Lecture 4 Flashcards
Why proteins as a catalyst?
Greater reaction specificity (chirality), capacity for regulation (inhibitors), higher reaction rates, and milder reaction conditions
Enzymes
catalytically active biological macromolecules. Provide an active site within which a given reaction can proceed more rapidly
Michaelis complex
the enzyme substrate complex.
v = ( vmax * [S] ) / (Km + [S])
Transition state
fleeting molecular moment in which events such as bond breakage/formation or change formation have proceeded to the point where decay to either substrate or product is equally likely.
T or F: Rate is dependent on the magnitude of the activation energy
True. The higher the activation energy, the slower the reaction. And enzymes can affect the activation energy.
Transition state and free energy change
a large negative free energy change favors product formation and vice versa
Rate limiting step
step with the highest activation energy
3 ways enzymes lower activation energy
rearrangement of covalent bonds during catalysis, organize reactive groups into close proximity, and stabilizing the transition state
3 types of proximity effect and speed in relation to each other
bimolecular reactions, unimolecular reactions flexible, and unimolecular reactions inflexible
k(cat)
turnover number - number of substrate molecules that one enzyme can convert per second
K(m)
Michaelis constant = disappearance of the substrate complex / formation of the substrate complex.
Thus lower Km, the greater the affinity.
Sequential mechanism
enzyme reaction occurring in random or ordered method of substrate binding.
Ping-pong mechanism
The enzyme gets modified by the first substrate, releasing the product, allowing the second substrate to come. Think phosphorylation.
3 types of enzyme inhibition
competitive, uncompetitive, noncompetitive (mixed)
Competitive inhibition
substrate and inhibitor compete for the binding site of the enzyme. intersect at y-axis. Km increases and Vmax stays the same.
Uncompetitive inhibition
inhibitor binds to the substrate complex. Substrate will cause a conformational change of the enzyme allowing the inhibitor to bind at an allosteric site. Parallel lines. Km is increased and Vmax decreases.
Noncompetitive inhibition (mixed)
The inhibitor can bind to the enzyme first or the substrate can bind to the enzyme first. left of y-axis. Km stays the same and Vmax decreases
Chymotrypsin
produced in pancreas. Cleaves peptide bond on the C-terminal side of the aromatic amino acids. does through hydrolysis. Adjacent amino acid can’t be Pro
Catalytic triad
Serine 195, Histidine 57, Aspartic acid 102.
3 important aspects of Chymotrypsin
Catalytic triad, hydrophobic pocket confers substrate specificity, and oxyanion hole present to stabilize the transition state
Oxyanion hole
Serine and glycine will hydrogen bond to the oxyanion, stabilizing the transition state
General base catalysis
proton extraction by a weak base. Typically via groups other than -OH from water
Specific base catalysis
Proton extraction by a strong base. Typically via the -OH group from water.
Enolase and its cofactors
dehydration key in glycolysis. 2 Magnesium ions which stabilize the oxyanion
Enolase’s important residues
Lysine and glutamate
Lysozyme
cleavage of the cell wall leads to lysis of bacteria. Cleaves the glycosidic bond through hydrolysis
Lysozyme’s important residues
Glutamate and aspartic acid
