Introduction to Bioorganic Chemistry and Chemical Biology
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.
-O
OCH3
P
O
O
-O
:O -
OCH3
P
O
O
..
-O
anti
syn
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Answer
4.2
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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.
H B
HO ..
NH2
B:
H O
N
N
HO:
N
N
NH2
R
NH3+
R
O-
-O
O-
N
R
N
N
N
B:
O
H O
H B
- O ..
NH2
NH2
N
O-
R
..
O-
N
R
O
H B
NH
N
R
O
N
N
R
N
O
:O -
NH3+
N
R
..
O-
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Answer
4.3
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A
3' C U C G G GG
5' G A G C CC UG
CU
C U G U C G 5'
C A C A G C 3'
AG
stem loops
U
C
3' C U C G G A
G CC U G U C G 5'
5' GA G C C GG AG A C A G C 3'
UC
"kissing complex"
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5'
3'
1
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).
G CU
A
U
U
U C GG
C C
G G UG
C GC U
3' A
C CA
U
G
CGG CUCC
A CG
G
5' G C C G A G G
U G C C U A AA
UA
CGA
G CA
C G
C U GA
U A
C G
A A
G
U
U G
UG
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Answer
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four types of base pairs: A•T, C•G, G•C, or T•A
5' N N N N N N N N N N
3' N N N N N N N N N
four types of unpaired bases: A, C, G, or T
N
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
Total possibilities = 47• 44• 12
= 411• 12
= 50,331,648
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Answer
4.6
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RNA
RNA
O H
:B
RNA
RNA
O
.. O
O
O
N
O
-O
..
O
N
CH3
O
O
O
O
-
O
N
.. CH
3
CH3
H B
RNA
O
O ..
O
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RNA
O
N+
CH3
H
O
O
H
N
CH3
Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 4
Answer 4.7
O
O
Gua Cyt
O
-O
O
P O
OH O
Ade Thy
O
-O
O
P O
OH O
template
strand
O
Ura Ade
RNA Pol
Mg
O O
O
O
P
P O O
P
O
-O
O
O
Gua Cyt
O
-O
O
P O
O
HO
OH O
OH
O
5'
Gua Cyt
O
-O
Ade Thy
P O
OH O
Ura Ade
Cyt Gua
Mg O
.. 3' OH
O
Mg O P O
+
HO
OH
O
O
O
O
P
P
-O
O
O
O
O
Cyt
O
template
strand
O
-O
Gua
HO 3' OH
leaving group
O
5'
O
P O
OH O
Ade Thy
O
OH O
-O
O
P O
template
strand
Ura Ade
O
-O P O
Mg
O
O
O
P O
P
O
-O
O
O
OH O
HO
3'
Cyt Gua
OH
Answer 4.8
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Triphosphates
highly susceptible to nucleophilic attack, particularly in the presence
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2+
of Mg ions (not shown). The 2ʹ-hydroxyl group of a 3ʹ-nucleotidyl triphosphate would
cyclize to give an unstable cyclic 2ʹ,3ʹ-phosphate.
HO
O
Cyt
O .O
. H
O P
O
-O
O P
-O
O
O P
OH
-O
HO
O
Cyt
O
O
P
O O-
OH
O P
-O
O
O P
OH
-O
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Answer
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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).
RNA library
GAL4
DNA-binding
domains
MS2 viral
coat protein
iron regulatory
protein
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transcription
3
Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 4
Answer 4.10
. OH
O H
O.
O
.
N
H
N
H
. O O.
O
.
N
H
N
H
O
H
N
.
O
O
H
H N
N H
H
.
N H
H
O
H
N
O
. O OH
O
N
H
H
N
O
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.
NH2
N
N
N
(S)-configuration
+H N to Bioorganic Chemistry and
+H | N
N Chemical Biology
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3
3 A4105
O
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-O C
-O C
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S
HO
2
:
OH
NH2
SAM
2
O
S
H3C
HO
N
N
N
OH
:
N
:
4
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Answer
4.12
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lariat
O
O
B
Ade
..O
n O
P
-O
O O
O
O P OO
this P–O bond is
P
-O
O
cleaved by
O
O
exposure to base
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The
phosphate indicated with the arrow still has an adjacent
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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.
Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 4
Answer 4.13
5'-GATCCGCACCGAGTTCAAGAACACCTTTTCAAGAGAGGTGTTCTTGAACTCGGTGTTCTTTTTTTCTAGAG-3'
transcription
sense
U UU
A
A
GUGGCUCAAGUUCUUGUGG
3'-GAGAUCUUUUUUUCUU
AG G
A
antisense
5'-GAUCCG CACCGAGUUCAAGAACACCU
Answer 4.14
N
H
N G2447
N
H
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N
N
N
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1
1
N
3
..N
N
H
O
N H
H
O P O
O
A2450
N
A2451
3
: ..N
H O
N
H
N
N
H
N
A2451
N G2447
N
O
H O P O
O
A2450
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Answer 4.15
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Cyt
Watson–Crick
base pair
H
Ura
N
O
N
H
N
H
N
N
H
H
O
H
N R
N
Gua
N
N
O
H
N
O
H
N
H
N
N
ManQ
wobble
base pair
O
H
N R
N
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Answer
4.16
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ATG GGC CGC CGC CCC GCC CGT TGT TAC CGG TAT TGT AAG AAC
AUG GGC CGC CGC CCC GCC CGU UGU UAC CGG UAU UGU AAG AAC
Met 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
A A
A
G G
C
5'-G CA GCT G CT G CT CCA G TT-3'
Ala Thr Asp Gly Ala Ala
or
or or or
or or
Glu Ala Ala Ala Pro Val
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So
number
possiple hexapeptides coded by these sequences is 26 = 64.
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5
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.
peptide
deformylase
active
site
Zn
O
peptide
deformylase
active
site
Zn
actinoin
+
O
-
H
N
N
H
O
HO
~
~
N
HO:
H
O
+
O
hydroxide anion
S protein/peptide
O
O
H
N
N
N
H
O
R
NH
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Answer
4.19
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A
oxocarbenium ion
HO
HO
OH
HO
OH
O
HO
:
H2NOC
O:
O+
:
N
+
:
6
Me3
NAD+
N
H
H2NOC
O
O
N+
Me3N+
N
N+
N
H
H2NOC
N
NH H
O
O
N
NH H
EF-2
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The enzyme lowers
the
entropic barrier by bringing
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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 enthalpic 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-3ʹ
B
3ʹ-CATGGTGGT-5ʹ
5ʹ-GUACCACCA-3ʹ
Answer 4.23
B
*A
5'
3'
5'
3'
UA A G G C
C G G C C G GA
CU GU
G
C CU
CA C UG
AG CC A
G
G G
U U
C U
G C
A C
G
G
C
C
G C
UG C
G C
G UG
G G
A C
GA C
CG
Introduction to Bioorganic Chemistry and Chemical Biology: Answers to Chapter 4
Answer 4.24
*A
O ONa
P
O
O
*B
O ONa
P
O
C
O
H2O
100 °C
O
P
ONa
+ HO
ONa
1 M NaOH
OH
O
1 M NaOH
OH
H2O
100 °C
+
O
NaO
P
ONa
OH
O
Ura
OH
*Answer
4.25
O
(excess)
ONa
1 M NaOH
AdeB
O
CCG A
CCG
G
OH
G
A
O
G
G
A NaO P O
A
A
H2OA
P OA
A
O
G
GNaO
G
G
100 U
°C
U O
HO
G
G
OH
A
A
C
C
G
C
G
C
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Chemical Biology
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U
AG
ribozyme to Bioorganic
AG Chemistry andribozyme
A
C
A
C
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5'-GCGCAGC ACGGC-3'
5'-GGCGACC
ACCGU-3'
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3'-CGCGUCGCUGCCG-5'
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3'-CCGCUGGCUGGCA-5'
NaO P O
O
A
substrate
Ura
O
HO
+
OH
ONa
NaO P O
O
substrate
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©*Answer
4.28
Note that the presence of start and stop codons confirms that the reading frame is
correct.
ACCESSION X69154; Glycine max ENOD40-1 mRNA.
1
61
121
181
241
301
361
421
481
541
601
661
gaauuccgcu
GCUCACAACC
gugcucacuc
cugaucaaca
cuccgacgga
uggacuccau
uguaauaaua
uuacucaauu
uaggcaauuu
uguuuguguu
ucaguuuagg
aaaaaaaaaa
aaaccaaucu
AUCCAUGGUU
cucacacucc
agggaugugu
ggagaggcuu
uggggucucu
aacaaaguug
ugcagcugac
gugaucacuc
guuaguuaug
auuguauucu
aaaaaaaaa
aucaaguccu
CUUGAagaag
cucacuuaaa
ucuaacauuc
ggcuacagcc
auggcuaugu
gucuuccuuu
uagaauuccu
ccuucccuuu
accuuaugag
auugaacuuu
gauuaaucug
cuuggagaga
acaguuuguu
uuucuugagu
uggcaaaccg
agugcucaug
ugagaaguua
uucucucuuc
ucaugucuuc
gaaauaaaag
auuagaaaag
gugagcAUGG
aaggggugug
uuggcuuagc
ggcggaagca
gcaagucaca
uaguucuucu
ccagcuuuug
aguuucugca
uguguucccu
aauaguacaa
uuuccagagu
AGCUUUGUUG
agaggagagg
uuuggcuucu
gauacacauu
aaaaaggcaa
ugcuguagaa
cuguccaaaa
gaugaguagg
uuuccaugcu
uucuaguccc
ccuuucuaaa
Peptide A (highlighted)
AUGGAGCUUUGUUGGCUCACAACCAUCCAUGGUUCUUGA
MetGluLeuCysTrpLeuThrThrIleHisGlySerSTOP
Peptide B (underlined)
AUGGUUCUUGAagaagcuuggagagaaaggggugugagaggagagggugcucacuccucacacucccucacuuaa
MetValLeuGluGluAlaTrpArgGluArgGlyValArgGlyGluGlyAlaHisSerSerHisSerLeuThrSTOP
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*Answer 4.31
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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.
HO
HO
Tris
..
NH2
OH
O
+
EtO
pH 8
O
O
OEt
HO
HO
O
N
H
OH
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OEt
O
HO
Ade
OH
7