PROTEINS Dr. Nasim. Standard Amino Acids Building blocks of proteins More then 300 AA have been described Only 20 AA are found in mammalian tissue

PROTEINSPROTEINS

Dr. NasimDr. Nasim

Standard Amino AcidsStandard Amino Acids

Building blocks of proteinsBuilding blocks of proteins More then 300 AA have been describedMore then 300 AA have been described Only 20 AA are found in mammalian tissueOnly 20 AA are found in mammalian tissue These 20 AA are called primary or standard AAThese 20 AA are called primary or standard AA


Each AA contain a amino group (NH2), Each AA contain a amino group (NH2), carboxyl group (COOH) and a distinct side carboxyl group (COOH) and a distinct side chain exception to this rule is Proline chain exception to this rule is Proline which contains Imino group (NH) instead which contains Imino group (NH) instead of amino groupof amino group


PhenylalaninePhenylalanine TryptophanTryptophan ValineValine ThreonineThreonine LeucineLeucine IsoleucineIsoleucine MethionineMethionine SerineSerine


HistidineHistidine ArginineArginine LysineLysine LeucineLeucine AlanineAlanine CysteineCysteine Glutamic acidGlutamic acid Aspartic acidAspartic acid

Non Standard Amino AcidsNon Standard Amino Acids

These Amino acids do not take part in the These Amino acids do not take part in the protein synthesis but play important role in protein synthesis but play important role in the body.the body.

Non Standard Amino AcidsNon Standard Amino Acids

CitrullineCitrulline OrnithineOrnithine TaurineTaurine DOPADOPA GABAGABA

Classification of Standard Classification of Standard Amino AcidsAmino Acids

Amino acids with Aromatic side chainAmino acids with Aromatic side chain Amino acids with aliphatic side chainAmino acids with aliphatic side chain Amino acids with side chain containing Sulphur Amino acids with side chain containing Sulphur

atomatom Amino acids with Acidic side chainsAmino acids with Acidic side chains Amino acids with Basic side chainsAmino acids with Basic side chains Amino acids with side chain having OH groupAmino acids with side chain having OH group Imino AcidImino Acid

Amino acids with Acidic Side Amino acids with Acidic Side ChainsChains

These are mono amino dicarboxylic These are mono amino dicarboxylic Aspartic acidAspartic acid Glutamic acidGlutamic acid

Amino acids with Basic Side Amino acids with Basic Side ChainsChains

These are diamino monocarboxylic These are diamino monocarboxylic ArginineArginine HistidineHistidine LysineLysine

Amino Acids with Aliphatic Amino Acids with Aliphatic Side ChainSide Chain

• GlycineGlycine• AlanineAlanine• ValineValine• LeucineLeucine• IsoleucineIsoleucine

Amino Acids with Side Chain Amino Acids with Side Chain Having OH GroupHaving OH Group

• SerineSerine• ThreonineThreonine

Amino Acids with Side Chain Amino Acids with Side Chain Containing Sulphur AtomContaining Sulphur Atom

CysteineCysteine CystineCystine MethionineMethionine

Amino Acids with Aromatic Amino Acids with Aromatic Side ChainSide Chain

PhenylalaninePhenylalanine TyrosineTyrosine TryptophanTryptophan

Classification of ProteinsClassification of Proteins

Simple ProteinSimple Protein AlbuminAlbumin GlobulinGlobulin ProlaminProlamin HistoneHistone ProtamineProtamine

Albumins Albumins

These are water – soluble proteins These are water – soluble proteins Occur in both plant and animal kingdoms. Occur in both plant and animal kingdoms. Coagulated by heatCoagulated by heat Examples: Examples:

Serum albumin Serum albumin OvalbuminOvalbumin LactalbuminLactalbumin

GlobulinsGlobulins

Insoluble in water Insoluble in water They are found in animalsThey are found in animals E.g. E.g.

Lacto globulinLacto globulin Serum globulins Serum globulins LeguminLegumin

GlobulinsGlobulins

Globulins are more easily precipitated Globulins are more easily precipitated than albumins and this can be done by than albumins and this can be done by only half- saturation with ammonium only half- saturation with ammonium sulfate. sulfate.

Thus half-saturation with ammonium Thus half-saturation with ammonium sulfate can be used to separate sulfate can be used to separate globulins from albumin; this process is globulins from albumin; this process is called salting out.called salting out.

GlobinsGlobins

These are rich in histidine but are not These are rich in histidine but are not basic. basic.

They unite with heme to form hemoglobinThey unite with heme to form hemoglobin Hemoglobin of different species differs Hemoglobin of different species differs

only with respect to goblin, but the heme only with respect to goblin, but the heme part is the same in all cases. part is the same in all cases.

Prolamins Prolamins

These are soluble in 70 to 80% ethanol These are soluble in 70 to 80% ethanol but insoluble in water and absolute but insoluble in water and absolute alcoholalcohol

Examples are gliadin of wheat and zein Examples are gliadin of wheat and zein of maize. of maize.

These are rich in the amino acid praline These are rich in the amino acid praline but deficient in lysine.but deficient in lysine.

HistonesHistones

These are very strongly basic proteinsThese are very strongly basic proteins They are rich in arginine They are rich in arginine In combination with deoxyribonucleic acid In combination with deoxyribonucleic acid

(DNA) they form Nucleoproteins or (DNA) they form Nucleoproteins or Nucleohistones which occur in nuclei Nucleohistones which occur in nuclei forming chromatin materialforming chromatin material

HistonesHistones

The association of DNA and Histone The association of DNA and Histone gives rise to complex called gives rise to complex called nucleosomes, 10nm in diameter, in nucleosomes, 10nm in diameter, in which DNA strands wind around a core which DNA strands wind around a core of Histone molecules. of Histone molecules.

Histones are soluble in water but not in Histones are soluble in water but not in ammonium hydroxide. ammonium hydroxide.

These proteins contain little or no These proteins contain little or no tryptophantryptophan

ProtaminesProtamines

These are present in sperm cellsThese are present in sperm cells They are of relatively smaller sizeThey are of relatively smaller size They are basic protein and resemble They are basic protein and resemble

but unlike them arebut unlike them are Soluble in ammonium hydroxide Soluble in ammonium hydroxide Like Histone they form nucleoproteins Like Histone they form nucleoproteins

with nucleic acids and are rich in with nucleic acids and are rich in arginine. These proteins lack in both arginine. These proteins lack in both tyrosine and tryptophantyrosine and tryptophan

Functions of ProteinsFunctions of Proteins

Catalytic Proteins, e.g. EnzymesCatalytic Proteins, e.g. Enzymes

Regulatory ProteinsRegulatory Proteins

Structural Proteins, e.g. hairs, Nail etcStructural Proteins, e.g. hairs, Nail etc

Transport Proteins, e.g. AlbuminTransport Proteins, e.g. Albumin

Functions of ProteinsFunctions of Proteins

Defensive Proteins, e.g. ImmunoglobulinDefensive Proteins, e.g. Immunoglobulin

Contractile Proteins, e.g. Actin, MyosinContractile Proteins, e.g. Actin, Myosin

Genetic Proteins, e.g. NucleoproteinsGenetic Proteins, e.g. Nucleoproteins

Storage ProteinsStorage Proteins

Structural Classification of Structural Classification of ProteinsProteins

Derived ProteinsDerived Proteins Primary derived proteins (denatured Primary derived proteins (denatured

proteins)proteins) Secondary derived proteins (hydrolytic Secondary derived proteins (hydrolytic

proteins)proteins)

Primary StructurePrimary Structure

The sequence of amino acids in a protein.The sequence of amino acids in a protein.

Peptide bondPeptide bond


Peptide bondPeptide bond Amide linkage between the Amide linkage between the αα-carboxyl -carboxyl

group of one AA & the group of one AA & the αα-amino group of -amino group of another.another.

It is a very stable bond.It is a very stable bond. Not broken by conditions that denature Not broken by conditions that denature

proteins such as heating or high proteins such as heating or high concentration of urea.concentration of urea.

Primary StructurePeptide Bond (Cont.)


Peptide bond (Cont.)Peptide bond (Cont.) Non enzymatically hydrolyzed by prolong Non enzymatically hydrolyzed by prolong

exposure to strong acid or base at exposure to strong acid or base at elevated temperature.elevated temperature.

All AA sequences read from amino All AA sequences read from amino terminal to carboxyl terminal of the peptide terminal to carboxyl terminal of the peptide bond.bond.


Peptide bond (Cont.)Peptide bond (Cont.) Polypeptide chainPolypeptide chain Linkage of many AA through peptide bond Linkage of many AA through peptide bond

results in un branched chain.results in un branched chain. Each AA in a polypeptide chain is called Each AA in a polypeptide chain is called

as a residue or moiety. as a residue or moiety.

Primary Structure

Peptide bond (Cont.) Trans-configurationTrans-configuration Uncharged but polarUncharged but polar Partial double bondPartial double bond Lack of rotation around the bondLack of rotation around the bond

Primary Structure

Peptide bond (Cont.) Trans-configurationTrans-configuration

Primary Structure

Peptide bond (Cont.) Uncharged but polarUncharged but polar - C=O & - NH groups of the peptide bond neither

accept nor give proton over the pH range of 2 to 12

So charge is present only on N-terminal amino group and carboxyl group on C-terminal & any ionized group present in R.

Primary Structure

Peptide bond (Cont.) Partial double bondPartial double bond Because it is shorter in length then single Because it is shorter in length then single

bond.bond.

Primary Structure

Peptide bond (Cont.) Lack of rotation around the bond.Lack of rotation around the bond. This is a rigid bond prevents ant rotation This is a rigid bond prevents ant rotation

around carbonyl carbon and the nitrogen around carbonyl carbon and the nitrogen of the bond. of the bond.

Secondary Structure of Secondary Structure of ProteinsProteins

Alpha HelixAlpha Helix Beta sheetsBeta sheets Beta bends (reverse turns)Beta bends (reverse turns) Non-repetitive secondary structureNon-repetitive secondary structure Super-secondary structures (Motifs)Super-secondary structures (Motifs)


Alpha HelixAlpha Helix A spiral structureA spiral structure Consist of coiled polypeptide chain back Consist of coiled polypeptide chain back

bone core with the side chains extending bone core with the side chains extending outward from the central helix.outward from the central helix.

E.g. keratinE.g. keratin


Alpha HelixAlpha Helix Hydrogen bond Hydrogen bond Between carbonyl oxygen & amide Between carbonyl oxygen & amide

hydrogen's .hydrogen's . Function of Hydrogen bond.Function of Hydrogen bond. Individual Hydrogen bond is weak but Individual Hydrogen bond is weak but

collectively serve to stabilize the helix.collectively serve to stabilize the helix.


Alpha HelixAlpha Helix AA per turn 3.6 AA.AA per turn 3.6 AA. AA that disrupts the Alpha HelixAA that disrupts the Alpha Helix Proline (Imino gp)Proline (Imino gp) Glutamate, Aspartate, Histidine, Lysine, arginine Glutamate, Aspartate, Histidine, Lysine, arginine

(charged)(charged) Tryptophan (bulky side chain)Tryptophan (bulky side chain) Valine, Isoleucine (branch at beta carbon)Valine, Isoleucine (branch at beta carbon)


Beta sheetsBeta sheets Contain 2 or more peptide chains or Contain 2 or more peptide chains or

segments of polypeptide chains that are segments of polypeptide chains that are fully extended.fully extended.

There may be a single polypeptide chain There may be a single polypeptide chain which is folding on itself.which is folding on itself.

Arrangement of the polypeptide chains Arrangement of the polypeptide chains may be parallel of anti-parallel.may be parallel of anti-parallel.


Beta sheets (Cont.)Beta sheets (Cont.) All peptide bond components are involved All peptide bond components are involved

in the hydrogen bonding.in the hydrogen bonding. Hydrogen bonds are perpendicular to the Hydrogen bonds are perpendicular to the

polypeptide back bone core.polypeptide back bone core. Hydrogen bond may be inter-chain or intra Hydrogen bond may be inter-chain or intra

chain.chain.


Beta bends (reverse turns)Beta bends (reverse turns) Generally composed of 4 AAGenerally composed of 4 AA Mostly contain Proline & GlycineMostly contain Proline & Glycine Stabilized by the Hydrogen & ionic Stabilized by the Hydrogen & ionic

bonding.bonding. Connect the successive strands of anti Connect the successive strands of anti

parallel Beta sheetsparallel Beta sheets


Non-repetitive secondary structureNon-repetitive secondary structure Less regular structure usually in the shape Less regular structure usually in the shape

of a coil.of a coil.


Super-secondary structures (Motifs)Super-secondary structures (Motifs) Produced by packing side chains from Produced by packing side chains from

adjacent secondary elements close to adjacent secondary elements close to each other.each other.

MotifsMotifs

Proteins that binds to DNA contains one or Proteins that binds to DNA contains one or more of a limited number of motifs.more of a limited number of motifs.

The zinc motif is common, found in The zinc motif is common, found in number of proteins that functions as number of proteins that functions as transcription factor.transcription factor.

DomainsDomains

Fundamental functional & three dimensional Fundamental functional & three dimensional structural units of polypeptides.structural units of polypeptides.

Those polypeptide chains which contains more Those polypeptide chains which contains more then 200 AA in length generally consists of 2 or then 200 AA in length generally consists of 2 or more Domains.more Domains.

Folding of peptide chain within a Domain is Folding of peptide chain within a Domain is independent of folding in other Domains. independent of folding in other Domains.

Tertiary StructureTertiary Structure

The structure of a globular protein in the The structure of a globular protein in the aqueous environment is compact.aqueous environment is compact.

High density atoms in the core of the High density atoms in the core of the molecule.molecule.

Hydrophobic side chains are buried in the Hydrophobic side chains are buried in the interior.interior.

Hydrophilic groups are usually present on Hydrophilic groups are usually present on the exterior or surface.the exterior or surface.

Tertiary Structure Tertiary Structure

Stabilized by:Stabilized by: Hydrophobic interactionsHydrophobic interactions Hydrogen bondsHydrogen bonds Electrostatic interactionsElectrostatic interactions Disulfide bondsDisulfide bonds


Hydrophobic interactionsHydrophobic interactions If the protein molecules is present in the If the protein molecules is present in the

aqueous environment.aqueous environment. AA with the Hydrophobic side chains are AA with the Hydrophobic side chains are

buried in the interior.buried in the interior. AA with the Hydrophilic groups are usually AA with the Hydrophilic groups are usually

present on the exterior or surface.present on the exterior or surface.


Disulfide bondsDisulfide bonds A covalent linkage formed from the A covalent linkage formed from the

sulphydryl group (- SH) of each of the 2 sulphydryl group (- SH) of each of the 2 cysteine residues. cysteine residues.

Immunoglobulins contains many Disulfide Immunoglobulins contains many Disulfide bonds. bonds.


Hydrogen bond:Hydrogen bond: AA side chain having O2 or N-bound H2 AA side chain having O2 or N-bound H2

(alcohol group of serine & Threonine) can (alcohol group of serine & Threonine) can form H-bond with electron rich atoms (O2 form H-bond with electron rich atoms (O2 of a carboxyl group)of a carboxyl group)

Tertiary structureTertiary structure

Ionic interactions:Ionic interactions: Negatively charged groups, such as the Negatively charged groups, such as the

carboxyl group (-COO-) in the side chain carboxyl group (-COO-) in the side chain of aspartate or glutamate can interact with of aspartate or glutamate can interact with the + charged groups such as Amino the + charged groups such as Amino groups (-NHgroups (-NH33+) in the side chain of lysine.+) in the side chain of lysine.

Protein FoldingProtein Folding

Information needed for the folding is Information needed for the folding is located in primary structure of polypeptide.located in primary structure of polypeptide.

Folding begin along with the synthesis Folding begin along with the synthesis instead of waiting for synthesis of entire instead of waiting for synthesis of entire chain to be completed.chain to be completed.

Factors which contribute to the folding Factors which contribute to the folding include, include,

Protein Folding (Cont.)Protein Folding (Cont.)

Charge on the side chains of AA.Charge on the side chains of AA. Hydrophobic interactionsHydrophobic interactions Hydrogen bondsHydrogen bonds Electrostatic interactionsElectrostatic interactions Disulfide bondsDisulfide bonds Chaperones Chaperones

Protein Folding (Cont.)Protein Folding (Cont.)

Chaperones: Chaperones: Also known as Heat shock proteins.Also known as Heat shock proteins. Assist foldingAssist folding Protect Protect Some times keep protein unfolded until Some times keep protein unfolded until

synthesis is complete.synthesis is complete.

Quaternary Structure Quaternary Structure

Stabilized by:Stabilized by: Hydrophobic interactionsHydrophobic interactions Hydrogen bondsHydrogen bonds Electrostatic interactionsElectrostatic interactions

DenaturationDenaturation

Loss of secondary and tertiary structure.Loss of secondary and tertiary structure. This lead to loss of function.This lead to loss of function. Denaturant include, Denaturant include, Urea, extremes of pH, organic solvents.Urea, extremes of pH, organic solvents.

Denaturation (Cont.)Denaturation (Cont.)

2 types of Denaturation.2 types of Denaturation. Reversible Denaturation Reversible Denaturation Irreversible Denaturation Irreversible Denaturation Some proteins can refold upon removal of Some proteins can refold upon removal of

denaturant.denaturant. Other can’t refold upon the removal of Other can’t refold upon the removal of

denaturant.denaturant.

Documents

PROTEINS Dr. Nasim. Standard Amino Acids Building blocks of proteins More then 300 AA have been described Only 20 AA are found in mammalian tissue