Biochemistry Final Flashcards
9-17
where is glycine a good buffer?
-glycine has two spots where it can go from positive to negative cahrge and experience net charge of zero
- one region where it has a net charge of zero is between about ph 4 adn ph 8, that is where zwitterionic form will be
2 and 9 when moelcules become protonated and deprotonate dthey can act as a buffer they are the moelcules absorbing a hydrogen ion and as a result the ocnentration of hydronium in solution does not change and the pH remains relatively well buffered* around the pKa where these molecules can accept or donate a hydrogen ion to become protonated or deprotonated this is where these molecules will function as a buffer, because glycine has 2 pkas for aminoum and carboxylate 2 ph distint regionds where it will function as a buffer
9-17 Do you think it is energenically favorable or unfavorable to form amide bonds?
so from the 3 aa do you think its exogonic or endergonic? for 3 aa to brign together to form polymer chain energentically unfavorable and will not happen sponateously in fact we find there is a favorable release of free energy when we hydroyzle the amide bond why we develop these tyrosine crystals as we age cheese overtime and individual protein chains begin to degrade into 3 amino acids..?
- Energetically nto favorable to form these amide bodns, take home message: polypeptides are thermodynamically unstable but we have been talking about the fact that thermodynamics is not kinetics, so even though there is a tendency towards hydrolysis of peptide chain but the half life of amide bodn is at ph 7 is 7 yeasr, so kinetically these things are stable and when our cells synthesis protein it is reasonably stable overtime even if present over aqueous conditions when can presumably be hydrolyzed, we will see this over and over again when a molecule or pathway is under kinetic control, that the cell is able to create enzymes that can conditionally speed up these reactions so that the cell is actually able to control the rate at which these reactions can happen
- protein may be kinetically stable, cell may want to degrade particular protein product, cells have mechanism to target proteins for destruction and degrade them at relatively fast rates*
why trans amide bond?
9-17
The answer is that there are steric clashes =
There are steric clashes btw sidechain groups when we have the amide group in the cis confirmation, where we create that zero degrees for the amide bond we will see tht the side chain groups particularly at the c beta position, and create steric clash, that clash is alievaiated if we rotate bond in opposite orientation creating trans amide bond, now we position sidechain groups on opposite side of polypeptide chain, like aleiviating that steric clash just like elevating eclipsing interaction btw methyl and protane??
9-17 why proline 10% cis?
- Polypeptides have a strong preference for this trans arrangement, except for one amino acid in which this preference is not so strong
- Its b/c it’s a cyclic side chain wraps around and forms a covalent bond back to the backbone nitogen
- side chain not only takes off from calpha position it also is attached onto the backbone nitrogen as well, cis-amide in proline is more prevalent than in amides from primary amines
- In the cis orientation this shows the steric clash we tend expect btw two substituents at backbone C alpha positions, but here have to understand that even in the trans confirmation of amide group we still have a steric clash this time its with the portion of proline side chain that is covalently attached to the backbone nitrogen
- So because we have some extent of steric clash in both cis and trans, for proline groups the energeic difference for porlene is less than other 18 amino acids and as a result the energy difference is much less, the prediction would be then if take a look at protein structures, you would expect to see proline residues would have a significant observable population in which the dihedral angle corresponds to cis amide bodn where omega dihedral angle would be zero, that’s exactly what we see, the majority of those amide bonds are trans and omega angle is 180, and we have a significant population of cis amide bonds and protein structures and vast majority of those are formed by proline amino acids* so now we understood omega bond
9-17
phi and psi
- Need to think about types of steric clashes that may come about as we rotate around this phi and psi dihedral angle, if remember amide bond constitutes planes can think of polypeptide chains as a set of these planes connected through hinge elements, we will rotate these planes relative to one another as we rotate these phi and psi dihedral angles
- Rotations in psi and phi determine overall confirmation of backbone, these amide groups can see on plates/planes relatively rigid and we can then rotate these plates relative to one another by rotating around the phi and psi angles
- Again we should be able to identify which bonds are being rotated around as we rotate around phi and psi, rotation of psi is around c-c bond and rotation around phi bond is around the nitrogen c apha position
9-17 Linus Pauiling exam 1 info
- he began to think about how can we put together polypeptide chain that would minimize steric clashes and maximize number of H bonds that can ne formed by the polypeptide amide oxygen NH groups and repeating amide groups in a polypeptide, he was in England caught a cold because of miserable weather lying in bed sickwith his cold began to sketch a polypeptide chain, and tried to fold that piece of paper in such a way to point carbonyl oxygen toward the amide NH group to form an amide bond and tried to see whether he could create a repeating pattern of h bonds in that origami folded piece of paper depening this poly peptide chain, allowed him to predict helical structure of protein
- also i and i+4 positioning!
a. But which dihedral angles are favored in a protein chain? Minimize steric clahses, maximize H bonds!
9-17 Ram plot what he was trying t do
what he did was he began to consider at what angles for psi and phi could he alleviate the steric clashes in a polypeptide chain, and what he saw was that there were actually very specific regions that correspond to low energy structures
9-17
Ram 2
- plotd them out realized oculd make a 2d plot for each position in polypeptide chain that sepcizlies in A psi and A phi dihdeal angles and some of these pairs will alleviate the clashes**
- Plot dark green low energy states, light green more accessible and white denotes high energy confirmations
- Dark green are favorable regions and other regions give rise to clahses and these are disfavored or high energy states, and these plots witht eh dark green show low energy states, light green energetically accessible states and white is the disfavored states, so particular regions in this plot named after him associated with repeating arrangements of the polypeptide chain*
- thser egions, like with blue spots, are part of repeating units that are part of secondary structure elements*
- w e can assocaite them with different secondary strcuture elements, this combination for ex of phi and psi is associate withteh alpha helix* etc.
9-17 alpha helix
-Repeating pair of phi and psi dihedral angles do it at every position create a helix, see one full turn of polypeptide chain every 3.6 residues within the protein
-We also see that as we create this particular arranagment we position backbone atoms to form a repeating network of h bonds btw amide carbonyl oxygens and amide h groups oriented in exact arrangement that can give rise to this network of hydrogen bonds
What defines an alpha helix=phi and psi dihedral angles about negative 60-50 in Rha’s plot allowed regions, we have all amide H and carboxy groups hydrogen bodned to one another except for those at the end of the helix for which there is no particular partner, as a result the termini of alpha helixes have exposed amide /NH and exposed carbonyl oxygens and these tend to be POLAR and located on the surface of proteins8 tned ot be locate don the surfaces of proteins
e. so our characteristic pattern of hydrogen bonds if we take the carbonyl oxygen of one amide group and create a hydrogen bond in this arrangement specified by the alpha helix we will make the h bond with the nh group of the residue at the 4th position down the chain, take that carbonyl walk 1,2,3,4 down chain form h bond to that Nh group creates regular pattern, do that at each and every position as go down the peptide chain, we make that network repeating hydrogen bonds and that is what defines an alpha helix, see this all the time I to i+4
9-17 left handed helix
- we see this rarely becuase it is such high energy state
9-17
i to i+3/ or i+4
- i is at close proximity of side chains as positions i+3 to i+4 amide groups in backboen but also possibility to create interactions between chemical groups within th die chains, which amino acids at position i are going to interact with i+3 and i+4 becuase they are on teh same side of that cylinder formed by the helix SOO side chain groups can then pariticipate in electrostatic interactions, pie stacking and van der waals intearctions*
Side chains at i position can interact with side chains at i+3/i+4 positions using salt-bridges, hydrogen bonding, pi-stacking or van der Waals interactions
9-17 alpha helix hydrophobic/hydrophilic details
- Helices are often amphipathic
- Helices often have a hydrophobic face, which points into the protein interior, and more charged/polar faces, which point into solution.
- this turns out to be very nice when packing secondary elements into protein structure, in this situation take individual helix and barring it into the interior of folded proteins, we see a typical arrangement will be for all of the amino acids to be hydrophobic very foten we will see helix at the surface where one face of the helix is exposed to solvent other face of helix is pointing inward towards protein so tends to be amphiphilic
- orient amide groups along alpha helix position to create H bonds to one another as we do that we align individual dipoles in each amide group and get them all pointing in the same direction, as a result overall dipole associated with alpha helix call that a helix dipole
9-17
helical wheel
- the charged and polar groups oritented on one side of the helical wheel and other side is hydrophobic residues other individual helices fully exposed to solvent very often all of those amino acids around the helix are fully charged and polar amino acids
- 3.6 residues per turn
- Two turns of the helix bring sidechains into the same projection from the helix axis
- Residues at i, to i + 7 are in proximity
9-17
Linus pauling i and i+4
- he though about how he can fold up this chain so that every oxygen is associated with a H bond with soem other NH group in the chain, realized forvable arrangement but also instead of bending paper aroudn could also bend it around to go from i+3 amide NH group results in different secondary structure will talk about in next lecture
9-17
Some residues prefer to be in the helical conformation more than others
- Helix propensity is favored by Ala, destabilized by Gly or Pro.
- Leu stabilizes helix more than I or V. Crowding Cβ is less favorable.
- Side chains interact at spacing of i,i+3 and i,i+4: acid base bridges (E,D to K,R) stabilize helix, hydrophobic groups too.
rectiation 2pm 9-28
know diff btw chaperonins and chaperons, what are their mechanisms of action, what stage they act
- know for CHAPEroNES* which are typically smaller proteins they actually do not REFOLD misfolded proteins, hwo they act during the process of protein folding, the chaperones bind to specific some patches of aa along backbone of polypeptide, they help prevent misfolding of proteins so chaperones do not refold misfolded proteins they help a polypeptide chain fold to its correct confirmation by preventing misfolded states from being populated, the ATP hydrolysis in this case is used for a slightly different purpose, chaperones actually use energy of ATP hydrolsys to undergo confirmational change to either bind to polypeptide or release polypeptde
- but with chaperinons each 7 subunits within the chamber hydrolzyign atp to undergo also confirmational change but in that case each confirmational change created a new interaction with polypeptide chain so chain either extending out or getting a chance to refold back**
9-15 I think?
addition of salt for ex can be used to alter protein structure and participate proteins as we purify them?
Yes because salts have positive and negative charges, if you out a bunch of negative charges by the protein cause poisitive chrges t be attract t them or opposite so that can change the confirmation of the protein that way
Groel vs GRoES-
confirmation change that chamber undergoes, as ATP hydroylzed to ADP chamber expands and as it expands expsoes hydrophobic surface area on the interior, that is complementary to the hdyriphobic groups in the improperly folded protein now gives that improeply folded proteins ubstrate and opportunity to open up to detach hydrophobic interactions that are intermolcualr and incorrect and reasocate them with the envirornment* this in essence unfolds the protein from a properly folded sate, once it does that essentially whats going on it has been puled back up to top of that energy funnel** folding funnel he showed us before** so that hydrolysis of atp is paying energy to create a new environment inside that chamber and to pull that protein into an expanded form from which it can try again to fold properly*** partial polypeptide chain pulled apart, and let fo pulled apart and let fgo- while that happens in lower chamber ti chamber left open, not happening in top
champeron versus champeronin
- Any small protein, dimer- clamp like chameprone
- Any big like structure whith chamber like structure inside it is champeronin
- Clamplike chaperones
heat shock proteins
- Small proteins, ehat shock proteins because way discovered when ppl raised the growth temerpature of bacteria cultures to higher temperatures saw expression of proteins in bacterial cells, as if bacterial cells trying to do something to mitigate effect of inc temperature, so we know when temp of system high proteins start to be unstable or amy unfolded protein has harder time folding into its structure
- So these proteins called heat shock proteins were making higher amounts inside bacterial cells to prevent misfolding of other proteins or to help other proteins folding into the correct structure** so first tthign to remember HSP heat shock protein DO NTO REFOLD MIS FODLED PROTEINS*****
- They act DURING the folding reaction of a polyp chain to prevent chainf rom going to misfolded state, or they try to bias folding reaction ofpolypepyide chain toward folded structure, if piolyup misfolded cannto rescule polypepyides into correctly folded structure
aggregate proteins why need chaperons
- So say a polypeptide is folding into its 3 structure, generates intermediate structure say a bunch residues unstructured still say many are hydrophobic regions, these hydrophobic regions instead of forming hydrophobic interior cluster, hydrophobic regions btw diff polyp chains can nonspeiically interact with each other to give rise to a bunch of aggregates proteins, thse aggregates are not stabilized by intarmolecualr interactiosn they are stabilized by INTER moelcuarl lnteractions btw two polypeptide chains by hydrophobic residues by some other interaction generating aggregates
- Polypeptides in misfolded state in aggregates have no use to us, in order to prevent the folding intermediates or actual initial protein starting protein reaction to form aggregates what we can do if have certain prptein grabs onto folding polypeptide chain covers up region that can potentially undergo intermolecular interactiosn what will happen is these clamp proteins prevent intermeolcaurl interactiosn from happening and gives polypepide chance to generate intramoelcualr itneractiosn for correct strucurre or drive protein to right pathway by forming right pathway itnermediates, grab on undergo confirmational change, clamp like champerones
chaperones
are in more extended confirmation when bond to atp, when interact in open bdingin cliff interact with bidnign peptides can either bidn to completely unfolded peptides or trapped folded intermeidiates
-once interact with bidnign clamp, hydrolysis ATP undergoes and results in confirmational change in clamp like proteins that go from closed state to an open state, in that closed state it has a much higher affinity for plypeptide bidnign to, ithodsl onto the polypeptide, rest gets a chance ot generate folded structure or intetermeidate, and after a little bit a new protein come sin calld ncueltoide change factor kicks out ADP generated by hydrolysis of atp chamber like protein and replaces it with another atp molecule then clamp like goes back ot original confirmation elases paritally foled or almost totally foldd protein, then protein biased to form intermolecular contacts to give rise to native structure and clamp like champerone is recycled boudn to atp and in open cofniramtion when this another poilypeptide can hit another protein and go through same process
o Pulloing entire reaction towards favorign folded state of protein because its preventing surfaced exposed regins of folding intermediates ot fold itnermeocluarl interactions that can lead ot aggregations ormisfodld structures of intermediates*
o If already misfolded calmp cant do anything, but they can bind to it and deliver to chaperoneins
Two conditions happen if misfolded:
If conditions of cell are not condusive to recovering misfolded protein then prteins can be sent to degregation pathway were certain small tags given to protein sent to proteosome death chamber, under certain conditions instead of degrading proteins given a second chance to correctly fold back into native structure
o A bunch of chaperones bidn to these misofodled structure and send them to chaperonins*
How do you ensure only misfolded protein gets into GorEL complex??
So what happens is when proteins misfolding happens which is a huge area of study by itself, when proteins are NOT in their most stable confirmation in their cell, they have certain residues* that are exposed on tehri surface, in many cases many different types of residues exposed many cases hydrophobic residues typically should be buried inside protein, because of misfolded or stable misfolded intermediate they are exposed on surface, so there are certain proteins which just like the chaperones we talked about before this, groel groes examples of chaperonin proteins, also something called chaperons that help proteins fold, smaller soluble proteins that help other proteins fold o class of chaperoines that bind to hydrophobic surface of misfolded proteins and delivery these misfolded proteins to these chambers in the absence of these additional chaperon proteins, the chances of the misfolded protein being delivered to the groel groes complex would be much lower as opposed to higher probability of being degraded, if proteins chaperons not to bind and deliver to champeronins those misfoled proteins would actually be sent to different protein chamber inside the cell called proteosome where they are degraded, death chamber o there is a continuous partitioning of misfolded proteins between either going to degraded pathway or chaperon mediated refolding pathways**
groel groes 2
- Small chamber like structure GroEL open confirmation or closed confirmation, GRoES assocaton of seven proteins, 7 subunit chamber like exactly identical arrangement in bottom half, so can think of it as two parts each made up of 14 proteins*/ 7 form big chamber and 7 form top cap part, chamber GRoEL and cap part GROES
- Although symmetric structure at top and bottom look identical, they are structurally identical but not doing the same thing at the same time***
- top chamber open so a bunch of misfolded proteins and polypeptides can be delivered into chamber by other heat shock proteins, notice while this top chamber is open something going on in the bottom chamber, its not allowing anything new to come in cap closed on bottom chamber os bottom chamber at this point is busy trying to unfold the misfolded protein and give it a chance to refold
- each 7 units in bottom chamber bound to atp contiuosuly burning through cycles of ATP hydrolyzed ot ADP* then the whole structure of the chamber changes and whithint eh chamber polypeptides are puled apart and release dback os itgets a chance ot refold into correct structure*
groel vs groes 3
- Once polypeptide in chamber reaches stable folded structure becomes energetically ufnvaorable to unfold it keep in energentic state, at that point cap comes off polypepyide released, at that point groel closes on top chamber, so at sam time cant have both chambers closed**
- When top closed bottom not right orientation to fit cap, once top opens up bottom goes through confirmational change so cap fits on, by that time top has a protein come in refolded once in stable confirmation allos folded polypeptide to go out and when that happens and top chamber opens up another rufnodled or misfolded polypeptide has entered the bottom caber and whole process keeps repeating, unfolding and refolding going on in both chambers but only at one hcamber at a time** atp alters itneractiosn of aa lining up inner wall of chamber with misfodld polypeptide inside chamber because that cell essentially triedto fold and rfold polypeptide*
groel-groes 4
what is the function of symmetric architecture with two parts the top and bottom?
-we call the cap the groES and the chamber the groEL each made up of 7 subunits,
• there are different things going on in top and bottom chamber at the same time point
• as shown in top left hand corner, we have a top chamber where the chamber is open and the cap is not present, say partially folded protein entering at this point bottom chamber is actually closed, cap is closed what the bottom chamber is doing, the bottom chamber each subunit is continuously hydrolyzing atp to adp make that peptide fold and unfold, backbone of polypeptide side chains are interacting with aa that line interwall of side chamber, interactions of polypeptide those lining inner cavity of chamber continuously changing because of atp hydrolysis and associated conformational change* * visualize it in a way that partially peptide chain is being pulled apart and let go and pulled apart and let go, by doing that giving it a change to refold into proper structure
• while that is happening in lower, same thing not happening in top part, protein has reached stable confirmation from which it becomes energetically unfavorable to fold and unfold as oppose to keeping it in folded state at that point cap of chamber opens up of lower chamber, lets go of folded protein stable intermediate structure, at that point top chamber undergoes conformational change, in its ATP bound state, and that conformational change allows it to close the cap on top of it, so whatever misfolded protein enters the top chamber gets trapped in, the bottom chamber is open, now top chain does ATP hydrolysis cycles to open up and try to fold it back, while that process is happening in top chamber the bottom chamber is still opening
• so once it reaches stable structure on top, cap comes off lets that go and by that time another partially folded protein or misfolded protein has reached inside cavity of bottom chamber, so when the cap of top one comes off the cap on the bottom goes back on, process repeated, both chambers doing the same thing not at the same time, take turns in either remaining open or closed***
Limolene question from quiz
Q: dissolving nonpolar susbtances dissolving loimnune solution- when for clathrates UFNAVORABLE BECAUSE water molecule ordered becomes ordered when hydrpphobic effect energetically favorable because water moelcuels don’t have to order as much, so why is delta S is negative for limnuole because if visualize whats going on in terms of trying to dissolve nonpolar molecule in water, when trying to dissolve it in water, the limoluene moelcules themselves are not interacting with water, so you ar tryuing to fore them in water, so since wate rmoelcules are not interacting with limolene instead they are interacting btw themselves to form this network surrounding the limolene its trapped inside a cage the cage made up of water moelcuels and not interacting with limolene, if limolene trapped isndie cage itself cant be free to move around, watermolecuels hydrogen bodnign to eachother in that clathrate structure are also NOT free to move around, so that’s the reason if you start form situation where water moelcules randomly diffusing around and limolene just added to solution you end up in situation where entropy of water molecule as well as limolene IS LOWER WHY HAVE DELTA S NEGATIVE FOR LIMOLENEwhy have delta S negative for limolene**
hydrophobic effect, so two diff situaton oen where limolene interacting with istelf the other interacting with water
• Now the other question hydrophobic effect is a slightly diff thing what we are talking about here happens ot nonpolar moelcules in solution, hydropbobic effect consequence of this, have high cocnentraiton of nonpoar moelcuels they tend ot cluster together and when they cluster together the water moelcuels that were otherwise at this interface of the clusters and forming cage like structure snow when two hdyrophobci groups come together the water moelcuels from that interface are released so after you have a hydrophobic interaction or have two hydrophobic groups packed against each other its at that point, have net number of wate rmoelcules released from this interface, so inc the overall entropy of wate rmoelcules, so the reduction in entriopy of wate rmoelcuels when they form a clathrate around the individual limoleuen moelcuels is what is entripoically unfavorable so tthats why delta S is negative, why if have high enough cocnetnration of limoelen moelcuels would rather cluster together, eliminat as much water from surface as possible instad of remaining indivdaully in solution, two diff sitations limolene by itself or interacting with another limolene molecule**
• What stabilizies interact ion btw two limolene moelcules in an aq solutionc
answer to that would be that when two limolene come together the water moelculs releated by clathrates at interface increase the entropy of overall bulk molecule and that’s what makes the interaction btw limolene moelcules overall energically favorable because of inc in entropy of wate rmoelcuesl** by being released by clathrate structures at interface
-but if question is just asking you whether just adding limolene to water is entroigcally fvaporable or not then the answr is NO B/C when add JUST limolene to water, not asking if limolene is forming hydrophobic interactions are not, we are just asking you if add limolene to water by itself without interacting ohter limolene moelcules is that entropically favorable? No its no other nopolar moelcyules is that an entropicly favorable process or not? In that case its entropically unfvaorable because of clathrate system**
if there is a high concentration of limolene and let reaction proceed to equilibrium eventually will it reach some sort of a thermodyanmci favorable situation or not
if you do have a high enough concentration of hydrophobic moelcules so can interact with each other or IF just let enough time pass so at some point the hydrophobic molecules will interact with eachother, can only keep them stabilized in solution because of inc ientrpy of wate rmoelcules at the end of the day
Ram plot 2
- The reason this is important is because we know that when a polypeptide chain folds** not all confirmations are equally and energetically fvaorble because in certain confriamtions can expect a lot of stric crowding, repulsion btw simairly charged side chains
- If you have certain oreintations of side cahins/ oreintations of the groups are around alpha C or backbone certain orientations create a high energy sitiaton when collision btw side chains and groups on backbone and certain lower energy combination of torsion angles create lower energy situaiton which are thermodynamically more favorable**
ram plot 3 why do we care?
you care about these- values of phi and psi is to come up with a way to predict with backbone confrimations would be more favorabel than others when a polypeptide chain folds* in modern days more importantly when working on solving structure of protein often from experimental data generate a model, when trying to piublsih that model you cant publish it if majority of torsion angles calcautled form that model are in violation of Ram plot*** so plot is a benchmark that tells you that there are certain combinations of torsion angles in backbone of polypeptide chain that will be energetically more favorable than others and certain combinations that are absolutely not allowed, so if your model shows there is a torsion angle combination btw angle phi and psi that is allowed and unless you have a really good reason why its true, model would not be accepted for publication it would eb flat out rejected, more practical use of it
6 atoms
6 atoms can be thought of as relatively coplanar, distribtued around central amid ebond the CN bond in the C of carbonyl part of amide, and N being the nitrogen part of amide
- CN bond becuase its paritally double bonded in nature other atoms coplanar with it C alpha attached to carbonyl carbon and C alpha also attached to N of amide bond so if thinkign of polypeptide backbone, these two C alphas represent the amino acid rpeciding and follwoign amide bond, all tehse six atoms can think of them as being more or less on the same plane*
Ram plot 4
-Some phi and psi combiantions are v unfavorable: STERIC CROWDING of bkacbone atoms with other atoms in the backbone or side chains
-Some phi and psi angle combinatns are more favorable: FORM FAVORABLE H BOND INTERACTIONS ALONG THE BACKBONE**
o instead there is a limited region that is energentically favorable because we have to worry about steric clashes btw different groups in the peptide those two angles actually don’t get an opportunity to explore the different possibilities they essentially are binned, confirmatonal possibilities fall inyo particular low energy values in that landscale, those are the message get from rhamashamdra plot, then can use those to understand the features of the most common structures we observe in proteins that o fhte alpha helix and the beta strand*
rotating bonds in peptide
only phi or psi bonds can rotate, capable fo free rotaiton connects C alpha to nitrogen of preceeding amide bond or the C alpha connects amino acid to next carbonul carbon of next amide bond, cant rptate around amide bond itself because partially doubel bonded in character so cannot rotate it itself, almost always stuck in transf confirmation, too C alphas in side of two planes are potinign in opposite directins trans, or sometimes cis when both C alphas pointing in same directin***
ram plot 5 summary
ultimately
- phi and psi combinations are very unfavorable: STERIC CROWDING of backbone atoms with other atoms in the backbone or side chains
- some phi and psi combinations are more favorable: form favorable H bond interactions along the backbone
- polypeptide cahins fold in ways so as to minmize collison between side chains hence only certain values of torision angles are energetically allowed**
how to read ram plot from Mitra
- since two torsion angles go from 180-0-180 can plot 2 d plot, way to look at this looking at intersectin of two axis, vertical axis Y acis represents all possible values of torsion agnle psi, if go form center of this Y axis to the top go from o to +180, 0 to minus 180 values of psi, same as x axis which intersects y axis, it start at midpoint of that sectiona dn go to right you are talking about al the phi values that go frm zero to plus 180 and go from zero to negative side of x axis 0 to -180** of values of phi torsion angle
- so since now defiend this interspace using a coordinate system of vertical axis and hroizotnal axis itnersectign each other, v precise values of axis can represent any combination of phi and psi in coordinate system where say phi is +150 and psi is say plus 120+ so should be able immediately to look at what quandrant* where is that combination such that that point represents psi +150 and phi 120 should obviously first look at positive places on this x axis, psi going from 0 to 180 reprsents positive avlues so the quantrand focusing on is top righthand coordinate becuae positive present values of pho and psi going from 0 t +180** so if find out where ont eh phi axis +150 is, and wherw on psi axis +120 is and then drop a lien from where they meet would represent coordination points that defines phi +150 and psi +120 that’s how youcome up with these figures, so ones that gve you more steric hindrance he indicated them by poijnt on diagram and essentially at the end of the day can see clear map that results from that, all regions shown in blue are regions represent energetically favorable confirmation phi and psi angles
- darker blue color better in terms of energetic stability represent much lower energy combinations, lighter bleuu indicates still allowed but energies are still slightly higher* still negative energy but slightly higher, then any area blank white all represent phi/psi combos which would create significant steric collisions btw side chaisn or backbone and WOULD NOT be energetically allowed*
Buffers
* see sharp change in ph as function of adding base start devaitign and enter plateaued region flat, plato region in titration indictes buffer*8 whatever molecule is there in solution is resisting a change in pH why?
- Because in beginning when add in a little amount of base sharp rise in pH once get to flat area need a lot more base to achive the same change in ph because entered range where carbxolic acid is undergoing reversible dissocaiton asscoaiton
- so everytime add base it is trying to before contributing abse to aq solution to inc ph a part of the base is forcing deprotonation of COOH so proton released by COOH is bidnign to that base to restore neutral water meocluel* so as long as you are in that range of the pka value of carboxylic acid, will need a lot more base in order to achieve the same amount of rise in pH if compared to basene of anything trying to slow down that rise* so that is why right around tha tpka value have a whole region of pH values or base concengratiosn wher eneed a lot fo abse to change the pH of the solution once pH of the solution ahs goen beyond tha point, COO fully deprotoatnd, ntohign preventing base from contributing more hydroxide ions to solution so even with small additions of OH get sharp inc in pH fo solution until hit second ionazbel group of gylcine the amino group
- if keep adding base instead of contributing to raising pH of solution will try to deprotonate alpha amino gorp, whatever base adding deprotonates alpha amino group, OH bidns to H grenerates H20 instead of adding to basicity of solutont aht entire range exists over 1 unit ok pka of amino group once ph of solution goes beyond that nothing else to reduce to create that effect of absorbing hydroxide ions so now even with a little addition of hydroxide ions see an inc in pH
- so why for glycine 2 regions in soltuin where glycine moelcuel tries to reseit change in pH of the soluton becuas ethsoe ranges correspond to pka of those ionazble groups** so like hsitide does the same thing but now will do that at 3 different ranges of pH values so if trying to generate a buffer where want buffer to acta s buffer not just at 1 ph range but at mutlipel* then moelcuels like amino acids amphiptes mutlipel ionizable groups can eb really good interms of buffering abilties*
tyrosine and cysteine are special* why?
- Tyrosine net charge 0 but because goes from an OH to O-, two grousp ionize at higher pH and give moelcuel negative charge going frm 0 to -1
- But only two aa that take you from 0 to -1 which are cystine and tyrosine**
- Cystine we know deprotonates around 8.3 or so so when cystine exists in protonated form is SH uncharged, if deprotonate is S- thiolate form gives you negative charge, provided Cystine not in a disfulded bond state if by itself as thiol group
- For tyrosine in order to figure out what would be charge at ph 10 so if carbxolic acid deproronate at 3, so keep raising pH of solution that carboxilic acid gets deprotoatned at ph of 3 get negative charge on carboxyclic acid at 4, ph 8 enter deprotonate amino acid, by time at 8.5 or higher will be deprotonated, so by time get pH of 9 alpha amino completely deprotonated, carbox acid still protaonte so have net minus charge from just those two groups
- the phenolate group, as start to get to ph of ten protonate hydroxyl group goes from 0 to -1** since pka of group is at 10 and ph of solution at as 10, IT WILL BE HALF DEPROTONATED SO will be negative half charge, so net charge on tyrosine at ph of 10 is -1 frm COO- then -0.5 from thiolate so -1.5, already lost positive charge by deprotonating alpha amino
- Only two groups cystine and phenol of tyrpsone** uncharged state has a zero charge if deprotonated go to phenolate anion -1 charge, or cystine thiol group if not disfuilde group if free thiol group has zero charge** if deprotoatned because thiol group of cysteine has pka of8, then thiolate anion negatively charged**
Rules for titration!
-two aa side cahins deprotonate at lower ph those are yoru acids* cabrxolic acids which will deprotonate at say pkas or ph around 4 if protonated form neutral when deprotonated they will make group negatively charged go from zero to minus 1 both happen*
o Lysine or arg go from +1 to 0
acids= 0 to -1
tyrosine and cystine go from 0 to -1*
coiled coiled
keratin fibrous protein made uo of coiled coil structures, have typical right handed helix but right handed helices wrapped around each other that is going in left handed, each alpha helix is right handed but two wrapped around each other then that helical wrapping would be left handed* so actually have opposite coordination compared original handedness of individual helices
o Typically speaking if helices have specific right handed ior left hadnedness, the triple helix will be the opposite the overall quarntary assocaiton of coiled coiled will hve the oppsite, of he indiivudla helix*
same for collagen, so collage individual helices are left handed overall structure right handed triple helix
collagen helix
triple helical structure, individual helices are left hadned, but when they are helically intertwined with each other that overall helical strucutre is right handed so called right handed triple helix*
o Typically speaking if helices have specific right handed ior left hadnedness, the triple helix will be the opposite the overall quarntary assocaiton of coiled coiled will hve the oppsite, of he indiivudla helix*
- when make coil coiled we take two alpha helixces adn twist around each other, see quite a lot of examples in which there are hydrophobic interactions present at the interface* and can interdigitate* with respect to one another*
collage 2
h bodnignw ithin each chain but so within typical right handed helix have I to I+4 rule, collagen doesn’t follow that rule much more extended structure means have to go over more aa to complete one full circle longer H bodnign interaction but also weaker btw individual chains
- what is actually holding them together is when, if just take a single strand of three strand structure v hard ot get into left handed helical confirmation, that left handed helical confiramtion is uniquely formed when all three wrapping each other in righted handed confirmation b/c special groups like hdyroporline. and amid ebonds btw backboens optimal h bond pattern stabilzign triple helical structure within context of that structure, within that strucutre they are left handed helixes, unless part of right handed overlal structure the individual left handed structure wouldn’t be stable
- H bodnign btw backbones of the individual helices to each other as well as hydrogen bond of hydroxprolines btw the chains*
- Think of triple helix as more like a beta strand interaction with h bonding btw the strands in this case not strands they are forming helices, but h bonds more btw strands as opposed to within the same strand**
**hydroxyprolines have hydroxyl group which can hydrogen bond as well which has lone pairs on the oxygen*
quiz question urea 2
h bonds with wate rmolecules, so dec entropuy makes it rigid
- there is a net entrooy and entrpy change with respect to urea and indivdiaul water molecules, so if take solid urea and dissolve in water actually breaking lattic of crystal structure of urea and dissolving in water to so they become more mobile in water, but in this case we were saying when urea is in water what happens? not solid state of urea
- urea very polar molecule, has to interact with water so no way it cannot effect entropy of urea as long as its in water
- delta s engative if consdie rtwo sititosn wate rwithotu urea and water with urea, no urea nothing holding wate rmoelcuesl to each other othe than hydrogen bonds extremely transient, as soon as add urea bunch of urea tighly holding on to water moelcules tightly holding onto it, each urea can form bonds, amide hydrogens with another two so like 6 water moelcuels surround urea separate from clathrate structure hydration layer, so all wate rmoelcuesl sticking around urea have lowered entropy of water moelcule*
quiz question urea versus limolene
urea quiz question cnt.
different from limonene b/c limolene is NOT interacting with water molecules but entropy of water moelcuesl still reduced water molecules were forming cage like structures by formign H bonds btw themselves, in this case watermoelcueslf ormign hydrogen bodns with solute still results in dec of those wate rmolecules adding to solvation layer around urea
delta s positve ? NO not possible, if lots of wate rmolecuels forming tight interactiosn with polar surrounding it cant inc ability of water molecules
random diffusion not possible so correct answer is B, so we know urea interacts with water so d wrong, and e is wrong becuase random motion of urea signicantly inc in water, because when urea is in solid state doesn’t have high entropy but moment dissolve it in water then its entropy is inc
-solid urea versus urea in water dissolved, entropy will inc when add to solution, but once equilbiruatedf rom poitn of addition at that poitn entropy would not be high, each urea moelcule surrounded by water moelcule, although more mobile than they would be in solid state where urea molecuyles cant move at all, then in that perspective yes can see where confusion is, more mobile than solid satte a cant move at all, liquid can still move around, then their entropy would inc compared to solid state, but inside the water if you compare solvated molecule vs unsolvated moelcuel then solvated entropy is lower than nonsovlated*
