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

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.

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.

• 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.

Mechanism of enzyme action:

• Substrate → Product

• Lowering down of activation energy.

• Do not alter the equilibrium.

• Enzymes are biocatalyst.

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.