Download Midterm for Bio98B A1 (1) Enzymes accelerate reactions by

02/11/08 Bio98B Midterm
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Midterm for Bio98B
A1 (1) Enzymes accelerate reactions by decreasing the free energy input needed to
achieve
the ____________________________________ of the reaction.
A2 (1) All but one amino acid have at least one chiral carbon center, which amino acid
does not have a chiral center (3-letter code).
______________
A3 (2) There are two amino acids which have a chiral carbon center on their side chain.
Draw one of these amino acids and draw an arrow to the chiral carbon center on the side
chain.
A4 (2) Rhinoceros myoglobin has a P50 for O2 of 40 mm Hg. What PO2 is needed to
saturate 60% of the myoglobin. ______________________
A5 (3) Draw the structure of the following lipid, 8:1cΔ6
Would 8:1cΔ6 have a melting temperature higher or lower than 8:0?
_______________
02/11/08 Bio98B Midterm
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B1 (4) a) For the plot shown below, estimate the Km _______________________
and the Vmax
_______________________________
(no units – no credit!)
b) Draw a dotted line to indicated the relative position of the data if the same enzyme
reaction was studied in the presence of a competitive inhibitor.
c) If the total enzyme concentration is 5 x 10-5 moles, what is the k2 (kcat) of the reaction
(or rate of turnover)? _________________
(no units – no credit!)
B2 (3) Draw the structure of the dipeptide Asp-Ala at pH 7.0. Indicate which bonds
along the polypeptide chain have a) freedom to rotate (arrow with FREE written next to
it), and b) no freedom to rotate (arrow with No FREE written next to it). Hint: There are
2 bonds that rotate, and 1 that does not.
02/11/08 Bio98B Midterm
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C1 (4) a) Which of these disaccharides does not have an hemiacetal group?
___________
b) Circle the carbon of the hemiacetal group on the other disaccharide.
c) O-glycoside bond is a bond between a ___________ group and an _________ group.
A
B
C2 (3) In chymotrypsin, the active site amino acid ________ serves as nucleophile to
form a _____________ bond with the substrate while the active site amino acid
_____________ serves to donate and accept protons several times during one reaction.
C3 (4)
Protein(s) ____________ has/have all helices
Protein(s) ____________ has/have all sheets
Protein(s) ____________ has/have a mixture
of sheets and helices
Write the correct letter A, B, C or D in the
space provided.
There may be more than one protein per
answer
C4 (2) You have two peptides with the following sequences
Arg-Glu-Ala-Leu-Ser-Ile-Gln-Tyr-Asp-Glu
Met-Phe-Gln-Asn-Val-Thr-Ile-Leu-Arg
You want to separate these 2 peptides using chromatographic methods at neutral pH.
Would you use gel filtration or ion-exchange chromatography?
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02/11/08 Bio98B Midterm
D1 (2) In 2-dimensional chromatography, the first electrophoresis step separates proteins
on the basis of __________ while the second electrophoresis step separates on the basis
of ___________.
D2 (3) A particular metabolic pathway converts compound A to F in a series of
enzymatic steps using enzymes E1, E2 etc. Compound __________ is most likely to be a
feedback __________ of enzyme ____________.
D3 (1) The compound shown to the right is a
A
B
C
D
E
steroid
glycerophospholipid
sphingolipid
fatty acid
triacylglycerol
D4 (1) A spectrophotometer set to a wavelength of 280nm will most easily detect
peptides that contain (circle one).
Gly
Asp
Trp
Val
Cys
Lys
D5 (1) One of the proteins exhibits homotropic allostery
A
B
C
E
myoglobin
hexokinase
chymotrypsin
hemoglobin
D6 (1) Which of the following best describes the role of the oxyanion hole in
chymotrypsin.
A
B
C
D
F
Stabilizes the positive charge on the substrate carbonyl carbon
Assists in the transfer of the proton to the peptide leaving group
Stabilizes the tetrahedral intermediate
Serves as a nucleophile to help break the peptide bond
Operates as an acid/base catalyst
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02/11/08 Bio98B Midterm
E1 (1) The tertiary structure of many proteins is stabilized by covalent bonds between
the side chains of?
His
Cys
Ala
Phe
Ile
Gln
E2 (1) Which is the C-4 epimer of D-glucose?
E3 (6) Trypsin cleaves a peptide at Lys (C) and cyanogen bromide cleaves at Met (C)
A
B
C
D
E
F
QQYHHPLMGEK
IAAGGYKQQYHHPLM
LI
AFHGMIAAGGYK
GEKLI
AFHGM
Which two peptides are generated after cleavage with trypsin ________ & ______
Which two peptides are generated after cleavage with cyanogen bromide _____ & ____
Which two peptides are from the C-terminal of the protein _______ & _________
Piece together the sequence of the protein using the alphabetic letters of the cyanogen
bromide cleaved peptides ie. A+B+D
E4 (3) a) This structure is called a ________________________ .
b) Draw arrows to the hydrophobic portions and hydrophilic portions.
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02/11/08 Bio98B Midterm
F1 (2) You want to make a pH = 7 phosphate buffer. You have 0.1M KH2PO4. What
concentration of K2HPO4 do you need?
HPO4-2 + H+
H2PO4-
pKa = 6.86
F2 (2) This is the sigmoidal curve of oxygen binding for hemoglobin. Draw in two
curves if the subunits of hemoglobin were stuck in its T-state or R-state and label.
F3 (7) An enzyme (E) catalyzes the reversible formation of B from A. To start the reaction, A is dissolved
in a buffer at 25oC. Enzyme is then added and the reaction is allowed to proceed to equilibrium,
whereupon, the concentrations of A and B are found to be 1.5 x 10-5 M and 4.5 x 10-4 M, respectively.
Calculate Keq for the reaction, the starting concentration of A, and the value of ΔGo for this reaction (at
25oC, RT = 2.479 kJ/mol).
Keq
=__________________
[A]initial =___________________
o
ΔG
o
If ΔG is negative (not ΔG )
If ΔS is negative
If ΔH is negative
If ΔH is positive and ΔG > ΔH
=___________________
Is the reaction favorable?
Yes No
Is the reaction entropically favored? Yes No
Is the reaction enthapically favored? Yes No
What is ΔS?
negative
positive