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FUN E > E4 Protein function and enzymes > Flashcards

E4 Protein function and enzymes Flashcards

1
Q

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

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

what is a tetramer? give an example of one

A
  • 2 pairs of identical polypeptides working together in a protein complex
  • eg. haemoglobin
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3
Q

compare and contrast haemoglobin and myoglobin

A
  • 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
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4
Q

compare myoglobin and haemoglobin’s affinities for oxygen

A
  • 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
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5
Q

describe the structure of haemoglobin

A
  • 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
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6
Q

describe the function of haemoglobin

A

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

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7
Q

describe the binding of oxygen in haemoglobin

A
  • 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
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8
Q

describe the structure of myoglobin

A
  • 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
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9
Q

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

A
  • 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
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10
Q

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

A

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

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11
Q

how can protons affect the affinity of haemoglobin to oxygen?

A
  • 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
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12
Q

what kind of molecule are enzymes?

A
  • most enzymes are proteins
  • however, a few are RNA (ribozymes)
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13
Q

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

A
  • 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)
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14
Q

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

A
  • stabilise the transition state
  • also lower Gibbs free energy of activation
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15
Q

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

A
  • entropy
  • orientation
  • distortion
  • solvation
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16
Q

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

A
  • the amount of disorder in the system
  • enzymes reduce this disorder
17
Q

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

A
  • ensures the substrate is able to interact in a specified way
18
Q

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

A
  • all the amino acids and cofactors are able to interact and work on the substrate
  • this causes distortion
19
Q

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

A
  • the solvent in which the chemistry is done in the pocket of the enzyme
  • eg. water
20
Q

in enzyme kinetics, what is Vmax?

A

the maximum reaction rate

21
Q

in enzyme kinetics, what is Km?

A

substrate concentration where V = 1/2Vmax

22
Q

describe the Michaelis-Menten equation

A
  • 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
23
Q

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

A

a hyperbolic curve

24
Q

what is Km in enzyme kinetics?

A
  • Michaelis constant
  • an inverse measure of affinity of the enzyme for the substrate
  • the lower the Km, the higher the affinity
25
Q

what does the induced fit model for enzyme action require?

A

a conformational change in the enzyme

26
Q

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

A
  • acid-base (proton donation / abstraction)
  • temporary covalent bond formation
  • redox effects
  • electrostatic effects
  • orientation / proximity effects and straining effects
27
Q

what are cofactors?

A
  • 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
28
Q

give examples of organic and inorganic cofactors

A

organic
- ATP
- NADH

inorganic
- magnesium ion
- zinc ion

29
Q

what are coenzymes?

A

cofactors that bind loosely and are chemically altered by the enzyme

30
Q

how can cofactors that tightly bind be considered?

A
  • considered part of the enzyme
  • enzyme without cofactor bound is called apoenzyme
  • enzyme with cofactor bound is called holoenzyme
31
Q

state 4 ways that enzyme activity can be regulated

A
  • competitive inhibition
  • non-competitive inhibition
  • covalent modification
    allosteric regulation
32
Q

describe competitive inhibition of enzymes

A
  • 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
33
Q

describe covalent modification as a method of regulating enzyme activity

A
  • 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
34
Q

describe allosteric regulation as a means of regulating enzyme activity

A
  • 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
35
Q

how is the mechanism of statins involving enzymes?

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

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