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2011-05-06 10:27:57
Chapter Microbiology Chang

Chapter 13 Microbiology Dr. Chang
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  1. The _______ is the entire complement of genetic information
  2. What elements does the genome include?
    Protein coding genes, regulatory sequences and noncoding DNA
  3. What is genomics?
    Discipline of mapping, sequencing, analyzing and comparing genomes
  4. ______ is the science that applies powerful computational tools to DNA and protein sequences
  5. What is the purpose of bioinformatics?
    To analyze, store and access sequences for comparative purposes
  6. What type of analysis allows for predictions of metabolic pathways and transport systems?
    Comparative analysis
  7. In Prokaryotes, which type of genes are the most abundant?
    Metabolic genes
  8. Which type of genes are typically prevalent in Prokaryotes?
    Nontranslated RNA genes (rRNA, tRNA, small regulatory RNAs)
  9. Number of genes with roles that can be clearly identified in a given genome is ____ or less of total ORFs detected.
  10. What are hypothetical proteins?
    uncharacterized ORFs; proteins that likely exist but whose function is presently unknown.
  11. Hypothetical proteins likely encode ______ genes and make up ____ of the genome.
    Nonessential; 30%
  12. ______ is the entire complement of RNA produced under a given set of conditions.
  13. What are microarrays?
    Small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern.
  14. What can be learned from microarray experiments?
    • Global gene expression
    • Expression of specific groups of genes under different conditions
    • Expression of genes with unknown functions
    • Comparison of gene content among closely related organisms
    • Identification of specific organisms
  15. What is proteomics?
    Genome-wide study of the structure, function and regulation of an organism's proteins.
  16. ________ is the technique used for the separation, identification and measurement of all proteins present in a sample
    Two-dimensional (2D) polyacrylamide gel electrophoresis
  17. In 2-D polyacrylamide gel electrophoresis, what happens in the first (horizontal) dimension?
    Proteins are separated by difference in isoelectric points.
  18. In 2-D polyacrylamide gel electrophoresis, what happens in the second (vertical) dimension?
    Proteins are separated by size.
  19. Proteins with ____ sequence identity typically have similar functions while proteins with ____ sequence identity almost certainly have similar functions
    >50% ; >70%
  20. ______ homology is a much more accurate determination of gene similarity than ______ homology
    Protein ; DNA
  21. What is the metabolome?
    The complete set of metabolic intermediates and other small molecules produced in an organism.
  22. ______ is one of the primary techniques used for monitoring metabolites.
    Mass spectrometry
  23. What does homologous mean?
    Related in sequence to an extent that implies common genetic ancestry.
  24. ____ are groups of gene homologs.
    Gene families
  25. What are paralogs?
    Genes within an organism (species) whose similarity to one or more genes in the same organism is the result of gene duplication
  26. What are orthologs?
    Genes found in one organism (species) that are similar to those in another organism but differ because of speciation.
  27. What is the difference between paralogs and orthologs?
    Paralogs are genes similar to organisms within the same species and orthologs are genes similar to organisms in a different species.
  28. What is horizontal gene transfer?
    • The transfer of genetic information between organisms, as opposed to vertical inheritance from parental organisms.
    • -May be extensive in nature
    • -May cross phylogenetic domain boundaries
  29. _____ may transfer DNA between different organisms
  30. _____ mediate large-scale chromosomal changes within a single organism
    • Transposons
    • -Presence of multiple insertion sequences (IS)
    • -Recombination among identical IS can result in chromosomal rearrangements
  31. _____ are regions of bacterial chromosome of foreign origin that contain clustered genes for some extra property such as virulence or symbiosis
    Chromosomal islands
  32. What are pathogenicity islands?
    Chromosomal islands containing genes for virulence
  33. What are symbiosis islands?
    Chromosomal islands containing genes for symbiosis
  34. What is the "pan"/"core" concept and describe the two genomes to which it refers?
    • Bacterial species consist of two components:
    • -Core genome: shared by strains of the species
    • -Pan genome: includes all the optional extras present in some but not all strains of the species
  35. What is the core genome?
    Genome shared by all strains of the virulent species
  36. What is the pan genome?
    Genome that includes all the optional extras present in some but not all strains of the virulent species