Enzymes Flashcards
1
Q
describe the common features of an active site
A
- 3D cleft formed by R groups of a.a in a polypeptide
- active site has a specific 3D conformation that is complementary to substrate (accounts for specificity of type of substrate enzyme acts on)
- takes up a small volume of enzyme, a.a are relatively far apart along the polypeptide chain but are brought closer together through folding
- substrate binds to enzyme at active site through weak interactions (hydrogen bonds, ionic bonds, hydrophobic interactions)
- specificity of binding depends on arrangement of amino acids in active site
2
Q
describe the four types of a.a residues in an enzyme
A
- binding residues are found at active site and binds to the substrate (holding substrate in correct orientation and position): consist of charged basic or acidic R groups that form ionic bonds with substrates/polar R groups that form hydrogen bonds with substrates, resulting in specificity of enzymatic action
- catalytic residues found at active site and catalyse the reaction
- supporting residues form the support structure for the active site
- non-essential residues have no specific role
3
Q
explain how enzymes help lower activation energy
A
- proximity effect: temporary binding of substrates next to each other on an enzyme increases chances of reaction occurring (uncatalysed reactions depend on random collisions between substrates)
- strain effect: temporary binding of substrate to active site strains bonds in substrate, increasing chances of breakage
- orientation surface: substrate held in such a way that exposes it for reaction
- microenvironment effect: hydrophobic amino acids create a water-free zone for non-polar substrates to react more easily
- acid-base catalysis: acidic and basic amino acids in active site facilitate the donation of protons to/acceptance of protons from substrate
4
Q
explain the lock and key hypothesis
A
- 3D conformation of active site of enzyme and substrate are exactly complementary
- enzyme and substrate collide in right orentation to form a short-lived enzyme-substrate complex
- once reaction has occurred, product and free enzyme are released from former ES complex. product unable to fit into active site and is released from enzyme into surrounding medium
- enzyme is again available and remains unchanged, ready to combine with substrates/catalyse another reaction
5
Q
explain the induced fit hypothesis
A
- when substrate binds with active site of enzyme, this induces a 3D conformational change in the enzyme structure. enzyme ‘wraps around’ the substrate to form a more stable structure, catalytic groups are more correctly aligned for catalysis
- enzyme and substrate do not fit together exactly. enzyme undergoes a 3D conformational change upon substrate binding, which improves fit between substrate and enzyme
6
Q
explain the effect of enzyme co-factors on enzyme’s mode of action
A
- many enzymes require non-protein co-factors for efficient activity
- although co-factors are required for enzyme activity, they are not catalytic on their own
- co-factors are smaller than their associated enzymes and are required in small amounts
- inorganic ions can be tightly or loosely associated with their enzymes, moulding the active site into a conformation for easy formation of ES complex, increasing chances of reaction occurring
- co-enzymes are non-protein, organic co-factors that are loosely associated with their enzymes and are derived from vitamins
- prosthetic groups are non-protein, organic co-factors that are tightly bound to the enzyme permanently
7
Q
describe how to measure rate of enzyme-catalysed reaction
A
measure amount of product formed/amount of substrate disappeared over a period of time
8
Q
describe the enzyme concentration on rate of reaction
A
- at a high substrate concentration, given that other factors remain constant, rate of reaction is proportional to enzyme concentration
- reactions are normally catalysed by enzymes at concentrations that are much lower than substrate concentrations
- as enzyme concentration increases, number of available active sites increases, more effective collisions, increasing rate of formation of ES complex, higher rate of enzyme action
9
Q
describe the effect of substrate concentration on rate of enzyme action
A
- for a given enzyme concentration, with all factors remaining constant, rate of reaction increases with increasing substrate concentration, up to a point where any further increase in substrate concentration does not produce a significant increase in rate of reaction
- at low substrate concentrations, many of the available enzymes have their active sites unoccupied
- at high concentrations of substrate, active sites at any given time will be virtually saturated with substrates, extra substrate molecules will have to wait for the ES complex to dissociate into its product and free enzyme before it can form an ES complex with the enzyme. this is known as the maximum reaction rate. enzyme concentration and dissociation time of ES complex are limiting factors
- michaelis constant is the substrate concentration when reaction rate is half of its maximum. each combination of enzyme and its particular substrate have its own michaelis constant
- michaelis constant is a measure of an enzyme’s affinity for its substrate. a high michaelis constant means the enzyme has a low affinity for its substrate while a low michaelis constant means the enzyme has a high affinity for its substrate
10
Q
describe the effect of temperature on rate of enzyme action
A
- at low temperatures, enzyme is inactivated. lowering temperatures lowers KE of molecules. frequency of effective collisions between substrate and enzyme decreases, rate of formation of ES complex decreases, rate of product formation decreases
- as temperature increases, KE of molecules increases as well. this increases frequency of effective collisions between substrates and enzymes, rate of formation of ES complex increases, rate of product formation increases
- at optimum temperature, reaction rate is highest (maximum)
- above the optimum temperature, reaction rate falls off sharply. enzymes are protein in nature so their 3D conformation is held together by weak forces (hydrogen bonds, ionic bonds, hydrophobic interactions). high temperatures can break these weak bonds. extreme heat irreversibly changes the secondary, tertiary and quaternary structure of protein enzyme, causing a change in the 3D conformation of the enzyme. active site is no longer complementary to substrate and enzyme is unable to function properly. enzyme is denatured
- high temperature irreversibly denatures the enzyme while low temperature inactivates it
11
Q
describe the effect of pH on rate of enzyme action
A
- enzymes function within a narrow pH range, when pH is altered above or below this range, rate of enzyme activity decreases. at optimum pH, rate of reaction is a maximum
- changes in pH change ionic charges of acidic and basic R groups of a.a residues on enzyme. these pH changes can be inhibitory to binding/catalysis by causing ions to reassociate
- pH changes may disrupt ionic and hydrogen bonds that maintain the structure of the active site. this changes the 3D conformation of the active site, and the substrate no longer fits. hence, enzyme activity decreases
- at extreme pH, enzyme denatures
12
Q
describe reversible and irreversible inhibition
A
- reversible inhibitors do not permanently affect the enzyme. when the inhibitor is removed, enzyme can resume its function. reversible inhibitors bind to the enzyme through weak interactions (hydrogen bonds, ionic bonds, hydrophobi cinteractions)
- irreversible inhibitors bind to enzymes permanently, making it difficult to resotre enzyme activity. these inhibitors cause the enzyme proteins to precipitate. irreversible inhibitors bind to the enzyme through strong covalent bonds
13
Q
describe the structure and effect of competitive inhibitors
A
- competitive inhibitors bear structural resemblance to substrate molecules and are complementary to the specific 3D conformation of the active site. therefore, competing for binding at the same active site
- when substrate concentration increases, there is a larger number of substrates than inhibitor molecules, to out-compete the inhibitor molecules as they have a greater probability of binding to the active site, as compared to competitive inhibitor. rate of reaction increases until Vmax is achieved at very high substrate concentrations
14
Q
describe the structure of non-competitive inhibitors
A
- have no structural similarity to substrate molecules, bind to a site on the enzyme other than the active site
- binding of non-competitive inhibitor causes enzyme to change its 3D conformation, causing active site to no longer be complementary to substrate
- by altering enzyme’s active site, enzyme is unable to bind to substrate. inhibitor may also disrupt function of catalytic sites on enzyme, such that the enzyme may bind to the substrate but catalysis cannot take place
- increasing substrate concentration has no effect on rate of reaction as number of available active sites has reduced. rate of reaction will continue to decrease with an increase in inhibitor concentration
- when inhibitor saturation is reached, rate of reaction will be almost zero
15
Q
is non-competitive inhibition the same as allosteric inhibition?
A
- regulatory enzymes are usually allosteric enzymes
- allosteric enzymes are enzymes made up of two or more polypeptide chains and have an allosteric site that is different from its active site. molecules can bind to the allosteric site and act as allosteric effectors
- allosteric enzyme can exist in two conformations: active state (when an activator binds, it activates catalysis) and inactive state (when an inhibitor binds, it inactivates catalysis)
- in allosteric regulation, the allosteric enzyme can be activated or inhibited depending on type of effector that binds. binding of effectors can enhance/inhibit binding of substrate at active site
- allosteric activation: when an activator binds, it stabilises the active form of the enzyme and increases the affinity of enzyme for its substrate
- allosteric inhibition: when an inhibitor binds, it stabilises the inactive form of the enzyme and decreases the affinity of the enzyme for its substrate
