This document discusses the classification and structure of proteins. It describes the four levels of protein structure: primary, secondary, tertiary, and quaternary. The primary structure is the linear sequence of amino acids. The secondary structure involves local folding patterns stabilized by hydrogen bonds. The tertiary structure is the overall three-dimensional shape of a protein determined by interactions between amino acid side chains. Quaternary structure refers to the arrangement of multiple protein subunits. The document also categorizes proteins based on their biological functions and physical properties.

3. Structure
Biological function
Shape and solubility
Composition
Nutritional basis

4. CLASSIFICATION
BY
STRUCTURE

5.  The primary structure of proteins is defined
as a linear sequence of amino acids joined
together by peptide bonds.
 Peptide bonds and disulfide bonds are
responsible for maintaining the primary
structure.

7.  The secondary structure of a protein is
defined as a local spatial structure of a
certain peptide segment, that is, the relative
positions of backbone atoms of this peptide
segment.
 H-bonds are responsible for stabilizing the
secondary structure.
 Repeating units of Ca-C(=O)-N(-H)-Ca
constitute the backbone of peptide chain.
 Six atoms, Ca-C(=O)-N(-H)-Ca, constitute a
planer peptide unit.

9.  The tertiary structure is defined as the
three-dimensional arrangement of all
atoms of a protein.

11.  The quaternary structure is defined as
the spatial arrangement of multiple
subunits of a protein.
 These subunits are associated through
H-bonds, ionic interactions, and
hydrophobic interactions

14.  Those proteins which are highly
specialized in their function with
catalytic activity.
 These proteins regulate almost all
biological reactions going on inside all
living cells.
 There are about 2000 different enzymes
has been recognized; each capable of
catalyzing a different kind of
biochemical reaction.

15.  are those proteins which help in transportation
of life sustaining chemicals vital gases and
nutrients.
 Carry essential substances throughout the
body.
 Example:
- Haemoglobin is a globular protein present in
RBC of blood can binds with oxygen when
blood passes though longs and distributes
oxygen through out the body cells to affect
cellular respiration.
- Blood plasma contains lipoprotein which
carries lipids from the liver to other organs.

16.  are those stored inside the cells or
tissue as reserved food and can be
mobilized at the time of nutrient
requirement to provide energy.
 Store nutrients.
 Example:
- Casein stores protein in milk.
- Ferritin stores iron in the spleen and liver.

17.  Move muscles.
 the ability to contract to change the shape or
to move about.
 These proteins includes. Actin and myosin;
which are present in form of filamentous
protein in muscle cells for functioning in the
contractile systems.

18.  This type of protein form major component of
tendons, cartilages and bones.
 These are fibrous proteins named collagen.
Ligaments are contains special structural
protein capable of stretching in two
dimensions called as elastin.
 Hairs finger nails, feathers of birds consists of
tough insoluble protein named keratin.
 Major component of silk fibers, threads of
spider web contain structural protein named
fibroin.

19.  Many proteins in body of organisms
posses defending action against the
invasion and attack of foreign entities or
protect the body from injury.
 Among these proteins special globular
protein named immunoglobulin's or
antibodies in vertebrate’s body is the most
indispensible protein.
 It synthesized by lymphocytes and they
can neutralize the foreign protein produced
by bacteria, virus and other harmful
microbes called antigens through
precipitation or glutination.

20.  Some proteins help to regulate cellular or
physiological activity. Among them are
many hormones, such as insulin; which is
a regulatory protein formed in pancreatic
tissue help to regulate the blood sugar
level.
 Growth hormones of pituitary and
parathyroid hormones regulate Ca++ and
phosphate transport in body. Other
proteins called repressors regulate
biosynthesis of enzymes.

21.  There are number of proteins whose functions
are not yet specified and are rather exotic.
These includes –
 Monelin: - A protein of an African plant has an
intensely sweet taste and used as non toxic
food sweetener for human use.
 Antifreeeze: A protein present in blood
plasma of Antarctic fisher which protect their
blood freezing in ice cold water.
 Resillin: A type of protein present in wing
hinges of some insects with elastic properties.

23.  these proteins have a rod like structure. They
are not soluble in water.
(a) These are made up of polypeptide chain
that are parallel to the axis & are held together
by strong hydrogen and disulphide bonds.
(b) They can be stretched & contracted like
thread.
 Examples:
-Collagen
-Keratin
-Fibrinogen
-Muscle protein

24.  these proteins more or
less spherical in nature.
Due to their distribution
of amino acids
(hydrophobic inside,
hydrophillic outside) they
are very soluble in
aqueous solution.
 Examples
Myoglobin, albumin,
globulin, casein,
haemoglobin, all of the
enzymes, and protein
hormones.

25.  These are protein which are in association
with lipid membranes.
 Those membrane proteins that are embedded
in the lipid bilayer have extensive hydrophobic
amino acids that interact with the non-polar
environment of the bilayer interior.
 Membrane proteins are not soluble in aqueous
solution.

27.  are those which on hydrolysis yield only amino
acids and no other major organic or inorganic
hydrolysis products. They usually contain
about 50% carbon,7% hydrogen, 23% oxygen,
16% nitrogen and 0–3% sulphur.
 Example:
-Egg (albumin)
-Serum (globulins)
-Wheat (Glutelin)
-Rice (Coryzenin)

28.  are those which on hydrolysis yield not only amino
acids but also organic or inorganic components. The
non-amino acid part of a conjugated protein is called
prosthetic group.
 Conjugated proteins are classified on the basis of
the chemical nature of their prosthetic groups.

31.  A complete protein contains an adequate amount of
all of the essential amino acids that should be
incorporated into a diet.
 Some protein contains all the amino acids needed to
build new proteins, which generally come from
animal and fish products. A complete protein must
not lack even one essential amino acid in order to be
considered complete.
 Sources: The following foods are examples of
complete proteins, which need not be combined with
any other food to provide adequate protein: Meat,
Fish, Poultry, Cheese, Eggs, Yogurt, Milk

32.  An incomplete protein is any protein that
lacks one or more essential amino acids in
correct proportions. These can also be
referred to as partial proteins.
 Even if the protein contains all the
essential amino acids, they must be in
equal proportions in order to be considered
complete. If not, the protein is considered
incomplete.
 Sources of Incomplete Proteins: Grains,
Nuts, Beans, Seeds, Peas, Corn

33.  By combining foods from two or more
incomplete proteins, a complete protein can
be created. The amino acids that may be
missing from one type of food can be
compensated by adding a protein that
contains that missing amino acid.
 When eaten in combination at the same meal,
you are providing your body with all the
essential amino acids it requires. These are
considered complementary proteins when
they are combined to compensate for each
other's lack of amino acids.

34.  create a complete protein in one meal include:
 Grains with Legumes - sample meal: lentils and rice with
yellow peppers.
 Nuts with Legumes - sample meal: black bean and peanut
salad.
 Grains with Dairy - sample meal: white cheddar and whole
wheat pasta.
 Dairy with Seeds - sample meal: yogurt mixed with
sesame and flax seeds.
 Legumes with Seeds - sample meal: spinach salad with
sesame seed and almond salad dressing.

35. •Physical Properties
•Chemical Properties

36.  contains carbon, hydrogen, oxygen, nitrogen and
small amount of sulphur.
 composed of amino acids that are linked together
by peptide bonds
 act as catalysts, enzymes that speed up the rate of
chemical reactions
 provides structural support for cells
 transports substances across cell membrane
 provides a defense mechanism against pathogens
(antibodies)
 responds to chemical stimuli
 secretes hormones.

37. •In order to determine the nature of the molecular and
ionic species that are present in aqueous solutions at
different pH's, we make use of the Henderson -
Hasselbalch Equation.

38.  the negatively and positively charged
molecular species are present in equal
concentration. This behavior is general for
simple (difunctional) amino acids.

40.  The distribution of charged species in a
sample can be shown experimentally by
observing the movement of solute molecules
in an electric field, using the technique
of electrophoresis.

42.  Denaturation of Proteins
Denaturation is a process in
which proteins or nucleic acids lose
the quaternary structure, tertiary
structure and secondary structure which is
present in their native state, by application of
some external stress or compound such as a
strong acid or base, a
concentrated inorganic salt, an organic solvent
(e.g., alcohol or chloroform), radiation or heat.

44.  Denaturation occurs because the bonding
interactions responsible for the secondary
structure (hydrogen bonds to amides) and
tertiary structure are disrupted.
 In tertiary structure there are four types of
bonding interactions between "side chains"
including: hydrogen bonding, salt bridges,
disulfide bonds, and non-polar hydrophobic
interactions. which may be disrupted.
 Therefore, a variety of reagents and conditions
can cause denaturation. The most common
observation in the denaturation process is the
precipitation or coagulation of the protein.

45.  Heat can be used to disrupt hydrogen bonds
and non-polar hydrophobic interactions. This
occurs because heat increases the kinetic
energy and causes the molecules to vibrate so
rapidly and violently that the bonds are
disrupted. The proteins in eggs denature and
coagulate during cooking. Other foods are
cooked to denature the proteins to make it
easier for enzymes to digest them. Medical
supplies and instruments are sterilized by
heating to denature proteins in bacteria and
thus destroy the bacteria.

46.  Hydrogen bonding occurs between amide groups in
the secondary protein structure. Hydrogen bonding
between "side chains" occurs in tertiary protein structure in
a variety of amino acid combinations. All of these are
disrupted by the addition of another alcohol.
 A 70% alcohol solution is used as a disinfectant on the
skin. This concentration of alcohol is able to penetrate the
bacterial cell wall and denature the proteins and enzymes
inside of the cell. A 95% alcohol solution merely
coagulates the protein on the outside of the cell wall and
prevents any alcohol from entering the cell. Alcohol
denatures proteins by disrupting the side chain
intramolecular hydrogen bonding. New hydrogen bonds
are formed instead between the new alcohol molecule and
the protein side chains.

47.  Salt bridges result from the neutralization of an
acid and amine on side chains. The final
interaction is ionic between the positive
ammonium group and the negative acid group.
Any combination of the various acidic or amine
amino acid side chains will have this effect.
 The denaturation reaction on the salt bridge by
the addition of an acid results in a further
straightening effect on the protein chain as
shown in the graphic on the left.

48.  Heavy metal salts act to denature proteins in much the same
manner as acids and bases. Heavy metal salts usually
contain Hg+2, Pb+2, Ag+1 Tl+1, Cd+2 and other metals with high
atomic weights. Since salts are ionic they disrupt salt bridges
in proteins. The reaction of a heavy metal salt with a protein
usually leads to an insoluble metal protein salt.
 This reaction is used for its disinfectant properties in external
applications. For example AgNO3 is used to prevent
gonorrhea infections in the eyes of new born infants. Silver
nitrate is also used in the treatment of nose and throat
infections, as well as to cauterize wounds.
 Mercury salts administered as Mercurochrome or Merthiolate
have similar properties in preventing infections in wounds.

49. Acids
 Acidic protein denaturants
include:
 Acetic acid[8]
 Trichloroacetic acid 12% in
water
 Sulfosalicylic acid
Solvents
 Most organic solvents are
denaturing, including:
 Ethanol
 Methanol
Cross-linking reagents
 Cross-linking agents for
proteins include:[citation needed]
 Formaldehyde
 Glutaraldehyde
 Chaotropic agents
 Chaotropic agents include:
 Urea 6 – 8 mol/l
 Guanidinium chloride 6 mol/l
 Lithium perchlorate 4.5 mol/l
Disulfide bond reducers[edit]
 Agents that break disulfide
bonds by reduction
include:[citation needed]
 2-Mercaptoethanol
 Dithiothreitol
 TCEP (tris(2-
carboxyethyl)phosphine)
Other
 Picric acid
 Radiation
 Temperature

50. Example of denaturation that occurs in our
living:
1. Denaturation of human hair
 The extent to which fatty acid oxygenases are
activated in the normal epidermis is not known
2. In cooking eggs
 cooking eggs turns them from runny to solid
 cooking food makes it more digestible.
3. Milk forms a solid curd on standing
 · bacteria in milk grows
 · forms lactic acid
 · protonates carboxylate groups
 · becomes isoelectric
 · coagulates into a solid curd

51. 1. Chromatography – the method of separating amino acids
on the basis of differences in absorption, ionic charges, size
and solubility of molecules
2. Electrophoresis – effects separation in an electric field on
the basis of differences in charges carried by amino acids
and proteins under specific condition
3. Ultracentrifugation – effects separation on the basis of
molecular weight when large gravitational forces are applied
in the ultracentrifuge.
4. Precipitation Methods – salts as sodium sulfate,
ammonium sulfate, cadmium nitrate, silver nitrate and
mercuric chloride at specific conc. precipitate some proteins
while others remain in solution
5. Dialysis – is for the removal of small, crystalloidal
molecules from protein solution.

52.  Much of modern biochemistry depends on the use
of column chromatographic methods to separate
molecules.
 Chromatographic methods involve passing a
solution (the mobile phase) through a medium (the
immobile phase) that shows selective solute
components.
 The important methods of chromatography are:
1. Ion-Exchange Chromatography
2. Antibody Affinity Chromatography
3. Gel Filtration Chromatography
4. HPLC (High Performance Liquid Chromatography)

59.  Proteomics is the science of protein
expression of all the proteins made by a cell
 Proteome pertain to all proteins being made
according to the transcriptome (RNA profile).
It is often visualized by a system interaction
map as seen in the proteogram.

60.  Commonly used procedures by Proteomics
are:
 Mass Spectrophotometry – detects exact
mass of small peptides (molecular weight).
 X-ray Crystallography – determines 3D
shape of molecules mathematically
 NMR Spectroscopy – magnetic signal
indicates distances between atoms

61. Amino
Acids
Systematic
name
Importance
Glycine Aminoetha-
noic acid
Helps trigger the release of oxygen to
the energy requiring cell-making
process
Important in the manufacture of
hormones for strong immune system
Alanine α-amino
propanoic
acid
Important AA as it is an energy source
for the liver, muscles, and CNS
Strengthens the immune system by
producing antibodies
Helps in the metabolism of sugars and
organic acids

62. Valine α-amino 3-
methylbutanoic
acid
Essential AA
Promotes mental vigor,
muscle coordination and
calm emotions
Leucine α-amino
4-methyl
pentanoic acid
Essential AA
Provides necessary
substances for energy
production
Stimulants to the upper
brain and helps to be
more alert
Isoleucin
e
α-amino 3-
methylpentanoi
c acid
Essential AA
Same functions as
leucine

63. Phenylalanine α-amino 3-
phenylpropanoic
acid
Essential AA
Used by the brain to produce
norepinephrine,
Reduces hunger pains
Functions as antidepressant
Helps improve memory
Tyrosine α-amino 3-(4-
hydroxyphenyl)pro
panoic acid
 Transmits nerve impulses to the brain;
helps overcome depression; improves
memory; increases mental alertness;
promotes the healthy functioning of the
endocrine glands
Tryptophan α-amino 3-indole
propanoic acid
Essential AA
A natural relaxant, helps alleviate insomia by
inducing normal sleep
Reduces anxiety and depression
Helps in the treatment of migraines and
headaches
Helps stabilize the immune system
Helps reduce risk of artery and heart spasms
Works with lysine in reducing cholesterol levels

64. Methionine α-amino 4-
methyl thiol
butanoic acid
Essential AA
Principal supplier of sulfur which
prevents disorder of the hair, skin
and nails
Helps lower cholesterol levels by
increasing the liver’s production of
lecithin
A natural chelating agent for heavy
metals
Regulates the formation of
ammonia and creates ammonia-free
urine which reduces bladder
irritation
Influences hair follicles and
promotes hair growth

65. Cysteine 2-amino 3-
mercaptopropanoi
c acid
Functions as an antioxidant and is a
powerful aid to the body in protecting
against radiation and pollution
Helps slow down the aging process,
deactivate free radicals, neutralizes toxins
Aids in protein synthesis and promotes
cellular repair
Necessary for skin formation, in the
recovery from burns and surgical operations
Serine 2-amino 3 hydroxy
propanoic acid
A storage source of glucose by the liver
and muscles
Helps strengthen immune system by
providing antibodies
Synthesizes fatty acid sheath around
nerve fibers
Threonine 2-amino 3 hydroxy
butanoic acid
Essential AA
Important constituent of collagen,
Assists metabolism and assimilation
Helps the digestive and intestinal tracts
functions normally
Helps prevents fat build-up in the liver

66. Histidine α-amino 3 (1H-
imidazol-4-yl)
propanoic acid
Essential AA
Found abundantly in hemoglobin
Used in the treatment of rheumatoid
arthritis, allergic diseases, ulcers, anemia
Lysine 2,6 diamino
hexanoic acid
Essential AA
Insures adequate absorption of calcium
Helps form collagen (which makes up
bone and cartilages)
Aids in the production of antibodies,
hormones and enzymes
Arginine α-amino 5-
guanidino
pentanoic acid
Helps improve immune responses to
bacteria, viruses and tumor cells
Promotes wound healing and
regeneration of the liver
Causes the release of growth hormones
Crucial for optimal muscle growth and
tissue repair

67. Aspartic Acid α-amino
butanedioic acid
Most easily used as energy source
Aids in the expulsion of toxic ammonia
from the body
Located most closely to the TCA cycle,
the site of energy production
Found in increased levels in people with
epilepsy and in decreased amounts in
some cases of depression
Glutamic
acid
α-amino
pentanedioic acid
Considered to be nature’s “brain food” by
improving mental capacities
Helps speed the healing of ulcers; gives
a “lift” from fatigue
Helps control alcoholism, schizophrenia
and the craving of sugar, Parkinson’s
disease, mental retardation, and muscular
dystrophy
Asparagine α-amino 3
carbamoyl
propanoic acid
Found in the surfaces of proteins where
they can interact with water molecules

68. Glutamine α-amino 4
carbamoyl
butanoic acid
Found in the surfaces of proteins where
they can interact with water molecules
The polar amide groups can also form
hydrogen bonds with atoms in the side
chains of other polar amino acids
Proline Pyrrolidine-2-
carboxylic acid
Non-essential AA
Important for the proper functioning of
joints and tendons
Helps maintain and strengthen heart
muscles
Helps repair processes after cell injury or
for any type of wound healing
Hydroxy
lysine
Hydroxy
hexanoic acid
It is a hydroxy derivative of lysine.
It is most widely known as a component
of collagen

69. Protein No. of
AA
Function
Insulin 51 Enzyme for sugar
metabolism
Cytochrome C 104 Enzyme for cell respiration
Growth hormone 191 Used as anti-aging treatment
Hemoglobin 574 Oxygen transport in blood
Hexokinase 730 Enzyme for glycolysis
Gamma globulin 1320 Part of immune system in
blood
Myosin 6100 Muscle action

70. Albumins Create osmotic pressure and
transport other molecules
Immunoglobulins Participate in immune system
Fibrinogens Blood coagulation
Alpha-1-Antitrypsin Neutralize trypsin that has
leaked from the digestive
system
Regulatory proteins Regulation of gene
expression