Chapter 6 Flashcards
(25 cards)
How do enzymes lower activation energy?
- enzyme active sites are the complementary to the transition state of the reaction
- enzymes bind transition states better than substrates
- stronger/ additional interactions with the transition state as compared to the ground state lower the activation barrier
describe acid-base catalysis
give and take protons
Describe covalent catalysis
-A transient covalent bond between the enzyme and the substrate
-Requires a nucleophile on the enzyme
Can be a reactive serine, thiolate (organosulfur), amine, or carboxylate
-Changes the reaction Pathway
describe metal ion catalyses
Involves a metal ion bound to the enzyme
Interacts with substrate to facilitate binding
Stabilizes negative charges
Example: two-step reaction catalyzed by enolase
describe 1st order reactions
For a reaction where A goes to P, rate is the loss of A over time, or the gain of P over time:
V = -ΔA/ΔT = ΔP/ΔT
Related to the concentration of A by k, the rate constant:
V = k[A]
If directly proportional to [A], then first order equation, units are s-1
describe zero order reactions
rate is not dependent on the concentration of reactant [A]
V= k
Describe the effect of substrate concentration on enzyme kinetics
- Most cases the relationship of enzyme activity to substrate concentration is hyperbolic (those enzymes with a single active site).
- At low substrate concentrations, the reaction rate is first order (activity increases approximately linearly with increase in substrate concentration)
- At very high substrate concentrations, the rate of reaction approaches zero order (increase in substrate concentration has very little effect on the rate of reaction.)
- At intermediate substrate concentrations, the order is intermediate between zero and first order
What is V0
it is the initial velocity
what is Vmax
it is the velocity observed when virtually all the enxyme is present as the ES complex and [E] is very very small
what is Km
the substrate conc required for an enzyme to operate at 1/2 vmax
Why is it useful to use Lineweaver-Burk plot to extrapolate info from V0 vs [S] data or to visualize the effects of inhibitors
The Lineweaver-Burk plot represents a linear model of the Michaelis-Menten equation
What are reversible inhibitors?
-bind to and can dissociate from the enzyme
-They are often structural analogs of substrates or products
-They are often used as drugs to slow down a specific enzyme
-Can be competitive, uncompetitive or mixed
Reversible inhibitor can bind:
-to the free enzyme and prevent the binding of the substrate
-to the enzyme-substrate complex and prevent the reaction
What are irreversible inhibitors?
- react with the enzyme
- One inhibitor molecule can permanently shut off one enzyme molecule
- They are often powerful toxins but also may be used as drugs
- bind covalently with or destroy a functional group on an enzyme that is essential for the enzyme’s activity. This class of inhibitors can also form stable non-covalent associations
Describe competitive inhibition
-Enzyme can bind substrate or inhibitor, but not both
-Inhibitor often resemble substrate, binds to active site
-Reduces catalytic rate by reducing available enzyme molecules
-Can be reversed by adding more substrate (e.g. ethanol treatment
for methanol poisoning)
-Lineweaver-Burk: lines intersect at the y-axis
Describe uncompetitive inhibition
- Inhibitor binds only to ES complex
- Can not be relieved by adding more substrate
- Lineweaver-Burk: lines are parallel
Describe mixed inhibition
- Inhibitor and substrate can bind at the same time, to different sites
- Can not be relieved by adding more substrate
- Differs from uncompetitive in that substrate does not have to bind
- Lineweaver-Burk: lines intersect left from the y-axis
What are suicide inhibitors
are a special class of irreversible inhibitors. These inhibitors bind at the active site, begin catalytic reaction but then generate reactive intermediate that covalently modifies and inactivates enzyme or cofactor
What are transition state analogs
mimics the transition state
What kind of inhibitor is penicillin and how does it work?
- irreversible inhibitor; form of suicide inhibitor
- inhibits transpeptidase
- Transpeptidase is an enzyme that catalyzes the crosslinking of the peptidoglycan layer of proliferating bacterial cells.
describe how β-Lactamases and β-lactamase inhibition works
Pathogenic bacteria have evolved to express β -lactamases, enzymes that cleave β -lactam antibiotics.
Lactamases inactivate antibiotics such as Penicillin.
HIV protease and protease inhibitor
HIV protease breaks protein down into peptides so that protein combines with the virus’s genetic material to form new virus
Protease inhibitor inhibits protease from doing this
Allosteric regulation of some enzymes
- activity of enzymes can be modulated through activators or inhibitors
- In many allosteric enzymes the substrate binding site and the modulator binding site(s) are on different subunits, the catalytic (C) and regulatory (R) subunits, respectively.
- When a Modulator (M) bindes to the regulatory subunit, it causes a conformational change in the catalytic subunit, allowing the Substrate (S) to bind with higher affinity.
Reversible covalent modifications
- phosphorylation
- adenylation
- acetylation
- myristoylation
- ubiquitination
- ADP-ribosylation
- methylation
Describe zymogens
- A zymogen, or pro-enzyme, is an inactive precursor that requires activation to become functional.
- activated by irreversible covalent modification
- Digestive enzymes, such as chymotrypsin and trypsin, are examples of how zymogens work
