Enzymes Flashcards
enthalpy
the total energy in a system
free energy
the amount of energy that is AVAILABLE in a system to use
entropy
the tendency for ordered things to become random
how do enzymes serve as catalysts?
they speed up chemical reactions (increase the rate of reaction) by lowering the activation energy; ex: the enzyme glucokinase holds ATP and glucose together which stabilizes it so the enzyme can place the phosphate onto glucose
activation energy
the minimum amount of energy required to overcome the energy barrier and achieve transition state
part of the transition state complex which is where the energy required to raise the substrate energy to the transition state
the minimum amount of energy required to convert a normal stable molecule into a reactive molecule
transition state
a high energy state; the apex when the molecules have the highest potential energy; the most unstable point for the molecules
transition state complex
specifically while the substrate is held in its active site, since substrates need to be activated; after binding and before it’s released
inversely proportional to the rate of the reaction
substrate binding site
where the substrate binds (the whole “mouth” that also contains the active site)
lock and key
substrate binding site creates a 3-D shape that is complementary to the substrate (ensures a perfect match since enzymes are so specific)
induced fit
substrate binding to the enzyme induces a conformational change; this still relies on complementarity
helps to reposition the functional groups to promote the reaction
when is a reaction exergonic
if the product (P) has less free energy than the starting reagents (A and B), the G is (-), reaction will go forward spontaneously, and energy is released
when is a reaction endergonic
if the product P has more free energy than A and B, the G is (+), reaction will not occur spontaneously, and energy needs to be added for the reaction to occur
what does delta G predict?
it predicts the DIRECTION of a reaction; it does not affect the rate at which the reaction occurs!!!!!
what does the RATE of a reaction depend on?
the activation energy! the lower the activation energy, the faster the rate of reaction
why is ATP used so much?
it is highly exergonic because ripping off that third phosphate group releases a lot of energy, and we can couple this exergonic reaction with endergonic ones so the overall G for the coupled reaction remains negative
where do the functional groups in the active site come from?
they can be from the protein (enzyme) itself or from other bound cofactors (coenzymes)
what kind of bonds form between the substrate and the substrate binding site?
non covalent bonds with the amino acids from the enzyme or cofactors
why are additional bonds formed with the enzyme?
to stabilize the substrate in its transition state; adding bonds increases the stability of the substrate which directly relates to a lower activation energy
how do enzymes lower the activation energy?
by stabilization! (a.k.a. more chemical bonds with the substrate, which makes it more stable and ready to proceed in the reaction)
what kind of non covalent interactions occur between the enzyme amino acids and / or cofactors with the substrate?
hydrophobic, electrostatic, H-bonds, etc
what does “lowering the amount of energy” mean?
in the transition state complex, it means more molecules at any given time are more apt to reach the transition state so the reaction can occur
functional groups found in the active site
amino acid side chains, coenzymes, metal ions
covalent catalysis amino acids
serine, cysteine, lysine, histidine
polar amino acids in the side chains of functional groups
nucleophilic catalysis (an electron rich molecule that donates electrons)
coenzymes
non-protein organic molecules (vitamins)
what processes do coenzymes do to the substrate?
activation transfer or oxidation-reduction
activation transfer
form covalent bond with substrate it, then activate it for transfer
activation transfer (remember…this is how vitamins / coenzymes work)
form covalent bond with substrate it, then activate it for transfer
ex: biotin - uses N to attach to CO2 groups in carboxylases
coenzyme A - uses its sulfhydryl group (in the cysteine) to do nucleophilic attacks
thiamine pyrophosphate - contains carbon with dissociable proton
oxidation-reduction
functional groups accept or donate electrons
similar to activation transfer, but no covalent bond is formed
metal ions
electrophiles (they are positively charged, so they liked to accept electrons)
participate in substrate binding, stabilizing anions, and donating/accepting electrons in redox reactions
inhibitors
compounds that decrease the rate of an enzymatic reaction
types of inhibitors
covalent inhibitor, transition state analogs, non-covalent
covalent inhibitor
form covalent (very tight) bond with functional groups in the active site
transition state analogs
bind more tightly to the enzyme than substrates or products; the best kind of inhibitors and often used in medicine
why are transition state analogs so effective?
more bonds are being made (can be covalent or not) so it’s harder to rip apart
