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Enzymes Flashcards

1
Q

What are enzymes ?

A

Biological catalysts that increase the rate of biochemical reactions without being changed at the end of the reaction

Lowers the activation energy of the reaction, allowing it to proceed at lower temperatures

Globular protein with specific 3D conformation which includes an active site with a specific shape and charge that recognises specific substrates

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2
Q

What are intracellular enz ?

A

Enz that are made and retained in cell, synthesised by free ribosomes

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3
Q

What are extracellular enz ?

A

Enz made in cell by ribosomes attached to the rER and are then passed through the endomembrane system to be secreted out of the cell

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4
Q

What are co-factors of enzymes ?

A

Non-protein components that are required for enz to function

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5
Q

What are the 6 properties of enz ?

A

Effective in small amounts

Remain chemically unchanged at the end of the reaction, thus can be reused repeatedly

Extremely effective, 1000-100000000 times faster than non-catalysed reaction

Globular protein with (at least) tertiary structure, soluble in aqueous solution

Specific active site in terms of shape, configuration and charge

Enz activity affected by changes in temperature, pH, substrate concentration, enzyme concentration and presence of inhibitors

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6
Q

(ANS FORMAT)
How to explain enz mode of action ?

A
  1. active site has specific shape and charge complementary to specific substrate
  2. Only specific substrate can bind ( enz specificity)
  3. Binding of substrate to active sire forms enzyme-substrate complex
  4. ESC lowers the Ea of the reaction
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7
Q

What is the active site (AS) of an enz ?

A

A small portion of the enz molecule (3-12 AA residues) which come into direct contact with substrates

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8
Q

What are the two groups of AA grouped into at the AS ?

A

Contact residues
Catalytic residues

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9
Q

What are contact residues ?

A

AA that form the shape of the AS that is complementary to the substrate, with complementary charges to the substrate

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10
Q

What do contact residues contribute to ?

A

Enz specificity
- facilitate substrate binding

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11
Q

What do catalytic resides contribute to ?

A

The ability of the enz to catalyse biochemical reaction

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12
Q

What do catalytic enz do ?

A

They increase the reactivity of the substrates by altering the charges on them

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13
Q

Other than the AA at AS, what do the other AA do?

A

They help maintain teh globular shape of the enz which helps maintain a the shape of the AS
Some form other binding sites (allosteric site)

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14
Q

Are the AA that form the AS close to each other in the primary structure ?

A

Not necessarily
- extensive folding of the polypeptide will bring them together

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15
Q

How does the ESC form ?

A

Binding of substrate to enz occurs as a result of effective collisions between enz and substrate molecules where substrate sits into the AS which has a complementary charge and shape to that of the substrate

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16
Q

What is the lock and key hypothesis

A

The substrate is completely complementary in shape to the AS - prefect fit
There is no change in shape when substrae binds

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17
Q

What is the induced fit hypothesis ?

A

In initial shape of the AS is not complementary to the shape of the substrate
Substrate binding to AS causes slight conformation change in the enz that enables the substrate to fit more snugly into the AS

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18
Q

What does the lock and key hypothesis explain?

A

How enz are specific to their substrate

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19
Q

What does the induced fit hypothesis explain ?

A

How enz lower the Ea of the reaction and perform their catalytic function more effectively

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20
Q

What is activation energy (Ea) ?

A

The amount of energy needed to bring 1 mole of substance to the transition state at a particular temperate

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21
Q

What does Ea represent in a reaction ?

A

The energy barrier that has to be overcome before a reaction an take place

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22
Q

How does formation of ESC lower Ea

A

Substrate fits snugly into AS and the R groups of the catalytic resides at the AS will increase the reactivity of the substrate

Different substrate molecules held in the AS are forced together in the correction orientation for reaction to occurs - facilitates bond formation

Certain bonds in the substrate molecules may be placed under physical stress (bending of bond) which increases the likelihood that the bond will break

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23
Q

How does catalytic AA increase reactivity of the substrate in the AS ?

A

Change the charge on the substrate, alter the distribution of electrons within the bonds of the substrate or cause other changes that will increase the reactivity of the substrate

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24
Q

What are the factors affecting rate of reaction ?

A

Enz concentration, substrate concentration, pH, temperature

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25
What happens are low enzyme concentration ?
Enz concentration is the LF since all the AS are filled Enz molecules present are saturated and working at the maximum rate An increase in and concentration leads to an increase in rate as more AS are available for more effective collision between enz and substrate molecules, thus forming more ESC
26
What happens at high enz concentration ?
Substrate concentration becomes the LF since there are insufficient substrate molecules to bind to empty AS Increase in enz concentration does not increase rate of effective collision of formation of ESC resulting in contain rate of reaction
27
What happens at Low substrate concentration ?
Substrate concentration is the LF Increase in substrate concentration leads to proportional increase in rate of reaction as AS are avaliable, more effective collisions between enz and substrate molecules, forming more ESC
28
What happens at high substrate concentration ?
Enz concentration becomes LF as all teh AS are used up an enz are fully saturated, working at max rate Substrate molecules must wait for free AS to be available to bind to Increase in substrate concentration does not increase rate of effective collision or formation of ESC resulting in constant rate of reaction
29
What does the temperature of a reaction indicate ?
The amount of kinetic energy (KE) that reactants molecules have
30
What happens are temperatures below optimum ?
The enz is inactive as there is little KE available for effective collision to occur As temperatures increase, the KE of substrates and enz increase meaning that they are moving at higher speeds - more effective collision between enz and substrate molecules, formation of more ESC
31
What is teh temperature coefficient (Q10)?
Measures change in rate of reaction when temperature increases by 10º
32
What is the Q10 for enzyme reactions that are below optimum temperature ?
2 - as temperature increases by 10ºc, rate of reaction increases by 2 times
33
What happens at the optimum temperate ?
Rate of enz reaction is at its max
34
What happens above optimum temperature ?
As temperature increases beyond optimum, rate of reaction decreases rapidly as the enz undergoes denaturation - the gain of large amounts of KE causes excessive vibration of AA residues in polypeptide chain of enz, disrupting weak ionic bonds, H bonds, hydrophobic interactions between R groups of AA thus causing the enz to lose its 3D conformation Shape of the AS affected, prevents effective collision between enz and substrate thus enz is unable to form ESC with substrate Enz is non-functional
35
Are the optimum temperatures for all enz the same ?
No, each enz has its own optimum temp
36
How does pH affect enz ?
Large changes in pH will cause enz to precipitate out, since enz work in a narrow pH range
37
What is the optimum pH for intracellular enz ?
Neutral
38
What is the optimum pH range for extracellular pH ?
Acidic or alkaline
39
What happens are optimum pH ?
Rate of enz reaction is at max Bonds maintaining the 3D conformation of enz are intact and shape of AS is complementary The rate of effective collisions between enz and substrate and formation of ESC is the highest
40
What happens at pH lower or higher than optimum ?
As pH deviates from optimum, concentration of H+ will be different Ionic bonds and H bonds between R groups of AA are disrupted meaning that enz molecules lose their specific 3D conformation, shape of the AS is affected as well Chagne in concentration of H+ affect the charges of AS and substrate thus they may no longer have opposite electrostatic charges AS no longer complementary in shape and charge to substrate, preventing effective collision between enz and sub, ESC is not formed
41
What is Vmax?
Max rate of an enz reaction at given enz concentration, temp and pH in presence of excess substrate
42
What is Km?
The michaelis-menten constant Teh substrate concentration that enables the enz reaction to proceed at half its max rate (Vmax)
43
What does 1/Km represent?
The affinity of an enz or a substrate
44
What does a larger value of Km mean ?
Smaller affinity for the substrate
45
What is an inhibitor ?
Substance that prevents enz from catalysing its reaction
46
How does inhibitor reduce rate of reaction ?
By combining with enz to form an enzyme-inhibitor complex which then cannot combine with substrate
47
What are the four types of reversible inhibition ?
Competitive inhibition Non-competitive inhibition Allosteric inhibition End-product inhibition
48
What does reversible inhibition mean ?
Removal of inhibitor from enz will restore enz function
49
What is competitive inhibition ?
Where inhibitor has close structural resemblance to substrate, thus complementary to enz AS Inhibitor will compete with substrate molecules for AS of an enz, blocks the substrate from binding to AS while it remains attached
50
Where does the inhibitor in competitive inhibition bind to on the enz ?
AS
51
Why does increase in substrate concentration decrease the effect of a competitive inhibitor ?
There is a higher probability of forming ESC than EIC , the substrate outcompetes the competitive inhibitor to bind to the AS
52
What happens at Low substrate concentration with competitive inhibitor ?
Probability of inhibitor binding to enz is lower than substrate binding - AS of enz is blocked by competitive inhibitor Lowe r frequency of effective collision between enz and sub, lower rate of ESC formation
53
What happens when substrate concentration increase under competitive inhibition ?
More sub molecules to compete with competitive inhibitor for enz AS Rate of effective collision increase, formation of ESC increase thus rate of reaction increase
54
What happens are very high substrate concentration with competitive inhibitor ?
Substrate out-competes competitive inhibitor to bind to AS Most of the AS is bound by substrates to form ESC Rate of reaction is at its maximum and competitive inhibition has been overcome by high substrate concentration
55
What is the difference in Vmax of a reaction without competitive inhibitor and one with it ?
Vmax is the same but occurs at much higher substrate concentration for reaction with inhibitor
56
What is the difference in Km of a reaction with competitive inhibitor and one without ?
Km of reaction with inhibitor is higher than that without since the presence of competitive inhibitor causes the enz to have a lower affinity for the substrate
57
What is non-competitive inhibition ?
There is no structural resemblance of the inhibitor to the substrate of the enz, it binds to enz at allosteric to site
58
What does binding of inhibitor in non-competitive inhibition result in ?
Conformation change of enz molecule, thus a change in configuration of AS causing the enz to be non-functional
59
Can an increase in substrate concentration overcome non-competitive inhibition ?
No : non-competitive inhibition lowers the effective enz concentration
60
Is Vmax of reaction with non-competitive inhibitor and one without different ?
Different
61
Is the Km of a reaction with non-competitive inhibitor and one without the same ?
Same
62
What is allosteric inhibition ?
Specific for allosteric enz
63
What is the structure of an allosteric enz ?
Usually large, consists of more than 1 polypeptide chain Each polypeptide chain makes up one submit of enz, each subunit has its own AS and allosteric site
64
What are the two forms that the allosteric enz alternate between?
High-affinity active form Low-affinity inactive form
65
Why does allosteric enz alternate between two forms ?
Due to binding of inhibitor or activator at allosteric site or of substrate at AS
66
What is cooperativity ?
Substrate binding to AS of 1 subunit causing a change in the conformation of the while enz to the active form, which facilitates substrate binding to other AS in other subunits
67
What is bound at where to result in active form of enz ?
Binding of allosteric activator at allosteric site
68
Binding of what to where results in inactive form of allosteric enz ?
Binding of allosteric inhibitor at allosteric site
69
What shape is the enz graph for allosteric enz ?
Sigmoidal (S-shaped) graph
70
What is a metabolic pathway ?
Series of enz catalysed reactions which can be organised into cycles or chains
71
What is anabolic ?
Energy is required to build larger molecules from small molecules
72
What is catabolic ?
Energy is released to break down larger molecules into smaller ones
73
What is ABCD in context of metabolism ?
Anabolic Build Catabolic Destroy
74
When does end-product inhibition occur ?
When end product of a pathway accumulates, it can act as inhibitor of an enz in the pathway stopping synthesis of end-product
75
Why is end-production inhibition important ?
Helps prevent wastage of resources as it stops synthesis of end product beyond what is necessary Allows intermediates in the pathway ot be channelled into other pathways to produce other end products Helps prevent potential adverse effects of the excess accumulation of end product
76
Why does metabolic pathways occur in a series of steps ?
Feedback inhibition by end product Metabolic pathways allows for greater level of regulation as pathway si controlled at each enz, allowing for finer control Intermediates from one pathway can become substrates for other pathways Smaller release of energy in each step (rather than sudden large release) allows for better utilisation of energy and prevents damage to cells

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