exam 2 protein structure and function: enzymes Flashcards
how does enzyme catalysis work
by stabilizing the reaction’s transition state
what are some non-protein components that enzymes require for function
cofactors and prosthetic groups
what are the ways enzymes are highly regulated
by covalent modification and binding of non-substrate ligands
what type of proteins are enzymes
catalytic proteins - speeding up cellular reactions to allow life
do enzymes alter delta G
NO
what can enzymes link to each other
an energy producing reaction with an energy-requiring reaction to directly transfer the energy from one to the other
what can enzymes not do
cannot make a reaction occur spontaneously if it is thermodynamically unfavorable
cannot alter the concentrations of reactants and products in a reaction mixture that is at equilibrium
cannot extract more useful energy per mole of reactants - they can only extract it faster
what do enzymes do kinetically
they change the kinetics of a reaction, not the thermodynamics
what exactly is a chemical reaction
break some bonds to start a reaction, which requires an input of energy
what do you recover if a reaction is spontaneous
all activation energy + more energy
what do you recover if a reaction requires energy
you will get some back but not as much as you put in
what do enzymes lower and why
the amount of activation energy because the energy is a main barrier to initiating a reaction, which sets the speed of the reaction
as a catalyst, what is an enzyme also
only required in small amounts
must be left uncharged at the end of a reaction so that it can cycle back to bind more substrate
catalyzes equally the forward and reverse reactions
how does enzyme function begin
by binding the substrate through reversible, weak bonding to a stereo-specific active site, which forms an enzyme-substrate complex
where can ribosomes make peptide bonds form
between L amino acids
what can enzymes of metabolism only work with
D glucose
what happens after enzyme function has begun
the substrate is chemically converted to product, forming an enzyme product complex
what is the last step of enzyme function
the product is released and enzyme can bind another molecule of substrate
what is the reaction of enzymes all together
enzyme binds to substrate, making enzyme-substrate complex
then enzymes performs catalysis to convert substrate to product
then enzyme releases product to generate enzyme and product separately and repeats
what is the limiting rate for enzyme
the first step of binding of enzyme to substrate
what happens with more substrate
the more there is, the easier it is to bang into an enzyme and begin the reaction
what is the rate of a reaction limited by
the ability of the substrate to interact with the enzyme
what is V(max)
the rate when enzyme is saturated with substrate
what is V(max) dependent on
how many molecules of enzyme is in solution
what is turnover rate
the number of molecules of substrate that can be converted to product per second per molecule of enzyme
what is K(m)
the Michaelis Constant - approximately equal to the dissociation constant for the enzyme-substrate complex
what does a low K(m) mean
enzyme has a high affinity for its substrate
what is the equation for K(m)
1/2 V(max)
what does V(max) represent
how fast the enzyme can convert substrate to product
what is K(m) a measure of
how well the enzyme binds to the substrate
what happens if the K(m) is reduced
the binding interaction between the enzyme and substrate becomes stronger and the amount of substrate required to half-saturate the enzyme is lowered
what is the amount of substrate required to half-saturate the enzyme dependent on
the binding affinity of the substrate for the enzyme
what has to happen for a reaction to occur
substrate molecules have to pass through a series of intermediate states
what happens in intermediate states
3D geometry of reactants needs to be adjusted for optimal interaction
electrons among reacting atoms must begin to become redistributed
what happens with higher energy of a system
it’s less stable
what happens when you lower the energy of a transition state
you stabilize it, allowing a reaction to proceed more rapidly
what is the transition state for a reaction
an intermediate form between product and reactant with a specific structure
how can you reduce activation energy using a transition state
by providing an alternative pathway to reach a product
how do enzymes function
by stabilizing specific transition states of the substrate
what state has a higher energy than either reactants or products
as they react, substrates will go through a state with a higher energy level before the reaction occurs
what happens when enzymes stabilize transition states
they lower activation energy
what is the result of products binding to enzymes
they’re oriented in the correct way and can reach transition states
what do enzymes facilitate
redistribution of electrons - will bring in positively and negatively charged amino acids to help change electrons
what happens when enzymes put physical stress on molecules
they favor the formation of the transition state - transition state relives the stress
what is the full way enzymes mechanisms of stabilizing the transition state works
- enzymes binds to two substrate molecules and orients them precisely to encourage a reaction to occur between them
- binding of substrate to enzyme rearranges electrons in the substrate creating partial negative and positive charges that favor a reaction
- enzyme strains the bound substrate molecules, forcing it toward a transition state to favor a reaction
what are prosthetic groups
non-protein (non-organic) molecules which aid in some protein function
how can prosthetic groups be used
covalently or non-covalently bound by the protein
what are cofactors
enzyme prosthetic groups
what are coenzymes
organic molecules that act as cofactors
what are molecular tunnels
the structures of enzymes that perform multiple sub-reactions that must occur at distinct active sites to direct intermediate products from one active site to the next
what do molecular tunnels do
they prevent diffusion of intermediates and decomposition of unstable molecules and speed up reaction rates
what do molecule tunnels do for intermediates
they provide a direct route for intermediates to go from one catalytic site to the next one without interacting with other reactive components, thus speeding up the reaction rate over all
what do metabolic pathways require from reactions
reactions to occur in specific , highly regulated order
how are enzymes in the metabolic pathway organized
into higher-order multi-enzyme complexes
what occurs within a multi-enzyme complex
the product of the first enzyme is passed to the second enzymes, where it is the substrate, and so on
what does regulation of key enzymes involve
multiple inputs to be turned on and off when needed
what is feedback control with enzymes
a downstream product regulates an upstream enzyme in a given pathway
when is feedback control implemented
when product concentrations reach sufficient levels and there’s no more need for more product
what do irreversible inhibitors do
covalently bind to an amino acid residue, which usually lowers Vmax by inactivating and removing active enzyme molcules
how common are irreversible inhibitors
rare in nature
what do competitive reversible inhibitors do
reversibly bind to active site and compete with substate, though can be displaced by a very high [S]
how common are reversible inhibitors
common in nature
what do competitive reversible inhibitors do to Km
increase Km - lower affinity
Vmax is not affected, but Km is
what do non-competitive reversible inhibitors do
reversibly bind away from active site to cause change in enzyme structure that lowers catalytic efficiency
what do non-competitive reversible inhibitors do to Km
lowers Vmax, but does not affect Km or substrate binding
what does phosphorylation allow for
a rapid, reversible mode of regulation that can be coded by a short, linear amino acid sequence
what is an allosteric regulator
a regulatory molecule that binds at a site away from the catalytic site
what is conformational change in protein structure
the binding of one molecule to one region of an enzyme influences the binding of another molecule to a different region of the enzyme
what can an allosteric site be a part of
the same protein chain as the active site or may be in a regulatory subunit
what does binding result in
a change in the conformation of the catalytic site
what can conformational changes in the catalytic site do
activate (promote substrate binding/catalysis) or inhibit (prevent substrate binding/catalysis)
are allosteric inhibitors competitive or non-competitive
both - competitive affects substrate binding and non-competitive affects catalysis
what does allosteric regulation change
the shape of the enzyme to control its function and that can be either negative or positive
