Bmsc 210 mid2 p1

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Bmsc 210 mid2 p1
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Bmsc 210 mid2 p1
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  1. Three informational macromolecules in the cell
    – DNA– RNA– Protein
  2. Replication:
    DNA is duplicated
  3. Transcription:
     information from DNA is transferredto RNA
  4. mRNA (messenger RNA):
    encodes polypeptides
  5. tRNA (transfer RNA):
    -Brings amino acids to ribosome in protein synthesis
  6. rRNA (ribosomal RNA):
    plays role in protein synthesis
  7. Translation:
    information in RNA is used to build polypeptides
  8. Eukaryote transcription
    each gene is transcribed individually
  9. Prokaryotes transcription
    multiple genes may betranscribed together
  10. Four nucelotides found in DNA
    • – deoxyadenosine (A)
    • – deoxyguanosine (G)
    • – deoxycytidine (C)
    • – deoxythymidine (T)
  11. Pyrimidine bases (single ring)
    • Cytosine
    • Thymine
    • Uracil
  12. Purine Bases (Two ring)
    Adenine Guanine
  13. Backbone of DNA chain is alternating ______ and the pentose sugar ______
    • phosphates
    • deoxyribose
  14. Adenine–Thymine pair has ______ hydrogen bonds and Guanine–Cytosine pair has ______  hydrogen bonds
    • two
    • three
  15. denaturation
    High heat breaks hydrogen bonds, causing denaturation
  16. Genome:
    entire complement of genes in cell or virus
  17. Viruses Genetics
    -genomes
    -shape
    • -contain either RNA or DNA genomes
    • – Can be linear or circular– Can be single or double stranded
  18. Plasmids:
    • -replicate separately from chromosome
    • – Great majority are double stranded
    • – Most are circular
    • – Generally beneficial for the cell (e.g., antibioticresistance)
    • – NOT extracellular, unlike virusesa genetic element that isexpendable and rarely contains genes required for growth under all conditions
    • - Genetic information encoded on plasmids may confer a selective growth advantageunder certain conditions
    • -In several pathogenic bacteria, virulence characteristics are encoded by plasmid genes
  19. Chromosome
    genetic element with“housekeeping” genes– Presence of essential genes is necessary fora genetic element to be called a chromosome
  20. Avg gene length is ___ base pairs
    1000
  21. episome
    • plasmids that can integrate into the cell chromosome; similar to situation seen with prophages
    • -essentially all can do this
  22. curing plasmids
    Removal of plasmids from host cells can result from various treatments
  23. Conjugative plasmids
    -can be transferred between suitable organisms via cell-to-cell contact between closely related, or distantly related bacteria (broad host range)
  24. Conjugal transfer controlled by ___ genes on plasmid
    tra
  25. R plasmids
    • – Resistance plasmids; confer resistance toantibiotics and other growth inhibitors(Figure 6.12)
    • – Widespread and well-studied group ofplasmids
    • – Many are conjugative
  26. 4 characteristics of Virulence factors
    • – Enable pathogen to colonize
    • – Enable pathogen to cause host damage
    • – Hemolysin-destruction of red blood cell
    • – Enterotoxin-dehydration of intestinal wall (diarrhea)
  27. Bacteriocins
    • – Proteins produced by bacteria that inhibit or kill closely related species or even different strains of the same species
    • – Colicin, nisin
    • - Genes encoding bacteriocins are often carried on plasmids
  28. psuedomonas
    • -famous bacteria for ability to eat anything due to plasmid genes
    • -common soil bacteria
  29. Transposable Elements
    • – Segment of DNA that can move from one site to another site on the same or a different DNA molecule
    • – Inserted into other DNA molecules
  30. Three main types of Transposable Elements
    • • Insertion sequences
    • • Transposons-multiple genes besides transpose genes
    • • Special viruses
  31. 3 DNA Replication components
    • 􀅖 Templates and Enzymes
    • 􀅖 The Replication Fork
    • 􀅖 Bidirectional Replication and the Replisome
  32. semiconservative DNA replication
    – Each of the two progeny double helices have one parental and one new strand
  33. Start codon
    AUG
  34. Stop Codon
    UTR
  35. Precursor of each nucleotide is a __________
    deoxynucleoside 5′-triphosphate
  36. Replication ALWAYS proceeds from the _′ end to the _′ end
    • 5
    • 3
  37. DNA polymerases
    • DNA polymerases catalyze the addition of dNTPs
    • - Five different DNA polymerases in E. coli –
    • - DNA polymerases require a primer
  38. DNA polymerase III
    primary enzyme replicating chromosomal DNA
  39. Primer made from RNA by ___
    primase
  40. DNA synthesis begins at the ______ in prokaryotes
    origin of replication
  41. Replication fork:
    -zone of unwound DNA where replication occurs
  42. DNA helicase
    unwinds the DNA
  43. Extension of DNA
    • – Occurs continuously on the leading strand
    • – Discontinuously on the lagging strand
    • • Okazaki fragments are on lagging strand
  44. Transcription of genes
    • -Only one of the two strands of DNA are transcribed by RNA polymerase for any gene
    • - Genes are present on both strands of DNA, but only one of the strands at any given location has correct code

    - RNA polymerase recognizes DNA sites and starts transcription at sites called promoters
  45. Transcription (DNA to RNA) is carried out by ___ ___
    RNA polymerase
  46. RNA polymerase uses ___ as template
    DNA
  47. - RNA polymerase has ___ different subunits
    five
  48. RNA precursors(4)
    ATP, GTP, CTP, and UTP
  49. Promoters
    • -site of initiation of transcription by DNA polymerase
    • –Recognized by sigma factor (sub unit of RNA polymerase)
  50. transcription terminators
    specific sites Transcription stops at
  51. Unlike DNA replication, transcription involves _______ units of DNA
    (size)
    • -smaller
    • – Often as small as a single gene
    • – Allows cell to transcribe different genes at different rates
  52. Sigma factors recognize two highly conserved regions of promoter
    • -Pribnow box
    • -35 region
  53. Pribnow box:
    located 10 bases before the start oftranscription (-10 region)
  54. 35 region
    located ~35 bases upstream of transcription
  55. Termination of RNA synthesis is governed by a specific _____ sequence
    DNA
  56. Intrinsic terminators
    • transcription is terminated without any additional factors
    • -hairpin in mRNA followed by uuuuu
  57. Rho-dependent termination
    Rho protein recognizes specific DNA stop sequences and causes a pause in the RNA polymerase
  58. Unit of transcription
    • -part of chromosome that is transcribed
    • -can contain code for more than one gene
  59. Most genes encode _______, but some RNAs are not translated (i.e., rRNA, tRNA)
    proteins
  60. Three types of rRNA:
    • 16S, 23S, and 5S
    • (s is a unit os size=svedburg)
  61. 2 very stable RNA types
    rRNA and tRNA
  62. tRNA cotranscribed with _____ or ______
    • rRNA
    • other tRNA
  63. mRNAs have ______ half-lives
    • short
    • (a few minutes or seconds)
  64. Prokaryotes often have genes clustered together
    – These genes are transcribed all at once as a single _____
    mRNA
  65. polycistronic mRNA
    An mRNA encoding a group of cotranscribed genes (multygene)
  66. 2 types of functioning proteins in cell
    • – Catalytic proteins (enzymes)
    • – Structural proteins
  67. Genetic code:
    • a triplet of nucleic acid bases (codon) encodes a single amino acid
    • – Specific codons for starting and stopping translation
  68. Degenerate code:
    • -multiple codons encode a single amino acid
    • -many have 6 codons
  69. Anticodon
    • -three bases of tRNA that recognize three complementary bases on mRNA
    • - Fidelity of recognition process between tRNA and aminoacyl-tRNA synthetase is critical (Figure 6.34)
    • – Incorrect amino acid could result in a faulty or nonfunctioning protein
  70. Wobble:
    • -irregular base pairing allowed at third position of tRNA (Figure 6.31)
    • -first two letters of an amino acid code are the same
    • -the third can vary creating a weaker bond with tRNA or a wobble
  71. Stop codons:
    terminate translation (UAA, UAG,and UGA)
  72. Start codon:
    translation begins with AUG (methionine)
  73. Reading frame:
    -triplet code requires translation to begin at the correct nucleotide because there are no spaces in code
  74. Shine–Dalgarno sequence (ribosomal binding site):
    sequence upstream of start sequence ensures proper reading frame
  75. Open reading frame (ORF):
    -AUG followed by a number of codons and a stop codon in the same reading frame
  76. at least _____ tRNA per amino acid
    one
  77. – Bacterial cells have _____ different tRNAs
    – Mammalian cells have ______ different tRNAs
    • 60
    • 100–110
  78. Specific tRNA for both a ______ and its _____ amino acid
    • codon
    • cognate
  79. tRNA and amino acid brought together by __________
    (enzyme)
    • aminoacyl-tRNA synthetases
    • – ATP is required to attach amino acid to tRNA
  80. tRNA is ______ in shape
    cloverleaf
  81. Ribosomes: sites of ______ synthesis
    – (amount) of ribosomes per cell
    – Composed of two subunits ( ___and___ in prokaryotes)
    – S = ______
    – Combination of ____and _____
    - E. coli has __ distinct ribosomal proteins that make up the sub units
    • protein
    • thousands
    • 30S and 50S
    • Svedberg units
    • rRNA and protein
    • 52
  82. Three main steps of translation
    • 1. Initiation:
    • 2. Elongation: 
    • 3. Termination:
  83. Initiation:
    • two ribosomal subunits assemble with mRNA
    • • Begins at an AUG start codon
  84. Elongation:
    • -amino acids are brought to the ribosome and are added to the growing polypeptide
    • • Occurs in the A and P sites of ribosome
    • • translocation: movement of the tRNA holding the polypeptide from the A to the P site
  85. Translocation:
    movement of the tRNA holding the polypeptide from the A to the P site
  86. Release factors (RF):
    • recognize stop codon and cleave polypeptide from tRNA
    • -causes ribosome to break apart
  87. Termination:
    • occurs when ribosome reaches a stop codon
    • • Release factors (RF): recognize stop codon and cleave polypeptide from tRNA
    • • Ribosome subunits then dissociate
    • • Subunits free to form new initiation complex andr epeat process

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