Chapter 5 CMB

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Chapter 5 CMB
2010-10-19 18:36:05
Cellular molecular biology

Chapter 5
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  1. DNA polymerase synthesizes DNA in the __ to __ direction.
    5' to 3'
  2. A incoming _______ ________ is added one by one to the DNA strand growing 5' - 3'. The 3' end contains an exposed ____ group, and the 5' end contains the exposed ___ group.
    deoxyribonucleoside triphosphate; 3'-OH; 5'-triphospate
  3. Mutation rates are extremely low -
    only ~_ nucleotide change per ___ nucleotides each time DNA is replicated.
    ~1: 109
  4. There are _ proofreading mechanisms in DNA replication. Name them.
    • 1) DNA polymerase checks the exact base pair geometry before it catalyzes the addition of a nucleotide to the growing DNA chain.
    • 2) Exonucleolytic Proofreading provided by another catalytic site on the DNA polymerase called a 3'-to-5' proofreading exonuclease. SELF-CORRECTING enzyme
    • 3) Stand-directed mismatch repair; detects distortion in the double helix caused by mismatches base pairs
    • -recognizes which is the template strand to remove a mismatched nucleotide
  5. a new ___ primer synthesized by DNA primase is added to prime the DNA for replication in the __ to __ direction. The only primer is eventually replaced by _____ polymerase in _____ species. However in Eukaryotic cells a special ____ ____ enzyme replaces the old ____
    RNA: 5'-3' direction; DNA repair enzyme; RNA
  6. To seperate DNA strands the enzyme DNA ____ binds to the DNA to split it using ____ _____ as an energy source to break the hydrogen bonds.
    Helicase; ATP hydrolysis.
  7. ____ straighten the region on DNA chain for DNA polymerase to synthesize. If they were absent the DNA template woulf form short base-paired _____
    SSB single strand binding proteins ; hairpins. Makes it difficult for DNA polymerase to slide down the template smoothly.
  8. How does the DNA polymerase remain attached to the template strand?
    A sliding clamp + clamp loader utilize energy (ATP) to load and clamp DNA polymerase to the template for synthesis . The clamp loader dissociates as the clamp + polymerase synthesize in the 5'-3' direction.
  9. In Bacteria, 2 enzymes ; DNA primase and DNA helicase link to form _____
  10. This enzyme releases torsional strain from unwinding DNA. Describe how it works. Where does it bind?
    Topoisomerase. Covelently attaches to DAN phosphate, breaking a phosphodiester linkage in one DNA strand. It binds downstream from the replication fork.
  11. When topoisomerase breaks a phosphodiester bond to relieve torsion tension, how is the DNA rebonded?
    • The original phosphodiester bond energy is stored in the phosphotyrosine linkage, making the reaction reversible.
    • spontaneous re-formation of the phosphodiester bond regenerates both DNA helix and the DNA topoisomerase.
  12. On the DNA strand, a exposed _____ group is found on the 5' end while an exposed ___ group is found on the 3' end.
    Phosphate on 5' end and OH group on the 3`end
  13. A doubled-ring nucleotide base consiting of Adenosine and Guanine
  14. A single-ring nucleotide base consisting of cytosine, uracil, and thymine
  15. Okazaki fragments are ___ np long in prokaryotes, and ____ long in eukaryotes
    • 1000-2000 np long in prokaryotes
    • 100-200 np long in eukaryotes
  16. True/false: DNA synthesis is driven by a large favourable energy-free change
    True. Caused by the release of pyrophosphate via hydrolysis of A-triphosphate
  17. the ____ nucleotide has greater ____ for DNA polymerase then does the ______ nucleotide; makes the correct pairing more energetically favourable
    correct; affinity; incorrect
  18. ____ does not need a self-correcting mechanism
  19. the catalytic site for exonucleolytic removal is in the ___ of DNA polymerase
  20. exonucleolytic proofreading is in the ___ to ___ direction
  21. ___ ____ synthesizes RNA primers on the lagging strand
    DNA primase
  22. An enzyme that joins the 3' end of the newer (formerly RNA primer) DNA fragment to the 5' end of the previous DNA fragment
    DNA ligase catalyzes a covalent link
  23. An advantage to using a RNA primer of DNA is;
    • ·
    • : the ribonucleotides in the primer
    • automatically mark these sequences as “suspect copy” to be efficiently removed
    • and replaced. A self-correcting enzyme cannot start synthesis of chains de novo. Any enzyme that primes will of
    • necessity make a relatively inaccurate copy. Therefore mutation rates would be
    • enormous.
  24. In eukaryotes, the RNA primer is erased by _____ _. The gap is filled by ____ and covalently joined by ___
    • RNase H; DNA polymerase; DNA ligase.
    • Okazaki fragments are 100-200 np's long in eukaryotes
  25. DNA helicase can only unwind in the 5' to 3' direction?
    False. DNA helicase can unwind 5' to 3' as well as 3' to 5'
  26. what two proteins are needed to open up the double-helix?
    DNA helicase and SSB proteins
  27. In regards to DNA helicase, ATP hydrolysis causes?
    a shape change to propel itself rapidly alonf a single strand of DNA
  28. SSB proteins bind to? Do they cover the whole DNA strand molecule?
    Bind to the phosphate back bone and leave the bases exposed. The straighten the strand preventing formation of short hair pin helices
  29. Another word for helix-destablilizing proteins?
    Single-stranded binding proteins
  30. True/false: On their own DNA polymerase quickly synthesizes DNA from the DNA template strand.
    False. On their own DNA polymerase woulf quickly dissociate. An accessory protein, sliding ring clamp, keeps DNA polymerase firmly help to the template strand but dissociates when DNA polymerase encounters a double-stranded region
  31. In reality most of the proteins are held together in a large and orderly ________ complex that rapidly synthesizes DNA
    multienzyme complex
  32. The close association of proteins of the multienzyme complex at the replication fork _____ efficiency.
    Increases. This is made possible by the folding back of the lagging strand. Also, the clamp loader and the lagging strand DNA polymerase are kept in place as part of this protein machine even when they dissociate from the strand
  33. Strand-directed mismatch detects _____
    distortion in the DNA from misfit noncomplimentary base pairs. Recognizes the template and removes the newly synthesized nucleotide.
  34. Describe the 3-step process of strand-directed mismatch repair
    • 1) recognition of mismatch
    • 2) excision of DNA segment containing the mismatch from the newly synthesized strand
    • 3) resynthesis of the excised base using the old strand as a template
  35. Strand directed mismatch repair system reduces the number of errors made in DNA synthesis by a factor off ___
  36. 2 proteins involved in strand-directed mismatch repar. What is their role?
    • MutS - binds specifically to the mismatch
    • MutL - scans nearby DNA for a nick. Once the nick is found, it triggers degradation of the nick strand all the way back to the mismatch
  37. Where does topoisomerase I bind on the DNA strand?
    to the phosphate back bone
  38. Topoisomerase I requires ATP hydrolysis?
    False, the covalent linkage that joins the DNA topoisomerase protein to the DNA phosphate retains the energy of the cleaved phosphodiester bond, amking resealing rapid without energy input. Unlike DNA ligase of which joining requires ATP hydrolysis.
  39. 3 steps topoisomerase II releases a intertwined doubled strand. What is the energy source to drive the reaction?
    • 1) it breaks one double helix reversibly to create a DNA gate
    • 2) it causes the second nearby double helix to pass through this break
    • 3) it reseals the break and dissociates from DNA

    ATP hydrolysis is used as an energy source.
  40. Replication of DNA begins with ____ _____ _____
    special initiator proteins
  41. Bacterial chromosomes typically have __ origin of replication
  42. there are always _ replication fork(s).
    2 replication forks.
  43. In prokaryotes, describe the method to govern the amount of replication.
    The original OR is double methylated. As the OR is seperated and a new strand is synthesized, the double helix is now only hemi-methylated. (A-nucleotides are methylated). Hemi-methylated regions are resistant to replication. The OR is bound by an inhibitor protein, blocking access of the origin to initiator proteins.
  44. This enzyme methylates OR's.
    DNA methylase enzyme
  45. In eukaryotes, replication occurs only during which phase of the cycle?
    S phase - synthesis phase
  46. Heterochromatin is ____ found in the ___ ___ phase.
    condensed; late S phase.
  47. Euchromatin is ___ _____ and is found in ____ S pahse
    less condensed; early S phase
  48. Telomeres consists of tandem repeats rich in _ nucleotides located at the ___ end
    G nucleotides; 3'
  49. this enzyme is similar to reverse transcriptase
  50. telomerase consists of a ___ template and ___ that acts as reverse transcriptase
    RNA; protein
  51. telomeres function to prevent a ___ of DNA
  52. This protein is associated with telomeres and helps protect the end of chromosomes
    Shelterin - found in association in the t-loop on the telomere
  53. chromosomal shortening of telomere sequences to the point where coding region
    is affected. Exceptions include?
    Replicative cell senescence (aging); exceptions include cancer cells- where genes that code for telomerase become activated
  54. Hydrolytic attack , oxidative damage, and uncontrolled methylation are examples of?
    spontaneous DNA alterations that lead to DNA repair
  55. ______ is the most common change; releases
    a guanine, as well as adenine from DNA by hydrolytic attack
  56. This alteration converts a cytosine to an altered base Uracil
  57. a covalent bond forms between 2 pyrimidines to
    form a _____. The common cause is UV damage in skin cells. The
    most common ?
    pyrimadine dimer. The most common is a thymine dimer
  58. 2 types of accidental strand breaks can occur. Name them
    • Non-homologous double strand break: often involves short deletions or insertions that result in a loss of DNA
    • Homologous recombination: use the sister chromatid as a template to restore the double-strand break. More difficult to accomplish
  59. Genetic recombination occurs through 3 mechanisms:
    • 1) Homologous recombination : meiosis
    • 2) Transposition
    • 3)Conservative site-specific recombination

    • Mechanisms 2+3 use mobile genetic elements to translocate DNA
  60. What is a mobile genetic element?
    Elements used in genetic recombination from mechanisms like transpositon and conservative site-specific recombination. They are moved from one location to another location within a genome or to another genome. To another genome includes virsuses ect.
  61. A transposon moves ____ a genome
  62. encoded by the transposon, an enzyme called ____ moves the transposon
  63. transposase can move a transposon via 2 pathways. Name them
    cut-and-paste pathways and replicative pathways
  64. Non-retro retroviral transposons utilize what enzyme(s)?
    Reverse transcriptase and endonucleases. Moves via RNA intermediate
  65. a tranposon is how long?
    1,000 to 12, 000 np's
  66. True/false: Cut-and-paste mechanisms of a transposon can alter DNA causing a mutation.
    True. The donor chromosome is identified through inverted repeat DNA sequences. The repeat sequences are brought together to form a loop and excised. The staggered breaks are repaired via DNA polymerase and DNA ligase. As a result, the insertion site is marked by short repeat sequences of the target DNA. Although the break from the donor chromosome is repaired, the process alters the DNA sequence, causing a mutation at the original site of the excised transposable element.
  67. Describe the mechanism of replicated transposons.
    DNA-only transposon. Transposon DNA is replicated from the original site and is inserted to the new site. The original transposon remains at the original site. Similar to cut-and-paste mechanisms.
  68. True/false: Some transposons can move in both replicative and cut-and-paste mechanisms.
  69. Cut-and-paste transposons can move only with additional energy input?
    False. This mechanism can move without the input of external energy. The reaction begins and ends with the same number of phosphodiester bonds, it can occur without the additional input of energy
  70. DNA-only transposons are so named because?
    They only involve the movement of DNA. Predominant in bacteria
  71. Cut-and-paste transposons leaves behind a hole in the chromosome. 3 situations can occur to fill this hole. Describe them
    • 1) can be healed via homologous repair provided the chromosome has just been replicated and an identical copy of the damaged host sequence is available; restores the transposon to the original situation
    • 2) in a diploid organism, the damage can be recombinationally repaired using the chromosome homolog - transposon will NOT be restored
    • 3) Non-homologous end joining reaction can reseal the break; producing a mutiation at the site where the transposon was excised
  72. DNA polymerase I is found in _____ cells and functions to;
    • prokaryotic
    • removes and replaces RNA primers (also in excision repair of damaged DNA)
  73. DNA polymerase ___ is the main polymerase for synthesis on the leading strand, as well as Okazaki fragments on the lagging strand.
  74. This enzyme is found in _____ cell types and functions to make RNA oligonucleotides that are primers for DNA synthesis
    both cells ; DNA primase
  75. Initiator proteins are found in _____ cells and function to;
    • both
    • bind to the replication origin and initiate unwinding of DNA double helix
  76. Telomerase is found in _____ cell types. It functions to;
    • eukaryotic
    • using an RNA template, its protein part synthesizes DNA for extension of telomeres causing a 3' overhang that will be converted to double-stranded DNA
  77. Another name for transposons that move within a genome
    jumping genes
  78. Viruses consist of nucleoc acid surrounded by a ____
    capsid (protein coat)
  79. Define bacteriophage
    A virus that infects bacteria
  80. Retroviral-like retrotransposons require these enzymes for movement and move via which molecule?
    • Reverse transcriptase and integrase (transposase)
    • moves via RNA intermediate produced by the promoter in LTR ( long terminal repeats) at each end
  81. If a virus does not have a ____ it will not leave the host cell
  82. Jumping gene exist/extinct in human genes
    extinct. They no longer exist
  83. Nonretroviral retrotransposons use a protein complex composed of?
    reverse transcriptase and endonuclease
  84. In nonretroviral retrotransposons; RNA is attacked on the ___ end of the hnRNA.
    3' poly-AAAA tail
  85. Viruses enter the cell, then exit via ____ of the host cell
  86. A viroid is?
    • small circular ssRNA molecule
    • no protein coat present
    • use RNA polymerase II to replicateinfect cetrain plant types
  87. A plasmid is typically circular _____ molecule that self-replicates in the cytoplasm of many ______ and the _____ of some eukaryotic species cells.
    dsDNA; prokaryotic; nucleus