enzymes Flashcards
LOs:
what is the active site
region of the enzyme = has a specific 3D conformation that is complementary in shape and charge to a specific substrate
what are the residues found in the active site and their functions
contact residues: help to position the substrate in the correct orientation via weak interactions (hydrogen, ionic bonds and hydrophobic interactions)
catalytic residues: have specific R groups which act on bonds in the substrate and help to catalyse the conversion of substrate to product (catalytic activity)
what are the residues found in the enzyme and their functions
structural residues: interact with each other to maintain the overall 3D conformation of the protein
describe lock and key hypotheis
enzyme: lock
specific substrate: key
1. the enzyme’s active site has a conformation which is complementary in shape and charge to a specific substrate
2. enzyme and substrate collide in correct orientation
3. substrate binds to active site to form a enzyme substrate complex
4. catalysis occurs = products no longer fit active site = leave active site
5. active site available for another substrate molecule to bind
describe induced fit hypothesis
- binding of substrate to the enzyme active induces a conformational change in active site of enzyme
- enzyme’s active site now provides a more precise fit for the substrate
- enzyme can perform its catalytic action more effectively
what are the effects of temperature on an enzyme catalyzed reaction
as temperature increases,
1. kinetic energy* of enzyme and substrate molecules increase
2. frequency of effective collisions* between substrate and enzyme increase = forms enzyme-substrate complex
3. number of molecules having sufficient energy to overcome the activation energy barrier and
to form the products of reaction increases;
4. Reaction rate increases with temperature up to the optimum temperature where rate of rxn will peak
5. For enzyme-catalysed reactions within physiological temperatures, the rate of chemical reaction
doubles for each 10ºC rise in temperature (Q10 = 2);
6. Each enzyme has an optimal temperature* (humans 25oC – 40oC)
7. at optimum tempetaure: the greatest number
of effective molecular collisions occurs = max rate of reaction; Beyond optimum temperature, 8. kinetic energy of enzyme and substrate molecules continue to increase
9.intramolecular vibrations of enzyme molecule increase
10. hydrogen, ionic
bonds and other weak interactions that stabilizes the conformation of enzyme are disrupted
11. The enzyme denatures = the active site no longer complementary to shape and charge the substrate
12. rate of formation of enzyme subtrate complexes decreases = the rate of reaction
decreases;
what are the effects of enzyme concentration on an enzyme catalyzed reaction and the respective graph shape
when [enzyme] is increasing - linear graph
1. frequency of effective collisions btwn enzymes and substrate molecules increase
2. rate of enzyme-substrate complex formation increases = rate of reaction increases
when [enzyme] is limiting - linear graph
3. increasing [enzyme] will result in a steep increase in the rate of rxn
curved graph
4. rate of reaction increases at decreasing rate = [enzyme] is not the only limiting factor
plateau
5. [enzyme] no longer limiting factor = incresing [enzyme] will ot affect rate of rxn
what are the effects of [substrate] on an enzyme catalyzed reaction and the respective graph shape
linear shape
1. when [substrae] is low, active sites of enzymes are readily available and [substrate] is limiting
2. as [substrate] increases, frequency of effective collisions between enzyme and substate molecules increases
3. rate of enzyme substate complex formation increases = rate of rxn increases
plateau
4. at certain [substrate], all active sites of enzymes are saturated with substrate at any one point of time
5. [substrate] no longer limiting, [enzyme] is limiting
6. rate of rxn remains constant and reaches maximum velocity Vmax
what is michealis constant (Km)
[substrate] required to make the reaction attain half its maximum rate (1/2 Vmax) = is a measure of the affinity of the enzyme for its substrate
constant for an enzyme, but varies across enzymes
what does low Km mean
high affinity betwenn enzym and substrate = low [substrate] needed to attain 1/2 Vmax = enzyme is more efficient at catalysing the reaction even with low [substrate]
what does high Km mean
low affinity between enme and substrate = high [substrate] needed to attain 1/2 Vmax = enzyme is less efficient at catalysing the reaction at low [substrate]
how does pH level affect enzyme-catalysed reactions
at optimum pH
1. conformation of active site is most ideal for substrate binding and rate of reaction is highest
deviation from optimum pH
2. excess H+ or OH- affects ioniation of thr R groups of amino acid residues
3. excess H+ results in COO- groups becoming -COOH
4. excess OH- results in -NH3 becoming -NH2
5. ionic bonds and hydrogen bonds that maintain the conformation of the active site are disrupted = enzyme denatures
6. interaction between substrate and catalytic residues in active site is disrupted = rate of formation of enzyme substrate complex decrease
7. rate of reaction decreases
how does pH level affect contact amino acid residues in an enzymatic reaction
the specific* charge of the contact/binding residues* in the active site are affected =no longer complementary to charge of substrate = may
affect the temporary binding between the enzyme and substrate → no enzyme-substrate-complex* formed = may affect the catalytic process itself
how does pH level affect catalytic amino acid residues in an enzymatic reaction
pH changes the specific* charge of the R groups* of the catalytic residues* in the
active site* = catalytic activity of enzyme may be lost;
how does the pH level affect the structural residues in an enzymatic reaction
charges on the residues change = iformation of ionic and hydrogen bonds which determine the tertiary structure of the protein is disrupted = specific 3D conformation of the enzyme active site is changed = enzyme is denatured
how does pH level affect an enzymatic reaction if the substrate is a protein as well
charges on the residues of the proteins will change = affects substrate interaction with the enzyme active site and/or catalysis
function of the enzyme cofactors inorganic ions
mould enzyme or substrate = allows enzyme substate complex to form more easily
how do enzymes lower activation energy of reaction
- proximity effects: temporary binding of substrates in close proximity in enzyme active site increases chances of a reaction
- orientation effects: substrates are held by enzymes in their active sites in an orientation that will enable the bonds in substrates to be exposed to chemical attack
- strain effects: slight distortion of substrates when they bind to thr active site = strains the bonds in substrates that need to be broken for products to form
- microenvironment effects: provide a favourable environement for catalysis
- acid-base catalysis: R groups of acidic and basic amino acids in enzymes facilitate catalysis
functions of the enzyme cofactors prosthetic groups
they are permanently bound to enzymes and transfers atoms/chemical groups between active site of enzyme and substance
what are the enzyme cofactors coenzymes and their functions
- are organic molecules that are required by certain enzymes to carry out catalysis
- bind to active site and participate in catalysis - but not considered substrates of reaction
- function as intermediate carriers of electrons/specific atoms that are transferred in overall rxn
describe competitive inhibition
inhibitor and substrate have similar structure = both compete for active site of enzyme = reduces availability of active sites for substrate binding = rate of rxn decreases
effects of increasing [substrate] on competitive inhibition
- at high [substrate]: higher proportion of substrate molecules compared to inhibitor = effectively outcompetes inhibitor for active site
- effects of inhibition are overcome
- Vmax can be reached at high [substrate]
- Vmax reamins the same, Km increases
structure of competitive inhibitor
complementary to active site
similar to substrate
consits of 1 subunit with 1 active site
structure of allosteric activator/inhibitor
complementary to allosteric site
multmeric: has multiple active sites and allosteric sites
describe non competitive inhibition
inhibitor binds to a site other than the active site = conformational change in enzyme active site = substrate can no longer bind to active site = rate of reaction decreases
structure of non competitive inhibitor
complementary to site other than the active site
consists of 1 subunit with 1 active site
effects of increasing [substrate] on non competitive inhibition
- when inhibitor binds to site other than the active site, it changes the confomation of active site
- forms inactive enzyme-inhibitor complex= effectively decreases available [enzyme]
- incresing [substrate] = more inactive enzyme-inhibitor complexes are formed
- effects of inhibition cannot be overcome by increasing [substrate]
- Vmax decreases, Km remains the same
describe allosteric activation
activator binds to allosteric site of enzyme = results in conformational change in enzyme = stabilises enzyme in active state (shifts curve to left) = enzyme has higher affinity for substrate
describe allosteric inhibition
inhibitor binds to allosteric site of enzyme = results in conformational change in enzyme = stabilises enzyme in inactive state (shifts curve to right)
effect of increasing [substrate] on allosteric inhibition/activation
- substrate binding further stabilises enzyme in active conformation (even when inhibitor is bound to enzyme) = opposes effect of inhibitor = Vmax can be reached at high [substrate]
- substrate binding is cooperative: binding of asubstrate to first subunit changes conformation of other subunits = easier to accept subsequent substrates
