enzymes Flashcards
what do enzymes do?
they lower the activation rate
increase the rate of the reaction
they’re not consumed in the reaction
they don’t affect the equlibrium
what are the stages of an enzyme-catalysed reaction?
the substrate enters the active site
the substrate is held in the active site by weak interactions
substrates are then converted into products
then the products are released and the active site is free for more substrates to bind
what are the properties of an active site of an enzyme?
the position of the substrate is in the mouse favourable position
it’s complementary to the transition state
the amino acid side chains help to stabilise the electron distribution of the transition state
the transition state very quickly turns into products
the products have a low affinity for the active site
there are non-covalent interactions between the substrate and the amino acid side chains in the enzyme
what are the properties of an active site of an enzyme?
the position of the substrate is in the mouse favourable position
it’s complementary to the transition state
the amino acid side chains help to stabilise the electron distribution of the transition state
the transition state very quickly turns into products
the products have a low affinity for the active site
there are non-covalent interactions between the substrate and the amino acid side chains in the enzyme
what does the catalytic site do?
it donates/ withdraws electrons and stabilises/generates intermediates and forms temporary covalent bonds
what does the catalytic site do?
it donates/ withdraws electrons and stabilises/generates intermediates and forms temporary covalent bonds
what are the 2 ways that enzymes work?
lock and key
induced fit
what features are important for binding of the enzyme to the substrate?
shape
conformation
charge
what is ‘specific activity’?
its the activity of an enzyme/mg of total protein in the enzyme preparation (μ mol min-1 mg-1)
what are the units of enzyme activity?
1 enzyme unit (EU)= 1 μ mol min-1
this is the no. of micromolecules of substrate converted per min under standard conditions
what are co-factors?
they’re non-protein molecules found in enzymes
like metal groups- Mg2+
what are coenzymes?
theyre tightly bound (but not covalently bound) organic molecules (like NAD)
what are holo-enzymes?
theyre enzyme proteins with prosthetic groups ot co-enzymes
they’re catalytically active
what are apoenzymes?
its the protein part of the holo-enzyme that doesn’t have the prosthetic group
its also catycally inactive
what are oxidoreductases?
theyre enzymes involved in redox reactions
what are dehydrogenases?
they remove/ add H
what are oxidases?
they transfer 2 electrons to make H2O2 or H2O (if only half an O molecule is present)
what are oxygenases?
they incorperate O2 into the product
what are hydroxylases?
they incorperate half the O2 into the product in the form of -OH (in order to form H2O at the end
what are peroxidases?
they use H2O2 as an oxygen donor to form H2O
what are transferases?
they transfer the chemical group from one substrate to another
what are kinases?
they transfer P from ATP onto the substrate
what are hydrolases?
they cause hydrolysis to occur
what are some examples of hydrolases?
esterases, proteases, phosphatases and thioesterases
what are lysases?
they add molecules accross the C=C bond
what are isomerases?
theyre intramolecular rearrangements
what are synthetases?
they form bonds between the substrates and are often linked to using ATP
what are the factors which affect enzyme activity?
pH
temperature
concentration of enzyme
how does pH affect enzyme activity?
the binding of the substarte and the isonisation state of the amino acid side chains are affected
the binding of the substrate and catalyisis means its important for the proteins to be at the right pH so that they have the right conformation
how does temperature affect enzyme activity?
chemical reactions happen quicker at higher temps as the molecules have a higher chance of colliding and the electrons gain energy easier
the optimum temperature depends on the time of incubation
high temperatures can also denature enzymes which leads to the loss of H bonding, then unfolding and then precipitation
how does varying the amount of enzyme affect enzyme activity?
the active enzyme could disassociate low concentrations
there’s a linear increase in reaction rate when you increase the amount of enzyme present
how do you calcukate the reaction rate?
Vmax= max rate / velocity of the reaction
1/2 Vmax =Km (this is the typical value to see how well en enzyme works)
what does a low and a high Km mean?
high =the molecules haveing low affinities for the substrate
low = the molecules having high affinities for the substrate
what is a sequnetial reaction?
its a reaction with an enzyme which has 2 substrates and the reactions happen in turn, one after another
what is a ternary complex?
its a complex which has 3 different molecules in it
what is dihydrofolate reductase?
this has loop and domain movements (it works on e.coli dihydrofolate reductase)
what is a ping-pong reaction?
its when one substrate reacts and modifies the enzyme then the second substrate reacts with the modified enzyme and so on, it produces parallel lines on the graph because one reaction cant happen until the last one has
what are allosteric enzymes?
there enzymes which have binding sites separate from the active site
the bonding of the substrate to the active site causes a conformational change and allows the next substrate to bind to the other binding sites
what does it mean if an enzyme is sigmoidal?
it means that it has more than one active site in the complex
what do enzyme inhibitors do?
they lower the enzymes abiltiy to bind to the substrate and lower its catalytic ability
what do reversible inhibitors do?
these non-covalent bond to the enzyme
they work by blocking the binding or hindering the catalytic steps
what are irreversible inhibitors?
theyre also called inactivators
they covalently bond to the inhibitor and then the transition state intermediate isn’t able to break down
its also called a suicide inhibitor
what are competitive inhibitors?
they compete for binding at the active site
these can be overridden by increasing substrate concentration
what happens to Vmax and Km in competitive reversible inhibition?
Vmax stays the same andq Km increases if there’s enough substrate added to overcome the inhibitor
what are non-competive inhibitors?
they bind to the enzyme at a position separate from the active site and there isn’t any competition for binding with the substrate
