enzyme Flashcards
Define the term enzymes
Biocatalysts synthesized by living cells, colloidal, and thermolabile in character, and specific in their action
Define a Catalyst
A substance which increases the rate of a chemical reaction but remains unchanged at the end of the reaction
List the six major classes of enzymes based on IUBMB
- Oxidoreductases (oxidation-reduction reactions) (alcohol dehydrogenase)
- Transferases (transfer a functional group) (hexokinase)
- Hydrolases (hydrolysis) (lipase)
- Lyases (addition or removal of water, ammonia, CO2) (Aldolase)
- Isomerases (isomerisation reactions) (D-GA3P)
- Ligases (two molecules are joined together and ATP is used) (Glutamine synthetase)
Describe the types of enzyme specificity with examples
- Substrate specificity
- Enzyme is specific to a particular substrate
- e.g oxidoreductase - Bond and group Specificity
- Pepsin (peptide bond, amino group)
Define the term activation energy
Activation energy is the amount of energy that is required to start a reaction.
Enzymes reduce the activation energy of a reaction. Net effect of increasing the rate of reaction.
Compare the changes in free energy of a reaction in presence and absence of an enzyme with a graph. Emphasize on transition state
The free energy of activation refers to the difference in energy between the reactant and the Transition State. In the presence of an enzyme, the free energy of activation is lower than when an enzyme is absent.
The Transition State is where the high-energy intermediate is formed during the conversion of reactant to product. In the presence of an enzyme, the Transition State is lower than when an enzyme is absent
The total change in free energy refers to the difference between the free energy of the products and the reactants. The total change in free energy is the same for when an enzyme is present and absent.
Why is the rate of reaction of enzyme catalysed reactions faster?
1.In the presence of an enzyme, the Transition state of a reaction is decreased as a result of the enzyme providing an alternate reaction pathway with lower free energy of activation.
2. Thus, the proportion of the population of substrates that are able to achieve the free energy of activation is increased.
3. Altogether products are created faster, and thus the rate of reaction is accelerated
4. The enzyme does not alter the free energy of reactants or products. Hence, not changing equilibrium.
Describe the active site of an enzyme
The specific region, on the enzyme, that the substrate binds to. This is the location where the catalytic activity will take place.
- Pocket / cleft like site
- Containts a.a side chains that participate in substrate-binding catalysis
- Flexible template that binds the substrate and initiates its conversion to transition state.
- Stabilizes the substrate.
Describe the Lock and Key model to describe the active site of an enzyme
Lock and key model (Fischer’ template)
- The structure / conformation of the enzyme is rigid.
- The substrate fits to the binding site (specifically).
- ES union depends on a reciprocal fit between molecular structure of E and S
- No scope for flexible nature of enzymes (causing this model to fail)
Describe the Induced fit theory and its model of the active site
Induced fit theory (Koshland’s model)
- Active site is not rigid and pre-shaped.
- Substrate binding site are present at the nascent active site.
- Interaction of S with E induces a conformation change in the enzyme (resulting in the formation of a strong substrate binding site)
- Used for X-ray diffraction studies
List 3 factors that affect the enzyme catalyzed reactions
- Substrate concentration
- pH concentration
- Temperature
Describe the effect of substrate concentration on enzyme catalyzed reactions
- Initially, rate of enzyme reaction increases with increasing substrate concentration. At a very high substrate concentration, the active sites are saturated with the substrate. Any extra substrate has to wait for the enzye to release the product.
- Rate of a biochemical reaction is defined as the change in the [reactant] or [product] per unit time.
- Graphs for rate of reaction is initial velocity (V) vs substrate concentration [S]. Most of these curves show a hyperbolic curve (Michaelis-Menten kinetics).
- The rate of an enzyme-catalyzed reaction increases with increase in [S] until a maximum velocity is reached.
Explain the effect of substrate concentration with the Michelis Menton plot.
The Michaleis Menton Equation describes the rate of reaction as:
v = Vmax*[S] / (Km + [S])
v - measured velocity
Vmax - maximum velocity
[S] - substrate concentration
Km - Michelis Menten constant
What is the Michaelis Menten constant (Km)
The Michaelis-Menten constant (Km) is defined as the substrate concentration to produce half-maximum velocity in an enzyme catalysed reaction.
Describe the velocity of a reaction vs substrate concentration graph in relation to the linewearver-burk plot
- For the determination of the Km value, the substrate saturation curve is not very accurate.
- Since Vmax is approached asymptotically.
- To counteract this, you can take the reciprocals of the equation. This will give you a straight line graphic representation.
The equation then becomes
1/v = (Km/Vmax x 1/[S]) + 1/[Vmax]
(y=mx+c)
- This means that the gradient of the curve will be Km/Vmax and the y-intercept will be 1/Vmax
- X intercept is 1/Km
- Y value is 1/ v
- X value is 1/[S]
Describe first order and zero order reactions
First Order reactions:
- [S] < Km
Zero order reactions:
- [S] > Km
- This means the rate of reaction is independent of the substrate concentration and the reaciton is said to be zero order
Describe the significance of Low and high Km
Low Km:
- A lower [S] is needed to half-saturate the enzyme active sites.
- This reflects a high affinity of enzyme
High Km:
- This means that a higher [S] is needed to half-saturate the enzyme active sites
- This reflects a low affinity of enzyme for its substrate.
Explain the significance of the Km value in relation to Glucokinase and hexokinase
- Glucokinase and hexokinase are isoenzymes, meaning they catalyze the same reaction.
- Both phosphorylate glucose in glycolysis.
- Glucokinase has a higher Km for glucose (10mmol/L) and Hexokinase has a lower Km for gluxose (0.2mmol/L)
- This means that glucokinase has a high Vmax and Hexokinase has a lower Vmax.
- This means that hexokinase is able to operate at 50% with a much lower level of glucose. This allows hexokinase to be active even at low glucose levels (fasting states)
- Glucokinase is active when there is a high glucose levels (faster reaction at higher concentration), which makes it effective after a meal.
Explain the effect of Temperature with graph and examples
- The rate of enzyme reaction is doubled for every rise of 10 degrees C.
- As the temperature increases, the rate increases up to a certain level where the enzyme activity is maximum (this is known as the optimum temperature, about 37-40 degrees).
- If the temperature is increased above this level, the rate of reaction drops sharply as high temperature may denature thie enzyme.
At very high temperatures (above 70 degrees C) most enzymes become inactive. Exceptions are enzymes from thermophilic bacteria like Taq polymerase from T aquaticus.
