Proteins - Lecture Nine Flashcards
Why are enzymes essential for life?
∆G < 0
Energy released, products dominate
∆G > 0
Energy required, substrates dominate
∆G = 0
At equilibrium, substrates and products at equal concentration
∆H
Enthalpy
∆S
Entropy
To favour forward reaction (∆G < 0)
Either enthalpy must decrease (∆H < 0) or entropy must increase (∆S > 0)
Cellular integrity
Decrease in entropy in the cell, so energy from elsewhere is required. Enzymes control where and when energy is released to maintain the cell.
Activation energy (∆G˚‡)
Enquired to reach the transition state, this determines rate
Free energy (∆G˚)
Sets ratio [P]/[S] at equilibrium
Aldolase
Very positive ∆G˚, but big rate enhancement
Adenylate kinase
∆G˚ near zero, big rate enhancement
Cleavage of DNA phosphodiester backbone
Negative ∆G˚
Classes of enzymes
Oxidoreductases Transferases Hydrolases Lyases Isomerases Ligases
Oxidoreductases
Redox
Transferases
Transfer of a functional group
Hydrolases
Hydrolysis reactions (using water), this includes many things that break down peptide bonds (proteases), or burn ATP
Lyases
Non-hydrolytic breaking or making of bonds (not using water)
Isomerases
Transfer to atoms/groups within a molecule to yield an isomeric form
Ligases
Join two molecules together
Enzyme-substrate binding
Occurs at a specific site on the enzyme, the active site
The active site
Has amino acid side chains projecting into it
Binds the substrate via several weak interactions
Determines the specificity of the reaction
Types of enzyme-substrate bonds
Ionic bonds, hydrogen bonds, van der Waals interactions and covalent bonds
Ionic bonds (aka salt bonds)
Make use of charged side chains
Hydrogen bonds
Side chain or backbone O and N atoms can often act as hydrogen bond donors and acceptors
Van der Waals interactions
Between any protein and substrate atoms in close proximity, weakest of the interactions, but abundant
Covalent bonds
Relatively rare but much stronger than the other bonds
Lock and Key model
When the active site is already perfectly shaped for the substrate to fit, they are already complementary
Induced Fit model
When the active site isn’t completely complementary but they can make small adjustments as the substrate fits into the active site
Many, weak interactions ensure specificity and reversibility;
Several bonds are required for substrate binding - specificity.
Weak bonds can only form if the relevant atoms are precisely positioned.
Weak bonds allow reversible binding.
How is ∆G˚‡ lowered?
- Ground state destabilisation
- Transition state stabilisation (picture)
- Alternate reaction pathway with a different (lower-energy) transition state
1 and 2 can be achieved by having an active site that has shape/charge complementarity to the transition state, not the substrate.
Strategies for catalysis
Acid-base catalysis, adding or removing a protein to/from a substrate
Covalent catalysis, substrate ends up making a covalent bond with the protein
Redox and radical catalysis (metal ions), moving protons/electrons around
Geometric effects (proximity and orientation),
Stabilisation of the transition state
Cofactors with activated groups, e.g. electrons, hydride ion (H-), methyl groups (CH3), amino groups (NH2). Acts as carriers
Proximity and Orientation Effect
For two molecules to react they need to be close together AND in the right orientation
Cofactors
Many enzymes require other non-protein factors to help them catalyse reactions, there are two classes; metal ions and coenzymes
Metal ion catalysis
More than a third of known enzymes require metal ions
Specific coordination geometry orients substrates
As Lewis acids, metals accept an electron pair to polarise H2O and functional groups
Transfer electrons in oxidation-reduction reactions
Mg2+
DNA polymerase; hexokinase; pyruvate kinase
Zn2+
Alcohol dehydrogenase; carbonic anhydrase
Fe2+ or Fe3+
Cytochrome oxidase; peroxidase
Mn3+ or Mn4+
Photosystem II
Hexokinase using Mg2+ as a cofactor
Establishes orientation of phosphates of ATP by octahedral coordination of Mg2+ ion
‘Electron withdrawing’ Lewis acid: stabilises electrons on oxygen, making phosphorous a better electrophile
Coenzymes
Are small organic molecules
Are co-substrates
Are carriers (of electrons, atoms, or functional groups)
Are often derived from vitamins
Pyruvate dehydrogenase
Provides acetyl-CoA in aerobic conditions:
Multienzyme complex composed of 30 copies of enzyme E1, 60 copies of E2 and 12 copies of E3, each with cofactors.
Net reaction is an oxidative decarboxylation.
