Micro Exam 2

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Micro Exam 2
2011-04-01 00:11:01
Micro Exam

Micro Exam 2
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  1. Eukaryotic cells (3)
    • 10-100 um
    • Nucleus with linear chromosomes, surrounded by 2 lipid bilayer membranes
    • Nuclear membranes have pore complexes and are contiguous with rough ER
  2. Eukaryotic Genome Size
    varies greatly, from 2.9 million BP to 2,800 million BP
  3. How many linear chromosomes are found in Eukaryotic cells?
    3 to 50
  4. Describe Chromosomes in Eukaryotic Cells (5)
    • 3 to 50 linear chromosomes
    • Basic unit of chromosomes is DNA coiled around histones
    • Visible by electron microscopy
    • reside in nucleus
    • get replicated every time the cell divides
  5. Genome size of Eukaroytic organisms
    2.9 million BP to 2,800 million BP
  6. "Junk DNA"
    Tandom-Repeated DNA
  7. Subcellular organelles that have their own DNA
    • Chloroplasts
    • Mitochondria
  8. Three RNA Polymerases in eukaryotes:
    • rRNA, in nucleolus, amanitin - resistant
    • mRNA, amanitin - very sensitive
    • tRNA, aminitin - somewhat resistant
  9. Regions of gene not coding for AA:
  10. The structure of a nuclear pore complex in a Eukaryotic cell consists of (5):
    • Basket
    • Inner Ring
    • Outer Ring
    • Anchor Protein
    • Active Trasporter
  11. Eukaryotic Ribosomes
    sensitive to diptheria toxin and cycloheximide, not sensitive to tetracycline or chloroamphenicol
  12. Separation of DNA Strands in Eukaryotic cells:
  13. Prokaryotic molecular biology
    • Most have a single circular chromosome
    • few thousand genes located on it
    • single origin of replication
  14. Molecular Biology of Archaea
    • Chromosome circular, haploid
    • Genome Size: 0.5 to 5.8*10^6 BP
    • Most DNA are supercoiling
    • DNA Gyrase is like bacteria
    • 1-3 origins of replication
  15. Archaea Transcription
    • No introns in most genes
    • mRNAs not spliced, but translated directly
    • Promoter- TATA-Box, TATA-Binding Protein like Eukarya
    • RNA Polymerase: 1, like Eukaryotic RNA Poly II
    • Rifamipin-Insensitive, Like Eukarya
  16. Archaea Translation (4)
    • Ribosomes 70S
    • sensitive to diphtheria toxin
    • resistant to most antibacterial inhibitors of protein synthesis (tetracyclines, chloroamphenicol)
    • AUG start codons use methionine
  17. Eukaryotice Translation (6)
    • Ribsosmes are 80S
    • Large subunit has 3 rRNAs, not just 2
    • Ribosomes not inhibited by most bacterial inhibitors of protein sysnthesis
    • are sensitive to diphtheria toxin
    • No shine Delgarno site by start codon (AUG)
    • first amino acid is methionine
  18. Plasmids (3)
    • replicate independently of the chromosome
    • may be present in several copies
    • typically have genes which are not essential for the cell under basic conditions, however may assist in resistance to antibiotics, etc (these are specialized genes)
  19. Bacterial Chromosome
    • In a circle/star shape
    • Super coils are tangled together and held together by proteins
    • Few million BP long
  20. Processing of Eukaryotic Pre-mRNA (3):
    • Attach 5-Methylguanosine Cap
    • Attach Poly-Adenosine Tail
    • Splice out Introns
  21. Exons Code for
    Folding/ FunctionalDomains of Polypeptide
  22. DNA Synthesis Needs (4)
    • Primer
    • Template Strand
    • dATP, dCTP, dGTP, dTTP
    • Enzyme: DNA Polymerase
  23. Restriction Endonucleases:
    • Cleave DNA at specific 4-6 ntsequences.
    • Methylation canprotect from them.
  24. Bacterial Ribosomes
    • 70S
    • Some antibiotics block protein synthesis only in bacterial ribosomes
  25. A Site
    tRNAs with amino acids enter
  26. P site
    tRNAs with amino acid form peptide bond
  27. E Site
    empty tRNAs leave
  28. Compare Bacteria, Archaea, and Eukarya in terms of: Range of genome size
    Bacteria has a slightly greater range than archaea
  29. Compare Bacteria, Archaea, and Eukarya in terms of: Chromosome number and topography
    Eukaryotes usually have a greater chromosome number. In bacteria it is usually one circular chromosome
  30. Compare Bacteria, Archaea, and Eukarya in terms of: Extent of extragenic regions in DNA
    Only present in eukaryotes.
  31. Compare Bacteria, Archaea, and Eukarya in terms of: Presence of histones
    Bacteria does not have true histones, but Eukaya and some Archaea do.
  32. Compare Bacteria, Archaea, and Eukarya in terms of: Number of RNA Polymerases, and their structure
    • Bacteria has one polymerase with two sub unit parts
    • Many sub units in Eukarya
    • Archaea have one polymerase but the one polymerase has 8-12 sub units (so is more similar in structure to eukaryotic polymerase)
  33. Compare Bacteria, Archaea, and Eukarya in terms of: Presence of genes in operons
    Eukarya and bacteria have genes in operons
  34. Compare Bacteria, Archaea, and Eukarya in terms of: Presence of introns in genes
    Only in Eukarya
  35. Compare Bacteria, Archaea, and Eukarya in terms of: Size of ribosomes
    Eukarya 80S; Archaea 70S; Bacteria 70S
  36. Compare Bacteria, Archaea, and Eukarya in terms of: Sensitivity of ribosomes to cycloheximide vs tetracycline
    • Eukaryotic insensitive to cycloheximide, sensitive to tetracycline.
    • Archaea are sensitive to cycloheximide and not tetracycline.
  37. Enzymatic Pathway
    • Generally starts with a material being acted on by an enzyme converting it to an intermediate.
    • Process continues until an end product is reach.
    • Process can be regulated at various steps.
  38. Allosteric Regulation of Enzymes
    • Allosteric molecule binds to an allosteric site.
    • Catabolic pathways: starting material may be allosteric activator of enzymes, may activate transcription of genes.
    • Anabolic pathway: end-product mat act as allosteric inhibitor, decrease transcription of genes.
  39. Two-component Transcriptional Regulatory System:
    • 1. Sensor kinase in plasma membrane.
    • 2. Response regulator acts as transcriptional activator when phosphorylated.
  40. Negative regulation:
    A repressor protein can bind operator, blocking binding of RNA polymerase to promoter-blocks transcription.
  41. Positive Regulation:
    A transcription activator protein must bind near promoter, and assist RNA poly binding at promoter.
  42. Example of positive transcriptional regulation
    • E. Coli prefers glucose as energy source
    • Glucose used up, cAMP produced
    • Signals to switch to other sugars (like lactose)
    • cAMP binds Catabolite Activator Protein
    • Stimulates transcription
  43. Attenuation
    another mechanism of regulating transcription of the trp operon
  44. Control of Transcription in Archaea
    • Mainly similar to Bacteria
    • Repressor proteins bind TATA box and nearby BRE regions near promoter
    • Block access of (TBP) and TFB general transcription factors
    • Transcriptional activator proteins enhance binding of TBP at promoter
  45. RNA Longevity
    Most mRNAs in bacteria have a short half-life, and are degraded by ribonucleases, some of which target secondary structures.
  46. Operons regulated by repressor proteins are known from some:
  47. Transcriptional activators known from some:
  48. Post-Transcriptional Regulationof Gene Expression:
    • mRNAs degraded by RNAases
    • Antisense RNAs bind to mRNAs
  49. Viral Genome
    Total size from less than 2 kBP to over 200 kBP (3-100 genes)
  50. Viral Capsid
    • protein coat
    • may be helical, Icosahedral, or complex
  51. Viral Envelope
    • consists of host membrane lipids and viral proteins
    • may have role in binding and infection of host cells
  52. Viral Life Cycle (5)
    • virus binds to a host cell
    • viral Genome is replicated
    • viral proteins are made on host cell ribosomes
    • new virions are assembled
    • mature virions are released from the host cell
  53. Bacteriophages (4)
    • Viruses of bacteria
    • have virions binding to cell wall of host
    • inject DNA genome into host cytoplasm
    • capsid remains outside
  54. Eukaryotic viruses
    entire virion taken into the host cell by endocytosis or membrane fusion
  55. DNA viruses (dsDNA)
    • Includes many bacterial viruses (bacteriophages)
    • (–) strand DNA is template for making mRNA by RNA polymerase
    • Genome of dsDNA replicated by DNA polymerase
  56. DNA Viruses (ssDNA)
    • must first make complementary DNA
    • then DNA can replicate
    • (–) strand serves as template for making viral mRNA
  57. RNA genome viruses
    May involve 2 kinds of RNA dependent RNA polymerases (Transcriptase & Replicase)
  58. Transcriptase
    transcribes (-)strand RNA into mRNA
  59. Replicase
    transcribes (+) strand RNA into ds replicative form (RF) RNA
  60. Retroviruses
    • Have a RNA genome which is made into a DNA copy.
    • The DNA copy is then made back into an RNA copy. An example is HIV.
  61. Transposons
    Can replicate - move to new location in chromosome or plasmid
  62. Lytic Cycle
    kills host cell
  63. Lysogenic cycle
    DNA integrates
  64. Transduction
    bacterial DNA carried alongin phage from cell to cell.
  65. Virions
    Replicating, infectiousRNAs, encode no proteins.
  66. Prions
    Misfolded proteins, infectious, catalyse misfolding of intact proteins
  67. ´╗┐What accounts for the high rate of mutation in RNA genome viruses?
    • DNA Polymerase has a mechanism where it
    • changes mutations – RNA does not check.
  68. Viral taxonomy determined by (4)
    • type of nucleic acid
    • capsid and envelope characteristics
    • genome size and sequence
    • host infected
  69. What unique kinds of enzymes and unique information flow occur in life cycles of RNA genome viruses?
    Genome RNA → + RNA / - RNA → - RNA
  70. Bacteriophage T4 of E. Coli (5)
    • has a genome that is moderatly large (~160k base pairs)
    • icosahedral head, a stalk, and a base plate
    • has a linear genome
    • has a unique base in to prevent destruction of phage by host restriction endonucleases
  71. Bacteriophage Lambda (3)
    • About 48k base pairs long
    • one of the earliest genomes to be sequenced
    • looks like the other phages, but does not have the base plate
    • rolling-circle replication mechanism
  72. M13 Bacteriophage (4)
    • single strand of DNA genome
    • cylindrical virus that binds to the sex phylos that are produced to do conjugation
    • viral DNA is transcribed to produce viral proteins
    • host cell survives the entire process
  73. M2 Bacteriophage (5)
    • Have 3600 base pairs
    • RNA can be translated directly by the host cell
    • To replicate, replicase must be used.
    • Takes single-stranded RNA and makes a (-) copy to make more (+) strand genomes.
    • Kills host
  74. Mutations
    Change in Physical Structure of DNA- such as changes in nucleotidesequence.
  75. Spontaneous Mutations
    Errors in DNA polymerase but DNA poly. can proofread
  76. Induced Mutations
    • UV light, X-rays, Ionizing Radiation, Chemicals.
    • Excision-repair enzymes can fix some damage
  77. Prototrophic
    can grow on minimal, defined media with minerals (N, P, S sources) and C-source (glucose)
  78. Auxotrophic
    • Can’t grow on minimal media
    • Mutation in a biosynthetic pathway, require amino acid, vitamin, ect.
  79. Influenza (5)
    • (-) stranded RNA genome
    • The virus binds to receptors and is brought into the host cell by endocytosis.
    • genomes then get into the nucleus of the host cell
    • negative strands of RNA are transcribed by Transcriptase and assembled by Replicase
    • Replicase does not proofread.
  80. Antigenic Drift in Influenza virus:
    • Host anitbodies no longer protect against virus.
    • surface proteins will change
  81. What is a sigma factor?
    is a prokaryotic transcription initiation factor that enables specific binding of RNA polymerase to gene promoters.
  82. How does a sigma factor influence transcription of genes?
    Initiates transcription