E4 Protein function and enzymes Flashcards
what is the difference between a heterodimer and a homodimer protein complex?
- homodimer is 2 of the same polypeptide bonded to form a dimer
- heterodimer is 2 different polypeptides bonded to form a dimer
what is a tetramer? give an example of one
- 2 pairs of identical polypeptides working together in a protein complex
- eg. haemoglobin
compare and contrast haemoglobin and myoglobin
- haemoglobin is an oxygen TRANSPORT protein and myoglobin is an oxygen STORAGE protein
- very similar 3D structures
- both bind oxygen via the haemorrhage prosthetic group
compare myoglobin and haemoglobin’s affinities for oxygen
- myoglobin’s affinity for oxygen is higher
- after haemoglobin binds oxygen in the lungs, it is then taken by myoglobin for storage in the muscles
describe the structure of haemoglobin
- tetrameric
- consists of 4 polypeptides (2 alpha chains and 2 beta chains, each chain folds into 8 alpha helices)
- has a haem prosthetic group (protoporphyrin IX)
- has a central iron (II) ion
describe the function of haemoglobin
transports oxygen in the blood via erythrocytes (red blood cells)
describe the binding of oxygen in haemoglobin
- cooperative
- first oxygen binding causes a conformational change from tense to relaxed state (T to R)
- ease of binding is increased for the rest of the oxygen molecules to other subunits of the haemoglobin molecule
- this is called allostery
describe the structure of myoglobin
- monomeric
- single polypeptide of 153 amino acids (folded into 8 alpha helices)
- has a haem prosthetic group (protoporphyrin IX)
- has a central iron (II) ion
describe the conformational change of haemoglobin in terms of what happens when oxygen binds
- when oxygen isn’t bound, the iron ion is out of haem plane
- when oxygen is bound, it pulls the iron ion into the haem plane
- binding of oxygen also pulls the His F8 ligand and the F helix
why does allostery have more of an effect on haemoglobin than myoglobin?
haemoglobin has 4 polypeptides where allostery can occur so the effect is quadrupled compared to myoglobin
how can protons affect the affinity of haemoglobin to oxygen?
- when protons bind to haemoglobin, its affinity for oxygen is lowered
- therefore, more acidic blood (with more carbon dioxide from respiration) means more oxygen dissociates from the blood to the respiring tissues
what kind of molecule are enzymes?
- most enzymes are proteins
- however, a few are RNA (ribozymes)
what needs to be overcome for a biochemical reaction to occur? why is this energy needed?
- an energy barrier (activation energy)
- energy is needed to transform the substrate molecules into a transition state (highest free energy state in the reaction pathway)
what do enzymes do to a transition state of a reaction?
- stabilise the transition state
- also lower Gibbs free energy of activation
what are the 4 principle mechanisms of how enzymes lower activation energy
- entropy
- orientation
- distortion
- solvation
describe entropy in terms of being a principle of how enzymes lower activation energy
- the amount of disorder in the system
- enzymes reduce this disorder
describe orientation in terms of being a principle of how enzymes lower activation energy
- ensures the substrate is able to interact in a specified way
describe distortion in terms of being a principle of how enzymes lower activation energy
- all the amino acids and cofactors are able to interact and work on the substrate
- this causes distortion
describe solvation in terms of being a principle of how enzymes lower activation energy
- the solvent in which the chemistry is done in the pocket of the enzyme
- eg. water
in enzyme kinetics, what is Vmax?
the maximum reaction rate
in enzyme kinetics, what is Km?
substrate concentration where V = 1/2Vmax
describe the Michaelis-Menten equation
- at low [S], doubling [S] leads to doubling of initial velocity (linearly proportional)
- as [S] increases, the enzyme will become saturated so increasing [S] causes very small changes in initial velocity
what kind of curve does a plot of V0 against [S] give?
a hyperbolic curve
what is Km in enzyme kinetics?
- Michaelis constant
- an inverse measure of affinity of the enzyme for the substrate
- the lower the Km, the higher the affinity
what does the induced fit model for enzyme action require?
a conformational change in the enzyme
state some catalytic mechanisms by which an enzyme can facilitate lowering of an activation energy and achieves transition-state complexes
- acid-base (proton donation / abstraction)
- temporary covalent bond formation
- redox effects
- electrostatic effects
- orientation / proximity effects and straining effects
what are cofactors?
- non-protein molecules that are required for a reaction to take place in addition to the enzyme and the substrate
- can be organic or inorganic
give examples of organic and inorganic cofactors
organic
- ATP
- NADH
inorganic
- magnesium ion
- zinc ion
what are coenzymes?
cofactors that bind loosely and are chemically altered by the enzyme
how can cofactors that tightly bind be considered?
- considered part of the enzyme
- enzyme without cofactor bound is called apoenzyme
- enzyme with cofactor bound is called holoenzyme
state 4 ways that enzyme activity can be regulated
- competitive inhibition
- non-competitive inhibition
- covalent modification
allosteric regulation
describe competitive inhibition of enzymes
- a molecule competes with the substrate for the active site
- can be reversible or irreversible
- inhibitor is similar to the substrate and you need to outcompete the substrate
- some drugs follow this and outcompete substrates for enzymes in order to fight a disease
describe covalent modification as a method of regulating enzyme activity
- chemical modification of amino acid residues or removal of modifications
- eg. methylation, acetylation, phosphorylation
- can increase or decrease enzyme activity
- some drugs work this way eg. aspirin acetylates cyclooxyrgenase and inactivates it to reduce pain
describe allosteric regulation as a means of regulating enzyme activity
- non-covalent binding of a molecule to the enzyme that doesn’t directly compete with substrate binding
- binding is away from active site but causes conformational change
- can increase or decrease enzyme efficacy
how is the mechanism of statins involving enzymes?
- inhibit enzymes involved in cholesterol metabolism
- block the steps involved in cholesterol metabolism
- statin has minimal side effects
