enzymes Flashcards
What is an Enzyme?
Globular protein
Biological catalyst that differs from a chemical catalyst
enzymes: ribozymes
catalytic RNA molecules with no protein component
enzymes are biological catalysts that
- Catalyses very high reaction rates
- Shows great reaction specificity
- Work in mild temperature/pH conditions
- Can be regulated
Cofactor =
Non-protein component needed for activity
eg- ions
cofactor in glucose-6-phosphate
Mg2+
cofactor in pyruvate kinase
K+
cofactor in catalase, peroxidase
Fe2+, Fe3+
Coenzyme
Complex organic molecule, usually produced from a vitamin
coenzyme from riboflavin
FAD
coenzyme from Niacin
NAD+
coenzyme from pantothenate
Coenzyme A
Prosthetic group =
Cofactor covalently bound to the enzyme or very tightly associated with the enzyme
eg- haem in haemoglobin
Apoenzyme =
The protein component of an enzyme that contains a cofactor
Holoenzyme =
“whole enzyme” – the apoenzyme plus the cofactor(s)
Substrate =
Molecule acted on by the enzyme
Active site =
Part of the enzyme in which the substrate binds and is acted upon
Oxidoreductases - type of reaction
Transfer e-
Transferases - type of reaction
Group transfers
Hydrolases - type of reaction
Hydrolysis (transfer chemical groups to water)
Lyases - type of reaction
Form, or add groups to double bonds
Isomerases - type of reaction
Transfer groups within molecules (form isomers)
Ligases - type of reaction
Formation of C-C, C-S, C-O and C-N bonds (coupled to ATP cleavage)
Enzymes do not
- Move reaction equilibria
- Make a non-spontaneous reaction spontaneous
Enzymes do
- Increase rates of spontaneous reactions
- Lower the activation energy of biochemical reactions
- Accelerate movement towards reaction equilibrium
“Useful” energy generated from cellular reactions is termed
Gibbs Free-Energy (G), originally called “available energy”
Spontaneous reactions must have a
–ve ΔG value as they will decrease enthalpy (H) and/or increase entropy (S)
Spontaneous reaction isn’t
instantaneous because of the energy barrier
Energy barrier =
energy required to position chemical groups correctly, bond rearrangements, e- rearrangements, etc…
Transition state shows
the moment that chemical bonds are formed and broken. the top bit of curve.
Addition of an enzyme to a spontaneous reaction
lowers the activation energy
Enzymes allow the reaction to proceed via different route
Enzymes form non-covalent bonds with
substrate molecules, called the “binding energy” allowing them to take the reaction through a different path of reaction intermediates
No enzyme =
high activation energy ( high delta G)
CATALYSIS =
Active site complementary to transition state
How do enzymes reduce activation energy?
- Entropy reduction
- Desolvation
- Induced fit
Explain Entropy reduction
- Molecules in free solution will only react by “bumping” into one another
- Enzymes “force” the substrate(s) to be correctly orientated by binding them in the formation they need to be in for the reaction to proceed
Explain Desolvation
Weak bonds between the substrate and enzyme essentially replace most or all of the H-bonds between substrate and aqueous solution
Explain Induced fit
Conformational changes occur in the protein structure when the substrate binds
If we changed the substrate concentration [S] we would change
the initial rate of a reaction.
More substrate = higher initial rate of reaction
- As the reaction proceeds, the substrate is used up and the rate of reaction changes
- Initial velocity (V0) can be studied if we assume that initial [S] does not change – this only really works if you have loads of S
When substrate concentration becomes so large that V0 changes are vanishingly small you get
maximum reaction velocity, Vmax.
Vmax occurs because all of the enzyme active sites are saturated with substrate
Michaelis-Menten equation
when you plot V0 against substrate concentration you get a
hyperbolic curve.
formation of an enzyme-substrate complex (ES)
Michaelis-Menten equation
Model states that the first part of the reaction (to produce ES) occurs reversibly
Second part of the equation (to produce E and P) occurs more slowly than the first part - rate limiting step
Michaelis-Menten equation:
If 2nd part is slower it must
limit the rate of the overall reaction, so the overall rate of reaction must be proportional to the amount of ES
- In other words, more ES would give a higher overall reaction rate and less would give a slower overall reaction rate
V0 usually equates to the
steady state of a reaction, so study of these initial rates of reaction is termed “steady state kinetics”
M-M equation was derived from their hypothesis that t
he rate-limiting step of an enzymatic reaction is the breakdown of the ES complex to give free enzyme and product
V0 =
initial reaction velocity
Vmax =
maximum reaction velocity
What’s the point of the M-M equation?
The equation accounts for the hyperbolic curve you see when a reaction proceeds
- At low [S] (i.e. the [S] is much less than Km) the M-M equation looks like,
V0 = Vmax[S]
Km
At high [S] ([S] is much greater than Km) the equation looks like,
V0 = Vmax
Km is equivalent to
the substrate concentration at which the initial reaction rate is half of the maximum reaction rate