10.4 2.6 – log 4.0 = 0.60
Asp 9.8 2.1 3.9 log 4.5 = 0.65
Glu 9.7 2.2 4.2 log 5.0 = 0.70
His 9.2 1.8 6.0 log 5.5 = 0.74
Cys 10.8 1.8 8.3 log 6.0 = 0.78
Tyr 9.1 2.2 10.0 log 6.5 = 0.81
Lys 9.0 2.2 10.5 log 7.0 = 0.85
Arg 9.0 2.2 12.5 log 7.5 = 0.88
log 8.0 = 0.90
R = 8.3 X 10-3 kJ/K•mol log 8.5 = 0.93
log 9.0 = 0.95
25°C = 298K log 9.5 = 0.98
log 10.0 = 1.00

©2015 Charles S. Gasser, may not be reproduced without expressed permission of author.
Name Key A (White) BIS102-001, Spring '15, Page 2 of 8
Last, First C. S. Gasser

Question Scantron Short Answer Score (short answer)

1 35 0
2 18 0
3 20 0
4 12 0
5 0 18
6 0 16
7 0 26
8 0 5
Total 85 65

1. (35) Indicate the one most correct answer to each of the following on your Scantron.

SC.1. (5) You have 2 ml of protein solution collected from a column that is in 10 mM Tris pH7.8
and 200 mM NaCl. You want to dialize the sample against 10 mM Tris pH7.8 to remove the
NaCl. Which of the following would be most effective if each dialysis step is taken to
completion?

A. Dialyze once against 1 liter of the Tris buffer. 1:500 ->0.4 mM

B. Dialyze three times against 50 ml of the Tris buffer. 1:25 -> 8 mM->0.32->0.0128
C. Dialyze once against 500 ml of Tris buffer. 1:250 -> 0.8 mM
D. Dialyze twice against 200 ml of Tris buffer. 1:100 -> 2 mM -> 0.02 mM
E. Can't tell, it depends on the nature of the protein.

SC.2. (5) A detergent can dissolve a membrane because it:

A. has positive charges that counteract the negative charges on membrane lipids.
B. can cleave the fatty acids off of the membrane lipids and trap them in micelles.
C. denatures the proteins in the membrane.
D. can disrupt the interactions of the hydrophilic head groups and water.
E. can form micelles that can contain and solubilize the hydrophobic parts of membrane
lipids.

SC.3. (5) Which of the following is NOT a function of SDS (sodium dodecyl sulfate) in SDS
polyacrylamide gel electrophoresis?

A. binds to hydrophobic amino acids in a protein.

B. gives all proteins in a sample a uniform charge/mass ratio.
C. makes all proteins in a sample negatively charged.
D. denatures proteins.
E. ensures that larger proteins have a less charge so that they migrate more slowly than
smaller proteins.

©2015 Charles S. Gasser, may not be reproduced without expressed permission of author.
Name Key A (White) BIS102-001, Spring '15, Page 3 of 8
Last, First C. S. Gasser

SC.4. (5) Isoelectric focusing gel electrophoresis (IEF):

A. leads to proteins running off the gel if run for too long.
B. separates proteins by hydrophobicity.
C. can be eluted with a pH gradient.
D. will often separate proteins even if they are exactly the same size.
E. does not work for a protein that has no amino acid side chains that can carry a charge.

SC.5. Chaperonins facilitate protein folding by:

A. Increasing the ΔS of protein folding to facilitate this process.

B. Preventing interactions with surrounding proteins to prevent aggregation.
C. Using the negative ΔG of hydrolysis of ATP to make the overall folding process
spontaneous.
D. Extracting individual proteins from aggregates and refolding them.
E. Favoring α-helicies over ß-sheets to achieve the proper folded structure.

SC.6. The parallel ß-pleated sheet protein secondary structure is primarily stabilized by:

A. Peptide bonds between amino acids.

B. Salt bridges between aspartate and arginine residues.
C. Hydrogen bonds between carbonyl oxygens and hydrogens bound to nitrogens.
D. Hydrogen bonds between nitrogens and hydrogens in alcohol groups.
E. Hydrophobic interactions between amino acid side-chains.

SC.7. Which lipid is least likely to be found in the plasma membrane of erythrocytes (red blood
cells).

A. triacylglycerol
B. phosphatidyl serine
C. cholesterol
D. a glycosphingolipid
E. phosphadidyl ethanolamine

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Name Key A (White) BIS102-001, Spring '15, Page 4 of 8
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2. (18) For each statement below, mark “A” on your scantron sheet if the statement is true and
“B” if the statement is false. (3 pts each)

SC.8. T F A protein with a ΔH of folding of -224 kJ/mol and a ΔS of folding of -0.78

kJ/K•mol will be denatured at 68°C.
ΔG=-224-(68+273)•-0.78 = +4.2 so unfolding favored
SC.9. T F Spontaneous folding of a protein in aqueous solution will usually raise the
temperature of the solution. ΔH is negative so solution heats up

SC.10. T F All proteins with quaternary structure have more than one amino terminus.
One for each subunit.
SC.11. T F A threonine residue can inhibit α-helix formation because its side chain can form
a salt bridge that interferes with those that normally stabilize the helix.
Forms and H-bond
SC.12. T F All proteins that exhibit cooperative binding of ligands have multiple ligand
binding sites.
SC.13. T F A disadvantage of immumoaffinity chromatography for protein purification is
that you have to know the structure of a compound that is bound by the target protein.
This is a disadvantage of ligand affinity chromatography
3. (20) You are experimenting with a tube containing human hemoglobin (Hb) initially in
equilibrium with the air. Under these initial conditions, the Hb is 90% saturated. You are
interested in testing the effects of various changes on the solution and the hemoglobin. For
each of the following, on your Scantron mark A for unchanged (U), B for increased (I), C for
decreased (D), or D for need more information (N) to say how the indicated parameter would
be altered (or not) by the treatment. (4 pts. each).

A B C D (Scantron marks)
SC.14. U I D N the P50 of the hemoglobin in response to an increase in the pH of the
solution. pH up, [H+] down, less deoxy, so more O2 binding, so P50 is lower

SC.15. U I D N the amount of CO2 bound by the hemoglobin in response to an increase

in the concentration of BPG (2,3 –bisphosphoglycerate).
BPG up, favors deoxy, favors CO2 binding so more CO2 bound
SC.16. U I D N the pH of the solution in response to a decrease in the PO2 over the
solution. Less O2, more deoxy, deoxy binds more H+, less H+ in solution, pH increases

SC.17. U I D N the oxygen saturation of the hemoglobin in response to an increase in the

+
concentration of H in the solution. More H+, more deoxy, less O2 bound

SC.18. U I D N the average pKa of the hemoglobin in the mixture in response to an

increase in PCO2 over the solution. More CO2 favors deoxy, deoxy will bind more H+
because it has an increased pKa

©2015 Charles S. Gasser, may not be reproduced without expressed permission of author.
Name Key A (White) BIS102-001, Spring '15, Page 5 of 8
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4. (12) For each of the following pairs of fatty acids determine which one in each pair will have
the higher melting point. Circle A or B on your scantron to indicate which has the higher
melting point. (3 pts. each).

A B
SC.19. stearic acid oleic acid

SC.20. linoleic acid 18:3Δ9,12,15

SC.21. 20:1Δ 9 20:2Δ9,12

SC.22. 20:0 18:0

5. (18) A biochemist is attempting to purify a large amount of the grasshopper, SEX LETHAL
protein (SXL, a protein that is known to bind RNA) from a grasshopper cellular extract. This
protein has never been previously purified. The biochemist has partially purified the protein,
but it still is contaminated with other proteins with the following properties:

pI (isoelectric pt.) Molecular weight binds RNA?

protein A 5.1 38,400 yes
protein B 9.4 82,000 yes
protein C 9.5 38,500 no
SXL 9.5 38,500 yes

For each of the following pairings write the name of a protein separation method that would
be suitable for efficient preparative separation of large quantities of the pair of proteins
from each other based on the information provided above. Also next to the method give
the basis upon which that method separates proteins, (6 pts. each).
Method Separation basis
Gel electrophoresis methods will not work for "large amount" purification.
a) SXL from protein A Ion exchange pI
chromatography

b) SXL from protein B Gel filtration size (molecular weight)

c) SXL from protein C ligand affinity binding of RNA

on an RNA
column

©2015 Charles S. Gasser, may not be reproduced without expressed permission of author.
Name Key A (White) BIS102-001, Spring '15, Page 6 of 8
Last, First C. S. Gasser

6. (16) In a startling discovery, life is found under a layer of ice on one of the moons of Jupiter.
Biochemists on earth extract compounds from the discovered organisms. One researcher
studies lipids and isolates the molecule below from a sample of this extraterrestrial organism.
(drawing ignores chiral considerations)
1
H2C O (CH 2 ) 15 CH 3
O 2
H H H H
HC O C (CH 2 ) 7 C C (CH 2 ) 2 C C (CH 2 ) 5 CH 3

H 3N+ O
HC CH 2 O P CH2
-
CO 2 O- 3

a) (4) If a significant quantity of this molecule was vigorously mixed with water, what
structures would you expect it to spontaneously form? (CIRCLE ONE ANSWER)

micelles extensive bilayer

liposomes dissolved in solution

fatty globules can’t be predicted

b) (12) The structure of this molecule resembles some typical glycerophospholipids found in
organisms on earth, but differs from these in several ways. Below, list three ways the
above lipid differs from such lipids of earth organisms. Circle the regions of the
molecule you are referring to and write numbers to indicate the corresponding
descriptions.

1. There is an ether linkage in place of an ester linkage.

2. There are two methylenes instead of one between the two double bonds
(unsaturations).

3. There is a direct P–C linkage instead of a phosphoester bond (an "O" should be
between the P and C).

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7. (26) A sample of human blood at pH 7 the hemoglobin (Hb) was assayed for oxygen binding.
PO 2 2
It was found to bind oxygen according to the equation Θ = PO 2 2 +P50 2
where P50 = 30 mm Hg.
If PO2 in the lungs was 90 mm Hg and in the tissues was 35 mm Hg, how many moles of O2
would be delivered to the tissues through a single cycle of one mole of this Hb from the lungs
to the tissues (assume pH and PCO2 are constant in the blood of this individual)?
€
First determine what fraction of binding sites delivered O2 .

90 2
Lungs : Y = = 0.90
90 2 + 30 2

35 2
Tissues : Y = = 0.58
35 2 + 30 2

Binding sites delivering O2 = 0.90 – 0.58 = 0.32

4 binding sites/Hb -> 0.32 • 4 moles of binding sites = 1.28 moles of O2 delivered
€
Moles O2 = 1.28

b) (10) In fact, pH and PCO2 do vary in the blood. So the real situation in this individual is
such that the P50 of the Hb in the lungs is 30 mm Hg, but in the tissues it is 40 mm Hg.
The PO2 in tissues and lungs is as in part a). The exponent does not change. Under these
conditions how many moles of O2 would be delivered to the tissues by a single cycle of
one mole of this Hb?

Lungs unchanged = 0.90 saturation

35 2
Tissues : Y = = 0.43
35 2 + 40 2

Binding sites delivering O2 = 0.90 – 0.43 = 0.47

€ 4 binding sites/Hb -> 0.47 • 4 moles of binding sites = 1.88 moles of O2 delivered

Moles O2 = 1.88

©2015 Charles S. Gasser, may not be reproduced without expressed permission of author.
Name Key A (White) BIS102-001, Spring '15, Page 8 of 8
Last, First C. S. Gasser

8. (5) Sequences A, B, and C below derive from related proteins of different organisms. The
sequences are aligned with each other in pairs and the symbols “|”, “:” and “.” indicate
identity, strong similarity, and weaker similarity for the aligned amino acids. Use this
information to answer the question below.

A LRNLEGKLERT
|:||| .||:
B LKNLEIHLEKI

C LRNLEGRLERS
||||||:|||:
A LRNLEGKLERT

C LRNLEGRLERS
|:||| .||:
B LKNLEIHLEKI

Which of the following phylogenetic trees best represents the relationships among the sequences
(circle one).
A B

B C
C A

A A

B C
B
C

©2015 Charles S. Gasser, may not be reproduced without expressed permission of author.