Prepared by: Mohamed kasala

Senior lecturer
Ph.D. candidate, B.Sc., PGDE, M.Sc.
Unit Four
Amino Acids and Proteins
Overview
Amino acids are the building blocks that make up proteins. There are
twenty common amino acids, and they can be joined together, much like
beads on a string, to form proteins. Proteins are the “workers” in the cell.
There are thousands of proteins, because amino acids can join together in
various combinations and to almost any length. In this unit, you will
learn what the amino acids look like, and about their ionic behavior. You
will also learn about the structures and functions of proteins.
Unit Four is divided into
Amino Acids
Proteins—Primary Structure
3-D Structure of Proteins I—Secondary Structure
3-D Structure of Proteins II—Tertiary and Quaternary Structures
Objectives
After completing this unit, you should be able to
identify the twenty common amino acids.
explain how amino acids are joined to form a protein.
describe how the physicochemical properties of the amino acids
determine the three-dimensional structure of a protein.
define the terms “primary structure,” “secondary structure,” “tertiary
structure,” and “quaternary structure,” as applied to proteins.
list the diverse roles proteins play in biological systems
Introduction to Amino Acids
 Amino acids are the building blocks of proteins,
the biomolecules found in all living organisms.
 Amino acid molecules can join together to form
chains called peptides.
 As many as 300 amino acids occur in nature Of
these, only 20—known as standard amino acids are
repeatedly found in the structure of proteins,
isolated from different forms of life animal, plant
and microbial.
Definition of Amino Acids
 Amino acids are a group of organic
compounds containing two functional groups
amino and carboxyl. The amino group (—NH2)
is basic while the carboxyl group (—COOH) is
acidic in nature.
General structure of amino acids
 The general structure of amino acids includes
an amino group and a carboxyl group, both of
which are bonded to the Alpha-carbon (the one
next to the carboxyl group). The Alpha-carbon
is also bonded to a hydrogen and to the side
chain group, which is represented by the letter
R.
 The R group determines the identity of the
particular amino acid
 Amino acids all contain carbon (C), oxygen
(O), nitrogen (N), and hydrogen (H).
 amino group the —NH2 functional group
 carboxyl group the —COOH functional
group
 side chain group the portion of an amino
acid that determines its identity
Classification of amino acids
 There are different ways of classifying the
amino acids based on the structure and chemical
nature, nutritional requirement, metabolic fate etc.
A. Amino acid classification based on the
structure :
1.Amino acids with aliphatic side chains :
 This group consists of the most simple amino
acids— glycine, alanine,valine, leucine and
isoleucine.
2. Hydroxyl group containing amino acids :
 Serine, threonine and tyrosine are
hydroxyl group containing amino acids.
 Tyrosine—being aromatic in nature—is
usually considered under aromatic amino acids.
3. Sulfur containing amino acids :
 Cysteine with sulfhydryl group and
methionine with thioether group are the two
amino acids
4. Acidic amino acids and their amides :
 Aspartic acid and glutamic acids are
dicarboxylic monoamino acids while asparagine
and glutamine are their respective amide
derivatives.
5. Basic amino acids :
 The three amino acids lysine, arginine and
histidine are dibasic monocarboxylic acids. They
are highly basic in character.
6. Aromatic amino acids :
 Phenylalanine, tyrosine and tryptophan are
aromatic amino acids. Besides these,histidine may
also be considered under this category.
7. Imino acids :
 Proline containing pyrrolidine ring is a unique
amino acid. It has an imino group ( NH), instead
of an amino group ( NH2) found in other amino
acids. Therefore, proline is an Alpha-imino acid.
B. Nutritional classification of amino acids :
 The 20 amino acids are required for the synthesis
of variety proteins, besides other biological
functions.
 However, all these 20 amino acids need not be
taken in the diet.
Based on the nutritional requirements, amino
acids are grouped into two classes—essential and
nonessential.
1. Essential amino acids :
 The amino acids which cannot be synthesized by
the body and, therefore, need to be supplied
through the diet are called essential amino acids.
They are required for proper growth and
maintenance of the individual. The ten amino acids
listed below are essential for humans are
Arginine, Valine, Histidine, Isoleucine, Leucine,
Lysine, Methionine, Phenylalanine, Threonine,
Tryptophan.
 The two amino acids namely arginine and histidine can
be synthesized by adults and not by growing children,
hence these are considered as semi–essential amino acids
2. Non-essential amino acids :
 The body can synthesize about 10 amino acids
to meet the biological needs, hence they need not be
consumed in the diet.
 These are glycine, alanine, serine, cysteine,
aspartate, asparagine, glutamate, glutamine, tyrosine
and proline.
C. Classification according to polarity of side chain (R):
 Amino acids are classified into 4 groups based on their polarity.
Polarity is important for protein structure.
1.Non-polar amino acids :
 These amino acids are also referred to as hydrophobic
(water hating). They have no charge on the ‘R’ group.
 The amino acids included in this group are — alanine, leucine,
isoleucine, valine, methionine, phenylalanine,
tryptophan and proline.
2.Polar amino acids with no charge on ‘R’ group :
 These amino acids, as such, carry no charge on the ‘R’ group. They
however possess groups such as hydroxyl,sulfhydryl and amide this
group are— serine, threonine, cysteine, glutamine, asparagine .
3. Polar amino acids with positive ‘R’ group :
 The three amino acids lysine, arginine and histidine
are included in this group.
4. Polar amino acids with negative ‘R’ group :
 The dicarboxylic monoamino acids—aspartic acid
and glutamic acid are considered in this group.
Properties of amino acids
 The amino acids differ in their physico– chemical
properties which ultimately determine the
characteristics of proteins.
A. Physical properties
1. Solubility : Most of the amino acids are
usually soluble in water and insoluble in organic
solvents.
2. Melting points : Amino acids generally
melt at higher temperatures, often above 200°C.
3. Taste :
 Amino acids may be sweet (Gly, Ala, Val),
tasteless (Leu) or bitter (Arg, Ile).
 Monosodium glutamate (MSG; ajinomoto) is
used as a flavoring agent in food industry, and
Chinese foods to increase taste and flavor.
4. Optical properties :
 All the amino acids except glycine possess optical
isomers due to the presence of asymmetric carbon atom.
Some amino acids also have a second asymmetric carbon
e.g. isoleucine, threonine. The structure of L- and D-amino
acids in comparison with glyceraldehydes has been given
5. Amino acids as ampholytes :
 Amino acids contain both acidic ( COOH) and
basic ( NH2) groups.
 They can donate a proton or accept a proton,
hence amino acids are regarded as ampholytes.
Zwitterion or dipolar ion : The name zwitter
is derived from the German word which means
hybrid. Zwitter ion (or dipolar ion) is a hybrid
molecule containing positive and negative ionic
groups.
B. Chemical properties of amino acids:
1- Reactions due to COOH group:
 Salt formation with alkalis,
 Ester formation with alcohols,
2- Reactions due toNH2 group:
 The amino groups behave as bases and combine with
acids (e.g. HCl) to form salts
Determination and reaction with ninhydrin reagent.
 Ninhydrin reagent reacts with amino group of amino
acid yielding blue colored product. The intensity of blue
color indicates quantity of amino acids present.
 Synthesis of -amino acids
• A variety of methods have been developed
• Important in industry due to the commercial relevance
 bodybuilding supplements (for big musles)
 sources of vitamins not only for human also for animals
To be Continued