Protein chemistry

LECTURE-03
 Learning Objectives

1.Tertiary structure of protein

2.Quaternary structure of protein
3.Classification of protein
 Tertiary Structure
⚫ Three dimensional structure of the whole protein.
⚫ It will have single polypeptide chain ‘’Backbone’’ with
one or more secondary structure.
⚫ Stabilized by covalent bond other than peptide bond.
Usually by Disulfide bonds.
Ex. Alcohol dehydrogenase, G3PDH, LDH.
 3 D structure of
Lactate dehydrogenase
Interactions stabilizing tertiary structure :
⚫ 1. Disulfide bonds
⚫ 2. Hydrophobic interactions
⚫ 3. Hydrogen bonds
⚫ 4. Ionic interactions
⚫ 5. Vander Waals force
Hydrogen bond

⚫ H bonds are weak which

allows to be broken and
reformed easily.
⚫ Allows structural change
and produces ‘functional’
molecules.
Disulfide bond
⚫ In Globular proteins:
Tertiary interactions are frequently stabilized by sequestration
of hydrophobic amino acids residues in the protein core.
⚫ Ions on R groups form
salt bridges through ionic
bonds.
⚫ • NH3 +and COO- areas
of the protein attract and
form ionic bonds.
 Globular proteins
⚫ Myoglobin is a globular protein that stores oxygen in the
muscles.
⚫ Myoglobin is a single peptide chain that is mostly alpha-helix
⚫ O2 binding pocket is formed by a heme group and specific
amino acid side-chains that are brought into position by the
tertiary structure
 Fibrous Proteins
⚫ Consist of long fibers and are mainly structural proteins
Ex. Alpha Keratins are fibrous proteins that make hair, fur,
nails and skin.
⚫ Hair is made of twined fibrils, which are braids of three alpha-
helices.
⚫ Helices are held together by disulfide bonds
 Quaternary structure
⚫ Includes majority of functional proteins
⚫ Each peptide form a subunit.
⚫ The arrangement of protein subunits in 3D complexes in a
multi subunit protein.
⚫ The interactions within multi subunits are the same as
that found in tertiary and secondary structures
⚫ Quaternary structure adds stability by decreasing the
surface/volume ratio of smaller subunit
⚫ Ex. Haemoglobin
 FUNCTIONAL CLASSIFICATION
CATALYTIC Digestive and cellular enzymes
CONTRACTILE Muscle actin and myosin
STRUCTURAL Keratin: Hair, nail, hoof
Elastin: connective tissue
Collagen: Bone, cartilage
Cell wall
GENE REGULATORY Histone, nuclear protein

HORMONAL GH, Glucagon, insulin

TRANSPORT Transferrin(Fe), Hb(Oxygen),

Ceruloplasmin(Cu), Lipoprotein(lipid),
Transcortin(Cortisol)
REGULATORY Calmodulin

STORAGE In seeds : zein, corn

Gliadin/glutelin: wheat
PROTECTIVE Fibrin,
14 immunoglobins
CLASSIFICATION OF PROTEINS: ON CHEMICAL PROPERTIES AND SOLUBILITY
SIMPLE, CONJUGATED, DERIVED

SIMPLE : on hydrolysis yield only amino acid

CLASS CHARACTERISTICS EXAMPLE
Albumin Sol in water, coag by heat, ppt by Sr albumin, egg albumin
amm SO4. Product of plants, animal, Myogen(muscle)
def in glycine Lact alb, leucosin
Globulin Insol in water, sol in dil neutral Sr globulin, myosin
salts/alk/acids, coag – heat, glycine edestin
present ppt ½ sat Plant + animals vitellin(egg)
Glutelin Insol in water, sol in dil alk/acids Glutelin(wheat)
Mostly plant proteins Oryzenin (rice)
Prolamins Insol in water/abs alcohol sol 70- Gliadin(wheat)
80% alcohol. Plant proteins Zein(maize)
Histones Sol water, insol in dil ammo. Not Globin(Hb)
readily coag BASIC prot Thymus
Nucleic acids Gladus
Protamins Sol water, dil acid, alk. Non coag Salmine (salmon sperm)
Simplest low BASIC prot
Scleroprotein Insol in water/ dil acid – alk/alc. Keratin(hair)
s exoskeleton Elastin (Con Tissue)
Collagen, Spongin
15 Fibroin(silk
CONJUGATED PROTEINS : SIMPLE + NON PROTEIN (prosthetic group)

CLASS CHARACTERISTICS EXAMPLE

Nucleoprotein SP + All cells with nucleus
Protamin/ histone + nu acid sol in
water
Lipoprotein SP + Milk, blood, membrane,
Lipids; Lecithin, Cephalin, chloroplast, bacteria,
Chylomicron, VLDL, LDL, HDL, IDL antigen
Mucoprotein SP + Mucin(saliva),
Mucopolysaccaride; Connective ovomucoid(egg),
tissue, bones, cartilage, tendon osseomucoid,
tendomucoid, blood
group subs, GH
Chromoprotei SP + Hb, Cytochrome, Fp,
n Colored pigment with porphyrin myoglobin, catalase,
+metal ion visual purple, peroxidase
Phosphoprote SP + Phosphoric acid (with serine of Caseinogen (milk)
in protein) Vitellin (egg yolk)

Metalloprotei SP + metal ions (Fe, Mn, Cu, Co, Mg, Siderophyllin(Fe)

n Se) Transferrin,
ceruloplasmin,
16 metalloenzymes
DERIVED PROTEINS : Formed from simple and conjugated protein
by physical , chemical or enzyme action

I] PRIMARY DERIVED – DENATURED COAGULATED PROTEINS

CLASS CHARACTERISTICS EXAMPLE

Proteans Derived in the early stage of All cells with nucleus
hydrolysis of proteins by dil
acid, alk, enzyme
Meta Derived in later stage of Milk, blood,
proteins proteins hydrolysis by slightly membrane,
stronger acid, alkali chloroplast, bacteria,
antigen
Coagulated Denatured protein formed by Mucin(saliva),
proteins heat, X-ray, UV ray etc ovomucoid(egg),
osseomucoid,
tendomucoid,
blood group subs, GH

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II] SECONDARY DERIVED –
DUE TO PROGRESSIVE HYDROLYSIS OF PROTEIN

CLASS CHARACTERISTICS EXAMPLE

Proteoses Formed by action of pepsin, Albumose from
trypsin, ppt`ed by ammo SO4, Albumin
non coag by heat. Glubulose from
Globulin
Peptones Further stage of cleavage than
proteoses, sol in water, non
coag. by heat, not ppt by ammo
SO4
Peptides Composed of 2 more AA, Di, Tri, Di, Tri, Tetra peptide
Tetra peptides, water soluble,
non conj by heat, not ppt`ed by
ammo SO4

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 CLASSIFICATION
Depending on Overall shape
Or axial ratio ie. Ratio of length : breath

GLOBULAR PROTEINS: axial ratio<10

Cross linked and with molecule
folded in 3 dimensional structure

FIBROUS PROTEINS: axial ratio>10

Coiled in spiral or helical form

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Globular and Fibrous Proteins
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Globular proteins Fibrous proteins

“spherical” shape long,. thin fibers
Insulin
Hair
Hemoglobin
Wool
Enzymes
Skin
Antibodies Nails