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

  

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.