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hellsite-proteins · 5 months ago

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I have a bio exam in about six hours (in the afternoon, this is an appropriate hour for me to be awake) and I don't wanna study so I'm gonna recite everything I know about proteins to you.

Proteins can have CHONS, Carbon Hydrogen Oxygen Nitrogen Sulfur. Made up of amino acids. Amino acids have NH2-R-C-H-COOH. NH2 is the amino group and COOH is the uhh carboxyl group? Amino acids exist as zwitterions, with the NH2 becoming NH3- and COOH becoming COO-. Because electronegativity and stuff. There are 20 amino acids (in my syllabus).

Proteins have primary structure (polypeptide chain, the specific sequence of amino acids) listed from N terminus to C terminus. Maintained by peptide bonds. Which is a condensation reaction. The COOH and the NH2 form a bond that looks like CONH. Then secondary structure, which is alpha helixes and beta sheets. Both are maintained by hydrogen bonds. Beta sheets can be parallel or antiparallel, though most of the ones in your blog or antiparallel (but also very short). Alpha helixes are more common and recognisable.

Next is tertiary structure. Four types of bonds in this one: Hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interactions. In increasing order of strength, hydrophobic<hydrogen<ionic<disulfide. Disulfide bonds are covalent bonds and very heat stable. Formed by disulfide bridges. Very strong. Sulfur is found on Cysteine so the more cysteine is in a molecule the more heat stable it is likely to be. The single letter code for Cysteine is C. If I say CCCCCCCCCCCC, will disulfide bridges form in my protein? Hm. Ionic bonds is when uhh. Charged particles. Shit I forgot I need to revise this part. Hydrogen bonds are easier, I can identify them by identifying differences in electronegativity- in chem I remember these as FON and H, but in amino acids there's only O and N, no Fluorine. Very common, in most secondary structures. In polar particles or R groups. Ionic bonds are for charged particles, hydrogen bonds are for polar particles. Lastly in hydrophobic interactions, not to be confused with homophobic interactions. Which is when hydrophobic side chains- most commonly stuff with lots of carbon, or sometimes sulfur- gather in the middle of the protein, away from the aqueous exterior.

Next is Quaternary structure, which is when there are MULTIPLE polypeptide chains. Only when multiple polypeptide chains, if not it's tertiary. Not all proteins have these. Bonds are mostly the same as tertiary, I think?

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There are globular, fibrous, and membrane proteins. But mostly I have to focus on the globular and fibrous part. My case study for globular proteins is haemoglobin. Haemoglobin has four polypeptide chains in it's quaternary structure, two alpha two beta. It is unclear if the names of the chains have anything to do with whether there are alpha helixes or beta sheets in them. It also has a prosthetic group, a haem group in this case, of iron- I think an Fe2+ molecule? Yeah. Which oxygen binds to. And once oxygen is bound to it it causes a change in confirmation in all four parts allowing it to bind to oxygen more easily. I need to know about sickle cell disease, which is when one of the amino acids- glutamic acid I think- is replaced with a hydrophobic one. Serine? Either way when oxygen is bound to it it's fine but when there's no oxygen there's a hydrophobic patch sticking out, which it doesn't like so the haemoglobin will change confirmation to hide, causing the haemoglobin to clump together in a way that causes the red blood cell to appear "sickle shaped". Also I was wrong it's not serine it's valine.

For fibrous, I have collagen. Which is mostly a repeating sequence of three amino acids- shit I forgot which ones I need to get my notes- glycine-X-Y. Glycine has a very small R group which allows it to fit in the small tight part in the alpha helix. X-Y is usually proline and hydroxyproline. Alpha helix, hydrogen bonds formed. Proline and hydroxyproline have relatively inflexible and bulky R groups which gives the structure rigidity. That's the secondary structure. But collagen is unique in that it has a secondary and quaternary structure, because in tropocollagen it's like three of these alpha helixes wound together. Then each tropocollagen cross links to neighbouring tropocollagen molecules. This is covalent bonds involving lysine residues. Lysine??? Where tf did Lysine come from??? I don't see it anywhere else on the page. This is worrying. Uhh this increases tensile strength and the staggered or overlapping arrangement of tropocollagen minimises points of weakness along the length of the fibrils. It's like, collagenchain-tropocollagen-fibrils-fibres. The staggering gives the bundle of fibrils a banded appearance. There was... A part where they talk about how the cell produces it on the outside... No, wait, that's cellulose. Carbohydrate. Completely different.

Then we move on to enzymes which is a whole different chapter and this is already a very long ask which I imagine will take very long to load. Thank you for letting me ramble in your inbox. CCCCCCCCC. I'm going to ramble about DNA&genomics to hellsitegenetics in a bit but first I need to finish looking through mitosis and meiosis. Ugh. I hope this protein has a high success rate and that my exam has an even higher success rate. Thank you for your time.

this sounds great and i bet you did awesome on your exam! i find explaining things to someone else helpful when studying, so i hope that doing this helped you as well. without even looking at it i can guarantee that your exam was much more successful than whatever proteins i'll get out of this.

i actually had to split this into two proteins and run them completely separately because it was simply too long. i am both excited and absolutely terrified to see what we get from all those cysteines

letter sequence in this ask matching protein-coding amino acids:

protein 1:

IhaveaieaminatsihrsintheafternnthisisanapprpriatehrfrmeteawakeandIdntwannastdysImgnnareciteeverythingIknwatprteinstyPrteinscanhaveCHNSCarnHydrgenygenNitrgenSlfrMadepfaminacidsAminacidshaveNHRCHCHNHistheamingrpandCHisthehhcarylgrpAminacidseistaswitterinswiththeNHecmingNHandCHecmingCecaseelectrnegativityandstffThereareaminacidsinmysyllasPrteinshaveprimarystrctreplypeptidechainthespecificseqencefaminacidslistedfrmNterminstCterminsMaintainedypeptidendsWhichisacndensatinreactinTheCHandtheNHfrmandthatlkslikeCNHThensecndarystrctrewhichisalphaheliesandetasheetstharemaintainedyhydrgenndsetasheetscaneparallelrantiparallelthghmstfthenesinyrlgrantiparalleltalsveryshrtAlphaheliesaremrecmmnandrecgnisaleNetistertiarystrctreFrtypesfndsinthisneHydrgenndsinicndsdislfidendsandhydrphicinteractinsInincreasingrderfstrengthhydrphichydrgeninicdislfideDislfidendsarecvalentndsandveryheatstaleFrmedydislfideridgesVerystrngSlfrisfndnCysteinesthemrecysteineisinamleclethemreheatstaleitislikelyteThesinglelettercdefrCysteineisCIfIsayCCCCCCCCCCCCwilldislfideridgesfrminmyprteinHmInicndsiswhenhhChargedparticlesShitIfrgtIneedtrevisethispartHydrgenndsareeasierIcanidentifythemyidentifyingdifferencesinelectrnegativityinchemIrememertheseasFNandHtinaminacidstheresnlyandNnFlrineVerycmmninmstsecndarystrctresInplarparticlesrRgrpsInicndsarefrchargedparticleshydrgenndsarefrplarparticlesLastlyinhydrphicinteractinsnttecnfsedwithhmphicinteractinsWhichiswhenhydrphicsidechainsmstcmmnlystffwithltsfcarnrsmetimesslfrgatherinthemiddleftheprteinawayfrmtheaqeseterirNetisQaternarystrctrewhichiswhenthereareMLTIPLEplypeptidechainsnlywhenmltipleplypeptidechainsifntitstertiaryNtallprteinshavethesendsaremstlythesameastertiaryIthink

protein 2:

CCCCCCCCCCCCCCCCTherearegllarfirsandmemraneprteinstmstlyIhavetfcsnthegllarandfirspartMycasestdyfrgllarprteinsishaemglinHaemglinhasfrplypeptidechainsinitsqaternarystrctretwalphatwetaItisnclearifthenamesfthechainshaveanythingtdwithwhethertherearealphaheliesretasheetsinthemItalshasaprstheticgrpahaemgrpinthiscasefirnIthinkanFemlecleYeahWhichygenindstAndnceygenisndtititcasesachangeincnfirmatininallfrpartsallwingittindtygenmreeasilyIneedtknwatsicklecelldiseasewhichiswhenneftheaminacidsgltamicacidIthinkisreplacedwithahydrphicneSerineEitherwaywhenygenisndtititsfinetwhentheresnygentheresahydrphicpatchstickingtwhichitdesntlikesthehaemglinwillchangecnfirmatinthidecasingthehaemglintclmptgetherinawaythatcasestheredldcelltappearsickleshapedAlsIwaswrngitsntserineitsvalineFrfirsIhavecllagenWhichismstlyarepeatingseqencefthreeaminacidsshitIfrgtwhichnesIneedtgetmyntesglycineYGlycinehasaverysmallRgrpwhichallwsittfitinthesmalltightpartinthealphaheliYissallyprlineandhydryprlineAlphahelihydrgenndsfrmePrlineandhydryprlinehaverelativelyinfleileandlkyRgrpswhichgivesthestrctrerigidityThatsthesecndarystrctretcllagenisniqeinthatithasasecndaryandqaternarystrctreecaseintrpcllagenitslikethreefthesealphahelieswndtgetherTheneachtrpcllagencrsslinkstneighringtrpcllagenmleclesThisiscvalentndsinvlvinglysineresidesLysineWheretfdidLysinecmefrmIdntseeitanywhereelsenthepageThisiswrryinghhthisincreasestensilestrengthandthestaggeredrverlappingarrangementftrpcllagenminimisespintsfweaknessalngthelengthfthefirilsItslikecllagenchaintrpcllagenfirilsfiresThestaggeringgivesthendleffirilsaandedappearanceTherewasApartwheretheytalkathwthecellprdcesitnthetsideNwaitthatscelllseCarhydrateCmpletelydifferentThenwemventenymeswhichisawhledifferentchapterandthisisalreadyaverylngaskwhichIimaginewilltakeverylngtladThankyfrlettingmeramleinyrinCCCCCCCCCImgingtramleatDNAgenmicsthellsitegeneticsinaittfirstIneedtfinishlkingthrghmitsisandmeisisghIhpethisprteinhasahighsccessrateandthatmyeamhasanevenhighersccessrateThankyfryrtime

protein guy analysis:

protein 1 looks absolutely awful. it barely has any secondary structure, and absolutely no tertiary structure to speak of. the horrifying loops have some strings of cis bonds, and there is not a single disulfide bond. i hate this so much. the long string of C's just looks off putting. protein 2 is the same but worse. there is one disulfude, but otherwise barely any structure exists. the single alpha helix feels almost mocking. overall, this is miserable and disgusting.

predicted protein structure:

protein 1 cartoon

protein 1 surface

close up of cysteines on protein 1

protein 2 cartoon with disulfide bond in orange

protein 2 surface

#science #biochemistry #biology #chemistry #stem #proteins #protein structure #science side of tumblr #protein asks #protein info

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