genetics 4

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genetics 4
2013-04-14 17:45:45

exam 4
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  1. conservative DNA replication
    two strands one old, one new

    incorrect mode
  2. semiconservative DNA replication
    one new strand, one old strand, coiled together

    correct mode of replication
  3. dispersive DNA replication
    mixture of old and new on one strand

    incorrect mode
  4. DNA replication in prokaryotes
    -Meselson- Stahl experiment

    -DNA replication is semi-conservative

    -each new strand of DNA consist of one old strand and one newly synthesized strand
  5. Taylor- Woods-Hughes experiment
    demonstrated that DNA replication is semiconservative in eukaryotes
  6. DNA replication in prokaryotes
    begins at one origin of replication

  7. replicon
    length of DNA that is replicated following one initiation event at a single origin
  8. bidirectional
  9. unidirectional
  10. DNA polymerase
    catalyzes DNA synthesis and requires a DNA template and all four dNTPs
  11. Can DNA polymerases I, II, III initiation of chain synthesis?
  12. does DNA polymerase I, II, III have 5-3' polymerization?
  13. does DNA polymerase I,II,III have 3'-5' exonuclease activity?
  14. which DNA polymerase has 5-3' exonuclease activity?
    polymerase I
  15. What does DNA polymerase 1,2,3 need to elongate an existing DNA strand
  16. which DNA polymerase initates DNA synthesis?
  17. exonuclease activity
    proof reading, fixes wrongly matched polymers
  18. DNA polymerase1 is responsible for:
    removing the primer

    the synthesis that fills gaps produced during synthesis
  19. DNA polymerase 3 if responsible for:
    5'-3' polymerization essential in vivo

    3'-5' exonuclease activity allows proof reading

    10 subunits

    not involved in repair
  20. 1. Unwinding of the helix
    • Step one
    • DnaA intial steps in unwinding
    • DnaB and DnaC further opens and destabilizes the helix
    • Energy from hydrolysis of ATP used to supply these proteins
  21. Single-stranded binding proteins (SSBPs)
    Stabilize the open helix

    Step one- unwinding the helix
  22. helicases
    proteins that open DNA structure

    DnaA, DnaB, DnaC
  23. 2. Reducing increased coiling generated during unwinding
    • Step 2
    • The unwinding creates super coiling
    • DNA gyrase stops super coiling
  24. DNA gyrase
    • Stops supercoiling
    • A DNA topoisomerases
  25. 3. synthesis of a primer for initiation
    • Step 3
    • Elongation requires a primer with a 3'-hydroxyl group
    • Primase used
  26. Primase
    • Enzyme
    • Synthesizes an RNA primer that provides the free 3' hydroxyl required by DNA polymerase 3
  27. 4. synthesis of DNA strand
    • Step 4
    • Replication fork moves, one strand is used for template for continuous DNA synthesis
    • Opposite strand undergoes discontinues DNA synthesis
  28. Leading strand
    • Undergoes continues DNA synthesis
    • Enlongated
  29. lagging strand
    • Undergoes discontinues DNA synthesis
    • Synthesized into Okazaki fragments-¬† (small fragments each with an RNA primer
  30. 5. removal of the RNA primers
    • DNA polymerase 1
    • Removes the primers on the lagging strand
    • Replaces the missing nucleotides (fills gaps)
  31. 6. joining of the gap-filling DNA to the adjacent strand
    • Step 6
    • Fragments of lagging strand joined by DNA ligase
  32. DNA ligase
    fills gaps, binds lagging strands of DNA
  33. 7.Proof reading
    Fix any possible mistakes
  34. DNA synthesis at single replication fork involves:
    • DNA polymerase 3
    • Single-stranded binding proteins
    • DNA gyrase
    • DNA helicase
    • RNA primers
    • DNA ligase
  35. B- subunit clamp
    prevents the core enzyme from falling off the template during DNA synthesis
  36. Eukaryotic DNA synthesis
    • More complex
    • More DNA than prokaryotic cells
    • Chromosomes are linear
    • DNA complexed with proteins
    • Multiple origins of replication=faster
  37. autonomously replicating sequences (ARSs)
    involved in efficient initiation
  38. what major forms of enzymes are involved in initiation and elongation ?
    pol alpha and gamma
  39. Pol alpha
    • Low processivity
    • Synthesis of RNA primers during initation on leading and lagging strand
  40. processivity
    length of DNA synthesized by an enzyme before it dissociated from the template
  41. Telomeres
    • Found on ends of linear chromosomes
    • Long stretches of short repeating sequences
    • Preserve the integrity and stability of chromosomes
    • Problematic to replication
    • Can cause gap in replicated strands
  42. Telomerase
    • Directs synthesis of the telomere repeat sequence to fill the gap
    • Ribonucleoprotein with RNA
    • Serves as a template for the synthesis of its DNA complement
  43. Homologous recombination
    • Genetic exchange at equivalent position along two chromo. with substantial DNA sequence homology
    • AKA general, homologous, recombination
    • Two chromo. similar sequences
  44. Genetic recombination involves?
    • Endonuclease nicking
    • Strand displacement
    • Ligatioin
    • Branch migration
    • Holliday structure
  45. Holliday structure
    • Duplex seperation
    • Miosis
    • Holliday junction
  46. recombinant duplexes
    sequences similar but mixed

    Ab Bb
  47. gene conversion
    • Consequence of DNA recombination
    • Nonreciprocal genetic exchange between two closely linked genes
  48. DNA is transcribed into
  49. RNA is translated into
  50. The genetic sequence of RNA consists of
    A U C G
  51. coding strand aka
    nontemplate strand
  52. non-coding strand aka
    template strand
  53. triplet codon
    • Specifies one amino acid
    • Provide 64 codes to specify the 20 amino acids
    • Contains start and stop signals
  54. Stop codons for DNA
    • UGA
    • UAA
    • UAG
    • Do not code for any amino acid
  55. start codon for DNA
  56. fameshift mutations
    • Insert 1 or 2 nucleotide, protein sequence completely changes
    • Insert multiples of 3 it does not completely change
  57. triplet binding assay
    • Determines specific codon assignments
    • Ribosomes bind to a specific codon
  58. genetic code is degenerate:
    • Many amino acids specified by more than one codon
    • Only tryptophan and methionine are encoded by a single codon
  59. Wobble hypothesis
    3 and 1 position in mRNA and tRNA can be modified
  60. different initiation points can create
    overlapping genes, 2 different gene sequences
  61. RNA serves as the intermediate molecule between
    DNA and proteins
  62. RNA is synthesized on a DNA template during
  63. in a prokaryote translation and transcription occur
    at the same time
  64. in an eukaryote transcription and translation occur
    • Different times
    • Different places
  65. RNA polymerase
    • Directs synthesis of RNA using DNA template
    • No primer required in initiation
    • Uses ribonucleotides instead of deoxyribonucleotides
  66. RNA transcription in procaryotes requires
    • RNA polymerase enzyme holoenzyme
    • Promoter sequence on DNA template
    • Ribonucleotides
  67. Initiation of RNA transcription
    • RNA polymerase binds to promoter
    • Start sequence TTGACA and TATTAT
  68. Elongation in RNA transcription
    sigma dissociates and elongation begins with core enzymes
  69. termination
    • Transcription terminates due to hairpin formation in the RNA
    • Some depend on Rho termination factor
  70. five steps of transcription in prokaryotes
    • 1. RNA polymerase binds to promoter
    • 2. short sequence of DNA is unwound
    • 3. RNA synthesis begins
    • 4. sigma factor dissociates
    • 5. RNA elongates
  71. difference in eukaryote transcription from prokaryots
    • Eukaryotes
    • Transcription occurs in nucleus and not coupled translation
    • Requires chromatin remodeling
    • mRNA processing to produce mature mRNAs
    • RNA polymerase (I,II,III)
    • Promoter needed
    • Transcription factors
    • Enhancers and silencer
  72. Eukaryotic transcription requires: (1-5)
    • 1 promoter
    • 2.RNA polymerase
    • 3.transcription factors
    • 4.enhancer and silencer
    • 5. ribonucleotides
  73. Promoter in eukaryotic transcription
    • TATAA box -35 from start site
    • GGCCAATCT box -80from start site
  74. RNA polymerase in eukaryotic transcription
    • I, produces rRNA
    • II, produces mRNA,snRNA
    • III, produces 5S rRNA , tRNA
  75. transcription factors in eukaryotic transcription
    1. general transcription factors

    2. Gene-specific transcription factors
  76. general transcription factors
    required for all RNP II mediated transcription and help RNA polymerase II bind to the promoter and initiate basal level transcription
  77. gene-specific transcription factors
    influence the efficiency or the rate of RNP II transcription
  78. Enhancers and silencers in eukaryotic transcription
    • Can be upstream, within or downstream (anywhere)
    • Can modulate transcription from a distance
  79. initiation complex
    • RNA polymerase II + general transcription factors
    • 35 subunit at promoter
  80. mediator
    • Associates and enables either positive or negative regulation of initiation
    • 20 subunits after initiation complex
  81. introns
    • Regions of initial RNA transcript that are not expressed in amino acid sequence
    • Removed by splicing and exons joined by mature mRNA
  82. spliceosome
    spice out Pre-mRNA introns
  83. alternative splicing
    • Multiple ways to put genes together
    • Different exons are included in mRNA
    • Increases genetic expression
  84. amino acid
    • Carboxyl group
    • Amino acid
    • R (radical) group -refers to specific chemical properties
  85. peptide bond
    • Forms by dehydration reaction between the carboxyl group of the amino acid and the amino group of another
    • Bonds amino acids
  86. translation
    polymerization of amino acids into polypeptide chains
  87. translation requires
    • Amino acid
    • Messenger RNA (mRNA)
    • Ribosomes
    • Transfer RNA (tRNA)
  88. Prokaryotes have how many monosomes
  89. Eukaryotes have how many monosomes?
  90. Ribosomes 3 sites:
    • E-site: exit site
    • P-site: peptidyl site
    • A-site: amnioacyl site
  91. tRNA
    CCA sequence at 3' end is binding site for amino acid
  92. aminoacyl tRNA synthetase
    actives tRNAs with the appropriate amino acid
  93. 3 steps of mRNA translation:
    • Initiation
    • Elongation
    • Termination
  94. Initiation in prokaryotes requires:
    • Small and large ribosomal subunits
    • Initiation factors
    • Charged initiator tRNA
    • Mg
    • GTP
  95. Initiation codon in prokaryotes
    • AUG
    • Before it is AGGAGGU

  96. Elongation in Prokaryotes
    • Requires both ribosomal subunits with mRNA, form P (peptidyl) site and A (aminoacyl) site
    • Charged tRNA enter A site
    • Peptidyl transterase- catalyzes peptide bond between amino acid on tRNA A site and the peptide chain bound to tRNA P site
    • Uncharged tRNA moves to E site
    • tRNA bound to peptide chain moves to P site
  97. Termination in Prokaryotes is signaled by?
    • Stop codon
    • UAG
    • UAA
    • UGA
  98. what does GTP-dependent release factors do in termination?
    take off polypeptide chain from tRNA and release it from translation complex
  99. why is translation more complex in Eukaryotes?
    • Ribosomes are larger than in bacteria
    • Transcription and translation are in different locations at different times
    • Ribosomes are with endoplasmic reticulum instead of free floating
    • Ribosomes must have initiator sequence in proper order (Kozak sequence)
    • Requires more factors for initiation, elongation, and termination than bacteria
  100. Kozak sequence
    initiator tRNA in proper sequence
  101. Difference in initiation Prokaryotes 1:
    • Initation begins with methionine-not N-formyl-methionine
    • tRNA:tRNAi met
    • Initator tRNA bears unformylated methionine
  102. difference in initiation in prokaryotes 2:
    Contain no Shine-Dalgarno sequence to show ribosomes where to start
  103. differences in initiation in prokaryotes 3:
    requires more initation factors than eukaryotes
  104. difference in initiation in prokaryotes 4:
    • Eukaryotes contain 2 release factors
    • eRF1
    • eRF3
  105. Polysomes (polyribosomes)
    mRNAs with several ribosomes translating at once
  106. Prokaryotic regulation can be controlled under ?
    positive and negative conditions
  107. regulator elements in prokaryotic gene expression are located?
    • Upstream
    • cis-acting
  108. molecules that bind to cis-acting sites in prokaryotic gene regulation
    transacting elements
  109. lactose metabolism in E.coli is regulated by
    • An induced system
    • Enzymes responsible for lactose metabolism are induced
    • Lactose is the inducer
  110. Lac operon
    • Three structural genes lacZ, lacY, lacA
    • Upstream regulatory region with a promoter and operator
  111. permease
    • lacY
    • enzyme that facilitates the entry of lactose into the bacterial cell
  112. transacetylase
    • lac A
    • Involved in the removal of toxic by-products of lactose digestion from the cell¬†
  113. lacI gene regulates transcription of the structural genes by producting
    • repressor molecule
    • which is allosteric
  114. allosteric
    • interacts reversibly with another mlc.
    • Causes 3-D shape change and change in chemical activity
  115. no lactose present
    • =repressed
    • Repressor binds to operator
    • Blocks transcription
    • No transcription
    • No enzymes
  116. lactose present
    • = induced
    • No binding occurs
    • Transcription proceeds
    • Transcription > mRNA> translation > enzymes
    • Operator-binding region altered when bound to lactose
  117. Lac operon mutation Oc
    • Active=always on
    • nucleotide sequence of operator DNA is altered and will not bind with normal repressor
  118. Lac operon mutation I-
    • Active=always on
    • repressor protein is altered/absent and can not bind to operator region
  119. Lac operon mutation Is
    • Repressed= not on
    • Lactose binding region is altered, repressor always bound to operator
  120. Bacteria conjugation
    • Genetic info from one bacterium is transferred to another
    • F+ cells are donor
    • F- are recipients
    • Fertility factor (F factor)
  121. fertility factor
    • F factor
    • Can donate DNA during conjugation
  122. catabolite-activating protein (CAP)
    • Represses expression of lac operon when glucose is present
    • Used when there is enough lactose and glucose present
  123. Catabolite repression
    • repression of the expression of lac operon
    • Happens when there is enough lactose and glucose
  124. CAP positive control
    • Absence of glucose
    • Presence of lactose
    • CAP-binding site and RNA polymerase bind to promoter
    • Max expression=respressor not bound to operator and CAP bind CAP-binding site
    • Regulated by activator CAP
  125. cAMP is required for
    • CAP binding
    • levels increase as glucose decreases
  126. adenylyl cyclase
    • repressed by glucose
    • Catalyzes the production of cAMP
    • Prevents CAP from binding when glucose is present