Enzymes (EK B1 Ch1) Flashcards
oxidoreductases
reaction catalyzed= transfer of hydrogen and oxygen atoms or electrons from one substrate to another ex. dehyrogenases, oxidases, oxidation reduction reactions
Oxidoreductases (including dehydrogenases) catalyze redox reactions
transferases
catalyze reactions of the transfer of a specific group (a phosphate or methyl etc.) from one substrate to another ex. transaminase, kinase so groups are transferred from one location to another
hydrolases
regulate hydrolysis of a substrate / hydrolysis reactions ex. estrases, digestive enzymes
isomerases
change of the molecular form of the substrate/ transfer of groups within a molecule, with the effect of producing isomers ex. phospho hexo, isomarse, fumarase
lysases
nonhydrolytic removal of a group or addition of a group to a substrate
- so functional groups are added to double bonds or conversely, double bonds are formed via the removal of functional groups
ex. decarboxylases, aldolases
Lyases break covalent bonds using mechanisms besides hydrolysis
ligases (sythetases)
- joining of two molecules by the formation of new bonds
- catalyze condensation reactions coupled with hydrolysis of high energy moelcules
ex. citric acid synthetase
hexokinase
- lowers activation energy for the phosphorlyation of glucose
- enzyme that phosphorylates glucose as soon as it enters the cell
from metabolism ch1 (Ch 4 in entire packet)
Step 1: glucose is phosphorylated to glucose-6-phosphate by hexokinase
- ATP is the source of the phosphate group
- Glucose is trapped in the cell. Could go on through glycolysis or be stored as glycogen
- Hexokinase is in most cells, including muscle and brain
- Hexokinase has low Km (high affinity for glucose) but low Vmax
- Hexokinase will work even when glucose levels are low
saturation kinetics
as relative concentration of substrate inc, the rate of reaction also increases, but to a lesser and lesser degree until a maximum rate, Vmax has been achieved. = this occurs because as more substrate is added, individual substrates must begin to wait in line for an unoccupied enzyme
saturation kinetics workers ex
analogous to assemebly line workers -when there are more workers, more enzymes, the rate of production VMAX increases! -but there comes a point when there is just too much starting material (substrate) and the workers cannot go any faster -at this point the workers or enzymes are saturated and have reached Vmax
vmax
proportional to enzyme concentration
kcat
turnover number
- number of substrate molecules one active site can convert to product in a given unit of time when an enzyme solution is saturated with substrate
- provides a rough estimate of the catalytic efficiency of an enzyme
kcat
= vmax/Et (vmax/ enzyme concentration)
Km
= 1/2 vmax, it is the substrate concentration at which the reaction rate equals to 1/2 vmax
Km explanation
indicates how highly concentrated the substrate must be to speed up the reaction
- if a higher concentration of substrate is needed, the enzyme must have a LOWER AFFINITY for the substrate
- Km is inversely proportional to the enzyme substrate affinity****
- does not vary when the enzyme concentration is changed, unlike vmax** in other words, it is characteristic of the intrinsic fit between the enzyme and substrate, rather than reflecting amount fo substrate present
glucokinase
this and hexokinase add a phosphate to glucose, to form glucose-6-phosphate, which is trapped inside the cell
- has a significantly higher Km, meaning that it has lower affinity for glucose compared to hexokinase
- acts in liver, so high levels of blood glucose would be required to begin phosphorylating glucose in the heptocyte cytosol
- this lower affinity allows glucose to be phosphorylated in other cells, which use hexokinase!!! Only when glucose concentrations become high will the liver begin storing it as glycogen and fatty acids
temp affects rates of enzymatic reactions
as temp inc, the reaction rate initially goes up
- since enzymes are generally proteins, at some point the enzyme denatures and the rate of reaction drops off precipitously
- for enzymes in human body, optimal temp is around 37 C
pepsin
enzyme in stomach prefers pH of 2
trypsin
enzyme active in small intestine, works best at a pH btw 6 and 7
cofactor
for optimal activity some enzymes need cofactors to function -either minerals or coenzymes -nonprotein component
Enzyme regulation: 4 primary means
- proteolytic cleavage (irreversible covalent modification), ex zymogen
- reversible covalent modification, ex. amp, protein kinase when some enzymes activated or deactivated by phosphorylation or the addition of some other modifier such as AMP, removal of modifier is always accomplished by hydrolysis
- control proteins- protein subunits that associate with certain enzymes to activate or inhibit their activity, ex calmodulin and g proteins
- allosteric interactions
zymogen
many enzymes released into their environment in the INACTIVE FORM called a zymogen or proenzyme (greek pro= before) when specific peptide bonds or zymogens are cleaved, the zymogen become irreversibly activated. activation of zymogens may be instigated by other enzymes or by a change in environment, for ex, pepsinogen (“ogen” at the end indicating zymogen status) is zymogen of pepsin and is activated by low pH
allosteric interactions
allosteric regulation is the modification of an enzyme’s configuration through the binding of an activator or inhibitor at a specific binding site on the enzyme
pepsin zymogen
the release of pepsin as a zymogen that is activated only by low pH ensures that pepsin only digests proteins where it is supposed to, in the stomach!
zymogen- pepsinogen
active enzyme- pepsin
function-digestive protease
allosteric regulation
- products that exert negative feedback inhibition do not resemble the substrate of the enzymes that they inhibit and do not bind to the active site
- instead they bind to the enzyme and cause a conformational change, which can be exerted by both allosteric inhibitors and allosteric activators
- not all are noncompetitve inhibitors which alter Km without affecting Vmax
allosteric enzymes
- meaning enzymes that have sites for allosteric regulation -do not exhibit typical kinetics because they normally have several binding sites for different inhibitors, activators and enzymes
- at low concentrations of substrate, small inc in concentration inc enzyme efficiency as well as reaction rate
- first substrate changes the shape of the enzyme, allowing other substrates to bind more easily, this is called positive cooperativity, opposite phenomenon negative cooperativity also occurs =cooperativity in presence of allosteric inhibitor is what gives the oxygen dissociation curve of hemoglobin its sigmoidal shape*
competitive inhibitors
compete with substrate by binding reversibly with non-covalent bonds to active site
- only type of reversible inhibitor that binds directly to active site rather than a different site on enzyme
- raise the apparent Km but do not change vmax***
- rate of reaction can be inc to the original, uninhibited Vmax by inc the concentration of substrate, since inc concentration of substrate is required to reach Vmax, an inc concentration is also required to reach 1/2 vmax
- Km raised showing lower affinity for enzyme for substrate
the ability to overcome inhibition….
by inc substrate concentration is the classic indication of a competitive inhibitor
uncompetitive inhibitors
-bind at site other than the active site -regulatory molecules can also bind to a site other than the active site and exert a positive feedback effect, rather than an inhibitory effect - do not bind to the enzyme until it has associated with the substrate to form the ES complex -once bound, substrate remains associated with the enzyme -the apparent affinity of the enzyme for the substrate increases, meaning that Km decreases -because this only affects enzymes that have already bound substrate, adding more substrate does not overcome the effect of inhibitor! -vmax is lowered because the substrate stays bound to the enzyme for a longer period of time
mixed inhibitors
-bind at site on enzyme other than active site, so they do not prevent the substrate from binding
-their names comes from the fact that they can bind to either the enzyme alone or the enzyme-substrate complex
- most have preference for one or the other which dictates the effect on Km and Vmax
- act like competitive inhibitors by binding primarily to the enzyme before the substrate is associated inc Km, just as competitive inhibitors do
- in contrast, mixed act more like uncompetitive inhibitors by preferring to bind to the enzyme-substrate complex lower Km
- all lower Vmax to some extent
noncompetitive inhibitors
special kind of mixed inhibitor
- bind just as readily to enzymes with a substrate as to those without, bind noncovalently to an enzyme at a spot other than the active site and change the conformation of the enzyme
- do not resemble the substrate, they commonly act on more than one type fo enzyme, they cannot be overcome by excess substrate, so they lower Vmax
- they do not however lower the enzyme’s affinity for the substrate because they bind to a site other than the active site, so Km remains the same
competitive inhibitors
- binding site= enzyme active site -inhibits binding of substrate
- effect on km= inc -effect on Vmax= no change
uncompetitive inhibitors
-binding site= Enzyme substrate complex -inhibits binding of substrate= NO -effect on Km= decrease -effect on Vmax= decrease
mixed inhibitors
- binding site= Enzyme substrate complex or enzyme
- inhibits binding of substrate= NO
- effect on Km= decrease or increase -effect on Vmax= decrease
noncompetitive inhibitors
- binding site= Enzyme substrate complex or enzyme
- inhibits binding of substrate= NO
- effect on Km= no change
- effect on Vmax= decrease
Line weaver burke
x intercept= -1/Km (correlates with enzyme substrate fit) y intercept = 1/vmax (max rate of catalysis) slope = km/vmax
Line weaver burke competitive
km inc, Vmax constant
Line weaver burke noncompetitive
Km stays the same/constant, vmax dec
kinase
enzyme that phosphorlyates a molecule, often phosphoryaltes another enzyme in order to activate or deactivate it
can also be called a= Transferases catalyze transfer of a chemical group from one molecule (donor) to another (acceptor). Most of the time, the donor is a cofactor that is charged with the group about to be transferred. Examples include kinases and phosphorylases.
Which specific class of enzymes is primarily responsible for the release of free glycerol from stored triglycerides?
Q13 Blueprint exam 4
Lipases
-Lipases are the enzymes that digest lipids (fats). Most dietary fats originally exist in the form of triglycerides.
The diagram below depicts the six major classes of enzymes. Since lipases typically catalyze hydrolysis reactions, they are a subclass of the hydrolases.
B. Carboxylases= Carboxylases add carboxyl groups to their substrates.
C.
Phosphorylases= A phosphorylase is a transferase enzymes that moves phosphate groups between species. It does not relate to the digestion of fats.
D.
Kinases= A kinase is a transferase enzymes that moves phosphate groups between species. It does not relate to the digestion of fats.
Oxidoreductases 2
Oxidoreductases catalyze oxidation-reduction reactions where electrons are transferred. In metabolism, these electrons are usually in the form of hydride ions or hydrogen atoms. When a substrate is being oxidized, it is the hydrogen donor. Examples include reductases, oxidases, and dehydrogenases.
Lyases 2
Lyases catalyze reactions where functional groups are added to break bonds in molecules or they can be used to form new double bonds or rings by the removal of functional group(s). Decarboxylases are examples of lyases.
Lyases break covalent bonds using mechanisms besides hydrolysis
Isomerases 2
Isomerases catalyze reactions that transfer functional groups within a molecule so that a new isomer is formed to allow for structural or geometric changes within a molecule.
examples on graph
hydrolases 2
Hydrolases catalyze reactions that involve cleavage of a molecule using water (hydrolysis). This cases usually involves the transfer of functional groups to water. Hydrolases include amylases, proteases/peptidases, lipases, and phosphatases.
Hydrolases are responsible for the hydrolysis of bonds (proteases and lipase are examples)
Ligases 2
Ligases are used in catalysis where two substrates are stitched together (i.e., ligated) via the formation of C-C, C-S, C-N or C-O bonds while giving off a water (condensation) molecule.
Ligase joins two nucleic acid pieces
vmax 2
enzyme limit, where all active sites become saturated, if change how much enzyme you have can change vmax, premise is that you have limited amount of enzyme which limits your vmax* if Km high more falling apart less sticky, how fast going away of es complex versus how fast going toward which is opposite of affinity, why Km high thing falling apart low affinity
K2+ K3/ K1
Vmax = maximal reaction velocity = maximal turnover rate reached at saturating [S]
reversible inhibition
- usually noncovalent bonds*** 3 categories compeitive, mixed (also includes noncompeitive), uncompetitive
- Reversible inhibition typically involves noncovalent interactions between inhibitor and enzyme
Reversible inhibition may be competitive, uncompetitive or mixed (including noncompetitive)
- Inhibition: may be reversible or irreversible
Consider Enzyme B at a point below Vmax. As substrate concentration is increased and an allosteric activator is added, how will reaction rate and Vmax be affected?
A.Both Vmax and the reaction rate will remain constant.
B.Both Vmax and the reaction rate will increase.
C.Vmax will remain constant, while the reaction rate will increase.
D.Vmax will increase, while the reaction rate will remain constant.
C.
Vmax will remain constant, while the reaction rate will increase.
CORRECT Vmax is not dependent on substrate concentration, and it does not change upon addition of an activator. In fact, Vmax would increase only if more enzyme were added. However, increased substrate concentration does raise the reaction rate, as is shown by the graph; exposure to an activator should have the same result.
