Cell Bio Exam 2

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irishdancer123
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177823
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Cell Bio Exam 2
Updated:
2012-10-20 17:10:56
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Cell Biology
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Midterm 2
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  1. nuclear envelope
    two lipid bilayers (inner and out nuclear envelope)
  2. Interstitial space (define and say what it is connected to)
    lumen of nuclear envelope; continguous with the lumen of the endoplasmic reticulum
  3. nucleoplasm
    • fluid phase interior of nucleus
    • contiguous with cytoplasm but there is no free flow
  4. nuclear strucutre
    conferred by a system of proteins in and out of the nucleus
  5. KASH
    integral membrane protein that spans the outer envelope of the nucleus
  6. SUN
    integral membrane protein that spans the inner envelope of the nucleus
  7. intermediate filaments
    cytoskeletal molecules that are not A/GTPases
  8. nuclear lamins
    • intermediate filament proteins that live just inside the surface of the inner nuclear envelope
    • phosphorylation induces disassembly
  9. Histones (list, charge, pH)
    • family of proteins: H1 [H2A,H2B,H3,H4]
    • positive charge
    • basic pH
  10. nucleosome
    • DNA looped around histone complex (10nm)
    • connected by linker sequences
  11. solenoid (define and what holds it together)
    • coil wound into a tightly packed helix
    • histone H1 holds it together
  12. chromatin
    combination of DNA and the proteins associated with it (eg histones)
  13. heterochromatin
    • very dark, dense, and very protein rich; tighly packed
    • generally not unraveled
    • found at telomeres and centromeres
  14. euchromatin
    • lighter/less dense than heterochromatin both in the amount of DNA present and the amount of protein present
    • partially unwrapped chromosomes
    • makes the genes for proteins to transcribe them (transcriptionally active)
  15. aceylation
    adding an acetyl group to a histone to neutralize some of its positive charge to allow thte histones to release the DNA partially so it can unravel
  16. semiconservative replication
     conserve half of the genetic material
  17. Licensing/priming
    When?
    What?
    Why?
    • occurs during G1
    • building up components around the origin for replication
    • limites replication to a single cycle by building up the martials that will be used for replication
  18. ORI
    • origin
    • a DNA sequence that is A-T rich (easier to separate than C-G)
    • 1000s in eukaryotes are scattered throughout chromosomes
  19. ORC
    • origin recognition complex
    • pre-replication complex; structural molecule
    • six proteins (ORC1-ORC6)
    • binds origin; serves as a landmark
  20. Cdc6p
    • pre-replication complex; structural molecule
    • protein that binds to the ORC complex and Cdt1
  21. Cdt1
    • Cyclin dependent transcript #1
    • pre-replication complex; structural molecule
    • binds Cdc6p and MCM
  22. MCM
    • mini-chromosome-maintenance
    • heterohexomer (MCM 2-7)
    • provide helicase activity to separate DNA strands
    • activated by Cdc45p
  23. Cdc45p
    binds MCM complex and activates it
  24. RPA
    • Replication Protein A
    • binds single stranded DNA (ssDNA) and stabilizes it in its single stranded form
  25. DNA dependent DNA polymerases
    phosphodrestal bond: bond with 3' hydroxyl of one base and the 5' phosphate of another base
  26. DNA polymerase a(lpha)
    • contains primase activity
    • first few bases are RNA primary followed by DNA primer bases
    • error prone
  27. RFC
    • Replication Factor C
    • recognizes primer and binds to it
    • binds to PCNA
  28. PCNA
    • Proliferating Cell Nuclear Antigen
    • binds RFC; wraps around DNA
    • binds DNA polymerase d(elta)
  29. DNA polymerase d(elta)
    • longer runs
    • requires a primer
    • proofreading activity
    • low error rate (1/10,000,000)
  30. DNA ligase
    seals the gaps in DNA
  31. Toporsomerase I
    cuts a nick in one strand of DNA to unwind strands (relieve stress)
  32. Toporsomerase II
    cuts two strands and ties them back together (requires ATP)
  33. What happens in early G1 stage?
    • ORC is bound to the origin
    • Cdc6 and Cdt1 bind
    • recruit MCM (but don't turn it on)
  34. Early S-Phase (part 1)
    • cdc45p binds MCM complex and activates its helicase activity
    • replication bubble is opened p
    • ORC, cdc6 and cdt1 leave the complex
    • ORC returns at the end of S-phase; cdc6 and cdt1 do not return until G1
  35. Early S-Phase (part 2)
    • replication forks start to extend
    • RPA is recruited (keeps strands separate)
    • DNA polymerase a(lpha) is recruited
    • primase synthesizes primer (RNA - DNA) reading 5'-3'
  36. Early S-Phase (Part 3)
    • RFC is recurited by primer and is bound to it
    • RFC recruits PCNA
    • PCNA recruits DNA polymerase d(elta)
  37. RNA portion of primer in replication is removed by ____
    RNAase H
  38. what limits the amount of times a cell can replicate its DNA?
    shortening of telomeres
  39. What is a difference between RNA and DNA?
    the presence/absence of hydroyl on C2 ribo/deoxynucelic acid
  40. RNA
    • shorter sequences
    • base pairs w/ it self creating hairpin loops (short) and stem looks (large)
    • tertiary structure in some RNAs
    • can be catalytic
  41. ribozymes
    splicing of mRNA catalyzed by RNA
  42. Transcription:
    Read:
    Write:
    • Read: 3'-5'
    • Write 5'-3'
  43. Differences between replication and transcription
    • 1. entire genome is not transcribed
    • 2. Takes place throughout most of the cell cycle
    • 3. primers are not required
    • 4. RNA polymerases are much less accurate than DNA polymerases (b/c molecules are disposable)
  44. RNA Polymerase I
    makes rRNAs
  45. RNA Polymerase II
    mkaes mRNAs
  46. RNA Polymerase III
    makes tRNA and snRNA (small nuclear RNA)
  47. promoter (transcription)
    • just upstream from coding sequence
    • transcriptional machinery binds here
  48. TATA box
    • 7-9bps long
    • specific binding site and recognition site for transcription factors
  49. core promoter
    • inside promoter
    • builds transcriptional machinery
  50. Regulatory Sequences
    upstream from the gene. Serves as a recruting element for transcription factors
  51. Transcription facors
    proteins bonding DNA-> recruiting/activating polymerase
  52. General transcription factors
    • required for transcription of all genes
    • bind in promoter region (TATA box)
  53. promoter-proximal elements
    DNA sequences of transcriptional start site
  54. TFII-D
    • transcriptional factor
    • TBP-TATA box binding protein
  55. TFII-A,B,F
    • transcriptional factor
    • bind to each other, the TATA box, and PolII(makes mRNAs)
  56. TFII-E
    • transcriptional factor
    • binds TFII-H and PolII(makes mRNAs)
  57. TFII-H
    • binds to TFII-E and Pol II
    • binds helicase and kinase(phosphorylated PolII)
    • opens strands + transcription bubble
  58. Polymerase Pol II
    • makes mRNA
    • needs to be phosphorylated before it can be activated
  59. CAC
    • capping enzyme complex
    • binds to the 5' base of mRNA
  60. 5'cap (3)
    • stabilizes mRNA
    • serves as a signal for nuclear export
    • signals translation of gene
  61. splicing (what is it and what is used to do it)
    • occurs after transcription with a spliceosom (composed of RNA and proteins)
    • cuts out introns and ligates exons back together
  62. What happens during termination of transcription?
    • 1. Polyadenylation signal (AATAAA) signals polymerase II to slow down and stop
    • 2. Termination facts bind polymerase II and mRNA to cleave the mRNA
  63. polyadenylation
    • Poly A polymerase binds 3' end of mRNA and adds 100-300 As (polyAtail)
    • serves as a timer- when too many As have fallen off, the mRNA is enzmatically destroyed
  64. translation error rate
    1/1000 amino acids
  65. where does tranlation take place?
    cytoplasm in ribosomes (mRNA must be translocated through nuclear pores out to the cytoplasm)
  66. mRNA is read __ to __ in translation
    amino acids chain is synthesized ___ to ___
    • 5'-3'
    • N-terminal to C-terminal
  67. when in the cell cycle does translation take place?
    whenever
  68. start codon for translation (and what it codes for)
    • AUG
    • methionine
  69. stop codons
    UAA UAG UGA
  70. A
    P
    E
    translation sites
    • A(dd): new tRNA enters ribsome here
    • P(olypeptide): contains tRNA that is linked to a growing polypeptide chain
    • E(xit): bound to tRNA that has lost its amino acid
  71. tRNAs have a ____ structure
    cloverleaf
  72. what code do tRNAs end with a the 3' end? what is attached at the 3' end?
    • CCA
    • amino acid
  73. MIFs
    • mRNA Initiation Factors
    • bind 5' cap and recruit small ribosmal subunit
  74. eIF2
    • Eukaryotic Initation Factor 2
    • when turned on (bound to GTP) it prevents translation until the GTP is hydrolysized to GDP (when AUG is reached) (allows large ribosomal subunit to bind)
  75. g-protein
    • small proteins that serve as switches
    • bound to GTP (on) until hydrolysis is trigged externally (GDP-off)
  76. EF1
    • elongation factor 1
    • it is an activated g-protein that prevents peptide bond formation unless the codon and anticodon match (GTP is hydrolyzed when there is a match)
  77. EF2
    • Elongation Factor 2
    • an activated g-protein that ensures that peptide bond formation is physically coupled to ribosome translocation in the 3' (->) direction down mRNA
  78. what catalyzes the peptide bond between amino acids in translation? what happens after that?
    • large ribosomal subunit
    • EF2 hydrolyzes GTP allowing ribosome to move forward 3 bases (1 step)
  79. how does translation end?
    • stop codon is reached
    • termination factor enters A site
  80. signal
    primary piece of information received by the cell
  81. 3 types of signals
    • hormones (chemical)
    • damage (physical)
    • cell to cell contact (physical)
  82. signal transduction system
    • the component that receives and responds to the signal
    • can be a single cell, group of cells, tissue, organism
  83. 4 types of cell signaling
    • 1. endocrine
    • 2. paracrine
    • 3. juxtacrine
    • 4. autocrine
  84. endocrine signaling
    • longest range
    • chemical (eg hormone)
    • source: gland
    • gets to target through blood
  85. paracrine signaling
    short ranges (less than a mm)
  86. juxtacrine
    • very short rainge (direct cell to cell contact)
    • signal produced on surface of cell
  87. autocrine signaling
    • cell signals to itself
    • signal released is received by a receptor in its own plasma membrane
  88. general mechanism of signal transduction (5)
    • 1. receptor-ligand bonding
    • 2. phosphorylation
    • 3. use of g-proteins
    • 4. 2nd messengers
    • 5. localization
  89. phosphorylation
    addition of a phosphate group (rapid, catalytic)
  90. kinsase
    • enzyme that phosphorylates proteins
    • many; protein specific
  91. phosphatases
    • proteins that remove phosphates
    • low in number, less protein specific than kinases
    • always active unless turned off
  92. Familes of kinases
    • 1. serine-threonine kinases (S/T) (most common)
    • 2. tyrosine kinsase (Y)

    (a few kinases also have duality)
  93. GEFs
    • Guanine nucleotide Exchange Factor
    • knocks off GDP from g-protein and allows GTP to attach
  94. GAP
    • GTPase Activating Protein
    • binds to GTP-bound g-protein and causes it to hydrolyze GTP to GDP
  95. examples of second messengers (4)
    • ions (Ca2+)
    • lipids (PIP2)
    • carbohydrates (IP3)
    • nucleotides (CAMP)
  96. receptors are ________ proteins (name domains)
    • tripartite
    • n-terminal, middle, c-terminal
  97. n-terminal of receptor
    • transcriptionally active domain (TAD)
    • recruiting factor for activators of transcription
  98. middle domain of receptor
    DNA binding domain

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