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.