BIOCHEM

• Enzymes


  Catalysts that are not consumed in the reactions
• Enzymes


  • They are proteins that act as a catalyst for biochemical reactions
  • The human body has 1000s of enzymes
  • They are the most effective catalysts known
  • Most enzymes are globular proteins
  • A few enzymes are ribonucleic acids (RNA)
• Enzyme activity


  Dramatically affected by alterations in pH, temperature, and other protein denaturants
• Simple enzyme


  Composed only of protein (amino acid chains)
• Conjugated enzyme


  • Has a nonprotein part in addition to a protein part
  • Apoenzyme: Protein part of a conjugated enzyme
  • Cofactor: Nonprotein part of a conjugated enzyme
  • Holoenzyme: Biochemically active conjugated enzyme (apoenzyme + cofactor)
• Cofactors


  • Important for the chemically reactive enzymes
  • Small organic molecules or inorganic ions
  • Organic molecule cofactors are also called co-enzymes or co-substrates and are derived from dietary vitamins
  • Inorganic ion cofactors are derived from dietary minerals
• Enzyme nomenclature


  • Most commonly named with reference to their function, the type of reaction catalyzed, and the identity of the substrate
  • Suffix -ase identifies it as an enzyme
  • Prefix indicates the type of reaction catalyzed
  • Substrate identity is often used in addition to the type of reaction
• Six major classes of enzymes

  • Oxidoreductases (catalyze oxidation-reduction reactions)
  • Transferases (catalyze functional group transfer reactions)
  • Hydrolases (catalyze hydrolysis reactions)
  • Lyases (catalyze reactions involving addition or removal of groups to form double bonds)
  • Isomerases (catalyze isomerisation reactions)
  • Ligases (catalyze bond formation reactions coupled with ATP hydrolysis)
• Oxidoreductase


  Catalyzes an oxidation–reduction reaction where oxidation and reduction are always linked, and requires a coenzyme that is either oxidized or reduced as the substrate
• Transferase


  Catalyzes the transfer of a functional group from one molecule to another, with two major subtypes: transaminases (transfer amino groups) and kinases (transfer phosphate groups)
• Hydrolase


  Catalyzes a hydrolysis reaction involving the addition of a water molecule to a bond to cause bond breakage, central to the process of digestion
• Lyase


  Catalyzes the addition of a group to a double bond or the removal of a group to form a double bond, without involving hydrolysis or oxidation

  
• Isomerase


  Catalyzes isomerization (rearrangement of atoms) reactions
• Ligase


  Catalyzes the formation of a bond between two molecules, requiring the input of energy from ATP hydrolysis
• Enzyme active site


  Relatively small part of an enzyme's structure that is actually involved in catalysis, where the substrate binds
• Enzyme-substrate complex


  Intermediate reaction species formed when substrate binds with the active site, with orientation and proximity favourable for fast reaction
• Lock-and-key model


  Enzyme has a pre-determined shape for the active site, only a specific substrate can bind
• Induced fit model


  Substrate contact with enzyme will change the shape of the active site to accommodate the substrate
• Forces determining substrate binding

  Hydrogen bonding, hydrophobic interactions, electrostatic interactions
• Types of enzyme specificity

  • Absolute specificity (one substrate)
  • Stereochemical specificity (distinguish stereoisomers)
  • Group specificity (structurally similar compounds with same functional groups)
  • Linkage specificity (particular type of bond)
• Factors affecting enzyme activity

  • Temperature (higher temperature increases activity up to an optimum, then decreases)
  • pH (most enzymes have optimal activity in pH range 7.0-7.5, except digestive enzymes)
  • Substrate concentration (activity increases with concentration up to saturation)
  • Enzyme concentration (activity increases with concentration)
• Enzyme inhibition


  • Competitive inhibitors compete with substrate for active site
  • Noncompetitive inhibitors bind to enzyme at a location other than active site
  • Reversible inhibition can be overcome by increasing substrate concentration, irreversible inhibition permanently inactivates the enzyme
• Regulation of enzyme activity

  • Proteolytic enzymes and zymogens (inactive precursors)
  • Covalent modification (e.g. phosphorylation/dephosphorylation)
  • Feedback control by allosteric regulation
• Allosteric enzymes


  • Have quaternary structure with distinct substrate and regulator binding sites
  • Binding of regulators causes changes in 3D structure and enzyme activity (activators or inhibitors)
• Antibiotics


  Inhibit specific enzymes essential to bacterial life processes
• Covalent modification


  A process in which enzyme activity is altered by covalently modifying the structure of the enzyme
• Covalent modification of enzymes

  1. Involves adding or removing a group from an enzyme

  2. Most common: addition and removal of phosphate group

  3. Phosphate group often derived from ATP

  4. Addition of phosphate (phosphorylation) catalyzed by kinase enzyme

  5. Removal of phosphate (dephosphorylation) catalyzed by phosphatase enzyme

  6. Phosphate group added to/removed from R group of serine, tyrosine, or threonine amino acid residue
• Antibiotic


  A substance that kills bacteria or inhibits their growth
• Antibiotics


  • Usually inhibit specific enzymes essential to life processes of bacteria
• Families of antibiotics


  • Sulfa drugs
  • Penicillins
• Sulfa drugs


  Derivatives of sulfanilamide that exhibit antibiotic activities
• Sulfanilamide


  • Structurally similar to PABA (p-aminobenzoic acid), a compound needed by bacteria to produce folic acid
  • Sulfanilamide competitively inhibits enzymes responsible for converting PABA to folic acid
  • Folic acid deficiency retards bacterial growth and kills them
  • Sulfa drugs don't affect humans because we absorb folic acid from diet
• Transcription occurs in the nucleus, while translation takes place on ribosomes.
• Enzyme inhibitors can affect the rate of enzyme-catalyzed reactions by binding to the enzyme.
• The three-dimensional structure of proteins is determined by the primary, secondary, tertiary, and quaternary structures.
• The Michaelis-Menten equation is a commonly used model to describe enzyme kinetics.
• Enzyme kinetics studies the rates at which enzymes catalyze chemical reactions.
• Sucrose is a disaccharide made up of one molecule of alpha-D-glucose and one molecule of beta-D-fructose.
• Protein synthesis involves transcription (DNA to mRNA) and translation (mRNA to protein).
• Competitive inhibition involves an inhibitor molecule competing with substrate for active site binding.