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NBME 21 Answers

nbme21/Block 3/Question#28 (63.1 difficulty score)
A 1-year-old girl is admitted to the hospital ...
Disruption of the secondary structure of collagen molecules🔍
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I inhtk it hsa sniogtemh ot od htwi clygnie (edu to tsi mlsla seiz ti nca fti in yamn aeplcs hrwee htero nomai dscia anc tno nda cheen ti svrepido “tsrtualruc cessmpcn”aot to eht eg,acnoll ie.. tup a kikn ni eht alaph il)h.xe fI elnciyg si apmlsdeic yb semithgon ,eles I t’dno thnki aeopl-locrng acn morf tsi tcreocr areondycs ttrruuec.s

jotajota94  True! also, glycine is 1/3 of collagen alfa chains, so it makes sense that substitution with alanine (which is much bigger) would lead to disruption in the alpha helix formation. +  
jotajota94  True! also, glycine is 1/3 of collagen alfa chains, so it makes sense that substitution with alanine (which is much bigger) would lead to disruption in the alpha helix formation. +  
thepacksurvives  Glycine is small and bendy, which allows it to form the fibrils for the triple helix +  
brasel  Also in general (FA 2018 pg 50) OI is from problems forming the triple helix which is secondary structure. Fortunately, they gave us something to reason with in the question (Gly->Ala) +1  



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I diur,efg Xg-y-Yclein is ichatcelnyl endoscider a r“mripay oniam iadc euttrcrus of a t”rionep scein teh dteonfiini fo a rPrymai uutrcrest fo a iotpren is a“ raenli iahnc fo inmao .cds”ai fI uyo smse ihtw the Prmiary utsr,rtuec as in eth enisoutq set,m uyo otncna fmro hte ayoeSdncr uttrrusce of het entpiro, ichwh is nieedtrdme by teh -dibngneghonyord whhic srcuoc neeewtb hte tideppe cbnoekab, dientpnnede fo hte R rsogup. I epho hist dmae .eness

mFor aiediwpki: coraS“deny uurtertcs si famrylol dnefdei by eth erattpn fo dnorhyeg bnsdo nweeebt het ionam gdehnroy and ycaorxbl gxnoye satom in teh depipte ecabnkbo”. isaesh(mp n)mei


From Molecular Biology of the Cell:

Biologists distinguish four levels of organization in the structure of a protein. The amino acid sequence is known as the primary structure of the protein. Stretches of polypeptide chain that form α helices and β sheets constitute the protein’s secondary structure. The full three-dimensional organization of a polypeptide chain is sometimes referred to as the protein’s tertiary structure, and if a particular protein molecule is formed as a complex of more than one polypeptide chain, the complete structure is designated as the quaternary structure.

https://www.ncbi.nlm.nih.gov/books/NBK26830/#A406

+/- drdoom(646),


 +3  upvote downvote
submitted by hungrybox(791),
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Due ot yne'gcsil samll izse, ti erecsat "k"knis in eth animo icad nese.ecuq sThee kisnk rea ndeeed to yrcltcoer mfro eth oaryencsd esurt.ctru

hrteO asrnw:es

  • e"kwednae crtntaioien btewene egcnalol dan yoo"gnacltpre - olgnceal + yngrotoacple = lalr.gatcei heT qonetsui etms mneotnsi ynma esetdfc ni bEON t(yep I anlceo)gl but no eotinnm of scetedf ni WrlagaTleOc py(te II cgle)olna



 +3  upvote downvote
submitted by usmle11a(65),
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ok gsyu adn i uqote from wmots:acnfiuisph4.isbcsditstcsmtte/oaeh/gt1r0/-errp2otlww.//leeoeeop

0"%9 eavh na leedibaitifn etcgien noaitmut CO L A11 dna COL 1A2
seusc a maanblor ceglolna scngilns-roik vai a cnliyeg isbitttnousu ni eth olnlogepcar ceullmoe "

whcih samen ttha OI sha a cglnyei iibtuussottn dna ohrfrete tsi elabun ot rmof a ncdreysoa u.cersruttu




 +0  upvote downvote
submitted by drdoom(646),
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eHesr’ eon awy ot me-aoiniopstrs-celef a“dedceers ybrhongd-eond tfn:aroom”i ’mI not a gbi fna fo isth ieln of oair,senng utb aecilncytlh alenani as a dise grpuo has roem *edhrogsny fro oeniattlp nryegodh obinndg than glynice:

elanan:i H3C—
lic:ygne H—

So, “ihle,lnyat”cc nenaila wlodu reimpt mero drn-boyehdong r,oaimnoft whhic gimht lawlo uyo to nemilteia hatt coce.ih

Tath ds,ai it ssmee salotm iimebpsols to rlue out uwiohtt( eyvr lhacintec dgnekwelo or seom idovpdre ixeeamptlnre t)aad htta teh yghstlil alrrge naealni sode otn rpmaii ydrgoneh nndgbio neteewb oallcneg mleeuclso iav isetcr )spl(tiaa e.inrneertefc nI eplsirm semtr, esinc enlaian si ,geralr ouy uwldo think tath it sumt omowseh enteerrfi tihw teh dgbongenroihdy-n htta ocrusc hwti teh wlditey-p yilnceg.

---
ylSrc*tti ,gisnkaep ’ist ton eth umrneb of yehdrgosn btu aslo the ttghnres fo the leoipd htta tietcsflaai gehdrnoy ndnibo:g a grdneohy odnub ot a gtloryns eeetlecgvotrina lceuolme klie elrfouni liwl p”rape“a orem oevpsiit n,ad ,stuh oenbdhog-ndry eomr nygrostl whit a renaby xognye mecpoa(dr ihwt a nhydoger ecotdecnn to cr,nboa orf am.exel)p

Frehtru dre:gnai

  1. elwpddq/epsiomutlhndtbt/mwuhlhigu/.he./:wccuhpe/sd.r.
hungrybox  Appreciate the effort but this is far too long to be useful. +14  
drachenx  hungrybox is a freaking hater +  
drdoom  @drachenx haha, nah, coming back to this i realize i was probably over-geeking lol +  
blueberrymuffinbabey  isn't the hydrogen bonding dependent on the hydroxylated proline and lysine? so that wouldn't really be the issue here since those aren't the aas being altered? +  
drdoom  @blueberry According to Alberts’ MBoC (see Tangents at right), hydroxylysine and hydroxyproline contribute hydrogen bonds that form between the chains (“interchain”, as opposed to intra-chain; the chains, of course, are separate polypeptides; that is, separate collagen proteins; and interactions between separate chains [separate polypeptides] is what we call “quaternary structure”; see Tangent above). And in this case, as you point out, the stem describes a Gly->Ala substitution. That seems to mean two things: (1) the three separate collagen polypeptides will not “pack [as] tightly” to form the triple helix (=quaternary structure) we all know and love and (2) proline rings will fail to layer quite as snugly, compromising the helical conformation that defines an alpha chain (=secondary structure; the shapes that form within a single polypeptide). +  
tadki38097  also you can't H bond with carbon, it's not polar enough +  

From Molecular Biology of the Cell:

Hydroxylysines and hydroxyprolines are infrequently found in other animal proteins, although hydroxyproline is abundant in some proteins in the plant cell wall. In collagen, the hydroxyl groups of these amino acids are thought to form interchain hydrogen bonds that help stabilize the triple-stranded helix. Conditions that prevent proline hydroxylation, such as a deficiency of ascorbic acid (vitamin C), have serious consequences. (Emphasis mine)

https://www.ncbi.nlm.nih.gov/books/NBK26810/#A3555

+/- drdoom(646),

From Molecular Biology of the Cell:

The primary feature of a typical collagen molecule is its long, stiff, triple-stranded helical structure, in which three collagen polypeptide chains, called α chains, are wound around one another in a ropelike superhelix (Figure 19-43). Collagens are extremely rich in proline and glycine, both of which are important in the formation of the triple-stranded helix. Proline, because of its ring structure, stabilizes the helical conformation in each α chain, while glycine is regularly spaced at every third residue throughout the central region of the α chain. Being the smallest amino acid (having only a hydrogen atom as a side chain), glycine allows the three helical α chains to pack tightly together to form the final collagen superhelix (see Figure 19-43).

https://www.ncbi.nlm.nih.gov/books/NBK26810/#_A3551_

+/- drdoom(646),


 +0  upvote downvote
submitted by nmb29(0),

I might be overthinking it but, H bond formation of aa's makes the secondary structure of the protein (collagen in this case). The Gly to Ala substitution does result in less H bond formation, but of individual aa's not between collagen molecules (that might be more for quaternary structure)

lpp06  I think the key is in the answer phrasing, the answer mentioning H-bonds says "Disruption of H-bonds between collagen molecules" Although collagen does undergo H-bonding to support the triple helix, this is done within the same collagen molecule. Linking different collagen molecules occurs via the lysine - hydroxylysine links done in the ECM +1  
kevin  this is the one comment that finally helped me understand why that was incorrect. thank you +  



Gly-X-Y is backbone for collagen alpha chain. 3 collagen alpha chains spiral to form triple helix. Glycine has no R group, allowing for flexibility and formation of triple helix. No glycine prevents this continuous spiraling, preventing the formation of collagen secondary structure.

Recall that alpha-helices and beta-sheets are examples of secondary structures. This can be thought of a manifestation of the alpha helix.




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het ywa I tthgohu obtua ti, si ttah hte sitOseensoge fIcetampre lussert ni cdfvetiee teiodso dutpooircn hhicw is a orndyesca ucurtesrt to aeollncg shtinessy




 -2  upvote downvote
submitted by lilmonkey(19),

Gly is polar, Alanine is nonpolar and hydrophobic. Missense nonconservative mutation. These AAs have different chemical properties which lead to disrupted protein folding (secondary structure). Similar to Glu - Val substitution in Sickle Cell Disease.