241 - 31, Comparative genomics and proteomics

Question 1

In some areas, long stretches of DNA (>1mb) are completely devoid of any know genes. Called _____ _____

Answer 1

gene deserts

Question 2

gene deserts size

Answer 2

> 1mb

Question 3

segmental duplication size

Answer 3

> 1kb

Question 4

Vertebrates have MORE / LESS protein diversity than do invertebrates.

Answer 4

more

Question 5

Vertebrate genomes DO / DO NOT encode more protein domains than do invertebrates.

Answer 5

do not (dependent on combinations)

Question 6

Explain protein diversity between vertebrates and invertebrates

Answer 6

greater diversity in vertebrae, because domains in more combinations

Question 7

regions where the order of genes within variously sized blocks is the same as their order in the most recent common ancestor of the two species

Answer 7

syntenty

Question 8

_______ are closely related genes.

Answer 8

homologs

Question 9

_______ refers to homologs inherited from a common ancestor.

Answer 9

orthologs

Question 10

_______ are genes that are related by gene duplication event in a genome.

Answer 10

paralogs

Question 11

proteomics (2)

Answer 11

2D gel

yeast 2-hybrid interaction screen

Question 12

Proteins are separated first by electric charge (first dimension) and then by molecular weight (second dimension) in a ___ ___

Answer 12

2D gel

Question 13

The DNA binding domain and activation domain of a transcription factor is fused to two proteins of interest. If the two protein interact, a functional transcription activator will be reconstituted.

Answer 13

Yeast 2-hybrid interaction screen

Question 14

most prokaryotic genome are . . .

Answer 14

single circular chromosome

Question 15

prokaryote genomes (3)

Answer 15

single circle (most common)
single linear
two circles

Question 16

prokaryotes have about _ kb per gene (this is DENSE / NOT DENSE)

Answer 16

1; dense

Question 17

A process by which both closely and distantly related bacterial species periodically exchange gene information over evolutionary time.

Answer 17

horizontal gene transfer

Question 18

one mechanism of horizontal gene transfer is ________

Answer 18

transformation

Question 19

repetitive DNA is frequently ___% of the total DNA in ________

Answer 19

> 50; eukaryotes

Question 20

_________ have many introns

Answer 20

eukaryotes (human)

Question 21

gene density: pro vs eu

Answer 21

pro - high

eu - low

Question 22

yeast __ kb per gene

humans __ kb per gene

Answer 22

2; 125

Question 23

genes found within introns are common in . . .

Answer 23

highly evolved plants

Question 24

gene density IS / IS NOT uniform

Answer 24

is not

Question 25

gene deserts (devoid of known genes) are how large?

Answer 25

> 1 mb

Question 26

why do vertebrates have more protein diversity than invertebrates?

Answer 26

assembled into more cominations (not because they have more domains [ they don't])

Question 27

number of protein domains between species is SIMILAR / VARIED

Answer 27

similar

Question 28

BLAST stands for

Answer 28

basic local alignment search tool

Question 29

_____ is an alignment value – more points for long matches, points deducted for interruptions or gaps.

Answer 29

BLAST

Question 30

“_____” value is like __-score–the probability that similarity between genes is random.

Answer 30

"expect"; p

Question 31

better matches have: HIGH / LOW BLAST score HIGH / LOW expect value

Answer 31

HIGH | LOW

Question 32

regions where the order of genes within variously sized blocks is the same as their order in the most recent common ancestor of the two species

Answer 32

synteny

Question 33

protein expression directly determines ______

Answer 33

phenotypes

Question 34

analysis of what proteins are translated in a certain cell type, or under certain experimental conditions

Answer 34

proteomics

Question 35

2-D gels separate ______ by what two variables

Answer 35

proteins; mass and charge

Question 36

yeast two-hybrid system used for detecting _____-______ interactions

Answer 36

protein-protein

Question 37

________ - linking a gene's sequence information to other information about its function and expression, the protein that it encodes, and information on similar genes in other species

Answer 37

annotation

Question 38

________ - all of the RNA molecules transcribed from a genome

Answer 38

transcriptome

Question 39

______ - all proteins encoded by a genome

Answer 39

proteome

Question 40

orthologs vs paralogs

Answer 40

ortholog - evolved from same gene in a common ancestor | paralog - duplication of a gene in evolutionary past (same organism)

Question 41

genes affecting a particular characteristic or function can be identified by using a genome wide ________ _____ and ________ ________

Answer 41

mutagenesis screen and positional cloning

Question 42

``` order the following for a mutagenesis screen: 1 - verify genetic basis 2 - positional cloning 3 - mutagenesis 4 - identify mutants ```

Answer 42

3, 2, 4, 1

Question 43

horizontal gene transfer has played a major role in _______ genome ________

Answer 43

bacterial genome evolution

Question 44

For multi-cellular eukaryotic organisms, what's the relationship between organismal complexity and amount of DNA?

Answer 44

None

Question 45

humans have vary long ______, as compared to other species

Answer 45

introns

Question 46

____ ________ precisely determines the molecular mass of a molecule; used to measure amount of each protein present

Answer 46

mass spectrometry

Question 47

Closely related genes are referred to as ________

Answer 47

homologs

Question 48

the somatic cells of a human male is made into a library and subjected to whole-genome sequencing. After the completion of the project, the number of contigs should be

Answer 48

24

Question 49

the somatic cells of a human female is made into a library and subjected to whole-genome sequencing. After the completion of the project, the number of contigs should be

Answer 49

23

Question 50

________ - regions where gene order in 2 species is the same as in the most common ancestor

Answer 50

synteny

Question 51

what 2 methods are used in conjunction in proteomics

Answer 51

2D gel followed by mass spectrometry