subject guide notes
C1.1.1—Enzymes as catalysts
enzymes can speed up the rate of reaction
they do this by lowering the activation energy (the energy barrier a reaction has to overcome)
this allows the reaction to occur more easily
but they’re not changed or used up in the reaction
so they can catalyse chemical reactions over and over, without being used up
cells can control the rate of metabolic reactions, by producing more or less of the enzyme
C1.1.2—Role of enzymes in metabolism
due to enzyme specificity, different types of enzymes are required by organisms
1 enzyme aids with 1 chemical reaction
C1.1.3—Anabolic and catabolic reactions
anabolism includes monomers undergoing condensation reactions, in order to form macromolecules
ex: protein is made from amino acids that undergo condensation reactions
starch is made from glucose units that undergo condensation reactions
anabolism requires energy
catabolism releases energy through hydrolysis reactions
ex: hydrolysis of macromolecules into monomers during digestion
or breakdown of sugars or fats, in order to release energy
C1.1.4—Enzymes as globular proteins with an active site for catalysis
active site is composed of a few amino acids & is where catalysis occurs
interactions between the amino acids in the 3D structure of the enzyme, ensures that the active site has the necessary properties for catalysis
active site is result of folding of polypeptide chains
specific binding of the substrate & active site can occur, because they both share similar chemical & physical properties
the shape of the active site is also specific, so the substrate that matches the shape, can bind to the active site
C1.1.5—Interactions between substrate and active site to allow induced-fit binding
the induced fit-model states that when the substrate binds to the enzyme, it triggers a structural change in the enzyme, which allows a tighter fit
is called an induced fit
is possible cuz of the flexibility of the protein molecules that make up the enzyme
when the enzyme & substrate fit together, the enzyme will weaken the bonds within the substrate
this lowers the activation energy needed for the reaction
once the reaction has occurred, substrate converted to product(s)
these products no longer fit in the active site & are released from enzyme
enzyme’s active site returns to its original shape & is empty
C1.1.6—Role of molecular motion and substrate-active site collisions in enzyme catalysis
enzymes and substrate mix & bump into each other
if the active site & substrate collide with enough energy & in the correct orientation, a chemical reaction occurs
however, there are some exceptions
if the substrate is immobilised, then enzyme has to more to substrate
if enzyme is immobilised, then substrate has to move to it
enzyme could be immobilised if it’s embedded into the membrane & therefore cannot move
C1.1.7—Relationships between the structure of the active site, enzyme–substrate specificity and denaturation
certain enzymes can bind to only one substrate, while other enzymes can bind to multiple substrates
enzyme-substrate specificity is caused by the matching chemical & physical properties of both the active site & substrate
the shape of the substrate should also match the shape of the active site
enzymes are proteins, so they can be denatured
denaturation destroys tertiary & quaternary conformation of protein
if temp is high enough or pH is extreme enough, the secondary conformation could also be destroyed
denaturation typically permanently prevents the enzyme from functioning
C1.1.8—Effects of temperature, pH and substrate concentration on the rate of enzyme activity
temperature
low temp = molecules move slow = less chance of collision between enzymes & substrates
high temp = molecules move quick = higher change of collision
each enzyme has optimal temperature, where the rate of enzymatic reaction is highest
if temp is higher than optimal - enzyme can be denatured
enzymatic reaction quickly declines
pH
each enzyme has optimal pH, where rate of enzymatic reaction is highest
alter active site = denaturation
affects charges on amino acids in the active site
amino acids won’t be attracted to each other
substrate concentration
increase in substrate concentration = more chances of collision = slow increase in enzymatic reaction
but this increase is stopped when all active sites are occupied by substrates
after this point, adding more substrates has no effect on the rate of reaction
C1.1.9—Measurements in enzyme-catalysed reactions
just know independent variable & dependent variable
C1.1.10—Effect of enzymes on activation energy
in order for substrate to be converted to products, it has to pass a transition state
activation energy is the minimum amount of energy needed, in order to reach the transition state
the bonds in the substrate are broken & the reaction continues to form products
however note that the overall energy released during the reaction, is the same in catalysed & uncatalyzed reactions
can check interactive in this section in kognity
C1.1.11—Intracellular and extracellular enzyme-catalysed reactions
intracellular and extracellular metabolic pathways are two pathways to carry out different metabolic reactions
intracellular reactions are catalysed by enzymes that’re produced by free ribosomes
ex: glycolysis - breaks down glucose into 2 pyruvate molecules, releasing energy in the process
ex: Krebs cycle - oxidises acetyl-CoA to produce carbon dioxide, electron carriers & energy-rich molecules
extracellular reactions are catalysed by enzymes that’re produced by bound ribosomes & secreted outside the cell through exocytosis
ex: digestive enzymes such as lipase, amylase and proteases are secreted extracellularly by acinar cells in the pancreas in order to catalyze digestive reactions in the gut
C1.1.12—Generation of heat energy by the reactions of metabolism
metabolic reactions aren’t 100% efficient, meaning some energy is always ‘lost’ as heat
so, heat generation is inevitable (it will definitely occur cuz metabolic reactions aren’t completely efficient)
warm-blooded organisms rely on this generation of heat in order to maintain a constant body temp
C1.1.13—Cyclical and linear pathways in metabolism
linear pathways involve a series of complex steps, which produce an end-product
ex: glycolysis
cyclical pathways are linked to other pathways
they also involve a starting compound being converted into an intermediate product, which is then processed to regenerate the original starting compound
ex: Krebs cycle, cuz glycolysis is linked directly to the Krebs Cycle
C1.1.14—Allosteric sites and non-competitive inhibition
when non-competitive inhibitors bind to the allosteric site, the enzyme’s shape changes
this means the substrate can no longer bind to the active site
so fewer enzymes are available to catalyse the reaction
the rate of reaction with a non-competitive reaction, is lower
binding is reversible
increasing concentration of substrate has no effect on the non-competitive inhibitor’s impact
C1.1.15—Competitive inhibition as a consequence of an inhibitor binding reversibly to an active site
competitive inhibitors compete with substrate for active site
increase in substrate concentration = increase in rate of reaction cuz there’s more substrate than inhibitors
so the substrates can bind to the active site before the inhibitors
competitive inhibitors are also chemically similar to the substrate, which means they match the chemical composition of the active site & can bind to it
ex: statin drugs
these drugs inhibit the enzyme HMG-CoA reductase
they bind to its active site, preventing cholesterol production
C1.1.16—Regulation of metabolic pathways by feedback inhibition
when the end-products of a reaction are no longer needed, they can function as non-competitive inhibitors & bind to the allosteric reaction
this prevents the function of the first enzyme that catalyses the reaction
prevents the reaction from occurring again
ex: isoleucine is an essential amino acid
once it’s produced, it can allosterically bind to the enzyme that catalyses the first step
so the substrate can no longer bind to the enzyme
C1.1.17—Mechanism-based inhibition as a consequence of chemical changes to the active site caused by the irreversible binding of an inhibitor
mechanism-based inhibition is irreversible
inhibitor binds to the active site through a covalent bond
the enzyme permanently loses its catalytic activity
ex: penicillin
this binds to transpeptidase (which is an enzyme that maintains the rigidity of cell wall)
this inhibits transpeptidase’s function, meaning the cell wall is weakened & the bacterial cells burst & are killed