10 Flashcards
Where does enzyme substrate binding occur
Active site
How does the active site bind to substrate
Active sitre bind to substrates via several weak interactions
What determines the specify of the reaction
The active site
What do many weak interactions ensure
Specificity and reversablitly
Contridion for weak bonds to form
Weake bonds can only form if real ent atoms are precisely postitioned
It is ____ to break weak bonds
It is easier to break weak bonds
Molecular ______ between ___ and ____ is critical
Molecular complementarity between exhume and substrate is critical
Enzymes show
Geometric and stereospecififity
Two models for enzyme-substrate binding
-Locke and key
- induced fit
Provided the ____ of the ____ _____ is _____, the enzyme can ______ between ______ groups on the _______
Provided the shape of the active site is asymmetric, the enzyme can distinguish between identical groups on the substrate
Ezymes are _____ not. _____
Dynamic not static
Types on enzyme substrate bonds
- ionic bonds
- hydrogen bonds
- van der walls interations
- covalent bonds
Ionic bonds (salt bridges)
- uses charges side chains (Asp,Blu,Arg,Lys)
Hydrogen bonds
Side chain or backbone O and N atoms can often act as hydrogen bond acceptors and donors
(Only happen when two groups are in correct orientation)
(- connections between substrates and active site redidues within enzymes)
- need side chains for diversity
Van der walls interactions
Between any protein and substrate atoms in close proximity: weakest of all interations
Not much specificity
Weakest interactions
Van der walls
Example of realises weak interactions and covalent interations
- ionic bonds
- hydrogen bonds
- van der walls interactions
- covalent
Covalent bonds
- between active sites and amino acid side chains
- relatively rare - much stronger then other bonds
What happens when hexokinase binds a substate
Conformational change
3 wats active energy is lowered
- Groundstate destabilisation (trough up)
- Transition state stabilisation (trough down)
- Alternate reaction pathway with a different “(or lower energy) transition state
1 and 2 can be achieved the same way: by having an active sire that has shape/charge complementarity to the TS, not the substate
Catalytic mechanisms (common to all enzymes vs specific to reaction pathway)
- Preferential binding of the transition state
- Proximity and orientation effects
- Acid-base catalyst
- Metal ion catalysis
- Covalent catalysis
How prefectural binding of the transistor state happens
An enzyme bind the transition state more tightly then it binds the substate
Transition states are transient and cannot be isolated (they are very high energy) —> need to design and synthesise an analogue
An analogue is something the looks like the transition state but cannot be turned into a substrate
Enzymes catalyse thrermodyntmaclly favourable reactions
by lowering the activation enenery
Transition state shit - maybe go over this
transition state analogues as drugs - how?
Lipitor = powerful cholesterol-lowing drug
- it inhibits HMG-CoA reductase (within the biosynthetic pathway for chlolesterol)
- Liptor is a transition state analogue of the HMG-CoA reductase reaction pathway
- Lipitor looks more like the transition state so it binds to active site
If you want an inhibitor…
Use something that looks like the transition state
How transition state analogues are good drugs
- enzymes are often targets for drugs and other beneficial agents
- transition state analogues often make ideal enzyme inhibitors
What does analapril and aliskiren do?
- lower blood pressure
What do statins do?
Lower serum cholesterol
What are protease inhibitors?
AIDS drugs (transition state analogue of transition state hiv proteases)
What is a Juvenile hormone esterase
A pesticide target (
What is Tamiflu ?
An inhibitor of influenza neuraminidase (transition state
For two molecules to react they need to be
- close together (proximity)
- in the correct orientation
The reaction hexokinase catalyses and how it shows probity and orientation hexokinase is enabling through chemical reaction
- taking a phosphate off an atp and put onto glucose
- hexokinase has evolved An active site that binds glucose in its complementary way and also bind ATP adjacelntly with its phosphate group postitoned at its perfect place to be transferred onto the hydroxyl of the glucose
What does acid-base catalysis involve?
Proton H+ transfer (must have side chains that can exchange protons
- end=zyems with these residues in their active sites might have high or low activity depending on the pH of the solution and the environment at the active site
Which amino acid is particularly suitable to acid base reactions?
Histidine
Why is histidine so suitable for acid base reactions
- pKa (his) ~ 6.5 (close to physiological pH)
- depending on the environment of the active site, his can dontate or accept a proton
At least a third of known enzymes require ____ _____ for catalytic activity
Metal ions
Metal ions provide:
- substrate orientations -> due to their specific coordination geometry
- ability to act as a Lewis acid (electron acceptors) to polarise H2O molecules or other functional groups
- sites for electron transfer ( redox reactions)
Metal ions may be ______ at active enzyme sites
Cofactors
Hexokinase uses ___ as a cofactor
Mg2+
At the active site of hexokinase - diagram
What does Mg2+ do in the active site of hexokinase
Mg2+ ion balances negative charge of the transition state
What is covalent catalysis?
- involves the formation of a reactive, short-lived intermediate, which is covalently attached to the enzyme
- can have a nucleophillic side chain form a short lived intermediate which is covalent with the substrate
- b gets cleaved off
- water can then atack that bond and A is also then cleaved
The enzyme - substrate interaction relies on
multiple, weak interactions and (often) induced fit
Ezymes preferentially bind and ______ the _____ ______
Enzymes preferentially bind and stabilise the transition state
There are a variety of _____ _____, for providing alternate reaction routes compacted to the ________ ______
There are a variety of catalytic mechanisms,for providing alternate r reaction routes compared to the uncatalysed reaction
