2.1.4 - enzymes Flashcards
what are enzymes?
- 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
how does formation of ESC’s affect activation energy of metabolic reactions?
it lowers it
define ‘hydrolysis’
any chemical reaction in which a molecule of water ruptures one or more chemical bond
can enzymes have more than one active site?
yes
the reactants, intermediates and products in a reaction are known as what?
metabolites
give an example of an enzyme that catalyses intracellular reactions
- catalase
- hydrolyses / catalyses decomposition of hydrogen peroxide into water and oxygen
give 2 examples of enzymes that catalyse extracellular reactions
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)
state the general function of enzymes
- control all metabolic pathways in body
- speed up reactions without being altered, destroyed or used up (biological catalysts)
- specific to certain substrates
describe the structure of an enzyme
- 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
define ‘anabolic’
binding 2 or more substrates together
define ‘catabolic’
breaking down a substrate
explain the ‘induced fit’ model of enzyme action
- 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
explain the ‘lock and key’ model of enzyme action
- 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
define ‘activation energy’
energy required for a reaction to take place
how do enzymes lower required activation energy?
- they hold reacting ‘R’ groups in the optimum position
- the destabilisation of bonds in a substrate makes it more reactive
define ‘enzyme substrate complex’ / ESC
substrate has just joined active site / enzyme
define ‘enzyme product complex’ / EPC
substrate has separated into products but is still attached to active site
name 5 factors that affect the rate of enzyme controlled reactions
- enzyme concentration
- substrate concentration
- concentration of inhibitors
- pH
- temperature
why might there be lack of enzymes in an organism?
- 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
how does substrate concentration affect rate of reaction?
- 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
how does enzyme concentration affect rate of reaction?
- 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
how does temperature affect rate of enzyme controlled reactions?
- 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
what is the temperature coefficient?
- Q10 = R2 / R1 (where R represents rate)
- measures the change in rate of reaction per 10 degrees temperature increase
how does pH affect rate of reaction?
- 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
describe how an enzyme breaks down a substrate
- 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
when does ‘inhibition’ occur?
- 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
how do competitive inhibitors work?
- 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
how do non-competitive inhibitors work?
- 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
what is end product inhibition?
- 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
what are irreversible inhibitors?
- 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
what are reversible inhibitors?
- 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
define ‘metabolic poison’?
substance that damages cells by interfering with metabolic reactions, usually an inhibitor
what are cofactors?
non protein compounds required for enzyme activity:
- coenzymes
- inorganic cofactors
- prosthetic groups
what are coenzymes?
- 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
name an example of a metabolic poison and describe its action and effect
- cyanide
- non-competitive, irreversible, inhibits cytochrome c oxidase
how do some medicinal drugs act as inhibitors?
- 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
what are inactive precursors in metabolic pathways?
- 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
what are inorganic cofactors? give an example
- 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
what are prosthetic groups? give an example
- tightly bound cofactors act as a permanent part of enzymes binding site, binded covalently
- e.g. zinc for carbonic anhydrase
how do cofactors help enzymes?
- 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
give two examples of coenzymes
- 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
are active sites hydrophobic or hydrophillic?
most are hydrophobic
