Monday, May 26, 2008

RNA Polymerase




In all organisms, DNA carries the information needed to produce proteins that make the structure and do the work of the cells, and pass along this information to the next generation. In order to produce proteins, the DNA must be copied to RNA which takes the information to other molecules for further processing.


The picture above shows DNA (orange) being copied by a protein called RNA polymerase (pronounced po-LIM-er-ace) which in the picture is blue. The green is then the messenger RNA, so-called because there are several kinds of RNA and this is the one that comes right off the DNA. It may be modified later, but it eventually gets to other parts of the cell and is used to act as a template for protein production.


The RNA polymerase (blue in picture) is made up of amino acids in specific order. I have listed this order before but will do it again here. For the fruit fly, it's found on the Uniprot site at number A8JUY3:


10 20 30 40 50 60
MPKEQFRASA LNKKISHVQF GISGADEIQQ EALVRIISKN LYQAQRQPVP YGVLDRRMGI

70 80 90 100 110 120
STKDAMCETC GQGLNECIGH FGYLDLALPV FHIGHFRSTI NILQMICKVC AHVMLKPEDR

130 140 150 160 170 180
QLYEKKLHNP NFSYLGKKAL HVQMLAKAKK VTKCPHCGSP NGGVKKGPGL LKILHDPYKG

190 200 210 220 230 240
RKMDSLFTSN MNEMLRSTQT NRDLNSTLGN YSTAEELTPL MVLDLFEQIP QRDVALLGMC

250 260 270 280 290 300
SHDAHPKHLI VTRVFVPPAC IRPSVLSEVK AGTTEDDLTM KQSEILLIND VIQRHMATGG

310 320 330 340 350 360
KIELIHEDWD FLQLHVALYF HSEISGIPIN MAPKKTTRGI VQRLKGKQGR FRCNLSGKRV

370 380 390 400 410 420
DFSGRTVISP DPNLMINQVG VPVRVAKILT YPERVNPANI RHMRELVRNG PSMHPGANYV

430 440 450 460 470 480
QQRGSSFKKY LAYGNREKVA QELKCGDVVE RHLRDGDIVL FNRQPSLHKM SIMCHRAKVQ

490 500 510 520 530 540
PQRTFRFNEC ACTPYNADFD GDEMNLHLPQ TEEARAEALI LMGNQSNLVT PKNGEILIAA

550 560 570 580 590 600
TQDFITGGYL LTQKEVFLTK EEAMQLAACF LANEDSTMHI KLPPPALLKP RRLWTGKQMF

610 620 630 640 650 660
SLLMRPNDDS QVRLNMVNKG RNYTRNKDLC SNDSWIHIRN SELMCGVMDK ATMGSGTKQC

670 680 690 700 710 720
IFYLLLRDFG ESHATKAMWR LARNRGFSFG ISDVTPSKKL LQHKELLLNN GYAKCNEYIE

730 740 750 760 770 780
LLKAGTLQCQ PGCTPEETLE SVMLRELSAI REQAAKTCFA ELHPTNSALI MALSGSKGSN

790 800 810 820 830 840
INISQMIACV GQQAISGKRV PNGFENRALP HFERHSAIPA ARGFVQNSFY SGLTPTEFFF

850 860 870 880 890 900
HTMAGREGLV DTAVKTAETG YLQRRLVKCL EDLVVHYDGT VRNAVNEMVD TIYGGDGLDP

910 920 930 940 950 960
VSMETRNKPV DLVHQYDNLR AQHPQGKDRP LNAEEMSEAL ETLLRTPEFA EARDDFKLDV

970 980 990 1000 1010 1020
RNHINTVSKR IGQLQKRYEK CIDLCHQIEC LTTEQLLQFV RRINDRYNRA VTEPGTAVGA

1030 1040 1050 1060 1070 1080
IAAQSIGEPG TQMTLKTFHF AGVASMNITQ GVPRIVEIIN ATKTISTPII TAELENCHSM

1090 1100 1110 1120 1130 1140
EFARQVKARI EKTTLAELSS YVEVVCGPYS CYLAIGVDMA RIKLLGLHID LDTIVFSILK

1150 1160 1170 1180 1190 1200
SRMRVKPTQV EVVASQSRIV VRVEATRTST INAELARLAL SLQNVVVAGL PNINRAVIAV

1210 1220 1230 1240 1250 1260
DDARQPPTYK LCIEGYGLRD VIATYGVVGK RTRSNNICEI YQTLGIEAAR TIIMSEITEV

1270 1280 1290 1300 1310 1320
MEGHGMSVDW RHIMLLASQM TARGEVLGIT RHGLAKMRES VFNLASFEKT ADHLFDAAYY

1330 1340 1350 1360 1370
GQTDAINGVS ERIILGMPAC IGTGIFKLLQ QHEDKQVPPI EPTICSSLNL LPSKTT



And here on the right is one of the amino acids of the protein chain, L-Aspartic Acid. For every D abbreviation in the list above, this would be inserted. The letters stand for atoms. H=hydrogen, O=Oxygen, C=Carbon (understood to be at the corners of the connected lines) and N=nitrogen. The others are in the Wikipedia link to amino acids at right.





The picture of RNA polymerase at the top is not necessarily based exactly on the fuit fly, but the function is general throughout biological life. As you can see, there are 1376 amino acids in the fruit fly RNA polymerase. These are in specific order so the RNA polymerase molecule can do its own specific job. The number of amino acids in the bacteria E. coli is only slightly less with 1342. The 20 amino acids that are found in living cells make different kinds of chemical bonds. One of the connections of the bonds has to do with the spirial shape of the protein. Others affect the "folding" of the entire protein which gives it an over-all shape. So these amino acids have to connect in a certain way and be specific distances apart from each other to give the protein the shape that gives it the ability to function, among other considerations. This is why we can use mathematics to assess the probabilities of a protein being able to function. Not all combinations of amino acids would give the shape this needs. In fact, it's been estimated only 1 in 10^77 to about 1 in 10^63 will give a shape that works. 10^77 is a 1 with 77 zeroes after it, 10^63 a 1 with 63 zeroes after it. (See link to Stephen Meyer article at right for more details).

I believe that God created this world. My husband and I will be attending a Memorial Day service at our church's cemetery today in conjunction with the other Catholic churches of our area. Though I would believe in God whereever I lived, I am grateful for the sacrifices of the men & women of the armed forces that allow me to freely express my belief as I do.


Update: as of 2/22/2012, the number of amino acids for a fruitfly is listed at Uniprot as 1383.

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