M.Sc.

Computational Statistics and Data Analytics

DIGITAL ASSIGNMENT -1

CHY-1005 Allied Chemistry

Name: KISHORE.K
REG.NO: 20MIY0004
Chemistry & Functions of Amino Acids &
Proteins

AMINO ACIDS:

Amino acids are organic compounds that contain amino (–NH2)

and carboxyl (–COOH) functional groups, along with a side chain (R
group) specific to each amino acid.

The key elements of an amino acid

carbon (C), hydrogen (H), oxygen (O), and nitrogen (N), although
other elements are found in the side chains of certain amino acids.
About 500 naturally occurring amino acids are known as of
1983 (though only 20 appear in the genetic code) and can be
classified in many ways.
They can be classified according to the core structural
functional groups' locations as alpha- (α-), beta- (β-), gamma- (γ-) or
delta- (δ-) amino acids; other categories relate to polarity, pH level,
and side chain group type (aliphatic, acyclic, aromatic,
containing hydroxyl or sulfur, etc.).
 In the form of proteins, amino acid residues form the second-
largest component (water is the largest) of human muscles and
other tissues. Beyond their role as residues in proteins, amino acids
participate in a number of processes such
as neurotransmitter transport and biosynthesis.
In biochemistry, amino acids which have the amine
group attached to the (alpha-) carbon atom next to the carboxyl
group have particular importance.

They are known as 2-, alpha-, or α-amino

acids (generic formula H2NCHRCOOH in most cases, where R is
an organic substituent known as a "side chain");often the term
"amino acid" is used to refer specifically to these.
They include the 22 proteinogenic ("protein-
building") amino acids, which combine into peptide chains
("polypeptides") to form the building blocks of a vast array
of proteins. These are all L-stereoisomers ("left-handed" isomers),
although a few D-amino acids ("right-handed") occur in bacterial
envelopes, as a neuromodulator (D-serine), and in some antibiotics.

General structure
the structure shown at the top of the
page, R represents a side chain specific to each amino acid.
The carbon atom next to the carboxyl group is called the α–carbon.
Amino acids containing an amino group bonded directly to the alpha
carbon are referred to as alpha amino acids. These include amino
acids such as proline which contain secondary amines, which used to
be called "imino acids".
Here is the structure of twenty amino acids with their chemical
formula.

Essential and non-essential

Nutritionists divide amino acids into two groups -

essential amino acids (must be in the diet because cells can’t
synthesize them) and non-essential amino acids (can be made by
cells).
This classification of amino acids has little to do with
the structure of amino acids. Essential amino acids vary considerable
from one organism to another and even differ in humans, depending
on whether they are adults or children.
 Some amino acids that are normally nonessential, may
need to be obtained from the diet in certain cases. Individuals who do
not synthesize sufficient amounts of arginine, cysteine, glutamine,
proline, selenocysteine, serine, and tyrosine, due to illness, for
example, may need dietary supplements containing these amino
acids

Classification of Amino Acids

Amino Acid can be classified based on their structure and the structure
of their side chains i.e. the R chains. Now two basic subcategories are

1] Non-Polar Amino Acids

These are also known as Hydrophobic. The R group can be either of
Alkyl groups (with an alkyl chain) or Aromatic groups. The acids falling
in this group are stated below. Numbers one to seven are Alkyl and the
last two are aromatic

i. Glycine (H)
ii. Alanine (CH3)
iii. Valine ( CH (CH3)2 )
iv. Methionine ( CH2CH2SCH3 )
v. Leucine ( CH2CH(CH3)2 )
vi. Isoleucine ( -CH(CH3)CH2CH3 )
vii. Proline (special structure)
viii. Phenylalanine
ix. Tryptophan
2] Polar Amino Acids
If the side chains of amino acid contain different polar groups like
amines, alcohols or acids they are polar in nature. These are also
known as Hydrophilic Acids. These are further divided into three further
categories.

a) Acidic: If the side chain contains an extra element of carboxylic acid

component these are acid-polar amino acids. They tend to donate their
hydrogen atom. These are:

i. Aspartic Acid ( CH2COOH)

ii. Glutamic Acid ( CH2CH2COOH )
b) Basic: These have an extra nitrogen group that tend to attract a
hydrogen atom. The three basic polar amino acids are

i. Histidine
ii. Lysine ( CH2(CH2)2NH2 )
iii. Arginine
c) Neutral: These are neither acidic nor basic. They have an equal
number of amino and carboxyl groups. Also, they have at least one
hydrogen component connected to electronegative atoms. Some of
these neutral acids are

i. Serine ( CH2OH )
ii. Threonine ( CH(OH)CH3 )
iii. Asparagine ( CH2OHNH2 )
iv. Glutamine ( CH2CH2CONH2 )
v. Cysteine ( CH2SH )
 vi. Tyrosine

Non-protein functions
In humans, non-protein amino acids also have important roles
as metabolic intermediates, such as in the biosynthesis of
the neurotransmitter gamma-aminobutyric acid (GABA). Many amino
acids are used to synthesize other molecules, for example:

 Tryptophan is a precursor of the neurotransmitter serotonin.

 Tyrosine (and its precursor phenylalanine) are precursors of
the catecholamine neurotransmitters dopamine, epinephrine
and norepinephrine and various trace amines.
 Phenylalanine is a precursor of phenethylamine and tyrosine
in humans. In plants, it is a precursor of
various phenylpropanoids, which are important in plant
metabolism.
 Glycine is a precursor of porphyrins such as heme.
 Arginine is a precursor of nitric oxide.
 Ornithine and S-adenosylmethionine are precursors
of polyamines
 Aspartate, glycine, and glutamine are precursors
of nucleotides. However, not all of the functions of other
abundant nonstandard amino acids are known.
Functions of Amino Acids
 Functions of Essential Amino Acids
o Phenylalanine helps in maintaining a healthy nervous
system and in boosting memory power.
o Valine acts as an important component in promoting
muscle growth.
o Threonine helps in promoting the functions of the immune
system.
o Tryptophan is involved in the production of vitamin B3 and
serotonin hormone. This serotonin hormone plays a vital
role in maintaining our appetite, regulate sleep and
boosts our moods.
o Isoleucine plays a vital role in the formation of
haemoglobin, stimulating the pancreas to synthesize
insulin, and in transporting oxygen from the lungs to the
various parts.
o Methionine is used in the treatment of kidney stones,
maintaining healthy skin and also used in controlling
invade of pathogenic bacteria.
o Leucine is involved in promoting protein synthesis and
growth hormones.
o Lysine is necessary for promoting the formation of
antibodies, hormones, enzymes and in the development
and fixation of calcium in bones.
o Histidine is involved in many enzymatic processes and in
the synthesizing of both red blood cells (erythrocyte) and
white blood cells (leukocytes).

 Functions of Non-Essential Amino Acids

o Alanine functions by removing toxins from our body and in
the production of glucose and other amino acids.
o Cysteine acts as an antioxidant provides resistance to our
body and inhibits the growth of hair, nails, etc.
 o Glutamine promotes a healthy brain function and is
necessary for the synthesis of nucleic acids – DNA and
RNA.
o Glycine is helpful in maintaining the proper cell growth, its
function and it also plays a vital role in healing wounds. It
acts as a neurotransmitter.
o Glutamic acid acts as a neurotransmitter and is mainly
involved in the development and functioning of a human
brain.
o Arginine helps in promoting the synthesis of proteins and
hormones, detoxification in the kidneys, in healing
wounds, and in maintaining a healthy immune system.
o Tyrosine plays a vital role in the production of the thyroid
hormones -T3 and T4, in synthesizing a class of
neurotransmitters and melanin, which is natural pigments
found in our eyes, hair, and skin.
o Serine helps in promoting muscle growth and in the
synthesis of immune system proteins.
o Asparagine is mainly involved in the transportation of
nitrogen into our body cells, formations of purines and
pyrimidine for the synthesis of DNA, in the development of
the nervous system and in improving our body stamina.
o Aspartic acid plays a major role in metabolism and in
promoting the synthesis of other amino acids.
o Proline is mainly involved in the repairing of the tissues in
the formation of collagen, preventing the thickening and
hardening of the walls of the arteries (arteriosclerosis) and
in the regeneration of new skin.

Deficiency of Amino Acids

amino acids are the building blocks of proteins and
proteins plays a fundamental role in almost all life processes.
Therefore, it is necessary to include all nine essential amino acids in
our daily diet to maintain a healthy and proper function of our body.
The deficiency of amino acids may include different pathological
disorders including:

 Edema.
 Anemia.
 Insomnia.
 Diarrhea.
 Depression.
 Hypoglycemia.
 Loss of Appetite.
 Fat deposit in the liver.
 Skin and hair related problems.
 Headache, weakness, irritability, and fatigue.
Protein:
Proteins are large biomolecules and macromolecules that comprise
one or more long chains of amino acid residues. Proteins perform a
vast array of functions within organisms, including catalysing
metabolic reactions, DNA replication, responding to stimuli,
providing structure to cells and organisms, and transporting
molecules from one location to another.
Proteins differ from one another primarily in their
sequence of amino acids, which is dictated by the nucleotide
sequence of their genes, and which usually results in protein
folding into a specific 3D structure that determines its activity.A
linear chain of amino acid residues is called a polypeptide.
A protein contains at least one long polypeptide. Short
polypeptides, containing less than 20–30 residues, are rarely
considered to be proteins and are commonly called peptides, or
sometimes oligopeptides. The individual amino acid residues are
bonded together by peptide bonds and adjacent amino acid residues.

Protein Structure
Proteins are a polymeric chain of amino acid residues. The structure
of a protein is mainly composed of long chains of amino acids. The
structure and position of amino acids give particular properties to the
proteins. Amino acids are made up of an amino functional group (-
NH2) and a carboxyl group (-COOH)
 Amino acids are linked together to form
polypeptide chains. One or several of such chains fold differently to
form a protein. Amino acids are substituted methane, where the four
valencies of the α- carbon are occupied by hydrogen, amino group,
carboxyl group, and the fourth valency is fulfilled by a variable R-
group.
Depending on the R-group, there are different
types of amino acids, out of which 20 are found in a polypeptide
chain. All these properties of amino acids decide the ultimate
structure and function of proteins.
The structure of the protein is classified at 4 levels:-
  Primary – The primary structure of a protein is the linear
polypeptide chain formed by the amino acids in a particular
sequence. Changing the position of even a single amino acid will
result in a different chain and hence a different protein.
 Secondary – The secondary structure of a protein is formed by
hydrogen bonding in the polypeptide chain. These bonds cause
the chain to fold and coil in two different conformations known
as the α-helix or β-pleated sheets. The α-helix is like a single
spiral and is formed by hydrogen bonding between every fourth
amino acid. The β-pleated sheet is formed by hydrogen bonding
between two or more adjacent polypeptide chains.
 Tertiary – The tertiary structure is the final 3-dimensional shape
acquired by the polypeptide chains under the attractive and
repulsive forces of the different R-groups of each amino acid.
This is a coiled structure that is very necessary for protein
functions.
 Quaternary – This structure is exhibited only by those proteins
which have multiple polypeptide chains combined to form a
large complex. The individual chains are then called subunits.


Four major types of attractive interactions determine the shape and

stability of the tertiary structure of proteins.
(a).Ionic bonding- Ionic bonds result from electrostatic attractions
between positively and negatively charged side chains of amino
acids. For example, the mutual attraction between an aspartic
acid carboxylate ion and a lysine ammonium ion helps to maintain
a particular folded area of a protein.

(b).Hydrogen bonding-Hydrogen bonding forms between a highly

electronegative oxygen atom or a nitrogen atom and a hydrogen
atom attached to another oxygen atom or a nitrogen atom, such as
those found in polar amino acid side chains. Hydrogen bonding (as
well as ionic attractions) is extremely important in both the intra- and
intermolecular interactions of proteins
©.Disulfide linkages- Two cysteine amino acid units may be brought
close together as the protein molecule folds. Subsequent oxidation
and linkage of the sulfur atoms in the highly reactive sulfhydryl (SH)
groups leads to the formation of cystine disulfide linkages are found
in many proteins, including insulin and have a strong stabilizing effect
on the tertiary structure.

(d).Dispersion forces.- Dispersion forces arise when a normally

nonpolar atom becomes momentarily polar due to an uneven
distribution of electrons, leading to an instantaneous dipole that
induces a shift of electrons in a neighboring nonpolar atom.
Dispersion forces are weak but can be important when other types of
interactions are either missing or minimal).
This is the case with fibroin, the major protein in silk,
in which a high proportion of amino acids in the protein have
nonpolar side chains. The term hydrophobic interaction is often
misused as a synonym for dispersion forces.
Hydrophobic interactions arise because water
molecules engage in hydrogen bonding with other water molecules
(or groups in proteins capable of hydrogen bonding). Because
nonpolar groups cannot engage in hydrogen bonding, the protein
folds in such a way that these groups are buried in the interior part of
the protein structure, minimizing their contact with water.
 When a protein contains more than one polypeptide
chain, each chain is called a subunit. The arrangement of multiple
subunits represents a fourth level of structure, the quaternary
structure of a protein.

Hemoglobin, with four polypeptide chains or subunits,

is the most frequently cited example of a protein having quaternary
structure. The quaternary structure of a protein is produced and
stabilized by the same kinds of interactions that produce and
maintain the tertiary structure. A schematic representation of the
four levels of protein structure.
 The Quaternary
Structure of Hemoglobin. Hemoglobin is a protein that transports
oxygen throughout the body.

The primary structure consists of the specific amino

acid sequence. The resulting peptide chain can twist into an α-helix,
which is one type of secondary structure.

This helical segment is incorporated into the tertiary

structure of the folded polypeptide chain. The single polypeptide
chain is a subunit that constitutes the quaternary structure of a
protein, such as hemoglobin that has four polypeptide chains.

Functions of Protein
Proteins play multiple functions in the body and its structure gives it
its functionality. Some prominent functions are:-

1. Digestion – Digestion is carried out by the digestive enzymes

which are basically proteinaceous in nature.
2. Movement – Myosin is a protein found in muscles which enables
the contraction of muscles making movement possible.
3. Structure and Support – Keratin is the structural protein which
makes our hair, nails, and horns in animals.
4. Cellular communication – Cells communicate with other cells
and the external environment via receptors present on the
surface of cells. These receptors are made of proteins.
5. Act as a messenger – These proteins function as the chemical
messengers, which help in the communication between the
cells, tissues, and organs.