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Amino acids, Peptides,

and Proteins
ada D. Son

What are proteins?
Building blocks
Properties of Amino
Uncommon Amino
Reactions of Amino

Protein Basics
Proteins are the most abundant biological
macromolecules, occurring in all cells and
all parts of cells.
Proteins also occur in great variety;
Proteins are the molecular instruments
through which genetic information is

Protein Basics
Proteinsare biologicalmacromolecules
made ofamino acidsarranged in a linear
chain and folded into varius 3D structures.
The amino acids in apolymerchain are
joined together by thepeptide
thecarboxylandaminogroups of adjacent
amino acidresidues
The sequence of amino acids in a protein
is defined by thesequenceof agene,
which is encoded in thegenetic code

Protein Basics
Proteins are polymers of amino acids, with
each amino acid residue joined to its
neighbour by a specific type of covalent
An amino acid is any organic molecule with
at least one carboxyl group (organic acid)
and at least one amino group (organic base).
Several hundreds of different amino acids
are known to be present in plant and animal
cells. Only those 20, are genetically coded
for incorporation into proteins.

Amino Acids

pH = 7.4

A chiral molecule is a type of molecule
that lacks an internal plane of
symmetry and has a nonsuperimposable mirror image.
The feature that is most often the cause
of chirality in molecules is the presence
of an asymmetric carbon atom
Two mirror images of a chiral molecule
are called enantiomers or optical


Chirality for Amino Acids

For all the common amino acids except glycine, the carbon is bonded to four different groups: a carboxyl
group, an amino group, an R group, and a hydrogen atom.
The -carbon atom is thus a chiral center. Because of
the tetrahedral arrangement of the bonding orbitals
around the -carbon atom, the four different groups can
occupy two unique spatial arrangements, and thus amino
acids have two possible stereoisomers.
Since they are nonsuperimposable mirror images of each
other, the two forms represent a class of stereoisomers
called enantiomers. All molecules with a chiral center
are also optically activethat is, they rotate planepolarized light.

Determining theD/Lisomeric
form of an Amino Acid
the "CORN" rule
The groups: COOH, R, NH2 and H (where
R is a variant carbon chain)are arranged
around the chiral center carbon atom.
Sighting with the hydrogen atom away
from the viewer, if these groups are
arranged clockwise around the carbon
atom, then it is theD-form.
If counter-clockwise, it is theL-form.

The D and
s for the
amino acid,

In Biological systems L-form of the amino
acids is prefered.
D-alanine and D-glutamate are first
discovered in short peptides of cell walls of
Gram-negative bacteria.
D-valine is present in peptide antibiotics:
valinomycine, actinomycin D, gramicidin A.
D-aspartate is isolated in human teeth, eye
lenses, erythrocytes and some tumors.
D-serine is isolated from mammalian brain
where it functions as neurotransmitter.

Amino Acids Can Be Classified

by R Group

Nonpolar, Aliphatic R Groups The R groups in this

class of amino acids are nonpolar and hydrophobic.
Aromatic R Groups Phenylalanine, tyrosine,
and tryptophan, with their aromatic side chains,
are relatively nonpolar (hydrophobic). All can
participate in hydrophobic interactions. The hydroxyl
group of tyrosine can form hydrogen bonds.
Polar, Uncharged R Groups The R groups of these
amino acids are more soluble in water, or more
hydrophilic, than those of the nonpolar amino acids,
because they contain functional groups that form
hydrogen bonds with water.

Amino Acids Can Be Classified

by R Group
Positively Charged (Basic) R Groups The
most hydrophilic R groups are those that are
either positively or negatively charged.
Negatively Charged (Acidic) R Groups The
two amino acids having R groups with a net
negative charge at pH 7.0 are aspartate and
glutamate, each of which has a second
carboxyl group.

Uncommon Amino Acids Also Have

Important Functions
In addition to the 20 common amino acids, proteins
may contain residues created by modification of
common residues already incorporated into a
Among these uncommon amino acids are:
6-NMethyllysine is a constituent of myosin, a
contractile protein of muscle. Another important
uncommon amino acid is -carboxyglutamate, found
in the bloodclotting protein prothrombin and in certain
other proteins that bind Ca2 as part of their biological
More complex is desmosine, a derivative of four Lys
residues, which is found in the fibrous protein elastin.

21st amino acid

peroxidase enzyme


22nd amino acid

enzyme of a
freshwater bacteria
contains this amino


Selenocysteine is a special case. This rare amino

acid residue is introduced during protein synthesis
rather than created through a postsynthetic
modification. It contains selenium rather than the
sulfur of cysteine. Actually derived from serine,
selenocysteine is a constituent of just a few known
Some 300 additional amino acids have been found in
cells. They have a variety of functions but are not
constituents of proteins.
Ornithine and citrulline deserve special note
because they are key intermediates (metabolites) in
the biosynthesis of arginine and in the urea cycle.

Amino Acids Can Act as Acids

and Bases

When an amino acid is dissolved in water, it

exists in solution as the dipolar ion, or zwitterion
(German for hybrid ion). A zwitterion can act as
either an acid (proton donor) or a base (proton
Substances having this dual nature are
amphoteric and are often called ampholytes
(from amphoteric electrolytes).
A simple monoamino monocarboxylic -amino
acid, such as alanine, is a diprotic acid when fully
protonatedit has two groups, the -COOH group
and the NH+3 group, that can yield protons.

Ionizable Groups

Titration of an amino acid

Two ionic forms of Histidine may be

present in vivo. Which one would be
predominant at a pH of 7.4?

pH = pKa + log ( [A-]/ [HA] )

Two Cysteine
residues react with an
The amino acid cysteine has an SH (sulfhydryl) group on the side chain.
This -SH group
of cysteine
react under
oxidizing conditions
with an SH a
to can
of another cysteine forming a disulfide bond. This covalent bonding
A reducing
between bond.
cysteines becomes
important in protein
the cleavage of the disulfide bond to

Peptide Bond

Primary Structure