Module 6 - Enzymes: function, reaction mechanisms, and kinetics Flashcards
How do enzyme active sites work?
provide chemical environments that facilitate catalytic reactions by excluding excess solvent (such as water)
What are the three parameters of enzyme function?
enzymes bind substrates with high affinity and specificity, binding to active sites induce structural changes, and enzyme activity is highly regulated in cells (to balance catabolic and anabolic pathways)
How is the catalytic efficiency of glycogen phosphorylase increased?
noncovalent binding of allosteric regulators like AMP and covalent attachment of a phosphoryl group on Ser14
How do enzymes effect the conversion of hydrogen peroxide to water and oxygen?
half life of H2O2 would be 3 years, but by adding a free iron the half life is only 11.6 minutes
How does catalase increase reaction rate?
assist in proton movement and oxidation of Fe3+ to Fe4+
catalase reaction is 10,000,000 more efficient than Fe alone
How do catalysts and enzymes effect reaction energy?
lower the transition state
What are cofactors vs. coenzymes?
cofactors are typically metal ions (Cu2+, Zn, etc.), while coenzymes are larger vitamin derivatives (NAD, FAD, CoA, etc.)
What kind of cofactor does nitrite reductase have?
A Cu2+ ion cofactor between two His residues that hold it in an optimal position for catalyzing the reaction
What is lipoamide?
a coenzyme that is covalently attached to a lysine residue in the decarboxylase enzyme
What are the three ways that enzymes increase reaction rate?
stabilize the transition state, provide an alternate path for product formation via stable intermediates, and optimal substrate orientation and increased local concentration
Uncatalyzed reactions require collisions that are…
at the right orientation and sufficient energy
What are the two main functions of enzyme active sites?
- provide optimal orientation
- exclude excess solvent (water) that can interfere with the reaction
What is demonstrated by the aldolase reaction?
the importance of favorable spatial arrangements, and the formation of a covalent substrate-enzyme intermediate
In hexokinase, what happens at the active site?
when glucose binds, water is excluded to prevent nonproductive phosphoryl transfer from ATP to water
How do hydrophobic substrate channels work?
prevent water from entering the buried active site
What is the difference between specific and non specific acid base catalysis?
specific - involves water
non specific - proton transfer involving a functional group
RNA cleavage with pancreatic ribonuclease involves…
two histidine residues and a general acid base catalysis using the addition of water
What is the unique aspect of covalent catalysis?
a transient covalent bond forms between the substrate and the enzyme that can also be used for create an unstable intermediate
the other reactant will react more strongly with the unstable enzyme intermediate than it would with the original reactants
What is an example of covalent catalysis?
1,3 BPG formation using the coenzyme NAD+
What is an example of metal ion catalysis?
the carbonic anhydrase reaction uses a Zn 2+ ion as a catalytic group to yield the bicarbonate product
What is the difference between redox reactions at C-O bonds vs. C-C bonds?
C-O: NAD+/NADH
C-C: FAD/FADH2
both transfer 2 electrons
What are the three types of metabolite transformations?
isomerization:
reactions do not change the molecular formula of the product compared to that of the substrate
condensation:
reactions combine two substrates to form a larger molecule
hydrolysis or hydration: hydration or dehydration using water
What are two examples of reversible modifications?
insulin signaling stimulates phosphoinositide-3-kinase activity which is turned off when phosphatase and tensin homolog removes the phosphate
DNA methyltransferases use the metabolite adenosyl-I-methionine as a methyl donor to add a methyl to deoxycytidine. The demethylation of deoxycytidine by a DNA glycosylase is associated with gene activation.
Describe chymotrypsin reactions
Chymotrypsin is a serine protease that cleaves proteins using acid-base and covalent catalysis. Serine, histidine, and aspartate form a catalytic triad.
Consists of three peptide chains, with serine on the C chain and histidine and aspartate on the B chain.
Describe enolase reactions
Enolase is a metalloenzyme with each active site containing two divalent metal ions that are required for the reaction. Lys acts as a general base and Glu acts as a general acid, overall resulting in the formation of phosphoenolpyruvate (PEP)
Describe HMG-CoA reductase
tetrameric enzyme in the cholesterol biosynthetic pathway
atorvastatin is a cholesterol lowering drug
two hydride transfers involving two molecules of NADPH coenzyme with the active site stabilizing the transition state
What are statin drugs?
treatments for artherosclerosis by lowering LDL levels
all are similar to HMG-CoA with different functional groups
What does the rate constant, k, of a reaction indicate?
how quickly a substrate molecule is converted to product under defined conditions
What is the equation for velocity of the reaction?
v=k[S] or v=k[S][Y]
v is amount of product formed per unit time, k is rate constant, and [S] and [Y] are concentration of substrates
In Michaelis-Menten Kinetics, how is substrate concentration held “constant”?
the concentration of substrate is much greater than the concentration of enzyme, so it stays relatively the same
What are the three assumption of Michaelis-Menten Kinetics?
- no product has been generated
- product released is assumed to be a rapid step
- concentration of ES remains approximately constant because [S]»>[E]
What is Km? What does it mean about an enzyme?
the Michaelis constant, or the concentration of substrate at which velocity is 1/2 Vmax
low value means high catalytic activity
What is the Michaelis-Menten equation? What does it represent?
Vo = Vmax [S] / Km + [S]
represent the hyperbolic curve of initial velocity and substrate concentration
What is the Lineweaver-Burk plot?
graph that can be used to obtain the Michaelis-Menten parameters
slope = Km/Vmax
x intercept = -1/Km (same for all substrate concentrations)
y intercept = 1/Vmax
What is kcat?
the turnover number, or the catalytic rate
What value is best used for describing how well the enzyme works?
kcat/Km, the specificity constant
How does pH and temperature affect enzyme activity?
Changes in pH can affect chemistry of enzymes because seven amino acids have ionizable side chains that could gain or lose a proton
Changes in temperature can affect catalytic properties, but also structure of the protein
