Chapter 5-7 Flashcards
(51 cards)
Apoenzyme vs coenzymes
apoenzyme- enzyme without its cofactor
coenzyme- cofactors that are small organic molecules
What is a prosthetic group
tightly bound coenzymes
what is a holoenzyme
apoenzyme(enzyme w/o cofactor) + cofactor
How does a reaction occur spontaneously
only if delta g is negative 8
how do enzymes accelerate reactions
by stabilizing the transition state and lowering the activation energy
lock and key vs induced fit
lock and key is perfect fit between substrate and enzyme
induced fit the enzyme will undergo conformational change to fit substrate
What are the 3 assumptions made in deriving Michaelis Menten equation?
1) steady state; the breakdown of ES equals the rate of formation for ES
2) Free ligand: substrate concentration is much greater than enzyme concentration
3) irreversibility: only consider the initial velocity and assume that little or no back reaction occurs
Name the slope, intercept and x intercept, x axis and y axis
linear form of MM equation
What is K2 or Kcat
the turnover number of the enzyme, which is the number of substrate molecules into product per second
Sequential displacement (orders vs random) vs double (ping-pong) displacement
sequential ordered- substrate molecules bind to active site in specific order and products released in specific order
random-order of substrate binding and release does not matter
ping pong- 1st substrate bind and changes enzyme to produce ES intermediate complex this then converts substrate into first product. 2nd substrate binds into active site forming second intermediate complex the second substrate then transformed into a second product and released
How does temperature affect enzyme activity?
rates of enzyme catalyzed reactions increase as temperature increases, this trend continues until protein is denatured and catalytic activity ceases
Reversible vs irreversible inhibitors
reversible: CUN(t) Competitive, uncompetitive, noncompetitive
irreversible: suicide inhibitor (penicillin), affinity label inhibitors (TPCk)
group specific reagent inhibitors ( DIPF)
Compare the reversible inhibitors
Competitive- inhibitor is similar shape of substrate and competes for active site, inhibitor prevents binding of substrate
uncompetitive- binds to ES complex once substrate is bound to enzyme
Noncompetitive- inhibitor can bind to enzyme and ES complex with equal affinity
describe the Km and Vmax of each reversible inhibitor
How is Ki calculated
Types of Enzymes
Ligase
Isomerase
Lyase
Hydrolysis
Oxi/red
Transferase
Specify the type of inhibitor
competitive, uncompetitive, noncompetitive
Compare the irreversible inhibitors
Group specific Reagent(least specific)- Inhibitor reacts only with specific side chains of AAs
e.g iodoacetamide with cysteines
Affinity labeling- Inhibitor resembles substrate allowing them to fit inside active site of enzyme, once inside they modify the catalytic residue covalently, inhibiting enzyme function
Suicide Inhibitor (most specific)-bind to active site and initiate catalysis process as if natural substrate, however, at some point a reactive intermediate is formed that modifies the residue on the active site covalently, inhibiting enzyme irreversibly
transition state analog
Transition State analog- ( enzymes are optimized to bind to the transition state) these inhibitors are similar to the transition state and bind with higher affinity than regular substrate
Transition state molecules require high energy the enzymes are optimized to bind to them to stabilize them
What is penicillin and what does it do?
Penicillin mimics what substrate?
Draw the mechanism by which the transpeptidase reacts with penicillin
penicillin is suicide inhibitor of glycopeptide transpeptidase that prevents final step of bacterial wall formation, the cross linking of peptidoglycan strands
penicillin mimics D-Ala-D-Ala peptide
How to draw Iodoacetamide
group specific reagent
Draw TPCK
affinity label inhibitor
Catalytic strategies
Covalent Catalysis- active site contains a reactive group typically a strong nucleophile that can for covalent bonds with substrate
general acid base catalysis- proton donor or acceptor other than H2O that can activate nucleophiles for catalysis, stabilize charged groups, or increase LDF to stabilize transition state
catalysis by approximation- active site bings substrates close together
metal ion catalysis- metal ions used as cofactors by enzymes lose electrons easily and exist as cations that can stabilize intermediate structures, assist in forming strong nucleophiles. .and hold the substrate inside active site
Proteases:
Carbonic Anhydrases:
Restriction Enzymes
Mysoins
facilitate a difficult reaction
make a fast reaction faster
highly specific DNA cleavage
Coupling ATP hydrolysis to mechanical work
Draw DIPF. What is it for?
DIPF reacts with Ser195 to inactivate chymotrypsin
covalent catalysis
