Chapter 7: Microbial Genetics

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marley9233
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Chapter 7: Microbial Genetics
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2011-10-18 18:37:45
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Microbial genetics DNA RNA Transcription Translation marley
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Exam 2
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  1. Structure of Prokaryotic Genomes
    • Chromosomes-haploid, circular molecule of DNA in nucleoid, Archaeal DNA is wrapped around globular proteins called histones
    • Plasmids-small molecules of DNA that replicate independently
  2. Types of plasmids in Prokaryotes
    • fertility factors
    • resistance factors
    • bacteriocin factors
    • virulence plasmids
  3. Structure of Eukaryotic Genome (Nuclear Chromosomes)
    • typically more than one chromosome per cell
    • linear
    • sequestered within the nucleus which is surrounded by nuclear envelope
    • diploid
  4. Extranuclear DNA of eukaryotes
    • DNA molecules of mitochondria and chloroplasts
    • resemble chromosomes of prokaryotes
    • only code for about 5% or RNA and proteins
    • Some fungi and protozoa carry plasmids
  5. Semiconservative replication
    New DNA is composed of one original strand and one daughter strand
  6. DNA Replication begins where? In which direction?
    • begings at the origin
    • DNA polymerase replicates 5' to 3'
    • strands are antiparallel
  7. Leading Strand
    • synthesized continuously
    • moves toward the replication fork
    • begins with addition of RNA primer to provide a 3' hydroxyl end
    • DNA polymerase III synthesizes strand by adding nucleotides
  8. Lagging strand
    • goes against replication fork
    • still replicates 5' to 3'
    • replicates in short fragments called Okazaki fragments
    • DNA polymerase I removes RNA primers, synthesizes DNA, ligase joins fragments together
  9. Helicase
    breaks hyrdrogen bonds in order to unzip DNA
  10. Topoisomerases
    reduces tension caused by supercoils
  11. Bidirectionality
    • characteristic of DNA replication in prokaryotes
    • replication begins on both sides, happening in opposite directions
    • 
  12. How is Eukaryotic replication of DNA differ from prokaryotic?
    • uses four DNA polymerases
    • thousands of replication origins
    • shorter okazaki fragments
  13. Transcription
    information in DNA is copied as RNA
  14. Translation
    Polypeptides synthesized from RNA
  15. Central Dogma of Genetics
    • DNA transcribed to RNA
    • RNA translated to form polypeptides
  16. Central Dogma of Genetics Diagram
  17. Events in Transcription
    • Four types of RNA transcribed from DNA
    • Occur in nucleoid of prokaryotes
    • there are three steps
  18. Four types of RNA transcribed from DNA
    • RNA primers
    • mRNA
    • rRNA
    • tRNA
  19. RNA primers
    for DNA polymerase to use during DNA replication
  20. mRNA
    carry genetic information from chromosomes to ribosomes
  21. rRNA
    combine with ribosomal polypeptides to form ribosomes
  22. tRNA
    deliver correct sequence of amino acids to ribosomes based on nucleotide sequence in mRNA
  23. Three steps in Transcription
    • Initiation
    • Elongation
    • Termination
  24. Initiation of Transcription
    • RNA polymerases are enzymes that synthesize RNA
    • polymerases bind to specific nucleotide sequences called promoters located near beginning of gene
    • primase
  25. Sigma Factor
    • in bacteria
    • polypeptide subunit of RNA polymerase
    • necessary for recognition of promoter
  26. Elongation of Transcription
    • triphosphate ribonucleotides align with their DNA complements and RNA polymerase links them together, synthesizing RNA
    • no primer is needed
  27. Differences between RNA and DNA polymerase
    • RNA unwinds and opens DNA itself, no helicase required
    • RNA does not need a primer
    • Transcribes only one of the DNA strands
    • slower than DNA polymerase III
    • useds ribonucleotides instead of deoxyribonucleotides
    • uracil incorporated instead of thymine nucleotides
    • proofreading function is less sufficient
  28. Termination of Transcription (Two ways)
    • Self-termination
    • Enzyme-dependent termination
  29. Self-Termination of Transcription
    transcription of DNA terminator sequences causes the RNA to fold, loosening the grip of polymerase on DNA
  30. Enzyme-dependent Termination
    • Rho pushes between polymerase and DNA, releasing polymerase, RNA transcript and Rho.
    • *Rho is a termination protein
  31. Conccurrent RNA Transcription
    • once an RNA polymerase molecule has cleared the promoter, another molecule of polymerase can recognize the promoter and initiate transcription
    • thus, many moleucles of polymerase are able to transcribe the same gene
  32. Difference in transcription of Eukaryotes
    • RNA transcription occurs in the nucleus (not cytosol)
    • also occurs in mitochondria and chloroplasts
    • 3 types of RNA polymerase (m,r, and tRNA)
    • numerous transcription factors (instead of sigma) and elongation factors
    • mRNA processed before translation
  33. Capping
    • a modified guanine nucleotide is added to the 5' end of the mRNA
    • capping ensures the mRNAs stability while it undergoes translation
  34. Polyadenylation
    • 100-250 adenine nucleotides are added to the 3' end
    • helps produce matures messeneger RNA
  35. Splicing
    removing all the introns to make a functinal mRNA containing only coding regions called exons
  36. Introns
    • nucleotide sequence within a gene that is removed by RNA splicing to generate a final mature RNA product
    • non-coding
  37. Exons
    • nucleic acid sequence that make up a mature form of RNA
    • coding
  38. Translation
    process where ribosomes use genetic information of nucleotide sequences to synthesize polypeptides
  39. Codons
    triplets of mRNA nucleotides that code for specific amino acids
  40. Start Codon
    AUG
  41. Stop Codon
    • UAA
    • UAG
    • UGA
  42. Differences in eukaryotic and prokaryotic RNA
    • Eukaryotic cells produce pre-mRNA to make mRNA
    • one molecule of eukaryotic mRNA contains instructions for one polypeptide
    • transcription and translation do not occur simultaneoulsy in eukaryotes (transcription in nucleus, translation- cytoplasm)
  43. Transfer RNA
    • sequence of 75 ribonucleotides
    • clover leaf structure with 3 main hairpin loops
    • transfers the correct AA to a ribosome during polypeptide synthesis
    • has an anticodon triplet in its bottom loop and an acceptor stem for a sepcific AA at it's 3' end
    • wobble hypothesis
  44. Anticodon
    a nucleotide triplet that is complimentary to mRNA codon for that AA
  45. Ribosomes and Ribosomal RNA
    • prokaryotes- 50S and 30S form 70S
    • eukaryotes- 60S and 40S subunits form 80S
    • smaller unit of ribosome shaped to accommodate 3 codons at one time
    • has three tRNA-binding sites
  46. Three tRNA-binding sites
    • A site- accommodates a tRNA delivering an AA
    • P site- holds a tRNA and the growing polypeptide
    • E site- discharged tRNAs exit from this site
  47. Three stages of Translation
    • Initiation
    • Elongation
    • Termination
  48. Initiation of Translation in Prokaryotes
    • small ribosome unit attaches to mRNA at a ribosome binding site so as to position a start codon at it's P site
    • tRNA attaches at the ribosomes P site (energy from GTP used to bind tRNA in place)
    • larger subunit attaches to form a complete initiation complex
  49. Elongation of Translation
    • tRNA delivers its specific AA to the Asite
    • ribozyme forms a peptide bond between terminal AA and new AA
    • ribosome moves one codon down the mRNA transferring each tRNA to the adjacent binding site
    • ribosome releases "empty" tRNA from the E site
    • appropriate enzyme "recharges" the tRNA with another AA, cycle repeats, each time adding another AA.
  50. Termination of Translation
    • does not involve tRNA
    • release factors recognize stop codons, severs the polypeptide from the final tRNA
    • ribosome dissociates into subunits
  51. Translation differences in Eukaryotes
    • innitiation occurs when ribosomal unit subunit binds to 5' guanine cap
    • first amino acid is methionine rather than f-methionine
  52. Mutation
    • change in the nucleotide base sequence of a genome
    • rare event
    • almost always harmful
    • rarley leads to a protein that improves ability of an organism to survive
  53. Two Types of Mutations
    • Point Mutations
    • Frameshift Mutations
  54. Point Mutations
    • most common
    • one base pair is affected
    • insertions, deletions, and substitutions
  55. Frameshift Mutations
    • nucleotide triplets after the mutation are displaced
    • insertions and deletions
  56. Silent Mutation
    do not result in a change to the amino acid sequence of a protein
  57. Missense Mutation
    • A point mutation in which a single nucleotide is changed
    • resulting in a codon that codes for a different amino acid
    • they can render the resulting protein nonfunctional
  58. Nonsense Mutation
    • A point mutation in a sequence of DNA that results in a premature stop codon
    • results in a incomplete, and usually nonfunctional protein product
  59. Mutagens (four kinds)
    • Radiation
    • Chemical Mutagens
    • Nucleotide-altering chemicals
    • Frameshift Mutagens
  60. Radiation Mutagens
    • ionizing radiation e.g. X-rays, gamma rays
    • Nonionizing radiation e.g. ultraviolet light
  61. Chemical Mutagens
    • Nucleotide analogs
    • Disrupt DNA and RNA replication
  62. Nucleotide-altering chemicals
    • result in base pair substitution and missense mutations
    • Aflotoxin- converts guanine nucleotides to thymine nucleotides
  63. Frameshift Mutagens
    acridine, ethidium bromide
  64. Pyrimidine dimer
    • molecular lesions formed from thymine bases in DNA via photochemical reactions
    • ultraviolet light
  65. DNA Repair Mechanisms
    • Light repair
    • Dark repair
    • Base excision repair
    • Mismatch repair
  66. Light repair
    Photolyase enzyme-functions only in the presence of light, it breaks up tiny thymers
  67. Dark Repair
    • does not require light
    • uses repair enzymes
    • excises bases
    • polymerase and ligase repair the gap
  68. Mismatch Repair
    completely go through the whole strand to find where the incorrect nucleotide was inserted, removes the area, ligase comes in and joins them
  69. Methods to recognize mutants
    • Positive Selection
    • Negative (indirect) selection
  70. Positive Selection
    • method to recognize mutants
    • sample is spread on two plates, one with penicillin and one without
  71. Negative (indirect) selection
    • method for recognizing mutants
    • grow sample on a plate
    • "stamp" innoculated plate onto two new plates one selective and the other not
  72. Genetic Recombination
    exchange of nucleotide sequences often mediated by homologous sequences
  73. Recombinants
    cells with DNA molecules that contain new nucleotide sequences
  74. Vertical gene transfer
    organisms replicate their genomes and provide copies to descendents
  75. Horizontal Gene Transfer
    • donor cell contributes part of gene to recipient cell
    • Three Types:
    • Transformation
    • Transduction
    • Bacterial Conjugation
  76. Transformation
    • cells that take up DNA are competent
    • results from alterations in cell wall and cytoplasmic membrane that allow DNA to enter cell
    • **Griffith's Experiment with mice
  77. Transduction
    • generalized-transducing phage carries random DNA segment from donor to recipient
    • specialized-only certain donor DNA sequences are transferred
    • bacteriophages carry them
  78. Bacterial Conjugation
    • takes place with help of a plasmid which contains fertility factor called f positive cells
    • cells that contain f plasmid have conjugation pillus
    • conjugation pillus draws the other cell in, then the tranfer of DNA takes place
    • this complimentary strand now contains DNA, both now become double stranded
    • F-negative cells now become F-positive cells because the plasmid has been transferred
  79. Conjugation involving an Hfr cell
    • High frequency of recombination cell
    • Plasmid that contains Fpositive cell, with help of sex pilus
    • this recombination is not complete- only a section of DNA is transferred so cell remaisn f-negative
    • becuase high frequency, replicate much faster (no time to transfer all DNA)-recipient cell still negative
  80. Transposons
    • Jumping genes
    • segments of DNA that move from one location to another in the same or different molecule
    • result is a kind of frameshift insertion (transposition)
    • **all contan palindromic sequences at each end (spelt same way forwords as backwards)
  81. Simple Transposons
    • insertion sequences
    • have no more than two inverted repeats and a gene for transposase
  82. complex transposons
    contains one or more genes not connected with transposition

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