8 -

back to the stupid ahh review paper -

thermodynamic box - read it. -

law of thermodynamics - protein folding and unfolding - enzyme catlysis -

to understand why protein folding occurs - is it faborable for a reaction to conver its reactant to protects. it will tell us if its spontanous or not. when we talk about protien folding . we are going from a to B. this is a chemcial reaction. most chemcial reactiosn are reversible same thing w protein folding. this is protien dneaturing or unfolding.

To make a prediction of system reaction, we are interest in enthlpy , entropy, and gibss free energy G. the first and second laws of thermodynmiacs first law the is the to amount of energy is constanst and that enregy cant be either created or destroyed / it can go from one form to another. from this law we can keep track of energty. delta H deponds on the bonds that have been broken or formed.. protein folding is an exothermic reaction with negative delta H . sometimes can fold even when delta H is postive.

Second law the entropy of the universe always incrases -

in exoertheric reaciotn entropu increases and delta S increases.

fuck no just read the article.

Delta G = Delta H - T delta S

energy

Delta s = entropy change

Delta H =

in its native or folded conformation, the black vs the white spheres. the plan is the hydrophobic and white is the hydrophilic. most protien folding process are spontaneous. the main driving force for folding and stabilizing is the hydrophobic effect. THe tendency of the hydrophobic resides to cluster together and form the core of the protein molecule. this is entropically favorable so water moelcules doent make a solvation later. structure water moleuls are low in entropy, they are thermodynamically unfavorable. the water molcuels then will be free. when a protein folds there are a lot of h bonds, van der wall, and these release heat/enthalpy. so in most cases the the process is enthalpically and entropically faborable. abosulte rule is that whatver combination of delta h and delta S u have as long as the delta g is negative then that process is spontanous. u can have a isutation where u have an enthopucally unfaborable process but as it is coupled to an entropically fabroed process rothter it will make the whole process faborable. and other way around.

for biochem process - it is improssibel what the delta h or delta S will be. protein folding orunfolding. when u boil and egg u start with liquid and as u boil it will be solid. u are unfolding the proeitns inside the egg. as u increase the temp u bring th ehydrophobic core out into the opena nd agregate and form insoble material. …

start over i feel anxious -

thermodynamix box. so we use this to understand wether protein folding happens or not. we use thermodynamics to know if a reaction will occur or if its fabroable for a reaction to conver its reactants into products. enthalpy H, entropy S, and gibbs free energy G. the first and the seocnd law of theremodynamics will help us understand. protein folding is a chemical reaction from A to B. protein folding is reversible like most chem reactions.

The first law says that the total amount of energy is constant and cant be created or destroyed but it can be tranfered. we can keep track of energy6. So going form unfolded to folded protein, we can keep track of heat ernegy that is lsto from a reaction as products are made, the energy of the system will go down. the energy of the surrounds will go up as heat energy is tranfered over. Change in heat is delta H. Delta H depends on the bonds that have been broken and new ones that have been made.

when. a bond is formed heat energy is released, and whenever it is broke it is taken up. to caculate delta H one must consider the sum of the broken bond energyes and the sum of the formed bond energy. if more energy has been realsed from bond forming then take up from breaking bonds. then energy will be -Delta H or exothermic. If elss energy has been released from bond formation and more has been taking up from bond breaking the delta H will e postiive and endothermic.

for proteinf folding the itneractison invovled are usually weak non covalent bonds . hydrophobic effect, h bonds, electrostatic, van der wall, etc. when a protien folds more energy is realsed than taken up . this is because more bonds are made. in most cases. in most cases protein folding is an exothermic with a -delta H. sometiems proteins can fold even when delta H is postiive(endothermic).

second law. the entropy of the universe always increases. in an exothermic reaction, energy is realsed to the surrounding and increases teh trnopy of the universe as the energy has no been dispered.

When heat is released, that is putting in energy to molcules in the universe. and the more energy these mocluels have the more disorderd they will be . releasing energy by forming bonds increases teh entropy of the univese. entropy of hte universe can increase through an increase in entropy of the system. or by making bonds and releasing heat. the heat goes into the surroundings and entropy increases. so change in the entropy of the universe is Delta S = -delta G/T… good thing is that we dont have to think about the universe scale. know that Delta G= delta H -T delta S. . .

Delta G is change of gibs free energy, delta H is the change in enthalpy, and T is temp in kalvenins, and delta S is the change in the entropy of the system.

dont meausre the chnage of entropy in the universe, only the system.

if we look at the left. the black is the hydrophobic and the white is the philic. spontanous process. most protein folding processes are. the main driving force for stabilizing a protien structure and as well for folding aprotein is hydrophobic effect. so they are going to cluster and form the core. this way the hydrophobic R groups are shielded by water and this is entropically favorable. structure water moleciules are low in entropy so thermodynamically unfaborable. so when the hydrophobic parts go into the middle it is enthapically and entropically faborable. thsi is because when a protein folds there are a lot o fhydrogen bonds and ionic interactions that are forming and therefore release energy, that energy releases to the system and increases entropy. so protein folding is entropically and enthalpically faborable. the absolutre rule is that whatver combination of delta H and delta S u have, as long as that detla G is negative then that process is spontanous.

U can have a situation where it is enthapolically unfaborable proecess but as long as it coupled and the delta G is - it is good. it is impossible what the delta H or delta s will be so they have to be measured.

Potein unfolding -

breaking - takes up energy

so wehn u boil and egg tranforms into solid.u are unfolding the proteins inside the egg. so before u cook it is solubale, the hydrophobic amino acids in teh core the hdyrophilic ont he surface. they interact with water. as u increase temp u open the core and agregate together and form insolubal ematiera. ovalbumin is the main protein component of egg white. it is an interesting protein , it has a defined tertiary structure. the sole prupose of olvalbumin is to provide. amino acid building blocks. so that the merbyo can use it to biuld proteins. So obtalb ium is going to provide amino acids. when the ovalbuminis broken down into indivual amino acids by protease, the fetus uses that. the yolk is called lipoportien, low and high density . LDL and HDL. in blood work u see the LDL level, that is corealted with cholestrol in your blood. it doesnt directly measure choelstrol level, it measure LDL whose funciton is to store lipids. cholestrol is a type of lipid. lipids are highly. insoluble molcules. they cannot be directly dissolved in blood. so this protien is going to store and and tranport lipids, including cholestrol. when u heat up the egg u are going to destroy and denature or unfold this prteoin and end up with this insoluble matierla.

Professor at UC irvine - they unboiled an egg, they started with a cooked egg and went to reverse to create this liquid egg. how did they do that, they added dtergent to disaggregate the aggrtegated protein.

when proein unfolding happens it is usually bad news. A membrena anchored protein called amyloid beta precursor protein. so the proein has a funciton and works outside of the cell. in some cases that protein unfols. and cleaves off the membrane and then it dentaures. and forms the firbous structure. this is a misfolded protein because it is not the native conromation. these are amyloid fibers and causes parkinsons and alzhimers. just like unboiling the egg, if we unboild the amygloid fiber that would cure the disease because we would bring it back to the native configuration. becuase it is inside our brains we cannot apply chemical that disaggregate this. the better way to appraoch thsi is to prevent it happening in the first place.

Protein dynamics - proteins are not rigid. they ar eydnaomic. humans are dynamic and maniquncs are static and rigid. proteins are large organic molcuels and theyll have atomic and molecular virbrations thats present in all chemical entities.

these are small movments and they are rapid and as long as tempurate is above aboslute 0, the atoms and bonds theyll ahve mvometn. what we are mostly concerted about is the second type. teh slow type of movmetn, these are movment realtive movmetn of the differne trdomains. the degree of meometn becomes more signifiacant. 0,.5 to 10 anstrongs. and its slower movmetn. the movmetn is induced by binding ingrteactsion. ligant to protien or protein to substran or to another protien.

T state and the state and u kow dpeoending on which fornoamtion the affinity is dfferent. as soon as the first o2 bind to any of the four poly pepetide chains it will enduce conformation chang ein the nmeighboring polypeptide chain and increase affinity. so that will keep going till all are fully saturated. we call proteins like this allosteric proeitns. for protein. to have allostry it has to have multiple ligand binding sites, and hemoglbin does. this is a case of postivie allosetry because the conromation change, enhances the binding of the ligand. it increasews the affinity of the ligand.

negative allostery - proteins are dynamic - it changes shape - feeback inhibition mechansim depeonds on thsi tyep of dynamic movment. moleucle a converst to a to them b amd b to c and c to d and d to e. there are four enzymes invovled. a to b and b to c. glycolysis is an exmaple. glucose gets broken down several steps to pyruvate. first enzume is hexokinases that convers a to b and has abinding site for b even tho b is not a substrate for a and when that b mocluel binds to a. final produce e binds to e and influcnes shape of enzyme thats less catlaytic. it slows down when there is. alot of B. thsi si negative allsotry, the ocnformation change causes the eneyzme to be less active.

intrinsically disordered protein -

some protiens are so dynamic they dont have a defined teritary strucutre. the whole protien is dirosred and takes on billions of dif types of shapes. these protiens are intrisially diffuclt to study in the lab. some instirally dirsoerd proeitsns when tehy find to partner protein they fold into a shape that is defined. anotehr itnersting thins is where the entire prietn is disorderde and not common. alsomst all proteins have regions withing the pritne that is like thsi. 90% of proietn will have a well defined strucutre, it oculd hav a small regions that is tetriary structure and disordered. this is consequentl and involved in the funciton of the protien.

go back and watch video lol

YOU MAKE A BOND U REALSE ENERGY.