Module 7 - Genomics

Question 1

What is a genome?

Answer 1

• entire complement of genes of a cell or virus that are found in its chromosomes

Question 2

What is genomics?

Answer 2

• attempt to understand content, organization, function and evolution of genetic information contained in whole genomes

Question 3

What is structural genomics?

Answer 3

• determine organization and sequence of genetic information

Question 4

What is a DNA library?
(aka genomic library)

Answer 4

• collection of clones containing all of the DNA fragments from one source

Question 5

What are the 2 types of DNA libraries?

Answer 5

• genomic & cDNA

Question 6

What is a cDNA library?

Answer 6

• cDNA = complementary DNA
• cDNA is the DNA sequence that is complementary to an mRNA
• cDNA library has sequences that only correspond to a transcribed gene (non-coding, introns, etc. are left out)
• useful in many instances

Question 7

How to make a cDNA library

Answer 7

• mRNA must be separated from other cellular RNAs
• mRNAs can be separated from other RNAs using oligo (dT) column
• this is a column packed with short fragments of DNA consisting entirely of thymine nucleotides. As RNA moves through the column, poly-A tails will bind
• at the end, mRNAs are eluted with an appropriate buffer
• one strand of cDNA is then made using reverse transcriptase. DNA Pol is then used to make the other strand
• finally, DNA fragments are cloned into vector of choice
• frequency of cDNA in library depends on the abundance of corresponding mRNA in a tissue/cell sample
• cDNA libraries are tissue/cell-type and stage-specific

Question 8

Screening a library

Answer 8

• purpose of screening a library is to find clones that contain DNA sequences/genes of interest
• common method is to add a labelled probe to replica of the library
• if labelled probe hybridizes to complementary DNA sequence in a colony in the library, then that colony will retain the label

Question 9

What are model organisms?

Answer 9

• are non-human organisms that have been studied extensively in order to understand human phenomena

Question 10

What are homologs?

Answer 10

• genes from the same or different organisms that have sequence similarity are called homologs
• not only are individual genes conserved between humans and model organisms, but whole signalling pathways are conserved too.

Question 11

What are the advantages of model organisms?

Answer 11

• model organisms are well-developed experimental systems
• allows researchers to explore possible causes/treatments when experimentation on humans would be unethical
• model organisms are easy to grow in the lab and have relatively short generation times

Question 12

Advantage of having sequenced genomes

Answer 12

• projects move ahead more quickly
• can do ‘reverse’ genetics
• allows the study of novel genes
• molecular evolution studies of individual genes and gene groups
• combining genomics and functional genomics allows the study of gene organization; possible co-regulation of expression of genes with similar expression patterns
• estimate number of genes in genomes of different species

Question 13

Forward genetics

Answer 13

• geneticists mutate a model organism and look for interesting phenotype
• then they try to identify and isolate the gene that lead to the mutant phenotype

Question 14

Reverse genetics

Answer 14

• knowing the sequences of all of the genes in a genome, scientists can start with the gene of interest, delete it, and then determine what, if any phenotype occurs
• knock out/deletion or knockout its function with RNAi

Question 15

What does chimera mean?

Answer 15

• genetic mix of two cell types