Chapter 9

Question 1

genome

Answer 1

entire complement of genetic info including genes, regulatory sequences and noncoding DNA

Question 2

genomics

Answer 2

discipline of mapping, sequencing, analyzing and comparing genomes

Question 3

first genome sequences in 1976

Answer 3

RNA citrus MS2; 5386 bp

Question 4

first cellular genome sequenced in 1995

Answer 4

haemophilus influenzae

Question 5

human genome contains..

Answer 5

3 billion pb and 25000 protein coding regions

Question 6

sequencing

Answer 6

determine the precise order of nucleotides in a DNA or RNA molecule

Question 7

generation

Answer 7

succesive major changes in sequencing technology that confer
-increase in speed, drop in cost of sequencing

Question 8

sanger method

Answer 8

first generation sequencing

Question 9

presently, most labs access _____ generation sequencing

Answer 9

second

Question 10

shotgun sequencing

Answer 10

entire genome is cloned, and resultant clones are sequenced

-sequencing is redundant

Question 11

genome assembly

Answer 11

connecting the DNA fragments in the correct order and eliminating overlap

Question 12

annotation

Answer 12

converting raw sequence data into a list of genes present in the genome

Question 13

bioinformatics

Answer 13

science that applies powerful computational tools to DNA and protein sequences for the purpose of analyzing, storing, and accessing the sequences of comparative purposes

Question 14

majority of genes encode

Answer 14

proteins

Question 15

functional open reading frame (ORF)

Answer 15

encodes a protein

Question 16

how do computer algorithms search for ORFs?

Answer 16

looks for start/stop codon and Shine-Dalgarno sequences

Question 17

hypothetical proteins

Answer 17

proteins that exists, but whose function is currently unknown and encode nonessential genes

Question 18

noncoding RNA

Answer 18

RNA that does not code for proteins; lack start codon and have multiple stop codons (tRNA, rRNA)

Question 19

unlike prokaryotes, eukaryotes genome contains….

Answer 19

large fraction of non coding DNA

Question 20

on average a prokaryotic genome is ____ bp long

Answer 20

1000

Question 21

as genome size increases, gene content….

Answer 21

proportionally increases

Question 22

smallest cellular genomes belong to…

Answer 22

parasitic or endosymbiotic prokaryotes

Question 23

estimates suggest minimum # of genes for a variable cell is…

Answer 23

250-300 genes

Question 24

many genes can be identifies by….

Answer 24

comparative analysis

Question 25

comparative analysis

Answer 25

identifying sequence similarities to genes found in other organisms

Question 26

most abundant class of genes

Answer 26

metabolic genes and gene coding for protein sequences

Question 27

what makes up a minor fraction of genome?

Answer 27

DNA replication and transcription genes

Question 28

number of genes with role that can be identified in a given genome is...

Answer 28

70% > total ORFs detected

Question 29

archaea typically devote a high percentage of their genomes to ___ than bacteria

Answer 29

higher

Question 30

archaea contain fewer genes for ___ than bacteria

Answer 30

carbohydrate metabolism or cytoplasmic membrane functions

Question 31

metagenome

Answer 31

total gene content of the organism present in an enviro

Question 32

transcriptome

Answer 32

entire complement of RNA produced under a given set of conditions

Question 33

interactome

Answer 33

- complete set of interactions among molecules | - data expressed in the form of network diagrams

Question 34

metabolome

Answer 34

the complete set of metabolic intermediates and other small molecules produces in an organism

Question 35

microbiome

Answer 35

- lyses and extract DNA - sequence DNA - assemble genomes

Question 36

microarrays

Answer 36

hybridization techniques can be used in conjunction with genomic sequence data to measure gene expression

Question 37

RNA sequence

Answer 37

deep sequencing of cDNAs allowing comprehensive quantitation of all RNAs in a cell

Question 38

what info can be derived from microarray

Answer 38

- global gene expression - expression of specific group of genes under different conditions - expression of genes with unknown function - comparison of gene expression - identification of specific strains

Question 39

homologous

Answer 39

related sequence that implies common genetic ancestry

Question 40

gene families

Answer 40

group of gene homologs

Question 41

paralogs

Answer 41

genes within organisms whose similarities to one or more genes in the same organism is the result of gene duplication

Question 42

orthologs

Answer 42

genes found in one organism that are similar to those in another organism but differ because of speciation

Question 43

gene analysis in the 3 domains suggests that...

Answer 43

many genes present in all organisms have common evolutionary roots

Question 44

horizontal gene transfer

Answer 44

1. transformation 2. transduction 3. conjugation elements: plasmids, phage, transposons and insertion sequences (isoelectric points)

Question 45

vertical gene transfer

Answer 45

gene replication and cell division (size)

Question 46

core genome

Answer 46

shared by all strains of the species

Question 47

pan genome

Answer 47

includes all the optional extras present in some but not all strains of the species

Question 48

polyacrylamide gel electrophoresis

Answer 48

technique used for the separation, identification, and measurement of all proteins present in a sample

Question 49

how are proteins separated in a 2D page?

Answer 49

1. horizontal--> isoelectric points | 2. vertical--> size

Question 50

interactomes

Answer 50

- complete set of interaction among molecules | - data expressed in the form of network diagrams

Question 51

what is the primary technique for monitoring metabolites?

Answer 51

mass spectrometry

Question 52

systems biology

Answer 52

integration of different field of "ohms" research - genomics - proteomics - transcriptomics - metabolomics