Introduction to Bioorganic Chemistry and Chemical Biology: Chapter 4 Answers

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.




m
OCH3 OCH3




er as
-O
P -O
P
O O




co
O O
..




eH w
-O
:O -
anti syn




o.
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Answer 4.2
rs e
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ou urc
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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.
o

H B
HO .. B: H O
aC s

NH2 NH3+
vi y re


N N
- N N
HO: NH2 R O- -O :O - O
R O- NH3+
H B NH
N N N
N N N N
ed d




H B ..
R O B: H O - O .. R O- R O R O
NH2 NH2
ar stu




N N
N N ..
R O- R O-
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is




Answer 4.3
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Th




A CU U
3' C U C G G GG C
C U G U C G 5' 3' C U C G G A
G CC U G U C G 5' 5'
5' G A G C CC UG C A C A G C 3'
AG 5' GA G C C GG AG A C A G C 3' 3'
UC
sh




stem loops "kissing complex"
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, 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
3' A C GC U
C CA U G
CGG CUCC
A CG
5' G C C G A G G G
UA U G C C U A AA
G CA CGA
C G C U GA
U A
C G
A A
G U
U G
UG
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m
four types of base pairs: A•T, C•G, G•C, or T•A




er as
co
5' N N N N N N N N N N
four types of unpaired bases: A, C, G, or T




eH w
3' N N N N N N N N N
N




o.
rs e 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
ou urc
Total possibilities = 47• 44• 12
= 411• 12
o
= 50,331,648
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aC s

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Answer 4.6
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RNA RNA RNA
O
.. -
O O -
RNA O O O O O O O
-O
.. O
O H :B N N N
ed d




CH3 CH3 .. CH
3
ar stu




H B




RNA RNA
is




-
O .. O
O O
O O H
Th




N+ N
CH3 CH3
H
sh




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