Section 3 Flashcards
(48 cards)
enzyme
biological macromolecule that acts as a catalyst for biochemical reactions (usually a protein but not always)
What is a catalyst?
- a chemical that increases the rate of a reaction without being consumed
- speeds up reaction rate
- essential for biological systems
What is meant by enzymes are specific?
enzymes will only catalyze one specific set of reactions
- > specificity is based on a series of weak interactions with the substrate (especially in the active site)
- > substrate and enzyme active site must be partly complimentary
What is a proteolytic enzyme? (proteases)
-> cleave peptide bonds
Where is trypsin located and what does it do?
- intestine
- cleaves only the peptide bond on the carbonyl side of Lys and Arg
What does papain do?
cleaves any peptide bond
Where is thrombin located and what does it do?
- blood
- cleaves only Arg- Gly peptide bonds
What is an active site? What does it contain?
- region of enzyme that binds to the substrate
- contains residues directly participating in the reaction
What are some characteristics of an active site?
- cleft in the enzyme made of residues from all over primary amino acid sequence
- take up small volume of enzyme
- water excluded from active site as it interferes with weak interactions
What are the 2 ways an enzyme and substrate can bind to eachother?
- ) lock and key -> active site is a full complimentary fit to the substrate (rare because the substrate won’t leave)
- ) induced fit -> enzyme isn’t perfect to substrate, but will recognize it, assume a matching shape and bind to it
True or false? The enzyme will match the substrate’s structure perfectly
false. It matches the transition state
Cofactor + example
- enzyme requires it to function
- > an inorganic ion or small organic compound required for enzymatic activity
- eg.) Fe2+ of myoglobin
What is a prosthetic group?
A cofactor that is tightly bound to an enzyme
eg.) Heme group tightly bound to myoglobin
apoenzyme
enzyme without its cofactor
holoenzyme
enzyme with its cofactor
Will enzymes lower deltaG?
- no, they obey the laws of thermodynamics
- can’t make a reaction more spontaneous
do enzymes alter the final equilibrium of a reaction to make more products?
no
How do enzymes speed up the rate of a reaction?
- accelerate reactions by lowering activation energy (aka deltaG(double dagger)) by facilitating the formation of the transition state (X(double dagger))
What does X(double dagger)) represent?
- transition state
- highest enery (delta G)
- lowest concentration ( hardest thing to form)
- energy needed to form transition state -> deltaG(double dagger)
What is the formula to get deltaG(double dagger)?
deltaG(double dagger)(substrate -> products) = G(x double dagger) - G(substrate)
What types of things is the reaction rate governed by?
Activation energy controls the reaction rate
-only a small fraction of the substrate will have enough energy to form the product
Is the activation energy part of the overall deltaG?
no, it is returned when the transition state is converted to products
How does an enzyme work mechanistically?
- enzymes interact with the transition state such that the activation energy is lower
- reaction will speed up since greater fraction of substrate has the energy to reach the transition state
What is deltaG(b)
- binding energy
- derived from noncovalent interactions between enzyme and substrate
- energy to lower activation energy comes from binding and stabilizing the transition state
- difference between deltaG(catalyzed) and deltaG(uncatalyzed)
