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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) – Rel small amt DNA • 5K to 182K base pairs (bp’s) – One chromosome • Chromosome = “packaged” DNA – Many circular 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 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 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? Fig.24-2 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) Fig.24-3 Fig.24-4 Supercoiling • DNA helix is coil – Relaxed coil is not bent – BUT can coil upon itself supercoil (Fig.249,10) • 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 Fig.24-9 Fig.24-10 Fig.24-11 Fig.24-13 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 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 Fig.24-7 1st Level Pakaging in Euk’s Is Around Histones • DNA bound tightly to histones (24-24) 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 Histones – cont’d • Must remove 1 helical turn in DNA to wind around histone (24-25) – Topoisomerases impt Histones – cont’d • Histones bind @ specific locations on DNA (24-26) – Most contact between DNA/histones: AT-rich areas 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 Fig.24-24 Chromatin • Repeating units of nucleosomes (24-23) • “Beads on a string” – Flexibly jointed chain 30 nm Fiber • Further nucleosome packing (24-27) • Yields ~100x compaction • Some nucleosomes not inc’d into tight structure 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) Fig.24-29 Fig.24-30 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 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 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 Definitions – cont’d • Replication Fork – cont’d – Bidirectional repl’n (25-3) • 2 repl’n forks simultaneously synth daughter strands 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 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 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?? 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) 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) Fig.25-4 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 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