PROTEINS

AA.
 What Are Proteins?
• Large molecules
• Made up of chains of amino acids
• Are found in every cell in the body
• Are involved in most of the body’s functions
and life processes(FUNCTIONS OF PROTEINS)
• The sequence of amino acids is determined by
DNA (GENE EXPRESSION)
 Structure of Proteins
• Made up of chains of amino acids; classified by
number of amino acids in a chain
– Peptides: fewer than 50 amino acids
• Dipeptides: 2 amino acids
• Tripeptides: 3 amino acids
• Polypeptides: more than 10 amino acids
– Proteins: more than 50 amino acids
• Typically 100 to 10,000 amino acids linked together
• Chains are synthesizes based on specific bodily DNA
• Amino acids are composed of carbon, hydrogen,
oxygen, and nitrogen
Structural Differences Between Carbohydrates, Lipids, and
Proteins

Figure 6.1
The Anatomy of an Amino Acid

Figure 6.2b
 AMINO ACIDS
• When an amino acid is dissolved in water, it exists in solution as the
dipolar ion, or zwitterion.
• Aromatic R Groups Phenylalanine, tyrosine, and tryptophan,
• Nonpolar, Aliphatic R Groups The R groups in this class of amino acids
are nonpolar and hydrophobic. The side chains of alanine, valine,
leucine, METHIONINE, PROLINE and isoleucine.
• Polar, Uncharged R Groups-serine, threonine, cysteine, asparagine,
and glutamine
• Positively Charged (Basic) R Groups-LSINE ARGININE AND HISTIDINE.
• Negatively Charged (Acidic) R Groups The two amino acids having R
groups with a net negative charge at pH 7.0 are aspartate and
glutamate,
Some Amino Acids
Some More Amino Acids
Still More Amino Acids
 Peptide Bonds Link Amino Acids
• Form when the acid group (COOH) of one
amino acid joins with the amine group (NH2)
of a second amino acid
• Formed through condensation
• Broken through hydrolysis
Condensation and Hydrolytic Reactions

Figure 6.3
 Essential, Nonessential, and Conditional

• Essential – must be consumed in the diet

• Nonessential – can be synthesized in the body
• Conditionally essential – cannot be
synthesized due to illness or lack of necessary
precursors
– Premature infants lack sufficient enzymes needed
to create arginine
 Structure of the Protein
• Four levels of structure
– Primary structure
– Secondary structure
– Tertiary structure
– Quaternary structure

Any alteration in the structure or sequencing

changes the shape and function of the protein
 Protein levels
• A description of all covalent bonds (mainly peptide bonds and disulfide
bonds) linking amino acid residues in a polypeptide chain is its primary
structure. The most important element of primary structure is the
sequence of amino acid residues.
• Secondary structure refers to particularly stable arrangements of
amino acid residues giving rise to recurring structural patterns. The
beta pleated sheets and the alpha helices.
• Tertiary structure
• describes all aspects of the three-dimensional folding of a polypeptide.

• When a protein has two or more polypeptide subunits, their

arrangement in space is referred to as quaternary structure.
 Primary Structure
• This is the linear sequence of amino acids in a polypeptide chain. It
determines the further levels of organization of protein molecule. In
primary structure, the amino acids are numbered from N-terminal
(which is always written on the left end) of the polypeptide chain.

• All the structural levels of a protein (secondary, tertiary and

quaternary) are ultimately determined by the primary structure
because all the information needed for the molecule to achieve its
conformation is imprinted within the primary structure. It is this
polypeptide chain (and its components) that determines where the
proteins bend, fold, and where they can link to another polymer chain.
 Secondary Structure
• It is formed when a polypeptide chain assumes a three-dimensional structure by folding or
coiling, and results from steric interrelationships between amino acids located near each other in
the chain. The tendency of the polypeptide chain is to arrange itself in space so as to form a
tightly compact structure. Three types of secondary structure are possible: α-helical, reverse turn,
and ß-pleated sheet.

• In α-helical structure, the polypeptide chain twists into a right-handed screw to form rod-
like structure. In the process it brings into close proximity the amino group of one amino acid
with carboxyl group of the fourth amino acid in the chain. It is stabilized by hydrogen bonds
between the amino and the carboxyl group. In the coiled polypeptide chain, non-polar
hydrophobic groups (side chains) tend to occupy the interior of the helix while polar hydrophilic
groups are oriented towards the periphery.

• In Reverse Turn structure, the polypeptide chain may fold back on itself to change or even
reverse the direction of the chain. Glycine and proline which have small side chains, offer
convenient spots in the polypeptide chain for folding to occur.

• In ß-pleated sheet structure, the polypeptide chains lie side by side in an extended state to
form sheets. It is stabilized by hydrogen bonds between amino and carboxyl groups in
neighbouring chains. The polypeptide chains may be parallel if they run in the same direction or
anti-parallel if the same chain takes a reverse turn and folds on itself.
 Tertiary structure
• It is formed when a polypeptide chain undergo extensive
coiling to produce complex rigid structure and results from
steric interaction between amino acids located far apart but
brought closer by folding, looping and binding.
• The final shape may be ellipsoid, globular or any irregular
shape which is determined by the intermolecular forces
involved, thus - hydrogen bonds, hydrophilic and hydrophobic
interactions, disulfide forces, ionic / electrostatic forces and
van der waals forces.
• The conformations are biologically active and are referred to
as native proteins.
 Quarternary structure

• Some protein molecules are complexes containing

more than one polypeptide chain.
• Each chain in the molecule has its own characteristic
tertiary structure and is called subunit or monomer.
• Two or more of the monomers are held together by
hydrophobic interactions, hydrogen bonds, and
electrostatic forces.
• The compound structure is called oligomer. For
example, hemoglobin is a tetramer.
 Denaturing
• Alteration of the protein’s shape and thus
functions through the use of
– Heat
– Acids
– Bases
– Salts
– Mechanical agitation
• Primary structure is unchanged by denaturing
 Classification of Proteins

• Proteins are classified into three groups, namely simple proteins, conjugated proteins and,
derived proteins.
• Simple Proteins

• These are proteins which contain amino acids only and have been sub-classified as:

 Albumins – are soluble in water and heat coagulable. E.g. egg albumin, serum albumin,
lactalbumin, and soya bean albumin.
 Globulins – are insoluble in water but soluble in dilute salt solutions and heat coagulable.
They occur together with albumins in same sources.
 Glutelins – are soluble in acids and alkalis but insoluble in neutral solvents. They are the
major proteins of wheat, rice and other cereals.
 Prolamines – are soluble in 70% alcohol and are rich in proline. They occur in cereals like
corn, barley and others.
 Scleroproteins – are also called albuminoids and are insoluble in most solvents. They are
animal proteins present in hair, hoof, horn, nails, cartilage and bone. E.g. collagen, keratin
and fibroin.
 Histones – are soluble in water, dilute acids and salt solutions and are rich in basic amino
acids like arginine. Examples, globin in hemoglobin and protein moiety of nucleoproteins.
 Protamines – have very low molecular weight but are strongly basic and rich in arginine.
They occur in nucleoproteins of the sperm.
 Conjugated Proteins

• These are proteins which contain other chemical components apart from
amino acids. The non-amino acid part is called prosthetic group. Conjugated
proteins are sub-classified according to the prosthetic group they contain.
•
 Nucleoproteins – contain nucleic acids as the prosthetic group. Example,
histones and protamines.
 Proteoglycans and glycoproteins – contain carbohydrate as the prosthetic
group. Example, Heparin, γ-globulin.
 Chromoproteins – contain coloured compound as the prosthetic group.
Example, hemoglobin, flavoprotein, visual purple.
 Phosphoproteins – the prosthetic group is phosphoric acid attached to OH of
serine or threonine. Examples, casein.
 Lipoproteins – contain mainly phospholipids as the prosthetic group. Example,
ß-lipoprotein of blood.
 Metalloproteins – contain metallic ions (e.g. Cu, Fe, Co, Mn, Zn, Mg) as the
prosthetic group. They are usually enzymes. Example, ferritin
 Derived Proteins
• These are sub-classified into two, namely primary and secondary derived
proteins.

 Primary Derived Proteins – are produced as a result of denaturation. Examples:

Proteans (e.g. fibrin); metaproteins, and coagulated proteins.
 Secondary Derived Proteins – are produced as a result of partial digestion of
proteins. Examples: proteoses, peptones and peptides.
Denaturing a Protein

Figure 6.5
 Protein Denaturation

• This is the loss of the specific three-dimensional conformation of proteins, and

may be temporary or permanent. It is caused by several agents:

 Heat or Radiation (e.g. IR, UV light). The kinetic energy supplied to the protein
causes its atoms to vibrate violently, thus disrupting the weak hydrogen bonds
and ionic bonds. The protein then coagulates.
 Heavy Metals (e.g. lead and mercury). Such cations form strong bonds with
carboxyl groups and often disrupt ionic bonds. They also reduce electrical
polarity of proteins and thus increase their solubility, causing them to
precipitate in solution.
 Strong Acids and Alkalis, and Concentrated Salts. Such solutions disrupt ionic
bonds and the protein coagulates.
 Organic Solvents and Detergents. These substances disrupt hydrophobic
interactions and form bonds with hydrophobic groups.