lecture 3: enzymes Flashcards
what is metabolism?
thousands of chemical reactions linked through metabolic pathways
what are reactions catalyzed by?
enzymes
what are enzymes?
biological catalysts
what do catalysts do?
speed up reaction by lowering activation energy
do spontaneous reactions need enzymes? why is this good for our body?
yes they do. it is good in our body, because we dont want these reactions happening at random times in our body. they regulate the reactions in our body.
what is activation energy?
initial input of energy required to break bonds in reactants and allow them to form products. amount of energy required for reactants to reach the transition state
true or false? in a spontaneous reaction the potential energy of products is higher than reactants.
false! in a spontaneous reaction, the potential energy of the products is lower than the potential energy of the reactants.
how does lowering activation energy catalyze a reaction?
it increases the number of molecules that have enough energy to react.
what is the transition state?
an in-between state when old bonds are being broken so that new bonds can be formed.
physically, how do enzymes help with reactions?
they grab onto reactants and bring them together with the right orientation.
do enzymes change delta G?
NOOOOOO
how do enzymes regulate reactions?
-enzymes for certain reactions are not created if not needed
-use phosphate group to change their shape which changes function (phosphorylation)
what is another word for reactants?
substrate
what do we mean by enzymes are substrate specific?
only bind to specific substrates
What does the reaction with an enzyme form?
what is the active site?
pocket or groove on the protein’s surface where the substrate binds
through which bonds does the substrate bind to the enzyme’s active site?
non-covalent interactions such as H-bonds and ionic bonds
are ionic bonds considered weak or strong in bio?
weak, cause you dont need enzymes to break them
what does the induced fit of an enzyme mean?
binding of substrate causes a change in the shape of the enzyme to bring amino acid side chains in position to catalyze the reaction
how do enzymes lower activation energy?
1) holding substrates in the correct orientation and+ close together for reaction to occur
2) stressing bonds in substrates (s) so that they are easier to break
3) create a micro-environment in the active site (ex: PH, can favour reaction by making active site basic or basic)
4) enzyme can be directly involved in reaction (the amino acid chains in active site are acting like reactants)
factors that affect reaction rate?
1) substrate concentration
2) enzyme concentration
3) environmental conditions (temperature, PH)
4) cofactors or coenzymes
What does increasing substrate concentration do to reaction rates?
Reaction rates increase until point of saturation cause there are no more active sites that can be used. it increases the chance of the enzyme and substrate finding each other
What does increasing enzyme concentration do to the reaction rate?
Increases rate of reaction
how does temperature affect reaction rates?
1) increasing temperature increases the frequency of collisions between substrates and active sites, therefore increasing reaction rate.
2) after a certain heat, reaction rate goes dow, as excess temperature denatures the enzymes
What would an increasing enzyme graph look like if we didn’t have an excess amount of substrate?
What does the graph of temperature increase vs reaction rate look like?
how does PH affect reaction rates?
enzymes are usually most active within a specific pH range. extreme pHs affect the ionization of amino acid side chains and causes the enzyme to denature.
what does the pH vs rate of reaction graph look like?
what are cofactor and coenzymes?
non-protein molecules that can bind permanently or reversibly to the enzyme. they help the enzymes
what’s the difference between cofactors and coenzymes?
-cofactors: inorganic metal ions
-coenzymes: organic molecules (ex: vitamins)
-bind weakly to enzyme
ex: NAD+, FAD coenzyme A
what type of enzyme inhibition exists?
irreversible and reversible
what is irreversible inhibition? give examples
-not good
-inhibitor attaches by a covalent bond (nerve gas, penicillin, some poisons)
what is reversible inhibition? give an example
-inhibitor attaches by weak, non-covalent bonds
-important part of regulating metabolism in our body
-example:ATP inhibits PFK enzyme
why are irreversible inhibitors not found in our bodies?
because the reactions in our body happen for a reason. they need to be regulated. enzymes need to be turned on and turned off
other than reversible and irreversible, what else can enzyme inhibitors be?
competitive/non-competitive
what are competitive inhibitors?
-inhibitor binds to active site and competes with substrates for binding
-can be overcome by increasing substrate concentration (more likely that the substrate will bond to enzyme instead of inhibitor because more substrate. mimics the substrate, competing for the active site
what are non-competitive inhibitors?
-inhibitor binds somewhere else on the enzyme (not the active site)
-causes enzyme to change shape so that it can no longer bind to substrate
-increasing substrate concentration does not overcome inhibition (enzyme cant bind to substrate anyways, because the change of its shape)
in which reaction has the competitive/non-competitive inhibitor been added?
what are allosteric enzymes?
-involved in regulation of metabolic pathways
-comprised of more than one polypeptide (each with own active site)
-special type of enzyme
what do enzyme inhibitors do?
they turn enzymes off
what are allosteric enzyme regulators?
-molecules that bind weakly to allosteric site
-can be inhibitor or activator of the enzyme
what is the difference between allosteric activators and inhibitors?
-inhibitors: stabilize the active form of the enzyme
-inhibitors: stabilize the inactive form of the enzyme
inhibitors and activators often compete for the allosteric site
what is negative feedback inhibition/feedback inhibition?
negative feedback inhibition happens when something near the end of a metabolic pathway inhibits the enzyme of a reaction early on in the pathway.
why does negative feedback inhibition make sense for regulation?
products shut down their own production when there’s enough. it prevents the wasting of cell resources. dont even need any external help.
how does allosteric regulation apply to ATP?
-ATP acts as an allosteric inhibitor of PFK
-AMP acts as an allosteric activator of PFK
