BIOL1021: Behaviour of Biomolecules
Dr. Ramon Rios: rrt1f11@soton.ac.uk
Behaviour of Biomolecules
Lecture 6: : Carbon-Carbon bond formation in the round-
1
bottomed flask, and in nature
,Lecture 1 – Chemistry of the carboxyl group
Specific learning objectives – the mechanism of substitution (nucleophilic attack,
followed by ejection of leaving group from a tetrahedral intermediate) and
reasoning based on these principles
Logic of the reaction:
O Y O Is ‘Y’ a good enough nucleophile?
O X R Y R Is the starting material sufficiently
X R
reactive?
OR X
Y
Which is the better leaving group, X or Y?
O Y O
Is the product more or less reactive than
X R X R the starting material?
Y These reactions are reversible
ester carboxylic acid
Reasoning based on mechanism
O H2O/H or NaOH (ester hydrolysis) O
MeO R ester formation MeOH/H HO R Should be able to predict (not learn!)
Na
N Me which of the possible substitution
2 or
Me
2 NH H/
H reactions will work
NaOEt or NaOMe or /H EtO is)
EtOH/H MeOH/H ly s H2O/H
on hy dro or NaOH Should be able to draw a mechanism for
Transesterification
ati ter
fo r m
OH
(es any of the substitution reactions (including
ter Na
es
/H
or
O
chymotrypsin)
O O
H2 NaNMe 2 or Me2NH/H
EtO R Me2N R Should be able to predict the product (if
2
ester amide any) from given reagents and conditions
, General mechanism of carboxyl substitution
To understand the biological process, e.g. amide hydrolysis by serine
proteases, we must understand the underlying chemical principles
General mechanism (addition-elimination):
tetrahedral intermediates
Under basic conditions
O Y O
X = OH (carboxylic acid), OR O X R Y R
(carboxylic ester), NR2 (amide)
X R OR X
Y = OH (hydroxide), OR
(alkoxide), NR2 (amide) Y
O Y O
X R X R
Need to consider: Y
‘Y’ a good enough nucleophile?
he starting material sufficiently reactive?
ch is the better leaving group, X or Y?
product more or less reactive than the starting material?
3
ese reactions are reversible
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