PHRD5025 Lecture 13 - Nucleic Acid Metabolism & DNA Replication

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PHRD5025 Lecture 13 - Nucleic Acid Metabolism & DNA Replication
2013-11-17 23:43:53
Nucleic Acid Metabolism DNA Replication

Nucleic Acid Metabolism & DNA Replication
Show Answers:

  1. What type of bond links nucleotides through sugar groups?
    phosphodiester bond
  2. The 5’ end terminates in a ______group and the 3’ end terminates in a _______group.
    phosphate; hydroxyl
  3. Chargaff’s rules (4)
    • •The base composition of DNA generally
    • varies between species.
    • •DNA isolated from different tissues of the same organism have the same base composition.
    • •Base composition of DNA in a given species does not change with age, nutrition or environment.
    • •In all DNAs, regardless of species, the # of A=T and G=C (or # purines = # pyrimidines, A+G = T+C)
  4. classic characteristics of DNA structure from the Watson-Crick model (5)
    • - right handed double helix 
    • - has major/minor grooves
    • - hydrophilic backbone
    • - phosphate backbone is on outside of
    • helix
    • - hydrophobic bases are inside the helix
  5. How RNA is different from DNA (6)
    • Thymidine (T) is replaced by Uridine (U)
    • Pentose sugar is ribose
    • Single-stranded
    • complex tertiary structures
    • Shorter half-life
    • Shorter (in terms of length) than DNA
  6. 3 types of RNA
    • mRNA
    • tRNA
    • rRNA
  7. limiting factor in cell division
    nucleotide synthesis
  8. what Glutamine-PRPP amidotransferase is inhibited by (3)
  9. During negative feedback regulation of purine
    biosynthesis, the ___________ enzyme in the pathway is usually rate-limiting and the ___________.
    first; most regulated
  10. NMPs are converted to NDPs by ____ nucleoside _____ kinases.
    specific; monophosphate
  11. NDPs are converted to NTPs by _____ nucleoside _____ kinases.
    ubiquitous; diphosphate
  12. The cancer chemotherapeutic Gemcitabine is an irreversible inhibitor of _____. This enzyme helps to synthesize deoxyribonucleotides from ribonucleoside diphosphates.
    ribonucleotide reductase
  13. Chemotherapy drug used to inhibit Thymidylate Synthase?
  14. Chemotherapy drugs used to competitively inhibit Dihydrofolate Reductase?
    Methotrexate or Aminopterin

    (binds w/ 100X higher affinity than dihydrofolate)
  15. Purines are degraded by Xanthine Oxidase into
    uric acid
  16. Disease in which B and T lymphocytes do not fully develop.
    Severe Combined Immunodeficiency Disease (SCID)
  17. In Lesch-Nyhan Syndrome, what does the lack of HGPT ultimately result in?
    Gout-like tissue damage (due to increased uric acid production)
  18. Which DNA Polymerase has 5’ > 3’ exonuclease
    DNA Polymerase I
  19. 3 stages of DNA replication
    • initiation
    • elongation
    • termination
  20. Requires primer to start, helicase unwinds DNA,Topoisomerase II relieves helical tension, stage can be regulated.
  21. DNA Polymerases duplicate the lagging and leading strands.
  22. Termination sequence encountered and stops
    replication, Topoisomerase IV unlinks the two intertwined strands.
  23. only stage of DNA replication that is regulated
  24. _____________ relieves helical stress caused by unwinding of dsDNA during replication.
    topoisomerase II (DNA gyrase)
  25. Compared to prokaryotes, eukaryotes have DNA molecules which are (smaller / larger) and are (circular / not circular)
    larger; not circular
  26. DNA viruses such as Parvovirus, herpes virus pox viruses and HPV undergo _____ replication.
    classical semi-conservative
  27. Retroviruses involve the +RNA virus being reverse transcribed by _____ specifically known as RNA-dependent DNA polymerase, (RDDP). This  produces a RNA/DNA hybrid intermediate.
    viral reverse transcription (RT)
  28. _____ RNase activity removes the RNA strand while synthesizing a new DNA strand to produce _____.
    RT; dsDNA intermediate
  29. What must happen before “prodrugs” can become activated?
    they must first be phosphorylated
  30. 3 components of a nucleotide
    • nitrogenous base
    • pentose (ribose or deoxyribose)
    • phosphate
  31. nucleoside
    nucleotide without a phosphate
  32. connects purine/pyrimidine to pentose
    -glycosidic bond
  33. effect of cAMP as a secondary messenger
    • "fight or flight"
    • caffeine effects (inhibits phosphodiesterase)
  34. effect of cGMP as a secondary messenger
    • vasodilation
    • (Viagra inhibits cGMP PDE)
  35. part of DNA that is constant
    alternative pentose & phosphate backbone
  36. part of DNA that is variable
    base sequence
  37. what the 3' end of DNA terminates in
    hydroxyl group
  38. what the 5' end of DNA terminates in
    phosphate group
  39. orientation of 2 strands of DNA
  40. type of bonding between base pairs
    hydrogen bonding
  41. type of RNA that serves as an intermediate in gene expression
  42. type of RNA that serves as adapters in protein synthesis
  43. type of RNA that is an integral part of the structure of ribosomes that are involved in protein synthesis
  44. RNAs that have catalytic activity
  45. precursors for de novo nucleotide synthesis (4)
    • 1) amino acids
    • 2) ribose-5-phosphate
    • 3) CO2
    • 4) NH3
  46. when does nucleotide synthesis occur?
    during DNA replication
  47. nucleic acid purines
    adenine; guanine
  48. nucleic acid pyrimidines
    cytosine, thymine, uracil
  49. committed step in de novo purine biosynthesis
    PRPP -> 5-phospho--D-ribosylamine (by glutamine-PRPP amidotransferase)
  50. primary regulatory enzyme in de novo pyrimidine synthesis
    • aspartate transcarbamoylase (ATCase)
    • **1st step
  51. inhibits de novo pyrimidine synthesis
    CTP (end-product)
  52. energy requirement for purine synthesis
    6 NTPs
  53. energy requirement for pyrimidine synthesis
    0-3 ATPs
  54. how CTP is formed
    amination of UTP
  55. 2'-2' difluorodeoxycytidine (dFdC)
    • Gemcitabine
    • cancer chemotherapeutic
    • nucleoside analog prodrug
    • irreversible inhibitor of ribonucleotide reductase (RNR)
    • suicide inhibitor
  56. how dUMP is converted to dTMP
    methylation by thymidylate synthase
  57. result of pyrimidine degradation
    ammonia & succinyl-CoA (->CAC)
  58. result of purine degradation
    uric acid (by xanthine oxidase)
  59. xanthine oxidase inhibitor
  60. cause of Lesch-Nyhan Syndrome
    defect in purine salvage pathway leading to deficiency in HGPT
  61. when does mitochondrial DNA replicate?
    during cell division
  62. principle prokaryotic replication enzyme
    DNA Pol III
  63. cleanup and repair enzyme in prokaryotes
    DNA Pol I
  64. how leading strand begins during elongation (in prokaryotes)
    DNA primase adds RNA primer
  65. prokaryotic enzyme that separates catenated (interlinked circles) DNA
    Topoisomerase IV
  66. drug with selectivity for prokaryotic topoisomerase II and IV
  67. enzyme that links DNA fragments
    DNA ligase
  68. in eukaryotes, terminate replication and prevent premature shortening of chromosome ends
  69. eukaryotic polymerase that synthesizes Okazako fragments
    DNA Pol 
  70. eukaryotic polymerase involved in DNA repair
    DNA Pol 
  71. viruses with contain mRNA and can be immediately translated into proteins
    postive-strand RNA viruses
  72. viruses that must first be converted by RDRP contained within the virion
    negative strand RNA viruses
  73. viruses that utilize classical semi-conservative replication
    DNA viruses
  74. viruses that use RNA-dependent DNA polymerase (RDDP) to produce an RNA/DNA hybrid intermediate
  75. MOA of AZT against HIV
    inhibits reverse transcriptase (RDDP)