C1.1 Enzymes and metabolism

what is an enzyme

mainly proteins that function as biological catalysts

what is a catalyst

a substance that speeds up the rate of a chemical reaction, catalysts are effective in small amounts and remain unchanged at the end of the reaction

what allows reactions to occur at relatively high rates in cells

enzymes

in general, catalysts

are effective in small amounts, remain unchanged at the end of the reaction

what can cells do by making some enzymes and not others

cells can control what chemical reactions happen in the cytoplasm

what are metabolites

Include all the molecules synthesized or broken down by chemical reactions inside our bodies

what is anabolism

the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions

what is catabolism

the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers

how many substrates can fit into each enzyme

usually only one

how are enzymes usually classified

according to the type of reaction they catalyse and they can be named according to their substrate

what does metabolism consist of

chains and cycles of enzyme-catalysed reactions, such as we seen in respiration, photosynthesis and protein synthesis and in many other pathways

what are some examples of anabolism

the synthesis of proteins from amino acids, the synthesis of polysaccharides from simple sugars, photosynthesis

what are some examples of catabolism

hydrolysis of macromolecules into monomers in digestion, oxidation of substrates in respiration

what is a substrate

the starting substance in a reaction catalysed by an enzyme it is the molecule that the enzyme reacts with

what is the product

what the substrate is converted to in a reaction catalysed by an enzyme

what is the active site

the region of an enzyme molecule where the substrate molecule binds and catalysis occurs

what is the enzyme-substrate complex

a temporary structure formed when a substrate binds to the active site of an enzyme

what type of molecules are enzymes typically

large, globular protein molecules where the tertiary structure has given the molecule a generally rounded shape

how do enzymes work

by binding to the substrate molecule at a specially formed pocket in the enzyme, here the enzyme and substrate from an enzyme-substrate complex, the substrate is raised to a high energy transition state, this complex has the briefest of existences before the substrate molecule is formed into another molecule or broken down into others by the catalytic properties of the active site, then the products are released, together with the unchanged enzyme, the enzyme is available for reuse

how is it ensured that the active site has the necessary properties for catalysis

the interactions between the amino acids within the overall 3D structure of amino acids, including binding to the substrate molecule, holding onto it while the chemical reaction takes place and lowering the energy of the transition state

what is the size of most substrate molecules compared to the enzyme

quite small

what is induced fit

the binding of the substrate to the enzyme causes a change in the shape of the enzyme and the substrate, resulting in the proper alignment of the catalytic groups on its surface, which enables catalysis to take place

why are enzymes specific

because of the way they bind with their substrate at the active site

what happens as the substrate binds to the enzyme

a slight change of shape is induced in the enzyme and substrate molecules

what does the enzyme hexokinase catalyse

glucose + ATP -> glucose-6-phosphate + ADP

what is an immobilized enzyme

an enzyme attached to an inert, insoluble material, enabling recovery, reuse and improved enzyme stability

what is needed for a substrate molecule and an active site to come together

movement, the greater the kinetic energy of enzyme and substrate the greater the chance of collisions between molecules and the formation of enzyme substrate complexes

what method of enzyme use is widely used in food processing, pharmaceuticals and wastewater treatment

Enzymes immobilized on (or in) a membrane

what does the EIM system facilitate

recycling of the enzymes and also, often enhanced enzyme properties,

what does enzyme immobilization involve

the attachment of enzymes to insoluble materials which then provide support

what are the different enzyme immobilization techniques

entrapment, adsorption, covalent bonding, cross-linking, affinity

what are the advantages of using an immobilized enzyme in industrial processes

it permits reuse of the enzyme preparation, the product is enzyme free, the enzyme may be much more stable and long lasting due to protection by the inert matrix

when does denaturation occur

when the weak intramolecular interactions within a globular protein, formed between different amino acid, residues, break, this changes the 3D shape of the active sites

what bonds are not hydrolyzed during denaturation

peptide bonds

what happens when starch is hydrolyzed by the enzyme amylase

maltose is produced

is it sufficient to say when explaining the increase in the reaction rate of an enzyme, because there are more collisions with the enzyme

no, a better answer is, because there are more frequent collisions between the substrate and the active sites

do all enzymes have the same optimum temperature

no, bacteria in thermal springs can have enzymes with optimum temperatures closer to 0C

what is the optimum pH of enzymes often close to

pH 7, the point of neutrality

why does the effect of pH on enzymes occur

because the structure of a protein, and therefore the shape of the active site is maintained by various bonds and weaker intermolecular forces within the proteins structure, a change in pH from the optimum value alters the bonding patterns, progressively changing the 3D shape of the molecule, the active site may quickly be rendered inactive

are the effects of pH on the active sites normally reversible

yes, if the change in pH wasn't too extreme

why do some digestive enzymes have different optimum pH values from most other enzymes

some parts of the digestive system are very acidic so the enzymes must have a lower optimum pH

what do we do when measuring the rate of enzyme catalysed reactions

we measure the amount of substrate that has disappeared from a reaction mixture or the amount of product that has accumulated in a unit of time

what is convenient to measure when investigating the rate of enzyme activity of catalase

the rate at which oxygen accumulates

what is the relationship between the substrate concentration and the rate of reaction

at lower concentrations, the rate increases in direct proportion to the substrate concentration, at higher substrate concentrations, the rate of reaction becomes constant and shows no increase

what is the result of increased concentrations of substrate in terms of collisions

increased concentrations of substrate mean there are more frequent collisions between substrate and the enzyme with a higher likelihood of the substance binding with the active site of the enzyme and enzyme-substrate complexes forming, causing the reaction to take place

what happens when there is more substrate than enzyme

substrate molecules must queue up for access to an active site so there is no increase in the rate of reaction as the substrate concentration is further increased

what is activation energy

the energy required by a substrate molecule before it can undergo a chemical change

how do we represent the reaction between an enzyme and substrate including the transition state

E + S -> [ES] -> ES -> P + E

what happens in terms of energy when the substrate becomes the product

energy is released

how do enzymes work in terms of activation energy

they lower the amount of energy required to activate the reacting molecules by providing a new alternative reaction pathway

do enzymes remove the activation energy barriers

no, they just make it significantly smaller

what is an extracellular enzyme

an enzyme secreted by a cell that functions outside the cell

what is an intracellular enzyme

an enzyme that functions within the cell in which it was produced

what is an example of a type of enzyme that is exported from cells

digestive enzymes

how do extracellular enzymes leave the cell

through endocytosis

what are two of the main metabolic processes in respiration

glycolysis and the Krebs cycle

what happens in terms of energy when glucose is oxidized to carbon dioxide and water in aerobic cell respiration

energy is transferred from the store of chemical potential energy to heat energy

what is free energy

energy available to do work

what are exergonic reactions

reactions that release free energy

give an example of an exergonic reaction

the oxidation of glucose

what is inevitable in metabolic reactions

heat generation

what are endotherms

animals that depend on the release of heat from metabolic reactions for the maintenance of a constant body temperature

what are ectotherms

animals that cannot use metabolic heat to maintain a constant body temperature

what are endergonic reactions

reactions that require energy

what is an example of an endergonic reaction

the synthesis of a protein from amino acids

what is a linear metabolic pathway

a series of enzyme catalysed reactions that run in one direction, from reactant to product

what is a cyclical metabolic pathway

a circular series of enzyme catalysed reactions where there is no end to the series, one reaction leads to the next and eventually back to the starting point

what is a metabolic pathway

a sequence of enzyme catalysed biochemical reactions in cells and tissues

give an example of a linear metabolic pathway

glycolysis

give an example of a cyclical metabolic pathway

the Krebs cycle

what are the two sets of reactions in photosynthesis

the light dependent reactions and the light independent reactions

which cycle drives the light independent reactions in photosynthesis

the Calvin cycle

what is an enzyme inhibitor

a substance that slows or blocks enzyme action

what is a competitive inhibitor

a substance that binds to the active site of an enzyme, slowing or blocking enzyme action

what is a non-competitive inhibitor

a substance that does not bind to the active site but to another part of the enzyme, slowing or blocking enzyme action

what is the enzyme that catalyses the reaction between carbon dioxide and the acceptor molecule in photosynthesis

ribulose biphosphate carboxylase

what is ribulose biphosphate carboxylase competitively inhibited by

oxygen

what is an allosteric regulator

molecules that change the shape and activity of an enzyme by reversibly binding at a site on the enzyme

what does the binding of an allosteric activator do

temporarily stabilize the enzyme shape as an active an effective catalyst

what does the binding of an allosteric inhibitor do

change the enzyme shape into an inactive form

what is allosteric regulation a form of

reversible non-competitive inhibition or activation of an enzyme

what can subtle fluctuations in the concentration of activators and inhibitors do

fine tune the activity of a critical pathway as constantly changing conditions or requirements of cell metabolism demands

what is the name given to the specific substances that can bind to an allosteric site

effectors

what is the rate of an enzyme-catalysed reaction

the amount of substrate that has disappeared from a reaction mixture or the amount of product that has accumulated in a period of time

what is a statin

any class of drugs that lower the level of low density lipoproteins in the blood by inhibiting the activity of an enzyme involved in the production of cholesterol in the liver

what is competitive inhibition a consequence of

an inhibitor binding reversibly to an active site

what type of inhibitor are statins

competitive inhibitors

what do statins competitively inhibit

HMG-CoA reductase

what are statins similar in structure to

the substrate of HMG-CoA reductase

what are the two forms of cholesterol in the blood

low-density lipoproteins, high-density lipoproteins

what can result from excess blood cholesterol, present as LDLs

atherosclerosis

what is atherosclerosis

the progressive degeneration of the artery walls, a direct consequence of this is an increased likelihood of the formation and circulation of blood clots

what are statins taken for

to reduce LDLs in the blood and therefore reduce the risk of coronary heart disease

what is end-product inhibition

when the product of the last reaction in a metabolic pathway inhibits the enzyme that catalyses the first reaction of the pathway

how can individual pathways in metabolism by switched off

by the final product acting as a reversible inhibitor of the enzyme that catalyses the first step in the pathway

what can bacteria synthesize isoleucine from

threonine

explain the metabolic pathway for the synthesis of isoleucine

isoleucine acts as a non-competitive inhibitor by binding to the allosteric site of the enzyme threonine deaminase, threonine deaminase is an essential enzyme in the first stage of the metabolic pathway, its inhibition turns off isoleucine production, this regulates the production of isoleucine, initially, when isoleucine concentration is still low, the metabolic pathway can proceed as non competitive inhibition is low, as isoleucine concentration increases, non-competitive inhibition takes place and the metabolic pathway is regulated, as isoleucine is used in the cell for protein synthesis, its concentration falls and the allosteric sites of threonine deaminase are no longer occupied, so the enzyme can once again act in the conversion of threonine to isoleucine

what is mechanism based inhibition

a process that occurs when unreactive molecules are transformed into an active form through catalytic reactions, these active forms inhibit the enzyme, typically through covalent modification of the active site, it is an irreversible form of enzyme inhibition

what is a substrate analogue

a molecule that has a similar structure to the substrate

describe mechanism-based inhibition

a substrate analogue binds to the active site of the enzyme covalently, the substrate analogue is modified by the enzyme to produce a reactive group, which reacts irreversibly to form a stable inhibitor-enzyme complex