Biochem: Enzymes and G proteins Flashcards
(30 cards)
what is the range of the rate enhancement of enzymes?
5-17 orders of magnitude
What two factors contribute to the specificity of enzymes?
covalent bonds with the substrate and non covalent interactions that stabilise the enzyme-substrate complex, a major source of free energy, used to lower the reaction energy.
What is the function of transferase?
transferring functional groups between or within molecules
Function of oxidoreductase
NAD+ or electron transfer
Function of isomerase
transferring functional groups within molecules to create isomers
Function of lyase
breakdown of c-n, c-c, c-o bonds not via phosphorylation or hydrolysis
Function of ligase
generation of new c-n, c-c, c-o bonds by condensation using ATP
Function of translocase
translocation of molecules within the proximity of or attached to the membrane
What is the enzymatic mechanism of chymotrypsin?
acylation (phase1) and deacylation (phase2) on the sarin residue:
phase 1: the peptide bond is sliced and an Esther bond between the peptide’s carbonyl and the carbon in the enzyme.
phase 2: the Esther bond undergoes hydrolysis and the deacylated enzyme is regenerated
What happens in a general acid base catalysis and why is it important for enzymatic reactions?
a proton is transferred by a weak acid or base other than water. in the active site of the enzyme water might not be available as a proton donor or acceptor which is why a general acid base catalysis is important for generating the E-S complex.
What is a specific acid base catalysis?
Catalysis of the type that uses only the H+ (H3O+) or OH- ions present in water is referred to as specific acid-base catalysis.
What happens in a covalent catalysis and what enzymes can use this catalysis?
In covalent catalysis, a transient covalent
bond is formed between the enzyme and the substrate. enzymes with a nucleonic group X can be considered covalent catalyses.
A – B + X: -> (with water) A–X + B –> (with water) A + X: +B
What is the catalytic triad in chymotrypsin?
Ser195 linked to His57 and Asp102
What is the enzymatic reaction of chymotrypsin?
phase 1 acylation:
1. substrate enters the active site of the enzyme and due to the substrates aromatic residue it strengthens the bond between His57 and Asp102 due to conformational change
- this change changes the pKa of His from 7 to >12 which makes it a base that can receive a proton from ser195 hydroxyl group, so that it becomes elcoxide.
- elcoxide attacks the substrate’s carbonyl to generate a tetrahedral acyl-enzyme; the tetrahedral enzyme is unstable and collapses, so his57 donates an proton to the amino terminus and release the amino terminus from the substrate. so the complex is left with a bond between the carboxyl terminus of the substrate to the enzymes ser195 in an ester bond
- Water molecules enter the complex and undergo de-protonation in a general acid-base catalysis generates a OH- ion which generates another tetrahedral intermediate state on the ester bond
- De-acylation: the second unstable tetrahedral intermediate state collapses and a carboxylate ion is generated
- detachment if the enzyme from the substrate which regenerates the enzyme for the next round
What is the rate limiting factor of chymotrypsin?
De-acylation
What happens in the pre steady state?
The concentration of ES complex builds up, it is very short (in the µs range)
What is true according to the steady state assumption?
1. the rate of formation of ES is equal to half of the rate of its breakdown
2. the rate of formation of ES is equal to the rate of its breakdown
3. the rate of formation of ES is greater than the rate of its breakdown
- the rate of formation of ES is equal to the rate of its breakdown
k1([Et] - [ES])[S] = k-1[ES] + k2[ES]
What is the Michaelis Menten equation, and how is it changed when V0 = 1/2Vmax?
V0 = Vmax[S]/km + [S]
when V0 = 1/2Vmax:
Vmax/2 = Vmax[S]/km + [S] // :Vmax
1/2 = [S]/km + [S] // *2, *km + [S]
km+ [S] = 2[S] // - [S]
km = [S]
What happens in competitive, reversible inhibition?
the inhibitor competes with the substrate over the active site; can be overcome by increasing the [S]; therefore, Vmax won’t change, but Km with be higher
What happens in reversible, uncompetitive inhibitor?
the inhibitor binds at a site distinct from the substrate active site and, unlike a competitive inhibitor, binds only to the ES complex; therefore Vmax and km will decrease
What happens in mixed inhibition?
an inhibitor binds to a site distinct for the active site, but can bind both E and ES.
Vmax and km will increase
Describe the reaction catalysed by the enzyme hexokinase
Hexokinase is an bisubstrate enzyme, with both Glucose and ATP as substrates. The enzyme catalyses the formation of G6P from glucose (or other 6 carbon sugars), by adding the gamma (last) phosphate from ATP molecule to the hydroxyl group on carbon 6 of glucose. when glucose binds to hexokinase it changes the latter’s conformation (induced fit) to make it catalytically active, so that the ATP molecule won’t add its phosphate to random water molecules rather than to the glucose. The enzyme cannot work without Mg-ATP
what happens if you add a xylose molecule to a solution with hexokinase instead of glucose?
the enzyme will undergo conformational change (induced fit) but the ATP will phosphorylate a water molecule instead of the sugar, is it lacks carbon 6.
What is the difference between homotrophic and heterotrophic allosteric enzymes? + example
homotrophic - the substrate and the modulator are the same molecule
heterotrophic - the modulator is a different molecule from the substrate.
example: ACTase
it is involved in the synthesis of pyrimidine NAs. CTP, its intermediate substrate is an example for a negative allosteric, homotrophic modulation as high concentrations of this molecule binds to the allosteric site and slows down the enzymatic activity ; ATP is not its substrate and activates the enzyme by binding to an allosteric site
