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Biochemical Linkages
Linkages are formed from simple reactions
between two functional groups
•
•
Nucleophilic functional groups are amine, hydroxyl, sulfhydryl and acid
oxygens
Electrophilic groups are carbonyl and phosphoryl
•
Reaction types are condensation (reverse of hydrolysis), addition
(reverse of elimination) and oxidation (reduction)
•
Biomolecules are assembled by linking the functional groups from the
molecular components or “building blocks”
LINKAGES FROM NUCLEOPHILIC ADDITION OR SUBSTITUTION
CH 2 O
R
C
R
CH 2
CH 2 S
OH
R
H
C
R
hemiacetal
CH 2
CH 2 C
R
H
CH 2 N
CH 2
CH 2
R
R
CH 2 C
H
O
CH 2 R
O
P
O
CH 2 N
CH
CH 2
R
Schiff base (aldimine)
H
O
P
O
O
R
R
P
O
O
O
phosphoanhydride
R
CH 2 C
S
CH 2 R
thioester
O
O
O
CH 2
phosphoester
amide linkage
O
R
O
ester
H
R
H
O
N
CH
thiohemiacetal
O
R
OH
OH
CH 2 C
O
O
P
O
O
acyl phosphate
H
Carbohydrate Linkages
CH 2 O
R
C
OH
CH 2 H
R
CH 2 O
R
C
R
CH 2 H
hydroxyl
R
HC
R
CH 2
aldehyde
ADDITION
H
O
CH 2 O
O
CH 2 R
acetal
hemiacetal
CH 2 OH
O
R
C
R
CH 2 H
HO
CH 2
hydroxyl
hemiacetal
CONDENSATION
R
LINKING A CARBOHYDRATE
Acid catalysis gives carbocation from hemiacetal
+
H
O CH
+
H
O H
O
H
O CH
C
+
H
O H
O
H
O CH
C
H
H
O H
O
C
H
O
H
O CH
O H
C
H
H
Hydroxyl group attacks to yield acetal linkage
H
O CH
H
O H
O
O
H
C
+
H
O H
O CH
C
H
O
H
O CH
+
H
O H
C
H
O CH
+
H
H
H
O CH
H
+
O
H
H
+
O H
O
O
H
O H
H
+
O
O H
O CH
C
H
O CH
C
H
O CH
C
H
O H
C
H
Acid catalyst regenerated, water is leaving group
H
O H
O
C
H
Nucleotide Linkages
O
O
H
O
P
O
CH 2
R
H
O
P
phosphoester
P
P
O
O
OH
O
HO
CH 2
hydroxyl
phosphate
CONDENSATION
O
phosphoanhydride
O
O
O
O
O
H
O
R
H
O
P
O
OH
O
phosphate
HO
P
O
O
phosphate
CONDENSATION
T Zamis:
LINKING A NUCLEIC ACID
O
O
P
O
O
O
O
CH 2
O
P
H
O
O
H
O
O
O
CH 2
O
P
H
O
O
O
CH 2
O
P
H
O
H
O
O
O
O
CH 2
O
H
O
H
H
Nucleophilic attack by hydroxyl, leaving group is water
O
O
P
O
O
O
O
CH 2
O
P
H
O
O
O
CH 2
O
P
H
O
O
H
H
O
O
O
O
O
CH 2
O
P
H
O
O
H
O
CH 2
O
H
O
H
Phosphoester shown in red
O
O
P
O
O
O
O
CH 2
O
P
O
O
CH 2
O
P
O
H
H
O
O
O
CH 2
O
P
O
O
H
H
O
O
O
H
H
O
O
O
H
CH 2
O
H
Protein Linkages
O
R
R
CH 2 C
N
CH 2
R
H
R
CH 2 C
H
O
H
N
H
CH 2
H
carboxylic acid
S
amine
CONDENSATION
S
CH 2
R
disulfide bond
amide linkage
O
CH 2
H
R
R
CH 2
SH
sulfhydryl
HS
CH 2
sulfhydryl
OXIDATION
R
LINKING A PROTEIN
H
H
C
R
N
H
O
C
H
O
H
O
H
C
R
N
H
C
N
H
H
O
H
O
H
C
R
C
H
O
H
O
H
C
R
N
H
C
O
H
Nucleophilic attack by amine, water is leaving group.
H
N
H
H
C
R
O
C
O
H
H
H
C
R
N
H
O
C
N
H
H
O
H
H
C
R
O
C
O
H
H
N
H
O
H
C
R
C
O
H
Amide linkages shown in blue.
N
HH
H
C
R
O
C
N
H
O H
H
H
C
R
O
C
N
H
O H
H
H
C
R
O
C
N
H
O H
H
H
C
R
O
C
OH
Lipid Linkages
O
R
CH 2 C
O
O
CH 2 R
R
R
CH 2 C
O
H
O
carboxylic acid
S
CH 2 R
thioester
ester
O
CH 2 C
HO
CH 2 R
hydroxyl
CONDENSATION
R
CH 2 C
H
O
carboxylic acid
HS
CH 2 R
sulfhydryl
CONDENSATION
LINKING A PHOSPHATIDIC ACID
O
O CH 2
C
O
H
H
O
C
O
H
O CH
H
O
H2 C O
H
P
O
O
O H
H
Form two ester linkages and one phosphoester linkage
O
C
O
O CH 2
C
O
H
O CH 2
O H
H
O H
H
O
H
C
O CH
H O
O
O
C
O
H
H2 C O P
O CH
H
O H
O
H2 C O
H
H
O
P
O
O
O H
H
The actual linking reactions in
biochemical metabolism involve
activated building blocks.
O
O CH
H
O
H
H
O
C
O
H
P
O
O
acetal phosphate
H
N
H
The activated building blocks result
from reaction coupling with ATP
hydrolysis.
C
R
O
C
O
P
O
O
acyl phosphate
O
H
O
O
O
O
P
P
P
O
C
O
O
O
O
O
CH 2
O
H
O
O
O
H
P
O
O
H
ATP hydrolysis is how a cell
releases stored energy.
H2O + ATP
Biopolymer linkages result from
reaction coupling with activated
group hydrolysis.
O
ADP + Pi
R
CH 2 C
N
CH 2
R
H
AMP + PPi
ATP
2 ADP
H2O
2Pi
O
R
CH 2 C
R
O
C
R
CH 2 H
acetal
CH 2
CH 2 R
ester
amide linkage
CH 2 O
O
O
R
H
O
P
O
CH 2
O
phosphoester
R
BUILDING BLOCK
ACTIVATED BUILDING BLOCK
O
O
H
H
O CH
O CH
H
C
O H
H
O
C
O
P
O
acetal phosphate
monosaccharide
O
O
P
O
O
O
O
O
CH 2
O
O
O
H
O
H
P
nucleotide
O
P
P
O
O
H
O
CH 2
O
H
O
O
phosphoanhydride
O
H
O
H
H
N
H
C
C
R
O
H
H
O
H
N
H
C
R
O
C
O
P
O
O
acyl phosphate
amino acid
H
O
O
C
fatty acid
O
O
P
O
O
C
O
H
LEAVING GROUPS IN ORANGE
H