Lecture 4 Flashcards
protein function/ enzymes and kinetics
enzymes
complex biological molecules that behave as biological catalysts
functions of enzymes
-highly specialized proteins
-can accelerate chemical reactions
active site
one region on the enzyme directly responsible for interactions with the reacting molecules
enzyme classification:
oxidation-reduction reactions
oxidoreductases
enzyme classification:
transfer of functional groups
transferases
enzyme classification:
hydrolysis reactions
hydrolases
enzyme classification:
group elimination to form double bonds
lyases
enzyme classification:
isomerization
isomerases
enzyme classification:
bond formation coupled with ATP hydrolysis
ligases
ligand
molecules that reversibly binds to a macromolecules
what are the two things interaction specificity between ligand and enzyme are based on?
shape (geometric), charge (electronegativity)
the _ _____ of amino acids contribute to the shape and charge of both the ligand and the enzyme active sites
R groups
where does enzyme catalysis occur?
binding or active site
an enzyme and substrate can be modeled as a …
lock and key
what are the 2 models of ligand binding?
lock and key, induced fit model
which model is this?
the shape of a ligand or substrate must match exactly to the shape of the active site of an enzyme
lock and key model
which model is this?
a loosely bound ligand can interact with functional groups on the protein and cause the protein to alter its conformation so as to better fit and bind the ligand more tightly
induced fit model
how do enzymes accelerate reactions?
by stabilizing the transition state and reducing the free energy of the transition state
in the induced model, the enzyme can be seen as …
clay because of how it will mold to the substrate’s form
what type of catalysis is a proton donor?
acid catalysis
what type of catalysis is a proton acceptor?
base catalysis
covalent catalysis
a transient covalent bond forms between the enzyme and the substrate during formation of the transition state
simply binding substrates facilitates reactions in 2 ways:
- bring substrates into contact with each other and catalytic groups
2.enzymes bind substrates with a specific orientation that aligns the substrate and catalytic groups
what kind of catalysis involves metals tightly bound to the enzyme?
metal ion catalysis
what are common metal cofactors?
Fe2+, Fe3+, Cu2+, Mn2+, Co2+
what kind of reversible changes do metal ions do to mediate oxidation-reduction reactions?
-the metal’s oxidation state
-orient the substrate for reaction
-stabilize or shield negative charges
digestive enzymes that cleave peptide bonds have _____ catalytic mechanisms but _____ in substrate specificity
similar; differ
what type of curve results from when an enzyme becomes saturated as [S] increases
hyperbolic
Km measures…
substrate concentration
what is Km inversely related to?
the affinity of an enzyme for its substrate
the higher the affinity the lower the Km
what is the Michaelis-Menten equation?
V0= Vmax[S]
————
Km+[S]
What is the catalytic constant or Turnover number?
Kcat
what does Kcat describe?
-describes how quickly an enzyme can act
-how fast the ES complex proceeds to E + P
what does Kcat/Km represent?
catalytic efficiency
what does the catalyic efficiency describe?
-how avidly the enzyme binds its substrate
-how rapidly it converts it to product
what are two types of enzyme inhibition?
irreversible and reversible
what kind of inhibition results from binding to the enzyme so tightly that activity is blocked?
irreversible inhibition
what are the 3 types of reversible inhibition?
competitive, uncompetitive, mixed
small molecules that bind an enzyme at sits different than the substrate binding site and effects, positively or negatively, the activity of that enzyme
allosteric effectors
what are the two types of allosteric effectors?
allosteric activators
allosteric inhibitors
1 molecule acts as both the ligand and the allosteric modulator
homotropic enzyme
modulators are different than ligands with different binding sites
heterotrophic enzyme
what preferentially binds to a high affinity R state
ATP
what preferentially binds to a low affinity T state
CTP
