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Genes & Chromosomes

Genes & Chromosomes. Chapter 24. 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. Genome. Sum of all DNA Viruses (Table 24-1)

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Genes & Chromosomes

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  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

  3. 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

  4. Genome – cont’d • 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 • Eukaryotes – many chromosomes • Single human cell DNA ~ 2 m • Must be efficiently packaged

  5. 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

  6. 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?

  7. Fig.24-2

  8. 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)

  9. Fig.24-3

  10. Fig.24-4

  11. 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

  12. Fig.24-9

  13. Fig.24-10

  14. Fig.24-11

  15. Fig.24-13

  16. 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

  17. 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

  18. Fig.24-7

  19. 1st Level Pakaging in Euk’s Is Around Histones • DNA bound tightly to histones (24-24)

  20. 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? • 1o structures well conserved across species

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

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

  23. 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

  24. Fig.24-24

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

  26. 30 nm Fiber • Further nucleosome packing (24-27) • Yields ~100x compaction • Some nucleosomes not inc’d into tight structure

  27. 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)

  28. Fig.24-29

  29. Fig.24-30

  30. 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

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

  32. 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

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

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

  35. 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 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

  36. 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??

  37. 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)

  38. 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)

  39. Fig.25-4

  40. 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

  41. 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

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