BIOTEC E3 C9

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shockwave
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119654
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BIOTEC E3 C9
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2011-11-29 23:14:51
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BIOTEC E3 C9
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  1. Genomics is closely related to --------- which uses computers, computational tools, and databases to organize and analyze DNA and protein information
    bioinformatics
  2. T OR F ?
    One goal of genomics is compilation and organization of both expressed gene sequences and other
    non-expressed regions.
    TRUE
  3. INSULIN RESISTANT DIABETES AND HYPER CHOLESTREOLMIA (LDLR) GENES CAN BE FOUND ON WHAT CHROMOSOME?
    19
  4. CHROMOSOME 19 HAS ------- BASES.
    67 MILLION
  5. CHROMOSOMAL BANDING PATTERENS ARE CAUSED BY WHAT?
    differences in the ratio of the bases adenine and thymine to guanine and cytosine
  6. Karyotype is generated....HOW?
    by grouping all chromosomes of an individual together
  7. -------------- ------------- can be used to examine metaphase chromosomes (condensed version)
    Light microscopes
  8. HUMAN CHROMOSOME. HOW MANY?
    • 22 AUTOSOMES &
    • X AND Y SEX CHROMOSOMES.
    • (X IS BIGGER)
  9. DEFINE "CONTIG"
    CONTINUOUS SEQUENCE OF BP FROM ONE MARKER TO THE NEXT
  10. CONSTRUCT A CONTIG
    • 1. RFLP MARKER TO RESTRICTION SITE OF DISEASE.
    • 2. PROBE ON 5'
    • 3. ID SEQUENCE AND MAKE PROBE FOR 3'
    • 4. RUN AGAIN
    • 5. YOU NOW HAW A CONTINUOUS SEQUENCE OF BP FROM ONE MARKER TO THE NEXT.
  11. Genetic Linkage Maps
    NAME 3 POINTS
    • -Genes on the same chromosome
    • -phenotypictraits
    • -Genes can be followed from generation to generation within famlies, 5000 disorders have been studied this way
  12. IN A GENETIC LINKAGE MAP, genes A and B are separated by recombination 1% of the time (1:100) then they------ APART
    1 cM apart (1 million bp)
  13. Homologous recombination can occur during meiosis via ------- ------ events. HOW MANY PER PAIR?
    • crossing over
    • 1.5 cross overs per pair of chromosomes
  14. T OR F?
    IF GENES ARE LINKED CROSSOVER IS UNLIKLY, WHY?
    TOO CLOSE
  15. Frequency of cross over is a measure of the linear distance between ---- ----- ----- -----.
    genes on linkage map
  16. CROSSOVER UNITS (MEASUREMENTS)
    Distances are measured in centrimorgans (cM)
  17. WHEN DOES CROSSOVER OCCUR?
    DURING MEIOSIS.
  18. DISEASE GENE FOR BREST AND PROSTATE CANCER ARE ON WHAT CHROMOSOME?
    16
  19. Specific physical regions of the DNA with
    variations in DNA sequence within a specific region for different individuals...KNOWN AS WHAT?
    DNA POLYMORPHISM
  20. IF A DNA POLYMORPHISM IS LOCATED ON AN INTRON, WILL CHANGE BE PRECEIVABLE?
    • NO.
    • HAS TO BE ON CODEING GENE.
  21. T OR F?
    polymorphisms are detectable at the DNA level and can serve as markers
    TRUE
  22. Restriction fragment length polymorphisms (RFLPs) ARE DETECTED HOW?
    RESTRICTION ENDONUCLEASES
  23. YACs cloning vectors are used to
    fit the large fragments of about ------- TO --------- BP
    roughly 7,500 clones for the entire human genome
    3-400,000 bp
  24. ------- --------- ------ can be used to clone pieces of DNA of up to 200,000 base pairs in length
    • Bacterial artificial chromosomes
    • (BACs)
  25. THE ENTIRE GENOME IS STUDIED YSING A GENOMIC LIBARARY AND WHAT?
    Yeast Artificial Chromosomes (YACs)
  26. THIS PROCESS SHOWS THE ORIENTATION OF GENES ON INDIVIDUAL CHROMOSOMES
    • FISH
    • Fluorescence in situ hybridization
  27. DEFINE FISH
    • Fluorescence in situ hybridization.
    • PROBES FOR METAPHASE CHROMOSOMES IN 2 LOCATIONS.
  28. Localizes coding regions to specific chromosome regions or bands (exons) AND Combine
    linkage maps with this method to locate disease causing genes....MAP TYPE?
    cDNA (PHYSICAL MAP)
  29. -Also called bottom-up mapping
    -Chromosome cut into overlapping fragments
    -Clone fragments and determine order
    -Fragments will form continuous DNA blocks
    WHAT MAP TYPE ?
    HIGH RES PHYSCIAL MAP
  30. HOW TO YOU MAP A PART OF A CHROMOSOME?
    piece is cut out and restricted, fragments cloned in YACs, mapped and sequenced using standard methods
  31. map types range from course
    to fine resolution of genetic locations:
    NAME THEM FROM LOWEST TO HIGHEST
    • Lowest: genetic map
    • -Measures frequency of recombination between linked markers, genes or noncoding (GENES)

    • MID LOW: Restriction
    • - DNArestriction fragments:1-2 Mb fragments are separated and mapped.( BIG FRAGMENTS)

    • MID HIGH YAC
    • -0.4 cM to 1 cM fragments.
    • -subclones is 20,000 to 40,000 bp (SML FRAGS)


    • Highest: DNA base sequence map
    • -Separate each chromosome to make 24 libraries (22 autosomal + 1each for X andY)
  32. Human genome project REFERENCE SYSTEM, HOW MANY BP?
    • 200-500 of partially sequenced DNA are used to
    • identify clones, contigs, long stretches
  33. Standard markers used for physical mapping of DNA.
    • STS
    • SEQUENCE TAGGED SITES
  34. Can use cDNA region as STS that is called an
    ---------- --- -------
    • expressed-sequence tag (EST).
    • -ESTs are landmarks along the map
  35. T OR F ?
    HGP Goal to generate STSs every 100,000 bp for each human chromosome (30,000 STSs)
    TRUE
  36. Powerful method for finding location of genes that cause inherited diseases, and track chromosome walking.
    • polymorphic DNA markers
    • -Need flanking DNA markers as starting points, Hybridization to clones with contigs in the disease region...get 2 maps...compare and find region.
  37. All genes in the entire----- chromosome genome
    46
  38. Human genome contains
    -------- TO ------- genes on --- pairs of chromosomes
    • ~30,000-40,000
    • 23
  39. Smallest chromosome is ---- AT -------- BASE PAIRS
    Y at 50 million
  40. LARGEST CHROMOSOME?
    #1 WITH 250BP
  41. -------- bp in a haploid genome
    3 BILLION
  42. HGP HAS A GOAL TO MAKE TWO MAPS NAME THEM
    • Genetic linkage maps:
    • -Determine the relative arrangement and distances between genes and markers on chromosomes

    • Physical maps specify two things:
    • -The physical location, in base pairs
    • -Distance between genes or DNA fragments with unknown functions
  43. Distance between genes or DNA fragments with unknown functions
    WHAT MAP WOULD YOU LOOK AT?
    PHYSICAL MAP
  44. Genome Project Timeline

    ----- First physical map published.
    -----The public human genome sequence draft was published
    --------Close to 99.9%
    • 1994
    • 2001
    • 2003
  45. Potential Uses for Genome-Related Information
    • treatments and diagnostic methods
    • identification of all the genes and other
    • technologies to analyze genome-related information
    • understanding of human evolution, gene regulation.
    • genetic counseling
  46. T OR F?
    HGP.....DNA samples were from males, although female donors were used to refine DNA
    sequences in later stages of the project
    TRUE
  47. CRAIG VENTER'S COMPANY
    • CELERA.
    • SHOTGUN APPROACH
  48. The human genome contains a little more than ----- BP
    • 3 billion base pairs
    • (3164.7 million nucleotides)
  49. The number of genes found was close to one-third1/3 of the expected number of genes in the genome ------------------- ---------------- --------------- PREDICTED-------------- + more random than other genomes
    (23,000–30,000 protein-encoding genes rather than the predicted 80,000–100,000)
  50. approximately ----% of the human genome encodes for the production of -------- with similar protein families to other organisms
    • 1.5%
    • PROTEINS
  51. Repeated sequences that do not encode proteins make up at least ----% of the genome
    —they are thought to affect ------ ----------and dynamics and is a much higher %
    than all other organisms, but have stopped accumulating repeats (not so in mice)
    • 50%
    • chromosome structure
  52. The average length of a gene is
    ------- nucleotides, although sizes vary greatly
    3000
  53. T OR F ?
    Genes are not evenly distributed
    across a chromosome;Genes concentrate in random regions, with large amounts of noncoding DNA between them
    TRUE
  54. Gene-dense areas are composed primarily of --- & --- nucleotides.
    Gene-poor regions have more --- & ---- nucleotides
    • Gene-dense:G- and C
    • Gene-poor: A- and T
  55. Chromosome: FEWEST AND MOST GENES
    • Y 231 GENES
    • #1 2968 GENES
  56. Approximately ----- genes originated directly from --------.
    • 200
    • BACTERIA
  57. T OR F ?
    Human proteins are more complex than proteins with similar functions in lower
    organisms
    TRUE
  58. The germline mutation rate in ----- is two times higher than in -----
    MALES HIGHT THEN FEMALES
  59. The nucleotide sequence in all humans is ------% identical
    99.9%
  60. More than ------% of newly discovered genes have unknown functions
    50%
  61. How chromosomes are organized AND The roles of DNA that doesn’t code for proteins ARE NOT COMPLETELY UNDERSTOOD.
    TRUE
  62. Proteomics involve the following aspects:
    • -expression and id of proteins in a given cell
    • -structure of proteins (for example, tertiary folding)
    • - interactions with each other in the cell
  63. Proteomics is difficult...2 POINTS
    • each cell type has the same DNA complement, but a
    • different proteome

    proteome can change depending on the physiological state of the cell or the organism
  64. DEFINE Transcriptome
    Full complement of genes called “transcripts” that are made in a specific cell type under a specific set of conditions, revealing changes in transcription for every gene in the genome
  65. DEFINE Metabolome
    • Entire metabolic state of a cell, including the array of substrates, metabolites, and other small molecules that are made in different cells and tissues
    • EX:four varieties of Arabidopsis
  66. Pharmaceutical companies mostly use ------------------- in drug development
    pharmacogenomics
  67. An example of a DNA database is ------, which is hosted at the National Center for Biotechnology
    OTHERS 2 ARE----- AND ------
    • GenBank
    • European Molecular Biology Laboratory (EMBL)
    • DNA DataBank of Japan (DDBJ)
  68. Tools of Bioinformatics
    • DNA and protein sequences COMPARISON
    • Prediction of RNA secondary structure—RNA folding
    • Protein classification
    • Gene prediction using DNA sequences
    • Genome analysis
  69. MYTONIC DYSTROPHY...WHAT CHROMOSOME?
    19
  70. WHAT DOES ELSI MEAN?
    • The HGPs ethical, legal, and social implications (ELSI) working group established by the DOE and NIH
    • (HGP action plan co-sponsors)

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