Lecture 5 - trying to be positive but i miss my man

oxygen is a very importnat molecule for us. we use oxygen for metabolism . we use oxygen to conver thte food moclules into atp. atp is needed for biological work. o2 is critical we need it constantlyand in large amount . o2 is a hydrophobic insoluable molecule. its small and insoluable in water. we need large amount of it inside our body. diffusion through tissues is ineffective over large distances. transitionmetals are good at binding oxygen , metals like iron and copper. when u attach o2 to ionr and copper , these are charged ions, so they ar ehighly soluable, u solve the solubility problem. free ionr or free copper while it binds o2 well it tends to create hydroxyl radicals. these are highly reactive speicies that are very dangerous to have inside the cell especially for dna. using naked iron and naked copper is not a solution. instead of using free transition metals we use proteins that are evolved bind the metals.

your blood is red because we use iron to bind o2. this isnt the case for all animal animals like crabs have blue blood. octupus also have blue blood and shrimp. immune cells of horshe carbs are sensitive to viruses and bacteria, as soon as thsoe pathogens encounter the cells they are going to immediately coagulate. companies use horshe crab blood to test that their product is not contaminated with pathogen.

instead ofheomglobin these animals have hemocynainin at the active site it has two coppoer ions and in between the two coppers is werhe the o2 binds.

for us we use hemoglobin and myoglobin. these proteins have a molecule called protoprophryin . so protoporhrin plus ion atoms is goin to make a heme . so once u bind the iorn to protophrouin it is no lonver a problems where ion creates the hydroxyl.

the free heme is still not used to bind and cary o2 because it convers ionr form plus two state to the plus thre state and the plus threei snot good at binding oyxgene. so that is why we need hemoglobin protine , one u bind the heme in the protein then u solve all these problems.

some inrogainic chemcistry -

ionr atomcs form six coordination bonds and give them a coord numbe r of 6 and otahedral geometry. so at the gener is the ionr atom and there are six different entities bound to it.

hemoglobin ionr is bound to protpphrin . the ion is bound to protoporphryin and if u look at hemojglobin that ionri s boudn to four nitrogen atoms. thats prt of the protporphryin orgnai micluel so four out of the sox coordination moclules are occupies and this leave two left. one site is bound by the r group form the hemoglobin proitne it is going to be bound to the histidine group and the sixth psotion is going to be wehre the o2 binds. so the heme group binds o2 very well because the iron binds o2 very well.

there is a moleucl that heme binds more titlgy than o2 it is CO. it binds it 20,000 times more tighlty than it binds molcuelar o2. that is why we have co poisoning. hemoglobin iin ur proitne andmyobling if theres both o2 and co it is going to choose co. so carbon monoxidebinds a lot more tightl to heme .

if u look at o2 binds ot the heme it bind at and angle that is 120 degrees which is the opitmal binding geomtry for o2. which were not going to go into.

CO binds at 180 degree angle. o2 binds at an angle and Co binds orthogonally.

so when u ee a protein structure drawn with these cylinders the cylinders represent alpha helicies. so alpha helicies cna be drawn as a spiral that youve seen before in a cartoon representaiton or as these cylinders. myoglobin is a member of a larger fmaily of protiens called the globin protien family .

so the globin protien fmaily, if u look at their structure they allr esemblye the myoglobin strcture so they are evolutionarily conserved structure wise. they are made up of eight alpha helices , an most of these function in o2 tranport and o2 storage.

the different globin protien sin humans there are four major types myoglobin, is a monomeric protien it is a singel polypeptide chain therefore has no quaternary strcture. so theres one n temrinsu and one c tmerinus because theres only one polyepeptide chain. hemoglobin is a tetrameric proteins and repsonsibel for o2 trnaport in our blood. hemoglobin has a 4’ strcutre. it has multiple polypeptide chains that make up that single proitne. myoglobin does not have a 4’ strcuture. it only has a 3’ structure.

neuroglobin is going to be amonomeric and expressedi in neurons in the brain. our brain is senstivie to o2 levels so instead of relying in myo and hemoglobin for o2 storage . it makes sure that when theres not enoguh o2 being deliverd by hemoglobin u have sort of an emergency reservoir. cytoglobing is a monomeric globin protein. this is unique that it doenst bind or carry o2 but it binds and senses NO which is importnat singlingmolcule for muscle relaxation. .

myoglobin has 153 residues + 1 molecule of heme

helices are labeld, so alpha helices a,b,c,etc. the indivaul helcies ar elinked to one another through the fleixble loops. so they are named helix ab, bc, cd. thisis what max perutz did to name the loops.

it has an amino acid labeled his93 = that paritcular histiidne residue is 93rd amino acid in the priamry structure of myoglobin. ,

1553 amino acids in total. that particular histinde is the 93rd one in that structure.

o2 bound to myoglobin molcuel it will bind at an angle. there is histinde reisde withing myoglobin that i spostive so it can form a H bond with the o2 atom of hte second oxygen atom and that moleucalr oxygen. it forms a h bond. why is it imjportnt? because the h bond forming o2 binds to the heme more tightly than it would when there was no protein scaffold. so this contirbutes a lot to makeing the o2 bidning tighter . this effect applices to o2 and not CO. CO doesnt bind at an angle, it is vericle. so that hisitinde called distal histidine is not at the correct postion to form a H bond of CO. so in the context of myoglobin o2 affinity increase wher ehte affintity of CO is the same wehtehre u have just a naked heem versus that heme being part of myoglobin. the total effect of this is that now ur myoglobin moclules, same with hemoglobin bonds CO only 40 fodl more tihgtly nthan molcular o2. its still a substantial different. Myoglbin still perfers CO over o2 but only by 40 fold instead of 20k fold. withouth this effect we would have more popele dying each year from CO poisoning.

what is happening at the moelcular level,

myoglobin is undergoing a binding reaction or hemoglobin where it bidns o2 and makes. amyoglobin o2 complex and that binding reaction can use P plue L = reverse PL. P is the protien and L is the ligan so o2.

association constatn Ka.

equilibrium contnat. the conentiroal of all the prod over the concentiroan of all the reactats.

its a measure of the affinity of ligan L for the proiten. the higher the KA the higher affinity/tighter binding. the lower the value is the lower affinity or weak binding.

there is two ways of epression the equil of a reaction… u can use the rate of the forward reaction ove the rate of the revese reaction. Small ka / over small kd.

so the equilb constnat is the rate constate fo the forward over the reverse.

caseL the concentriaotn of o2 is much lareger than the convetration of myoglobin. so under that ocndision bindin o fhte ligan by the prodin does not aprreciably L. so if us tart with a large Ligan molecules if some of that binds to myoglobin, the number of free mcoluesl is constant.

this is

equaition 5-3 is multipling both sides by concentriaon of L this tells u that under the condition that L is larger than B. L is constant. ka by deifntion is a consonat. that means that the reation of pL over P is constant.

When L is not large then the ration is not constatn and isntead will dpeodn on the conentrioan of the free ligand in that system. youll see why this beocme simjpornta lter.

vitals -

o2 saturation levle. shows u what percetn of hemogli has o2 bound, u dont want it to drop drasitically. this is called oximeter. infrared singal - it calculates the o2 saturation level. this is meausring the total number of bidning site occupie by ligan over the otal binding sites that are avaible in the body. ( u add the binding sites that are occupied and the sites that are free.) that is percetn stuariaton. this is equaiton 5-4

what is reciprotal of the binding reaction it is the dissociation reaciton. the same equilibrium but looking at the dissociation. so u start with PL and become P + L. .. in practce we use KD which is the disscoation constatnt to express the affinity of protien for ligan. scientst ar emore concerned with Kd rather than ka. for most drugs mocluels once it binds to the target how well it stays bound rathe than how it strongly binds to a free target. that is why they are jmore concerned with kd. how well it stays bound vs affinity. the lowe rhte KD the higher teh affinity.

this descirbes a hyperbola. if u plt this y on the axis whichi s the percent saturation and L on the x acis. there is going to be a curve hyperoblic shape. on the y this percetn stauration when it reaches a value of one that means all the ligan binding sitres are occupied by the ligan. 0 means non of the binding sitres are occupied by ligand.

so the conentriaotn of the lgiand at which on half o the aviable ligan binding sitres are occupied corresponds to kd. or 1/ka…

so when the lgian concentriaotn is kd youll see that the side simpilies to 1/2. or .5.

so by defintion kd is the concentriaton of the lgain in which 50% occurapncy of all you proteins.

real life eamples of kd values. so at the top theres a preoitn called avidin which binds a ligand called biotin. this is famous for the highest affinity partners. so i fu look at hte kD of those two its 10 to the minus 15. its an emtremly smal lnumber and remembre for kd the smaller the value the tigher the binding . small kd is high affinity.

insuling receptor. so a protine that is on the surface of cells, they bind insuling, the dosscioate constatne is ten to the minus ten which is still small whcih is tigh binding reaciotn but comapred to avidina nd biotin is weaker by ten to the five fold weaker.

cal moduline binds to calium ions and the Kd is 3 times ot hte minus six and its a much alrger value than the other that wehave discussed so far. this realively weakly binding proitne and ligan pari.

percent staturaiton is y= o2/o2+kd

kd is o2 when ½ of the avaibel ligan binding sitres are occupies .

this is p50.

cncontriaton of o2 iw didifuclt o work with in the lab because there is no direct meausre of a gas. we cant measure o2 concentiroan direlty. we use partial pressue of o2. this is the pressure of the o2 mocluel in the gas pahsed that conatctint the oslution that youre trying to analyze. theres a direct correlation betwen the pressue of the gas moleucle above the liquid pahse and how much gets dissovled in that liquid pahse so/ we can sub the o2 conentriaonof ur blood with the o2 pressure of the atomospher that is conatctin the blood. that is the partiul pressure of o2 in ur lungs. if u plot the equiatn u cat a hyperbolic cuve. the hgiher the partal pressure of o2 the mro staurated your myoglobin or hemoglbin will be with the o2 . so when the o2 drop u put on a o2 mask on that patien that direclty increase the partial pressure of o2 thereby artifually increasing the satuaration level.

so in airplaes that o2 maskdrops to make sure ur body maintin a high level of o2 saturaiton . which is importnat