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83 Cards in this Set

  • Front
  • Back
What are enzymes?
Enzymes are specilaized proteins that efficiently accelerate chemical reactions with a high degree of specificity in biological systems. They act as catalysts.
What are cofactors?
They are inorganic ions necessary for catalytic activity( trace nutrients, vitamins, metals) that are required by some enzymes for their catalytic activity. Eg mg, selenium are critical accessories or cofactors.
What are Coenzymes?
Coenzymes are complex organic or metallo-organic molecules that are required by some enzymes for their catalytic activity.
What differentiate enzymes from cofactors?
Coenzymes are substrates for enzymes and do not form a permanent part of the enzymes' structures. This distinguishes coenzymes from cofactors, which are non-protein components that are bound to enzymes - such as iron-sulfur centers, flavin or heme groups.
What is a prosthetic group?
A prosthetic group is a coenzyme or metal ion that is very tightly or covalently bound to the enzyme protein. Eg heme.
What is the apoenzyme/apoprotein?
Apoenzyme/apoprotein is the protein part of the enzyme without cofactors, or prosthetic groups. The protein is catalytically inactive.
True or false? A particular enzyme is able to function in aqueous solutions that have wide range of temp. or pH.
False.
They are designed to fx in aqueous soln at our normal body temp. & pH.
Things go awry if we change the pH or the temp.
Define active site.
The active site is an area on the enzyme containing the AA side chains that are involved in catalyzing the reaction. That site is the area that the substrate finds most optimum. (The AAs lining the active site is just right for the substrate to bind to).
Define substrate.
Substrate is the molecule that is bound in the active site and is acted on by the enzyme to form the product. (The substrate is the molecule being acted upon by the enzyme).
How are enzymes named?
An enzyme's name is generally derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase. Example: urease catalyzes the hydrolysis of urea, and DNA polymerase catalyzes the polymerization of nucleotides to form DNA.
Based on its name, what type of reaction do suppose the enzyme oxidoreductase catalyzes?
It transfers electrions (hydride ions H atoms)
Based on its name, what type of reaction do suppose the enzyme transferases catalyzes?
Group transfer reactions.
Based on its name, what type of reaction does the enzyme hydrolases catalyzes?
Hydrolysis reactions (transfer of functional groups to water)
Based on its name, what type of reaction do suppose the enzyme lyases catalyzes?
Additon of groups to double bonds, or formation of double bonds by removal of groups.
Based on its name, what type of reaction does the enzyme isomerases catalyzes?
Transfer of groups within molecules to yield isomeric forms.
Based on its name, what type of reactions do you suppose ligase catalyzes?
Formation of C-C, C-O, C-S and C-N by condensation reactions coupled to ATP cleavage.
True/False?
An enzyme is changed after it completes its work in a reaction.
False.
After an enzyme finishes its work, it remains unchanged – it is just a conduit for speeding up the rxn.
How is the rate of a reaction defined?
The rate of a chemical reaction is the speed at which it takes place.
The rate is equivalent to the change in the number of moles of starting material or product generated per unit time.
What can cause catalytic activity to be lost
The integrity of the native protein conformation and primary, secondary, tertiary and quaternary structures are all essential to their catalytic activity. Catalytic activity is lost if the protein is denatured or dissociated into subunits. 
(1)Give two examples of covalent modification and (2)how does covalent modification affect enzyme activity?
Phosphorylation & glycosylation.
Enzyme activity can be regulated through covalent modification.
How does enzymes work?
Enzymes provide a specific optimized environment for chemical reactions to occur more rapidly.
What are the two distinguishing features of enzyme-catalyzed reactions?
(1)The reaction only takes place within the confines of a pocket called the ACTIVE SITE.
(2) The molecule bound selectively to the active site and acted upon by the enzyme is called the SUBSTRATE
Describe the surface of the active site?
The surface of the active site is lined with AAs with substituent (R) groups that bind the substrate and catalyze its chemical transformation.
(R-groups provide the specificity).
State the collision theory of chemical kinetics?
Collision theory of chemical kinetics states that the rate of reaction is proportional to the frequency of collisions between molecules.
(In order for rxns to take place, the molecules have to come in contact with one another).
In addition to coming into contact with each other, what else is needed for molecules to overcome repulsive forces?
They must have high enough energy to overcome the repulsive force that they experience when they are close together.
What is the ground state(ΔG)of a reaction?
It is the starting point for either a forward or reverse chemical reaction. It is the free energy contributed to the system by the average molecule under a given set of conditions: product (P) and substrate (S).
What does the equilibrium between S & P reflect?
The difference in the free energies of their ground state (ΔG).
What is activation energy?
It is the energy needed for a reaction to take place or break the energy barrier.
How does enzymes affect activation energy?
They lower activation energy.
When the energy at P is lower than that of S, what do we have?
When the energy at P is lower than that of S, the standard free energy change for the reaction is negative (exothermic) – it reflects a favorable reaction equilibrium, and the equilibrium favors P.
When the reaction is releasing energy, what is it called?
An exothermic reaction.
True/false?
The position and direction of equilibrium are not affected by any enzyme or catalyst.
True
What is the energy barrier/energy hill between S and P?
The energy required for formation of transient unstable charges, bond rearrangements, and other transformations required for the reaction to proceed in either direction.
In relationship to the energy barrier, what must happen for the reaction to occur (in either direction)?
The molecules must be raised to a higher energy level to overcome this barrier.
What is the transition state (‡):
When the molecules are raised to a higher energy level reach the top of the energy hill, the transition state (‡)is a fleeting point at which decay to the S or P state is equally probable.
What is the difference between the energy levels of the ground state and the transition state?
Activation energy (ΔG‡), it is the energy requirement for reaction to occur.
How does the rate of reaction reflects its activation energy?
A higher activation energy corresponds to a slower reaction.
What ultimately determines reaction equilibria?
The free energies of S and P ground state.
Reaction equilibria are linked to the standard free-energy change for the reaction (change in ΔG).
How does the reaction energy path affect the reaction?
Reaction energy path controls the reaction speed.
How does raising the temperature affect the rate of the reaction?
Rates can be increased by raising the temperature - this increases the free energy of ground state thereby increasing the number of molecules with sufficient energy to overcome the energy barrier.
Enzymes decrease the activation energy by forming enzyme-substrate (ES) complexes and enzyme-product (EP) complexes. How does this affect the reaction?
It accelerates the inter-conversion of S and P (this is a bi-directional catalyzing reaction). The final equilibrium point is unaffected.
What determines the overall rate of the reaction (the rate limiting step)?
When several steps occur in a reaction, the overall rate is determined by the step with the highest activation energy, this step is called the rate-limiting step.
When many enzymes are used and the rxn have several steps that have similar activation energies, how is the rate-limiting step determined?
The steps are all partially rate-limiting.
Although activation energies are energy barriers to chemical reactions, they are crucial and a benefit to life itself. What would happen if a reaction did not have to surmount this energy barrier?
Without this barrier, complex macromolecules would revert to much simpler molecular forms spontaneously, and the higher ordered structures and metabolic processes of cell could not exist.
How does enzymes help to ensure cell survival?
Enzymes selectively lower activation energies for reactions that are needed for cell survival to occur at the right place and at the right time.
True/false?
Enzymes can
enhance a reaction rate by as much as 17 orders of magnitude.
True.
Enzymes have extraordinary catalytic power.
Where does the energy come from for enzyme to dramatically lower the activation energies for specific chemical reactions?
Major source: binding energy from weak, noncovalent interactions between substrate and enzyme, as a specific enzyme-substrate (ES) complex is formed during reaction.
True/false?
The same forces (hydrogen bonds, hydrophobic and ionic interactions, etc. ) that stabilize protein structure also maintain the interaction between E and S in the ES complex.
True
What is binding energy?
Formation of these weak interactions in the ES complex is accompanied by release of a small amount of free energy that provides a degree of stability to the interaction. This is called binding energy.
How does enzyme discriminate between substrates with similar structure?
Thereotically this is explained by the lock and key theory: enzyme active sites are complementary to the target substrate in shape and ionic properties. In terms of structure, they fit to each other like a lock to a key.
If the lock and key theory is mostly thereotical, what is the reality?
The complementarity between enzyme and substrate is rarely perfect (as lock & key suggests). In-stead, enzyme active sites are complementary not to the substrates but to the its transition state during the reaction .
How does induced fit enhance specificity?
When the substrate approaches, the interaction of a enzyme with the
substrate often involves a change in conformation.
This brings specific functional groups on
the enzyme into the proper position to catalyze the reaction- this is an example
of induced fit.
What are enzyme inhibitors?
They are molecular agents that
interfere with catalysis, slowing or halting
enzymatic reactions.
What are the two broad classes of enzyme inhibitors?
Reversible (competitive or uncompetitive) and irreversible (noncompetitive) inhibitors.
Give an example of a (1)irreversible inhibitor and an (2)reversible inhibitor?
(1)ASA irreversibly inhibits the enzyme that catalyzes the first step in the synthesis of prostaglandins, so it is good for platelet inhibition.
(2)(1)Ibuprofen reversibly inhibits the same enzyme, so it is suited for control of periodic symptoms like headache and fever, but not platelet inhibition.
Competitive inhibitors
competes with the substrate for the active site of an enzyme. Why is this and what is the complex formed when the the enzyme binds to an inhibitor?
Many competitors resemble the substrate. When they combine with the enzyme they form an enzyme inhibitor (EI) complex, and catalysis is prevented.
How can competition for the enzyme be biased to favor the substrate?
By adding more substrate.
Give a clinical example of adding more substrate to displace a reversible inhibitor from an enzyme?
Medical therapy of slow
intravenous infusion of ethanol for treating patient who have ingested methanol.
How does irreversible inhibitors affect enzymes?
They bind covalently with or
destroy a functional group on an enzyme that is essential
for the enzyme’s activity.
What are suicide inactivators?
They are a special class of irreversible inhibitors that are relatively un-reactive until they bind to
the active site of a specific enzyme -> inactivation of the enzyme.
What is the process when the suicide inactivator bind to the enzyme?
It undergoes the first few chemical steps of the normal enzymatic reaction, but instead of being transformed into the normal product, the
inactivator is converted to a very reactive compound that combines irreversible with the enzyme.
A well designed suicide inactivator is specific for a single enzyme and is un-reactive until it is within that enzyme’s active site. What significance is this to pharmacology?
Drugs based on this approach can offer the important advantage of few side effects.
What is the initial velocity of a reaction dependent on?
The concentration of substrate.
Initially, as concentration of substrate increases, velocity (V) increases, when does the velocity stop increasing?
Velocity increases until the enzyme is completely saturated (binding sites are full).
How is enzyme activity quantified?
Enzyme activity is expressed as mmol of substrate converted to product per minute under assay conditions.
When all the active sites of an enzyme is filled with substrate then we are at _____
______
Maximum velocity (VMAX).
What are the enzyme kinetics rules for competitive
and non-competitive inhibition
1. Only one substrate can bind each enzyme at a time.
2. The substrate must remain bound for a fixed period of time before being transformed to a product.
3. There are fixed amts of binding sites.
Using the enzyme kinetics rules for competitive
and non-competitive inhibition, how is Vmax calculated?
Amt of enzyme /required amt of time at binding site.
What is Km?
Km = concentration of subtrate required to produce 50% of maximum velocity (Vmax).
True/false?
When a competitive inhibitor occupies the binding pocket of the enzyme,it is not changed by it.
True.
Competitive inhibitors are reversible.
How does a competitive inhibitor affect Vmax and Km?
The competitive inhibitor does not affect Vmax, but it increases the Km (conc of substrate that produces half max velocity).
When competitive inhibitor disassociates from the binding pocket it can be replaced by a molecule of the normal substrate. This increases the amt of substrate needed to displace the inhibitor & reach maximum velocity but does not affect the amt of maximum possible binding potential of the substrate.
Increase in Km, combined with the absence of effect on Vmax is a characteristic feature of which type of inhibition?
Competitive inhibition
True/false?
Vmax can be recovered by increasing substrate.
True.
How does non- competitive inhibitiors bind to enzymes?
Non-competitive (irreversible inhibitiors)form covalent bonds between the binding site and themselves.
When non-competitive inhibitiors bind to enzymes, can the binding sites be recovered?
Binding sites bound by non-competitive inhibitors are permanently taken out of commission.
Irreversible inhibitors lower the Vmax but not the Km. Why?
Because the inhibitor acts as if it removes active enzyme from the reaction, which would decrease max velocity due to lack of enzyme for available substrate.
True/false?
In the case of irreversible inhibitors, increasing substrate can rescue Vmax.
False.
.
What are regulatory enzymes?
In most multi-enzyme systems, they are the first enzyme of the sequence. They exhibit increased or decreased catalytic activity in response to certain signals & they have a greater effect on the rate of the overall metabolic sequence.
What are allosteric enzymes?
Allosteric enzymes are enzymes that change their shape, or conformation, upon reversible or noncovalent binding of a modulator like an allosteric effector. This modulates their activities.
What is the result of conformational changes induced by modulators on allosteric enzymes?
It can lead to more active or less-active forms of the enzymes. So the modulators for allosteric enzymes may be inhibitory (as with allosteric inhibitor)
or stimulatory (as with or allosteric activater).
How does phosphorylation affect regulatory enzymes?
It can regulated their activities by reversible covalent modification.
What are homotropic regulatory enzymes?
Homotropic: regulatory enzymes for which
substrate and modulator are identical.
What are heterotropic regulatory enzymes?
Heterotropic: regulatory enzymes for which the
modulator is a molecule other than the substrate