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Enzymes Flashcards

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1
Q

What is metabolism?

A

Sum total of catabolism (breakdown of molecules) and anabolism (synthesis of molecules)

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2
Q

What is a catalyst?

A

A substance that increases the rate of a chemical reaction by lowering the activation energy but remains chemically unchanged itself at the end.

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3
Q

What is an enzyme?

A

Biological catalysts that speed up biochemical reactions by lowering the activation energy of a reaction

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4
Q

What is the effect of an enzyme on a reaction?

A

Activation energy is lowered
More reactant molecules can surmount the energy barrier to reach the transition state to be converted to product molecules
But the total energy difference between reactant molecules and product molecules REMAIN THE SAME

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5
Q

What are substrates?

A

The reactants acted upon by an enzyme in an enzyme-catalysed reaction

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6
Q

Are enzymes effective in small amounts?

A

Yes!
Enzymes remain chemically unaltered at the end of the reaction and can be reused

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7
Q

How efficient are enzymes?

A

Highly efficient
Enzyme-catalysed reactions proceed 10^3 to 10^8 times faster than uncatalysed reactions

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8
Q

Enzymes have a high degree of specificity? True or false?

A

True! Most enzymes are specific to one typ of substrate molecule/a group of similar substrates

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9
Q

What are enzymes very sensitive to?

A

Temperature (can be denatured by heat, functions most efficiently at optimum temperature)
pH (function most efficiently at optimum pH)

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10
Q

How is enzyme activity regulated?

A

By activators and inhibitors

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11
Q

What is the structure of enzymes?

A

Globular proteins (mostly)
Have specific 3-dimensional conformaion
3d conformation must be maintained for an enzyme to remain functional
Denatured when bonds holding specific 3d conformation is disrupted

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12
Q

Enzymes are made of which 4 categories of amino acid residues?

A

Catalytic and acid residues
Binding amino acid residues
Structural amino acid residues
Non-essential amino acid residues

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13
Q

What are catalytic amino acids in enzymes?

A

R groups of catalytic amino acids are directly involved in catalytic activity (making/breaking of chemical bonds once substrate is bound)

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14
Q

What are binding amino acids in enzymes?

A

R groups of these amino acids hold the substrate(s) in position via non-covalent bonds while catalysis takes place

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15
Q

What are structural amino acids in enzymes?

A

Involved in maintaining the specific 3d conformation of the active site (nd the enzyme as a whole)

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16
Q

What are non-essential amino acid residues in enzymes?

A

No specific functions
Can be removed or replaced with the loss of enzyme’s catalytic function

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17
Q

What are enzyme cofactors?

A

An additional non-protein component that enzymes interact with via covalent bonds or weak interactions

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18
Q

Purpose of cofactors?

A

So that substrate molecules fit correctly into the enzyme’s active site (for catalytic reactions)

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19
Q

What are the 3 main types of cofactors? What purpose do they serve?

A

Inorganic metal ions
- mostly small, divalent ions
- can be a component of active site/ affect enzyme activity through allosteric regulation (allosteric enzymes have multiple subunits and though conformational changes, bind activators of inhibitors at sites other than the active site)
- usually bind reversibly to the enzyme by altering the enzyme’s active and/or allosteric sites to facilitate the catalytic reaction carried out by the enzyme
EG: salivary amylase activity is increased in the presence of chloride ions

Coenzymes
- loosely associates with the enzyme durin the reaction, act as transient carriers of specific functional groups/ydrogen/electrons
- most are derived from vitamins
EG: Nicotinamide adenine dinucleotide (NAD) is an important coenzyme in respiration

Prosthetic group
- tightly bound to the enzyme on a permanent basis
EG: prosthetic group of enzyme catalase is an iron-containing haem group

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20
Q

Wha is a holoenzyme?

A

Enzymes that require BOTH a coenzyme and one or more metal ions for activity
Holoenzyme refers to the complete, catalytically active enzyme together with its bound coenzyme and/or metal ions

Protein part of an enzyme: apoenzyme

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21
Q

What is the mode of action of enzymes?

A

In a solution containing both substrate and enzyme, molecules move around freely and collide with one another
1. When enzyme and substrate collide in the CORRECT ORIENTATION, substrate will be bound to the active site of the enzyme to form an enzyme-substrate complex (EFFECTIVE COLLISION)
2. Substrate molecule is held in the active site by non-covalent bonds (hydrogen/ionic bonds) between the R groups of the binding amino acids and the substrate molecule
3. R groups of the catalytic amin acid residues at the active site catalyse the conversion of substrate to product
4. Alteration in chemical conformation, product molecule released from active site as it is no longer complementary to active site, enzyme active site is free. For binding of another substrate molecule (reused)

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22
Q

Which 2 amino acid residues are found at the active site of an enzyme?

A

Catalytic and binding amino acid residues

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23
Q

How do enzymes lower activation energy?

A
  1. Orienting substrates in close proximity, in correct orientation, to undergo chemical reactions
  2. Straining critical bonds in substrate molecules, allowing substrates to attain their unstable transition state
  3. Providing a microenvironment that favours the reaction (specific amino acids/ions at active site may result in a specific set of molecular conditions that favours the formation/breakage of particular bonds)
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24
Q

What are the two mechanisms for enzyme action? (__hypothesis)

A

Lock and key hypothesis
Induced fit hypothesis

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25
What is the lock and key hypothesis?
An exact fit/complementary shape or conformation between the substrate and the active site of the enzyme (enzyme is viewed as very rigid) like how a key fits into a lock very precisely Explains enzyme specificity
26
What is the induced fit hypothesis?
Active site flexibility - Enzymes do not have a rigid conformation - flexible in conformation, can allow for more than one type of substrate to bind - not in precise complementary conformation to the substrate before binding to the substrate Interaction between enzyme and substrate - upon binding, active site changes conformation slightly to bind to substrate more firmly/snugly - R group of the catalytic amino acids at active site are moulded into a specific 3d conformation, brought to close proximity to chemical bonds in substrate to facilitate catalysis Explains group specificity
27
What is the rate of an enzyme catalysed reaction?
Amount of substrate converted to product by enzymes PER UNIT TIME
28
What to measure to obtain the rate of an enzyme-catalysed reaction?
Product formation Substrate usage
29
How to measure the initial rate of reaction when given a graph?
Calculate the INITIAL GRADIENT Initial mount of product formed or substrate used DIVIDED BY time duration
30
What are the 4 factors affecting rate of enzymatic reaction?
Substrate concentration Enzyme concentration Temperature pH
31
What is a limiting factor?
The factor in the shortest supply (the slowest reaction in the series
32
At low substrate concentration, assuming all other conditions are constant, what happens when substrate concentration increases? Why?
Proportional increase in the rate of reaction (substrate is limiting factor) Not all active sites of enzymes are occupied rate is limited by concentration of substrate Increase in substrate concentration, increases frequency of effective collision between enzyme active site and substrate molecules, increase the number of enzyme-substrate complexes formed per unit time, increases the amount of product formed per unit time
33
At high substrate concentration, assuming all other conditions are constant, what happens when substrate concentration increases? Why?
Further increase in substrate concentration DOES NOT result in an increase in the rate of reaction (graph reaches a plateau) Substrate availability is no longer the limiting factor (enzyme concentration is limiting factor) Rate is limited by saturation of enzyme active sites Any added substrates have to ‘wait’ until existing enzyme-substrate complexes dissociate to release their products and free enzyme molecules in order to form new enzyme-substrate complexes Rate of reaction can only increase with the addition of enzyme
34
What is the turnover number? Kcat?
The maximum number of molecules of substrate an enzyme can convert to product per catalytic site per unit time
35
At low enzyme concentration, assuming all other conditions are constant, what happens when enzyme concentration increases? Why?
Proportional increase in the rate of reaction Concentration of enzyme is the limiting factor Increase in enzyme concentration, more active sites Increasing frequency of effective collisions between substrates and active sites More enzyme-substrate complexes formed per unit time Increase in the amount of product formed per unit time Increase in rate of reaction
36
At high enzyme concentration, assuming all other conditions are constant, what happens when enzyme concentration increases? Why?
Further increase in enzyme concentration does not result in an increase in enzyme concentration (graph plateaus) Enzyme concentration no longer the limiting factor (substrate concentration is limiting) Not enough substrate molecules competing for active sites available Rate of reaction can be increased with addition of substrate
37
As temperature increases to the optimum temperature, assuming all other conditions are constant, how is the rate of reaction impacted? Why?
Low temperatures: enzymes inactivated Increasing temperature increase kinetic energy of substrate and enzyme molecules increases frequency of effective collisions between substrates and active sites increases formation of enzyme-substrate complexes per unit time Increases amount of product formed per unit time Increases rate of reaction
38
What happens at the optimum temperature?
Enzyme activity is highest Rate of enzyme-substrate complexes formation is highest
39
As temperature increases beyond the optimum temperature, assuming all other conditions are constant, how is the rate of reaction impacted? Why?
Decrease in rate of reaction DESPITE INCREASING FREQUENCY OF COLLISIONS Thermal agitation: disrupts hydrogen bonds, ionic ones and other non-covalent interactions that stabilise the specific 3d conformation of the protein molecule Loss in specific 3d conformation, loss of active site (no longer a complementary fit with substrate) Denatured! Loses catalytic function Frequency of effective collisions between substrates and active sites decrease, rate of formation of enzyme-substrate complexes drop, less product formed per unit time
40
What is the dual effect of temperature on enzyme activity?
1. Increasing effective collision of enzymes 2. Decreasing stability of the enzyme
41
How does a change in pH affect enzyme activity?
Alters the ionic charge of the acidic and basic R groups Disrupts the ionic/hydrogen bonds that maintain the specific 3d conformation of the enzyme, causing denaturation Lower pH, more hydrogen ions available to neutralise negative charges in enzyme Higher pH, less hydrogen ions available to neutralise negative charges in enzyme
42
How does a change in pH affect structural amino acids in an enzyme?
Conformation of active site is no longer complementary to substrate Cannot form enzyme-substrate complex
43
How does a change in pH affect binding amino acids in an enzyme?
Substrate cannot be held in is correct orientation in the active site for catalysis to occur
44
How does a change in pH affect catalytic amino acids in an enzyme?
R groups no longer possess the correct ionisation/charge to catalyse the required reaction
45
What is the optimum pH?
Rate of reaction is at a maximum Intra molecular bonds are intact, conformation of active site is ideal for binding Frequency of effective collision is the highest, largest amount of enzyme-substrate complexes formed Usually the pH of the environment the enzyme normally functions
46
Enzymes are very pH sensitive, so pH values only slightly above/below the optimum pH will see a marked decline in enyme activity. True or false?
TRUE! Slight change in pH, alters 3d conformation, affinity for substrate is decreased
47
Are the effects of pH change reversible?
Yes! Restoring the pH to optimu level usually restores the rate fo reaction
48
What is Vmax?
Maximal reaction velocity The maximum rate that a reaction can proceed in the presence of a specific concentration of enzyme and EXCESS SUBSTRATE
49
What is Km?
Michaelis constant Measured as the substrate concentration that allows an enzyme-catalysed reaction proceed at half the maximum velocity (1/2 Vmax)
50
What does the Km value represent?
Affinity of an enzyme for a particular substrate Low Km: high affinity for substrate High Km: low affinity for substrate
51
What are inhibitors?
A small variety of molecules which can reduce the rate of an enzyme-catalysed reaction
52
What is the structure of competitive inhibitors? What purpose do they serve?
Structurally similar to substrate molecule, compete with substrate for binding to the active site Remains bound to the active site prevents substrate binding to active site
53
Describe what happens when a competitive inhibitor is added to an enzyme-substrate reaction? Explain.
Describe: initial rate of reaction: reduced When substrate concentration is very high, both reactions (with and without competitive inhibitors) reach the same Vmax In presence of inhibitor, a longer period of time is required to produce the same amount of product Explanation Increase in substrate concentration, reduces effect of inhibitor Substrate and inhibitor are in direct competition for enzymes’ active sites greater proportion of substrate molecules Greater chance for substrate to outcompete the inhibitor to enter the active site Final rate of reaction almost equivalent to Vmax Final amount of product is the same (substrate continues to be converted by enzyme molecules that are unaffected by the inhibitor
54
What is the structure and purpose of a non-competitive inhibitor?
Bear no structural resemblance to substrate Does not compete with substrate for active site Binds to the part of the enzyme molecule that is NOT the active site Binding of inhibitor alters 3d conformation of enzyme molecules and active site Enzyme molecule no later has an active site that is complementary in conformation to substrate Substrate does not bind to enzyme active site, no enzyme-substrate complex can be formed
55
Describe what happens when a non-competitive inhibitor is added to an enzyme-substrate reaction? Explain.
Describe: Initial rate of reaction is reduced Even when substrate concentration is very high, initial rate of reaction with inhibitor DOES NOT REACH THE SAME Vmax Explanation: Binding of non-competitive inhibitor to a site other than the enzyme’s active site, change in 3d conformation, prevents substrate molecules from binding Proportion of enzyme molecules are rendered inactive (Vmax is lower) Substrate and inhibitor not in direct competition, increase in substrate has no effect on inhibition Km remains unchanged (affinity of enzyme for substrate is unaffected) Final amount of product formed is the same, substrate continues to be converted by an enzymes molecules that are unaffected by inhibitor
56
What is the difference in effect of increasing substrate concentration in competitive and non-competitive inhibition?
Competitive: inhibition can be reveresed, substrate molecules can out-compete the inhibitor for the active site Non-competitive: no effect
57
What is the difference in maximum rate of reaction in competitive and non-competitive inhibition?
Competitive: Vmax is reached at higher substrate concentration Non-competitive: Vmax is less than that of reaction even at high substrate concentration
58
What is the difference in change of Km value in competitive and non-competitive inhibition?
Competitive: larger Km (lower affinity) Non-competitive: Km is unchanged (affinity of substrate for normal enzyme remains unaffected) BUT FINAL AMOUNT OF PRODUCT FORMED IS THE SAME
59
What is allosteric regulation?
Regulation of an enzyme by the binding of molecules at an allosteric site (other than the active site) Called regulators (activators/inhibitors)
60
Allosteric regulators are enzymes that alternate between their active and inactive forms. True or false?
True Only the active form catalyse reactions
61
How does an allosteric regulator go from inactive to active?
Inactive form of allosteric enzyme has an active site that does not fit substrate Shape must be altered for substrate to fit into the active site
62
Most allosterically regulated enzymes are composed of two or more polypeptide chains (multi-unit). True or false?
True
63
What is allosteric activation?
When activator binds, stabilises active of enzyme, increases affinity of enzyme for substrate
64
What is allosteric inhibition?
Inhibitor binds to the same region, stabilises inactive form of the enzyme, decreases affinity of enzyme for its substrate
65
What is the shape of the graph for an allosterically activate enzyme reaction? Why?
Sigmoidal Binding of activator, induces favourable conformation change in active site of ALL SUBUNITS of enzyme (COOPERATIVITY, amplifies response of enzyme to substrate, primes an enzyme to accept additional substrates) Amplifies the response of enzyme to substrates Sudden steep rise in rate of reaction
66
What is reversible inhibition?
Binds to enzyme via weak non-covalent bonds (hydrogen bonds, hydrophobic interactions) Effect is inhibitor is temporary, can be easily removed and cause no permanent damage to the enzyme When inhibitor leaves, activity of enzyme will be restored to normal
67
What is irreversible inhibition?
Binds to enzyme via covalent bonds Causes permanent damage to enzyme molecule so it is unable to carry out catalytic activity
68
Where are enzymes located?
Intracellular (within the cell7 - cytosol or nucleus - inside membrane bound organelles - plasma membrane - membranes of organelles Extracellular enzymes - produced in the cell, packaged to be secreted out of the cell (digestive enzymes)
69
What are advantages of metabolic pathways catalysed by enzymes?
1. No accumulation of products, products become substrates of subsequent reactions 2. Modified in a series of small steps so that - energy can be released in controlled amounts - minor adjustments to be made to the structure of molecules - coupling of exergonic reactions to endergonic reactions 3. Each step catalysed by a specific enzyme allowing for REGULATION AND CONTROL of metabolism as each enzyme is A POINT OF CONTROL of the overall pathway. Enzymes specific to the reaction are regulated by different inhibitors/activators, allowing for finely balanced portioning of cell metabolites among different pathways 4. Spatially arranged, product of one reaction is ideally located to become the substrate of the next, permits the build-up of high local concentrations of substrate molecules and biochemical reactions can proceed rapidly (catalysed by multi-enzyme complex)
70
What is a multi-enzyme complex?
Team of enzymes for several steps of a metabolic pathway Orders sequence of reactions (product from the first enzyme becomes substrate of adjacent enzyme in the complex and so on) GREATLY INCREASES EFFICIENCY
71
What is end product inhibition?
When end product of metabolic pathway accumulates, cts as an inhibitor on enzymes controlling the preceding steps of the pathway Binding may - alter the conformation of the active site of the enzyme and lower its affinity for its substrate - block the entry of substrate into active site FURTHER PRODUCTION OF END PRODUCT IS INHIBITED BY ITSELF

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