Chapter 19 - Genomics

Question 1

Genomics

Answer 1

Field that studies the entire collection of an organism’s DNA or genome. Involves sequencing, analyzing and comparing information.

Question 2

Sequencing

Answer 2

determining the base order of an organism’s DNA or RNA. Often the first step to finding out detailed information about an organism.

Question 3

Bacterial genome range

Answer 3

130 kilobase pairs to over 14 megabase

Question 4

Viral genome range

Answer 4

0.859 to 2473 kilobase pairs

Question 5

Shotgun Sequencing

Answer 5

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.

Question 6

Second generation DNA sequencing

Answer 6

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

Question 7

Third and Fourth generation DNA sequencing

Answer 7

Involed sequencing of a single molecule of DNA. Known as post-light sequencing, utilizes methods other than optical detection for sequencing

Question 8

Bioinformatics

Answer 8

Combines many fields together to use the power of computers to analyze information contained in the genomic sequence.

Question 9

Genome Annotation

Answer 9

Locating specific genes within a genome

Question 10

Open Reading Frames (ORFS)

Answer 10

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)

Question 11

How long is an ORF?

Answer 11

Typically 100 codons before a stop codon, with 3’ terminator sequences.

Question 12

Functional ORF

Answer 12

One that is actually used by the organism to encode a protein

Question 13

GenBank

Answer 13

database of over 200 billion base pairs of sequences that scientist can access

Question 14

BLAST

Answer 14

Basic Local Alignment Search Tool .- programs for comparing both nucleotide sequences and amino acid sequences

Question 15

Comparative Genetics

Answer 15

Genomes assessed for information regarding size, organization and content. Shows that many genes are derived as a result of gene duplication.

Question 16

pan genome

Answer 16

represents all the genes found in all the members of species

Question 17

paralogs

Answer 17

genes within a single organism that likely came about because of gene duplication

Question 18

orthologs

Answer 18

genes acquired from a common ancestor

Question 19

functional genomics

Answer 19

placing the genomic information in context

Question 20

Transcriptome

Answer 20

the entire complement of RNA that a cell can make from its genome

Question 21

Proteome

Answer 21

All the proteins encoded by an organism’s genome

Question 22

Microarrays

Answer 22

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

Question 23

Proteomics

Answer 23

The study of the proteins of an organism

Question 24

two-dimensional gel electrophoresis

Answer 24

first separates proteins based on isoelectric points - by pH gradient. Then ran through polyacrylamide gel - provides second dimension as they’re separated by size

Question 25

Structural proteomics

Answer 25

focuses on three-dimensional structure of proteins. Often determined by protein modeling.

Question 26

Matabolomics

Answer 26

Strives to identify complete set of metabolic intermediates produced by an organism

Question 27

Metagenomics

Answer 27

environment genomics - extraction of pooled DNA directly from a specific environment

Question 28

metagenome

Answer 28

genome of all organisms that may be present

Question 29

phylotype

Answer 29

DNA sequence or group of sequences sharing level of similarity of a gene marker