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The structure of an alpha amino acid in its un-ionized form (1) and in ionized Each amino acid has a
form (2)
R side chains determine properties of proteins carboxyl group(-COOH), an
amino group (-NH2) and
distinctive side chain(R group)
bonded to the carbon atom
At physiologic pH ( 7.4), the
carboxyl group is dissociated,
forming the negativly charged
carboxylate ion (COO) and
the amino group is protonated
(-NH3+)
In proteins, almost all of these
carboxyl and amino groups are
combined in peptide
Classification of Amino Acids
Amino acids are generally divided into groups on the basis of
their side chains (R groups).
Amino acids are separated into:
Nonpolar
Neutral polar
Charged polar
Nonpolar amino acids
Alanine (Ala)
Phenylalanine (Phe)
Valine (Val)
Proline (Pro)
Leucine (Leu)
Tryptophan (Trp)
Isoleucine (Ile)
http://www.indstate.edu/thcme/mwking/amino-acids.h
The simplest amino acid is Glycine, which has a single
hydrogen atom as its side chain.
Alanine, Valine, Leucine and Isoleucine have saturated
hydrocarbon R groups (i.e. they only have hydrogen and carbon
linked by single covalent bonds). Leucine and Isoleucine are
isomers of each other.
Alanine Valine
Leucine Isoleucine
The side chain of Methionine includes a sulfur atom but
remains hydrophobic in nature.
Methionine Phenylalanine
Tryptophan is highly hydrophobic and tends to be found immersed
inside globular proteins.
Structurally related to Alanine, but with a two ring (bicyclic) indole group
added in place of the single aromatic ring found in Phenylalanine.
The ring is not reactive, but it does restrict the geometry of the
backbone chain in any protein where it is present.
Polar (Hydrophilic) R Groups
Serine (Ser) Cysteine
(cys)
Glutamine (Gln)
Tyrosine (Tyr)
http://www.indstate.edu/thcme/mwking/amino-acids.ht
Tyrosine is Phenylalanine with an extra hydroxyl (-OH) group
attached.
S S
Asparagine and Glutamine are the amide derivatives of
Aspartate (Aspartic acid) and Glutamate (Glutamic acid) - see
below. They cannot be ionised and are therefore uncharged.
Asparagine Glutamine
Negatively (Nonpolar) Charged R Groups
Lysine and Arginine both have pKs around 10.0 and are
therefore always positively charged at neutral pH.
Intermediates of
biosynthesis of arginin and
in urea cycle
The two stereoisomers of alanine
[H+] [A-]
Ka =
[HA]
[HA]
[H ] = Ka x
+
[A-]
[HA]
-log [H ] +
= -log Ka -log
[A-]
[A-]
pH = pKa + log
[HA]
Nonionic and zwitterion forms of amino acids
The zwitterion predominates at neutral pH
Week acid
Week base
mino acids have characteristic titration curves
Proto Proto
n n
donor accept
or
At the midpoint pK=9.60
+ there is equimolar
concentration of proton
donor and proton acceptor.
H O H O
+
+
H3N C C H3N C C
O O
CH3 H
Alanylglycine
H O H O
+
C C C C
H3N N O
CH3 H H
H O H O
+
C C C C
H3N N O
CH3 H H
N-terminus C-terminus
AlaGly
AG
Alanylglycine and glycylalanine
are constitutional isomers
H O H O
Alanylglycine
+ AlaGly
C C C C AG
H3N N O
CH3 H H
H O H O
Glycylalanine
+ GlyAla
C C C C GA
H3N N O
H H CH3
Alanylglycine
H O H O
+
C C C C
H3N N O
CH3 H H
TyrGlyGlyPheLeu
YGGFL
Oxytocin
4 5
3
IleGlnAsn C-terminus
2 Tyr
CysProLeuGlyNH2
6 7 8 9
1 Cys S S
N-terminus
SS bond