Amino acids

Associate professor Ljiljana

Andrijevi
Department of Biochemistry
 Amino acids

Twenty percent of the human body is made up of

protein. Protein plays a crucial role in almost all
biological processes and amino acids are the
building blocks of it.
A large proportion of our cells, muscles and tissue
is made up of amino acids, meaning they carry
out many important bodily functions, such as
giving cells their structure. They also play a key
role in the transport and the storage of nutrients.
Amino acids have an influence on the function of
organs, glands, tendons and arteries. They are
furthermore essential for healing wounds and
repairing tissue, especially in the muscles, bones,
skin and hair as well as for the removal of all
 Amino acids are building blocks of all proteins, and are
linked in series by peptide bond (-CONH-) to form the
primary structure of a protein. Amino acids possess an
amino group, a carboxylic acid group and a varying side
chain that differs between different amino acids.

There are 20 naturally occurring amino acids, which vary

from one another with respect to their side chains. Their
melting points are extremely high (usually exceeding
200C), and at their pI, they exist as zwitterions, rather
than as unionized molecules

Amino acids respond to all typical chemical reactions

associated with compounds that contain carboxylic acid
and amino groups, usually under conditions where the
zwitter ions form is present in only small quantities. All
amino acids (except glycine) exhibit optical activity due to
the presence of an asymmetric Carbon atom. Amino
acids with an L configuration are present in all naturally
Common to all -amino acids

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

Only carbon and hydrogen in their side chains.

Generally unreactive but hydrophobic.

Determining the 3-D structure of proteins, so they tend

to cluster on the inside of the molecule.
 Nonpolar (Hydrophobic) R Groups
Glycine (Gly) Methionine (Met)

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.

Phenylalanine is Alanine with an extra benzene (sometimes

called a Phenyl) group on the end. Phenylalanine is highly
hydrophobic and is found buried within globular proteins.

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 presence of the nitrogen group makes Tryptophan a little less

hydrophobic than Phenylalanine.
Proline is unique amongst the amino acids its side chain is
bonded to the backbone nitrogen as well as to the a-carbon.

Because of this proline is technically an imino rather than an

amino acid.

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)

Threonine (Thr) Asparagine (Asn)

Glutamine (Gln)
Tyrosine (Tyr)

http://www.indstate.edu/thcme/mwking/amino-acids.ht
Tyrosine is Phenylalanine with an extra hydroxyl (-OH) group
attached.

It is polar and very weakly acidic. Tyrosine can play an

important catalytic role in the active site of some enzymes.
Reversible phosphorylation of OH group in some enzymes is
important in the regulation of metabolic pathways

Serine and Threonine play important role in enzymes which

regulate phosphorylation and energy metabolism.
Cysteine has sulfur-containing side group.The group has the
potential to be more reactive.It is not very polar.

Cysteine is most important for its ability to link to another

cysteine via the sulfur atoms to form a covalent disulfide
bridge, important in the formation and maintenance of the
tertiary (folded) structure in many proteins.

COOH - CH- CH2- HS SH- CH2- CH - COOH

NH2 NH2

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

Aspartic acid (Asp) Glutamic acid (Glu)

Two amino acids with negatively charged (i.e. acidic) side

chains - Aspartate (Aspartic acid) and Glutamate (Glutamic
acid).

These amino acids confer a negative charge on the proteins of

which they are part.
 Positively Charged R Groups

Lysine (Lys) Arginine (Arg) Histidine (His)

Lysine and Arginine both have pKs around 10.0 and are
therefore always positively charged at neutral pH.

With a pK of 6.5, Histidine can be uncharged or positively

charged depending upon its local environment.

Histidine has an important role in the catalytic mechanism of

enzymes and explains why it is often found in the active site.
 Essential Amino Acids in Humans
Ten proteinogenic amino acids are called
essentialfor humans because they cannot be
created from othercompoundsby the human body
and so must be taken in as food
Required in diet
Humans incapable of forming requisite
carbon skeleton
Arginine* Lysine
Histidine* Methionine
Isoleucine Threonine
Leucine Phenylalanine
Valine Tryptophan

* Essential in children, not in adults

 MEMORY TIP
Any Help In Learning These
Little Molecule Proves Truly
Valuable

This stands for: Arginine, Histidine,

Isoleucine, Leucine, Threonine,
Lysine, Methionine, Phenylalanine,
Tryptophan, Valine
Non-Essential Amino Acids in Humans

Not required in diet

Can be formed from a-keto acids by
transamination and subsequent reactions
Alanine Glycine
Asparagine Proline
Aspartate Serine
Glutamate Cysteine (from Met*)
Glutamine Tyrosine (from Phe*)

* Essential amino acids

Uncommon Amino Acids

Hydroxylysine and hydroxyproline, are

found in the collagen and gelatin proteins.
Thyroxin and 3,3`,5-triiodothyronine,
iodinated a.a. are found in thyroglobulin, a
protein produced by the thyroid gland.
-Carboxyglutamic acid is involved in
blood clotting.
Finally, N-methylarginine and N-
acetyllysine are found in histone proteins
associated with chromosomes.
Uncommon amino acids found
in proteins

Intermediates of
biosynthesis of arginin and
in urea cycle
The two stereoisomers of alanine

a-carbon is a chiral center

Two stereoisomers are

called enantiomers.

The solid wedge-shaped

bonds project out of the
plane of paper, the dashed
bonds behind it.

The horizontal bonds project

out of the plane of paper,
the vertical bonds behind.
Optical Properties of Amino Acids

The -carbon of a.a.

is attached to four
different chemical
groups is a chiral or
optically active carbon atom.
Glycine is the exception.
Amino acids exist in two forms, D and L, that are
mirror images of each other.
All amino acids found in proteins are of the L-
configuration.
 ACIDIC AND BASIC PROPERTIES OF
AMINO ACIDS
Amino acids in aqueous solution contain weakly acidic
-carboxyl groups and weakly basic -amino groups.

Each of the acidic and basic amino acids contains an

ionizable group in its side chain.

So, both free and some of the combined amino acids in

peptide linkages can act as buffers.

The concentration of a weak acid (HA) and its

conjugate base(A-) is described by the Henderson-
Hasselbalch equation.
Buffer
s
Henderson/Hasselbach equation and pKa
Protonated form Unprotonated form (conjugate base)
HA H++ A-

[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

Zwitterion = in German for hybrid ion

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.

Dipolar ion Izoelectric point

At the midpoint pK1=2.34

+
there is equimolar
concentration of proton
donor and proton acceptor.
Proto Proto
Fully n n
protonated donor accept
form at wery or
 27.7
Peptides
 Peptides
Peptides are compounds in which an
amide bond links the amino group of
one -amino acid and the carboxyl
group of another.
An amide bond of this type is often
referred to as a peptide bond.
 Alanine and Glycine

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

Two -amino acids are joined by a

peptide bond in alanylglycine. It is
a dipeptide.
 Alanylglycine

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

The peptide bond

is characterized by
a planar geometry.
 Higher Peptides

Peptides are classified according to

the number of amino acids linked
together.
dipeptides, tripeptides,
tetrapeptides, etc.
Leucine enkephalin is an example
of a pentapeptide.
Leucine Enkephalin

TyrGlyGlyPheLeu

YGGFL
 Oxytocin
4 5
3
IleGlnAsn C-terminus

2 Tyr
CysProLeuGlyNH2

6 7 8 9
1 Cys S S

N-terminus

Oxytocin is a cyclic nonapeptide.

Instead of having its amino acids
linked in an extended chain, two
cysteine residues are joined by an
 Oxytocin

SS bond

An SS bond between two cysteines is

often referred to as a disulfide bridge.