BIOCHEM

Enzymes

• Biological catalysts that speed up biochemical reactions.
• Most are 3-dimensional globular proteins.
• Some RNA molecules also act as enzymes (Ribozymes).

Enzyme Structure

• Active site: Region that binds substrates, co-factors, and prosthetic groups.
  • Contains residues that help hold the substrate.
  • Has a specific shape due to the tertiary structure of the protein.
  • Divided into:
    • Binding site: Selects and binds the substrate.
    • Catalytic site: Performs the catalytic action of the enzyme.
• Co-factors: Non-protein molecules essential for some chemical reactions.
  • Cannot be performed by standard 20 amino acids.
  • Activate the protein.

Types of Cofactors

• Inorganic cofactors: Inorganic molecules needed for enzyme activity.
  • Example: Mg in Hexokinase.
• Organic cofactors: Organic molecules needed for enzyme activity.
  • Prosthetic groups: Tightly bound organic cofactors.
    • Example: Flavins, heme group, biotin.
  • Coenzymes: Loosely bound organic cofactors.
    • Example: NAD+

Holoenzymes/Holoproteins

• Complete enzymes, with the co-factor bonded.

Substrate

• Reactant in a biochemical reaction.
• Forms an enzyme-substrate complex when it binds to an enzyme.

NAD and NADH

• NADH: Reduced form (gained electrons)
• NAD: Oxidized form (lost electrons)

Enzyme Synthesis

• Synthesized by ribosomes attached to the endoplasmic reticulum.
• DNA carries information for enzyme synthesis.
• Some enzymes are intracellular (used within the cell itself).
• Some enzymes are extracellular (secreted for use outside the cell).
  • Example: Pancreatic digestive enzymes.

Enzyme Characteristics

• Speed up reactions.
• Do not alter the nature or properties of end products.
• Highly specific.
• Sensitive to changes.
• Have a turnover number, which represents the number of substrate transformed per minute by one enzyme.
  • Example: Catalase turnover number = 6 x 10^7 /min.

Enzyme Nomenclature

• Enzymes are classified by the International Enzyme Commission.
• Classified based on the reaction type.

Enzyme Action Mechanism

• Thermodynamic changes: Chemical reactions have energy barriers.
  • The difference between the transition state and substrate is the activation barrier.
• Active site processes: Enzymes facilitate reactions differently.
  • Covalent catalysis: Covalent linkages form between the enzyme and substrate. The enzyme is released unaltered after the reaction.
  • Acid-base catalysis: Histidine residues often participate as both a proton donor and acceptor.
  • Catalysis by proximity: Enzymes bring molecules close together so reactions can occur faster.
  • Catalysis by bond strain: Causes reorientation, and the bond between substrate is broken into product.

Enzyme Kinetics and Inhibition

• Enzyme kinetics: Studies the rate of enzyme-catalyzed reactions.
• Factors that affect enzyme reaction rates:
  • Temperature
  • pH
  • Substrate concentration
• Inhibition: Prevention of an enzyme process due to interactions with inhibitors.
  • Reversible: Inhibitor associates and dissociates from the binding site. Some subtypes include:
    • Competitive: Inhibitors compete with the substrate for the active site.
    • Uncompetitive: Inhibitors bind to another site on the enzyme.
    • Mixed: Inhibitors bind to either the enzyme or the enzyme–substrate complex
    • Non-competitive: Inhibitor has equal affinity for the enzyme and the enzyme–substrate complex.
  • Irreversible: Inhibitor forms a covalent bond with the enzyme, permanently inhibiting its activity.

Enzyme Activation

• Enzyme activation: Conversion of an inactive form of an enzyme to an active form to process metabolic activity.
  • Types:
    • Activation by cofactors: Often a non-protein (inorganic or organic) molecule.
    • Conversion of an enzyme precursor (inactive form of an enzyme): Zymogen is converted to an active enzyme through a proteolytic cleavage process, such as enteropeptidase acting on trypsinogen to produce trypsin.

Enzyme Specificity

• Enzymes are highly specific, interacting with one, or very few types of substrates.
  • Bond specificity: Enzyme acts on similar substrates (e.g., with a 1,4-glycosidic bond)
  • Group specificity: Enzyme is specific to the surrounding structure.
  • Substrate specificity: Enzyme acts on only one substrate.
  • Optical/stereo-specificity: Enzyme is specific for optical configuration(e.g., D-amino acid oxidase).
  • Dual specificity: Enzyme acts on one substrate via two reactions (e.g. isocitrate dehydrogenase).

Lipids

• Diverse group of chemicals, including fats and oily substances.
• Hydrophobic (water-repelling).
• Amphipathic : polar (water-loving) and nonpolar (water-repelling) regions
• Backbones include glycerol (C3H8O3).
• Classes include:
  • Simple lipids: Esters of fatty acids with alcohols.
    • Fats: Solid at room temperature; rich in saturated fatty acids.
    • Oils: Liquid at room temperature; rich in unsaturated fatty acids.
    • Waxes: Esters of long-chain fatty acids and long-chain alcohols.
  • Complex lipids: Lipids containing other components in addition to fatty acids and alcohols.
    • Phospholipids: Include phosphoric acid and nitrogenous bases and are major components of cell membranes.
    • Glycolipids: Have carbohydrates attached and are part of many cell membranes.
    • Lipoproteins: Conjugates of lipids and proteins that transport lipids in blood.
  • Derived lipids: Obtained by hydrolysis of other lipids
    • Fatty acids
    • Steroid
    • Cholesterol - common steroid building block.

Carbohydrates

• Polyhydroxyaldehydes or polyhydroxyketones.
  • Can be broken down (hydrolyzed) into simple sugars.
    • Monosaccharides: Simplest sugars that can't be hydrolyzed further.
      • Aldoses: Have an aldehyde group (e.g., glucose).
      • Ketoses: Have a ketone group (e.g., fructose).
      • Trioses: Simplest monosaccharides (e.g., glyceraldehyde).
      • Examples of monosaccharides: glucose, fructose, ribose.
    • Disaccharides: Two monosaccharides joined together (e.g., sucrose).
    • Oligosaccharides: Three to ten monosaccharides joined together.
    • Polysaccharides: Many monosaccharides joined together (e.g., starch, glycogen).

Nucleic Acids

• Biopolymers containing three types of monomer units:
  • Bases (derived from purines or pyrimidines)
  • Monosaccharides (pentose, typically deoxyribose in DNA)
  • Phosphate groups. Nucleotides are monomers of nucleic acids.