Genes & Genomes

Question 1

Define genomics

Answer 1

sequencing genomes of cultured organisms

Question 2

Define transcriptomics

Answer 2

sequencings expressed sequence tags - cDNAs

now is RNA-seq

Question 3

Define metagenomics

Answer 3

culture-independent sequencing from a community of organisms

Question 4

Define proteomics

Answer 4

large-scale analysis of proteins in mixtures

Question 5

What does proteomics require?

Answer 5

a reference genome

Question 6

Define metabolomics

Answer 6

study of small-molecule profiles

Question 7

What factors contributes the the RNA world theory?

Answer 7

1. DNA is modified RNA
2. RNA can store information
3. RNA is inherently more reactive than DNA and capable of 2ndary structure

Question 8

Why is RNA inherently more reactive than DNA?

Answer 8

2’-OH group on ribose sugar

Question 9

What are ribozymes?

Answer 9

naturally occuring RNA molecules capable of catalyzing reactions without protein presence

Question 10

The spliceosomes - complex can perform what reaction? What ribozyme does it share characteristics with?

Answer 10

u2-u6
splicing

GII introns

Question 11

Where do snRNAs originate from?

Answer 11

GII introns

Question 12

Homologs are genes/proteins that….

Answer 12

share common ancestry

Question 13

orthologs are genes/proteins that

Answer 13

evolve via speciation from a common ancestral gene

Question 14

paralogs are genes/proteins that

Answer 14

are related within a genome and evolve via duplication

Question 15

What are the four methods of gene duplication?

Answer 15

1. Tandem DNA-based duplication
2. Retroposition
3. DNA-based gene fusion
4. Tc-mediated gene fusion

Question 16

What is the mechanism of tandem gene duplication?

Answer 16

Unequal cross-over of transposable elements and produces a tandem gene by recombination

Question 17

What is the mechanism of retroposition?

Answer 17

mRNA is reverse transcribed and integrated into the genome as a retrogene

Question 18

What is the mechanism of DNA-based gene fusion?

Answer 18

juxtapositin of partial duplicates produce chimeric genes with fused sequences

Question 19

What is the mechanism of Tc-based gene fusion?

Answer 19

Different genes acquire intergenic Tc and splicing signals and produce a chimeric RNA which is then RT and intergrated into the genome

Question 20

What are orphan genes a.k.a. ORFans

Answer 20

genes without obvious homologs

Question 21

How do orphan genes arise?

Answer 21

1. gene duplication coupled with extreme divergence

2. from non-coding DNA

Question 22

What is the mechanism of orphan genes arising from non-coding DNA?

Answer 22

1. Mutations abolish a Proto-ORF’s frame disruptions

2. Proto-ORF acquires promoter and is transcriptionally active

Question 23

How are duplicated genes relatively similar in sequence and function?

Answer 23

via concerted evolution

Question 24

What factors influence the rate and fate of duplicated genes?

Answer 24

1. Rate of duplication
2. DNA recombination machinery
3. Gene structure
4. Population Size
5. Impact of new duplicate