Understanding Genes, Chromosomes, and the Central Dogma of Molecular Biology

1. Genes & Chromosomes Part III, Chapters 24, 25

2. Central Dogma • DNA replicates  more DNA for daughters • (Gene w/in) DNA transcribed  RNA • Gene = segment of DNA • Encodes info to produce funct’l biol product • RNA translated  protein

4. Genome • Sum of all DNA • Genes + noncoding regions • Chromosomes • Each has single, duplex DNA helix • Contain 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

5. 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?

7. Prokaryotic DNA • Viruses • Rel small amt DNA • 5K to 170K base pairs (bp’s) • One chromosome • Chromosome = “packaged” DNA • Many circular

8. Bacterial DNA -- larger than viral • E. coli -- ~4.6 x 106 bp’s • Both chromosomal and extrachromosomal • Usually 1 chromosome/cell • Extrachromosomal = plasmid • 103-105 bp’s • Replicate • Impt to antibiotic resistance

10. Chromosomes Complex Packaging reduces E.coli DNA 850x

12. Eukaryotic DNA • Many chromosomes • Single human cell DNA ~ 2 m • Must be efficiently packaged

13. Euk Chromosomes • Prok’s – usually only 1 cy of each gene (but exceptions) • Euk’s (ex: human) • Book: coding region (genes codinng for prot’s) ~ 1.5% total human genome • Exons

14. Euk’s (ex: mouse): ~30% repetitive • “Junk”? • Non-trascribed seq’s • Centromeres – impt during cell division • Telomeres – help stabilize DNA • Introns – “intervening” seq’s • Function unclear • May be longer than coding seq’s (= exons)

17. Supercoiling • DNA helix is coil • Relaxed coil is not bent • BUT can coil upon itself  supercoil • Due to packing; constraints; tension • Superhelical turn = crossover • Impt to repl’n, transcr’n • Helix must relax so can open, expose bp’s • Must unwind from supercoiling

22. Topoisomerases • Enz’s in bacteria, euk’s • Cleave phosphodiester bonds in 1/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

23. Type I

26. Type II

27. DNA Packaging • Chromosomes = packaged DNA • Common euk “X” “Y” type structures • Each = single, uninterrupted mol DNA • Chromatin = chromosomal material • Equiv amts DNA + protein • Some RNA also assoc’d

28. 1st Level Pakaging in Euk’s Around Histones • DNA bound tightly to histones

29. Histones • Basic prot’s • About 50% chromosomal mat’l • 5 types • All w/ many +-charged aa’s • Differ in size, amt +/- charged aa’s • What aa’s are + charged? • Why might + charged prot be assoc’d w/ DNA helix? • 1o structures well conserved across species

32. Must remove 1 helical turn in DNA to wind around histone • Topoisomerases impt

33. Histones bind @ specific locations on DNA • Mostly AT-rich areas

34. Nucleosome • Histone wrapped w/ DNA •  7x compaction of DNA • Core = 8 histones (2 copies of 4 diff histone prot’s) • ~140 bp DNA wraps around core • Linker region -- ~ 60 bp’s extend to next nucleosome • Another histone prot may“sit” outside • Stabilizes

36. Chromatin • Further-structured chromosomal mat’l • Repeating units of nucleosomes • “Beads on a string” • Flexibly jointed chain

37. 30 nm Fiber • Further nucleosome packing • ~100x compaction • Some nucleosomes not inc’d into tight structure

38. Rosettes • Fiber loops around nuclear scaffold • Proteins + topoisomerases incorporated • 20-100K bp’s per loop • Related genes in loop • Book ex: Drosophila loop w/ complete set genes coding for histones • ~6 loops per rosette = ~ 450K bp’s/ rosette • Further coiling, compaction  10,000X compaction total

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

42. DNA repl’n  daughter cell w/ own helix • 1 strand is parental (served as template) • 2nd strand is newly synth’d

43. Definitions • Template • DNA strand w/ 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: helix unwinding crucial to repl’n success

44. Repl’n Fork – cont’d • Bidirectional repl’n • 2 repl’n forks simultaneously synth daughter strands

46. At 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’ –PO4, 1 end 3’ –PO4 • REMEMBER: paired strands of helix antiparallel

47. Expected -- cont’d • Repl’n 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 2nd 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

48. But, exper’l evidence: • Repl’n ALWAYS 5’  3’ • Can envision at parental strand w/ 3’ end • What happens at other parental strand??

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

50. Called “lagging strand” • Takes longer to synth fragments + join them • Other parental strand, w/ continuous synth = “leading strand” • W/ repl’n, fragments joined enzymatically  complete daughter strand • Overall, repl’n on both strands occurs in 5’  3’ direction (w/ respect to daughter)