Quiz 2

Card Set Information

Author:
Cadence
ID:
284604
Filename:
Quiz 2
Updated:
2014-10-10 06:38:49
Tags:
Cell Biology
Folders:

Description:
Cell Bio
Show Answers:

Home > Flashcards > Print Preview

The flashcards below were created by user Cadence on FreezingBlue Flashcards. What would you like to do?


  1. Describe the function of primase in DNA replication
    • synthesizes short RNA molecule
    • reads DNA template and adds nucleotides in order to generate RNA primer
  2. Describe the function of DNA polymerase in DNA replication
    • synthesizes a new strand of DNA
    • adds nucleotides to the 3' end of the new strand
  3. Describe the function of helicase in DNA replication
    • separates double helix at replication fork
    • denatures template in front of replication fork
  4. Describe the function of DNA ligase in DNA replication
    • primer for DNA synthesis
    • Enzyme that joins two molecules of DNA together
    • closes the gap after repair, telomere extension or DNA synthesis
  5. List the GENERAL steps in the DNA repair process
    • Recognize the damage with special proteins
    • Remove the damage with nucleases
    • Fill in the missing DNA with DNA polymerase
    • Close the gap DNA ligase
  6. Explain why DNA synthesis is discontinuous on the lagging strand and a RNA primer is required repeatedly at the replication fork as it is opened
    The direction of DNA synthesis is 5'-3', so DNA synthesis must be discontinuous on the lagging strand in order to synthesize both strands of DNA at in the same direction
  7. Explain how it is possible for greater than 6 billion nucleotides of DNA in the human genome to be synthesized in a 8 – 10 hour period
    DNA synthesis occurs during the S phase of the cell, which usually lasts about 8 hours.  A human diploid cell contains 46 chromosomes which make up the human genome. At the end of S phase, each chromosome has been replicated to produce two complete copies.
  8. Describe Intracellular DNA damage and state the cellular mechanism used to remove the damage from the DNA.
    • damage due to “thermal collisions” and oxidative damage Depurination and deamination; Altered bases
    • Mismatch: Wrong base incorporated during replication (A not matched to G)
    • DNA mismatch repair system: Group of proteins that recognize and repair mismatchs
  9. Describe DNA damage due to environmental sources and state the cellular mechanism used to remove the damage from the DNA.
    • damage due to exposure to chemicals: DNA adducts
    • Radiation: UV dimers; double strand breaks
    • Nucleotide excision repair (NER): DNA adducts – bulky adducts added to the DNA
  10. Explain how DNA synthesis is initiated on eukaryotic chromosomes.
    • 1.  Initiation proteins bind at the replication origins. Denature the DNA
    • 2.  Helicase unwinds the double helix at the origin of replication
    • 3.  Single strand binding proteins bind and keep the strands apart
    • 4.  Primase forms a short 10 base RNA primer at the FORK on both strands
    • 5.  DNA polymerase adds bases to the 3’ end of the primers
  11. (1) After Initiation proteins bind at the replication origins and denature the DNA....
    (2) Helicase unwinds the double helix at the origin of replication
  12. (2) After helicase unwinds the double helix at the origin of replication...
    (3) Single strand binding proteins bind and keep the strands apart
  13. (3) After single strand binding proteins bind and keep the strands apart...
    (4) Primase forms a short 10 base RNA primer at the FORK on both strands
  14. (4) After primase forms a short 10 base RNA primer at the FORK on both strands...
    (5) DNA polymerase adds bases to the 3’ end of the primers
  15. Explain the function of telomerase in protecting the ends of the chromosomes
    • Telomerase binds to the template of the lagging strand at the end of the chromosome to facilitate the addition of telomeres.
    • Telomerase has a bound RNA template that adds telomeres to the ends of chromosomes  via RNA templated DNA synthesis.
    • The lagging strand is then completed by DNA polymerase via DNA templated DNA synthesis
  16. Single stranded biding proteins
    keeps the double strands apart until polymerase passes
  17. Topoisomerase
    • takes the kinks out of the DNA and rotates the strands ahead of the replication fork
    • removes kinks and tensions in front of replication fork
  18. RNA Primer
    10 base pair sequence formed by primase at replication fork during DNA synthesis
  19. Replication Orgin
    • Particular sequence of DNA  
    • Recognized by initiator proteins  
    • Causes DNA to melt and become denatured
    • Hydrogen bonds are broken and strands separated
    • Where DNA synthesis begins
  20. Replication Fork
    Y shape where the two DNA strands split apart during replication; come in pairs
  21. Telomeres
    G/T rich sequences on ends of chromosomes -GGGGTTA-
  22. Telomerase
    Enzyme which adds DNA to ends of chromosomes (onto telomeres)
  23. Explain why DNA polymerase requires a primer
    DNA polymerase can only add onto the 3' end of an -OH group and thus requires a primer to provide an -OH group on which to add the first nucleotide
  24. Phosphodiester bond
    between phosphate of 5'C of one nucleotide and -OH group of 3'C of other sugar
  25. Phosphodiester Bond
  26. DNA Polymerase
    Adds one nucleotide at a time  Adds to 3’ end of growing chain  Grows in 5’ to 3’ direction  Forms a phosphodiester bond  Reads the parental strand
  27. Describe the enzyme activity of DNA polymerase at the replication fork
    • incoming nucleotide pairs with a base in the template strand
    • DNA polymerase catalyzes covalent linkage of nucleotide into growing nucleotide strand
  28. Sliding clamp protein
    keeps DNA polymerase on the DNA
  29. Proteins involved in DNA replication
    • DNA polymerase
    • primase
    • DNA ligase
    • Sliding clamp protein
    • helicase
    • topoisomerase
    • single strand binding proteins
  30. DNA Damage: Mismatch
    Wrong base incorporated during replication
  31. Depurination and Deanimation
    • Leads to a change (mutation) in the DNA sequence
    • depurination: Loss of A and G; Spontaneous
    • deanimation of cytosine: spontaneous
  32. Proofreading by DNA polymerase
    checks each nucleotide after added Removes wrong nucleotide and re-adds 3’-5’ exonuclease activity 1 error every 107 nucleotides
  33. DNA mismatch repair system
    Group of proteins that recognize and repair mismatch
  34. Depurination
    • after replication deletion of base pair
    • loss of purine A
    • T not paired with A
    • after replication, A-T nucelotide pair deleted on one strand, but replicated correctly on the other
  35. Deanimation
    • deanimation of cytosine (C)
    • C turns to U
    • U pairs with G
    • after replication, one strand is made correctly, with G pairing with C, and the other incorrectly with U pairing with A
  36. DNA Damage: UV Exposure
    two thymines become one thymine dimer
  37. Base excision repair (BER)
    • modified bases or altered bases
    • U in the DNA
    • 8-oxo G
    • Methylated A
    • repairs deanimation
  38. Nucleotide excision repair (NER)
    • DNA adducts – bulky adducts added to the DNA
    • DNA repair systems for environmental damage and spontaneous changes mechanism
  39. RNA structure compared to DNA
    • Single stranded
    • U-A pairings possible
    • internal base pairing – leads to specific 3D RNA Structures
  40. Structure of a Gene
    • Promoter and Gene regulatory region
    • Start of transcription
    • Downstream
    • Upstream
  41. Promoter
    sequences involved in initiation of transcription
  42. Gene regulatory region
    sequences involved in regulating expression of the gene.
  43. Exon
    coding and noncoding sequences that will appear in the mature, processed mRNA
  44. Intron
    intervening sequences which are removed from primarytranscription; do not contain coding sequences
  45. Poly A addition site
    sequences (AAUAA) in which determines where polya tail will be added
  46. Termination site
    sequence at which RNA polymerase stops transcribing
  47. 5’ untranslated region (5’UTR)
    noncoding sequence contained in exon I, which comes before the start of translation
  48. 3’ untranslated region (3’ UTR)
    noncoding region contained in the final exon, which comes after the stop codon
  49. AUG (ATG)
    start of translation; 1st codon of the coding region; codes for methionine
  50. UGA, UAA, UAG (TGA, TAA, TAG)
    stop codon for translation - stops translation of the mature mRNA
  51. RNA Polymerase I
    transcribes most rRNA genes
  52. RNA Polymerase II
    all protein coding genes, miRNA genes, plus genes for other non-coding RNA (those in spliceosomes)
  53. RNA Polymerase III
    tRNA, 5S rRNA, genes for many other small RNAs
  54. Process of Initiation
    • 1. TFIID binds at TATA (via TBP –TATA binding protein)
    • 2. TFIIB’s binds to TFIID
    • 3. Binding of RNA polymeraseTFIIF, TFIIE, TFIIH
    • 4. Phosphorylation of RNA Polymerase and release of TF’s
  55. Transcription factors
    Proteins that bind to specific sequences in the promoter of the gene
  56. Promoter and Gene regulatory region
    • Contains control sequences for transcription
    • Binding site for RNA polymerase (Promoter)
    • Contains site of initiation (Promoter)
  57. Start of transcription
    Where first nucleotide comes in and transcription begins Referred to as +1
  58. Downstream
    Towards the coding region of the gene
  59. Upstream
    Away from coding region of the gene
  60. RNA Processing
    • 1.  Formation of 5’ cap
    • 2.  Addition of 3’ poly (A) tail
    • 3.  Removal of introns and joining of exons Splicing
  61. Formation of 5' Cap
    • Three bases of 5’ end are termed the 5’ cap
    • 1st of the 3 bases is added after transcription; guanine is added in opposite direction to last nucleotide on the pre-mRNA; 5’-5’ linkage
    • Important for translation
  62. Addition of 3' Poly (A) tail
    • Cut 10 to 20Nucleotides pass site on primary transcript
    • first nucleotide: +1sequence that tells us where to put polyA
  63. Function of Poly (A) tail
    • Length varies from 3 to 200 nucleotides
    • appears to be important for stability or half-life of mRNA; shorter tails - shorter half-life; longer tails - longer half-life
    • Tail gets shorter as mRNA ages Proteins associate with the poly (A) tail

What would you like to do?

Home > Flashcards > Print Preview