Week 6 Intro to enzymes

• What are enzymes?

  • They are catalysts that increase the rate of reaction without being used up
  • They are mostly globular proteins
  • however some RNA can catalyse reactions)
  • They are highly specific

  
• Rate enhancement by enzymes:

  • Shows how powerful enzymes are

  
• Lock and key model:

  A) substrate

  B) enzyme

  C) enzyme substrate complex

  D) active site

  
• Cofactors:

  • Small molecules that some enzymes require for activity
  • 2 types of cofactors
  • Coenzymes - organic molecules derived from vitamins
  • Metals
  • Prosthetic groups = tightly bound coenzymes
  • apoenzyme + cofactor = holoenzyme

  
• Reversible reactions and equilibria:

  X + Y → Z

  • irreversible reaction

  A + B ⇌ C + D

  S ⇌ P

  • reversible reaction

  A) concentration

  B) time

  
• Enzymes alter the reaction rate and not the reaction equilibrium

  A) with enzyme

  B) no enzyme

  
• Free energy change:

  A) negative

  B) positive

  
• Energy chnage during a chemical reaction:

  An energy barrier must be overcome in the conversion of A into B0

  A) activation energy

  
• The transition state:

  A) substrates

  B) transition state

  C) products

  
• Enzymes decrease the activation energy:

  • higher activation energy = slower reaction

  A) uncatalysed

  B) catalysed

  
• Stages in enzyme catalysis:

  • Enzyme binds the substrate (formation of ES complex)
  • Formation of a transition state
  • Product formation
  • Enzyme-product dissociation
• Enzymes accelerate reactions by facilitating the formation of the transition state:

  A) no enzyme

  B) substrate

  C) transition state

  
• Models of enzyme-substrate binding

  A) lock and key

  B) induced fit

  
• Active sites of enzymes

  • The active site is a three-dimensional cleft or crevice created by amino acids from different parts of the primary structure
  • The active site constitutes a small portion of the enzyme volume.
  • The interaction of the enzyme and substrate at the active site involves multiple weak interactions

  
• Rate (velocity) of a reaction (V):

  A) substrate

  B) product

  
• Rate equations:

  • V: rate of a chemical reaction
  • k: rate constant
  • rate equations must be determined experimentally

  
• Initial velocity

  • it is the rate of a reaction at the beginning

  A) product concentration

  B) time

  
• Relation between initial velocity and substrate conc:

  Experiment

  1. Mix enzyme + substrate
  2. Record rate of substrate disappearance/product formation as a function of time (the velocity of reaction)
  3. Plot initial velocity versus substrate concentration.
  4. Change substrate concentration and repeat

  
• Effects of substrate concentration

  A) product concentration

  B) time

  C) initial velocity

  D) substrate concentration

  
• Michaelis-Menten model:

  • Km (Michaelis constant) is equivalent to the substrate concentration at half maximum velocity . The enzyme is half saturated when [S] = Km

  
• Michaelis constant:

  A) enzyme

  B) substrate

  C) glucose

  D) fructose

  
• Turnover number:

  • kcat: turnover number of the enzyme
  • number of substrate molecules converted into product per second

  
• Enzyme inhibition:

  • major control mechanism in biologyical systems
  • inhibition by drugs
  • irreversible inhibition = inhibitor dissociates very slowly from enzyme because it is tightly bound to enzyme
  • reversible inhibition = inhibitor rapidly dissociates from enzyme
• Cell wall in Staphylococcus aureus:

  • cell wall is made up of a macromolecule called peptidoglycan

  Formation of cross-links in S. aureus peptidoglycan

  • Transpeptidase forms a covalent bond with its substrate (peptide)

  A) sugar

  B) glycine

  C) amino acids

  
• Penicillin forms a covalent bond with transpeptidase

  A) reactive bond

  B) penicillin

  
• Irreversible inhibition: Penicillin

  • Penicillin is the first antibiotic discovered
  • Penicillin inhibits growth of bacteria such as Staphylococcus aureus
  • Penicillin interferes with cell wall synthesis

  Penicillin is a suicide inhibitor

  • Penicillin binds to the transpeptidase because it resembles the substrate
  • As catalysis occurs, the enzyme modifies the substrate, converting it into an irreversible inhibitor
  • Transpeptidase participates in its own inhibition
• Types of reversible inhibition:

  • competitive inhibition
  • uncompetivitve inhibition
  • noncompetitive / mixed inhibition
• Competitive inhibition:

  • bind to active sit eof enzymes
  • can be relieved by increasing substrate concentration
  • example of methotrexate
  • A drug used to treat cancer
  • Inhibits a key enzyme of nucleotide synthesis (dihydrofolate reductase)
  • Structural analog of dihydrofolate, a substrate for dihydrofolate reductase
  • Binds to the enzyme 1,000 times as tightly as natural substrate

  
• Uncompetitive inhibition:

  • bind to a seperate site but only to enzyme substrate complexes

  
• Mixed inhibition:

  • bind at a separate site and may bind to enzymes or enzyme substrate complexes