Protein-Structure and its classification

Protein
(Unit-II)
Prepared by
Dr. A. Sudha,
Assistant Professor,
Department of Biotechnology,
Dr. Umayal Ramanathan College for Women,
Karaikudi.

Contents
1.Amino acids
 Definitions
 Properties
 Classification
 Functions
2.Essential and Non-essential amino acids
3.Proteins
 Definitions
 Classification
 Properties
 Biological functions
4.Structural Organization of proteins
 Primary structure
 Secondary structure
 Tertiary structure
 Quaternary structure

• An amino acid is a carboxylic acid-containing
an aliphatic primary amino group in the α
position to the carboxyl group and with a
characteristic stereochemistry.
• Proteins are biosynthesized from 20 amino acids
in a system involving strict genetic
control. Thus, amino acids are the basic unit
of proteins.
• All proteins are polymers containing chains of
amino acids chemically bound by amide
(peptide) bonds.
• Most organisms use 20 naturally-occurring
amino acids to build proteins.
Aminoacids

• The linear sequence of the amino acids in a protein is dictated
by the sequence of the nucleotides in an organisms’ genetic
code.
• These amino acids are called alpha (α)-amino acids because
the amino group is attached to the first carbon in the chain
connected to the carboxyl carbon.
• Amino acids constitute a group of neutral products clearly
distinguished from other natural compounds.

More than 300 amino acids are found in nature but only 20
amino acids are standard and present in protein because they
are coded by genes. Other amino acids are modified amino
acids and called non-protein amino acids.
Some are residues modified after a protein has been
synthesized by posttranslational modifications; others are
amino acids present in living organisms but not as constituents
of proteins.
The amino acids are classified by the polarity of the R group
side chains, and whether they are acidic or basic: – neutral,
nonpolar – neutral, polar – basic, polar (contains an additional
amino group) – acidic, polar (contains an additional
carboxylate group)
 All of the amino acids are also known by a three letter and
one-letter abbreviations.

Protein-Structure and its classification

• Stereochemistry of the Amino Acids:
• Since the amino acids (except for glycine) contain four
different groups connected to the α-carbon, they are chiral,
and exist in two enantiomeric forms:
The amino acids in living systems exist primarily in the L form.
Zwitterions:
Because amino acids contain both an acidic and a basic
functional group, an internal acid-base reaction occurs, forming
an ion with both a positive and a negative charge called a
zwitterion:

In solution, the structure of an amino acid can change with the
pH of the solution:
Lowering the pH of the solution causes the zwitterions to pick
up a proton:

Increasing the pH of the solution causes the zwitterions to
lose a proton:
Since the pH of the solution affects the charge on the amino
acid, at some pH, the amino acid will form a zwitterion. This is
called the isoelectric point.
Each amino acid (and protein) has a characteristic isoelectric
point: those with neutral R groups are near a pH of 6, those with
basic R groups have higher values, and those with acidic R
groups have lower values.

Properties of Amino acids
Physical Properties
Amino acids are colorless, crystalline solid.
All amino acids have a high melting point greater than
200o
c.
Solubility: They are soluble in water, slightly soluble in
alcohol and dissolve with difficulty in methanol, ethanol,
and propanol. R-group of amino acids and pH of the
solvent play important role in solubility.
• Because amino acids can react with both H3O+
and OH-
,
solutions of amino acids and proteins can act as buffers. (E.g.,
blood proteins help to regulate the pH of blood.)

Chemical Properties
Zwitterionic property
• A zwitterion is a molecule with functional groups, of which at
least one has a positive and one has a negative electrical
charge.
• The net charge of the entire molecule is zero. Amino acids
are the best-known examples of zwitterions.
On heating to high temperatures, they decompose.
All amino acids (except glycine) are optically active.
Peptide bond formation: Amino acids can connect with a
peptide bond involving their amino and carboxylate groups. A
covalent bond formed between the alpha-amino group of one
amino acid and an alpha-carboxyl group of other forming -CO-
NH-linkage.

They contain an amine group (basic) and a carboxylic group
(acidic).
The -NH2 group is the stronger base, and so it picks up
H+
from the -COOH group to leave a zwitterion or
ampholytes.
The (neutral) zwitterion is the usual form amino acids exist
in solution.

Amino acids can exist as ampholytes or zwitterions in
solution, depending upon pH of the medium.
The pH at which the amino acids exist as zwitterions, with
no net charge on them is called Isoelectric pH or Isoelectric
point.
In acidic medium, the amino acids exist as cations .
In alkaline medium , they exist as anions.
Isoelectric point:

The α carbon of each amino acid is attached to four
different groups and is thus a chiral or optically active
carbon atom.
Glycine is exceptional because there are two hydrogen
substituents at the α carbon, thus it is optically inactive.
Amino acids with asymmetric centre at the α carbon can
exist in two forms, D and L forms that are mirror images of
each other and are called Enantiomers.
All amino acids found in proteins are of L-
configuration.
D- amino acids are found in some antibiotics and in
bacterial cell walls.
Optical properties of amino acids:

Amphoteric property:
Amino acids are amphoteric in nature that is they act as both acids and
base since due to the two amine and carboxylic group present.
Ninhydrin test:
When 1 ml of Ninhydrin solution is added to a 1 ml protein solution
and heated, the formation of a violet color indicates the presence of α-
amino acids.
Xanthoproteic test:
The xanthoproteic test is performed for the detection of aromatic
amino acids (tyrosine, tryptophan, and phenylalanine) in a protein
solution. The nitration of benzoid radicals present in the amino acid
chain occurs due to reaction with nitric acid, giving the solution
yellow coloration.

• Reaction with Sanger’s reagent:
Sanger’s reagent (1-fluoro-2, 4-dinitrobenzene) reacts with a
free amino group in the peptide chain in a mild alkaline
medium under cold conditions.
• Reaction with nitrous acid:
Nitrous acid reacts with the amino group to liberate nitrogen
and form the corresponding hydroxyl.

• All 20 of the common amino acids are alpha-amino acids.
They contain a carboxyl group, an amino group, and a side
chain (R group), all attached to the α-carbon.
Structure of Amino acids

Exceptions are:
Glycine, which does not have a side chain. Its α-carbon contains two
hydrogens.
Proline, in which the nitrogen is part of a ring.
Thus, each amino acid has an amine group at one end and an acid
group at the other and a distinctive side chain. The backbone is the
same for all amino acids while the side chain differs from one amino
acid to the next.
All of the 20 amino acids except glycine are of the L-configuration,
as for all but one amino acid the α-carbon is an asymmetric carbon.
Because glycine does not contain an asymmetric carbon atom, it is
not optically active and, thus, it is neither D nor L.

General Classification of Amino acids
Standard amino acids :
Amino acids join together to form short polymer chains
called peptides or longer chains called either polypeptides
or proteins.
These polymers are linear and unbranched, with each
amino acid within the chain attached to two neighboring
amino acids.
Twenty-two amino acids are naturally incorporated into
polypeptides and are called proteinogenic or natural
amino acids. Of these, 20 are encoded by the universal
genetic code.
The remaining 2 are incorporated into proteins by unique
synthetic mechanisms.

Non-standard amino acids:
Aside from the 22 standard amino acids, there are many
other amino acids that are called non-proteinogenic or non-
standard.
They are either not found in proteins (for example
carnitine, GABA), or are not produced directly.
Non-standard amino acids that are found in proteins are
formed by post-translational modification, which is
modification after translation during protein synthesis.
These modifications are often essential for the function or
regulation of a protein; for example, the carboxylation of
glutamate allows for better binding of calcium cations

Amino acids can be classified in 4 ways:
1.Based on structure
2.Based on the side chain characters
3.Based on nutritional requirements
4.Based on metabolic fate
i) Aliphatic Amino Acids: a) Mono-amino mono-carboxylic
acids:
 Simple amino acids: Glycine , Alanine
Branched chain amino acids: Valine, Leucine and
Isoleucine
-OH group-containing amino acids: Serine and Threonine
Sulfur-containing amino acids: Cysteine, Cystine(Formed
by linking of two cysteine residues) and Methionine.
 Amide group-containing amino acids: Glutamine and
Asparagine
1. Based on structure

b) Mono-amino di-carboxylic acids:
Aspartic acid and Glutamic acid
ii ) Aromatic amino acids- Phenyl alanine and tyrosine
iii) Heterocyclic Amino Acids: Tryptophan and Histidine
iv) Imino acid- Proline
v) Derived Amino Acids:
 Non-α-amino acids e.g.: β-alanine, γ-amino butyric acid
(GABA), δ-amino Levulinic acid
 Derived and Incorporated in tissue proteins: e.g.:
Hydroxy-proline, hydroxy-lysine
 Derived but not incorporated in tissue proteins: e.g.:
Ornithine, Citrulline, Homocysteine, Argino succinic acid

A) Amino acids with a non-polar side-chain: e.g.: Alanine,
Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Proline
Each of these amino acids has a side chain that does not bind

or give off protons or participates in hydrogen or ionic bonds.
Side chains of these amino acids can be thought of as “Oily”

or lipid like, a property that promotes hydrophobic interactions.
B) Amino acids with a polar but uncharged side-chain: e.g.:
Glycine, Serine, Threonine, Tyrosine, Cysteine, Asparagine and
Glutamine.
 These amino acids are uncharged at neutral pH, although the
side chains of cysteine and Tyrosine can lose a proton at an
alkaline pH.
Serine , Threonine and Tyrosine each contains a polar
hydroxyl group that can participate in hydrogen bond formation.
2. Based on the side chain characters

 Side chains of Asparagine and Glutamine contain a
carbonyl group and amide group, they can also participate in
hydrogen bond formation.
C) Amino acids with a charged side-chain:
a)Amino acids with a positively charged side chain: The
basic amino acids- Lysine, Arginine and Histidine
b)Amino acids with a negatively charged side chain: The
acidic amino acids- Glutamic acid and Aspartic acid They
are hydrophilic in nature.

Nonpolar, Aliphatic amino acids: The R groups in this class
of amino acids are nonpolar and hydrophobic. Glycine,
Alanine, Valine, leucine, Isoleucine, Methionine, Proline.
Aromatic amino acids: Phenylalanine, tyrosine, and
tryptophan, with their aromatic side chains, are relatively
nonpolar (hydrophobic). All can participate in hydrophobic
interactions.
Polar, Uncharged amino acids: The R groups of these amino
acids are more soluble in water, or more hydrophilic, than
those of the nonpolar amino acids, because they contain
functional groups that form hydrogen bonds with water. This
class of amino acids includes serine, threonine, cysteine,
asparagine, and glutamine.

• Acidic amino acids: Amino acids in which R-group is acidic
or negatively charged. Glutamic acid and Aspartic acid
• Basic amino acids: Amino acids in which R-group is basic or
positively charged. Lysine, Arginine, Histidine

 Semi-essential amino acids: These amino acids can be
synthesized in the body but the rate of synthesis is lesser than the
requirement(e.g. during growth, repair or pregnancy) Examples-
Arginine and Histidine.
Non-essential amino acids: These amino acids are synthesized
in the body, thus their absence in the diet does not adversely affect
the growth. Examples- Glycine, Alanine, and the other remaining
amino acids.
3. Based on nutritional requirements
Essential amino acids: These amino acids cannot be
synthesized in the body and have to be present essentially in the
diet. Examples-Valine, Isoleucine, Leucine, Lysine, Methionine,
Threonine, Tryptophan and Phenylalanine.

The carbon skeleton of amino acids can be used either for
glucose production or for the production of ketone bodies.
Based on that,
I. Both glucogenic and ketogenic amino acids: Isoleucine,
Tyrosine, Phenylalanine and Tryptophan
II. Purely Ketogenic amino acids: Leucine and Lysine
III. Purely Glucogenic amino acids: The remaining 14 amino
acids are glucogenic.
4. Classification of amino acids on the basis of the metabolic
fate

• Glucogenic amino acids: These amino acids serve as
precursors gluconeogenesis for glucose formation. Glycine,
alanine, serine, aspartic acid, asparagine, glutamic acid,
glutamine, proline, valine, methionine, cysteine, histidine, and
arginine.
• Ketogenic amino acids: These amino acids breakdown to
form ketone bodies. Leucine and Lysine.
• Both glucogenic and ketogenic amino acids: These amino
acids breakdown to form precursors for both ketone bodies
and glucose. Isoleucine, Phenylalanine, Tryptophan, and
tyrosine.

Classification according to functions:
Anabolic/Catabolic Responses and Tissue pH Regulation :- –
Glutamic Acid – Glutamine
The Urea Cycle and Nitrogen Management
– Arginine
– Citrulline
– Ornithine
– Aspartic Acid
– Asparagine
Essential Amino Acids for Proteins and Energy
– Isoleucine
– Leucine
– Valine
– Threonine
– Histidine
– Lysine
– Alpha-Aminoadipic Acid

Sulfur Containing Amino Acids for Methylation and
Glutathione
– Methionine
– Cystine
–Homocysteine
– Cystathionine
– Taurine
Neurotransmitters and Precursors – Phenylalanine –
Tyrosine – Tryptophan – Alpha-Amino-N-Butyric Acid –
Gamma-Aminobutyric Acid
Bone Collagen Specific Amino Acids
– Proline
– Hydroxyproline
– Hydroxylysine

Precursors to Heme, Nucleotides and Cell Membranes
– Glycine
– Serine
– Sarcosine
– Alanine
– Ethanolamine
– Phospethanolamine
– Phosphoserine

Functions of Amino acids:
In particular, 20 very important amino acids are crucial for life
as they contain peptides and proteins and are known to be the
building blocks for all living things.
The linear sequence of amino acid residues in a polypeptide
chain determines the three-dimensional configuration of a
protein, and the structure of a protein determines its function.
 Amino acids are imperative for sustaining the health of the
human body. They largely promote the:
 Production of hormones
Structure of muscles
Human nervous system’s healthy functioning
The health of vital organs
Normal cellular structure

The amino acids are used by various tissues to synthesize
proteins and to produce nitrogen-containing compounds (e.g.,
purines, heme, creatine, epinephrine), or they are oxidized to
produce energy.
The breakdown of both dietary and tissue proteins yields
nitrogen-containing substrates and carbon skeletons.
The nitrogen-containing substrates are used in the
biosynthesis of purines, pyrimidines, neurotransmitters,
hormones, porphyrins, and nonessential amino acids.
The carbon skeletons are used as a fuel source in the citric
acid cycle, used for gluconeogenesis, or used in fatty acid
synthesis.

What is a peptide?
• A peptide is a short-chain made up of amino acid which,
together with other peptides, forms a protein.
• The number of amino acids in a peptide can range from two
amino acids to fifty amino acids.
• Based on the number of amino acids present in the peptide,
peptides are of many types; peptides with ten or fewer amino
acids are termed oligopeptides, and the peptides with more
than ten amino acids are termed polypeptides.
• Polypeptides with around 100 amino acids are then
considered proteins.

Peptide bond definition
• A peptide bond is a special type of amide bond formed
between two molecules where an α-carboxyl group of one
molecule reacts with the α-amino group of another molecule
releasing a water molecule.
• The peptide bond is also referred to as the isopeptide bond
where the amide bond forms between the carboxyl group of
one amino acid and the amino group of another amino acid at
other positions than the alpha.
• The process of formation of the peptide bond is an example of
a condensation reaction resulting in dehydration (removal
of water).

Peptide bonds are covalent bonds that exist between any two
amino acids resulting in a peptide chain.
A partial double bond exists between carbon and nitrogen of
the amide bond which stabilizes the peptide bond.
The nitrogen involved in the bond donates its lone pair to the
carbonyl group resulting in a resonance effect.
Thus, the resonance structure stabilizes the bond but also
limits the rotation around the amide bond due to the partial
double bond.
Peptide bonds have a planar configuration that undergoes very
little movement around the C-N bond but the other single
bonds on either side of the C-N bond exhibit a high degree of
rotational motion.

Peptide bond formation mechanism
• The mechanism of peptide bond formation is a dehydration
synthesis process.
• During the formation of a peptide bond, the carboxyl group of
one amino acid moves towards the amino group of another
amino acid.
• Subsequently, one hydrogen and one oxygen atoms are lost
from the carboxyl group (COOH) of the first amino acid. In
contrast, one hydrogen is lost from the amino group (NH2) of
the other amino acid.
• This results in the release of a water molecule (H2O) along
with the formation of an amide bond (C-N) between the two
amino acids.

• The process of formation of a peptide bond between two
amino acids results in a dipeptide molecule.
• Thus, a peptide bond is formed when the carboxyl group of
one amino acid condenses with the amino group of another
amino acid releasing in a water molecule.
• The formation of the peptide bond is an endergonic reaction
that requires energy, which is obtained from ATP in living
beings.
• Because this reaction involves the removal of a water
molecule, it is called a dehydration synthesis reaction.

Peptide bond degradation mechanism
• The degradation of the peptide bond takes place through
hydrolysis, thus requires the presence of water
molecules.
• The degradation reaction is very slow as the amide
bond between the amino acids is stabilized by
the partial double bond.
• Because of the partial double bond between carbon and
nitrogen molecule, carbon atom generates a slight
positive charge.
• In the presence of water, the OH–
ions of water attack the
carbon atom, which results in degradation of the peptide
bond.

• The remaining hydrogen ion of the water then attacks the
nitrogen atom resulting in the amino group.
• As a result of this, the peptide molecule is cleaved into two
units; one unit with the carboxyl group and another with the
amino group.
• The degradation of the peptide is an exergonic reaction that
releases about 8-16 Kjol/mole of energy.
• Because the protein degradation reactions are very slow, they
are usually catalyzed by proteolytic enzymes like proteases
and peptidases.
• Peptide bond hydrolysis is essential in the removal of those
toxins as well.
• Peptide bond hydrolysis is also an important step in the
digestion of proteins in living beings.

• Peptide bond hydrolysis is one of the mechanisms of peptide
bond degradation where polypeptides are either cleaved into
smaller peptides, or smaller peptides are degraded into
separate amino acids.
• Examples
• The peptide bond is present in all proteins that bind the amino
acid in the chain together.
• Monopeptide: having one amino acid
Dipeptide: having two amino acids
Tripeptide: having three amino acids
Tetrapeptide: having four amino acids
Pentapeptide: having five amino acids
Hexapeptide: having six amino acids
Heptapeptide: having seven amino acids
Octapeptide: having eight amino acids

 Short chains are referred to as peptides, chains of up to about 50 amino acids are
polypeptides, and chains of more than 50 amino acids are proteins. (The terms
protein and polypeptide are often used interchangeably.)
 Amino acids in peptide chains are called amino acid residues. – The residue with a
free amino group is called the N-terminal residue, and is written on the left end of
the chain. – The residue with a free carboxylate group is called the C-terminal
residue, and is written on the right end of the chain.
 Peptides are named by starting at the N-terminal end and listing the amino acid
residues from left to right. • Large amino acid chains are unwieldy to draw in their
complete forms, so they are usually represented by their three-letter abbreviations,
separated by dashes: – Gly-Ala (Gly = N-terminal, Ala = C-terminal) – Ala-Gly
(Ala = N-terminal, Gly = C-terminal) • The tripeptide alanylglycylvaline can be
written as Ala-Gly-Val. (There are five other arrangements of these amino acids
that are possible.) • Insulin has 51 amino acids, with 1.55x1066
different possible
arrangements, but the body produces only one.

• Proteins (Greek proteios, “primary” or “of first importance”)
are biochemical molecules consisting of polypeptides joined
by peptide bonds between the amino and carboxyl groups of
amino acid residues.
• Proteins perform a number of vital functions: – Enzymes are
proteins that act as biochemical catalysts. – Many proteins
have structural or mechanical functions (e.g., actin and myosin
in muscles). – Proteins are important in cell signaling, immune
responses, cell adhesion, and the cell cycle. – Proteins are a
necessary component in animal diets.
Proteins

•Proteins are the most abundant biological macromolecules,
occurring in all cells.
•It is also the most versatile organic molecule of the living
systems and occur in great variety; thousands of different
kinds, ranging in size from relatively small peptides to large
polymers.
•Proteins are the polymers of amino acids covalently linked
by the peptide bonds.
•The building blocks of proteins are the twenty naturally
occurring amino acids.

Characteristics of Proteins/Properties of proteins
• Size of Proteins -Physical
• Proteins are very large polymers of amino acids with molecular
weights that vary from 6000 amu to several million amu.
• – Glucose (C6H12O6 ) = 180 amu
• – Hemoglobin = 65,000 amu

• Proteins are too large to pass through cell membranes, and are
contained within the cells where they were formed unless the
cell is damaged by disease or trauma.
• Persistent large amounts of protein in the urine are indicative
of damaged kidney cells.
• Heart attacks can also be confirmed by the presence of certain
proteins in the blood that are normally confined to cells in
heart tissue.

Acid-Base Properties:
• Proteins take the form of zwitterions. They have characteristic
isoelectric points, and can behave as buffers in solutions.
• The tendency for large molecules to remain in solution or form
stable colloidal dispersions depends on the repulsive forces
acting between molecules with like charges on their surfaces.
• When proteins are at a pH in which there is a net positive or
negative charge, the like charges cause the molecules to repel
one another, and they remain dispersed.
• When the pH is near the isoelectric point, the net charge on the
molecule is zero, and the repulsion between proteins is small.
This causes the protein molecules to clump and precipitate
from solution.

Solubility in Water:
• The relationship of proteins with water is complex.
• The secondary structure of proteins depends largely on the
interaction of peptide bonds with water through hydrogen bonds.
• Hydrogen bonds are also formed between protein (alpha and
beta structures) and water. The protein-rich static ball is more
soluble than the helical structures.
• At the tertiary structure, water causes the orientation of the
chains and hydrophilic radicals to the outside of the molecule,
while the hydrophobic chains and radicals tend to react with each
other within the molecule (hydrophobic effect).

Denaturation and Renaturation:
Proteins can be denatured by agents such as heat and urea
that cause unfolding of polypeptide chains without causing
hydrolysis of peptide bonds.
The denaturing agents destroy secondary and tertiary
structures, without affecting the primary structure.
If a denatured protein returns to its native state after the
denaturing agent is removed, the process is called
renaturation.
Some of the denaturing agents include:
Physical agents: Heat, radiation, pH
Chemical agents: Urea solution which forms new hydrogen
bonds in the protein, organic solvents, detergents.

Protein Hydrolysis
Amides can be hydrolyzed under acidic or basic conditions.
The peptide bonds in proteins can be broken down under
acidic or basic conditions into smaller peptides, or all the way
to amino acids, depending on the hydrolysis time,
temperature, and pH
– The digestion of proteins involves hydrolysis reactions
catalyzed by digestive enzymes.
 – Cellular proteins are constantly being broken down as the
body resynthesizes molecules and tissues that it needs.

Denaturation
• Proteins are maintained in their native state (their natural 3D
conformation) by stable secondary and tertiary structures, and
by aggregation of subunits into quaternary structures.
• Denaturation is caused when the folded native structures
break down because of extreme temps. or pH values, which
disrupt the stabilizing structures. The structure becomes
random and disorganized.

Substances That Denature Proteins

Coagulation:
When proteins are denatured by heat, they form insoluble
aggregates known as coagulum. All the proteins are not heat
coagulable, only a few like the albumins, globulins are heat
coagulable.
Isoelectric point:
The isoelectric point (pI) is the pH at which the number of
positive charges equals the number of negative charges, and
the overall charge on the amino acid is zero.
At this point, when subjected to an electric field the proteins
do not move either towards anode or cathode, hence this
property is used to isolate proteins.

Molecular Weights of Proteins:
The average molecular weight of an amino acid is
taken to be 110.
The total number of amino acids in a protein
multiplied by 110 gives the approximate molecular
weight of that protein.
Different proteins have different amino acid
composition and hence their molecular weights differ.
The molecular weights of proteins range from 5000
to 109
Daltons.

Posttranslational modifications:
• It occurs after the protein has been synthesized on the
ribosome.
• Phosphorylation, glycosylation, ADP ribosylation,
methylation, hydroxylation, and acetylation affect the
charge and the interactions between amino acid
residues, altering the three-dimensional
configuration and, thus, the function of the protein.

Chemical Properties:
1. Biuret test:
When 2 ml of test solution is added to an equal
volume of 10% NaOH and one drop of 10%
CuSO4 solution, a violet col
our formation indicates
the presence of peptide linkage.
2. Ninhydrin test:
When 1 ml of Ninhydrin solu
tion is added to 1 ml
protein solution and heated, formation of a violet
colour indicates the presence of α-amino acids.

Classification of Proteins
• Based on the chemical nature, structure, shape and solubility,
proteins are classified variously.
• Historically based on SOLUBILITY of PROTEINS... Two
classes - SIMPLE & COMPLEX
• Simple proteins: They are composed of only amino acid
residue. On hydrolysis these proteins yield only constituent
amino acids. It is further divided into:
▫ Fibrous protein: Keratin, Elastin, Collagen
▫ Globular protein: Albumin, Globulin, Glutelin, Histones
• Conjugated proteins: They are combined with non-protein
moiety. Eg. Nucleoprotein, Phosphoprotein, Lipoprotein,
Metalloprotein etc.

SIMPLE PROTEINS: on hydrolysis include only amino acids:
1. Albumins - soluble in water (distilled), globular, most enzymes
2. Globulins - soluble in dilute aqueous solutions; insoluble in pure
distilled water
3. Prolamins - insoluble in water; soluble in 50% to 90% simple
alcohols
4. Glutelins - insoluble in most solvents; soluble in dilute
acids/bases
5. Protamines - not based upon solubility; small MW proteins with
80% Arginine & no Cysteine
6. Histones - unique/structural: complexed w DNA, high # basic
aa's - 90% Arg, Lys, or His

Complex Proteins:
on hydrolysis yield amino acids + other molecules
lipoproteins - (+ lipids)
blood, membrane, & transport proteins
glycoproteins - (+ carbohydrates)
antibodies, cell surface proteins
nucleoproteins - (+ nucleic acids)
ribosomes & organelles
7. Scleroproteins - insoluble in most solvents
fibrous structure - architectural proteins
of cartilage & connective tissue.
Collagen = high Glycine, Proline, & no
Cysteine when boiled makes gelatin.
Keratins - proteins of skin & hair high basic
aa's (Arg, His, Lys)

• Derived proteins: They are derivatives or degraded products
of simple and conjugated proteins. They may be :
▫ Primary derived protein: Proteans, Metaproteins,
Coagulated proteins
▫ Secondary derived proteins: Proteosesn or albunoses,
peptones, peptides.

Classification by Structural Shape:
Proteins can be classified on the basis of their structural shapes:
• Fibrous proteins are made up of long rod-shaped or string like
molecules that can intertwine with one another and form strong
fibers. – insoluble in water – major components of connective
tissue, elastic tissue, hair, and skin – e.g., collagen, elastin, and
keratin.
• Globular proteins are more spherical in shape – dissolve in
water or form stable suspensions. – not found in structural tissue
but are transport proteins, or proteins that may be moved easily
through the body by the circularoty system – e.g., hemoglobin
and transferrin.

Classification by Composition:
Proteins can also be classified by composition:
• Simple proteins contain only amino acid residues.
• Conjugated proteins also contain other organic or inorganic
components, called prosthetic groups.
– nucleoproteins — nucleic acids (viruses).
– lipoproteins — lipids (fibrin in blood, serum lipoproteins)
– glycoproteins — carbohydrates (gamma globulin in blood,
mucin in saliva)
– phosphoproteins — phosphate groups (casein in milk)
– hemoproteins — heme (hemoglobin, myoglobin,
cytochromes)
– metalloproteins — iron (feritin, hemoglobin) or zinc (alcohol
dehydrogenase)

Functions of Proteins
Proteins are vital for the growth and repair, and their functions are
endless. They also have enormous diversity of biological function
and are the most important final products of the information
pathways.
Proteins, which are composed of amino acids, serve in many roles in
the body (e.g., as enzymes, structural components, hormones, and
antibodies).
They act as structural components such as keratin of hair and nail,
collagen of bone etc.
Proteins are the molecular instruments through which genetic
information is expressed.
They execute their activities in the trans
port of oxygen and carbon
dioxide by hemoglobin and special enzymes in the red cells.

They function in the homeostatic control of the volume of the
circulating blood and that of the interstitial fluids through the
plasma proteins.
They are involved in blood clotting through thrombin,
fibrinogen and other protein factors.
They act as the defence against infections by means of protein
antibodies.
They perform hereditary transmission by nucleoproteins of the
cell nucleus.
Ovalbumine, glutelin etc. are storage proteins.
Actin, myosin act as contractile protein important for muscle
contraction.

Proteins perform crucial roles in all biological processes-
1. Catalytic function: Nearly all reactions in living organisms
are catalyzed by proteins functioning as enzymes. Without
these catalysts, biological reactions would proceed much more
slowly.
2. Structural function: In animals structural materials other
than inorganic components of the skeleton are proteins, such
as collagen (mechanical strength of skin and bone) and keratin
(hair, skin, fingernails).
3. Storage function: Some proteins provide a way to store
small molecules or ions, e.g., ovalbumin (used by embryos
developing in bird eggs), casein (a milk protein) and gliadin
(wheat seeds), and ferritin (a liver protein which complexes
with iron ions).

4. Protective function: Antibodies are proteins that protect the
body from disease by combining with and destroying viruses,
bacteria, and other foreign substances. Another protective
function is blood clotting, carried out by thrombin and
fibrinogen.
5. Regulatory function: Body processes regulated by proteins
include growth (growth hormone) and thyroid functions
(thyrotropin).
6. Nerve impulse transmission: Some proteins act as
receptors for small molecules that transmit impulses across the
synapses that separate nerve cells (e.g., rhodopsin in vision).
7. Movement function: The proteins actin and myosin are
important in muscle activity, regulating the contraction of
muscle fibers.

8. Transport function:
Some proteins bind small molecules or ions and transport
them through the body.
Serum albumin is a blood protein that carries fatty acids
between fat (adipose) tissue and other organs.
Hemoglobin carries oxygen from the lungs to other body
tissues.
Transferrin is a carrier of iron in blood plasma.
A typical human cell contains 9000 different proteins; the
human body contains about 100,000 different proteins.

Protein structure and its function
enzyme A
B
A
Binding to A
Digestion
of A!
enzyme
Matching
the shape
to A
Hormone receptor Antibody
Example of enzyme reaction
enzyme
substrates

Biological Functions of Proteins

Proteins are very versatile and have many different functions in
the body, as listed below:
Act as catalysts
Transport other molecules
Store other molecules
Provide mechanical support
Provide immune protection
Generate movement
Transmit nerve impulses
Control cell growth and differentiation
The extent to which the structure of proteins has an impact on
their function is shown by the effect of changes in the structure
of a protein. Any change to a protein at any structural level,
including slight changes in the folding and shape of the
protein, may render it non-functional.
Biological importance of protein

Protein has a critical physiological function. Protein is
primarily used in the body to build, maintain, and repair body
tissues.
In the event that protein intake is greater than that required by
the body for this primary function, excessive protein is converted
to energy for immediate use or stored in the body as fat.
Protein energy will be used only after other energy sources
(carbohydrate and fat) are exhausted or unavailable.
Protein is vital in the maintenance of body tissue, including
development and repair.
Protein is the major source of energy.
Protein is involved in the creation of some hormones, help
control body functions that involve the interaction of several
organs and help regulate cell growth.
Protein produces enzymes that increase the rate of chemical
reactions in the body.

Proteins transport small molecules through the organism.
Hemoglobin is the protein that transports oxygen to the cells and
it is called as transport protein.
Proteins called antibodies help rid the body of foreign protein
and help prevent infections, illnesses and diseases.
Protein help store other substance in the organism. For
example, iron is stored in the liver in a complex with the
protein ferritin.
Proteins help mediate cell responses, such as the protein
rhodopsin, found in the eye and involved in the vision process.
Proteins make up a large protein of muscle fiber and help in
the movement of various parts of our bodies.
Skin and bone contain collagen, a fibrous protein.

Protein Structure:
The structure of proteins is much more complex than that of
simple organic molecules.
Many protein molecules consist of a chain of amino acids twisted
and folded into a complex three-dimensional structure
The complex 3D structures of proteins impart unique features to
proteins that allow them to function in diverse ways.
1st
protein sequenced was Beef Insulin by Fred Sanger - 1958-
Nobel Prize winner. 2 polypeptides [21/30 aa's]

All proteins contain the elements carbon, hydrogen, oxygen,
nitrogen and sulfur some of these may also contain phosphorus,
iodine, and traces of metals like ion, copper, zinc and
manganese.
A protein may contain 20 different kinds of amino acids. Each
amino acid has an amine group at one end and an acid group at
the other and a distinctive side chain.
The backbone is the same for all amino acids while the side
chain differs from one amino acid to the next.
There are four levels of organization in proteins structure:
primary, secondary, tertiary, and quaternary.

1.Primary Structure of Proteins
• The primary structure of a protein is the linear sequence of the
side chains that are connected to the protein backbone. Proteins
are made up of a long chain of amino acids. Even with a
limited number of amino acid monomers – there are only 20
amino acids commonly seen in the human body – they can be
arranged in a vast number of ways to alter the three-
dimensional structure and function of the protein. The simple
sequencing of the protein is known as its primary structure.

Each protein has a unique sequence of amino acid residues
that cause it to fold into a distinctive shape that allows the
protein to function properly.
Eg: Primary structure of human insulin:

Amino acids are joined by peptide bonds.
Because there are no dissociable protons in peptide bonds, the
charges on a polypeptide chain are due only to the N-terminal
amino group, the C-terminal carboxyl group, and the side
chains on amino acid residues.
The primary structure determines the further levels of
organization of protein molecules.

2. Secondary Structure
The secondary structure includes various types of local
conformations in which the atoms of the side chains are not
involved.
Secondary structures are formed by a regular repeating pattern
of hydrogen bond formation between backbone atoms.
The secondary structure involves α-helices, β-sheets, and
other types of folding patterns that occur due to a regular
repeating pattern of hydrogen bond formation.
The secondary structure of protein could be :
Alpha-helix
Beta-helix

The α-helix is a right-handed coiled strand.
The side-chain substituents of the amino acid groups in an α-helix
extend to the outside.
Hydrogen bonds form between the oxygen of the C=O of each
peptide bond in the strand and the hydrogen of the N-H group of the
peptide bond four amino acids below it in the helix.
The side-chain substituents of the amino acids fit in beside the N-H
groups.
The hydrogen bonding in a ß-sheet is between strands (inter-strand)
rather than within strands (intra-strand).
The sheet conformation consists of pairs of strands lying side-by-
side.
The carbonyl oxygens in one strand hydrogen bond with the amino
hydrogens of the adjacent strand.

• The two strands can be either parallel or anti-
parallel depending on whether the strand directions
(N-terminus to C-terminus) are the same or opposite.
• The anti-parallel ß-sheet is more stable due to the
more well-aligned hydrogen bonds.

Secondary Structure —
The α-Helix
Hydrogen bonding causes
protein chains to fold and
align to produce orderly
patterns called secondary
structures. 42 • The a-helix
is a single protein chain
twisted to resemble a coiled
helical spring.

Secondary Structure — The β-Pleated Sheet • Another secondary
structure is the b-pleated sheet, in which several protein chains
lie side by side, held by hydrogen bonds between adjacent
chains:

Secondary structure
α-helix β-sheet
Secondary structures, α-
helix and β-sheet, have
regular hydrogen-bonding
patterns.

The β-pleated sheet structure is less common than the a-helix;
it is found extensively only in the protein of silk. • The figure
below shows both types of secondary structures in a single
protein.

The secondary protein structure depends on the local
interactions between parts of a protein chain, which can affect
the folding and three-dimensional shape of the protein. There
are two main things that can alter the secondary structure:
α-helix: N-H groups in the backbone form a hydrogen bond
with the C=O group of the amino acid 4 residues earlier in the
helix.
β-pleated sheet: N-H groups in the backbone of one strand
form hydrogen bonds with C=O groups in the backbone of a
fully extended strand next to it.
There can also be a several functional groups such as alcohols,
carboxamines, carboxylic acids, thioesters, thiols, and other
basic groups linked to each protein. These functional groups
also affect the folding of the proteins and, hence, its function in
the body.

The α-helix is held in this shape by hydrogen bonding
interactions between amide groups, with the side chains
extending outward from the coil. • The amount of a-helix coiling
in proteins is highly variable.
In α-keratin (hair, pictured below), myosin (muscles), epidermin
(skin), and fibrin (blood clots), two or more helices coil together
(supracoiling) to form cables. These cables make up bundles of
fibers that strengthen tissues in which they are found:

In a higher order structure, strands can be arranged parallel
(amino to carboxyl orientations the same) or anti-parallel
(amino to carboxyl orientations opposite of each other
Ribbon depictions of super secondary β-sheets (A-D) and α-helix
arrangements (E-F)

Turns (sometimes called reverse turns) are a type of secondary
structure that, as the name suggests, causes a turn in the structure of a
polypeptide chain. Turns give rise to tertiary structure ultimately,
causing interruptions in the secondary structures (α- helices and β-
strands) and often serve as connecting regions between two regions of
secondary structure in a protein. Proline and glycine play common
roles in turns, providing less flexibility (starting the turn) and greater
flexibility (facilitating the turn), respectively.
There are at least five types of turns, with numerous variations of each
giving rise to many different turns. The five types of turns are
• δ-turns - end amino acids are separated by one peptide bond
• γ-turns - separation by two peptide bonds
•β-turns - separation by three peptide bonds
•α-turns - separation by four peptide bonds
•π-turns - separation by five bonds
Of these, the β-turns are the most common form and the δ-turns are
theoretical.

β-turn: R-groups are shown in orange, hydrogens in yellow,
carbons in charcoal, nitrogens in purple, and oxygens in green. A
stabilizing hydrogen bond is indicated with the dotted line.

3. Tertiary Structure
Tertiary structure of a protein refers to its overall three-
dimensional conformation.
The types of interactions between amino acid residues that
produce the three-dimensional shape of a protein include
hydrophobic interactions, electrostatic interactions, and
hydrogen bonds, all of which are non-covalent.
Covalent disulfide bonds also occur.
It is produced by interactions between amino acid residues
that may be located at a considerable distance from each other
in the primary sequence of the polypeptide chain.
Hydrophobic amino acid residues tend to collect in the
interior of globular proteins, where they exclude water,
whereas hydrophilic residues are usually found on the surface,
where they interact with water.

• The tertiary structure of a protein refers to the bending and folding
of the protein into a specific three-dimensional shape.
The tertiary structure of proteins refers to the overall three-
dimensional shape, after the secondary interactions. These include
the influence of polar, nonpolar, acidic, and basic R groups that exist
on the protein.
• These structures result from four types of interactions between the
R side chains of the amino acids residues:
1.Disulfide bridges can form between two cysteine residues that are
close to each other in the same chain, or between cysteine residues in
different chains. These bridges hold the protein chain in a loop or
some other 3D shape.
2.Salt bridges are attractions between ions that result from the
interactions of the ionized side chains of acidic amino acids (—
COO-
) and the side chains of basic amino acids (—NH3 +
).

3. Hydrogen bonds can form between a variety of side chains,
especially those that contain:
Hydrogen bonding also influences the secondary structure, but
here the hydrogen bonding is between R groups, while in
secondary structures it is between the C=O and NH portions of the
backbone.
4. Hydrophobic interactions result from the attraction of
nonpolar groups, or when they are forced together by their mutual
repulsion of the aqueous solvent. These interactions are
particularly important between the benzene rings in phenylalanine
or tryptophan. This type of interaction is relatively weak, but since
it acts over large surface areas, the net effect is a strong
interaction.

The compact structure of globular proteins in aqueous
solution, in which the nonpolar groups are pointed inward,
away from the water molecules.

Types of Tertiary Structure
Globular Disordered Fibrous
Many insoluble
amino acids, protein
tends to minimize
surface/volume ratio
Interacts well with
water and takes up a
random configuration
Strong secondary
structure allows
protein to retain a
non-spherical shape

Some examples of 3D structure in proteins:
Lysozyme: MW 14,600 enzyme; egg white &
human tears -124 aa's with 4 S-S; that hydrolyses
polysaccharies in bacterial cell walls = bactericidal agent
Myoglobin: MW 16,700 - animal muscle protein -
stores O2
Cytochrome -C: MW 12,400 - heme binding single
polypeptide of 100 aa's in ETS of mitochondria
Ribonuclease : MW 13,700 enzyme of 124 aa w 4 S-S

4. Quaternary Structure
• Quaternary structure refers to the interaction of one or more
subunits to form a functional protein, using the same forces
that stabilize the tertiary structure.
• It is the spatial arrangement of subunits in a protein that
consists of more than one polypeptide chain.

Quaternary Structure of Proteins • When two or more
polypeptide chains are held together by disulfide bridges, salt
bridges, hydrogen bond, or hydrophobic interactions, forming a
larger protein complex. • Each of the polypeptide subunits has
its own primary, secondary, and tertiary structure. • The
arrangement of the subunits to form a larger protein is the
quaternary structure of the protein.
Hemoglobin
• Hemoglobin is made of four subunits: two identical alpha
chains containing 141 AA’s and two identical beta chains
containing 146 AA’s. Each subunit contains a heme group
located in crevices near the exterior of the molecule.
A hemoglobin molecule in a person suffering from sickle-cell
anemia has a one-amino acid difference in the sixth position of
the two b-chains of normal HbA (a glutamate is replaced with a
valine).

• This changes the shape of red blood cells
that carry this mutation to a characteristic
sickle shape, which causes the cells to
clump together and wedge in capillaries,
particularly in the spleen, and cause
excruciating pain.
Cells blocking capillaries are rapidly
destroyed, and the loss of these red blood
cells causes anemia.

The sequence of a protein is determined by the DNA of the gene
that encodes the protein (or that encodes a portion of the protein,
for multi-subunit proteins).
A change in the gene's DNA sequence may lead to a change in
the amino acid sequence of the protein.
Even changing just one amino acid in a protein’s sequence can
affect the protein’s overall structure and function.
For instance, a single amino acid change is associated with sickle
cell anemia, an inherited disease that affects red blood cells. In
sickle cell anemia, one of the polypeptide chains that make up
hemoglobin, the protein that carries oxygen in the blood, has a
slight sequence change. The glutamic acid that is normally the
sixth amino acid of the hemoglobin β chain (one of two types of
protein chains that make up hemoglobin) is replaced by a valine.
This substitution is shown for a fragment of the β chain in the
diagram below.

The quaternary protein structure refers to the orientation and
arrangement of subunits in proteins with multi-subunits. This is only
relevant for proteins with multiple polypeptide chains.
Proteins fold up into specific shapes according to the sequence of amino
acids in the polymer, and the protein function is directly related to the
resulting 3D structure.
Proteins may also interact with each other or other macromolecules in
the body to create complex assemblies. In these assemblies, proteins can
develop functions that were not possible in the standalone protein, such
as carrying out DNA replication and the transmission of cell signals.
The nature of proteins is also highly variable. For example, some are
quite rigid, whereas others are somewhat flexible. These characteristics
also fit the function of the protein. For example, more rigid proteins
may play a role in the structure of the cytoskeleton or connective
tissues. On the other hand, those with some flexibility may act as
hinges, springs, or levers to assist in the function of other proteins.

The forces that keep the quaternary structure are hydrogen
bonds, electrostatic bonds, hydrophobic bonds and van der
Waals forces.
Depending on the number of polypeptide chain, the protein
may be termed as monomer (1 chain), dimer (2 chains), tetramer
(4 chains) and so on. Each polypeptide chain is termed as
subunit or monomer.
Homodimer contains two copies of the same polypeptide
chain. Heterodimer contains two different types of
polypeptides as a functional unit. For example, 2 alpha-chains
and 2 beta-chains form the hemoglobin molecule. Similarly, 2
heavy chains and 2 light chains form one molecule of
immunoglobulin G. Creatine kinase (CK) is a dimer. Lactate
dehydrogenase (LDH) is a tetramer.

Some Common Quarternary Level Protein Shapes...
1. dimers - self recognizing symmetrical regions -
bind together @ identical binding sites
[ Catabolic Activator Protein* ]
homodimers - 2 identical subunits
heterodimers - non-identical subunits (as in PDH)
2. filaments - polymers of protein subunits each bound together
in an identical way forming a ring or helix
3. colied-coil - 2 parallel helices forming a stiff filament, linked
via a stripe of hydrophobic aa's.
4. tetramers - 4 identical
subunits... ex: neuraminidase and hemoglobin

Protein Structure Summary
Primary
Secondary
Tertiary
Quaternary
Assembly
Folding
Packing
Interaction
S
T
R
U
C
T
U
R
E
P
R
O
C
E
S
S

Protein Assembly
• occurs at the ribosome
• involves polymerization of
amino acids attached to
tRNA
• yields primary structure

Protein Folding
• yields secondary structure
• occurs in the cytosol
• involves localized spatial
interaction among primary
structure elements, i.e. the amino
acids

Protein Packing
• occurs in the cytosol (~60%
bulk water, ~40% water of
hydration)
• involves interaction between
secondary structure elements
and solvent
• yields tertiary structure

Protein Interaction
• occurs in the cytosol, in close proximity to other folded and
packed proteins
• involves interaction among tertiary structure elements of
separate polymer chains

Protein-Structure and its classification

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