Chapter 7 Flashcards
what are the 2 models to describe how enzymes and substrates fit together? what is the reality?
- lock and key
- induced fit
in reality is likely a mixture of both
what is the lock and key model? what does it rely heavily upon?
there is a perfect substrate for every enzyme; relies heavily on conformational selection
what is the induced fit model? what is it dependent upon?
says that enzyme and substrate change a little bith to fit together; depends upon noncovalten interactions but allows more freedom
what is the active site?
the area inside the enzyme where the REACTION HAPPENS
give an example of a reaction site
where a ligand binds to a protein
does hemoglobin have an active site?
NO! although O2 binds, no reaction occurs
what is a substrate?
the reactant the enzyme binds (AKA the ligand)
what is rate?
reactions per unit time; bigger is better
what is rate enhancement?
catalyzed rate divided by uncatalyzed rate; bigger is better
what is rate enhancement used for?
to compare enzymes
what are the 3 ways to change the rate of a reaction? how do these ways do this?
- temperature: via conformational selection and diffusion
- concentrationn: shifts equilibrium
- catalysts: lower activation energy
what are the 2 types of catalysts?
- enzymatic: biological catalysts
- nonenzymatic
what allows enzymes to bind with high affinity and selectivity?
the creation of an active site environment that is optimal for substrate binding
what does susbtrate binding do to the enzymes conformation? how (2)
substrate binding changes the enzyme’s conformation by
1. nonbonded interactions broken and formed
2. new conformation favors product formation
in what 2 ways is enyzme activity heavily regulated in cells?
- bioavailability
- signaling
what is a transition state?
a high energy intermediate state formed during conversion of substrate to product
how many molecules are in the transition state simultaneously?
only a few
is the transition state easy to isolae through conventional methods?
nope
describe how transition state relates to the path from reactant to product
reactions have to take a certain path from reactants to products; the transition state is at the height of the path
describe the energy and stability of the transition state
high energy, low stability
what is delta G double dagger?
the activation energ, or the difference between reactant ground state energy and transition state energy
what do catalysts do to the transition state?
stabilize transition state to lower associated energy and make transition state more favorable
can a catalyst affect overall delta G? why or why not?
no; because cannot affect equilibrium
give 4 things that help enzymes catalyze reactions
- amino acid side chains in active site
- cofactors
- coenzymes
- prosthetic groups
what are cofactors?
small molecules that aid in catalysis (Fe2+, Cu2+, Mg2+)
what are coenzymes?
cofcators that have organic components and include vitamin-derived species such as NAD+/NADH and FAD/FADH2
what are prosthetic groups?
coenzymes that are permanently attached to enzymes like heme and biotin
what are the 6 classes of enzymes?
- oxidoreductase
- transferase
- hydrolase
- lyase
- isomerase
- ligase
what do oxidoreductases do?
oxidation-reduction; transfer of H or O atoms
give 2 examples of oxidoreductases
oxidases, dehydrogenases
what do transferases do?
trasnfer of functional groups like methyls, acyls, aminos, phosphoryls
give 2 examples of transferases
kinases, transaminases
what do hydrolases do?
formation of two products by hydrolyzin a substrate
give two examples of hydrolases
peptidases, lipases
what do lyases do?
cleavage of C-C, C-O, C-N, and other bonds by means other than hydrolysis or oxidation
give two examples of lyases
decarboxylases, carboxylases
what do isomerases do?
intramolecular rearrangements, transfer of groups within molecules
give 2 examples of isomerases
mutases, isomerases
what do ligases do?
formation of C-C, C-O, C-S, or C-N bonds using ATP cleavage
give an example of a ligase
synthetases
list and describe 3 methods of catalysis
- stabilize transition state: lower activation energy (barrier height) via interactions with involved molecules
- provide an alternate path for product formation via formation o stable intermediates (like base camp to rest before continue climb)
- orient substrates for reaction to occur and reduce entropy
what is the active site microenvironment?
a small subenvironment away from other things for the reaction to occur
what 3 things can an enzyme to in the active site microenvironment?
- induce geometric fit via altering protein conformation
- use cahrged residues on amino acid side chains
- exlusion of solvent via a hydrophobic core
list the 3 enzyme mechanisms
- acid-base catalysis
- covalent catalysis
- metal ion catalysis
describe the acid base catalysis enzyme mechanism (4)
- protons transferred between protein and substrate
- requires an ionizable aino acid
- enzyme always regenerated at the end
- pH dependent mechanism
give an example and describe an amino acid involved in acid base catalysis enzyme mechanism
histidine, has a pKa of approximately 7, meaning it is readily found in either acid or base form at body pH; can act as proton donor or acceptor
what is a nucleophile?
a reactant that donates an electron pair to form a bond
what is an electrophile?
accepts an electron pair
describe covalent catalysis as an enzyme mechanism
involves formation of a transient covalent bond between enzyme and substrate to form an unstable intermediate
what 5 amino acids are typically involved in covalent catalysis enzyme mechanisms?
- serine
- tyrosine
- cysteine
- lysine
- histidine
describe metal ion catalysis enzyme mechanism
positively charge metal ions stabilize negatively charged intermediated
what are the 2 types of enzymes involved in metal ion catalysis? describe
- metal activated enzymes: loosely bound metal ions
- metalloenzymes: tightly bound metal ions
what 2 amino acids are typically involved in metal ion catalysis?
- cysteine
- histidine
describe enzyme binding affinity for the transition state
high
why is the transition state so unstable?
free energy is high
describe enzyme bindning affinity for products low and result of this
enzyme has low binding affinity for products, so products dissociate and enzyme regenerated
