Genetics Chapter 11

  1. important structural features
    • double helix
    • nucleotides
    • four bases
    • hydrogen bonding between bases
    • A-T & C-G
    • antiparallel alignment
  2. semi-conservative transcription
    one strand is original mother helix and the other strand is the daughter 
  3. bacterial DNA replication
    • signle origin of replication
    • synthesis of new daughter strand is bidirectional
  4. OriC
    origin of replication in bacterial chromosomes
  5. three types of DNA sequences in OriC
    • AT-rich region 
    • DnaA box (4-5)
    • GTAC methylation site
  6. the 5 DnaA box sequences serve as a binding site for DnaA protein
    • DnaA proteins bind to all 4-5 DnaA boxes 
    • stimulates the cooperative binding of an additional 20-40 DnaA proteins to form a large complex
  7. witht the aid of ____ and ____, the DNA bends around the complex
    • HU
    • IHF
  8. DnaA protein
    • the tension caused from the wrapping of DNA around the DnaA complex causes the AT-rich region to separate
    • after DnaA and DnaC proteins recruit DNA helicase to bind to site and being strand separation withing the OriC
  9. replication
    • helicase opens helix
    • DNA gryase alleviates supercoiling
    • polymerase III synthesizes leading strand
    • primase synthesizes RNA primer
    • polymerase III elongates primer; prodcues okazaki fragments
    • polymerase I excises RNA primer; fills gaps
    • DNA ligase links Okazaki fragments to form continuous strand
  10. DNA polymerase
    covalently attaches nucleotides in daughter strand
  11. E. coli has 5 distinct polymerases
    • pol I and pol III: normal DNA replication
    • pol II, IV, and V: DNA repair and replication of damaged DNA
  12. DNA polymerase I
    • single subunit
    • fills in small regions wehre RNA primers were located
  13. DNA polymerase III
    • 10 subunits
    • responsible for most DNA replication 
  14. holoenzyme
    enxyme that has many subunits to it
  15. two polymerase oddities
    • unable to initiate DNA synthesis by linking together two individual nucleotides (primase needed)
    • works only in 5' to 3' direction (no bidirectional synthesis)
  16. Okazaki fragments are on the _____ strand
  17. completion of okazaki fragments
    • RNA primers removed by DNA polymerase I (5'-3')
    • polymerase I fills in this region with newly synthesized DNA
    • DNA ligase covalently bonds to last nucleotide made by polymerase I and the first nucleotide in the next new DNA fragment
  18. DNA polymerase III is a ______ enzyme
  19. termination of sequences
    • opposite OriC are termination sequences (ter sequences)
    • T1 ter and T2 ter sequences work alternatively 
    • DNA ligase covalently links the two daughter strands, creating two circular, double stranded molecules
    • topoisomerases break DNA strands and then rejoin them after strands have become unlocked
  20. T1 and T2 ter sequences
    • T1- allows advncement of clockwise-moving forks, but prevents the movement of counter clockwise-moving forks
    • T2- permits the advancement of counter clockwise-moving forks, but prevents the advancement of clockwise-moving forks
  21. primosome
    DNA helicase and primase
  22. replisome
    primosome and two DNA polymerase holoenzymes
  23. dimeric DNA polymerase
    term used to describe two DNA polymerase holoenzymes that move as a unit toward the replication fork
  24. why does DNA replication exhibit a high degree of fidelity?
    • hydroen bonds between correct partners are more stable
    • induced fit phenomenon 
    • enzymatic removal of mismatch at 3' end of newly made strand (exonucleases)
  25. induced fit phenomenon
    polymerase less likely to catalyze bonds between nucleotides if there are mismatched bases
  26. subunit epsilon comes with subunits alpha and theta to do what?
    • identify and remove mismatched nucleotides
    • occurs in 3' to 5' direction
    • reduces error rate to 1 in 100 million
  27. under what optimum conditions can E. coli reproduce?
    • replication must be coordinated with cell division
    • mechanisms must regulate initiation of replication
  28. mechanism 1 of initiation
    • insufficient amount of DnaA peoteins to bind to all the DnaA boxes within the OriC 
    • prevents premature replication
  29. mechanism 2 of initiation
    • involves the temporary lack of adenine methylation in the GATC sites within OriC 
    • enzyme DAM (DNA adenine methyltransferase) methylates all the GATC sites in the newly replicated strands of DNA
    • replication does not occur until after it has become fully methylated
    • methyl group on parent strand but not daughter strand (hemimethylated)
  30. eukaryotic DNA replication
    • not as well understoood
    • common enzymes with prokaryotic replication 
    • appears to be substantially more complex 
  31. unique features of eukaryotic replication
    • multiple origins of replication
    • ARS elements (Autonomously Replicating Sequences)
    • origin of recognition complex (ORC)
  32. multiple origins of replication
    • occurs bidirectionally from many origins of replication
    • during S phase
    • forks eventually meet and complete process 
  33. ARS elements
    • Autonomously Replicating Sequences
    • ~50 base pairs
    • the high percentage of A and T bases in this sequence
    • consensus sequence ATTTAT (A or G) TTTA
    • ^ where replication bubble begins
  34. origin of replicatin complex (ORC)
    • 6 subunit protein complex that acts as the initiator of eukaryotic replication when it binds to the ARS in the G1 phase 
    • licensing factors bind to MCM
    • MCM helicase (minichromosome maintenence) must coat DNA for replication to begin
  35. removal of RNA primers- flap endonuclease)
    • DNA polymerase delta generates flap
    • flap endonuclease cuts the flap off
  36. synthesis of more histon proteins
    • needed for DNA replication
    • occurs in the S phase of cell cycle
    • histones are assembled into octamer structures and associate with newly made DNA very near the replication fork
    • each daughter strand contains a random mixture of new and old octamers
  37. telomere
    complex of telomeric sequences within the DNA and the special proteins that bind to it
  38. telomeric region
    • moderately repetitive tandem arraw with a 3' overhauling region (12-16 nucleotides)
    • many G's and T's
    • are a problem when it comes to replication because they have more hydrogen bonds
    • incomplete ends because the polymerase will not connect two nucleotides
  39. how to fix incomplete ends by polymerization
    • telomerase recognizes teomeric sequences at the ends of chromosomes and synthesize additional repeats of telemetric sequences
    • contains both proteins and RNA 
    • RNA sequence functions as a template allowing the attachment of a series of 6-nucleotide sequences
  40. telomerase and its protein component
    • ribonucleoprotein
    • a single RNA molecule is called TERC (telomeric RNA component)
    • its protein comoponent is TERT (telomere reverse transcriptase)
  41. telomerase is a ____ ______
    • reverse transcriptase 
    • sythesizes DNA from an RNA template 
    • only found in a few somatic cells
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Genetics Chapter 11
Genetics Chapter 11 Dr. Troy Bry