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Flashcards in Enzymes Deck (38)
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1

method of action of enzymes

  • Enzymes can couple a spontaneous reaction to a nonspontaneous one, to make the overall ΔG 
  • Reactions pass through high energy transition states.
  • Activation energy is required to reach the transition state.
  • Enzymes catalyse thermodynamically favourable reactions by lowering the activation energy
  • The overall ΔG for the reaction is not changed.

2

what are enzymes made of

usually proteins but occasionally RNA

3

6 enzyme classes

  1. oxidoreductase - used for redox
  2. transferase - transfer of functional group
  3. isomerases - transfer of atoms/groups withina molecule to form isomer
  4. lyases - non-hydrolytic breaking or making of bonds
  5. ligases - join two molecules together
  6. hydrolase - hydrolysis reactions

4

cofactors

non-protein factors which help catalyse reactions. Can be metal ions or coenzymes

5

metal ions as cofactors

  • Are Lewis acids (i.e. election acceptors), so they can participate in acid-base catalysis
  • Form coordination compounds with precise geometries (good for positioning reactants exactly where they need to be).
  • e.g. Mg2+ used for DNA polymerase

6

coenzymes

  • Small organic molecules.
  • Co-substrates - required for enzyme-substrate complex interaction, formation or stabilisation
  • Carriers (of electrons, atoms or functional groups)
  • Often derived from vitamins

7

features of active site

  • has amino acid side chains pointing into it
  • binds substrate via several initial weak interactions
  • determines specificity
  • initial weak bonds are remodelled to form transition state

8

types of ES bonds

 

  • ionic bonds - charged side chains
  • hydrogen bonds - O and N atoms in side chains or backbones
  • VDW's interactions - between any protein and substrate in close proximity, weakest
  • covalent bonds - rare, v strong

9

why are weak bonds advantageous

  • easy to break when complex breaks apart - reversibility
  • Weak bonds can only form if the relevant atoms are precisely positioned - specificity

 

10

what does stereospecificity mean?

enzymes can recognise between different enantiomers (chiral compounds)

11

lock and key model

Substrate and active site have exactly complementary shapes

12

induced fit model

  • Active site conformation changes slightly when substrate tries to bind
  • Shows that enzymes are dynamic, not static

13

3 ways ΔGe‡ is lowered

 

  1. Ground state destabilisation - free energy increases
  2. Transition state stabilisation - free energy decreases
  3. Alternate reaction pathway with a different (lower energy) transition state

(1) and (2) can be achieved the same way: by having an active site that has shape/charge complementarity to the TS, not the substrate

14

should an enzyme bind to substrate or transition state more tightly?

transition state however this is difficult because it is transient and cannot be isolated

15

5 catalytic mechanisms

  1. preferential binding of transition state
  2. proximity and orientation effects - need to be close together and right orientation to react
  3. acid base catalysis - His is particularly suitable because has pKa 6.5, close to body pH so can donate or accept a proton depending on environment of active site
  4. metal ion catalysis - provide substrate orientation, ability to act as Lewis acids, sites for electron transfer
  5. covalent catalysis - formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme

16

progress curve

  • measures the appearance of product (or disappearance of substrate) with time

  • Important to measure initial reaction velocity (rate) i.e. at time zero

  • passes through origin

17

factors affecting reaction rate

  • temperature - increases until optimum

  • pH - optimum

  • amount of enzyme is increased, the rate of reaction increases, provided substrate is in excess

  • As amount of substrate increases, rate of reaction increases linearly until all active sites are occupied, at which point rate stops increasing

18

Vmax

  • maximum velocity possible when [S] = infinity

  • on V vs [S] curve, this is horizontal asymptote

  • on Lineweaver-Burk plot, this is 1/y-int

19

what is Km

  • Michaelis constant
  • substrate conc at which V = Vmax/2

  • on Lineweaver-Burk plot, Km = -1/x-int

20

significance of Km

  • Substrate conc needed to reach half Vmax
  • Low KM = high affinity between E and S
  • High KM = low affinity
  • In the cell, for a particular enzyme-substrate interaction, [S] is often below the Km, allowing for rate control

21

kcat

  • number of substrate molecules converted to product, per enzyme, per unit of time, when E is saturated with substrate

  • If Michaelis-Menten model fits then Vmax = kcat[Etotal]

  • high kcat is good

22

michaelis-menten equation and assumptions

assumptions:

  • Product is not converted back to substrate.
  •  the rate of ES formation equals the rate of its breakdown hence no change in [ES]
  • Measuring initial rate means [S] does not change significantly (and [S] is greater than [E])

23

kcat/Km

overall measure of enzyme efficiency

24

irreversible inhibitor

  • Binds covalently to enzyme, permanently inactivating it
  • Inhibitor reacts with a specific amino acid side chain, usually in the active site, and forms a covalent bond
  • e.g. natural toxins

25

reversible inhibitor

  • not covalently bound to enzyme

  • can be competitive or non-competitive

26

competitive inhibition

  • Depends on relative concentrations of substrate and inhibitor
  • Competes directly with substrate for active site
  • No change in Vmax - Infinite [S] outcompetes the inhibitor
  • Increases KM - More substrate is needed to get to V = Vmax / 2

27

non-competitive inhibitor

  • Inhibitor binds does not bind to active site
  • Enzyme can bind substrate, or inhibitor, or both
  • can be pure non-CI or mixed non-CI

28

pure non-CI inhibitor

  • Binding of Inhibitor has no effect on the binding of S; i.e. the substrate binds to E and EI with the same affinity
  • Binding Inhibitor changes the structure of the active site such that S still binds, but transition state stabilisation is no longer optimal.
  • Vmax decreases; KM stays the same

29

mixed non-CI inhibitor

  • More commonly, binding of the inhibitor does affect binding of the substrate 
  • Vmax decreases; KM increases

30

methods of enzyme regulation

  1. Turn gene expression on or off
  2. Degrade enzyme
  3. Covalent modification e.g. phosphorylation
  4. Proteolytic cleavage
  5. Allosteric effects in multisubunit enzymes