Understanding Covalent Modification: The Power of Phosphorylation in Cellular Regulation

another method by which our cells can regulate and control the activity of enzymes and change the functionality of

proteins is known as covalent modification now generally speaking in covalent modification what happens is we

actually transfer a functional group a functional moiety from one molecule onto that target ends on that target protein

so we actually covalently attached a group onto that enzyme and that's precisely what changes the activity of

that enzyme or the functionality of that protein it can either turn on or in some cases turn off the activity of that

enzyme now there are many different types of covalent modifications that can take place inside ourselves so we can

modify the proteins in many different ways for instance we have processes like methylation of acetylene sulfonation and

many others that we're going to discuss in future lectures but the one that we're going to focus on is known as

phosphorylation and phosphorylation is a very common method of covalent modification it's a very common weapon a

method by which we actually control the activity of enzymes and change the functionality of proteins in fact it's

so common that nearly 30% of all the proteins and this includes enzymes in eukaryotic cells are actually for

sporulating now why is this method so common well as it turns out the sporulation

is a very effective very efficient and a very convenient process and we'll see why that is so in just a moment first

let's actually discuss the family of enzymes that are responsible for catalyzing controlling the rate of this

phosphorylation process so basically just like any biological process that takes place inside our bodies controlled

by enzymes this process of phosphorylation is also regulated by enzymes and the family of enzymes that

regulates this says this family is known as the protein kinase family in fact inside our body we

have over 500 homologous protein kinases which are responsible for regularly regulating the rates of this process so

basically these different protein kinases catalyze the phosphorylation of different substrate molecules different

proteins and different enzymes now what exactly does the process of as for elation actually entail well in this

process that functional group that we transfer from somali q on to that target enzyme a protein is the phosphorylate

now the question is what is the source of this forespore group what is that molecule that exists inside

our cells that we can actually detach the forespore group and attach it onto that protein well inside our body inside

our cells we have a very high abundance of high energy ATP molecules adenosine triphosphate which are produced by the

mitochondria of the cell and so because we have this abundancy of high energy ATP molecules that contain the PFAs for

allah cules that are the source of this forespore group so basically in this process the protein kinase catalyze the

transfer of a terminal force Forel group shown in red from that ATP molecule onto a hydroxyl containing group hydroxyl

containing sidechain found on that protein the target protein and because serine threonine and tyrosine all

contain hydroxyl groups on the side chains of these amino acids these are the three residues that are capable of

actually using the hydroxyl group to accept that transfer that force Forel group so in this process on the reactant

side we have an ATP molecule and the target enzyme or protein and then on the product side we

basically have the ADP molecule adenosine diphosphate we have a single H+ alia that comes from this oxygen here

and we have this modified residue that is part of that target enzyme the target protein so the red term of the spore

group has been transferred onto this oxygen now because inside ourselves we have this abundancy of ATP molecules

it's inside the cells that the proteins basically undergo this process and those proteins found outside the cells do not

actually undergo this process of as for elation because outside the cells ATP is not abundant so reversible

phosphorylation occurs inside the cells where the concentration of ATP is high and abundant but proteins found outside

the cells are not regulated in this method of phosphorylation because outside the cells we don't have an

abundant supply of ATP like we have inside the cells now the next topic that I'd like to discuss is why is

phosphorylation so common so why is this one of the more common methods of covalent modifications and as I

mentioned earlier it's because phosphorylation is very effective very efficient and very convenience the

question is why what makes its process so effective and so convenient well there are seven

things that have listed several reasons that I've listed on the board so let's quickly go through each one of these

reasons and let's begin with reason number one so in the process of phosphorylation what we actually do is

we transform a neutral residue to a residue modified residue that contains unmake ative charge and because of the

presence of the negative charge it can basically break the old interactions and form better interactions more stabilized

interactions and what that usually means is if this residue is found inside the

active side of the enzyme the presence of this modified forespore group what it basically does is it forms new

interactions with let's say the substrate molecule and that can enter and change the activity the rate in

which the enzyme actually catalyzes that particular reaction so number one is this process gives unnecessary and that

target substrate molecule and this leads us directly into reason number two as a result of this modified Negley

negatively charged group found on this residue because of this negative charge that essentially gives this modified

residue a high potential to form hydrogen bonds and so the negatively charged oxygen atoms of the

phosphorylated sidechain residue can form hydrogen bonds with other molecules for instance the target enzyme for the

target substrate molecule and so this can increase the specificity of the interaction between the active site of

the enzyme and that substrate molecule now number three is the protein kinases are actually able to easily adjust the

rates the kinetics of this reaction so depending on the physiological needs of the cells this reaction can take place

very very quickly in a matter of seconds or it can take place over a very long period of time and the rate at which it

actually did the rate at which it takes place and the rate at which the protein kinase is catalyzed the reactions

basically depends on the conditions found inside ourselves if we have to undergo this process the protein kinases

can basically allow the process to take place very quickly but if we don't want to carry out the process these protein

kinases can easily adjust the kinetics and slow down the speed at which this reaction actually takes

place now number four is actually what we spoke about previously it's the fact that inside ourselves we have these high

energy adenosine triphosphate molecules that can act as the source of that force for group so we see that phosphorylation

requires the transfer of this force for group from some molecule onto that residue of that enzyme and these

high-energy ATP molecules which are so abundant inside our cells can easily be used and very effectively be used to

actually transfer that force Forel molecule number five is and we'll discuss this in much more detail we have

the process of amplification that takes place whenever protein kinases are involved and that's because usually a

single protein kinase enzyme can actually catalyze many enzymes at once and so if each one of these enzymes

itself carries out some type of reaction the protein kinase by activating all these other enzymes basically amplifies

the result it amplifies all these different types of reactions and that greatly speeds up the number of

substrate molecules which are transformed to the product molecules and we'll discuss this in much more detail

in a future lecture so activated protein kinase is can be used to regulate many different enzymes and many different

reaction pathways and this can lead to an amplification effect in which we essentially amplify the amount of final

product that we produce now number six is whenever this reaction takes place because essentially what we're doing is

we're d phosphorylating this ATP molecule and the breakdown of the ATP molecule is a very exergonic reaction it

releases energy we see that this process is in fact thermodynamically stable and the ana

the products is lower than the energy of the reactants and in fact about half of the energy half of the free energy that

is released in the dephosphorylation of this ATP molecule is stored inside this protein for spoil group complex so

dephosphorylation of ATP is a very exergonic reaction and it releases a large amount of free energy and that's

precisely why this reaction itself is thermodynamically stable in fact because the products are so much more stable

than the reactants this reaction ultimately takes place in a single direction so it takes place this way and

this reverse reaction doesn't actually take place at least not at a very high rate and that leads us directly into

number seven so if the process of phosphorylation is to actually be a convenient process we have to actually

be able to reverse this process because if a sporulation let's say turns on a proteins activity we have to be able to

basically turn off the activity of that enzyme by for instance removing that force for group but as I mentioned just

a moment ago this process as shown here because this is so much more thermodynamically stable than the

reactants this process is essentially a one-way reaction so the question is how how can we actually reverse this process

well instead of using the protein kinase to actually reverse the reaction we use a different enzyme known as protein

phosphatases so inside our body it's these protein phosphatases which actually used to reverse the effects of

the protein kinases so protein kinases are responsible for phosphorylating that enzyme or the protein but the protein

phosphatase does you a completely different reaction mechanism a completely different

reaction pathway to actually reverse the effects of the protein kinase and remove this force for group and that can

basically either activate or deactivate the activity of that enzyme so if phosphorylation activates that enzyme

then dephosphorylation will deactivate the activity of that enzyme and protein kinase is basically phosphorylate while

protein phosphatases défis foreign lead and they use the following hydrolysis reaction so basically this is that

modified a residue of that enzyme and what protein phosphatases do is they use a water molecule to basically remove

this group and produce reform this enzyme that now contains this original residue that we basically had right over

there so these are the seven reasons for why phosphorylation is a very effective and a very convenient process so again

it produces a residue that is modified and contains a net negative charge and that's precisely what gives it a

potential to form many hydrogen bonds and that allows it to actually interact in a much more stabilizing fashion with

that substrate molecule number three is these protein kinases can easily adjust the rate at which the

reaction takes place and the rate really depends on the physiological conditions found inside the cell number four is we

have an abundancy of these high-energy ATP molecules that exist inside ourselves and so we can quickly and

effectively use them to actually transfer those phosphorylate EP molecule because the breakdown the

dephosphorylation of the ATP molecule is in fact an exergonic process is releases an ample amount of free energy that free

energy is used to basically drive this reaction and so the thermodynamic stability of the products

will shift the reaction all the way to the product side and so these products are much lower in energy than these

reactants now let's go back to number five whenever dealing with protein kinase is

typically a single protein kinase usually catalyzes many individual enzymes and so instead of catalyzing one

reaction catalyzes many reactions at once and so