Chapter 19 - Genomics Flashcards
Genomics
Field that studies the entire collection of an organism’s DNA or genome. Involves sequencing, analyzing and comparing information.
Sequencing
determining the base order of an organism’s DNA or RNA. Often the first step to finding out detailed information about an organism.
Bacterial genome range
130 kilobase pairs to over 14 megabase
Viral genome range
0.859 to 2473 kilobase pairs
Shotgun Sequencing
initially involves construction of a genomic library, followed by the gragments being sequences and analyzed by a computer, searching for overlapping regions to form a longer stretch of sequence. Eventually all are aligned to give geneome sequence.
Second generation DNA sequencing
uses massively parallel methods, where multiple samples are sequenced side-by-side. Sequences are amplified by PCR, then attached to small bead, so that each bead carries several copies. Beads put into plate and sequenced
Third and Fourth generation DNA sequencing
Involed sequencing of a single molecule of DNA. Known as post-light sequencing, utilizes methods other than optical detection for sequencing
Bioinformatics
Combines many fields together to use the power of computers to analyze information contained in the genomic sequence.
Genome Annotation
Locating specific genes within a genome
Open Reading Frames (ORFS)
denotes a possible protein-coding gene. For double-stranded DNA, there are six reading frames to be analyzed. (DNA is usually read in bases of 3, with two stands of DNA)
How long is an ORF?
Typically 100 codons before a stop codon, with 3’ terminator sequences.
Functional ORF
One that is actually used by the organism to encode a protein
GenBank
database of over 200 billion base pairs of sequences that scientist can access
BLAST
Basic Local Alignment Search Tool .- programs for comparing both nucleotide sequences and amino acid sequences
Comparative Genetics
Genomes assessed for information regarding size, organization and content. Shows that many genes are derived as a result of gene duplication.
pan genome
represents all the genes found in all the members of species
paralogs
genes within a single organism that likely came about because of gene duplication
orthologs
genes acquired from a common ancestor
functional genomics
placing the genomic information in context
Transcriptome
the entire complement of RNA that a cell can make from its genome
Proteome
All the proteins encoded by an organism’s genome
Microarrays
Gene chips - solid supports upon which multiple spots of DNA are placed. Each spot represents a single gene. Can be used to determine what genes might be turned on or off
Proteomics
The study of the proteins of an organism
two-dimensional gel electrophoresis
first separates proteins based on isoelectric points - by pH gradient. Then ran through polyacrylamide gel - provides second dimension as they’re separated by size
Structural proteomics
focuses on three-dimensional structure of proteins. Often determined by protein modeling.
Matabolomics
Strives to identify complete set of metabolic intermediates produced by an organism
Metagenomics
environment genomics - extraction of pooled DNA directly from a specific environment
metagenome
genome of all organisms that may be present
phylotype
DNA sequence or group of sequences sharing level of similarity of a gene marker
