TBL 2 - Enzyme catalysis, kinetics and regulation Flashcards
Kinase
Transfers phosphate group from high energy molecule to a substrate (ATP hydrolysis)
Phosphorylase
Adds inorganic phosphate to a substrate without using ATP
Dehydrogenase
Catalyzes oxidation-reduction reaction through the transfer of H
Ligase
Binds or adds ligands
Transferase
Transfers functional group from one molecule to another
Oxidoreductase
Catalyzes oxidation-reduction reaction through the transfer of electrons
Approximation
Enzyme brings reactants closer together
Covalent catalysis
A reactive group on the enzyme is covalently bonded to substrate
Acid-base catalysis
A reactive group on enzyme acts as proton acceptor or donor
Metal ion catalysis
Assists in electrophilic or nucelophilic interactions or bonds to the substrate
Transition state inhibitors
Drugs that resemble transition state and bind to enzyme
Example of transition state inhibitor
Tamiflu inhibits influenza A and B neuraminidase
Pcn inhibits bacterial enzyme glycopeptide transpeptidase
Co-factors
Inorganic ions that assist in enzyme catalysis
The binding of a substrate to enzyme results in ____ called ____
a release of free energy
binding energy
Co-enzyme
Small organic non-protein that assist enzymes
Ex of co-enzyme
FAD, NAD, coenzyme A, biotin
Many co-enzymes are a derivative of ____
vitamins
THF stands for ____ and is derived from ____ and functions in ____
Tetrahydrofolate
Folic acid
Methylation
Co factor ex
Iron (Fe) Copper (Cu) Zinc (Zn) Magnesium (Mg) Selinium (Se)
Magnesium is often a cofactor for which enzyme category?
Kinase
Prosthetic group
A non-protein group (organic or inorganic) that forms a covalent bond with a protein
Biotin catalyzes ___ reactions
carboxylation
____ is frequently present in enzyme catalysis involving acid-base catalysis
Histidine
Histidine has a pKa near ____
Physiological pH
Serine proteases
Chymotrypsin, trypsin, elastase
Family of enzymes that sequentially cleave peptide bonds between specific AAs
Chymotrypsin
Cleaves proteins on the carboxyl side of aromatic or large hydrophobic amino acids
Binding pocket lined with AA which have small or no side chains
Trypsin
Cleave Arg and Lys (postiively charged AA)
Binding pocket has Asp (negatively charged AA)
Elastase
Cleaves at the C-terminus at AAs with small side chains
Binding pocket lined with bulky AAs
Zymogen (proenzyme)
Enzyme precursor
Isozymes
Enzymes that catalyze the same chemical reaction but differ in AA sequence
Vmax
Reached when enzyme is saturated with substrate
Zero order reaction
Velocity is independent of [S]
First order reaction
Velocity is directly proportional to [S]
Michaelis-Menten eq
V0 = Vmax[S] / Km + [S]
Km =
Substrate concentration at 1/2 of Vmax
Low Km has _____ affinity for [S]
high
High Km has _____ affinity for [S]
low
Lineweaver-burk plot equation and interpretation
1/V0 = Km/Vmax * 1/[S] + 1/Vmax
y-int = 1/Vmax x-int = -(1/Km) slope = Km/Vmax
Kcat
Turnover number
Vmax/Et = Kcat
Catalytic efficency
Kcat/Km
Cats are efficient at jumping over the moon
Competitive inhibition
Km increases
Vmax stays the same
can be overcome by increased substrate
Examples of competitive inhibition
Methotrexate - dyhydrofolate reducatase
Statins - HMG CoA reductase
Ethanol - alcohol deydrogenase
Non competitive inhibition
Km stays the same
Vmax goes down
Inhibitor binds at allosteric site causing conformational change
Example of Non competitive inhibition
Allopurinol - xanthine oxidase
used in gout
Uncompetitive inhibition
Bind at the enzyme-substrate complex
decreases Km and Vmax
Examples of Uncompetitive inhibition
Lithium used to treat bipolar disorder
Arsenate
Irreversible inhibition
permanently inactivate enzyme
Covalently bound
Seen in the use of aspirin which inhibits COX
and ferrochelatase which is inhibited by lead
Km =
-1/x-intercept
Allosteric effector
Bind to a site other than active site on enzyme, causing a conformational change in the active site which either promotes or inhibits binding of substrate
Allosteric enzymes
Change their conformational upon binding of an effector, “cooperative”
Example of cooperativity and allosteric interactions
Hemoglobin
sigmoidal curve
Serine protease “catalytic triad”
Histidine, Aspartic acid, Serine
Cooperativity
BInding of one ligand will increase the affinity for binding another ligand
Feed back regulation
Positive feedback loop: product upregulates pathway
Negative feedback loop: products down regulates pathway
Feed foward regulation
Product that regulates an enzyme, which is further ahead of it in pathway
Coenzyme TPP helps to transfer _______
Aldehyde group
Coenzyme biotin helps to transfer _____
CO2
Coenzyme CoA-SH helps to transfer _____
Acyl group
Coenzyme NADH helps to transfer _____
Hydride group
Metal ion cofactor: Zn Mg Cu Fe Se
Which enzymes are they involved in?
Zn- superoxide dismutase Mg- ATPases, Kinases Cu- cytochrome c oxidase Fe- cytochromes Se- glutathione peroxidase
