AMINO ACIDS AND PEPTIDES
CADRH | 2019
3.1 Amino acids are three-dimensional
 20 proteins are formed from all of
the amino acids.
 general structure: amino group, and a
carboxylic group that are bonded to
the -Carbon, that is also bonded to
a hydrogen and to the side chain
group (R).
 R group identifies the identity of a
particular amino acid.
 Stereochemistry – 3D shape of
proteins
 Chiral – mirror image. Many
biomolecules are chiral, most
common chiral center is Carbon.
 All amino acids have a Carbon
Center except for Glycine. Glycine
has 4
 Achiral – not symmetrical.
 Stereoisomers – - Carbon has four
different groups bonded to it giving
rise to non-superimposable mirror
images.
 L- and D-amino acids (2 possible
stereoisomer for another chiral
compound)
 L-amino acid – Latin word, laevus =
left
 D-amino acid – Latin word, dexter =
right
 Amino group on the left or right side
of the -Carbon determines the L- or
D- destination.
 Amino acids in proteins are all of the
L form.
 D- amino acids occur in nature, in
bacteria cell walls and antibiotics =
they are not found in proteins.
 Stereoisomer is important to its
characteristics and functions.
 Sugar molecule in D- orientation
(sweet), L-orientation (bitter).
 Drug can be helpful in one
orientation, and poisonous on
another.
3.2 Structures and properties of Amino
Acids
 R groups and amino acids are
classified into:
1. polar or nonpolar nature of the side
chain.
2. Acidic or Basic group in the side
chain.
3. Presence of functional groups other
than acidic or basic ones in the side
chains and their nature.
 Aside from glycine, all of the
sidechains of other amino acids, are
larger and more complex than the -
Carbon.
Non-polar Amino Acids
 Most AA’s from this group namely
alanine, valine, leucine, and
isoleucine have a alipathic
hydrocarbon group side chain.
 Alipathic – absence of benzene ring.
o Proline has aliphatic cyclic
structure, Nitrogen is bonded
to two carbon atoms.
o In organic chem, proline is a
secondary amine, commonly
called as an imino acid.
 Amino groups of all other common
AA are primary amines.
o Phenylalanine – hydrocarbon
is aromatic, rather than
aliphatic.
o Tyrptophan – side chain
contains an indole ring,
aromatic.
o Methionine, side chain is a
sulfur atom in addition to
aliphatic hydrocarbon
groupings.
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CADRH | 2019
Acidic Amino Acids
Polar-Neutral Amino Acids
 Polar side chains that are electrically
neutral at neutral pH.
 Glycine is included for convenience
as it lacks a nonpolar side chain.
 Serine and Threonine, polar group is
Hydroxyl (OH) bonded to aromatic
hydrocarbon group that loses a
protein at higher pH.
 Cysteine, polar side contains a thiol
group (-SH) that can react to other
cysteine thiol groups to form
disulfide bridges (-S-S-) in an
oxidation reaction. Which then forms
cystine.
 Glutamine and Asparagine have
amide groups derived from
carboxylic groups in their side
chains.
o Can be considered as
derivatives of glutamic and
aspartic acid.
 Presence of carboxylate, their side
chains are Negatively charged at
neutral pH.
 Glutamic and Aspartic acid have
carboxyl groups in their side chains.
 Carboxyl group can lose a proton
forming a carboxylate anion,
glutamate and aspartate.
 AMINO ACIDS AND PEPTIDES
CADRH | 2019
Basic Amino Acids the protein thyroglobulin. Thyroxine
is then released as a hormone by
proteolysis of thyroglobulin.

3.3 Amino Acids Can act as Both Acids

and Bases
 In a free AA = carboxyl and amino
group are charged at a neutral pH.
 Carboxylate – negative; Amino –
positive.
 Zwitterion = AA without charged
groups on their side chains - no net
charge.
 Zwitterion = equal and positive
chargers; electrically neutral.

Titration of Amino Acids

 Side chains are positively charged at
neutral pH.
 Lysine – side chain amino group is
attached to an aliphatic hydrocarbon
tail.
 Arginine – side-chain basic group,
guadino group = more complex in
structure than the amino group. Also
bonded to an aliphatic hydrocarbon.
 Histidine – can be found in
protonated or unprotonated forms in
proteins.
Uncommon Amino Acids
 Derived from common amino acids,
produced by modification of the
parent amino acid is synthesized by
the organism in process called post-
translation modification.
 Hydroxyproline and Hydroxulysine
– has OH grps on their side chains
– found in a few connective tissue
proteins, such as collagen.
 Thyroxine differs from Tyrosine as it
has an extra iodine-containing
aromatic group on the side chain. It
is only produced in the thyroid gland
formed by posttranslational
modification of tyrosine residues in
 When AA is titrated – reaction of
each FG with the H ion is indicated
in the Titration Curve.
 ALANINE
o Very Low pH = alanine has a
protonated carboxyl group
and a positively charged
amino group that is also
protonated. = ALANINE
HAS A NET CHARGE OF
+1
o As base is added, carboxyl
group loses its proton and
becomes a negatively charged
carboxylate group, pH of the
solution increases. Alanine
now has no net charge. Sad.
o As the pH continues to
increase with the addition of
base, the protonated amino
group (weak acid) loses its
protein, and the alanine
molecule now has a charge of
-1.
o Titration curve of alanine is
that of a diprotic acid.
 HISTIDINE
 AMINO ACIDS AND PEPTIDES
CADRH | 2019
o Imidazole side chain =
titratable group.
o Low pH, charge +2 because
both the imidazole and amino
groups have positive charges.
o Base is added, pH increases,
carboxyl group loses a proton
to become carboxylate acid,
histidine charge +1.
o As more base is added,
charged imidazole group
loses its proton, histidine =
no net charge.
o Higher values of pH, amino
group loses its proton = same
with alanine and histidine.
o Titration curve - Triprotic
Acid
 Titratable groups of amino acids
have pKa values. In -Carboxyl
3.4 The peptide Bond
groups, pKa value is low, around 2.
 Covalent bonds – links the individual
 pKa value of amino groups are acids together
higher, from 9 to 10.5.  Bond is formed between the -
 pKa value of side chain groups Carboxyl group of one amino acid
including carboxyl and amino group, and the -amino group of the next
depend on the group’s chemical one.
nature.  Water is eliminated from the process,
 classification of amino acid as acidic linked amino acids residues remain
from the dehydration process.
or basic depends on the pKa on the  This bond is known as the Peptide
side chain. Bond.
 Peptides – compounds formed by
linking small numbers of amino
acids, from two to several dozens.
 Polypeptide Chain
- Common in proteins
- Peptide bonds linked together
 Amide = compound formed by the
reaction between an amino and
carboxylic group.
 Resonance structure – structures that
differ from one another in the
positioning of electrons.
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CADRH | 2019
3.5 Small peptides with Physiological
Activity
 Most important role = hormones,
hormonal control.
 Steroids are hormones.
 Some important peptide hormones
have cyclic structures
 Vasopressin and Oxytocin has many
common structural features.
- In each there is an -S-S- bond for
the cyclic structure.
- Difference is that: oxytocin has
an isoleucine residue at position
3, and a leucine residue at
position 8.
- Vasopressin has a phenylalanine
residue at position 3, and an
arginine residue at position 8.
o Each peptide has:
- Nine AA residues
- Each has an amide group at the
C-terminal end
- Each has a disulfide link between
cysteine residues at positions 1
and 6.
3A. Biochemical Connections
 Labor
- Oxytocin induces labor in
pregnant women, and controls
contraction of uterine muscle.
- In pregnancy, number of
receptors for oxytocin in the
uterine wall increases.
- Number of receptors for oxytocin
is great enough to cause
contraction in the presence of
small amounts of oxytocin =
contraction of the smooth muscle
of the uterus.
- Fetus = moves to the end of the
cervix of the uterus.
- Cervix stretches, sending nerve
impulses to the hypothalamus.
Once reached = positive
feedback = more release of
oxytocin by the posterior
pituitary gland.
- More oxytocin = stronger
contraction of uterus = fetus is
forced through the cervix.
 Milking
- Process of suckling send nerve
signals to the hypothalamus of
the mother’s brain.
- Oxytocin is released and carried
by the blood to the mammary
glands.
- Oxytocin = smooth muscles in
mammary glands contract, more
hormones are release = milk is
produced.
 Blood pressure | Vasopressin
- Regulates contraction of smooth
mascle
- Released by the action of the
hypothalamus on the posterior
pituitary gland.
- Stimulates reabsorption of water
by kidneys = antidiuretic effect.
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CADRH | 2019
- More water is remained = BP  Monogamous
increases. characteristics:
 Neuropeptides (any of a group of Paternal care,
compounds which act as Selective mate-
neurotransmitters and are short-chain preference, Mate
polypeptides). guarding.
- Affect behavior, esp. social o NASAL INHALATION
interaction of mammals, FOR HUMANS:
including humans.  Increase in trust
- Neuropeptides such as Oxytocin o In males (OXYTOCIN):
and Vasopressin affect  Trust and
personality, trust, altruism, social altruistic behavior.
bonding, and ability to recognize  Made choices that
and understand facial expression benefited others.
and feelings of others.  Forgiving.
o IN FEMALES: o ASDs, Autism spectrum
 Oxytocin – female disorder
social and sexual  Nasal inhalation
behavior: Intercourse, of oxytocin –
maternal attachment, improvement in
pair bonding. social cognition,
o IN MALES: empathy, and
 Vasopressin – reciprocity.
erection, ejaculation, o
aggression,
territoriality, and pair
bonding.
Both peptides have behavioral roles in both
genders.
o Manipulation of hormone
levels/hormone receptor
levels IN RATS:
 Infusion of oxytocin:
stimulates maternal
behavior to virgin
rats.
Only 3-5% of mammals are socially
monogamous, however if introduced to
oxytocin:
- Pair bonding, and mate
preference occurs.
o Manipulation of hormone
levels/hormone receptor
levels IN MALE PRIRIE
VOLES: