Exam I Flashcards
Oxidoreductases
catalyses oxidation-reduction reactions.
Transferases
Catalyses transfers of C- N , or P containing groups.
Hydrolases
Catalyze cleavage of bonds by addtion of water.
Isomerases
Catalyzes racemization of optical or geometric isomers.
Ligases
Catalyzes the formation of bonds between Carbon, O, S, N, coupled to hydrolysis of high energy phosphates. (ATP goes to ADP-Pi)
Why biocatalysis?
Higher reaction rates, greater reaction specificity, capacity for regulation, metabolites have many potential pathways of decomposition, enzymes make the desired one most favorable.
Lyases
Catalyzes cleavege of C-C , C-S, and certains C-N bonds.
What does enzymes do to the Rate of the reaction?
Rate acceleration
The enzymes lower the activation barrier compared to the uncatalyzed aqueous reaction. Enzymes do not change free energies of reactants and products, and therefore, do not change the equilibrium of the reaction
Enzymes catalyze biological reactions by
1- Increasing entropy of a system
2- Increasing substrate energy
3- Altering reaction equilibrium
4- Lowering total energy levels of reactants
5-Decreasing free energy of activation
5-Decreasing free energy of activation
What are inhibitors?
Name a type of Inhibitor
Inhibitors are compounds that decrease the rate of an enzematic reaction.
Transition-state analogs are extremely potent and specific inhibitors of enzymes because they bind more tightly to the enzyme than do substrates or products.
How does penicillin works?
The antibiotic peniciliin is a transition state analog that binds tightly to glycopeptidyl transferase, the enzyme required by bacteria for synthesis of the cell wall.
What kind of curve does Michaellis-Menten show?
What kind of curve do allosteric enzymes show?
Enzymes following Michaellis-Mentes show hyperbolic curve.
Allosteric enzymes show sigmoidal curves.
What means to affinity when you have a large Km? what about a small Km?
If we have a large Km, it means the enzyme affinity to the substrate is low. If we have a small Km it means the enzyme affinity to the subtrate is high.
What is Kcat?
The turn over number- How many substrate molecules can one ezyme conver per second.
What does the Km refers to?
An approximate measure of substrate’s affinity for enzyme.
What are irreversible inhibitors?
They are inactivators, react with the enzyme. One inhibitor molecule can permanently shut off one enzyme molecule. They are often powerful toxins but may also be used as drugs.
How do reversible inhibitors work?
Reversible inhibitors are often structural analogs of substrates of products. They can bind to, and can dissociate from the enzyme. They are usually used as drugs to slow down the enzyme.
How does the Km change with a competitive inhibitor?
Km increases when there is a competitive inhibitor.
What happens to Km with non-competitive inhibitors?
Km stays the same. But Vmax decreases.
What kind of inhibitor appears in this Lineweaver-Burk graph?
Non-competitive, Km doesn’t change. Only Vmax decreases.
How is the enzyme synthesis controlled?
The rate of enzyme synthesis is regulated by increasing or decreasing the rate of gene transcription.
How is protein degredation achieved?
Protein in the cell can be degraded with characteristic half-life within lysosomes, or via two specialized systems, proteosomes and caspases, which are highly selective and regulated.
LOCK-AND-KEY MODEL FOR SUBSTRATE BINDING
The substrate-binding site contains amino acid residues arranged in a complemen- tary three-dimensional surface that “recognizes” the substrate and binds it through multiple hydrophobic interactions, electrostatic interactions, or hydrogen bonds (Fig. 8.5). The amino acid residues that bind the substrate can come from very dif- ferent parts of the linear amino acid sequence of the enzyme, as seen in glucokinase. The binding of compounds with a structure that differs from the substrate even to a small degree may be prevented by steric hindrance and charge repulsion. In the lock-and-key model, the complementarity between the substrate and its binding site is compared to that of a key fitting into a rigid lock.
What is a holoenzyme?
It is an active enzyme with its nonprotein component.
What is an Apoenzyme?
An enzyme without its nonprotein moiety, and it is inactive.
What are coenzymes?
Explain the two types of coenzymes?
Coenzymes are small organic molecules that interact with the enzymes.
Cosubstrate: coenzymes that are only trasiently associated with the enzyme. They dissociate from the enzyme in an altered state.
Prosthetic group: coenzymes that are permanently associated with the enzyme, and returned to its original form.
When do enzymes show sigmoidal curve when plotted against substrate concentration?
When the substrate itself serves as an effector, the effect is
said to be homotropic. Most often, an allosteric substrate functions as a positive
effector. In such a case, the presence of a substrate molecule at one site on the
enzyme enhances the catalytic properties of the other substrate-binding sites. That
is, their binding sites exhibit cooperativity. These enzymes show a sigmoidal curve
when reaction velocity (vo) is plotted against substrate concentration ([S]), as
shown in Figure 5.16. This contrasts with the hyperbolic curve characteristic of
enzymes following Michaelis-Menten kinetics, as previously discussed. [Note: The
concept of cooperativity of substrate binding is analogous to the binding of oxygen
to hemoglobin.
