chapter 7

Question 1

coding sequences (CDS)

Answer 1

open reading frames (ORF) that appear to encode for proteins

Question 2

alignment

Answer 2

compairing coding sequences (CDS) to other coding sequences (CDS) to determine how similar each is to already known protiens

Question 3

BLAST (basic local alignment search tool)

Answer 3

a common program used for alignment of coding sequnces (CDS)

Question 4

orthologues

Answer 4

when a similar ORF is found in two organisms with a common acestor

Question 5

paralogues

Answer 5

from duplication of genes

Question 6

gene ontology

Answer 6

the field that descirbes the coding for protiens across organisms

Question 7

annotation

Answer 7

the process of identifying functional elements along a seqence of genome, giving meaning to it

Question 8

transcriptome anaylsis

Answer 8

Transcriptome analysis studies all of the organism’s RNA

Question 9

functional genomics

Answer 9

linking the genes to the function/physiology

Question 10

proteome analysis

Answer 10

proteome analysis studies the proteins produced by an organism at a given time in a particular environment.

Question 11

taxonomy

Answer 11

the science of classifying living organisms

Question 12

the 3 aspects of taxonomy

Answer 12

1. classification - organizing into groups
2. nomenclature - the vocabulary to make sure everyone knows the exact “thing” that is being classified
3. identification - the ‘fun’ part of finding and compairing new oraganisms

Question 12

phenetic classification

Answer 12

grouping together organisms based on phenotypical characteristcs

Question 13

genotipic classification

Answer 13

replaced phenetic classification by identifying organisms at the genome instead of phenotipical features

Question 14

binomial nomencalture

Answer 14

a system created by Carl Linneaus

italized name with two parts

pt1 (genus name) pt2 (species name)

if the organism is discovered to actually belong in a different taxa, only the genus name is changed.

Question 15

phylogenetic analysis

Answer 15

shows the evolutional development sometimes using phylogenetic trees

Question 16

Bergey’s Manual of Systematics of Archaea and Bacteria

Answer 16

a published manual for classification of bacteria and archaea species, initially developed by David Bergey and colleagues in 1923