Amino acids, Peptides, and

Proteins
BIOL420
ada D. Son
Outline
What are proteins?
Building blocks
Properties of Amino Acids
Uncommon Amino Acids
Reactions of Amino Acids

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 expressed.
Protein Basics
Protein Basics
Proteins are biological macromolecules made
of amino acids arranged in a linear chain and
folded into varius 3D structures.
The amino acids in a polymer chain are joined
together by the peptide bonds between
the carboxyl and amino groups of adjacent
amino acid residues
The sequence of amino acids in a protein is
defined by the sequence of a gene, which is
encoded in the genetic code

Protein Basics
Proteins are polymers of amino acids, with each
amino acid residue joined to its neighbour by a
specific type of covalent bond.

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
Chirality
A chiral molecule is a type of molecule that
lacks an internal plane of symmetry and has a
non-superimposable 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 isomers


Chirality
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 plane-polarized
light.
Determining the D/L isomeric 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
the D-form.
If counter-clockwise, it is the L-form.

The D and L
enantiomers
for the amino
acid,
Alanine.
Chirality
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 polypeptide.
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 Ca
2
as part of their biological
function.
More complex is desmosine, a derivative of four Lys residues, which
is found in the fibrous protein elastin.
www.ull.chemistry/uakron/bio
chem/04
21st amino acid
Mammalian glutathione
peroxidase enzyme contains
selenocysteine.
www.ull.chemistry/uakron/bio
chem/04
22nd amino acid
Monomethylamine
methyltransferase enzyme
of a freshwater bacteria
contains this amino acid.
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 proteins.

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 acceptor):

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 = pK
a
+ log ( [A
-
]/ [HA] )
The amino acid cysteine has an SH (sulfhydryl) group on the side chain. This -SH group of
cysteine can react under oxidizing conditions with an SH of another cysteine forming a
disulfide bond. This covalent bonding between cysteines becomes important in protein
three-dimensional structures.
Two Cysteine residues react with an oxidizing agent to form
Cystine containing a disulfide bond. A reducing agent AH2,
causes the cleavage of the disulfide bond to reverse the
reaction
Peptide Bond
Primary Structure