atp - harvard universitysites.fas.harvard.edu/~chem27/psets/2006/ps5assigned.pdf · 2006. 4. 7. ·...
TRANSCRIPT
-
ATP
M01
O-O COO
-
+NH3
OP
-O O-ADP
O-O32PO
COO-
+NH3
NR
O
NH2
H H
COO-
+NH2O HH
B
COO-
NHO H H B
H+COO-
NH
OHH+
COO-
+NH
NR
O
NH2
H HH+
+ NAD++ ADP
COO-
+NH2
M09
O
OHHO
AOPO
O-OP
O
O-OP
O
O--ON
CNH
+
O
OHHO
AOPO
O-OP
O
O-OP
O
O-OC
N
HN
H+
O
OHHO
AOPOPO
P O
O-O
OO-O
NH
O
NH
+
-
Chemistry and Chemical Biology 27 Practice Problems Solutions Page 82
M10 (a)
(b)
O Adenine
OHHO
OP
O O-
P
O O-
OP
O O-
-O
PAPSsynthase
SO42-
PAPSsynthase
SO42-
O Adenine
OHHO
OP
O
O O-
P
O O-
P
O O-
-O
inhibitor step 1inhibitor step 2
inhibitor step 1inhibitor step 2
NONE
OAdenine
OHHO
OP
O O-
OS
O O
O-
APS
OAdenine
OHHO
OP
O O-
OS
O O
O-
APS
O Adenine
OHHO
OP
OP
O
O O-O O-P
O
O O-S
O
O
O-
-O
OAdenine
OHO
OP
O O-
OS
O O
O-
O-P
O
O O-P
O
O O-
OAdenine
OHHO
OP
OP
O
O O-O O-
PO
O O-
H
H+
H+
B:
PAPS + ADP
-
M11
O
-O2C
H
FCO2-
O-OPO
O-O ADP
HB:
O-O2C
H
F
O PO32-
O
O-
O
-O2CHF
-
Nitrogen Bases
N02
N
NH
O
NH2
N
NR
NH
NH
O
NH2
N
NR
HO H
NH
NH
ON
NR
NH2O H NH
NH
ON
NR
H2OH2O
+
H+O
H+
N06
H
O
NHN
NRN
H
HN
N
NHR
O NN
O
O R
HN
N
O H
N HH
N
NR
(a) (b)
-
Chemistry and Chemical Biology 27 Practice Problems Solutions Page 88
N09 (a)
NN
NNR
NH
H
NN
H
O
O
CH3
RN
N
NNR N
N
N
O R
A T
HH
O
H
N HH
G C
(b)
NN
NNR
NH
H
NN
H
O
O
CH3
RN
N
NNR N
N
N
O R
HH
O
H
N HH
N
NO NH H
H
RN
N
CH3
O
R
OH
NN
NNR
NH
H
NN
H
O
O
CH3
R
A T
NO O
C
+
H
T
C+
T T
H3C R
A G
(c)
N
N
ON
NR
NH
H
HN
NO
N N R
NH
HH
N
N
ON
NR
NH
H
HN
NO
NNR
NH
H H
-
Chemistry and Chemical Biology 27 Practice Problems Solutions Page 90
N13 (a)
N
N
N
NR
NH
N
N
N
NR
NH O
HCl N
N
N
NR
N OH
N
N
N
NR
N
H2OOH
H2O
H
H+
B
H+
(b)
NN
N
N NRN
N
ON
NR
H
N H
H
-
Chemistry and Chemical Biology 27 Practice Problems Solutions Page 91
DNA and RNA
O01 (a)
O BO
OOPO
O18-O
H
O BO
OOPO18 O
-
O BO
OOPO18 O
-
O BO
OHO
O BO
OHO
PO-O18-O
PO-
O18 O-
B
-OH
-OH
(b) Note that the stereochemical information is lost if the reaction proceeds farther than shown since phosphorous no longer has 4 different things bonded to it:
O BO
OOP
18O O-
O02
-
O
O
O
NH
N
N
N
Me O
NH2
O
O
O
NH
N
O
NH2H2N
NMe
O
H
O
O
O
NH
N
N
N
Me O
NH2
HHOO
O
O OH
O
O
O
NH
N
N
N
Me O
NH2
H OH
O
O
O
NH
N
N
N
Me O
NH2
OH
H OH
O
O
O
NH
N
N
NH
Me O
NH2
O
H OH
HHOO
O
O
NH
N
O
OH2
at pH=10:
+
NH2
+
H2N
NMe
O
H
+
H2O
+
H2O
at pH=4:
OH OH2
-
O11
O
HO
O
O
O
Growing chain
5'
3'
5'
3'
Base
Base
Wrong Base
Wrong BasePPPO
PO
O-O
O
HO
OP
HO
O-O
O
O-
Growing chain
O-
The chain in a 3' → 5' synthesis lacks the necessary triphosphate group which is still possessed bythe chain in a 5' → 3' synthesis, so DNA synthesis cannot continue in a 3' → 5' synthesis.