Answers to Chapter 4 - Garland · PDF file2 Introduction to Bioorganic Chemistry and Chemical...
Transcript of Answers to Chapter 4 - Garland · PDF file2 Introduction to Bioorganic Chemistry and Chemical...
Introduction to Bioorganic Chemistry and Chemical Biology 1
Answers to Chapter 4(in-text & asterisked problems)
Answer 4.1
The bulky tert-butyl group has a strong equatorial preference, the following two conformations will be predominant. The anti isomer cannot hydrolyze through neighboring group participation; the syn isomer can hydrolyze through neighboring group participation.
Answer 4.2
There are two plausible mechanisms that avoid expulsion of an anionic H2N– group. Without some mechanistic data, you cannot predict which is the most likely.
Answer 4.3
Introduction to Bioorganic Chemistry and Chemical Biology | A4096Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz
O -
P-O
OO
OCH3
- O
P-O
OO
OCH3
:
..
anti syn
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NN
O -R
NH2HO
NN
O -R
NH3+- O
.. BH
..
NN
O -R
NH2OHB:
NN
O -R
NH2- O
..
.. BHNN
OR
NH2HO-:
NN
O -R
NH3+OHB:
NN
OR
O -
BH
:
NNH
OR
O
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5'3'5'
3'CGAUGCCGCGAGG
GUC5'3'C
GCG
UA
GC
UAGA
CCCU AGGGUC
GACC
CU
5'3'CGAUGCCGCG 5'
3'CGC
GUA
GC
UA
"kissing complex"stem loops
2 Introduction to Bioorganic Chemistry and Chemical Biology: ANsWers To CHApTer 4
Answer 4.4
The following figure shows the minimum free-energy structure from rNAfold and GeneBee and the second-lowest energy structure from MC-fold (the lowest-energy structure from MC-fold did not match).
Answer 4.5
Answer 4.6
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C GAUGCCG
UG
GUUGA A
AU
CG CGCGGCAU CGCG
A
AUGCCGCGGCUA
GUCAAAA
G
GU
UCUGG
CC
GG
CG
C
CUUA
UU
G
ACCA
5'
3'
Introduction to Bioorganic Chemistry and Chemical Biology | A4100Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz
N
N
NNNNNN
N
N
NN
NNNNNN
NN
5'
3'
four types of base pairs: A•T, C•G, G•C, or T•A
four types of unpaired bases: A, C, G, or T
Total possibilities = 47• 44• 12 = 411• 12 = 50,331,648
twelve types of mis-matches:A•A, A•C, A•G, C•A, C•C, C•T, G•A, G•G, G•T, T•C, T•G, T•T
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N
OO O
CH3
O -RNA
..
B: N
OO
O
CH3
ORNA
..-
N
OO
O
CH3
ORNA
..
H B
N
OO
O
CH3
ORNA
..-
-
H
+ NO
CH3
ORNA
H
ORNA
H
Introduction to Bioorganic Chemistry and Chemical Biology: ANsWers To CHApTer 4 3
Answer 4.7
Answer 4.8
Triphosphates are highly susceptible to nucleophilic attack, particularly in the presence of Mg2+ ions (not shown). The 2ʹ-hydroxyl group of a 3ʹ-nucleotidyl triphosphate would cyclize to give an unstable cyclic 2ʹ,3ʹ-phosphate.
Answer 4.9
There are two possible hybrid pairs: the DNA-binding domain–Ms2 and the activation domain–iron regulatory protein (as shown) or DNA-binding domain–iron regulatory protein and activation domain–Ms2 (not shown).
Introduction to Bioorganic Chemistry and Chemical Biology | A4102Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz
O
O
Ade
O
HOOP
O-O
Ura
3'
O
O
Ade
OOP
O-O
Ura
5'
3'
OMg
OP
O
POP
O- OO O
OO
OO
HO
CytMg ..
+
-
OP
OPO
O- O
O
MgO
HO
CytOP
O
O
O
-
O
HOOP
O-O
Cyt
O
O
Ade
O
OOP
O-O
Ura
3'OP
OPO
O- O
O
Mg
O-
O
O
Gua
OPO
-O
OH
OH
OH
O
Cyt
Thy
Ade
Gua
OH
OH
OH
OH
OH
OH
O
O
Gua
OPO
-O
OHO
5' O
O
Gua
OPO
-O
OHO
Cyt
Thy
Ade
Gua
OH
Cyt
Thy
Ade
Gua
leaving group
RNA Pol
templatestrand
templatestrand
templatestrand
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O
O
CytHO
OP
OP
- O OP
- OO
O
- OO
OH
H.
O
O
CytHO
O. PO O - OH
P- O O
P
O
- OO
OH
Introduction to Bioorganic Chemistry and Chemical Biology | A4104Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz
GAL4DNA-binding
domains
iron regulatoryprotein
RNA library
MS2 viralcoat protein
transcription
4 Introduction to Bioorganic Chemistry and Chemical Biology: ANsWers To CHApTer 4
Answer 4.10
Answer 4.11
The two lone pairs around the sulfur of the thioether are diastereotopic, as shown in the following structure. The enzyme is selective for one of these lone pairs, generating the diastereomer of sAM with a configurationally stable S configuration at sulfur. The reaction with methyl iodide reacts with both lone pairs at approximately equal rates, leading to a mixture of R and S sulfonium ions. The natural S diastereomer of sAM is a good substrate for methyltransferases, whereas the R diastereomer is not.
Answer 4.12
The phosphate indicated with the arrow still has an adjacent 2ʹ-oH group, whereas the other two phosphate diesters lack the adjacent 2ʹ-oH group. This 2ʹ-oH group can play a key role in mediating rNA cleavage, as discussed earlier in the chapter.
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NH
O H
NH
O.
NH
O
.
NH
O
.
HN
O
.NH
O HN
OH
H
O O. .
OH.
NH
O HN
OH
O OH.
.
NH
O HN
O
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S
O
HO OH
N
NN
N
NH2
+H3N
-O2C
: :
S
O
HO OH
N
NN
N
NH2
+H3N
-O2C
H3C
:
(S)-configuration
SAM
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OO
O
BO
OO
O
Ade
OPO
- O
PO
- OO
PO
O -
n-..
this P–O bond iscleaved by exposure to base
lariat
Introduction to Bioorganic Chemistry and Chemical Biology: ANsWers To CHApTer 4 5
Answer 4.13
Answer 4.14
Answer 4.15
Answer 4.16
ATG GGC CGC CGC CCC GCC CGT TGT TAC CGG TAT TGT AAG AACAUG GGC CGC CGC CCC GCC CGU UGU UAC CGG UAU UGU AAG AACMet Gly Arg Arg Pro Ala Arg Cys Tyr Arg Tyr Cys Lys Asn
(The three-letter abbreviations used here correspond to the first three letters of the amino acid, with the exception of asparagine and glutamine, which are abbreviated Asn and Gln to avoid confusion with aspartic acid and glutamic acid, respectively.)
Answer 4.17
so the number of possiple hexapeptides coded by these sequences is 26 = 64.
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5'-GATCCGCACCGAGTTCAAGAACACCTTTTCAAGAGAGGTGTTCTTGAACTCGGTGTTCTTTTTTTCTAGAG-3'
CACCGAGUUCAAGAACACCGUGGCUCAAGUUCUUGUGG
UU UUAAGAGA3'-GAGAUCUUUUUUUCUU
5'-GAUCCG
transcription
sense
antisense
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N
N
NH
H
N
N
A2451
NN
O
NN G2447
N HH O P
OO
OA2450
3
1
H
N
N
NH
N
N
A2451
NN
O
NN G2447
NH O P
OO
OA2450
H
H
H.. ..3
1
:
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Gua
N
N
N
NHN
O
R
H
H
HH
O N N
NCyt
H
ManQ
N
N
N
N
N
OH
R
H
H
H
N O
N
O
Ura
wobblebase pair
Watson–Crickbase pair
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G TAC G TGC CAGC
AGCT G T-C
T-G AAC5' 3'
Alaor
Glu
ThrorAla
AsporAla
GlyorAla
Alaor
Pro
Alaor Val
6 Introduction to Bioorganic Chemistry and Chemical Biology: ANsWers To CHApTer 4
Answer 4.18
The Zn2+ ion acts a Lewis acid, coordinating to both the formamide carbonyl and the hydroxide nucleophile. The Zn2+ ion activates the carbonyl group toward attack and brings the hydroxide nucleophile into proximity with the carbonyl carbon.
Answer 4.19
B The enzyme lowers the entropic barrier by bringing the reactive carbon of NADH into close proximity with the diphthamide residue. Carbocation formation is the rate-determining step in an sN1 reaction. The enzyme probably lowers the en-thalpic barrier to ionization by stabilizing the oxocarbenium ion.
Answer 4.20
Because chloramphenicol disrupts all protein translation, chloramphenicol will prevent the cells from expressing the plasmid-encoded protein (chloramphenicol acetyl transferase) that confers resistance. Allowing the cells to grow before exposure to chloramphenicol ensures an adequate supply of the proteins that confer resistance.
Answer 4.21
Number of 50-mer rNAs = 450 = 1.3 × 1030
Molecular mass of a 50-mer DNA = 50 × 305 g mol–1 = 15,250 g mol–1
500 × 10–6 g × 1 mol/15,250 g × 6.02 × 1023 molecules mol–1 = 1.9 × 1017
1.9 × 1017/1.3 × 1030 = 1.6 × 10–13 (!)
*Answer 4.22
A 3ʹ-CATAGCTGTCCTCCT-5ʹ 5ʹ-GUAUCGACAGGAGGA-3ʹB 3ʹ-CATGGTGGT-5ʹ 5ʹ-GUACCACCA-3ʹ
Answer 4.23
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NH
HN
O
S
H N
OO
OZn +
:HONHR
-HN
ONH
N
OHO
OO
Zn+
- ~~
peptidedeformylase
activesite
peptidedeformylase
activesite
actinoin protein/peptide
hydroxide anion
Introduction to Bioorganic Chemistry and Chemical Biology | A4113Van Vranken & Weiss | 978-0-8153-4214-4 © www.garlandscience.com design by www.blink.biz
ON
H2NOC
OHHO
NAD+
NH
N
H2NOC
Me3N+
NHNH
O
O
:
EF-2
:: O
OHHO
+
O
HO
HO
NH
N+
H2NOC
Me3N+
NHNH
O
O
:+
oxocarbenium ionA
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CU
C
G
GAG
GA
GCUC
CC
GUC
UG
CGG
CAG
GA
GGGA
GC
CCUCC
UA
GU
GCGG C
G
UGCC
GGA CCUA
GC
UA
GC
5'
5'3'
B*A 3'
Introduction to Bioorganic Chemistry and Chemical Biology: ANsWers To CHApTer 4 7
Answer 4.24
*Answer 4.25
*Answer 4.28
Note that the presence of start and stop codons confirms that the reading frame is correct.
*Answer 4.31
Most amine-containing buffers are tertiary trialkylamines that can form stable adducts through acylation or sulfonylation. Tris is a primaryl alkylamine that can react readily with DepC to form stable carbamates.
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OP
O
O ONa 1 M NaOH
H2O100 °C
*A
OP
O
O ONaOH
1 M NaOH
H2O100 °C
*B
OH
OH
O
O
Ura
O
O
HO
Ade
OPO
NaO
OH
PO
NaO(excess)
1 M NaOH
H2O100 °C
C
OP
ONa
O ONaHO
NaOP
O
O ONaOHOH
OH
O
HO
Ura
O
ONaP
ONaO
OH
ONaO
HO
Ade
OPO
NaO+
+
+
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3'-CCGCUGGCUGGCA-5'5'-GGCGACC ACCGU-3'
CUGAUGAGG
CCGAAAGGCCG
AA
3'-CGCGUCGCUGCCG-5'5'-GCGCAGC ACGGC-3'
CUGAUGAGG
CCGAAAGGCCG
AA
A B
substrate
ribozyme
substrate
ribozyme
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1 gaauuccgcu aaaccaaucu aucaaguccu gauuaaucug gugagcAUGG AGCUUUGUUG 61 GCUCACAACC AUCCAUGGUU CUUGAagaag cuuggagaga aaggggugug agaggagagg121 gugcucacuc cucacacucc cucacuuaaa acaguuuguu uuggcuuagc uuuggcuucu181 cugaucaaca agggaugugu ucuaacauuc uuucuugagu ggcggaagca gauacacauu241 cuccgacgga ggagaggcuu ggcuacagcc uggcaaaccg gcaagucaca aaaaaggcaa301 uggacuccau uggggucucu auggcuaugu agugcucaug uaguucuucu ugcuguagaa361 uguaauaaua aacaaaguug gucuuccuuu ugagaaguua ccagcuuuug cuguccaaaa421 uuacucaauu ugcagcugac uagaauuccu uucucucuuc aguuucugca gaugaguagg481 uaggcaauuu gugaucacuc ccuucccuuu ucaugucuuc uguguucccu uuuccaugcu541 uguuuguguu guuaguuaug accuuaugag gaaauaaaag aauaguacaa uucuaguccc601 ucaguuuagg auuguauucu auugaacuuu auuagaaaag uuuccagagu ccuuucuaaa661 aaaaaaaaaa aaaaaaaaa
AUGGAGCUUUGUUGGCUCACAACCAUCCAUGGUUCUUGAMetGluLeuCysTrpLeuThrThrIleHisGlySerSTOP
AUGGUUCUUGAagaagcuuggagagaaaggggugugagaggagagggugcucacuccucacacucccucacuuaa
MetValLeuGluGluAlaTrpArgGluArgGlyValArgGlyGluGlyAlaHisSerSerHisSerLeuThrSTOP
ACCESSION X69154; Glycine max ENOD40-1 mRNA.
Peptide A (highlighted)
Peptide B (underlined)
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NH2
O
OEtO OEt
O.. +
HO
HO
OHTris
NH
HO
HO
OH
OEt
OpH 8