Enzymes Flashcards
How do enzymes work to lower the energy to make products faster?
They lower the activation energy by forming an enzyme-substrate complex
What are the 3 substrate recognition hypotheses?
- Lock and key
- Induced fit - when the substrate binds to the enzyme it change shape to fit around it
- Conformational selection - when the right enzyme shape and the wrong shape are in equilibrium with each other
Describe the binding energy of a reaction:
The free energy that is released by the formation of weak bonds between the substrate and the enzyme. These interactions are maximised when the substrate is in the transition state - tightest interaction between enzyme and substrate. However the transition state is the least stable chemical form of the substrate
What is the rest of the amino acids for in an enzyme that are not involved in the active site?
- Positioning the active site residues correctly, sometimes in energetically unfavourable positions
- Providing the correct microenvironment in the active site e.g shifting of pKa values.
- Provides other sites for recognition and control e.g allostery
What are organic cofactors known as?
Co enzymes
What are the 2 types of enzymes?
- Enzymes made completely out of protein and fully active
- Enzyme that needs an associated non-protein component in order to be a catalyst. The protein alone is called ‘apo’ enzyme and the whole enzyme is known as ‘holo’ enzyme
What is the difference between a prosthetic group and a coenzyme/cofactor?
Prosthetic groups are bound all the time whereas cofactors and coenzymes can bind and dissociate during the catalytic cycle
What are the 3 ways that enzymes can be regulated?
- Proteolysis of proenzymes is a one-way “on” switch
- Transient modification e.g phosphorylation is a two way switc
- Allostery is a graded response to either substrates or other non-covalently bound regulatory molecules.
What does a small kd imply?
Tight binding
What is the michleis menten eqn?
V = (vmax [s]) / (Km + [s])
What are the 4 assumptions for the mechalis meneten eqn?
- Catalysis is the slowest rate limiting step ka>kcat
- There is much more substrate than enzyme
- The conc of ES is constant
- The reverse reaction is negligible
What are the features of the lineweaver burk transformation?
Axis are 1/v and 1/[s]. The point of intersection between the ine and the 1/v is the 1/vmax and the intersection between the line and 1/[s] is -1/Km.
What are the 3 types of reversible inhibitors and what is the type of unreversible inhibitor?
- Competitive
- Non-competitive
- Uncompetitive
- Covalent modification of enzyme
The smaller the ki value…..
The better the inhibitor
Describe the type of inhibition: competitive
Inhibitors compete for the active site so they must be chemically similar to the enzymes substrate. The decrease Kcat but inhibition can be overcome by increased substrate conc
Describe the type of inhibition: non-competitive
Inhibitors bind to a site that is distant from the active site which is not dependent on the formation of the enzyme substrate complex, it acts by reducing Kcat.
Describe the type of inhibition: uncompetitive
Inhibitors can bind to another site which is only accessible after the substrate has bound to the enzyme. It cannot be overcome by adding more substrate
How does this type of inhibition affect Km/Vmax and what is the apparent Km/Vmax: competitive
The Vmax stays the same but -1/Km increases so the real Km decreases
Km app = Km (1 + [I]/Ki)
How does this type of inhibition affect Km/Vmax and what is the apparent Km/Vmax: non-competitive
1/Km stays the same but 1/Vmax increases so the real Vmax decreases
Vmax app = Vmax / (1 + [I]/Ki)
How does this type of inhibition affect Km/Vmax and what is the apparent Km/Vmax: uncompetitive?
Both 1/vMax and -1/Km increase
Vmax app = Vmax / (1 + [I]/Ki)
Km app = Km / (1 + [I]/Ki)
How can we calculate Ki?
By using a secondary plot - with either the slope (competitive) or y axis intercepts (non-competitive) plotted against [I]. The intercept with the x axis will then be the Ki
What is the hill eqn?
V = (Vmax [s] ^h) / (K + [s]^h)
What does the hill plot show us?
The slope is h and the bigger h is, the more cooperative the process. The point of intersection is log k/h
What is the T state?
High k so lower affinity for s
