AMINO ACIDS, PEPTIDES, & PROTEINS
BIOCHEM- LECTURE
AMINO ACIDS
- α-Amino carboxylic acids
- The “building blocks” from which
proteins are made
- These 4 groups are
o Amino group
o COOH group
o Hydrogen atom
o Side chain (R)
- Note: except for GLYCINE (R = H), all
amino acids are chiral molecules.
- There are about 300 amino acids occur
in nature. Only 20 occur in proteins.
CHIRALITY
An object that cannot be superimposed on its
image.
CHIRAL MOLECULE:
- If a molecule has an atom bonded to
four different groups, it can be chiral.
ENANTIOMERS:
- A chiral molecule has left-and right-
handed isomers, called enantiomers.
AMINO ACIDS:
- The two enantiomers of each amino
acids are designated by D, L system.
- Naturally occurring amino acids
generally have the same configuration as
L-glyceraldehyde (S-configuration at the
α-carbon)
- Only the L-amino acids have been
found in proteins
D: Dextrorotation L: Levorotation
FUNCTIONS OF AMINO ACIDS
- The building blocks of protein
- Forming parts of coenzymes
- Precursor of biosynthesis of molecules
such as heme
- Serves as energy source
ACID-BASE PROPERTIES
- Since amino acids have both an acidic
functionality and a basic functionality,
we should expect the following
equilibrium:
- In fact, the equilibrium lies to the right
all amino acids are charged at any
pH.
- Such species that are overall neutral
molecules but contain charged ends
called zwitterions.
 CLASSIFICATION OF AMINO ACIDS DISULFIDE BONDS
Amino acids are classified on the basis of - SH group of two Cys in proteins can be
structure of R oxidized to form a covalent disulfide
bond.
 ALIPHATIC – hydrophobic - Disulfide bonds: play a special role in
 POLAR SIDE CHAINS – text the structure of many proteins by
classified as HO-, S-, and amide forming covalent links.
containing – hydrophilic
 ACIDIC – hydrophilic
 BASIC – hydrophilic DISULFIDE
 HETEROCYCLIC/AROMATIC – BONDS

hydrophilic or hydrophobic

ALIPHATIC SIDE CHAINS

Hydrophobic

ACIDIC
Hydrophobic
- Have carboxyl in their R-group

POLAR SIDE CHAINS

Text classifies as HO-, S-, and amide containing
-hydrophilic

BASIC
Hydrophilic
LYS, ARG, and HIS
R GROUPS POLYPEPTIDES AND PROTEINS

 Amino - In 1902, Emil Fischer proposed that

 Guanidino proteins are long chains of amino acids
 Imidazole joined by peptide bonds.
- Peptide bond: the special name given to
POSITIVELY CHARGED R GROUPS AT PH
the amide bond between the α-carboxyl
7.0
group of one amino acid and the α-
HETEROCYCLIC/AROMATIC amino group another

Hydrophilic or hydrophobic PEPTIDES

- Phe and Tyr: benzene rings  DIPEPTIDE: a molecule containing

- Tryptophan: indole ring two ammino acids joined by a peptide
bond.
 TRIPEPTIDE: a molecule containing
three amino acids joined by peptide
bonds
 POLYPEPTIDE: a macromolecule
containing many amino acids joined by
peptide bonds.
 PROTEIN – a biological
macromolecular weight 5000 g/mol or
greater, consisting of one or more
- The -OH group in Tyr is an important polypeptide chains
functional group in proteins.
(phosphorylation, hydrogen bond, etc.),
polar.
ESSENTIAL & NON-ESSENTIAL AMINO
ACIDS

- Essential amino acids (or

indispensable amino acids):
o Cannot be synthesized by the
humans, must be supplied in the
diet.
o 8:Phe, Val, Thr, Trp, Ile, Met,
Leu, Lys GLUTATHIONE (GSH)
- Semi-essential amino acids:
o 2: His and Arg - Tripeptide: glutamic acid, cysteine, and
o Required by infants and glycine.
growing children - Function: important in biological
oxidation-reduction reactions, has
reduced and oxidized form
- It’s the most important molecule you
need to stay healthy and prevent disease
 - Communication and defense (antibodies,
hormones, and neurotransmitter
receptors)

 Fireflies emit light catalyzed by

PEPTIDES luciferase
 Erythrocytes contain a large amount of
- The only other type of covalent bond hemoglobin, the oxygen-transporting
between amino acids in proteins and
proteins.
peptides is the disulfide linkage
 Rhinoceros, the protein keratin is the
between two cysteine units:
chief structural components of hair,
horn, wool, nails, and feathers.

THE CHEMICAL COMPOSITION AND

CLASSIFICATION OF PROTEINS:
COMPOSITION:
CONOTOXIN G I: - The element composition in proteins
are:
C: 75%; H: 7%; O: 23%; N: 16%; S: 0-
3%
- A peptide neurotoxin isolated from the - Protein(g)= Nitrogen in Protein (g) x
venom of the fish-hunting cone snail 6.25
Conus geographicus.
- It is a paralytic toxin that block nicotinic o This approach is based on two
cholinoreceptors. assumptions:
 Dietary carbohydrates
PROTEINS and fats do not contain
- The name of the protein derives from nitrogen;
the Greek protos, meaning “first” or  Nearly all of the
“foremost” nitrogen in the diet is
- Proteins mediate virtually every process present as amino acids
that takes place in a cell, exhibiting an in proteins
almost endless diversity of functions. CLASSIFICATION:
FUNCTIONS - Proteins can be classified as simple
- Mechanical support and cushioning proteins and conjugated proteins
(keratin, collagen, elastin) o SIMPLE PROTEINS:
- Catalysis (enzymes RNA, DNA,  Composed of only
polymerase) amino acids.
- Transport and storage (hgb, myoglobin, o CONJUGATED PROTEINS:
serum albumin)  Contain permanently
associated chemical
group (called as
 prosthetic group) in PRIMARY STRUCTURE
addition to amino acids.
The primary structure of the protein is the
AA sequence in a protein.
THE SHAPE AND SIZE OF PROTEINS: - The primary structure is usually shown
using abbreviations (three letters or one
- Proteins are described as fibrous protein
letter) for the amino acid residue, from
of globular proteins by shape. N-terminal (left) to C-terminal (right)
o FIBROUS PROTEINS mainly
as structural components in
living organisms, such as
collagen. They are less soluble
in water.
 For example: collagen,
elastin, keratins.
o GLOBULAR PROTEINS are
generally well soluble in water
and have various functions such
as enzymes catalysis SECONDARY STRUCTURE
 For example: albumins,
globulins, histones, and The “local” hydrogen-bonding scheme
so on
- Three common secondary structures
THE STRUCTURE OF PROTEINS o α-helices, β-pleated sheets,
turns, random coil
Protein structure have conventionally been
considered at four different levels. α-HELIX
 PRIMARY STRUCTURE (amino  The polypeptides backbone is tightly
acids sequence) wound around the long axis (rodlike)
 SECONDARY STRUCTURE (amino  R groups protrude outward from the
acids interactions) helical backbone.
 TERTIARY STRUCTURE (complex  3-6 amino acids per turn
folding)  Right-handed
 QUARTENARY STRUCTURE
(protein complexes)
 - Interaction between R-groups is
β-SHEET:
important
- Tertiary structure is considered to be
largely determined by the protein’s
primary structure, or the sequence of
amino acids of which it is composed.
- All intermolecular forces we have
studied are at play
- Tertiary Structure: Chemical bonds
β-TURN:
between cysteines
- (hairpin turn) is also a common
secondary structure found where a
polypeptide chain abruptly reverses its
direction
- It often connects the ends of two
adjacent segments of an antiparallel β-
pleated sheets.

Stability of the tertiary structure is

β-TURN
determined by Noncovalent
interactions & disulfide bond

QUARTENARY STRUCTURE

How protein subunits aggregate into a

RANDOM COIL: larger functional unit
- Random coil generally refers to those
undefined, irregular secondary structure
in proteins.
- Nonrepetitive, having a loop or coil
conformation

- Hemoglobin has two α and β subunits

that fit together to form a shole
hemoglobin molecule with four hemes
and their associated iron atoms to
TERTIARY STRUCTURE transport O2 and CO2.
- How the protein, with all of its regions
of secondary structure (α-helix, β-
sheets) has folded over upon itself.
 3 PROPERTIES OF PROTEIN
SOLUBILITY:
- Form colloidal solutions instead of true
solutions in water due to huge size of
protein molecules.
o Hydrophilic groups on the
surface form a hydration shell
o Hydration shell and electric
repulsion make proteins stable
in solution.
ISOELECTRIC PH (PL):
- The nature of amino acids (particularly
their ionizable groups) determines the pl
of a protein.
- At isoelectric pH, the proteins exist as
zwitterions or dipolar ions. They are
electrically neutral.
PRECIPITATION OF PROTEINS:
- Precipitation by salting out
o Salting out: adding a large
quantity of salts, such as
Ammonia sulfate, into the
protein solution will neutralize
the surface changes and destruct
the hydration shell of proteins,
causing them to precipitate.
o Diluted by water can dissolve
the precipitation. So, salting out
is a reversible process.
- Precipitation by salts of heavy metal
o Heavy metals ions like Pb2+,
Hg2+, Fe2+, Zn2+ cause
precipitation of proteins.
o This reaction is used in reverse
in cases of acute heavy metal
poisoning.
o In such a situation, a person
may have swallowed a
significant quantity of a heavy
metal salt.
- Precipitation by organic solvents
o Such as alcohol, acetone
o They dehydrate the protein
molecule by removing the water
envelope and cause
precipitation.
DENATURATION OF PROTEINS
- Denaturation is a process in which
proteins lose their three-dimensional
structure.
- Many means can cause protein to
denature
o STRONG ACID OR BASE
 Disrupt the salt bridge;
o HEAVY METAL SALTS
 Hg2+, Pb2+, Ag+;
o ORGANIC SOLVENTS
(ALCOHOL OR
CHLOROFORM)
 Disrupt H-bonds;
o HEAT
 Disrupt H-bonds and
non-polar hydrophobic
interactions;
o SOLUTES (UREA,
GUANIDINE)
- Denatured proteins can exhibit a wide
range of characteristics, from loss of
solubility to communal aggregation.
- Most biological proteins lose their
biological function when denatures
- If proteins in a living cell are denatured,
this results in disruption of cell activity
and possibly cell death
o Medical supplies and
instruments are sterilized by
heating to denature proteins in
bacteria and thus destroy the
bacteria
o A 70% alcohol solution is used
as disinfectant on the skin
REVERSIBILITY AND IRREVERSIBILITY
- In some proteins (unlike egg whites)
denaturation is reversible (the proteins
can regain their native state when the
denaturing influence is removed)
- Protein denaturation and
renaturation.
 HEMEPROTEIN
- HEMEPROTEIN: proteins that contain
heme (iron-porphyrin) as a tightly
bound.
- In myoglobin and hemoglobin, the heme
group serves to bind and deliver oxygen.

HEMOGLOBIN
- Hemoglobin is found exclusively in red
blood cells.
- Function: transport oxygen from lungs
to the capillaries of the tissues
- It is the heme group that gives blood
their distinct red color.
COLOR REACTIONS OF PROTEINS
- Sickle – cell anemia (sickle-cell
BIURET REACTION hemoglobin; HbS)

FIBROUS PROTEIN
- Proteins that tend to be insoluble and
strong and so play a structural role in
organisms for support or protection.
- Types:
(urea) (biuret) (violet colored complex)
o Collagen
- When biuret is treated with dilute copper o Keratins
sulfate in alkaline medium, a purple o Elastin
color is obtained
COLLAGEN
- Collagen is the most abundant protein
METHODS FOR THE ISOLATION AND in mammals.
PURIFICATION OF PROTEINS: o About 25% of the total protein
mass in mammals is collagen.
 Salting out o It is strong, extensible,
 Dialysis insoluble, and inert
 Ultracentrifugation o It is a major component of
 Electrophoresis tendons, the extracellular matrix
 Ion-exchange chromatography of the connective tissues (skin,
 Gel-filtration bone matrix), and the cornea of
the eye.
OXYGEN-BINDING PROTEINS KERATIN
KINDS FUNCTIONSE EXIST - The chief structural constituent of hair,
HEMOGLOBIN Carry O2 in the Erythrocytes horns, feathers, and hooves.
blood from - Keratins are rich in hydrophobic residue
lungs to the which makes the keratins insoluble in
other tissues
water.
MYOGLOBIN Store O2 Muscle
- The individual α-helices are cross linked
(cardiac &
skeletal) by interchain disulfide bonds.
- Permanent waving of hair is
biochemical engineering where
disulfide bonds between individual
chain are reduced, curled, and
reoxidized

ELASTIN
- Present in walls of large blood vessels
(such as aorta). It is very important in
lungs, elastic ligaments, skin, cartilage.

- It is elastic fiber that can be stretched to

several times as its normal length