1. Genes & Chromosomes Chapter 24

2. Central Dogma (p.906) DNA replicates  more DNA for daughters (Genes of) DNA transcribed  RNA –Gene = segment of DNA –Encodes info to produce funct’l biol. product RNA translated  protein

4. Genome Sum of all DNA Viruses (Table 24-1) –Rel small amt DNA 5K to 182K base pairs (bp’s) –One chromosome Chromosome = “packaged” DNA –Many circular

5. Genome – cont’d Bacterial DNA -- larger than viral –E. coli -- ~4.6 x 10 6 bp’s –Both chromosomal and extrachromosomal Usually 1 chromosome/cell Extrachromosomal = plasmid –10 3 -10 5 bp’s –Replicate –Impt to antibiotic resistance Eukaryotes – many chromosomes –Single human cell DNA ~ 2 m Must be efficiently packaged

6. Chromosomes Each has single, duplex DNA helix Contains many genes –Historical: One gene = one enzyme –Now: One gene = one polypeptide –Some genes code for tRNAs, rRNAs –Some DNA sequences (“genes”) = recognition sites for beginning/ending repl’n, transcr’n

7. Chromosomes – cont’d Most gene products are “proteins” –Made of aa’s in partic sequence –Each aa encoded in DNA as 3 nucleotide seq along 1 strand of dbl helix –How many nucleotides (or bp’s) needed for prot of 350 aa’s?

8. Fig.24-2

9. Euk Chromosomes Complex Prok’s – usually only 1 cy of each gene (but exceptions) Euk’s (ex: mouse): ~30% repetitive –“Junk”? –Non-trascribed seq’s Centromeres – impt during cell division (24-3) Telomeres – help stabilize DNA Introns – “intervening” seq’s (24-4) –Function unclear –May be longer than coding seq’s (= exons)

10. Fig.24-3

11. Fig.24-4

12. Supercoiling DNA helix is coil –Relaxed coil is not bent –BUT can coil upon itself  supercoil (Fig.24- 9,10) Occur due to packing; constraints; tension Superhelical turn = crossover Impt to repl’n, transcr’n (Fig.24-11) –Helix must be relaxed so it can open, expose bp’s –Must be able to unwind from supercoiling

13. Fig.24-9

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17. Supercoiling – cont’d Topoisomerases –Enz’s found in bacteria, euk’s –Cleave phosphodiester bonds in 1 or both strands Where are these impt in nucleic acids? Type I – cleaves 1 strand Type II – cleaves both strands –After cleavage, rewind DNA + reform phosphodiester bond(s) –Result – supercoil removed

18. DNA Packaging Chromosomes = packaged DNA –Common euk “X” “Y” type structures –Comprised of single, uninterrupted mol of DNA –Table 24-2 – Chromosome # Chromatin = chromosomal material –Equiv amts DNA + protein –Some RNA also assoc’d

19. Fig.24-7

20. 1 st Level Pakaging in Euk’s Is Around Histones DNA bound tightly to histones (24-24)

21. Histones – cont’d Basic prot’s About 50% of chromosomal mat’l 5 types all w/ many +-charged aa’s (Table 24-3) –Differ in size, amt +/- charged aa’s What aa’s are + charged? Why might + charged prot be assoc’d w/ DNA helix? 1 o structures well conserved across species

22. Histones – cont’d Must remove 1 helical turn in DNA to wind around histone (24-25) –Topoisomerases impt

23. Histones – cont’d Histones bind @ specific locations on DNA (24-26) –Most contact between DNA/histones: AT-rich areas

24. Nucleosome Histone w/ DNA wrapped around it –Yields 7x compaction of DNA Core = 8 histones (2 copies of 4 diff histone prot’s) ~140 bp length of DNA wraps around core Linker region -- ~ 60 bp’s extend to next nucleosome May be another histone prot “sits” at outside –Stabilizes

25. Fig.24-24

26. Chromatin Repeating units of nucleosomes (24-23) “Beads on a string” –Flexibly jointed chain

27. 30 nm Fiber Further nucleosome packing (24-27) Yields ~100x compaction Some nucleosomes not inc’d into tight structure

28. Rosettes Fiber loops around nuclear scaffold (24-29) –Proteins + topoisomerases incorporated ~75K bp’s per loop ~6 loops per rosette = ~ 450K bp’s/ rosette Further coiling, compaction   10,000X compaction total (24-30)

29. Fig.24-29

30. Fig.24-30

31. Semiconservative Replication 2 DNA strands/helix Nucleotide seq of 1 strand automatically specifies seq of complementary strand –Base pairing rule: A w/ T and G w/ C ONLY in healthy helix –Each strand can serve as template for its partner “Semiconservative” –Semi – partly –Conserved parent strand

32. Semiconservative Rep’n-cont’d DNA repl’n  daughter cell w/ own helix (25-2) –1 strand is parental (served as template) –2 nd strand is newly synth’d

33. Definitions Template –DNA strand providing precise info for synth complementary strand –= parental strand during repl’n Origin –Unique point on DNA helix (strand) @ which repl’n begins Replication Fork –Site of unwinding of parental strand and synth of daughter strand NOTE: Unwinding of helix is crucial to repl’n success

34. Definitions – cont’d Replication Fork – cont’d –Bidirectional repl’n (25-3) 2 repl’n forks simultaneously synth daughter strands

35. At the Replication Fork Both parental strands serve as templates –Simultaneous synth of daughter cell dbl helices Expected –Helix unwinds  repl’n fork –Get 2 free ends 1 end 5’ –PO 4, 1 end 3’ –PO 4 REMEMBER: paired strands of helix are antiparallel

36. At the Repl’n Fork – cont’d Expected -- cont’d –Repl’n of each strand at end of parent One strand will replicate 5’  3’ –Direction of active repl’n 5’  3’ –Happens @ parent strand w/ 3’ end –Yields 2 nd antiparallel dbl helix One strand will replicate 3’  5’ –Direction of active repl’n 3’  5’ –Happens @ parent strand w/ 5’ end –Yields antiparallel dbl helix

37. At the Repl’n Fork – cont’d But, exper’l evidence –Showed repl’n ALWAYS 5’  3’ Easy to envision at parental strand w/ 3’ end What happens at other parental strand??

38. Okazaki Fragments Discovered by Dr. Okazaki –Found near repl’n fork Small segments of daughter strand DNA synth’d 5’  3’ –Along parental template strand w/ 5’ end Get series of small DNA segments/fragments –So synthesis along this strand takes place in opposite direction of overall replication (or of unwinding of repl’n fork)

39. Okazaki Fragments—cont’d Called “lagging strand” –Takes longer to synth fragments + join them Other parental strand, w/ continuous synth, called “leading strand” As repl’n proceeds, fragments are joined enzymatically  complete daughter strand Overall, repl’n on both strands happens in 5’  3’ direction (w/ respect to daughter)

40. Fig.25-4

41. Okazaki Fragments—cont’d Don’t be confused w/ bi-directional repl’n –Bidirectional refers to >1 repl’n fork initiating repl’l simultaneously –At each fork, repl’n takes place along both strands –At each fork, repl’n in 5’  3’ direction ONLY along each strand

42. Enz’s that Degrade DNA Exonucleases – degrade DNA from one end of molecule –Some digest one strand 3’  5’ –Some digest in 5’  3’ direction Endonucleases – degrade DNA from any site