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Stanford CS 262 - Lecture Notes

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CS262: Computational Genomics J anuar y 14, 20 0 8 pag e 1 Lecture-2 : B i o l o g y I n tro d ucti o n G e o r g e A s i m e no s Scribe: Dipankar Acharya 1 B i o l o g y T he w o rd bio l o g y co m es f ro m the G reek w o rd β ί ο ς , w hich m eans l if e. T he f o l l o w ing are so m e o f the im po rtant m il esto nes in bio l o g y: • 1 6 8 3 – d isco v ery o f b a c t e r i a • 1 8 58 – D a r w i n’ s natu ral sel ectio n • 1 8 6 5 – M e nd e l ’ s l aw s • 1 9 53 – d o u b l e h e l i x m o d el o f DN A su g g ested by Watso n-C rick • 1 9 55 – d isco v ery o f DN A and R N A p o l y m e r a s e • 1 9 7 8 – seq u encing o f f irst g eno m e (5kb v iru s) • 1 9 8 3 – inv entio n o f P C R • 1 9 9 0 – d isco v ery o f R N A i • 20 0 0 – hu m an g eno m e (d raf t) Disco v ery o f R N Ai is the m o st im po rtant ev ent o f the 9 0 ' s and this is w hat Stanf o rd g o t N o bel P riz e f o r l ast year. So u rces o f bio l o g y inf o rm atio n: 1 . Web: a. http:/ / w w w .w ikiped ia.o rg / : K itchen sink o f al l inf o rm atio n, v ery u p-to -d ate b. http:/ / bio l o g y-pag es.inf o / : J o hn K im bal l ' s bio l o g y pag es, no t so u p-to -d ate, bu t v ery w el l -w ritten 2. G eo rg e' s f av o rite bio l o g y m eeting s are at C o l d Spring H arbo r: a. C SH L B io l o g y o f G eno m es b. C SH L G eno m e I nf o rm atics 3. C o nv ersatio n w ith bio l o g ists Abo u t B io l o g y (the su bj ect): • We stil l d o n’ t kno w a l o t abo u t bio l o g y: there is stil l a l o t to u nd erstand , secrets to u nco v er. • I t is real l y d if f erent f ro m C o m pu ter Science: the ex perim ental d ata are no n-d iscrete and hav e erro rs m o st o f the tim e. o We cant real l y tal k abo u t if a m o l ecu l e is m ad e o r no t: m o st o f ten it is no t a yes/ no q u estio n. Al m o st al w ays w e f ind f ind w hatev er w e are l o o king f o r. We can tal k o f the co ncentratio n: at w hat l ev el w e f ind it.CS262: Computational Genomics J anuar y 14, 20 0 8 pag e 2 o B ecau se o f erro rs, w e o f ten see big d if f erence in resu l ts w hen w e repeat an ex perim ent. • I t is hard to m o d el : f o r ev ery ru l e there is an ex ceptio n. P ro babl y f o r this ru l e as w el l ☺ 2 C e l l Figure 1 C el l A cel l is encl o sed in a pl asm a-m em brane and co ntains a nu cl eu s. T he m aterial betw een the nu cl eu s and the pl asm a-m em brane is cal l ed cyto pl asm . T here is DN A in the nu cl eu s and ano ther stru ctu re cal l ed the m ito cho nd rio n. T here are ~ 1 0 ^ 1 4 cel l s in the hu m an bo d y.CS262: Computational Genomics J anuar y 14, 20 0 8 pag e 3 3 C h r o m o s o m e s a n d D N A Figure 2 C h ro m o s o m e C hro m o so m es co ntain DN A w hich ho l d s the inf o rm atio n abo u t ho w o rg anism s are m ad e. At the m o l ecu l ar l ev el , DN A is a d o u bl e-hel ix . T he rig ht hand sid e o f F ig -2 sho w s the DN A d o u bl e-hel ix being repl icated . H isto nes are pro tein m o l ecu l es that pack DN A into a m o re ro bu st stru ctu re. F o u r histo ne m o l ecu l es, H 2A, H 2B , H 3 and H 4 (sho w n as bl ack spheres in F ig -2), f o rm a d isk-l ike stru ctu re, cal l ed nu cl eo so m e, aro u nd w hich DN A is w rapped . Ano ther histo ne, H 1 , packs these ev en m o re tig htl y. T hese are f u rther packed into chro m atin, w hich is a 3-d im ensio nal stru ctu re o f the packed nu cl eo so m es. C hro m atins (packed stru ctu re o f the chro m o so m e) f o rm z ig -z ag strand s o f chro m o so m es v isibl e in a m icro sco pe. I n the m id d l e …


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Stanford CS 262 - Lecture Notes

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