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2 - foundations in bio > 2.1.4 - enzymes > Flashcards

2.1.4 - enzymes Flashcards

1
Q

what are enzymes?

A
  • globular proteins that have a specific tertiary structure that determines the shape of the active site
  • act as biological catalysts - for intra and extracellular reactions
  • affect metabolism of cells and organisms
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2
Q

how does formation of ESC’s affect activation energy of metabolic reactions?

A

it lowers it

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3
Q

define ‘hydrolysis’

A

any chemical reaction in which a molecule of water ruptures one or more chemical bond

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4
Q

can enzymes have more than one active site?

A

yes

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5
Q

the reactants, intermediates and products in a reaction are known as what?

A

metabolites

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6
Q

give an example of an enzyme that catalyses intracellular reactions

A
  • catalase
  • hydrolyses / catalyses decomposition of hydrogen peroxide into water and oxygen
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7
Q

give 2 examples of enzymes that catalyse extracellular reactions

A

1 - amylase - (carbohydrase) catalyses / hydrolyses digestion of starch into maltose (in saliva / small intestine lumen)
2 - trypsin - (pancreatic endopeptidase) catalyses / hydrolyses proteins into smaller peptides by breaking peptide bonds (in small intestine lumen)

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8
Q

state the general function of enzymes

A
  • control all metabolic pathways in body
  • speed up reactions without being altered, destroyed or used up (biological catalysts)
  • specific to certain substrates
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9
Q

describe the structure of an enzyme

A
  • polymer of amino acids
  • precise secondary and tertiary structure
  • has at least one ‘cleft’ called the active site - the tertiary structure results in the active site being specific to certain substrates
  • inside the active site, there are a few amino acids with a reactive ‘R’ group - these can form temporary bonds with the substrate, producing an ESC
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10
Q

define ‘anabolic’

A

binding 2 or more substrates together

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11
Q

define ‘catabolic’

A

breaking down a substrate

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12
Q

explain the ‘induced fit’ model of enzyme action

A
  • shape of active site is not directly complementary to substrate and is flexible
  • when active site and substrate make contact, the enzyme moulds itself to a perfect shape - this is known as conformational changes
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13
Q

explain the ‘lock and key’ model of enzyme action

A
  • substrate fits into active site perfectly as the shapes are complementary
  • active site has rigid shape (determined by tertiary structure) so is only complementary to one substrate
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14
Q

define ‘activation energy’

A

energy required for a reaction to take place

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15
Q

how do enzymes lower required activation energy?

A
  • they hold reacting ‘R’ groups in the optimum position
  • the destabilisation of bonds in a substrate makes it more reactive
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16
Q

define ‘enzyme substrate complex’ / ESC

A

substrate has just joined active site / enzyme

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17
Q

define ‘enzyme product complex’ / EPC

A

substrate has separated into products but is still attached to active site

18
Q

name 5 factors that affect the rate of enzyme controlled reactions

A
  • enzyme concentration
  • substrate concentration
  • concentration of inhibitors
  • pH
  • temperature
19
Q

why might there be lack of enzymes in an organism?

A
  • enzyme synthesis might be slow - it sometimes depends on genes being switched on or off
  • enzyme degradation - they are constantly being remade in order to eliminate abnormally shaped molecules as well as to eliminate any surplus
20
Q

how does substrate concentration affect rate of reaction?

A
  • given that enzyme concentration is fixed, rate increases proportionally to substrate concentration
  • rate levels off when maximum number of ESC’s are formed / all active sites are occupied
21
Q

how does enzyme concentration affect rate of reaction?

A
  • given that substrate is in excess, rate increases proportionally to enzyme concentration
  • the greater the number of enzymes, the more successful collisions with substrates so more product produced
22
Q

how does temperature affect rate of enzyme controlled reactions?

A
  • rate increases as kinetic energy increases and peaks at optimum temperature
  • above optimum temperature, ionic and H-bonds in tertiary structure break, making the active site no longer complementary to substrate causing the enzyme to denature
23
Q

what is the temperature coefficient?

A
  • Q10 = R2 / R1 (where R represents rate)
  • measures the change in rate of reaction per 10 degrees temperature increase
24
Q

how does pH affect rate of reaction?

A
  • enzymes have a narrow optimum pH range
  • outside this range, excess H+ / OH- ions interact with H-bonds and ionic bonds in tertiary structure, affecting how the substrate binds and potentially denaturing the enzyme
25
Q

describe how an enzyme breaks down a substrate

A
  • substrate shape is complementary to active site
  • substrate enters and binds to active site
  • induced fit means enzyme moulds shape to fit perfectly with the substrate, forming and ESC
  • bonds in substrate destabilise to form an enzyme product complex
  • products leave active site
26
Q

when does ‘inhibition’ occur?

A
  • when the action of an enzyme is slowed down or stopped by the action of another substance which is known as an ‘inhibitor’
  • this can affect the way the substrate binds to the enzyme, or the enzymes turnover
27
Q

how do competitive inhibitors work?

A
  • they bind to the active site since they have a similar shape to the substrate
  • this temporarily prevents ESC’s from forming until the inhibitor is released
  • reduces number of free active sites, so slows rate of product formation
  • can be reversible or irreversible
  • increasing substrate concentration decreases their effect
28
Q

how do non-competitive inhibitors work?

A
  • bind at ‘allosteric’ binding site
  • trigger conformational change of active site
    making substrate no longer complementary
  • prevents formation of ESC’s
  • can be reversible or irreversible
  • increasing substrate concentration has no impact on their effect
29
Q

what is end product inhibition?

A
  • one of the products of a reaction acts as a competitive or non competitive inhibitor for an enzyme involved in the pathway
  • essentially a sequence of enzyme catalysed reactions
  • product of the last reaction normally binds to the first enzyme in the reaction
  • prevents accumulation of too much end product
  • prevents further formation of products
30
Q

what are irreversible inhibitors?

A
  • permanently prevent formation of ESC’s
  • heavy metal ions e.g. mercury cause disulphide bonds in tertiary structure to break
  • bind to enzymes by strong (covalent) bonds
31
Q

what are reversible inhibitors?

A
  • may be competitive or non-competitive
  • binds to enzyme temporarily (by H-bonds or a few ionic bonds)
  • ESC’s can form after the inhibitor is released
32
Q

define ‘metabolic poison’?

A

substance that damages cells by interfering with metabolic reactions, usually an inhibitor

33
Q

what are cofactors?

A

non protein compounds required for enzyme activity:
- coenzymes
- inorganic cofactors
- prosthetic groups

34
Q

what are coenzymes?

A
  • organic cofactors that do not bind permanently and often transport molecules or electrons between enzymes
  • frequently derived from water soluble vitamins
  • larger organic molecules
  • are chemically changed in reactions so need to be recycled
35
Q

name an example of a metabolic poison and describe its action and effect

A
  • cyanide
  • non-competitive, irreversible, inhibits cytochrome c oxidase
36
Q

how do some medicinal drugs act as inhibitors?

A
  • penicillin - non-competitive inhibitor of transpeptidase to prevent formation of peptidoglycan cross links in bacterial cell wall
  • aspirin - non-competitive, irreversible inhibitor of cyclooxygenase (COX) to prevent inflammation, swelling, pain and fever
37
Q

what are inactive precursors in metabolic pathways?

A
  • to prevent damage to cells
  • some enzymes in metabolic pathways are synthesised as inactive precursors e.g. proteases
  • one part of the precursor acts as an inhibitor, when this is removed ESC’s form
38
Q

what are inorganic cofactors? give an example

A
  • facilitate temporary binding between substrate and enzyme
  • often metal ions
  • e.g. chloride ions are the cofactor for amylase
  • e.g. calcium ions needed to catalyse the reaction of fibronigen into fibrin by the enzyme thrombin
39
Q

what are prosthetic groups? give an example

A
  • tightly bound cofactors act as a permanent part of enzymes binding site, binded covalently
  • e.g. zinc for carbonic anhydrase
40
Q

how do cofactors help enzymes?

A
  • they act as co-substrates -> they bind to the substrate making it the correct shape to fit into the active site of the enzyme
  • they alter charge -> they alter charge distribution on the surface of the substrate/surface of the active site making temporary bonds that make forming the ESC easier
41
Q

give two examples of coenzymes

A
  • coenzyme A -> needed for many metabolic pathways, including respiration
  • vitamin B3 -> needed for enzyme pyruvate dehydrogenase to catalyse a reaction for respiration, lack of B3 can cause pellagra
42
Q

are active sites hydrophobic or hydrophillic?

A

most are hydrophobic

2 - foundations in bio (6 decks)

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