Amino acids
• Amino Acids are the building blocks of proteins.
• All amino acids have the same basic structure.
• All amino acids contain an amino group, a carboxyl
group, an alpha H and a side chain designated as –R
• It is the side chain that distinguishes an amino acid
from the rest.
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• Amino acid: a compound that contains
both an amino group and a carboxyl
group
 -Amino acid has an amino group
attached to the carbon adjacent to
Amino Acids
the carboxyl group
 -carbon also bound to side chain
group, R
– R gives identity to amino acid
– Two steroisomers of amino acids are
designated L- or D-. Based on
similarity to glyceraldehyde
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AMINO ACIDS
• All organisms use the same 20
amino acids as building blocks
for the assembly of protein
molecules.
Amino Acids: Definition
• the amino group and the
carboxyl group are bonded to
the same carbon atom: the αcarbon atom
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The twenty alpha-amino acids that are encoded by the
genetic code share the generic structure…
Overall amino
acid structure

This structure is
common to all but
one of the α-amino
acids.
(Proline, a cyclic
amino acid, is the
exception.)
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IDENTIFYING THE CARBONS IN THE SIDE CHAIN
z
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Amino acid
stereochemistry
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PROPERTIES OF AMINO
ACIDS
1. Asymmetry/ chirality- 2 isomers result because of this
chiral Carbon (L amino acid and D amino acid) they are called
enantiomers.
Both have same physical properties and chemical properties
Differ in direction in w/c they rotate polarized light
Only the L isomers are found in proteins
D amino acids are found in cell wall of bacteria and peptide
antibiotics
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AMINO ACID CLASSIFICATION
(AS TO STRUCTURE OF THE SIDE CHAIN)
1. Hydrophobic: Amino acids are those with side chains that do not like to reside
in an aqueous environment. Hence, these amino acids buried within the
hydrophobic core of the protein.
Aliphatic: Hydrophobic group that contains only carbon or hydrogen atoms.
Glycine – the simplest amino acid, although placed under nonpolar and
aliphatic its small H don not contribute much to hydrophobic interactions
Aromatic: A side chain is considered aromatic when it contains an aromatic
ring system.
2. Polar: Polar amino acids are those with side-chains that prefer to reside in an
aqueous environment and hence can be generally found exposed on the
surface of a protein.
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The thiol group is a
weak acid and can
H bond with O or N
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Twenty Amino acids
TYR: Amphipathic
GLY: Unclassifiable
Hydrophobic (non polar)
Aliphatic
Aromatic
(ALA, VAL, LEU, ILE,
MET, PRO)
(PHE, TRP)
Polar
Polar Neutral
Amide
-OH
(ASN, GLN)
(THR, SER)
-SH
Charged
Acidic
(CYS) (ASP, GLU)
Basic
(HIS,
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LYS,ARG)
UNCOMMON AMINO ACIDS
g-carboxyglutamic acid
Hydroxyproline and
Hydroxylysine are found
mainly in collagen and gelatin
proteins. Collagen is a fibrous
protein of connective tissues.
Is found in proteins involved
in blood clotting.
Thyroxine is iodinated
AA found only in
thyroglobulin in the
thyroid gland.
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AMINO ACID DERIVATIVES NOT FOUND IN PROTEINS
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Biologically Active Amino Acid
Derivatives
Dopamine is an important chemical
messenger involved in reward,
motivation, memory, attention and
even regulating body movements.
Thyroxine is the main hormone secreted into the bloodstream by the thyroid
gland. It is the inactive form and most of it is converted to an active form called
triiodothyronine by organs such as the liver and kidneys.
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Figure 4-15
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GABA is a neurotransmitter that blocks impulses between nerve cells
in the brain. Low levels of GABA may be linked to:
•Anxiety or mood disorders
•Epilepsy
•Chronic pain
Researchers suspect that GABA may boost mood or have a calming, relaxing
effect on the nervous system.
Why do people take GABA?
People take GABA as a supplement to try to:
•Improve mood
•Relieve anxiety
•Improve sleep
•Help with premenstrual syndrome (PMS)
•Treat attention deficit hyperactivity disorder (ADHD)
They may also take GABA to try to:
•Relieve pain or discomfort from injuries
•Increase tolerance to exercise
•Lower blood pressure
•Burn fat
•Increase the growth of lean muscle mass
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Disulfide Bond Formation
(Cystine)
Reversible formation of a disulfide bond by the oxidation of 2
cysteine to form cystine (Cys). Disulfide bonds stabilize the
structures of many proteins.
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Hydroxylation converts pro and
lys to OH-pro and OH-lys
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Desmosine is a derivative of 4 lysine residues found in the
fibrous protein elastin.(con tissue prot)
Selenocysteine – a rare amino acid derived from serine. It
is introduced during protein synthesis and not a product of
modification. It contains selenium and not sulfur.
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Not uncommon amino acids in biochemistry, but they are not encoded
within the genetic code (meaning not incorporated into proteins)…
Two basic AAs found in the Urea cycle.
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Functions of Amino Acids
1. components of proteins
2. Formation of glucose (glucogenic AA)
3. Precursors of nitrogen containing compounds like Nbases of nucleic acids (purines/ pyrimidines), heme,
chlorophyll
4. Transport and storage form of ammonia (glN)
5. Buffer – histidine is best buffer at physiologic pH
6. Some amino acids and their derivatives function as
chemical messengers/neurotransmitters
7. Detoxification reactions – Gly, cys and met are
involved in detoxification of some toxic substs.
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Functions of Amino Acids
chemical messengers/neurotransmitters
GABA – g-amino butyric acid, functions as inhibitory neurotransmitter in
brain tissue, derived from glutamate
Serotonin and melatonin are derived from tryptophan. Serotonin is a
mono amine NT found in the GIT, platelets and CNS where it regulates
mood, appetite and sleep.
Serotonin is a NT with a calming effect, low levels – depression, high
levels produce a manic state; in the stomach it regulates peristalsis.
Melatonin controls the sleep and wake cycle, taken by long distance airline
passengers to reset their biological clocks
Catecholamines are neurotransmitters derived from tyrosine. Include
dopamine, epinephrine and norepinephrine.
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Classification of Amino Acids
According to essential or non-essential
Amino Acid: Classification
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CLASSIFICATION OF AMINO ACIDS
According to glucogenic or ketogenic
XXX
Amino Acid: Classification
Lysine
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From trp
1. Serotonin
2. Melatonin
3. Niacin
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From tyr
Dopa
Dopamine
Ep/ Norep
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AA Derived Compounds of Biological
Importance
COMPOUND
Dopamine
Epinephrine
GABA
Histamine
Melanin
Melatonin
Norepinephrine
Serotonin
Thyroxine
Precursor AA
Primary Function
Tyrosine
Tyrosine
Glutamate
Histidine
Tyrosine
Tryptophan
Tyrosine
Tryptophan
tyrosine
Neurotransmitter
Hormone
Neurotransmitter
Allergic reactions
Biologic pigment
Hormone
neurotransmitter
Vasoconstrictor
hormone
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Histamine
- A potent vasodilator
-Released as part of the immune response
- Increases localized blood volume for white blood
cells
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LEVELS OF PROTEIN
STRUCTURE
Primary structure = the complete set of covalent bonds within a protein
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INSULIN
GLUCAGON
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STRUCTURE OF PROTEINS
1. Primary structure – includes a description of all covalent bonds
(peptide and disulfide bonds) linking amino acids in the
polypeptide chain.
- refers to the sequence of amino acid residues from the N –
terminal to the C- terminal.
-determines how a protein folds into a unique 3-d structure.
2.Secondary structure – refers to stable arrangements of AA
residues giving rise to recurring structural patterns.
3.Tertiary structure – describes all aspects of 3- dimensional
folding of a polypeptide
4.Quaternary structure – describes the arrangement in space of a
protein consisting of 2 or more subunits.
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THE FUNCTION OF
PROTEINS
1. Proteins with different functions have different amino
acid sequences.
2. Human genetic diseases can be traced to production of
defective proteins. Defect could be
a. single change in AA sequence – Sickle cell anemia
b. deletion of a large portion of polypeptide – Duchenne
muscular distrophy (a large deletion in the gene
encoding the protein dystrophin results to premature
termination forming a shortened protein)
3. Alteration of primary structure, may affect the function.
4. Proteins with similar functions, often have similar AA
sequences
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LEVELS OF PROTEIN STRUCTURE
1°structure: the sequence of amino acids in a
polypeptide chain, read from the N-terminal end to
the C-terminal end
• 2°structure: the ordered 3-dimensional
arrangements (conformations) in localized regions
of Protein Structure
of a polypeptide chain;Levels
refers
only to interactions
of the peptide backbone
– e. g., -helix and -pleated sheet
• 3˚ structure: 3-D arrangement of all atoms
• 4˚ structure: arrangement of monomer subunits
with respect to each other
• PROTEIN SECONDARY
STRUCTURE
-refers to spatial arrangement of amino acids that are
adjacent in a segment of a polypeptide chain
- do not consider the side chains
- refers to local folding of the polypeptide backbone into
a. alpha helix
b. beta pleated sheets
c. beta turns
d. random coil
- Polypeptide backbone refers to covalently interconnected atoms of the peptide bonds and the alpha
carbons linking the amino acid residues
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1. -helix
•
3.6 AAs per turn (5.4 A) and a creating a pitch of 0.54 nm.
•
Side chains of AA residues protrude outward from the helical
backbone.
•
The hydrogen-bonds are parallel to the helical axis.
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The polypeptide backbone is tightly wound around an imaginary
axis
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Stabilized by H-bond between NH and C=O of the peptide bonds. All
peptide bond components participate in H- bonding.
•
Destabilized by adjacent (-) or (+) charged amino acids and those
with bulky side chains
•
Destabilized also by Proline and Glycine
•
PRO is a helix breaker
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The -CO group of residue n is H-bonded to the NH group of residue (n+4).
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Left-hand versus right-hand
Right handed
alpha helix is
more stable
than the left
handed
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Presence of pro and gly offers
constraints to formation of an a –
helix.
In proline, the N atom is part of
the rigid ring and rotation about
the N – Ca bond is not possible.
Proline introduces a destabilizing
kink in an a-helix. The N of
proline can not participate in Hbonding.
Glycine is infrequently found in
an -helix bec it tends to form
coiled structures different from an
-helix.
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2. -pleated sheet /  Conformation
• Organizes polypeptides into sheets
• An extended zigzag conformation of protein backbones
• Protein backbones are arranged side-by-side through
H-bonds.
• H-bonds are perpendicular to the backbone direction.
• The side chains of adjacent AAs protrude in opposite
directions.
• The adjacent protein backbones can be either parallel
or anti-parallel. The anti-parallel is more stable because
the H- bonds are colinear unlike in parallel where they
are slanted.
•  - keratins like silk fibroin and fibroin of spider webs
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Secondary: Beta pleated sheet
• extensive hydrogen bond network with their
neighbors in which the N-H groups in the backbone
of one strand establish hydrogen bonds with the
C=O groups in the backbone of the adjacent strands
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 Sheets
• Core of many proteins is the
 sheet
• Form rigid structures with
the H-bond
• Can be of 2 types
• Anti-parallel – run in an
opposite direction of its
neighbor (A)
• Parallel – run in the same
direction with longer
looping sections between
them (B)
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3.  Turns
 turns reverses the direction of a polypeptide chain
-Connect the ends of two adjacent segments of
antiparallel - sheet.
-The structure is a 180o turn involving four amino acid
residues, where the carbonyl group of the first residue
forms an H –bond with the amino group of the fourth.
-Glycine and Proline residues often occur in -turns
-Gly bec it is small and flexible; Pro N in peptide bonds
readily assume the cis configuration
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3.  Turns
Structures of 
turns
a.Type I usually
involves proline as
the 2nd amino acid
residue
b.Type II usually
have glycine as
the 3rd residue
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TERTIARY STRUCTURE
three dimensional globular structure formed by
bending and twisting of the polypeptide chain
Formation of domain: section of protein structure
sufficient to perform a particular chemical or
physical task
linear sequence of amino acids is folded into a
compact globular structure
stabilized by multiple weak, noncovalent interactions
Highest order for monomeric protein
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TERTIARY STRUCTURE
• Interactions include:
– Hydrophobic
interactions 
hydrophobic amino
acid side chains into
Tertiary structure
the interior of the
protein shielding them
from water
– Disulfide bonds
– Hydrogen bonds
– Electrostatic
interactions between
charged amino acid
side chains
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EXAMPLES OF TERTIARY
STRUCTURES
Examples of tertiary structure
myoglobin
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4. QUATERNARY STRUCTURE
• the association of the
polypeptide chains
• each polypeptide
chain in the protein is
called a subunit
(homo or hetero)
• Example: hemoglobin
4. Quaternary Structure
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SUMMARY OF LEVELS OF
PROTEIN STRUCTURE
Summary of Levels of Organization
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Biologically Important Peptides
oInsulin – pancreatic hormone consisting of 2 polypeptide chains
oGlucagon – pancreatic hormone that opposes insulin
oGastrin – local hormone produced by the stomach, stimulates the
secretion of gastric juice
oGlutathione is a tripeptide of glutamate, cysteine and glycine, it
is found in all mammalian cells except neurons.
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