BMB 401

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  1. describe what the phrase "semi-conservative DNA replication" means.
    one of each original strand is conserved in each progeny molecule
  2. describe what "semi-discontinuous" DNA replication means.
    the leading strand is replicated continuous and the lagging strand is replicated with okazaki fragments in a discontinuous fashion.
  3. what unwinds the double helix?
  4. what molecule compensates for DNA supercoiling?
    DNA gyrase
  5. when DNA pol I is described to catalyze 20 cycles of polymerization, what does this mean?
    this means that on average it will add 20 nucleotides to the growing molecule
  6. what is processivity
    processivity is the term that describes how well a polymerase synthesizes a DNA/RNA chain, add x amounts of bases
  7. what is the role of the 3' to 5' exonuclease of DNA pol I
    serves as a proofreading function to remove incorrect bases
  8. describe the process of nick translation
    occurs because of the 5'-nuclease acitivity working together with the polymerase to degrade the primer and fill in behind with bases to move to "nick" along
  9. why is DNA pol III holoenzyme considered the "real" DNA polymerase in E.coli?
    this is the real workhorse because it has a processivity of around 5 million bases
  10. what is the role of the Beta subunit of DNA polymerase III holoenzyme
    the beta dimer forms a ring around DNA to attach the core to do activity also called the beta clamp. could account for the huge processivity
  11. what are the differences between leading and lagging strand synthesis
    lagging strand synthesis requires repeated priming for okazaki fragments to be synthesized.
  12. what are okazaki fragments and their significance in semi-discontinuous strand synthesis
    they are pieces of synthesized DNA of the lagging strand that needed to be joined together during nick translation
  13. what is included in the A family of polymerases?
    polymerases involved in DNA repair in bacteria
  14. what is included in the B family of polymerases?
    polymerases involved in replication of the eukaryotic chromosome
  15. what is included in the C family of polymerases?
    polymerases involved in the replication of the bacterial chromosome
  16. what do the families X and Y include as far as polymerases?
    they contain polymerases that act in DNA repair pathways
  17. what does the RT family contain?
    this is the family that designates retrovirus polymerases
  18. what are the different phases of the cell cycle
    G1 phase, S phase where chromosomal duplication happens, G2 phase and mitosis
  19. what is a CDK
    a cyclin dependant kinase
  20. what does ORC stand for?
    origin recognition complex
  21. what activates replication?
    the actions of Cdc7-Dbf4 and S-CDK
  22. compared eukaryotic DNA polymerase delta to E coli DNA polymerase III holoenzyme in terms of subunit assemblies and their functions
    they are both the principal DNA replicases,
  23. what does the ORC help to form?
    a prereplication complex
  24. what proteins are recruited by the ORC after it binds the origen?
    Cdc6, Ctd1 and MCM proteins
  25. what is important, energy wise of the forming of the pre-RC?
    it is energy dependant
  26. what is geminin? and what is its function
    it is a molecule that inhibits replication by preventing the incorporation of MCM complexes into the pre-RC
  27. what is PCNA and what is its association with DNA synthesis?
    PCNA associates with the delta polymerase to assist with the high processivity, (is homologous with the beta sliding clamp)
  28. what is the function of telomerase and why is it important
    maintains telomere length by restoring telomeres at the 3' ends of chromosomes
  29. what is unusual about reverse transcriptase
    it transcribes the RNA template into a complementary cDNA strand to form an RNA DNA hybrid
  30. what is a mutation
    a change in nucleotides, can be due to a mistake intranscription
  31. what is the RecBCD complex's function?
    it initiates recombination has both helicase and nuclease activity
  32. what is important about energy with recombination?
    it is an ATP-dependent action
  33. how are different DNA adducts repaired
    • mismatch repair
    • base excision repair
    • nucleotide excision repair
  34. how does RecA protein act in DNA recombination
    it forms a nucleoprotein filament capable of strand invasion and homologous pairing
  35. what is a holliday junction
    the holliday junction is the point at strand invasion during recombination where the strands cross
  36. what proteins recognize the holliday junction and how do they act
    RuvA and RuvB recognize and bind to the holliday junction to help process it, A acts as a branch site and B acts as the supercoiling compensator
  37. what is genetic recombination of DNA
    it is the shuffling of genetic homologs within DNA
  38. why is recombination of DNA important
    it adds to genetic diversity
  39. what is a prion?
    a protein that acts as a genetic agent
  40. what is the functional importance of the classes of RNA, mRNA, tRNA and rRNA respectively
    • mRNA is the actual RNA that encodes for proteins
    • tRNA is the RNA molecule that transports bound nucleotides to be part of the chain
    • rRNA is the ribosomal RNA that assists with translation
  41. what is a primary transcript
    a primary transcript is a transcript that contains introns and exons
  42. what are the four stages in transcription?
    binding, initiation, elongation and termination
  43. what is an open promoter complex
    an open promoter complex is when the DNA is unwound and RNA polymerase is bound to the promoter
  44. what is a closed promoter complex
    when RNA polymerase is bound to a promoter and DNA is not unwound
  45. what consensus sequencs motifs are in a bacterial promoter Pribnow box (-10), and the -35 region
    pribnow box is rich in TA (TATAAT) to make it a nice area for unwinding due to weaker hydrgen binding forces and the -35 region has (TTGACA)
  46. describe the two mechanisms of chain termination in E. coli
    • Chain termination: with Rho termination factor, ATP-dependent helicase unwinds the DNA:RNA hybrid and releases RNA chain
    • intrinsic termination using stem-loop structure
  47. Alpha-amanitin is an octapeptide from Amanita phalloids and is poisonous. Why?
  48. what is an exon
    an exon is a sequence of the RNA that codes for a gene
  49. what is an intron
    an intron is an interrupting sequence
  50. what is the importance of alternative splicing
    it leads to one gene being able to code for many proteins
  51. what is an anit-codon
    part of a tRNA that reads the codon for amino acid placement
  52. what is a stop, or nonsense codon
    untranslatable codon to signal the stop of protein synthesis
  53. what are the four general features of the genetic code
    • the genetic code is triplet
    • it is degenerate
    • genetic code is universal
    • has no punctuation is read continuously
  54. what are the animo-acyl tRNA sythetases, and how do they recognize tRNAs
    they translate the genetic code, they recognize a tRNA by reading it through base pairing with its anti-codon loop
  55. what is the Shine-Delgarno sequence and what role does it play in prokaryotic translation
    is a purine rich segment that the ribosome binds to
  56. how does elongation occur, what factors are involved, and is energy consumed?
    the factors involved are elongation factors Tu and G GTP is consumed with these reactions
  57. what is the function of IF2, EF-Tu, and EF-G
    both initiation factors act to shuttle amino acids to be incorporated, and IF2 delivers tRNA
  58. how do termination release factors work
    they work to form a hydrolase to cleave the peptidyl chain from the tRNA carrier
  59. what is a polysome
    is a RNA molecule with many ribosomes attached and working
  60. why are streptomycin and tetra cyclin useful antibiotics
    block binding at the A site
  61. what is a chaperone
    chaperones are proteins that help other proteins fold
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BMB 401
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