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Chapter 3: Proteins

Proteins:

  • Proteins constitute most of the cell’s dry mass.

  • Cell’s building blocks and also execute the majority of cell’s functions.

  • Heteropolymer of amino acids.

  • After water, proteins are the major components of protoplasm.

  • Peptide bond is present.

  • Most abundant protein on earth: Rubisco

  • Most abundant protein in mammals: Collagen

  • Proteins embedded in the plasma membrane form channels and pumps that control the passage of small molecules into and out of the cell.

  • Proteins from a chemical point of view are very complex and functionally sophisticated molecules.

  • The location of each amino acid in the long string of amino acids that forms a protein determines its three-dimensional shape.

Shape and Structure of Proteins:

  • 20 different amino acids.

  • A protein molecule is a long un-branched chain of these amino acids.

  • Proteins are called polypeptides.

  • It consists of:

    • Peptide bond

    • Disulphide bridges

    • Hydrogen bond

    • Ionic bond

    • Hydrophobic interactions

structure of protein

Amino Acids:

  • Micro molecules/acid soluble pool.

  • Monomer of protein/building of protein.

  • Substitute of methane.

  • Amino acids consist of:

    • Amide group: basic group, positively charged.

    • R: variable group, decide name, nature, and properties of amino acid.

    • COOH: carboxylic acid, acidic group, acidic nature, negatively charged.

    • C: chiral carbon or alpha carbon.

Properties of Amino Acids:

  • Configuration of protein.

  • Amino acids are amphoteric in nature.

  • All amino acids are officially active, and they show optical isomerism-except glycine.

  • Zwitter ions: Dipolar ions

    • at low ph (acidic) = positive charge

    • at high ph (basic) = negative charge

Classification of L-alpha amino acid:

  • Acidic amino acid:

    • It contains an extra COOH group.

    • Aspartic acid, Glutamic acid.

  • Basic amino acid:

    • It contain extra NH2 group.

    • Histidine, Lysine, Arginine.

  • Neutral amino acid:

    • It contains one NH2 group and one COOH group.

    • Asparagine, serine, tyrosine, etc.

Classification of amino acids on the basis of functional group

  • Amino acid with aliphatic group: GAVIL

    • Glycine, Alanine, Valine, Isoleucine, Leucine

  • Amino acids containing hydroxyl (-OH) groups: ST

    • Serine, Threonine

  • Sulphur containing amino acids: CM

    • Cysteine, Methionine

  • Acidic amino group: AAGG

    • Aspartic acid, Asparagine, Glutamic acid, Glutamine

  • Basic: LAH

    • Leucine, Arginine, Histidine

  • Aromatic: PTT

    • Phenylalanine, Tryptophan, Tyrosine

  • Imino: Proline

  • Non-polar amino acids: They have no charge on the “R-group”.

  • Polar amino acids: Have charge on the “R-group”.

Classification of amino acids (on the basis of synthesis in the body)

  • Essential amino acid:

    • Not synthesized in our bodies.

    • Need to be taken in our diets.

  • Non-essential amino acids:

    • Synthesized in their body cannot be taken in diet.

  • Semi-essential amino acids:

    • Produced at a very slow rate can be synthesized by the adult body but not in growing children.

Proteins classified on the basis of chemical nature and stability:

  • Simple protein:

    • Made up of amino acids.

    • Protein part:

      • Globular: spherical/oval shaped.

      • Fibrous: Collagen, Kinetin, Actin

  • Conjugate protein:

    • Made up of protein + nonprotein part.

  • Derived protein:

    • Primary: Due to denaturation of protein.

    • Secondary: formed due to digestion.

  • Protein are also divided as:

    • Complete protein: All 20 essential amino acids present.

    • Incomplete protein: One/two essential amino acids lacking.

  • Monomeric protein: Made up of one polypeptide chain.

  • Oligomeric protein: Made up of two/more polypeptide.

Structure of protein

  • Primary structure:

    • It is a linear chain of amino acids linked by peptide bonds.

    • It is a newly formed protein on the ribosome.

    • This structure of a protein is highly unstable/not functional but decides the fate of protein.

  • Secondary structure:

    • It comprises of alpha helix and beta plated sheet.

    • The folding of linear polypeptide chains in a specific coiled structure is called secondary structure.

    • A new bond is formed: Hydrogen bond.

    • 2 bonds: hydrogen + peptide

    • Alpha helix:

      • a most common type of secondary structure and rigid rearrangement of polypeptide chain.

      • stable configuration.

      • right-handed helix.

      • bonds: intramolecular h-bonding, peptide bond.

    • Beta-plated sheet:

      • made up of 2 or more polypeptide chains are held together by intermolecular-H bonding.

      • zig-zag shape.

      • protein of secondary structure insoluble in water and fibrous in nature.

  • Tertiary structure:

    • protein of tertiary structure are highly folded and globular in nature.

    • soluble in water.

    • more folded than secondary.

    • bonds:

      • peptide bond

      • H-bond

      • disulfide bond

      • hydrophobic interactions

      • ionic bond

    • most of the proteins and enzymes show tertiary structure in protoplasm.

  • Quaternary structure:

    • it is made up of two or more than two polypeptide chain.

    • oligomeric protein in which R-group close to each other.

    • all types of bonds like intra, inter-H bonding, ionic bonding, covalent bond, hydrophobic interactions etc, are formed.

    • these protein play important/significant role in the regulation of metabolism and cellular function.

structures of protein

ENZYMES

  • Enzymes enhance the rate of biological chemical reaction by lowering down activation energy.

  • It is a biological catalyst.

  • Enzymes are biological middlemen.

  • All enzymes are proteinaceous except ribozyme and ribonuclease.

  • Enzymes show tertiary and quarternary structure and very specific for biological activity.

  • Maximum enzymes are found in mitochondria.

  • Small enzyme: Peroxidase.

  • Largest enzyme: Catalase

Characteristics features of enzymes:

  • Enzymes do not disturb reaction equilibrium.

  • Turn over (The number of substrate molecules transformed per min/per sec by one enzyme molecules)

  • Turn over no. depends on:

    • number of active sites of an enzyme.

    • fastest reaction

    • separation of product.

  • Active site catalytic is directly proportional to turn over number.

  • Maximum turn-over number: Carbonic anhydrase.

  • Minimum turn-over: lysozyme

  • Reversibility in nature:

    • Substrate + Enzyme → ES complex

  • Very specific in nature:

    • temperature specific:

      • high temperature: denaturation

      • low temperature: inactivation

    • ph specific

  • Molecular weight is high.

  • Amphoteric in nature.

Nomenclature and Classification of Enzymes

  • Nomenclature: suffix= ase

  • Source of extraction: from where it is extracted.

  • 6 classes of enzymes:

    • OTHLiL

    • Oxidoreductase:

      • enzymes involved in oxidation-reduction reaction.

      • alcohol dehydrogenase, cytochrome oxidase.

    • Transferase:

      • Enzyme that catalyze reactions the transfer of functional group.

      • e.g.: hexokinase, trans-aminase.

    • Hydrolase:

      • Enzyme catalyzing hydrolysis of ester, ether, peptides etc.

      • These enzyme breaks large molecules into smaller molecules by the introduction/presence of H2O molecules.

    • Lyases:

      • They break specific covalent bonds and remove a group without hydrolysis, oxidation etc.

      • e.g. Aldolase, fumarase.

    • Isomerase:

      • Rearrangement of molecular structure to form isomers.

    • Ligases:

      • Enzyme catalysing the synthetic reaction where two molecules are joined together.

Types of Enzymes:

  • Simple enzyme: consist of only proteins and catalyze their substrate specific reactions.

  • Conjugate enzyme/Holo enzyme: Made up of protein and non-protein parts.

    • Protein part: Apoenzyme

    • Non-protein part: Co-factor

      • Organic:

        • Coenzyme: A coenzyme is a loosely bound/organic co-factor. It can be easily removed.

        • Prosthetic group: A prosthetic group is tightly bound organic co-factor.

      • Inorganic: They form coordination bond with side-chain at the active site and the same time for one/more coordination bond with substrate.

Mode of enzyme action

Mostly enzymes are protein in nature.

The hypothesis regarding the mode of enzyme action

  • Lock and Key Hypothesis:

    • According to this theory:

      • Enzymes are rigid and pre-shaped.

      • Substrate fit to the active site just as a key fit into a proper lock.

lock and key hypothesis

  • Induced fit hypothesis/ theory:

    • Proposed by Kosh land.The monomer

    • Most accepted hypothesis on the basis of enzyme action.

    • Enzymes are not rigid and pre-shaped.

induced fit hypothesis

Mechanism of enzyme action:

  • Substrate → Product

  • Lowering down of activation energy.

  • Do not alter the equilibrium.

  • Enzymes are biocatalyst.

mechanism of enzyme activity

Factors affecting enzyme action:

  • Temperature:

    • at high temperature: denaturation

    • at low temperature: inactivation

    • optimum temperature: 25-40 degrees Celsius for enzymatic activity.

  • pH:

    • optimum pH = enzyme activity very high.

    • enzymes:

      • endoenzyme (inside cell)

      • exoenzyme (enzymes are synthesized inside in the cell but secreted from the cell to work externally).

  • Substrate concentration:

    • Enzyme is larger in size and bears several active sites with the increase in substrate concentration the velocity of the reaction rises in first and the reaction reaches a maximum velocity. (Vmax)

    • The velocity is not exceeded by any further rise in the concentration of substrate.

    • Michalis Menten Constant (Km):

      • It is a mathematical derivation/constant which indicate concentration of substrate at which reaction velocity reaches half of Vmax.

      • Km indicate affinity of the enzyme for its substrate.

      • A high Km indicate low affinity of enzyme and low Km indicate high affinity.

      • Km is inversely proportional to turn over number.

      • Allosteric enzymes do not obey Km.

Inhibitors:

  • It is chemical molecules inhibit enzyme activity.

  • Inhibitors are of two types:

    • Competitive inhibitors:

      • Inhibitors are structure similar to substrate.

      • They favor lock and key hypothesis.

      • Reversible in nature.

      • Km increase but Vmax remain constant.

  • Non-competitive inhibitors:

    • Some inhibitors do not compete for active site of enzyme but destroy the structure of enzyme, the physical structure of enzyme is altered as a result and do not form enzyme-substrate complex.

    • They favor induced-fit theory.

    • Irreversible in nature.

    • Km remain constant but Vmax change.

graph showing both competitive and non-competitive inhibitors

AK

Chapter 3: Proteins

Proteins:

  • Proteins constitute most of the cell’s dry mass.

  • Cell’s building blocks and also execute the majority of cell’s functions.

  • Heteropolymer of amino acids.

  • After water, proteins are the major components of protoplasm.

  • Peptide bond is present.

  • Most abundant protein on earth: Rubisco

  • Most abundant protein in mammals: Collagen

  • Proteins embedded in the plasma membrane form channels and pumps that control the passage of small molecules into and out of the cell.

  • Proteins from a chemical point of view are very complex and functionally sophisticated molecules.

  • The location of each amino acid in the long string of amino acids that forms a protein determines its three-dimensional shape.

Shape and Structure of Proteins:

  • 20 different amino acids.

  • A protein molecule is a long un-branched chain of these amino acids.

  • Proteins are called polypeptides.

  • It consists of:

    • Peptide bond

    • Disulphide bridges

    • Hydrogen bond

    • Ionic bond

    • Hydrophobic interactions

structure of protein

Amino Acids:

  • Micro molecules/acid soluble pool.

  • Monomer of protein/building of protein.

  • Substitute of methane.

  • Amino acids consist of:

    • Amide group: basic group, positively charged.

    • R: variable group, decide name, nature, and properties of amino acid.

    • COOH: carboxylic acid, acidic group, acidic nature, negatively charged.

    • C: chiral carbon or alpha carbon.

Properties of Amino Acids:

  • Configuration of protein.

  • Amino acids are amphoteric in nature.

  • All amino acids are officially active, and they show optical isomerism-except glycine.

  • Zwitter ions: Dipolar ions

    • at low ph (acidic) = positive charge

    • at high ph (basic) = negative charge

Classification of L-alpha amino acid:

  • Acidic amino acid:

    • It contains an extra COOH group.

    • Aspartic acid, Glutamic acid.

  • Basic amino acid:

    • It contain extra NH2 group.

    • Histidine, Lysine, Arginine.

  • Neutral amino acid:

    • It contains one NH2 group and one COOH group.

    • Asparagine, serine, tyrosine, etc.

Classification of amino acids on the basis of functional group

  • Amino acid with aliphatic group: GAVIL

    • Glycine, Alanine, Valine, Isoleucine, Leucine

  • Amino acids containing hydroxyl (-OH) groups: ST

    • Serine, Threonine

  • Sulphur containing amino acids: CM

    • Cysteine, Methionine

  • Acidic amino group: AAGG

    • Aspartic acid, Asparagine, Glutamic acid, Glutamine

  • Basic: LAH

    • Leucine, Arginine, Histidine

  • Aromatic: PTT

    • Phenylalanine, Tryptophan, Tyrosine

  • Imino: Proline

  • Non-polar amino acids: They have no charge on the “R-group”.

  • Polar amino acids: Have charge on the “R-group”.

Classification of amino acids (on the basis of synthesis in the body)

  • Essential amino acid:

    • Not synthesized in our bodies.

    • Need to be taken in our diets.

  • Non-essential amino acids:

    • Synthesized in their body cannot be taken in diet.

  • Semi-essential amino acids:

    • Produced at a very slow rate can be synthesized by the adult body but not in growing children.

Proteins classified on the basis of chemical nature and stability:

  • Simple protein:

    • Made up of amino acids.

    • Protein part:

      • Globular: spherical/oval shaped.

      • Fibrous: Collagen, Kinetin, Actin

  • Conjugate protein:

    • Made up of protein + nonprotein part.

  • Derived protein:

    • Primary: Due to denaturation of protein.

    • Secondary: formed due to digestion.

  • Protein are also divided as:

    • Complete protein: All 20 essential amino acids present.

    • Incomplete protein: One/two essential amino acids lacking.

  • Monomeric protein: Made up of one polypeptide chain.

  • Oligomeric protein: Made up of two/more polypeptide.

Structure of protein

  • Primary structure:

    • It is a linear chain of amino acids linked by peptide bonds.

    • It is a newly formed protein on the ribosome.

    • This structure of a protein is highly unstable/not functional but decides the fate of protein.

  • Secondary structure:

    • It comprises of alpha helix and beta plated sheet.

    • The folding of linear polypeptide chains in a specific coiled structure is called secondary structure.

    • A new bond is formed: Hydrogen bond.

    • 2 bonds: hydrogen + peptide

    • Alpha helix:

      • a most common type of secondary structure and rigid rearrangement of polypeptide chain.

      • stable configuration.

      • right-handed helix.

      • bonds: intramolecular h-bonding, peptide bond.

    • Beta-plated sheet:

      • made up of 2 or more polypeptide chains are held together by intermolecular-H bonding.

      • zig-zag shape.

      • protein of secondary structure insoluble in water and fibrous in nature.

  • Tertiary structure:

    • protein of tertiary structure are highly folded and globular in nature.

    • soluble in water.

    • more folded than secondary.

    • bonds:

      • peptide bond

      • H-bond

      • disulfide bond

      • hydrophobic interactions

      • ionic bond

    • most of the proteins and enzymes show tertiary structure in protoplasm.

  • Quaternary structure:

    • it is made up of two or more than two polypeptide chain.

    • oligomeric protein in which R-group close to each other.

    • all types of bonds like intra, inter-H bonding, ionic bonding, covalent bond, hydrophobic interactions etc, are formed.

    • these protein play important/significant role in the regulation of metabolism and cellular function.

structures of protein

ENZYMES

  • Enzymes enhance the rate of biological chemical reaction by lowering down activation energy.

  • It is a biological catalyst.

  • Enzymes are biological middlemen.

  • All enzymes are proteinaceous except ribozyme and ribonuclease.

  • Enzymes show tertiary and quarternary structure and very specific for biological activity.

  • Maximum enzymes are found in mitochondria.

  • Small enzyme: Peroxidase.

  • Largest enzyme: Catalase

Characteristics features of enzymes:

  • Enzymes do not disturb reaction equilibrium.

  • Turn over (The number of substrate molecules transformed per min/per sec by one enzyme molecules)

  • Turn over no. depends on:

    • number of active sites of an enzyme.

    • fastest reaction

    • separation of product.

  • Active site catalytic is directly proportional to turn over number.

  • Maximum turn-over number: Carbonic anhydrase.

  • Minimum turn-over: lysozyme

  • Reversibility in nature:

    • Substrate + Enzyme → ES complex

  • Very specific in nature:

    • temperature specific:

      • high temperature: denaturation

      • low temperature: inactivation

    • ph specific

  • Molecular weight is high.

  • Amphoteric in nature.

Nomenclature and Classification of Enzymes

  • Nomenclature: suffix= ase

  • Source of extraction: from where it is extracted.

  • 6 classes of enzymes:

    • OTHLiL

    • Oxidoreductase:

      • enzymes involved in oxidation-reduction reaction.

      • alcohol dehydrogenase, cytochrome oxidase.

    • Transferase:

      • Enzyme that catalyze reactions the transfer of functional group.

      • e.g.: hexokinase, trans-aminase.

    • Hydrolase:

      • Enzyme catalyzing hydrolysis of ester, ether, peptides etc.

      • These enzyme breaks large molecules into smaller molecules by the introduction/presence of H2O molecules.

    • Lyases:

      • They break specific covalent bonds and remove a group without hydrolysis, oxidation etc.

      • e.g. Aldolase, fumarase.

    • Isomerase:

      • Rearrangement of molecular structure to form isomers.

    • Ligases:

      • Enzyme catalysing the synthetic reaction where two molecules are joined together.

Types of Enzymes:

  • Simple enzyme: consist of only proteins and catalyze their substrate specific reactions.

  • Conjugate enzyme/Holo enzyme: Made up of protein and non-protein parts.

    • Protein part: Apoenzyme

    • Non-protein part: Co-factor

      • Organic:

        • Coenzyme: A coenzyme is a loosely bound/organic co-factor. It can be easily removed.

        • Prosthetic group: A prosthetic group is tightly bound organic co-factor.

      • Inorganic: They form coordination bond with side-chain at the active site and the same time for one/more coordination bond with substrate.

Mode of enzyme action

Mostly enzymes are protein in nature.

The hypothesis regarding the mode of enzyme action

  • Lock and Key Hypothesis:

    • According to this theory:

      • Enzymes are rigid and pre-shaped.

      • Substrate fit to the active site just as a key fit into a proper lock.

lock and key hypothesis

  • Induced fit hypothesis/ theory:

    • Proposed by Kosh land.The monomer

    • Most accepted hypothesis on the basis of enzyme action.

    • Enzymes are not rigid and pre-shaped.

induced fit hypothesis

Mechanism of enzyme action:

  • Substrate → Product

  • Lowering down of activation energy.

  • Do not alter the equilibrium.

  • Enzymes are biocatalyst.

mechanism of enzyme activity

Factors affecting enzyme action:

  • Temperature:

    • at high temperature: denaturation

    • at low temperature: inactivation

    • optimum temperature: 25-40 degrees Celsius for enzymatic activity.

  • pH:

    • optimum pH = enzyme activity very high.

    • enzymes:

      • endoenzyme (inside cell)

      • exoenzyme (enzymes are synthesized inside in the cell but secreted from the cell to work externally).

  • Substrate concentration:

    • Enzyme is larger in size and bears several active sites with the increase in substrate concentration the velocity of the reaction rises in first and the reaction reaches a maximum velocity. (Vmax)

    • The velocity is not exceeded by any further rise in the concentration of substrate.

    • Michalis Menten Constant (Km):

      • It is a mathematical derivation/constant which indicate concentration of substrate at which reaction velocity reaches half of Vmax.

      • Km indicate affinity of the enzyme for its substrate.

      • A high Km indicate low affinity of enzyme and low Km indicate high affinity.

      • Km is inversely proportional to turn over number.

      • Allosteric enzymes do not obey Km.

Inhibitors:

  • It is chemical molecules inhibit enzyme activity.

  • Inhibitors are of two types:

    • Competitive inhibitors:

      • Inhibitors are structure similar to substrate.

      • They favor lock and key hypothesis.

      • Reversible in nature.

      • Km increase but Vmax remain constant.

  • Non-competitive inhibitors:

    • Some inhibitors do not compete for active site of enzyme but destroy the structure of enzyme, the physical structure of enzyme is altered as a result and do not form enzyme-substrate complex.

    • They favor induced-fit theory.

    • Irreversible in nature.

    • Km remain constant but Vmax change.

graph showing both competitive and non-competitive inhibitors

robot