Proteins

1. Protein

2. • The word protein is derived from Greek word, proteious meaning
primary. So, proteins are the major components of any living
organism
• Out of the total dry body weight, 3/4ths are made up of proteins.
• Proteins are used for body building; all the major structural and
functional aspects of the body are carried out by protein molecules.
• Abnormality in protein structure will lead to molecular diseases with
profound alterations in metabolic functions.
• Proteins contain Carbon, Hydrogen, Oxygen and Nitrogen as the
major components while Sulfur and Phosphorus are minor
constituents.
• Nitrogen is characteristic of proteins. On an average, the nitrogen
content of ordinary proteins is 16% by weight. All proteins are
• polymers of amino acids

3. Introductd.contd
• Few proteins contain other elements such as I, Cu,
Mn, Zn
• and Fe, etc.
• Amino acids: Protein molecules are very large
molecules with a high molecular weight ranging
from 5000 to 25,00,000.
• Protein can be broken down into smaller units by
hydrolysis. These small units the monomers of
proteins are called as amino acids.
• Proteins are made up from, 20 such standard
amino acids in different sequences and numbers.
So an indefinite number of proteins can be formed
and do occur in nature.

4. BIOMEDICAL IMPORTANCE OF
PROTEINS
• Proteins are the main structural components of the cytoskeleton. They are the sole source
to replace Nitrogen
• of the body.
• Biochemical catalysts known as enzymes are proteins.
• Proteins known as immunoglobulins serve as the first line of defence against bacterial and
viral infections.
• Several hormones are protein in nature.
• Structural proteins furnish mechanical support and some of them like actin and myosin
are contractile proteins and help in the movement of muscle fibre, microvilli, etc.
• Some proteins present in cell membrane, cytoplasm and nucleus of the cell act as
receptors
• The transport proteins carry out the function of transporting specific substances either
across the membrane or in the body fluids.
• •Storage proteins bind with specific substances and store them, e.g. iron is stored as
ferritin.
• Few proteins are constituents of respiratory pigments and occur in electron transport
chain or respiratory chain, e.g. cytochromes, hemoglobin, myoglobin.
• Under certain conditions proteins can be catabolised to supply energy.
• Proteins by means of exerting osmotic pressure help in maintenance of electrolyte and
water balance in body.

5. Classification
• Classification
• Even though there is no universally accepted classification system, proteins may be
classified on the basis of their composition, solubility, shape, biological function and on their
three dimensional structure.
• I. Composition:-
A. Simple protein: Yields only amino acids and no other major organic or inorganic hydrolysis
products i.e. most of the elemental compositions.
• B. Conjugated Proteins
• Yields amino acids and other organic and inorganic components
• Nucleoprotein (a protein containing Nuclei acids) .These are proteins attached to nucleic acids,
e.g. Histones. The DNA carries negative charges, which combines with positively charged proteins
• Lipoprotein (a protein containing lipids) These are proteins loosely combined with lipid
• components. They occur in blood and on cell membranes
• Phosphoprotein (a protein containing phosphorous) These contain phosphorus. Casein of milk
and vitellin of egg yolk are examples. The phosphoric acid is esterified to the hydroxyl groups
of serine and threonine residues of proteins
• Metalloprotein (a protein containing metal ions of Fe2+) They contain a metal ion as their
prosthetic group. Several enzymes contain metallic elements such as Fe, Co, Mn, Zn, Cu,
Mg, etc. Ferritin: Contains Fe, Carbonic Anhydrase: Contains Zn, Ceruloplasmin:
Contains Cu.
• Glycoprotein (a protein containing carbohydrates). Glycoproteins include mucins,
immunoglobulins, complements and many enzymes.

6. • Chromoproteins: These are proteins with coloured
prosthetic groups. Hemoglobin (Heme, red);
Flavoproteins (Riboflavin, yellow), Visual purple (Vitamin
A, purple) are some examples of chromoproteins
• C. Derived proteins: These are the proteins formed
from native protein by the action of heat, physical
forces or chemical factors.
• 2. Solubility
• a) Albumins: These proteins such as egg albumin and serum
albumin are readily soluble in water and coagulated by heat.
• b) Globulins: these proteins are present in serum, muscle
and other tissues and are soluble in dilute salt solution but
sparingly in water.
• c) Histones: Histones are present in glandular tissues
(thymus, pancreas etc.) soluble in water; they combine with
nucleic acids in cells and on hydrolysis yield basic amino
acids

7. • Overall Shape
• A. Fibrous proteins
• In these protein, the molecule are constituted by several coiled
cross-linked polypeptide chains, they are insoluble in water and
highly resistant to enzyme digestion. The ratio of length to
breath (axial ratio) is more than 10 in such protein.
• A few sub groups are listed below.
• 1. Collagens: the major protein of the connective tissue,
insoluble in water, acids or alkalis. But they are convertible to
water-soluble gelatin, easily digestible by enzymes.
• 2. Elastins: present in tendons, arteries and other elastic
tissues, not convertible to gelatin.
• 3. Keratins: protein of hair, nails etc.
• B. Globular proteins: These are globular or ovoid in shape,
soluble in water and constitute the enzymes, oxygen carrying
proteins, hormones etc. the axial ratio is 3 to 4 or less.
Subclasses include:- Albumin, globulins and histones.

8. . Classification Based on Biological Functions
• 1. Catalytic proteins, e.g. enzymes
• 2. Structural proteins, e.g. collagen, elastin
• 3. Contractile proteins, e.g. myosin, actin.
• 4. Transport proteins, e.g. hemoglobin,
myoglobin, albumin, transferrin
• 5. Regulatory proteins or hormones, e.g. ACTH,
insulin, growth hormone
• 6. Genetic proteins, e.g. histones
• 7. Protective proteins, e.g. immunoglobulins,
interferons, clotting factors.

9. STRUCTURAL ORGANISATION
OF PROTEINS
• Protein structure is normally described at four levels of
• organisation.
• A. Primary Structure: Primary structure is the linear sequence of
amino acids held together by peptide bonds in its peptide chain.
• Primary structure denotes the number and sequence of amino acids in
the protein.
• The peptide bonds form the backbone and side chains of amino acid
residues project outside the peptide backbone.
• The free -NH2 group of the terminal amino acid is called as N-
terminal end and the free -COOH end is called as C-terminal end.
• It is a tradition to number the amino acids from N-terminal end
as No. 1 towards the C-terminal end.
• Presence of specific amino acids at a specific number is very
significant for a particular function of a protein. Any change in
the sequence is abnormal and may affect the function and
properties of protein.
• The primary structure is maintained by the covalent bonds of the peptide
linkages

10. Numbering of Amino Acids in Proteins
• In a polypeptide chain, at one end there will be one free alpha amino
group.
• This end is called the amino terminal (N-terminal) end and the amino acid
contributing the alpha-amino group is named as the first amino acid.
• Incidentally, the biosynthesis of the protein also starts from the amino
terminal end.
• The other end of the polypeptide chain is the carboxy terminal end (C-
terminal), where there is a free alpha carboxyl group which is contributed
by the last amino acid .
• All other alpha amino and alpha carboxyl groups are involved in peptide
bond formation.

11. Secondary Structure
• The secondary structure of a protein refers to the local structure of a polypeptide
chain, which is determined by Hydrogen bond.
• The Interactions are between the carbonyl oxygen group of one peptide bond and
the amide hydrogen of another near by peptide bond.
• There are two types of secondary structure, the ∝ - helix and the β- pleated sheet.
• The α - helix
• The α - helix is a rod like structure with peptide chains tightly coiled and the side
chains of amino acid residues extending outward from the axis of spiral.
• Each amide carbonyl group is hydrogen bonded to the amide hydrogen of a peptide
bond that is 4 - residues away along the same chain. There are 3.6 amino acids
residues per turn of the helix.
• This enable every = NH group to bind with a carbonyl O, fourth in line behind the
primary structure and the helix winds in a right handed manner in almost all
natural protein, i.e. turns in a clockwise fashion around the axis.
• Since all the carbonyl oxygen and peptide nitrogen are thus involved in the
hydrogen bonds, the hydrophilic nature of the helical region is greatly minimized.

12. • Thus in α-helix intra chain hydrogen bonding is present. The α-helices can
be either right handed or left handed. Left handed α-helix is less stable
than right handed α-helix because of the steric interference between the
C = O and the side chains
• Only the right handed α-helix has been found in protein structure.
• Small or uncharged amino acid residues such as alanine, leucine and
phenylalanine are often found inα-helix.
• Proline is never found in α-helix. The proteins of hair, nail, skin contain a
group of proteins called keratins rich in α-helical structure

14. β-pleated sheet structure
• A conformation called β-pleated sheet structure is thus formed when
hydrogen bonds are formed between the carbonyl oxygens and
amide hydrogens of two or more adjacent extended polypeptide
chains.
• Thus the hydrogen bonding in β-pleated sheet structure is
interchain.
• The structure is not absolutely planar but is slightly pleated due to
the angles of bonds.
• The adjacent chains in β-pleated sheet structure are either parallel
or antiparallel, depending on whether the amino to carbonyl
peptide linkage of the chains runs in the same or opposite direction.
• In both parallel and antiparallel β-pleated sheet structures, the side
chains are on opposite sides of the sheet.
• Generally glycine, serine and alanine are most common to form
-pleated sheet.
• A protein molecule may have both type of secondary configuration in
different parts of its molecule

16. Tertiary structure
• : The polypeptide chain with secondary structure may be further folded,
superfolded twisted about itself forming many sizes.
• Such a structural conformation is called tertiary structure.
• Thus the tertiary structure is constituted by steric relationship between
the amino acids located far apart but brought closer by folding.
• The tertiary structure is maintained by noncovalent interactions such as
hydrophobic bonds, electrostatic bonds and van der Waals forces.
• The tertiary structure acquired by native protein is always
thermodynamically most stable
• The bonds responsible for interaction between groups of amino acids are
as follows:
• Hydrophobic interactions: Normally occur between nonpolar side
chains of amino acids such as alanine, leucine, methionine,
isoleucine and phenylalanine.

17. • They constitute the major stabilizing forces for tertiary structure forming a compact three
dimensional structure.
• • Hydrogen bonds: Normally formed by the polar side chains of the amino acids.
• • Ionic or electrostatic interactions: These are formed between oppositely charged polar
side chains of amino acids, such as basic and acidic amino acids.
• • Van der Waal Forces: Occur between nonpolar side chains.
• • Disulfide bonds: These are the S–S bonds betweenn-SH groups of distant cysteine residues

18. Quaternary Structure
• Quaternary structure refers to a complex or an assembly of two or more separate
peptide chains that are held together by non- covalent or, in some case, covalent
interactions.
• The protein will lose its function when the subunits are dissociated
• 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 fuctional unit.
• 2 alpha-chains and 2 beta-chains form the hemoglobin molecule. Similarly, 2 heavy
• chains and 2 light chains form one molecule of immunoglobulin
• Creatine kinase (CK) is a dimer while Lactate dehydrogenase (LDH) is a tetramer
• If the subunits are identical, it is a homogeneous quaternary structure; but if there are
dissimilarities, it is heterogeneous. For instance insulin consists of A and B chain which
are different.
• Hemoglobin has 4 chains, two of them are α and two are β.

19. GENERAL PROPERTIES OF PROTEINS
• Taste: They are tasteless. However, the hydrolytic products (derived proteins) are bitter
in taste.
• Odour: They are odourless. When heated to dryness they turn brown and give off the
odour of burning feather.
• Molecular weights of some of the proteins are: Insulin (5,700); Hemoglobin
(68,000);Albumin (69,000); Immunoglobulins (1,50,000);
• Viscosity of protein solutions: The viscosity of protein varies widely with the
kind of protein and its concentration in solution. The viscosity is closely related
to molecular shape, long molecules (fibrous proteins) being more viscous
than globular proteins. Thus fibrinogen can form a more viscous solution
than albumin.
• • Hydration of proteins: Polar groups of proteins such as -NH2 and -COOH
become hydrated in presence of water and swell up when electrolytes, alcohol or
sugars that form complexes with water are added to protein solutions. There is
competition for water and the degree of hydration of protein is decreased. They
dehydrate protein and precipitate it from solution.
• • Heat coagulation of proteins: Several proteins coagulate forming an insoluble
coagulum. Coagulation is maximum at the isoelectric pH of the protein.
• During coagulation, protein undergoes a change called as denaturation.
Denatured proteins are soluble in extremes of pH and maximum
precipitation occurs at isoelectric pH (pI) of the protein.
• • Amphoteric nature of proteins: In any protein molecule there are amino acids

20. • In addition to the side chains of polar amino acids, N-terminal -NH2 group
and C-terminal -COOH group may also ionise.
• Depending on the pH few groups act as proton donors while few as proton
acceptors.
• Therefore proteins are ampholytes and act both as acids and bases. At a
specific pH called an isoelectric pH (pI) a protein exists as a dipolar ion or
“Zwitterion” or “Hybrid” ion, carrying equal number of positive and
negative charges on its ionizable groups.
• So the net charge on protein molecule at its isoelectric pH is zero.

21. References
• Solomon et al., (2004), Lecture notes on Medical
Biochemistry . Ethiopia Public Health Training
Initiative, The Carter Center, the Ethiopia Ministry
of Health, and the Ethiopia Ministry of Education.
• Vasudevan et al(2013). Textbook of
BIOCHEMISTRY for Medical Students
• (Seventh Edition)
• Chatterjea and Shinde (2012) Textbook of
Medical Biochemistry(Eighth Edition)