Chapter 6: Mechanisms of Enzymes Flashcards
what are the 4 chemical modes of enzymatic catalysis?
- polar amino acids in the active site
- acid-base catalysis
- covalent catalysis
- pH effects on enzymatic rates
what are the non-chemical modes of enzymatic catalysis?
- proximity effect
- weak binding of substrate to enzymes
- induced fit
- transition state stabilization
what are the mechanisms of action for serine proteases?
- zymogens
- catalytic triad
what is the mechanism of action for lysozyme?
substrate conformation and specificity
what is the mechanism of action for arginine kinase?
transition state analog as a tool to understand reactivity
- an electron rich ion or atom
- nucleus seeking
- has a negative charge or an unshared electron pair
nucleophile
- an electron poor ion or atom
- electron seeking
electrophile
what type of reactions are most biochemical reactions?
group transfer reactions
the nucleophile attacks while the leaving group leaves, creating an unstable transition state with five groups around the central atom
direct displacement reaction
- *can occur in two ways:
- the electrons of the breaking covalent bond stay with one atom (most common)
- the electrons split and one electron remains with each atom
cleavage reaction
reaction in which both electrons go in one direction
heterolytic cleavage
reaction in which both electrons go in opposite directions
homolytic cleavage
- the loss of electrons
- gain of C–O bonds
- loss of C–H bonds
oxidation
- the gain of electrons
- loss of C–O bonds
- gain of C–H bonds
reduction
causes oxidation and is reduced in the process
oxidizing agent
causes reduction and is oxidized in the process
reducing agent
what causes changes between the pKa values of the ionizable groups of amino acids residues compared to the same groups in a free amino acid?
the microenvironment of the active site
how many catalytic residues do enzymes have?
between 2-6
which residues account for almost 2/3 of all catalytic residues?
- *the charged residues (HDREK)
- histidine
- arginine
- lysine
- aspartate
- glutamate
how is reaction acceleration achieved?/
catalytic transfer of a proton
which residue is an ideal group for proton transfer at neutral pH?
histidine (side chain pka of 6-7)
what happens during covalent catalysis?
a substrate is bound covalently to the enzyme to form a reactive intermediate
what are the steps of Schiff base formation?
- attack of nucleophile on the carbonyl
- transfer of proton from weak acid to strong base
- protonation of -OH to establish leaving group
- leaving group departs, double bond forms
what can the effects of pH on enzyme activity tell us?
- effect of pH on the reaction rate of any enzyme can suggest which amino acid residues are in its active site
- sensitivity to pH reflects an alteration in the ionization state of one or more residues involved in catalysis
- a reaction that occurs with every collision between reactant molecules
- can only go as fast as two things bind to each other in solution
diffusion controlled reaction
- catalyzes the interconversion of dihydroxyacteone to glyceraldehyde 3-phosphate
- mechanism has 4 kinetically measurable steps
triose phosphate isomerase
- catalyzes the removal of the superoxide radical anion
- structure creates a positively charged pocket in the active site that enhances the formation of the ES complex
- happens in two steps during which a metal bound to the enzyme is reduced and then oxidized
superoxide dismutase
- enzymes are often called entropy traps since they collect highly mobile reactants from dilute solution and position them for reaction
- often involves the rotation of bonds
proximity effect
why can’t binding of substrate to enzyme be extremely tight?
- the enzyme decreases the activation energy, so if the substrate is bound tightly to the enzyme, it would take just as much energy to reach ES as it does without catalysis
- excessive ES stability is a thermodynamic pit
- if ES binding is too tight, products will not be formed
- the enzyme shifts from an inactive to active form
- not a catalytic mode, but rather a substrate specificity mode
induced fit
mimic the transition state
transition state analogs
- explains a large part of the rate acceleration of enzymes
- increased interaction of the enzyme with the substrate in the transition state
transition state stabilization
- cleave the peptide bond of proteins
- characterized by a serine residue in the active site
- regulated by zymogen activation
serine proteases
- inactive enzyme precursors that undergo hydrolysis to generate active enzyme
- also called proezymes
zymogens
enzymatic cleavage of specific peptide bonds
selective proteolysis
what are some examples of serine proteases?
- pepsin
- trypsin
- chymotrypsin
- elastase
trypsin, chymotrypsin, and elastase are all examples of ______ because they have ____________ in the active site
homologous proteins; the same 3 residues
what gives rise to structural differences/specificity in the enzyme pockets?
size and polarity
- the three amino acid residues that function together at the center of the active site of some enzymes
- generate a powerful nucleophile that eventually attacks a peptide bond
catalytic triad
catalyzes the hydrolysis of some polysaccharides, especially those found in bacterial cell walls
lysozyme
what is the most stable form of a six-membered ring?
chair conformation
- catalyzes the phosphorylation of arginine
- is an induced fit enzyme
arginine kinase
What are the residues in Chymotrypsin?
- tyrosine
- serine
What are the residues of trypsin?
- arginine
- aspartate
What are the residues of elastase?
- alanine
- valine
- threonine
- has a shallow pocket
