Proteins (4), Carbohydrates (6/8), and Lipids (9) Flashcards
Enzymes
Catalysts involved in biochemical reactions. Increase the rate of reaction without being consumed.
Substrates
Molecule that acts as the reactant in an enzymatic catalyzed reaction. Binds to the enzyme at the active site.
Active Site
The location where the enzyme binds to on the substrate which allows catalysis to occur.
Lock and Key model
Only the correct substrate will fit to he active site on the enzyme.
Induced Fit
Interaction of the substrate and enzyme helps form the active site.
Enzyme Classification: Oxidoreductases
Catalyze reactions involving the gain or loss of electrons.
Enzyme Classification: Transferases
Transfers one group to another
Enzyme Classification: Hydrolases
Cleave a bond with water
Enzyme Classification: lysases
Break double bond with other means than oxidation and hydrolysis.
Enzyme Classification: Isomerases
Rearrangement of the molecule.
Enzyme Classification: Ligases
Join two molecules.
The two assumptions of Michaelis-Menten Constant
- k2 is much slower than k-1, as this allows for the establishment of an equilibrium at the ES complex.
- The ES complex forms rapidly and exists at a relatively unchanging concentration as the reaction proceeds until substrates is depleted.
Vmax
Theoretical maximal velocity for a given concentration of enzyme.
KM
Michaelis Constant: measures binding affinity of the ES complex.
- Higher KM means lower affinity
- Lower KM means higher affinity
KM = (k-1 + k2) / k1
Michaelis-Menten Equation
vo = Vmax [S] / KM + [S]
Lineweaver-Burke Plot
1/vo = (KM/Vmax)*1/[S] + 1/Vmax
kcat
Turnover Number: number of reactions the enzyme can catalyze per unit of time. Measures catalytic efficiency.
kcat = Vmax / [E]tot
Diffusion Controlled Limit
Occurrence when rate-limiting step becomes the diffusion of enzyme and substrate together.
Rate must be between 10^8 and 10^9 M-1 sec-1.
Suicide Inhibitors
Covalently modifies the actives site of the enzyme, irreversibly block its function. Directly poisons the enzyme.
Competitive Inhibitors
Recognize molecules similar to the shape of the substrate that binds to the active site which competes directly with the substrates. Can be overcome with substrate concentration is high.
vo = Vmax * [S] / KM*a + [S]
a = 1 + [I] / KI
Dissociation Constant KI = [E][I] / [EI]
Increase KM and Vmax remains the same.
Uncompetitive Inhibitors
Binds to the ES complex
vo = Vmax * [S] / KM + [S]*a’
a’ = 1 + [I] / KI’
KI’ = [ES][I] / [ESI]
Decrease KM and Decrease Vmax.
Mixed Inhibitors
A combination of competitive and uncompetitive inhibitors.
vo = Vmax * [S] / KMa +[S]*a’
Decrease or Increase KM and Decrease Vmax.
Note: If a = a’, the line will intersect on the x-intercept with different Vmax but same KM. This is known as the non-competitive or pure mixed inhibition.
General Principles of Enzyme Catalyzed Reactions
- Enzymes bind to substrates with various weak forces (Van Der Waal, Ionic Bonding, Hydrogen Bonding, Dipole-Dipole Interaction) and entropy (delta S) decreases.
- Enzyme binds to substrates with large number of weak forces known as electrostatic catalysis (sum total of the weak forces acting on the substrate).
- In induced fit, enzyme bind substrates that favours the transition state.
Types of Catalysis: General acid-base catalysis
Amino acid side chains donate or accept protons. Polar and charged amino acids are important.
For example: Lysozyme (Glu and Asp)
Types of Catalysis: Metal ion catalysis
Active site metal ion can act as a redox active center. Site can also act as a Lewis base or acid.
For example: Anhydrase
Types of Catalysis: Covalent catalysis
Nucleophilic or electrophilic attack on an atom which results in a covalent intermediate. Involves Ser, Asp, Lys, Tyr, Cys, and other cofactors.
For example: Chymotrypsin (catalytic triad: Asp, Ser, His) and Chmotrypsinogen, the inactive form.
Proteases
Enzyme that degrades proteins.
Many have Trypsin fold which are structures comprised of two Beta barrel domains, the active site being at the interface.
Affinity Labeling
Technique used to specifically label residues on the active site. Label only one amino acid residue, suggesting that the label amino acid is not the same as other amino acid residues.
Enzyme Regulation: Covalent modification -) Proteolytic cleavage
An inactive enzyme becomes active through cleavage or digestion of proteins and peptides (Irreversible)
For example: Chymotrypsinogen (an inactive form) is activated by proteolytic cleavage to Chymotrysin
Enzyme Regulation: Covalent modification -) Phosphorylation
A form of protein activation, facilitated by protein kinases which add phosphate groups to the hydroxyl groups of serine, threonine, or tyrosine. Phosphatase remove phosphate groups. The regulation occurs through a series of singling steps termed a signalling cascade. (Reversible)
For example: Src
