BIOCHEM

Cards (172)

  • 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
    • Type of reaction catalyzed
    • Identity of the substrate
    • Suffix -ase identifies it as an enzyme
    • Suffix -in is still found in the names of some digestive enzymes
  • 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 reactions involving bond formation coupled with ATP hydrolysis)
  • Oxidoreductase
    Catalyzes an oxidation–reduction reaction where oxidation and reduction reactions 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 in a manner that does not involve hydrolysis or oxidation
  • Isomerase
    Catalyzes isomerization (rearrangement of atoms) reactions
  • Ligase
    Catalyzes the formation of a bond between two molecules involving ATP hydrolysis, as such reactions are energetically unfavorable
  • 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 favorable 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 increased concentration up to saturation)
    • Enzyme concentration (activity increases with increased 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 at least two binding sites (substrate and regulator)
    • Binding of regulator causes changes in 3D structure leading to changes in activity
  • Feedback control
    Activation or inhibition of first reaction in a sequence is controlled by a product of the sequence
  • Proteolytic enzymes and zymogens
    Proteolytic enzymes are generated in an inactive zymogen form and then converted to active form
  • Covalent modification of enzymes
    Involves adding or removing a group, most commonly phosphorylation/dephosphorylation catalyzed by kinases and phosphatases
  • Antibiotics
    Substances that kill bacteria or inhibit their growth by inhibiting 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 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 bacteria need to produce folic acid
    • Sulfanilamide competitively inhibits enzymes responsible for converting PABA to folic acid in bacteria
    • Folic acid deficiency retards bacterial growth and kills them
    • Sulfa drugs don't affect humans because we absorb folic acid from diet
  • Penicillins
    • Antibiotics with structures containing a four-membered Beta-lactam ring fused with a five-membered thiazolidine ring
    • Selectively inhibit transpeptidase by covalent modification of serine residue
    • Transpeptidase catalyzes formation of peptide cross links in bacterial cell walls
  • Ciprofloxacin (Cipro)

    • A broad-spectrum antibiotic effective against skin, bone, urinary, gastrointestinal, and respiratory infections
    • Bacteria are slow to acquire resistance to Cipro
    • Effective against anthrax
  • Medical uses of enzymes
    Diagnose certain diseases by detecting enzymes produced in damaged organs/tissues
  • General characteristics of vitamins
    • Organic compounds
    • Must be obtained from diet
    • Body can't synthesize in enough amounts
    • Essential for proper body functioning
    • Needed in micro and milligram quantities
    • 1 gram of vitamin B sufficient for 500,000 people
    • Balanced diet provides enough vitamins
    • Supplemental vitamins may be needed after illness
    • Many enzymes contain vitamins as part of their structures (conjugated enzymes)
  • Classes of vitamins
    • Water soluble
    • Fat soluble