E4 Protein function and enzymes

Question 1

what is the difference between a heterodimer and a homodimer protein complex?

Answer 1

• homodimer is 2 of the same polypeptide bonded to form a dimer
• heterodimer is 2 different polypeptides bonded to form a dimer

Question 2

what is a tetramer? give an example of one

Answer 2

• 2 pairs of identical polypeptides working together in a protein complex
• eg. haemoglobin

Question 3

compare and contrast haemoglobin and myoglobin

Answer 3

• 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

Question 4

compare myoglobin and haemoglobin’s affinities for oxygen

Answer 4

• 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

Question 5

describe the structure of haemoglobin

Answer 5

• 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

Question 6

describe the function of haemoglobin

Answer 6

transports oxygen in the blood via erythrocytes (red blood cells)

Question 7

describe the binding of oxygen in haemoglobin

Answer 7

• 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

Question 8

describe the structure of myoglobin

Answer 8

• 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

Question 9

describe the conformational change of haemoglobin in terms of what happens when oxygen binds

Answer 9

• 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

Question 10

why does allostery have more of an effect on haemoglobin than myoglobin?

Answer 10

haemoglobin has 4 polypeptides where allostery can occur so the effect is quadrupled compared to myoglobin

Question 11

how can protons affect the affinity of haemoglobin to oxygen?

Answer 11

• 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

Question 12

what kind of molecule are enzymes?

Answer 12

• most enzymes are proteins
• however, a few are RNA (ribozymes)

Question 13

what needs to be overcome for a biochemical reaction to occur? why is this energy needed?

Answer 13

• 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)

Question 14

what do enzymes do to a transition state of a reaction?

Answer 14

• stabilise the transition state
• also lower Gibbs free energy of activation

Question 15

what are the 4 principle mechanisms of how enzymes lower activation energy

Answer 15

• entropy
• orientation
• distortion
• solvation

Question 16

describe entropy in terms of being a principle of how enzymes lower activation energy

Answer 16

• the amount of disorder in the system
• enzymes reduce this disorder

Question 17

describe orientation in terms of being a principle of how enzymes lower activation energy

Answer 17

• ensures the substrate is able to interact in a specified way

Question 18

describe distortion in terms of being a principle of how enzymes lower activation energy

Answer 18

• all the amino acids and cofactors are able to interact and work on the substrate
• this causes distortion

Question 19

describe solvation in terms of being a principle of how enzymes lower activation energy

Answer 19

• the solvent in which the chemistry is done in the pocket of the enzyme
• eg. water

Question 20

in enzyme kinetics, what is Vmax?

Answer 20

the maximum reaction rate

Question 21

in enzyme kinetics, what is Km?

Answer 21

substrate concentration where V = 1/2Vmax

Question 22

describe the Michaelis-Menten equation

Answer 22

• 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

Question 23

what kind of curve does a plot of V0 against [S] give?

Answer 23

a hyperbolic curve

Question 24

what is Km in enzyme kinetics?

Answer 24

• Michaelis constant
• an inverse measure of affinity of the enzyme for the substrate
• the lower the Km, the higher the affinity

Question 25

what does the induced fit model for enzyme action require?

Answer 25

a conformational change in the enzyme

Question 26

state some catalytic mechanisms by which an enzyme can facilitate lowering of an activation energy and achieves transition-state complexes

Answer 26

- acid-base (proton donation / abstraction) - temporary covalent bond formation - redox effects - electrostatic effects - orientation / proximity effects and straining effects

Question 27

what are cofactors?

Answer 27

- 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

Question 28

give examples of organic and inorganic cofactors

Answer 28

organic - ATP - NADH inorganic - magnesium ion - zinc ion

Question 29

what are coenzymes?

Answer 29

cofactors that bind loosely and are chemically altered by the enzyme

Question 30

how can cofactors that tightly bind be considered?

Answer 30

- considered part of the enzyme - enzyme without cofactor bound is called apoenzyme - enzyme with cofactor bound is called holoenzyme

Question 31

state 4 ways that enzyme activity can be regulated

Answer 31

- competitive inhibition - non-competitive inhibition - covalent modification allosteric regulation

Question 32

describe competitive inhibition of enzymes

Answer 32

- 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

Question 33

describe covalent modification as a method of regulating enzyme activity

Answer 33

- 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

Question 34

describe allosteric regulation as a means of regulating enzyme activity

Answer 34

- 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

Question 35

how is the mechanism of statins involving enzymes?

Answer 35

- inhibit enzymes involved in cholesterol metabolism - block the steps involved in cholesterol metabolism - statin has minimal side effects