PROTEINS &

Amino Acids
Outline:
 Amino Acids
 Properties of Amino Acids
 Types of Amino Acids
 Protein Structure
 Protein Functions
Source of Proteins
 PROTEINS
 Proteins are polymers of amino acids

 Each amino acids in a protein contains a amino group, -NH2,

a carboxyl group, -COOH, and an R group, all the groups
bonded to the central carbon atom and arranged
tetrahedrally.
 The R group may be a hydrocarbon or they may contain
functional group.

 All amino acids present in a proteins are alpha-amino acids

in which the amino group is bonded to the carbon next to the
carboxyl group.
 Amino acids
are building
blocks of
protein

All proteins are made up

from the same set of 20
standard amino acids which
have different side-chains.
Groups of amino acids:

 Depends on the nature of their side-chain (R):

 Non-polar (hydrophobic)
 aliphatic amino acids
 aromatic amino acids
 Polar/uncharged amino acids
hydrophilic
 Polar/Electrically charged amino acids
hydrophilic
 acidic (negatively charged)
 basic (positively charged)
Groups of amino acids:
 The carbon at the centre of the amino acid
structure (apart from glycine) has four different
groups attached. In glycine, the "R" group is
another hydrogen atom.
Essential & Non-essential amino acids

 Plants and microorganisms can synthesize all of

the 20 standard amino acids.

 Mammals: cannot synthesize all amino acids;

obtain some in their diet

 Essential amino acids: those that are supplied in

the diet

 Non-essential amino acids: those that can be

synthesized by the organism
ESSENTIAL NON-ESSENTIAL

Arginine Alanine
Histidine Asparagine
Isoleucine Arpartate
Leucine Cysteine
Lysine Glutamate
Methionine Glutamine
Phenylalanine Glycine
Threonine Proline
Tryptophan Serine
Valine Tyrosine
 Acid-Base Properties of
Amino Acids
 Amino acids contain both an acidic group,
- COOH, and a basic group, -NH2.

 As a result of intermolecular acid base

reaction, a proton is transferred from the
–COOH group to the –NH2 group producing
a dipolar ion or zwitterions that has a positive
and also a negative charge and is thus
electrically neutral.
 Because of zweitterion, amino acids have
many properties that are common for salts.
 Such as:
 Amino acids crystalline
 Amino acids have high melting points
 Amino acids are water soluble.
 In acidic solutions (low pH), amino acid
zwitterion accept a proton on their basic group
to leave only the positively charged group.
 In basic solutions (high pH), amino acid
zwitterion loses a proton from their acidic
group to leave only the negatively charged
group.
 The pH at which the net positive and negative
charges are evenly balanced is the amino
acid’s isoelectric point- the overall charges is
zero.
 Stereoisomer/Optical Isomers
 Protein can exist in either the D or L
configuration (Enantiomers). Only the L
isomer is found in proteins. D-Amino
acids rarely occur in nature, but are found
in bacterial cell walls
MIRROR IMAGE OF
AMINO: These two isomers are
nonsuperimposable mirror images that can be distinguished
on the basis of their different rotation of plane-polarized

AA have
asymmetric
center or
chiral center
and has the
property of
chirality
 Peptide bond…
 The peptide bond is a covalent bond between the amino
group of one amino acid and the carboxyl group of
another
 When amino acids linked together will form a peptide
bond whereby water is released due to condensation
process and always exist in the trans configuration.
 dipeptide (2 residues);
tripeptide (3 residues);
oligopeptide (< 20 residues);
polypeptide (> 20 residues)
 amino-end & carboxyl-end

H2N-Gly-Ile-Val-Cys-........-His-Lys-
Asn-COOH
 variation in length & sequence of polypeptide’s a.a. :
determine protein’s biological structure & functions
 disulphide bond – occur between 2 cysteine residues,
through oxidation process to cystine

 e.g. of disulphide bond: insulin

 METHOD OF PROTEIN
CLASSIFICATION
 Some common methods used to group proteins are
based on:
 Level of protein structure
 Primary, secondary, tertiary & quaternary
 Shape
 Fibrous & globular protein
 Composition
 Simple & conjugate protein
 PRIMARY STRUCTURE
 Primary structure of a proteins is the linear
sequence of amino acids connected by peptide
bonds.
 Along the backbone of the proteins is a chain of
alternating peptide bonds and α-carbons and the
amino acid side chains are connected to these α-
carbons

 By convention, peptides and proteins are always

written with the amino terminal amino acid (N-
terminal) on the left and carboxyl-terminal amino
acid (C-terminal) on the right.
 Primary structure… 1
 The linear sequence of amino acids joined
together by peptide bonds is termed the
primary structure of the protein.
 Each type of protein has a unique
sequence of amino acids.

.
 linear sequence
of amino acid
residues read
from N-end to
C-end
 SECONDARY STRUCTURE
 The two most common types of secondary
structure are the α-helix and the β-pleated sheet.
 The α-helix is a cylindrical, rod-like helical
arrangement of the amino acids in the polypeptide
chain which is maintained by hydrogen bonds
parallel to the helix axis.
 In a β-pleated sheet, hydrogen bonds form
between adjacent sections of polypeptides that are
either running in the same direction (parallel β-
pleated sheet) or in the opposite direction
(antiparallel β- pleated sheet).
 SECONDARY STRUCTURE
 α-Helix:
A single protein chain
coiled in a spiral with a
righthanded (clockwise)
twist.

 β-Sheet:
The polypeptide chain
is held in place by
hydrogen bonds
between pairs of
peptide units along
neighboring backbone
segments
Secondary structure … 2°

-helix
 right-handed twist
 3.6 residues in one turn & 5.4Å pitch

β-sheet:
• side chains in opposite
direction with 2 residues
repeating in 7.0 Å length
TERTIARY STRUCTURE
 The overall three dimensional shape that
results from the folding of a protein chain.
Tertiary structure depends mainly on
attractions of amino acid side chains that are
far apart along the same backbone
(biologically active).
 Non-covalent interactions and disulfide
covalent bonds govern tertiary structure.
 A protein with the shape in which it exist
naturally in living organisms is known as a
native protein.
TERTIARY STRUCTURE
Tertiary structure … 3°
 QUATERNARY STRUCTURE

 Quaternary protein structure: The way in

which two or more polypeptide sub-units
associate to form a single three-dimensional
protein unit.
 Non-covalent forces are responsible for
quaternary structure essential to the function
of proteins.
QUATERNARY STRUCTURE
 Quatenary structure… 4°

 subunit arrangement –
monomer/chain  oligomer

 homotype – same/similar
polypeptide chains joined
together; dimer/tetramer form;
e.g.: haemoglobin, lactate
dehydrogenase

 heterotype – interactions between

different subunit’s structure &
function; e.g.: pyruvate
dehydrogenase multienzyme
complex
 Pyruvate dehydrogenase
multienzyme
(heterotetramer)

Lactate dehydrogenase
(tetramer)
 H
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Denaturation & Renaturation
Types of proteins…
 fibrous & globular proteins
 fibrous protein:
 hard, long (static) & fibrous; insoluble in
water
 e.g.: collagen, keratin, fibroin

 globular protein:
 compact, folded, soluble in water, groove
 e.g.: haemoglobin, enzyme, antibody
E.g. of fibrous (a) and globular (b), proteins
 Functions

 Biological catalysts
 Structural components
 Mechanical
 Storage & transport
 Coding for cell information
 Hormones/receptors
 Special functions – e.g. antibody