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課程名稱︰生物化學
課程性質︰化學系五選三必修
課程教師︰陳平
開課學院：理學院
開課系所︰化學系
考試日期（年月日）︰2012/05/29
考試時限（分鐘）：60mins
是否需發放獎勵金：是
（如未明確表示，則不予發放）
試題:
(Total 116 pts, maximum 105 pts)
1. Multiple Choice. There is only one correct answer for each question.
(13x pts; 39 pts)
__1. What causes a “burst” of activity followed by a steady state reaction
when chyrnotrypsin is studied by stop-flow techniques?
A) the peptide bond is cleaved in a two step reaction.
B) acyl enzyme intermediate formation is faster than its hydrolysis.
C) the hydrolysis of the acyl enzyme intermediate is faster than its formation.
D) A and B.
E) A and C.
__2. How is substrate specificity determined by chymotrypsin?
A) interaction of the catalytic amino acids with the substrate
B) binding of the N-terminus amino acid at the active site
C) covalent binding of a His residue to the substrate
D) conformational change upon binding of substrate
E) binding of the proper amino acid into a deep pocket on the enzyme
__3. Convergent evolution is attributed to similarities found between
A) trypsin and elastase.
B) chymotrypsin and elastase.
C) chymotrypsin and trypsin.
D) chymotrypsin and subtilisin.
E) trypsin and kinase.
__4. If you carried out site-directed mutagenesis of subtilisin. changing serine
221 (key nucleophile) to alanine, what would you expect?
A) a large change in K_M
B) a minimal change in K_M
C) a large change in K_cat
D) A and C
B) B and C
__5. Carbonic anliydrases are necessary because
A) spontaneous hydration and dehydration of carbon dioxide occur very slowly.
B) spontaneous hydration and dehydration of carbon dioxide arc reasonable in
rates, but are not rapid enough
C) hydration and dehydration of carbon dioxide are coupled to other biochemical
processes.
D) A and C.
E) B and C.
__6. Binding of a water molecule to the zinc ion in carbonic anhydrase induces
A) hydronium ion to form.
B) a large conformation change in the binding site.
C) ionizatiOn of a His residuc. which functions as a strong nucleophile.
D) a lowered pKa for water, which leads to formation of a zinc bound hydroxide
ion.
E) an altered K_M value.
__7. The catalytic specificity of EcoRV endonuclease is mainly due to
A) the initial binding affinity.
B) unwinding of the DNA.
C) interactions to form a kink in the cognate DNA.
D) hydrogen bonding of the enzyme to the DNA backbone.
E) magnesium bridges.
__8. Nucleotide monophosphate kinases function to
A) transfer the phosphate from NTP to NDP.
B) transfer the phosphate from NTP to NMP.
C) transfer the phosphate from NMP to NDP.
D) phosphorylate NADH.
E) transfer the phosphate from NTP to water.
__9. The sequence GIy-X-X-X-Gly-Lys is referred to as a P-loop because
A) it forms a lariat P shape.
B) it forms a high-energy bond.
C) it interacts with phosphoryl groups.
D) it interacts with a phenylalanine.
E) the loop becomes covalently bound to a phosphoserine residue.
__10. For restriction endonuclease cleavage of DNA:
A) in-line displacement occurs at the phosphorus.
B) direct hydrolysis occurs.
C) covalent catalysis occurs
D) A and B.
E) A and C.
__11. The relaxed form of an allosteric enme has ___ affinite for the
substrates compared to the tense form.
A) higher
B) equal
C) lower
__12. The effects of substrates on allostric enzymes are referred to
as __ effect
A) homotropic
B) heterotropic
C) allotropic
D) all of the above
E) none of the above
__13. Changes in ATCase conformation were detected by using a compound
PALA. What is PALA?
A) a radioactive tag that binds to the subunits
B) a bi-substrate analog that resembles the catalytic intermediate
C) a fluorescent substrate analog
D) all of the above
E) none of the above
II. Fill in the blanks (20x2 pts: 40 pts)
1. The four catalytic strategies employed by natural enzymes are
a)
b)
c)
d)
2. Name the major four different types of proteases.
a)
b)
c)
d)
3.Human chymotrypsin and human trypsin share a common fold. Which type of
homolog are they?___ (ortholog or paralog).
4. What is the main feature in chymotrypsin for stabilizing the
tetrahedral intermediate?
5. The six most common strategy(ies) enzymatic regulation are:
6. ATP is one of the substrates for a given enzyme. This enzyme will most
likely contain a kind of protein fold. What is this type of protein
fold called?
7. For ATCase alone, the curve is E. Please fill in the corresponding
curves for the statements below. (3x4 pts; total 12 pts)
a) The R state curve is __
b) The curve for addition of inhibitor CTP is
c) The curve for addition of promotor ATP is
III.Short question
1.Why is a metal ion required for the activity of NTP-dependent enzyme?
(5pts)
2. How does carbonic anhydrase achieve hydration rates (~1O^6 s^-1) that
exceed rationalization based on Zn(II)-bound water pKa and proton
diffusion rates?(4 pts)
IV. Structure drawing with stereochemistry. (26 pts)
1. Please draw the three amino acids in the catalytic triad of chymotrypsin.
(3x3 pts)
2. The CH3 group of Captopril binds the S1’pocket of the angiotensin
converting enzyme. Please draw the amino acid in the natural peptide
substrate that most likely binds the S1' pocket of this enzyme? (3 pts)
3. Please draw the structure of the bases involved in the A-T base pair with
the adenine methy1ated. Also, please include the hydrogen bonds and indicate
the major aWd minor grooves. (2x2 structure 2x1 H-bond; 2x1 grooves total 8 pts)
4. Draw the stucture of 5'-CTP and 5'-ATP (2x3 pts)
ans
I.DEDEE DCBCD AAB
II.
1.
covalent catalysis
general acid base catalysis
metal ion catalysis
catalysis by approximation
2.
cysteine proteases
serine proteases
aspartyl proteases
metallo proteases
3.paralog
4.oxyanion hole
5.
allosteric control
mutiple forms
reversible covalent modification
proteolytic activation
expression
neutral inhibitor
6.Rossman fold
7.BDC
III.
1.
NTP metal ion couple
neutral charge
conformation
recognition
2.
buffer
proton suffle system
IV.
1.Asp His Ser
2.Ala
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