c1.1 enzymes & metabolism Flashcards
what is metabolism?
metabolism is the sum of all chemical processes that occur within a living organism in order to maintain life. it is the web of all enzyme-catalysed reactions that occur within a cell or organism.
metabolic reactions serve two functions:
- they provide a source of energy or simple molecules for cellular processes
- they enable the synthesis and assimilation of new materials for use within the cell.
what is an enzyme?
enzymes are biological catalysts - they speed up metabolic reactions but aren’t used up.
what is the structure of an enzyme?
enzymes are globular proteins with an active site, where catalysis takes place.
the specificity of an enzyme is a result of the complementary nature between the shape of the active site on the active site on the enzyme and its substrates. the shape of the active site is determined by the complex 3D shape of the protein that makes up the enzyme.
why does all life depend on enzymes?
reactions such as oxidation do occur naturally, however living organisms need enzymes to help them happen quickly.
human cells contain around 1300 different enzymes. all enzymes are specific to their substrate. as such, every step of a metabolic pathway that generates a new intermediate compound needs a new enzyme.
each step along the pathway changes the energy level by a small amount. so reactions with large energy changes, such as respiration, need many steps.
what is anabolism?
anabolic reactions are involved with the building of large molecules from smaller ones. they often include condensation reactions. anabolic reactions are endergonic (requiring an input of energy to take place aka endothermic) meaning energy storing products are the end result.
examples include: photosynthesis, protein synthesis, formation of glycogen
what is catabolism?
catabolic reactions are involved with breaking down large molecules into smaller, simpler ones. they often include hydrolysis reactions. catabolic reactions are exergonic (releasing energy aka exothermic) meaning these reactions are often carried out to release energy for cellular processes and for the excretion of waste.
examples include: respiration, deamination, breakdown of macromolecules
what are the consequences of a mutation?
a mutation is a change in the sequence of bases in DNA. this results in different codon triplets and so we get a different sequence of amino acids, meaning we get a different shaped protein (or enzyme).
what is the induced fit model?
the induced fit model suggests that as the substrate enters the active site, it causes a conformational change in the protein structure. this movement either brings the reaction molecules together (anabolism) or stretches and weakens the bonds (catabolism).
how does kinetic energy link to catalysis?
in order for the substrate molecule to collide with an ultimately bind to the enzyme active site, movement is required. this is the result of the kinetic energy that molecules have. the greater the kinetic energy of the molecules, the faster the movement and the higher the probability of the enzyme and substrate colliding. this leads to more enzyme substrate complexes forming and the production of more product molecules.
what are immobilised enzymes?
in some cases, large substrate molecules are immobilised, while in other cases it is possible to immobilise enzymes by embedding them in membranes. these immobilised enzymes can be used in a range of industries such as food processing, environmental management, pharmaceuticals and manufacturing process.
what are the advantages of immobilised enzymes?
advantages of immobilised enzymes are that there is no enzyme in the product and therefore there is no need to further process or filter the end product. the immobilised enzyme can be reused multiple times which is both efficient and cost effective. immobilised enzymes have a greater tolerance of temperature and pH changes. substrates can be exposed to higher enzyme concentrations than when using enzymes in solution, increasing the rate throughout.
how are immobilised enzymes used in cells?
within cells, many of the enzymes involved in regulating metabolic processes are embedded in membranes such as the cristae of mitochondria or the thylakoids of chloroplasts.
the organelle can ensure the enzymes are located where internal processes that maximise the concentration gradients of the necessary substrates or supplies of ATP so that the reactions happen at their fastest rate.
what is denaturation?
enzymes can be denatured when it is exposed to high temperatures or extremes of pH. bonds holding the enzyme molecule in its precise 3D shape start to break. this causes the 3D shape of the protein to change and permanently changes the shape of the active site, preventing the substrate from binding.
explain the graph of enzyme activity against temperature
- as temperature increases, the particles have more KE. there are more successful collisions between enzyme and substrate. substrate binds more often with active site.
- optimum: temperature at which there is the fastest rate.
- denaturing of enzymes, substrate no longer complementary and reaction stops.
explain the graph of enzyme activity against pH
- denaturing at low pH, substrate no longer complementary and reaction stops.
- optimum: pH at which there is the fastest rate.
- denaturing at high pH, substrate no longer complementary and reaction stops.
explain the graph of enzyme activity against substrate concentration
- as concentration increases, there are more successful collisions between the substrate and active site.
- plateaus: all enzyme active sites are full and so any additional substrate has nowhere to bind. this is known as the saturation point.
what is the effects of enzymes on activation energy?
all chemical reactions, including metabolic pathways, are associated with energy changes. for a reaction to proceed there must be enough activation energy - the amount of energy needed by the substrate to become unstable enough for a reaction to occur and for new products to be formed. enzymes speed up chemical reactions because they reduce the stability of bonds in the substrate. they lower the activation energy needed to catalyse a reaction.
how do you calculate rate of reaction?
rate of reaction = change in amount (mol dm ^-3) / time (s)
rate of reaction = 1 / time taken (s^-1)
what are intracellular and extracellular enzymes?
enzymes can be intracellular or extracellular based on whether they are active inside or outside of the cell. extracellular enzymes are produced inside the cell and then packaged into vesicles before being secreted by the cell, where they will catalyse reactions outside the cell. most enzymes however are intracellular, meaning they are produced and function within the cell.
what are exergonic reactions?
reactions that release free energy are known as exergonic reactions. many metabolic reactions are exergonic, and some of the energy is released as heat because the energy transfer is not 100% efficient.
what are endergonic reactions?
reactions where energy is absorbed are called endergonic reactions. the products formed by these reactions will have more stored energy than the reactants. since endergonic reactions require an energy input, they are often linked to exergonic reactions in metabolism. ATP acts as the intermediate that links the energy yielding reactions to the energy absorbing ones.
what are linear and cyclical reactions?
metabolic pathways involve a series of small steps, each involving a chemical change. the enzyme catalysed reactions that make up metabolic pathways usually consist of linear or cyclical reactions. linear reactions are a linear sequence with a distinct beginning and end. cyclical reactions involve the end product starting the next cycle - these are less common than linear reactions.
what are enzyme inhibitors?
inhibitors are chemical substances that can bind to an enzyme and reduce its activity. inhibitors can be formed from within the cell or can be introduced from the external environment. increasing the concentration of an inhibitor reduces the rate of reaction and eventually the reaction will stop completely.
what are non competitive inhibitors?
non-competitive inhibitors bind to the enzyme at an alternative site which is not the active site. these sites are called allosteric sites and they are usually located far from the active site. binding to the allosteric site causes interactions within an enzyme which leads to conformational changes. this therefore prevents the substrate from binding to the active site.
how do non competitive inhibitors affect rate of reaction?
non-competitive inhibitors lower the initial and the maximal rate of reaction, meaning a lower amount of product is produced than normal.
increasing the substrate concentration for non-competitive inhibitors cannot increase the rate of reaction, as the shape of the active site remains unchanged and enzyme-substrate complexes are still unable to form.
what are competitive inhibitors?
competitive inhibitors have a similar shape to that of the substrate molecules. they bind to the active site of the enzyme, interfering with it and competing with the substrate for the active site.
how do competitive inhibitors affect rate of reaction?
a competitive inhibitor will lower the initial rate of reaction, whilst the maximal rate is not affected. eventually the same amount of product will be produced.
increasing the substrate concentration for competitive inhibitors can increase the rate of reaction but the substrate needs to reach a high enough concentration in order to displace the inhibitor.
what are statins?
statins are drugs that are prescribed to lower cholesterol levels by binding to the active site of the enzyme needed to synthesise cholesterol. this inhibits the enzyme from catalysing the reaction that synthesises cholesterol, leading to cholesterol levels decreasing in the blood.
what is end product inhibition?
end product inhibition occurs when the end product from a reaction is present in excess and itself acts as a non-competitive inhibitor of the enzyme. the end product binds to an allosteric site on the enzyme and causes inhibition of the pathway. they are important as they prevent the build up of intermediate products in a metabolic pathway, as each small step of the pathway may produce a new product. the product therefore does not accumulate and the pathway can continue.
how is isoleucine an example of end product inhibition?
the amino acid isoleucine can be synthesised from threonine in bacteria. isoleucine can bind to the allosteric site of the enzyme threonine deaminase. at the start of the process, isoleucine levels are low so the metabolic pathway can proceed without being inhibited. however, as the concentration of isoleucine increases, it begins to regulate the metabolic pathway by acting as a non-competitive inhibitor.
what is mechanism based inhibition?
molecules that are able to form covalent bonds with the active site of an enzyme are known as a substrate analogue. the substrate analogue can now be changed by the enzyme to produce a reactive group. this form of inhibition is called mechanism based inhibition and is irreversible.
how is penicillin an example of mechanism based inhibition?
penicillin is an antibiotic that is very effective at killing bacteria. penicillin inhibits the strengthening of a bacteria’s cell wall by stopping the formation of cross links between peptidoglycan molecules. it binds to an enzyme called transpeptidase, which permanently blocks the enzyme from creating more cross links. the cell wall will then burst as it can no longer withstand the pressure inside the cell.
bacteria may however develop resistance to penicillin. DNA mutations in the bacterial genome may lead to changes in the shape of the active site of transpeptidase, which makes it difficult for penicillin to bind and inhibit the enzyme.
