BCH 400
Spring 2004
Exam 1
February 9, 2004
Name:
Student I.D.#:
Notes: pKa of amino acid R-groups: cysteine = 8.4, tyrosine = 10.5, aspartate = 3.9,
glutamate = 4.1, lysine = 10.5, arginine = 12.5, histidine = 6.0, pKa of alpha amino
groups = 10, pKa of the alpha carboxyl group = 2
Multiple Choice (2 points/question)
1) The Buchner brothers _________________________.
a) synthesized urea in vitro.
b) coined the term “enzyme” for biological catalyst.
c) showed that extracts from killed yeast could catalyze the conversion of
glucose to ethanol.
d) won the WWF tag team wrestling championship in 1852.
2) The linkage that occurs between two consecutive nucleotides in an RNA molecule
is referred to as a ______________.
a) disulfide linkage
b) amide linkage
c) phosphodiester linkage
d) ester linkage
3) Ribosome assembly occurs within the ___________________________.
a) cytosol
b) peroxisome
c) golgi apparatus
d) nucleolus
4) Which of the following techniques would you use in an early stage of a protein
purification to enrich an extract from leaves for a protein specifically involved in
photosynthesis?
a) anion exchange chromatography
b) gel permeation chromatography
c) SDS PAGE
d) differential centrifugation
5) Hydrogen bonds can form between __________________.
a) the proton of an amino group and the proton of a hydroxyl group
b) the proton of an amino group and oxygen of a carbonyl group
c) the proton of a hydroxyl group and the oxygen of a carbonyl group
d) all of the above
e) b and c
6) The layer of water molecules surrounding the hydrophilic exterior of a protein is
referred to as a ___________________.
a) hydrophobic cleft
b) micelle
c) hydration shell
d) none of the above
7) In the frozen state, a single water molecule can form hydrogen bonds with
approximately ___________ other water molecules.
a) one
b) two
c) four
d) ten
8) Which of the following amino acids could serve as a buffer at pH 9?
a) glutamate
b) histidine
c) alanine
d) all of the above
e) none of the above
9) A weak acid _____________.
a) only partially ionizes in water
b) completely ionizes in water
c) can hydrolyze peptide bonds
d) none of the above
10) Binding of oxygen to one subunit of hemoglobin___________.
a) causes a conformational change in adjacent subunits
b) increases the affinity of the deoxygenated subunits for oxygen
c) shifts the conformation of that subunit from the T to the R form
d) all of the above
11) Which of the following is an allosteric effector of hemoglobin (22)
a) bisphosphoglycerate
b) proton
c) oxygen
d) a and b
e) all of the above
12) In the tissues of the body where oxygen concentrations are low relative to the
lungs, hemoglobin___________________.
a) is present in the T configuration
b) has a high affinity for oxygen
c) has a sickle cell conformation
d) a and b
13) In a beta sheet, the R-groups of consecutive (adjacent) amino acids in a beta
strand are oriented ______________ relative to each other.
a) on the same side of the beta sheet
b) on opposite sides of the beta sheet
c) anti-parallel
d) parallel
e) a and c
14) Which of the following are stabilized by hydrogen bonds?
a) alpha-helix
b) beta-sheets
c) beta-turns
d) all of the above
15) Which of the following secondary structures absolutely must have proline and
glycine present in order to maintain its conformation?
a) alpha helix
b) beta sheet
c) beta-turn
d) all of the above
16) Proteins are thermodynamically driven to ____________________.
a) fold into the most compact conformation
b) fold into the lowest energy state conformation
c) fold into the highest energy state conformation
d) the market by a elderly lady every Friday afternoon
17) Of the following protein folding intermediates, which occurs first during the
protein folding?
a) local secondary structures
b) motifs
c) domains
d) native conformation
18) At what pH is the concentration of a weak acid equal to the concentration of its
conjugate base?
a) when the pH is higher than the pKa
b) when the pH is within one point above or below the pKa
c) when the pH is lower than the pKa
d) when the pH is equal to the pKa
19) Isoelectric focusing can be used to determine ________________.
a) the molecular weight of a protein
b) the subunit conformation of a multimeric protein
c) the pH at which a protein is a zwitterion
d) the protein sequence of a protein
20) A protein with quaternary structure will by definition always be described as a
_______________.
a) multimeric protein
b) monomeric protein
c) fibrous protein
d) globular protein
21) Proteins with similar amino acid sequences will also have similar ________.
a) secondary structures
b) tertiary structure
c) quaternary structure
d) all of the above
Match the functional group or linkage with the term that best describes it from the
terms listed in questions 22- 25 (only one answer per question) (2 points/question)
A
D
B
C
22) primary amine _______
23) phosphoanhydride _______
24) phosphoester linkage ______
25) nucleotide triphosphate ______
Short answer (Please answer each question in the space below)
26) Draw the correct structure of the following peptide at pH 2 (20 points)
Methionine-Glutamate-Asparagine-Tyrosine-Isoleucine-Histidine-Tyrptophan-Arginine-Valine-Apartate
27) Write out the correct one letter amino code for the decapeptide above (5 points)
28) (15 points total) The figure below describes the titration curve for aspartate.
Aspartate has three ionizable groups and therefore three different pKa’s. 1) On the
graph below mark with a square and label each square with the appropriate pKa
value. 2) Calculate the pI value for aspartate. 3) Draw the correct structure of the
zwitterion specie. (Hint it may be worth drawing out the structures of the
three acid/base pair corresponding to each pKa) .
14
12
10
pH
8
6
4
2
0
1
2
OH- equivalents added
3
29) (5 points) Briefly describe why hydrophobic interactions are the primary driving force
involved in protein folding. How do they counter act the thermodynamically unfavorable
effect of a polypeptide chain being folded into a more ordered conformational?
30) (5 points) Briefly describe why polypeptides chains can fold into only a few different
types of secondary structure (i.e. alpha-helices, beta sheets, beta turns, and loops).
Extra Credit (5 points) You digested a protein with trypsin, chymotrypsin and CNBr. Each of the
proteolytic fragments were then sequenced and the data is shown below. From this data, list the
amino acids in the correct order to get the sequence of the undigested protein.
Trypsin digest:
T-Y-R
M-L-F-G-M-K
Chymotrypsin digest:
R-H-E
M-L-F
CNBr digest
L-F-G-M
M
H-E
G-M-K-T-Y
K-T-Y-R-H-E