Genes

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Genes Chromosomes

• Chapter 24

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Central Dogma (p.906)

• DNA replicates ? more DNA for daughters
• (Genes of) DNA transcribed ? RNA
• Gene segment of DNA
• Encodes info to produce functl biol. product
• RNA translated ? protein

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(No Transcript)
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Genome

• Sum of all DNA
• Viruses (Table 24-1)
• Rel small amt DNA
• 5K to 182K base pairs (bps)
• One chromosome
• Chromosome packaged DNA
• Many circular

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Genome contd

• Bacterial DNA -- larger than viral
• E. coli -- 4.6 x 106 bps
• Both chromosomal and extrachromosomal
• Usually 1 chromosome/cell
• Extrachromosomal plasmid
• 103-105 bps
• Replicate
• Impt to antibiotic resistance
• Eukaryotes many chromosomes
• Single human cell DNA 2 m
• Must be efficiently packaged

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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 repln, transcrn

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Chromosomes contd

• Most gene products are proteins
• Made of aas in partic sequence
• Each aa encoded in DNA as 3 nucleotide seq along
  1 strand of dbl helix
• How many nucleotides (or bps) needed for prot of
  350 aas?

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Fig.24-2
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Euk Chromosomes Complex

• Proks usually only 1 cy of each gene (but
  exceptions)
• Euks (ex mouse) 30 repetitive
• Junk?
• Non-trascribed seqs
• Centromeres impt during cell division (24-3)
• Telomeres help stabilize DNA
• Introns intervening seqs (24-4)
• Function unclear
• May be longer than coding seqs ( exons)

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Fig.24-3
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Fig.24-4
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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 repln, transcrn (Fig.24-11)
• Helix must be relaxed so it can open, expose bps
• Must be able to unwind from supercoiling

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Fig.24-9
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Fig.24-10
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Fig.24-11
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Fig.24-13
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Supercoiling contd

• Topoisomerases
• Enzs found in bacteria, euks
• 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

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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 assocd

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Fig.24-7
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1st Level Pakaging in Euks Is Around Histones

• DNA bound tightly to histones (24-24)

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Histones contd

• Basic prots
• About 50 of chromosomal matl
• 5 types all w/ many -charged aas (Table 24-3)
• Differ in size, amt /- charged aas
• What aas are charged?
• Why might charged prot be assocd w/ DNA helix?
• 1o structures well conserved across species

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Histones contd

• Must remove 1 helical turn in DNA to wind around
  histone (24-25)
• Topoisomerases impt

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Histones contd

• Histones bind _at_ specific locations on DNA (24-26)
• Most contact between DNA/histones AT-rich areas

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Nucleosome

• Histone w/ DNA wrapped around it
• Yields 7x compaction of DNA
• Core 8 histones (2 copies of 4 diff histone
  prots)
• 140 bp length of DNA wraps around core
• Linker region -- 60 bps extend to next
  nucleosome
• May be another histone prot sits at outside
• Stabilizes

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Fig.24-24
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Chromatin

• Repeating units of nucleosomes (24-23)
• Beads on a string
• Flexibly jointed chain

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30 nm Fiber

• Further nucleosome packing (24-27)
• Yields 100x compaction
• Some nucleosomes not incd into tight structure

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Rosettes

• Fiber loops around nuclear scaffold (24-29)
• Proteins topoisomerases incorporated
• 75K bps per loop
• 6 loops per rosette 450K bps/ rosette
• Further coiling, compaction ? ? 10,000X
  compaction total (24-30)

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Fig.24-29
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Fig.24-30
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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

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Semiconservative Repn-contd

• DNA repln ? daughter cell w/ own helix (25-2)
• 1 strand is parental (served as template)
• 2nd strand is newly synthd

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Definitions

• Template
• DNA strand providing precise info for synth
  complementary strand
• parental strand during repln
• Origin
• Unique point on DNA helix (strand) _at_ which repln
  begins
• Replication Fork
• Site of unwinding of parental strand and synth of
  daughter strand
• NOTE Unwinding of helix is crucial to repln
  success

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Definitions contd

• Replication Fork contd
• Bidirectional repln (25-3)
• 2 repln forks simultaneously synth daughter
  strands

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At the Replication Fork

• Both parental strands serve as templates
• Simultaneous synth of daughter cell dbl helices
• Expected
• Helix unwinds ? repln fork
• Get 2 free ends
• 1 end 5 PO4, 1 end 3 PO4
• REMEMBER paired strands of helix are
  antiparallel

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At the Repln Fork contd

• Expected -- contd
• Repln of each strand at end of parent
• One strand will replicate 5 ? 3
• Direction of active repln 5 ? 3
• Happens _at_ parent strand w/ 3 end
• Yields 2nd antiparallel dbl helix
• One strand will replicate 3 ? 5
• Direction of active repln 3 ? 5
• Happens _at_ parent strand w/ 5 end
• Yields antiparallel dbl helix

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At the Repln Fork contd

• But, experl evidence
• Showed repln ALWAYS 5 ? 3
• Easy to envision at parental strand w/ 3 end
• What happens at other parental strand??

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Okazaki Fragments

• Discovered by Dr. Okazaki
• Found near repln fork
• Small segments of daughter strand DNA synthd 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 repln fork)

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Okazaki Fragmentscontd

• Called lagging strand
• Takes longer to synth fragments join them
• Other parental strand, w/ continuous synth,
  called leading strand
• As repln proceeds, fragments are joined
  enzymatically ? complete daughter strand
• Overall, repln on both strands happens in 5 ?
  3 direction (w/ respect to daughter)

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Fig.25-4
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Okazaki Fragmentscontd

• Dont be confused w/ bi-directional repln
• Bidirectional refers to gt1 repln fork initiating
  repll simultaneously
• At each fork, repln takes place along both
  strands
• At each fork, repln in 5 ? 3 direction ONLY
  along each strand

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Enzs 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