01 Amino Acids

Amino Acids
Outline
• Introduction
• Structure and classification of amino acids
• Chemistry of amino acids
• Essential and non-essential amino acids
• Peptides
Intro...
• Amino acids are the building blocks of protein
molecules.
• Amino acids and their derivatives participate in
cellular functions such as nerve conduction and
synthesis of purines and pyrimidines.
• The human diet must contain adequate amounts
of these amino acids to support adequate
growth.
• There are twenty (20) amino acids.
Structure of aa.
• The basic structure of the

amino acid is composed of:
– An alpha amino group
– An alpha carbonyl group
– An R-group or a side chain
• All attached to a central
alpha carbon atom
Classification of aa.
• The amino acids are
classified based on the
properties of their ‘R-
group’:
– Amino acids with non-
polar side chains –
hydrophobic amino acids
– Amino acids with polar,
charged side chains
– Amino acids with polar,
uncharged side chains
• Amino acids with Non-
polar, hydrophobic side
chains
– do not ionize
– Do not participate in
hydrogen bonding
– Cannot participate in ionic
bonding
– Involved in hydrophobic
interactions
– Aromatic amino acids
absorb UV light
• Amino acids with Polar,
uncharged side chains
– Participate in hydrogen bonding.
– Uncharged at pH 7
– May contain –OH groups which
are points of attachment for
phosphate and carbohydrates
Which polar uncharged amino

acids are most commonly
involved in enzymatic
reactions?
• Amino acids with Polar,
charged side chains
– They are divided into two sub-
classes – acidic and basic
– The acidic amino acids have –
COOH and are able to donate
protons and can acquire a
negative charge.
– The basic amino acids have
amino (NH₃⁺) groups, are able
to accept protons and can
acquire a positive charge.
• There are also other modes of classification of amino
acids i.e. by the structure of the ‘R-group’.
– Amino acids with aliphatic side chains
– Amino acids with side chains containing hydroxylic (OH)
groups
– Amino acids with sulphur atoms
– Amino acids with side chains containing acidic groups of their
amides
– Amino acids with side chains containing basic groups
– Amino acids containing aromatic rings
– Imino acid
Chemistry of the aa.
• All amino acids except glycine has a tetrahedral
alpha-carbon bonded to four different groups.
• This makes all other amino acids chiral.
• Common amino acids are all L-stereoisomers
and human proteins are only made up of
these.
• It is not known why but it is observed that:
– Repetitive substructure in proteins (helices, sheets,
turns) require the same configuration
– Humans may have evolved from these amino acids
based on initial random choice.
Chemistry of the aa.
• Amino acids may have positive, negative or zero
net charge.
• Amino acids are weak acids
• At physiological pH, the carboxyl group will be
unprotonated and the amino group will be
protonated.
• The strength of the acid is determined by its pKa
that is the pH at which equal amounts of the acid
and its conjugate base are present.
Chemistry of aa.
• Henderson-Hasselbalch equation
• pH = pK + log [A⁻]⁄[HA]
Chemistry of aa.
• The side chains with basic groups have positive
charges
• The side chains with acidic groups have negative
charges
• The net charge on an amino acid is the algebraic
sum of the positive and negative charges of the
groups present.
• The net charge of and aa. depends on the pH of
its environment.
Chemistry of aa.
• The Isoelectric point (pI)
– The pH at which the amino acid has no net charge
– Can be calculated by taking the average of the two
pKa values closest to the uncharged state of the
aa.
• An amino acid with no ionizable R-group
would be neutral at physiological pH; this is
called a zwitterion.
Peptides
• The bond between two amino
acids is called a peptide bond;
these are formed via
condensation reactions.
• The peptide bonds are
uncharged due to the net loss
of one negative and positive
charge per bond formed.
• Peptides are charged due to
their terminal carboxyl and
amino group or the acidic or
basic R-groups.
• Peptide bonds are cleaved by
hydroxylation.
Peptides
• The amino acid are linked
together by the bonds to
form a protein.
• These proteins are formed in
one direction: from the N-
terminus to the C-terminus.
• the proteins are numbered
from the N-terminus
• The residues in the polymers
are named by replacing the
–ine with a –yl.
Peptides
• Peptides are extending by addition of aa. With
the resultant name depicting the number:
– Dipeptide, tripeptide
– Oligopeptide 10 -20aa.
– Polypeptide >20aa.
– One or more polypeptide chains connected to each
other
• Residue: an amino acid or peptide unit in an
oligopeptide, polypeptide or protein.
Peptides
• Some aa. Can be modified within the protein
by:
– Phosphorylation
– Acetylation
– Hydroxylation
– Glycosylation
– methylation
Essential and nonessential amino acids
• These terms are misleading, all 20 common amino
acids are essential for health.
• However 8 must be present in the human diet these
are the nutritionally essential aa.
• The other 12 are not necessarily required o be part of
the diet and as such are nutritionally nonessential aa.
• Protein deficiency illnesses such as kwashiokor are
common in Africa; where our diets are mostly grains,
poor in typtophan and lysine.
Reading assignments
• Why is proline and imino acid?
• What are non-standard amino acids?
• The 21st amino acid selenocysteine
• Cysteine amino acids spontaneously bonds
with adjacent cysteine molecules to form
what? and why?
Thank you

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Amino Acids

• The basic structure of the

Which polar uncharged amino

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