Enzymes Flashcards
What are functions of enzymes?
- reduces activation energy
- enables biological rections to proceed at faster rates
properties of enzymes?
- enzymes can be hydrolyzed by dilute acids or alkali to form free AA or low molecular weight peptides
- E can be broken down by proteases to form AA or peptides with participation of H2O
- E can respond to typical common protein tests (ie. ninhydrin and lowry)
- E is comprised of AA linked together by peptide bonds
what can hydrolyze enzymes?
what do they form?
dilute acids or alkali; or peptides
forms free AA or low molecular weight peptides
what links AAs together?
peptide bonds
sizes of collagen, myosin, trypsin, amylose?
collage: 100-400kDa
myosin: 200kDa
trypsin: 20kDa
amylose: 40-50kDa
def of proenzyme?
immature and inactive enzyme
def of holoenzyme?
complete enzyme that is active
it is bound to its cofactor
def of apoenzyme?
enzyme that requires a cofactor
it is inactive
becomes active when it is bound to a cofactor
def of a prosthetic group?
the non-protein part that forms a part of a protein
examples of prosthetic groups?
metal ions: Ca, Fe, Zn
relationship between holoenzyme and prosthetic group?
- sometimes, the holoenzyme is the whole protein
- other times, the holoenzyme needs the essential non-protein part for the protein to be active (ie. the prosthetic group)
what are features of the enzyme active site? (3)
small
3D
clefts/crevices
what are 2 events that occur at the active site?
binding and transformation
Relationship between binding and transformation?
- binding of substrate preceeds transformation
- not all binding leads to transformation
- no transformation occurs without binding
4 levels of enzyme specificity?
- bond specificity
- group specificity
- absolute specificity
- sterospecificity
how are enzymes bond specific?
- E acts on compounds with one type of bond (ie. lipase can act on lipids as long as they have an ester bond)
- can have relative or low specificity
How are enzymes group specific?
when an enzyme acts on a group of closely related compounds
- ie. pepsin can hydrolyze peptide bonds where there is are aromatic AAs
- ie trypsin can hydrolyze peptide bonds where there are basic AA
- moderate specificity
how are enzymes absolutely specific?
when enzyme acts on one single substrate
- ie lactase only acts on lactose. Sucrase only acts on sucrose
- very high specificity
how are enzymes sterospecific?
when enzyme acts on one isomer of a molecule
-ie L-AA oxidase acts only on L-AA
why is it necessary to understand specificity in a baking company?
- linear starch has alpha(1-4) bonds.
- branched starch has alpha (1-6) bonds
- linear starch is stickier than branched starch
how many enzyme classifications are there? what are these classifications based on?
6 classifications
based on recommendation of enzyme commission of the international union of biochemists
also based on types of reaction catalyzed
what is the numbering system that enzyme nomenclature
enzyme commission = EC
EC = (A.B.C.D) –> letters are digits
A = 1st group B = sub group C = sub sub group D = numbering
what are the 6 enzyme classifications?
- oxidoreductase
- transferase
- hydrolyse
- lyases
- isomerases
- ligases
what are oxidoreductases?
can catalyze oxidation or reduction reactions
ie. polyphenol oxidase (PPO), glycose odidase (GOX), peroxidase, lipoxygenase
what are transferases
transfers groups from one substrate (the donor) to another substrate (Acceptor)
eg. transglutaminase
what are hydrolyases
catalyzes cleavage or hydrolysis of larger molecules into smaller molecules with H2O as a co-reactant
eg. proteases and lipases
what are lyases
removes group from one molecule, leaving behind a product with a lower molecular weight (usually with unsaturated bonds)
eg. histidine decarboxylase, pectin, lyase
what are isomerases
catalyzes the conversion of molecules into their isomers
eg. glucose isomerase
what are racemases and epimerases?
isomerase enzymes that catalyzes the inversion of stereochemistry
racemases: catalyzes sterochemical inversion around the asymmetric carbon atom (in a substrate has only one center of asymmetry)
epimerases: catalyzes sterochemical inversion of the configuration around an asymmetric carbon (in a substrate with more than one center of assymmetry)
what are ligases
catalyzes the joining together of two or more molecules
eg. fatty acyl CoA synthase
why is it necessary to purify enzymes
to remove undesirable components from source materials (ie toxins and other enzymes)
steps in enzyme purification
extration then purification
describe the extraction process
- blend or homogenize raw materials in buffer solution
- filtration
- results in crude enzyme extract (But may still have other enzyme components: salt, nucleic acids, sugars, enzymes, minerals)
what are enzyme purification methods that are based on size differences
dialysis
ultrafiltration
centrifugation
gel filtration
describe the dialysis enzyme purification process
- uses a dialysis bag (semipermeable membrane with polysaccharide)
- sample is placed into dialysis bag
- bag is placed in beaker with solvent solution that is lower than conc that solution in bag
- small molecules in sample travel through pore to outside of dialysis bag, but larger molecules stay inside bag
- process continues until equilibrium concentration
is the dialysis process efficient?
no because molecules can still re-enter into bag at equilibrium concentration
describe the ultrafiltration process
- purification based on size difference
- uses semi permeable membrane
- uses pressure from gas (N2) or vacuum to force small molecules through pores in membrane
describe the centrifugation process
- purification based on size difference
- uses centrifugal force for large molecules o go to the bottom as fast as possible
- larger and heavier molecules sediment faster than small and light molecules
in centrifugation, which molecules sediment faster?
large/ heavier are faster than small and light
describe the gel filtration chromatography
- purification based on size difference
1. place resin in column
2. apply sample on top of column
3. sample will migrate down column
large molecules elute faster than small ones
in gel filtration, what size molecules pass through (or elute) faster
large molecules elute faster
what are 3 methods of purification based on solubility differences
- isoelectric precipitation
- salt fractionation
- solvent precipitation
describe isoelectric precipiation
at the isoelectric point, E has minimal solubility
when Pi = pH of an enzyme, the enzyme will precipitate
describe salt fractionation
type of protein separation based on SOLUBILITY DIFFERENCE
- adding neutral salts (eg ammonium sulfate) to compress the solvation layer and increase protein-protein interactions.
- charges on surface of protein interacts with the salt –> exposes hydrophobic patches on protein surfaces –> causes protein to fall out of solution –> aggregation and precipitation
- ionic strength increases –> proteins interact via hydrophobic pathes on surface
why is ammonium sulfate used in salt fractionation
since it preserves protein activity and promotes precipitation at lower concentrations than other salts
describe what salting in and out is. (salt fractionation)
salting in: when protein solubility increases (at low salt concentrations)
salting out; when protein solubility decreases (at high salt concentrations)
describe solvent precipitation
type of protein separation based on SOLUBILITY DIFFERENCE
- adding miscible solvents (eg ethanol or methanol) to cause proteins in solution to precipitate. (Miscible organic solvents decrease dielectric constant to water, which allows proteins to come close together)
- solvation layer around protein decreases as the organic solvent displaces water from protein surface and binds it in hydration layers around the organic solvent molecule
what is the use of miscible organic solvents in solvent precipitation?
they decrease dielectric constant to water
allows two proteins to come close together
what are protein separation methods based on charge differences
- ion exchange chromatography
- electrphoresis
- isoelectric focusing (IEF)
what are protein separation methods based on specific binding sites
- affinity chromatography
- hydrophobic interaction chromatography (HIC)
- hydrophillic interaction chromatography (HILIC)
describe ion exchange chromatography
type of protein separation based on CHARGE DIFFERENCE
- purifying a negatively charged enzyme using IEX
1. resin is positively charged
2. apply sample
3. negatively charged enzyme binds resin
4. positively charged enzymes won’t bind and will elute using buffer
5. bound enzymes are removed by charging the pH or ion strength of the elution buffer
describe electrophoresis
type of protein separation based on CHARGE DIFFERENCE
- restriction enzymes cleave DNA into smaller segments of various sizes
- DNA segments are loaded into wells in a porous gel
- gel floats in buffer solution within a chamber between two electrodes
- an electric current is passed through the chamber –> DNA gragments move towards pos-charged cathode
- similar DNA segments move faster and farther than larger DNA segments
describe isoelectric focusing (IEF)
type of protein separation based on CHARGE DIFFERENCE
- uses a gel made of AA and peptides
- pH gradient gel is generated by ampholyte
- apply electric current
- E with different charges will migrate up to a pH point in the gel until overall charge of the E is 0
- sample with pos charge moves toward cathode. Sample with neg charge moves towards anode
what are anion and cation exchanges (in ion exchange chromatogrpahy)?
anion exchange: pos charged particles that bind with negatively charged resin
cation exchanges: neg charged particles that bind with pos charged resin
what is SDS page
involved in ion exchange chromatography
mobility is related to size of enzyme
aka polyacrylamide gel electrophoresis (used to separate molecules based on electrophoretic mobility)
what does amypholyte do in IEF?
generates a pH gradient gel
describe affinity chromatography
enyzmes with specific binding will bind to substances in resin
unbound enzymes will elute from column first
bound enzymes can be washed out of column by changing the pH or ion strength of elution buffer
describe hydrophobic interaction chromatography (HIC)
- Hydrophobic groups are attached to stationary column. If stationary phase is too weak in water, buffers (ie. Na2SO4 and NaCl) are added)
- Proteins with hydrophobic AA side chains on their surfaces interact with and bind to groups on the column
- Buffer with high ionic strength (eg. Ammonium sulfate) is applied to the column –> reduces solvation of sample solutes –> solvation decreases and hydrophobic regions are absorbed by the medium
(higher hydrophobicity = less salt is needed)
- molecules elute in order of increasing hydrophobicity
describe hydrophillic interaction chromatography (HILIC)
- separates polar and hydrophillic compounds with an amide/amino bonded phase column
- involves polar stationary (retains polar compounds) phase and mobile phase
in HIC, higher hydrophobicity means ___ salt is needed
less
how do enzymes facilitate reactions?
by reducing the energy barrier
In the transition state theory, what is the activation energy?
minimum energy needed to overcome the energy barrier to get to the activated complex of the transition state
delta G = (energy of transition – energy of substrate)
what does a higher activation energy mean?
harder for reaction to occur
how do enzymes lower activation energy?
Decreases the delta G to achieve the transition state (delta G catalyzed is much smaller than delta G un-catalyzed)
E can transiently bind with S to produce a transition state “ES” having a lower energy of activation that the transition state of un-catalyzed reaction
S + E ES –> E+P
how can we measure enzyme activity?
rxn rate of enzymatic reaction
how can we measure rxn rate?
- measure rate of disappearance of S
2. measure rate of formation of P (normally used)
describe the state of substrates and products during at the beginning of a reaction
- S is saturated
- P production is increasing in a linear relation with t
Rx = delta [P] / delta t
(constant slope)
describe the state of substrates and products after some time after the beginning of a reaction
- S is saturated
- P is increasing but slowing down
Rx = delta [P] / delta t
(Rx is decreasing)
describe the state of substrates and products after a long time after the beginning of a reaction
- S is finished
- P is 0 (no production of enzyme. Amount of enzyme remains constant)
- thus, Rx = 0 (slope becomes horizontal)
what are the 2 types of initial rate experiment?
- continuous method: with catalysis taking place, measuring the Rx rate within the linear period
- discontinuous method (aka end point method): after catalysis takes place, some chemicals (ie acids, alkali, inhibitors) are added to stop the reaction
what does the overall reaction rate depend on?
[E], [S], T, stability of ES, [P], pH, etc…
if the enzyme concentration increases, catalysis ___?
increases
if the substrate concentration increases, catalysis ___?
increases up to a certain point until the enzyme is saturated
a lower KM means ____ affinity
higher
how do you increase rxn rate? how to decrease rxn rate?
increase: raising temperature or pressure
decrease: catalysts (lowers activation energy)
a high Vmax/Km ratio means…?
high efficiency
what is competitive inhibition
when compounds compete for same active site
will decrease amount of substrates bounded and products produced
what is non-competitive inhiibtion
inhibitor can bind anywhere other than active site (doesn’t affect substrates or products)
what is uncompetitive inhibition
inhibitor binds to site on enzyme which becomes available only after substrate has bound to active site
how to relieve competitive inhibitions
increase [s]
how to relieve non-competitive inhibitions
remove inhibitors using separation techniques
how to relieve un-competitive inhibitions
dilute [s] or add [E]
describe the bell shaped graph (effect of temperature on enzyme catalysis)
- low temp slows down enzyme catalysis
- as temp increases, enzyme catalysis increases (Q10 rule)
- after optimal temp, catalysis of enzyme decreases
- extreme high temp denatures enzymes
what is optimum enzyme pH
5-8
optimum oH of pepsin?
1.5
what enzyme has a broad optimum pH range?
papain (papaya proteinase)
beneficial aspedts of enzymes in food industry
- natural and non toxic
- specific (uniform product)
- efficient
- enzymes can be inactivated by heat or pH
- enzymes can be re-used
what is an immobilized enzyme
protein hydrolyzed by trypsin to get protein hydrolates
waht are undesirable effects of enzymes
- enzymatic browning by PPO
- spoilage
3, safety issues
what are enzymes that cause flavor change in spoilage?
- lipooygenase (LOX): catalyzes oxidation of unsat FA causing odors in foods (unsat FA + O2 –> Fa hydroperoxide)
- lipase: causes rancid odor in FA that are not stable
- proteases: can form bitter peptides in protein foods
what are undesirable effects of safety issues of histidine?
histidine is toxic and gives an off-odor
disirable and undesirable effects are….?
relative
what are desirable effects of PPO?
black tea and coffee
desirable effects of LOX?
blanching flour by degrading pigments
what is the most common source of industrial enzymes?
microbial sources
80-90%
grows fast and needs only limited space and nutrients
eg amylase and transglutaminase
what is transglutaminase:
catalyzes cross linking of proteins to form firm texture
used in meat recombination and restructing
use of glucose isomerase?
converts glucose to fructose in corn syrup
chemical reactions in oxidoreductases?
- PPO
- peroxidase
- LOX
- glucose oxidase
- ascorbic acid oxidase
what does glucose oxidase do? what is it?
it is an oxidoreductase
oxidizes glucose into gluconic acid
describe fresh broccoli sterilization using peroxidase
can be used to determine if broccoli treatment involved heat
if peroxidase activity is how, it means they used high sterilization temp
