Understanding Enzyme Mechanisms: The Role of Catalysis in Biological Reactions

thus far in our discussion on enzymes we kept our discussion very general we generalized the idea of what enzymes

actually do so we said that enzymes are these biological catalysts that speed up the rates of all different types of

reactions that take place inside our cells and we said that the way that they achieve this is by basically binding

that substrate molecule into a special environment we call the active side and inside the active side there's a

confirmational change that takes place and that stabilizes not only the substrate molecule but it also

stabilizes the transition state in that particular reaction and by stabilizing the transition state that releases a

certain amount of binding energy into the environment and that decreases the energy of that transition state it

lowers the energy of the transition state and that's what lowers the activation energy and by lowering the

activation energy we speed up the rate of that particular reaction so this is the general mechanism by which enzymes

actually function now we know the general idea of what Mech of what enzymes actually do

but what exactly happens inside the active sides of these enzymes so we have all these different types of enzymes

found inside our body they all carry out the same general idea they basically decrease the activation energy of the

reaction but how exactly is that achieved and what are some mechanisms what are some methods that enzymes use

to achieve this decrease in activation energy so four of these methods are listed in the board and we have many

more but these are the four most important ones and enzymes can use one of these methods or they can use a

variety of these different methods so let's begin by focusing on the first one we call coent catalysis so in some

enzymes such as for example Tron kimot Trion other digestive enzymes as well as the enzyme we're going to focus in this

lecture glycopeptide transpeptidase in some enzymes inside the active side we have catalytic residues these amino

acids part of the active side of the enzyme that are responsible for actually forming a temporary calent Bond now why

would we want to form a calent bond well one reason is to basically keep that substrate molecule in place inside the

active s so many enzymes contain active sites with catalytic residues that can form temporary calent bonds with the

substrate molecule and that can be used to basically keep that molecule in place for the time being until that reaction

actually takes place now at the end of the reaction because we always have to regenerate our enzyme the enzyme is

never used or depleted or changed in any reaction we have to break that Bond and that's exactly why we call this Bond a

temporary or a transient calent Bond now in our discussion on irreversible suicide Inhibitors we discussed

penicillin and we said that penicillin is an antibiotic that affects a specific bacterial enzyme found in bacterial

cells known as glycopeptide transpeptidase and when we discussed this molecule we said that inside the

active site of glycopeptide transpeptidase is this catalytic residue namely this cerine molecule and the cine

amino acid basically plays the catalytic role of actually forming a coent a temporary coent Bond between the oxygen

and this carbon so in this reaction in the first step this molecule actually forms a bond between the oxygen and this

carbon kicking off this terminal amino acid to form the following temporary transient AEL intermediate molecule now

at the end of the reaction of course this bond is actually broken but we formed the bond to basically keep this

group attached into the active side so that another substrate can move in and grab this group so the bacterial enzyme

glycopeptide transpeptidase utilizes coent canalysis and as we'll see in just a moment another enzyme that we can

basically uh we can basically uh label as using coent canalysis is katriin and this is an important digestive enzyme

that exists inside our digestive system and we'll disc discuss much in much more detail what kimot Trion actually does

inside the active side now let's move on to Method number two catalysis by proximity and catalysis by orientation

so if we recall the Collision Theory from basic chemistry based on the Collision theory for a reaction to

actually take place what must happen well first of all those two substrate molecules that are about to react

must actually Collide so they must Collide they must collide with enough energy and they must collide with the

proper orientation so only when the Collision actually takes place with the proper orientation and with the right

amount of energy do we actually form the product molecule now what the active side does

what enzymes actually do is they bring the substrate molecules into this very small region of space that creates a

micro environment for that reaction so inside the active side we create a micro environment that not only brings those

substrate molecules in close proximity but it also orients those substrate molecules in the proper orientation so

that reaction can actually take place for instance if we go back to coent canalysis another reason why coent

canalysis might might take place is because once we attach this group onto the active side that orients that group

in just the proper orientation for the next step in the reaction to actually take

place so many biological reactions involve two or more substrate molecules and this implies that for a reaction to

actually take place they must be close enough and must also have the proper orientation and what active sides of

enzymes provide is they provide that small region of space that micro environment that brings the substrate

close enough for the collisions to actually take place at a high enough frequency in addition the active sites

may also Orient the molecules in the proper orientation for that bond to actually form and for us to form those

products now method number three is called acidbase catalysis and in acidbase catalysis we basically have a

transfer of an H ion now there are many residues that are involved or there are specific residues found in active sites

that might be involved in the transfer of an H ion and one specific residue is the histadine amino acid so the

histadine molecule has a pH that is relatively close to the normal physiological pH and many en enzymes

inside our body as we'll see in the next several lectures utilize tadine to actually transfer H ion so active sides

may contain residues such as histadine that can participate in transferring hydrogen ions now why would we want to

transfer an H ion well in some cases if we transfer an H ion from one molecule to another molecule we basically create

a strong nucleophile and that's strong nucleophile might be needed in that particular biological reaction so by

transferring the hydrogen ion the active site May activate a nucleophile that is required in that catalysis

process Now by transferring an H ion we can also actually stabilize different types of groups that might be found

inside the active side that contain charges and the transfer H ions can also be used to increase the electrostatic

interactions that take place within that active site and that can enter and stabilize things like the transition

state inside that chemical reaction now one particular example of an enzyme that uses acid-based catalysis is kyrion

inside kyrion inside the active side we have a searing residue that acts as a nucleophile but to create a strong

nucleophile what must happen is the H the H atom the H ion from the oxygen of cine must be taken away and so what

happens is a nearby histadine in the active side participates in actually taking away that H atom and so we see

that the H atom is transferred onto this nitrogen and the positive charge is now essentially delocalized among these

different atoms in the histadine side chain but this one now contains a full negative charge and now this became a

very strong nucleophile and this can participate in forming a coent a temporary coent Bond so as we'll see in

the next several lectures kimat tripson which this basically describes uses not only acid-based catalysis but it also

uses Cove valent catalysis in decreasing the activation energy of that particular chemical reaction that is what it

participates in is breaking different types of peptide bonds breaking different types of proteins that we

ingest into our body and finally the final mechanism by which our enzymes can decrease the activation energy and

therefore increase the rates of reactions is called metal ion catalysis so what's so special about Metal ions or

metal atoms well many enzymes and many proteins inside our body for example when we spoke about myoglobin and

hemoglobin we saw that these proteins use metal atoms and in fact enzymes utilize metal atoms as

co-actors now what's so special about these metal metal atoms well metal atoms have the ability to lose electrons very

easily and by losing electrons they gain a positive charge so because they are deficient electrons they have a positive

charge and this positive charge can be used to interact with different types of molecules found inside the active side

and so the positive charges on metal ions as we'll see in more detail in the future lectures they can be used to

basically stabilize the transy transition States as well as the intermediate molecules that are formed

within that active side they can also be used to assist in actually forming a strong nucleophile for instance one will

discuss uh Carbonic and hydrates we'll see that in Carbonic and hydrates inside the active side we have a zinc metal

atom that is used to actually form a strong nucleophile the hydroxide nucleophile and finally this metal atom

can actually be used to hold that substrate molecule in place so in the same way that we can use Cove valent

canalysis to basically Orient that substrate and hold in place we can also use the positive charge of these metal

atoms to actually bring the substrate molecules in the proper orientation and hold them in place inside the active

side so that reaction can actually take place at a reasonably High rate so we see that our enzymes inside our body use

a variety of different types of methods and mechanisms to basically carry out the general reaction of decreasing the

AC acation energy of that biological process so we can have coent catalysis we can have catalysis by proximity we

can have acid base catalysis and we can also have metal ion catalysis and we'll discuss many examples of enzymes that

utilize these different methods in the next several lectures