AMINO

General
Structure
α-carboxyl
group
H
α-
carbon

2
Side chain
confers the
α-amino identity of
group the amino
acid
General
Structure
General
Structure
At Neutral pH (pH = 7)
• Predominantly dipolar or
Zwitterions
General
Structure
ZWITTERIONIC FORM
• Explains the physical properties of amino
acids

 Crystalline solid
 Very high
melting point
 High solubility
in water
General
Structure
• Except for glycine, amino acids
have an asymmetric carbon

atoms bonded to the α-

 Four different groups of

carbon
 Chiral molecule
 Optically active

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General
Structure
STEREOCHEMISTRY
• Amino acids can exist as a pair of
Enantiomers

• D- and L- are absolute configurations

around the chiral carbon
General
Structure
STEREOCHEMISTR
Y
• D and L
configuration
General
Structure
STEREOCHEMISTRY
• Amino acid residues in naturally
occuring protein molecules are
exclusively L-isomers
• D-amino acids are found only in a few
peptides (eg. bacterial cell wall and some
antibiotics)
Classifying Std. Amino
Acids
Based on Nutritional Requirement
• ESSENTIAL amino acids – must be
supplied in the diet since they cannot
be synthesized by the human body
tryptophan valine threonin
e
isoleucine leucine lysine
phenylalanine methionine histidine
arginine
• NON-ESSENTIAL amino acids –
can be synthesized by the body
Classifying Std. Amino
Acids
Based on Structure (functional groups
in the side chain)
• Alkyl/Aliphatic
• Sulfur-containing
• Alcohols
• Aromatics
• Acidic
• Basic
• Amides
Alkyl/Aliphatic
• Stabilize proteins through
hydrophobic interaction

Glycin Alanin
Prolin
e e
e
(Gly, (Ala,
(Pro,
G)
• Proline A)
limits structural flexibilityP)because
of its rigid ring
Alkyl/Aliphatic
• Stabilize proteins through
hydrophobic interaction

Valin
Leucin e
Isoleuci (Val,
e ne
(Leu, V)
(Ile, I)
L)
Sulfur-Containing
• Methionine is
very
hydrophobic
• Cysteine is
Cystei responsible for
ne disulfide bridges
(Cys, in proteins
C)
Methioni
ne
(Met, M)
Alcohol
s
• Stabilize
protein and
interact with
the aqueous
environment
Threoni
through
ne
hydrogen
(Thr, T)
bonding
Serin
e
(Ser,
S)
Aromatics

Phenylalanin
e Tyrosin
(Phe, F) e Tryptoph
(Tyr, Y) an
• Stabilize protein
(Trp, W)
• through
Tyr (—OH)hydrophobic
can participate in H-
interaction
bonding
Aromatics
• Trp and Tyr account for absorbance of
light exhibited by most proteins at
280 nm.
Aromatics
• Absorbance at
280 nm is used
for
spectrophotomet
ric
determination of
protein
concentration
Acidic
• Have —COOH
side chains
which are
ionized at pH 7
Aspartic • Negatively
Acid/ charged
Aspartate Glutamic
(Asp, D) Acid/
Glutamate
(Glu, E)
Basi
c

Histidi
ne
Lysin
(His, H)
e Argini
(Lys, ne
K) 2 side chains
• Have —NH (Arg,
which are
R)
protonated at pH 7; positively charged
Amide
s
• Amide
counterparts of
acidic amino
acids
• Can stabilize
Asparagi protein by
ne Glutami hydrogen
(Asn, N) ne bonding
(Gln, Q)
You
must…
• Be familiarized with the structures of
the 20 standard amino acids
• Remember their classifications
• Memorize their names – both the three-
letter and single letter names
Some Uncommon Amino
Acids 4-
hydroxyproline
can be found
in plant cell
wall proteins

Both are
found in
collagen
Some Uncommon Amino
Acids

-found in
myosin

-found in
prothrombin (blood
clotting protein
Some Uncommon Amino
Acids

-found in
elastin
Some Uncommon Amino
Acids

-metabolites in the biosynthesis of

arginine and in the urea cycle
Paper Electrophoresis
• Can be used to separate amino acids
on the basis of net electric charge

• Spots can be visualized using

ninhydrin
PEPTIDES
Formation of a Peptide
Bond
• Peptide bonds are formed by
condensation reaction of amino acids
Some
terminologies
PEPTIDES/OLIGOPEPTIDES
• continuous chains of a few amino
acids usually not more than 50
residues
POLYPEPTIDES
• amino acid chains with MW <
10,000 Da
PROTEINS
• amino acid chains with MW ≥
10,000 Da
Peptides

Amino- or N- Carboxyl- or C-
terminal residue terminal residue
Drawing Peptides
• Serine (N-terminal residue) → glycine →
phenylalanine → alanine → leucine (C-
terminal residue)

O O O O O
H3N CH NH NH CH C NH CH C NH CH C
O
CH3
CH2
C CH
CH
CH2OH H3C
CH CH3
Naming
Peptides
• Start with the N-terminal residue
• Replace –ine of names with –yl for all
residues except that for the C-terminal
residue
• Write
O the whole nameO as one
O word O
O
H3N CH2OH CH C NH CH C
NH CH C NH CH C
NH CH C OH H3C CH3

CH2 CH3

ser glyc
CH phenylala alan leucin
2

yl yl nyl yl e CH
Sequence of Peptides
• Three-letter or single-letter designations
may be used
• Sequence: N-terminal to C-terminal
residue
O O O O
O
H3N CH2OH CH C NH CH C
NH CH C NH CH C
NH CH C OH H3C CH3

CH2 CH3
ser-gly-phe-
CH 2
ala-leu CH
SGFAL
Acid-Base Properties of
• All α-NH and α-COOH involved in
Peptides 2
peptide (amide) bond formation are
not anymore basic/acidic.
• Ionizable groups in a peptide include:
 Amino group of the N-terminal
residue
 Carboxyl group of the C-terminal
residue
 side chains of the acidic and basic
amino acids
Biological Activities of
some Peptides
• As HORMONES
(chemical
messengers of the
body)

• INSULIN –
responsible for
the absorption
of glucose from
the blood biology-
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stream
Biological Activities of
some Peptides
• As HORMONES
(chemical
messengers of the
body)

• OXYTOCIN – a
nonapeptide
that stimulates
uterine
contraction
Biological Activities of
some Peptides
• As HORMONES
(chemical
messengers of the
body)

• VASOREPRESSIN – a
nonapeptide
that prevents
urination at
night
Synthetic Peptides
• ASPARTAME – a dipeptide
aspartylphenylalanyl methyl ester used
as artificial sweetener
Referenc
es
Nelson and Cox. Lehninger’s Principles of Biochemistry, 4th
ed.