Enzymes Flashcards
What is the role of an enzyme
They act as catalysts, lowering the activation energy of a reaction.
What are the six maor classes of enzymes?
Isomerase oxidoreductase hydrolases lyases ligases transferase
What does an isomerase do?
Transfer of groups within the same molecule. Molecular structure changes but nor molecular formula
Ex: Glucose-6-phosphate -> fructose-6-phosphate by phosphoglucoisomerase
What does an oxidoreductase do?
Catalyzes redox reactions, dehydrogenase is a type of oxidoreductase
Ex: Lactate + NAD+ -> Pyruvate + NADH
by lactate dehydrogenase
What do hydrolases do?
Cut bonds by using H20
Ex: Urea + H20 -> 2 NH3 + CO2
by Urease
What do lyases do?
Cut C-C, C-S, and some C-N bonds
Ex: CH3-CO-COO- -> CH3-COH + CO2
What do Ligases do?
Catalyzes formation of C-O, C-N, C-C and C-S bonds
Ex: CH3-CO-COO- + CO2 -> (COO-)-CH2-CO-COO-
What do transferases do?
Catalyzes group transfer.
glucose + ATP -> glucose-6-phosphate + ADP
by a kinase
What is Kcat
Turnover # - How quickly the substrate is used in the enzyme
Holoenzyme
The active enzyme with the non-protein portion
Apoenzyme
The inactive enzyme - without the non-protein portion
cofactor
an ion like Zn+2 or Fe+2 that binds to an enzyme to activate it.
coenzyme
a small organic molecule that binds to an enzyme to activate it.
prosthetic group
When a coenzyme binds covalently with an enzyme
What do enzymes change?
They change the activation energy of the reaction (ΔG* or Ea)
What don’t enzymes change?
ΔG, ΔH, Equilibrium, Keq constant, or product amount
Km
The affinity of the enzyme for it’s substrate.
It reflects the substrate concentration that allows us to achieve 1/2 Vmax
What does a large Km mean? What does a small one mean?
A large Km means that an enzyme has a low affinity for the substrate, it takes a lot more substrate to achieve 1/2 Vmax
A small Km means that an enzyme has a high affinity for the substrate, it doesn’t take a lot of substrate to achieve 1/2 Vmax
Explain how Vmax is affected by concentration of solutes
At the very beginning of the addition of solute, there is a linear relationship with Vmax, a 1st order relationship. Then as more solute is added the relationship becomes mixed order (no longer linear) at Vmax the relationship is 0 order meaning that the reaction has achieved the max speed and adding more solutes won’t increase the rate of reaction.
What does the Kcat / Km ratio tell us?
It tells us enzyme efficiency.
We want a high Kcat and a low Km to be highly efficient.
High Kcat means the enzyme catalyzes the substrate quickly, and a low Km means the enzyme has a high affinity for the substrate.
What is a competitive inhibitor and how does it affect Vmax and Km
A competitive inhibitor binds to the same active site as the substrate inhibiting the substrate from being catalyzed.
Vmax is unchanged. You could eventually add enough substrate that the max reaction rate could be reached.
Km is changed. It affects the apparent Km, increasing it because the affinity of the enzyme to bind with the substrate is in essence changed.
What is a non-competitive inhibitor and how does it affect Vmax and Km
A non-competitive inhibitor binds to a site distant from the active site. This changes the conformation of the enzyme, making it no longer functional.
Vmax decreases because the enzymes are essentially removed from the equation when they’re inhibited. Increasing substrate won’t overcome this change and so the new Vmax is only calculated with the remaining enzymes
Km is unchanged. It cannot be overcome by adding more substrate.
What is an un-competitive inhibitor and how does it affect Vmax and Km
Similar to non-competitive inhibition, it binds to a site away from the active site, but an uncompetitive inhibitor only binds to the enzyme when it is an Enzyme substrate complex.
The Vmax is lowered because the enzyme undergoes a conformational change making it useless.
Km decreases because as the E-S complexes are inhibited they become an ESI complex completely different from the initial reactants. Le Chatliers principle moves the direction toward the formation of more ES complex, in essence changing Km in the direction of higher affinity (lower Km)
Zymogen
The inactive form of an enzyme.
Can be converted to Zymogen by uncompetitive or noncompetitive inhibition.
Zymogens are often activated by proteolytic cleavage (the breaking of a peptide bond)
Zymogen-ABC –cut–> Active Enzyme-A + BC
What is the difference between digestion and denaturing?
In digestion, the 1º, 2º, 3º, and 4º structure of the protein is changed.
In denaturing, only the 1º, 2º, 3º, and 4º structure of the protein is changed.
How does temperature affect protein?
Temperature increases - disrupts bonding interactions
How does radiation affect protein?
Disrupts native conformation
How does mechanical agitation affect protein?
Violent mixing like in a blender, or shaking. Will cause polypeptide chains to unfold.
How does pH affect protein?
Causes groups to gain or lose charges, disrupting bonding interactions
How do salts of heavy metals affect protein?
Pb++, Hg+, Ag+ in particular react with SH (sulfhydyl groups) and prevent disulfide bond
How do organic solvents (soaps, detergents, urea, alcohol) affect protein?
disrupts bonding interactions like hydrogen bonds
ex: alcohol passes through the cell wall of bacteria and destroys their proteins
How do oxidizing and reducing agents affect protein?
Can form disulfide bonds or destroy them.
isozymes
Enzymes that catalyze the same reactions, but differ in structure. They may differ a bit in Km and Vmax values
Feedback inhibition
The final product will start to bind with an enzyme at the beginning of the reaction series in an inhibition to slow down the reaction.
allosteric enzyme
An enzyme that undergoes a conformational change when binding with inhibitors or activators
They do not follow the same Vmax curve. They have a sigmoidal curve instead
