Enzymes Flashcards
Enzymes Function
extract energy from glucose, burning hydrocarbon fuels, nitrogen fixation, digesting breakfast
Two ways to accelerate a reaction
adding heat, adding a catalyst
adding heat
increases the number of reactants with sufficient energy to overcome the activation energy barrier
adding a catalyst
decreases the activation energy barrier nut does not react
Enzymes as proteins
typically globular, structure is determined by the same forces
enzymes as catalysts
accelerate reaction rates, regenerated, specific
nomenclature
ending in -ase, usually describe process
what need you need for a reaction to proceed (think in energy terms)
free energy of products is less then the free energy of the reactants (products less then reactants) (exergonic and spontaneous)
reaction speed effector
determined by the size of the activation energy barrier
how do enzymes effect free energy
reduces the free energy of the TS (NOT the free-energy change of the reaction)
How do enzymes reduces the free energy of the transition state (4 ways)
- removing substrates from aqueous solution (desolvation)
- proximity and orientation effects
- taking part in the reaction mechanism
- stabilizing the TS
active sites
region of enzyme where catalysis occurs. determines affinity specificity, and rate, complementary to substrate
desolvation
exclusion of water
3 desolvation advantages
- removal of water shell accelerates reactions
- enhances polar interactions
- prevents side reactions
induced fit
some change shape when substrate binds
- close activation site
- bring catalytic reactive groups together
(like a waffle iron surrounding dough when it cooks)
proximity and orientation
active sites bind close to eachother and in the right geometry (needed for reactions to occur)
participation in reaction
enzymes (some) position functional groups near the substrates in the activation site (maybe function as:
acid/base catalysis
covalent catalysis
metion ion catalysis)
AA side chains in Acid/Base catalysis
Asp, Glu, His, Lys,
Cys, Tyr (not usually - more so nucleophilic)
AA side chains in Nucleophilic Catalysis (covalent catalysis)
Ser, Try, Cys, Lys, His
(in deprotonated form these can act as nucleophiles)
sub groups of cofactors
coenzymes and metal ions
sub groups of coenzymes
cosubstrates and prosthetic groups
sub groups of metal ions
prosethic group and loosely bound
Apoenzyme
polypeptide without the prosthetic group
holoenzyme
polypeptide with the prosthetic group to form the functional tertiary structure
transition state stabilization
- binding the TS aids in lowering the DG(double dagger)
- parts of the protein interact with the unstable transition state
- enzyme activity sites bind the TS better then the substrate
tighter enzyme binding with TS
greater catalytic activity
regulation of enzyme activity (effect intrinsic activity)
competitive inhibiton, allostery, reversible covalent modification, ionic signals
regulation of enzyme activity (do not effect the intrinsic activity)
regulation of gene expression, changes in subcellular localization
competitive inhibitors
- bind reversibly in the activation site
- resemble TS or substrate but do not react
- physically blocks activation site (fewer sites available, lowers reaction rate)
how can you get over the decrease in reaction rate of competitive inhibitors
increase substrate concentration
allosteric enzymes
mulit subunit
activity may be cooperative
stabilize T - state
inhibitor
stabilize R state
activator
covalent modification of AA residue
changes the tertiary structure of a polypeptide (effect affinity) (phosphorylation is a great example)
