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The _______ is the entire complement of genetic information
Genome
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What elements does the genome include?
Protein coding genes, regulatory sequences and noncoding DNA
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What is genomics?
Discipline of mapping, sequencing, analyzing and comparing genomes
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______ is the science that applies powerful computational tools to DNA and protein sequences
Bioinformatics
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What is the purpose of bioinformatics?
To analyze, store and access sequences for comparative purposes
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What type of analysis allows for predictions of metabolic pathways and transport systems?
Comparative analysis
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In Prokaryotes, which type of genes are the most abundant?
Metabolic genes
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Which type of genes are typically prevalent in Prokaryotes?
Nontranslated RNA genes (rRNA, tRNA, small regulatory RNAs)
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Number of genes with roles that can be clearly identified in a given genome is ____ or less of total ORFs detected.
70%
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What are hypothetical proteins?
uncharacterized ORFs; proteins that likely exist but whose function is presently unknown.
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Hypothetical proteins likely encode ______ genes and make up ____ of the genome.
Nonessential; 30%
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______ is the entire complement of RNA produced under a given set of conditions.
Transcriptome
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What are microarrays?
Small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern.
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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
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What is proteomics?
Genome-wide study of the structure, function and regulation of an organism's proteins.
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________ is the technique used for the separation, identification and measurement of all proteins present in a sample
Two-dimensional (2D) polyacrylamide gel electrophoresis
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In 2-D polyacrylamide gel electrophoresis, what happens in the first (horizontal) dimension?
Proteins are separated by difference in isoelectric points.
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In 2-D polyacrylamide gel electrophoresis, what happens in the second (vertical) dimension?
Proteins are separated by size.
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Proteins with ____ sequence identity typically have similar functions while proteins with ____ sequence identity almost certainly have similar functions
>50% ; >70%
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______ homology is a much more accurate determination of gene similarity than ______ homology
Protein ; DNA
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What is the metabolome?
The complete set of metabolic intermediates and other small molecules produced in an organism.
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______ is one of the primary techniques used for monitoring metabolites.
Mass spectrometry
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What does homologous mean?
Related in sequence to an extent that implies common genetic ancestry.
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____ are groups of gene homologs.
Gene families
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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
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What are orthologs?
Genes found in one organism (species) that are similar to those in another organism but differ because of speciation.
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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.
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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
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_____ may transfer DNA between different organisms
Transposons
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_____ 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
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_____ are regions of bacterial chromosome of foreign origin that contain clustered genes for some extra property such as virulence or symbiosis
Chromosomal islands
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What are pathogenicity islands?
Chromosomal islands containing genes for virulence
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What are symbiosis islands?
Chromosomal islands containing genes for symbiosis
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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
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What is the core genome?
Genome shared by all strains of the virulent species
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What is the pan genome?
Genome that includes all the optional extras present in some but not all strains of the virulent species
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