Enzymes Flashcards
Ligase
Catalyze joining of two molecules.
Example: DNA ligase catalyzes phosphodiester bond formation between Okazaki fragments.
Isomerase
Catalyze conversion between isomeric forms.
Example: Conversion between glucose-6-phosphate and fructose-6-phosphate in the glycolysis pathway.
Oxidoreductase
Catalyze redox (reduction-oxidation) reactions.
Example: NADH dehydrogenase catalyzes the NADH → NAD+ reaction in the electron transport chain.
Hydrolases
Catalyze hydrolysis reactions.
Example: proteases cleave peptide bonds.
Lyases
Catalyze cleavage reactions other than hydrolysis reactions (handled by hydrolases) and oxidation reactions (handled by oxidoreductases). These reactions form double bonds.
Enzymes ending in the suffix -lase are lyases.
Example: Fructose-1,6-bisphosphate → GADP + DHAP is catalyzed by an aldolase in glycolysis.
Proteins that catalyze reactions, meaning they increase
reaction rate
Enzyme effects
Enzymes decrease the activation energy of a reaction by binding to substrates (reactants), and stabilizing the transition state.
They do not change the concentrations of the products/reactants at equilibrium.
Active site
The site of catalysis where the enzyme and substrate interact.
Substrate interaction theories
Lock and key theory: enzyme and substrate fit together exactly.
Induced fit theory: enzyme and substrate will conform shapes to fit together.
Cofactors
Cofactors are additional molecules, such as metal cations, required by some enzymes.
A cofactor that is an organic molecule is called a coenzyme.
Example: lipoic acid is a cofactor for pyruvate dehydrogenase.
Enzyme activity
Enzyme activity can be affected by pH and temperature, as extreme conditions can cause denaturation of the enzymes.
Lineweaver-Burk plot principles
These are linear graphs derived from rearrangement of the Michaelis-Menten equation.
Michaelis-Menten graphs record observed values while Lineweaver-Burk curves describe theoretical values which are more precise.
Axes of Lineweaver-Burk plot
- X-axis: 1 / [S]. Inverse of substrate concentration.
- Y-axis: 1 / V. Inverse of reaction rate.
Intercepts of Lineweaver-Burk plot
- X-intercept: - 1 / Km. Negative reciprocal of Michaelis constant Km.
- Y-intercept: 1 / Vmax. Reciprocal of maximal reaction rate.
- Slope: Ratio of Km / Vmax
Michaelis-Menten equation
Vo = (Vmax [S]) / (Km + [S])
Michaelis-Menten curves
Parameters
- Vmax represents the maximum reaction rate.
- Km represents the substrate concentration necessary to achieve half the maximum reaction rate.
- Km is also a measure of enzyme-substrate binding affinity. A higher Km indicates a lower binding affinity.
Graphical representation Michaelis-Menten curves
Michaelis-Menten curves are graphed with V (reaction rate) on the y-axis and [S] (substrate concentration) on the x-axis.
The height of the plateau on the curve represents Vmax.
The point on the x-axis at half the maximum height of the curve represents Km.
Three major assumptions of the Michaelis-Menten equation:
- Irreversibility assumption: Product concentration [P] and reverse reaction rate are negligible.
- Steady state assumption: Concentration of enzyme-substrate complex [ES] is constant throughout reaction. Rate of formation = rate of consumption.
- Free ligand assumption: Concentration of substrate must be much higher than concentration of enzyme; otherwise enzyme cannot be saturated. In other words [S]»_space;»> [E].
Transferases
Class of catalyst that catalyzes the transfer of functional groups between molecules.
Kinases and phosphatases are subclasses of transferases.
Subclasses of transferases
Kinase
Catalyzes the addition of a phosphate group from ATP.
Example: Phosphofructokinase catalyzes the committed step of glycolysis, fructose-6-phosphate → fructose 1,6-bisphosphate.
Subclasses of transferases
Phosphatase
Catalyzes the removal of a phosphate group.
Example: Dephosphorylation of the PDC in the citric acid cycle.
Subclasses of transferases
Phosphorylase
Catalyzes the addition of an inorganic phosphate group, like HPO4.
Example: glycogen phosphorylase in glycogenolysis.
Cooperative enzymes
Cooperative enzymes have multiple active sites, and binding to one changes the affinity of others for the substrate.
Cooperative enzymes
Effect on activity curves
Enzymes with positive cooperativity have sigmoidal-shaped activity curves.
Enzymes with negative or no cooperativity have hyperbolic-shaped activity curves.
Cooperative enzymes
Hill coefficient
A quantitative measure of cooperativity, derived from the Michaelis-Menten equation.
Hill coefficient > 1 indicates positive cooperativity.
Hill coefficient < 1 indicates negative cooperativity.
Suicide inhibition
Binds to active site by a covalent bond, causing irreversible inhibition. Generally slower compared to reversible inhibition.
Feedback inhibition
The product of a reaction pathway “feeds backwards” and inhibits an enzyme.
Also called end-product inhibition.
Allosteric effector
A substance that binds to the allosteric site of an enzyme (away from the active site) and changes the conformation of an enzyme and its active site.
This changes the kinetics of the reaction (e.g. the Michaelis-Menten curve).
Zymogen
An inactive precursor to an enzyme which can be activated under certain conditions.
Example: pepsinogen is activated to pepsin at low pH in the stomach.
Competitive inhibition binding and kinetics
Uncompetitive inhibition binding and kinetics
Noncompetitive inhibition binding and kinetics
Mixed inhibition binding and kinetics
Principles of kinetics
Kcat (turnover number)
Represents rate of substrate conversion to product under conditions of saturation.
kcat = Vmax / [E]
Principles of kinetics
Catalytic efficiency
Given by the equation:
Efficiency = kcat / Km
↓ Km results in ↑ efficiency
Principles of kinetics
Relation to Vmax
Vmax = kcat * [E]
