1. What are the biochemical functions of the human versions of the two protein A

Question

1. What are the biochemical functions of the human versions of the two protein A and protein B shown below? Use the following websites to help you solve this problem. Google searches may also be helpful http://blast.st-va.ncbi.nlm.nih.gov/Blast.cgi http://en.wikipedia.org/wiki/BLAST Protein A MDTDLDVPMQDAVTEQLTPTVSEDMDLNNNSSDNNAEEFSVDDLKPGSSG ADHKSSKPLELNNTNINQLDQWIEHLSKCEPLSEDDVARLCKMAVDVLQ FEENVKPINVPVTICGDVHGQFHDLLELFKIGGPCPDTNYLFMGDYVDRG YYSVETVSYLVAMKVRYPHRITILRGNHESRQITQVYGFYDECLRKYGSA NVWKMFTDLFDYFPITALVDNKIFCLHGGLSPMIETIDQVRELNRIQEVP HEGPMCDLLWSDPDDRGGWGISPRGAGFTFGQDVSEQFNHTNDLSLIARA HQLVMEGYAWSHQQNVVTIFSAPNYCYRCGNQAAIMEVDENHNRQFLQYD PSVRPGEPSVSRKTPDYFL Protein B MPAENQNTGQDRSSNSISKNGNSQVGCHTVPNEELNITVAVRCRGRNERE ISMKSSVVVNVPDITGSKEISINTTGDTGITAQMNAKRYTVDKVFGPGAS QDLIFDEVAGPLFQDFIKGYNCTVLVYGMTSTGKTYTMTGDEKLYNGELS DAAGIIPRVLLKLFDTLELQQNDYVVKCSFIELYNEELKDLLDSNSNGSS NTGFDGQFMKKLRIFDSSTANNTTSNSASSSRSNSRNSSPRSLNDLTPKA ALLRKRLRTKSLPNTIKQQYQQQQAVNSRNNSSSNSGSTTNNASSNTNTN NGQRSSMAPNDQTNGIYIQNLQEFHITNAMEGLNLLQKGLKHRQVASTKM NDFSSRSHTIFTITLYKKHQDELFRISKMNLVDLAGSENINRSGALNQRA KEAGSINQSLLTLGRVINALVDKSGHIPFRESKLTRLLQDSLGGNTKTAL ATISPAKVTSEETCSTLEYASKAKNIKNKPQLGSFIMKDILVKNITMEL AKIKSDLLSTKSKEGIYMSQDHYKNLNSDLESYKNEVQECKREIESLTSK NALLVKDKLKSKETIQSQNCQIESLKTTIDHLRAQLDKQHKTEIEISDFN NKLQKLTEVMQMALHDYKKRELDLNQKFEMHITKEIKKLKSTLFLQLNTM QQESILQETNIQPNLDMIKNEVLTLMRTMQEKAELMYKDCVKKILNESPK FFNVVIEKIDIIRVDFQKFYKNIAENLSDISEENNNMKQYLKNHFFKNNH QELLNRHVDSTYENIEKRTNEFVENFKKVLNDHLDENKKLIMQNLTTATS AVIDQEMDLFEPKRVKWENSFDLINDCDSMNNEFYNSMAATLSQIKSTVD TSSNSMNESISVMKGQVEESENAISLLKNNTKFNDQFEQLINKHNMLKDN IKNSITSTHSHITNVDDIYNTIENIMKNYGNKENATKDEMIENILKEIPN LSKKMPLRLSNINSNSVQSVISPKKHAIEDENKSSENVDNEGSRKMLKIE 2. All cells are surrounded by a lipid bilayer. The interior of the lipid bilayer is a strongly hydrophobic environment. Many proteins are embedded in the lipid bilayer, where they execute important functions The polypeptide chain of these proteins must cross the lipid bilayer. This presents a problem because the peptide bond is polar in nature. It turns out that in virtually all cases where an amino acid chain crosses a lipid bilayer it does so as an alpha helix. Why is this the case? 3. What unique property of histidine makes it an important amino acid? 4. The pKa values for amino acid side chains measured using purified amino acids can be quite different from the pKa values of the same amino acids in the context of a folded protein. Explain why this is the case

Explanation / Answer

Q3)  Histidine is a generally considered to be a polar amino acid, however it is quite unique with regard to properties, meaning that it does not particularly substitute well with any other amino acid. Histidine has a pKa near to that of physiological pH, meaning that it is relatively easy to move protons on and off of the side chain (i.e. changine the side chain from neutral to postive charge). This flexibility has two effects. The first is that it means Histidines is rather ambiguous about whether it prefers to be buried in the protein core. The second is that it is an ideal residue for protein functional centres. Histidines are the most common amino acids in protein active or binding sites. They are very common in metal binding sites (e.g. zinc), often acting together with other amino acids.

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