intro
O
R
C
OH
R
carboxylic acid
C
O
S
thioester
R
C
R
O
carboxylate
O
R
O
O
R
C
C
O
R
R
O
acyl phosphate
R
N
O
O
O R
C
R
amide R
ester
O
O P
O
C
Cl
acyl chloride
R
C
O
O
C
R
acid anhydride
12.1A
acetyl group
formyl group
12.1A
O
carboxylic acid
'peptide bond'
(amide)
OH
CH3
O
O
ester
CH3
H
protein
N
protein
O
CH3
acetylsalicylic acid
(aspirin)
carboxylate
O
O
stearate
12.1A
NH2
thioester
N
O
H3C
S
O
O
N
N
H
H
OH
O
O
O P
O P
O
O
O
O
HO
N
N
N
OH
acetyl-CoA
12.1A
Nucleophilic acyl substitution
R1
O
O:
O
X
R1
Nu
X
R1
Nu
+
X
:Nu
12.1B
Acyl transfer (another way of looking at the same
reaction type)
O
O
H3C
O
+ CH3OH
H3C
OCH3
+
HO
Transesterification
(Acetyl group transferred from isopentanol to methanol)
O
O
H3 C
O
+ HOH
H3C
OH
+
HO
Ester hydrolysis (acetyl group transferred to water)
12.1B
O
O
+ HOH
O2C
NH2
NH3
glutamine
O2C
OH
+
NH3
NH3
glutamate
Amide hydrolysis
(acyl group transferred from amine to water)
12.1B
12.1B
Acid derivatives are less reactive electrophiles
than ketones/aldehydes
O
O
ketones / aldehydes
R
R
R
R
O
O
O
acetic acid derivatives
R
X
R
X
R
X
lone pair on acyl X group makes
carbonyl carbon less electropositive
12.1C
O
R
O
O
O
carboxylate
least reactive
R
NR2
amide
R
O
OH
carboxylic acid
R
O
OR
ester
R
O
SR
thioester
R
O
O P OR
O
acyl phosphate
most reactive
12.1C
acyl phosphates: activated acyl groups
12.1C
12.2A
uphill reaction: won't work directly!
O
O
H3N
H 3N
X
O
NH2
CO2
CO2
glutamate
glutamine
NH3
O
R
O
O P O
O
'activated glutamate'
(fig not in text)
12.2A
O
R
O
O P
O
O
O
R
O
O P
H2N
O
H
R
O
NH2
+
O P
O
O
glutamine
O
H
N
O
H
:B
these are both downhill reactions
energy of one ATP has been ‘spent’
NH3
ATP
O
shorthand:
H3 N
O
CO2
glutamate
Pi
ADP
O
H3N
NH2
CO2
glutamine
12.2A
a slightly different example: acyl-AMP
O
Mg
H3N
O
O
O
O P
O P
O P
O
O
O
O P
CO2
O
ribose-A
O
O
ribose-A
aspartyl - AMP
+
ATP
H3N
O
O
CO2
O
O
O
O
P
O P
O
O
O
aspartate
pyrophosphate
12.2B
This time, NH3 comes directly from glutamine hydrolysis!
H
H3N
NH2
H
O
O
+
H3N
NH2
CO2
CO2
glutamine
O
O
O
H3N
A
:NH3
O
CO2
H
:B
H
glutamate
:B
(Glutamine is a carrier of NH3)
12.2B
from hydrolysis of glutamine
:NH3
O
O
H3 N
O P
CO2
O
O
H3N
ribose-A
O P O
ribose-A
O
CO2 O NH2
O
aspartyl - AMP
H3N
NH2
CO2
O
asparagine
O
+
O P O
ribose-A
O
AMP
12.2B
Condensed:
glutamine
H2O
ATP
H3N
O
CO2
O
aspartate
glutamate
PPi
AMP
H3N
NH2
CO2
O
asparagine
All this is happening in a single enzyme!
12.2B
Building purine (G/A) bases in DNA/RNA
O
+
O P O
NH3
O
ATP
O
H3N
O
ADP
O
H3N
H
O
O
PO
N
O P O
O
O
glycine
HO
O
PO
HO
NH2
OH
glycinamide ribonucleotide
OH
5-phosphoribosylamine
12.2C
NH3
H
PO
N
O
HO
OH
glycinamide ribonucleotide
many steps
NH2
N
PO
N
O
HO
OH
AMP
O
N
N
N
PO
N
O
HO
NH
N
NH2
OH
GMP
12.2C
Activated acyl groups in the lab
O
O
+
R
OH
Cl
S
O
Cl
R
O
Cl
+
O
O
R
OH
(3 equivalents)
O
R
P
Cl
R
Cl
O
+
Cl
HO
P
OH
H
(3 equivalents)
H
O
SOCl2
OH
HCl(gas)
(gas)
O
Cl
+
+
S
R
R
Cl
N
O
R
R
N
R
+ HCl
R
12.2D
Thioesters are also reactive acyl groups:
important in lipid metabolism
O
R
O
O
O
carboxylate
least reactive
R
NR2
amide
R
O
OH
carboxylic acid
R
O
OR
ester
R
O
SR
thioester
R
O
O
P
OR
O
acyl phosphate
most reactive
NH2
N
O
HS
O
N
N
H
H
OH
O
O
O P
O P
O
O
O
O
HO
N
N
N
OH
Coenzyme A
(HSCoA)
12.3A
O
H3C
O
OH
acetic acid
H3C
SCoA
acetyl-SCoA
acetic acid - important central
metabolite (in acetyl-CoA form)
O
OH
palmitate
O
SCoA
palmityl-SCoA (activated fatty acid)
12.3A
Activation of fatty acids
R
O
R
O
O
O P
O
O
palmityl-AMP
palmitate
O
R
O
P O
O
SCoA
H
:B
palmityl-SCoA
O
ri
b
o
se
-A
R
O
R
CoA S
O
O
P
O
+
O
ri
b
o
se
-A
O
SCoA
O
O P
O
AMP
O
ri
b
o
se
-A
O
PPi
ri
b
o
se
-A
ATP
12.2B
Fatty acids need to be activated in order to be transferred onto glycerol
O
O
R
OH
O
OH
OH
R
SCoA
O
O
R
glycerol
fatty acyl-SCoA
O
O
R
triacylglycerol
12.3C
First, the fatty acyl group is transferred to a cysteine group on the enzyme
(transthioesterification)
O
R1
SCoA
S
enzyme
O
H
:A
R1
S
enzyme
H
SCoA
O
A
+ HSCoA
R1
S
enzyme
covalent substrate-enzyme intermediate
12.3C
transfer to glycerol:
O
O
O
O
R1
S
enzyme
R2
+
+
OH
fatty acyl-enzyme
O
R2
OH
monoacylglycerol
OH
O
diacylglycerol
HS
enzyme
O
R1
downhill reaction!
12.3C
a transthioesterification rxn in fatty acid synthesis
12.3D
Thioester hydrolysis
HO CO2 O
HO CO2 O
O2C
SCoA
(S)-citryl-SCoA
SCoA
O2C
O H
H
:B
O
H
HO CO2 O
+ HSCoA
O2C
O
(citric acid cycle)
citrate
12.3E
Esterification
laboratory: acid-catalyzed
O
H3C
O
H2SO4
OH
+
HO
H3C
+ H2O
O
isopentyl acetate
(‘banana oil’)
12.4A
Question: is base-catalyzed esterification feasible?
12.4A
Esters often smell very good!
O
O
H3 C
H3C
O
propyl acetate
(pear)
O
O
H
benzyl acetate
(peach)
O
OH
O
ethyl butanoate
(pineapple)
O
isobutyl formate
(raspberry)
O
O
CH3
methyl salicylate
(wintergreen)
12.4B
basic ester hydrolysis
12.4B
Base-catalyzed ester hydrolysis: saponification
O
O
R
H2O
NaOH
O
O
R
O
OH
O
O
3 R
O
+
fatty acid
OH
OH
glycerol
R
triacylglycerol
soap!
O
O
a common fatty acid (stearate)
lipase enzymes catalyze the same reaction
micelle
12.4B
Enzymatic ester hydrolysis: acetylcholinesterase and sarin
acetylcholinesterase: breaks down acetylcholine in synapse
after it triggers nerve impulse
O
H3C
O
CH3
N CH3
O
CH3
acetylcholine
CH3
O
H3C
+
enzyme
covalent intermediate
HO
N CH3
CH3
choline
H2O
HO
enzyme
active site serine
O
O
H3C
acetate
12.4C
Sarin nerve gas irreversibly inactivates acetylcholinesterase
O
O P
F
H3C
sarin
B:
enz
O
H
RO
O
P
H3C
enz
F
O
O P F
RO CH3
O
enz
O
P OR
CH3
disabled acetylcholinesterase
12.4C
Resolution of enantiomers by lipase
O
O
O
O
+
SRS enantiomer
RSR enantiomer
lipase
O
OH
O
+
RSR enantiomer
(hydrolized by lipase)
SRS enantiomer
(not recognized by lipase)
12.4D
haloalkane dehalogenase
12.4D
Transesterification -the molecular action of aspirin
O
O
O
O
O
OH
CH3
+ HO
enzyme
+
H3C
O
enzyme
O
aspirin
serine on prostaglandin
H2 synthase
O
aspirin acetylates (thus inactivating) an enzyme that makes
prostaglandin, a signaling molecule that initiates
inflammation
12.4E
Nonenzymatic transesterification - biodiesel from
vegetable oil
O
O
CH3O
O
O
O
R
OH
O
R
Na
3 R
OCH3
+
OH
O
OH
glycerol
R
triacylglycerol
(eg. used french fry oil?)
biodiesel
(fatty acid methyl ester)
H3CO
O
stearic acid methyl ester
12.4E
Peptide bonds
O
H
N
Rn+1
H
O
N
N
Rn
H
O
Rn+3
N
Rn+2
H
O
O
H
N
O
H
N
N
CH3
H
O
O
O
N
H
O
HO
Ala-Phe-Ser-Asp
12.5A
Formation of a new peptide bond (on the ribosome):
essentially, amine plus carboxylate to amide plus water!
Step 1 - activating amino acid
ATP
O
H3N
O
R1
PPi
O
H3N
O
ribose-A
O P O
R1
O
activated acyl-AMP intermediate
12.5A
Step 2 - attach aa to tRNA
NH2
tRNA
N
N
O
O P
O
O
N
N
abbreviation:
O
HO
HO
O
H3 N
ribose-A
O
O
+
HO
OH
O
O P
R1
tRNA
O
H3N
O
O
R1
tRNA +
ribose-A
O P O
O
(AMP)
tRNA
12.5A
Step 3 - form new peptide bond
new peptide bond
O
O
H3N
R2
O
R1
tRNA1
+
O
H3N
O
tRNA2
H3N
R2
O
N
R1
H
tRNA2
O
+
HO
tRNA1
12.5A
Step 4 - repeat for each new aa on the growing chain
O
H3N
O
R2
O
N
R1
H
O
tRNA2
H3N
R2
R1
H
O
N
N
O
O
tRNA3
R3
+
+
O
H3 N
H
HO
O
tRNA2
tRNA3
R3
12.5A
Step 5 - hydrolize final amino acid
12.5A
Puromycin mimics tRNA-Phe, blocks active site
tRNA
N
O
N
O
O
N
N
N
N
O
O P
H3C
NH2
HO
N
O
CH3
N
N
H3 C O
O
OH
HN
O
O
NH3
tRNA - phenylalanine
OH
NH3
puromycin
ester linkage replaced by amide - less reactive
synthesis machinery in mammals is different - puromycin has
no effect
12.5A
peptide bond hydrolysis - proteases
12.5B
HIV protease hydrolizes cell-surface proteins on virus
‘aspartyl protease’
O
O
O
Asp1
O
O
O
H
H
H
O
O
O
N
H
H
O
Asp1
Asp1
O
Asp2
O
OH
+
H2N
O
H
O
H
N
H
H
O
Asp2
Asp2
O
O
12.5B
The action of penicillin - breaks peptidoglycan
cell wall of bacteria
yellow: sugar
red: peptide
blue: glycine bridges
Normal peptidoglycan synthesis forming the glycine bridge
step 1:
O
H
N
H3 C H
H CH3
O
N
H
O
O
H
N
O
enz
H3C H
cell wall polypeptide
+
+
H CH3
HO
enz
transpeptidase enzyme
O
H3 N
O
12.5C
step 2:
O
H
N
O
H3C
H
enz
H3 C H
+
H
O
H
N
H
H3N
H H
N
H
H
N
O
linked polypeptide
+
H
N
O
HO
enz
2nd polypeptide
12.5C
Penicillin acts as a target electrophile for active site
serine nucleophile
Ph
O
HN
H
S
lactam
N
O
CO2
benzyl penicillin
12.5C
Activated amides
NH3
H
N
O
O
citrulline
O
NH2
NH3
O
O
H
N
H
N
NH2
CO2
CO2
argininosuccinate
+
H2N
ATP
H2O
AMP
PPi
CO2
CO2
aspartate
12.6
NH3
H
N
O
O
citrulline
NH3
O
O
O
ribose-A
NH2
O
O
O
O P
O P
O P
O
O
O
O
ATP
O
H
N
O P O
NH2
ribose-A
+
PPi
O
'activated amide'
12.6
:B
AMP
H
R
H
N
O AMP
NH2
H
N
R
CO2
CO2
CO2
O HN
N
H
CO2
NH2
aspartate
R
H
N
O
H
N
NH2
CO2
CO2
argininosuccinate
+
O
P
O
ribose-A
O
AMP
12.6