Lecture 24

Question 1

Forward genetics

Answer 1

We choose a phenotype and try to find out what gene controls it, what exactly causes it, etc

Question 2

How can you begin to decipher a sequences genome, a random sequence of 4 nucleotide bases

Answer 2

There are many markers/gene elements like promoters, regulatory regions, introns exons etc, but few are actually detectable
Best bet is to find an ORF, a stretch of genetic info that does not contain a stop codon, you’re looking for an exon or a gene
Note: you have to look at different frames! What is a start codon in one frame is a stop or nothing in the next, gotta shuffle it

Question 3

How can you tell if an open reading frame is actually involved in a gene or if its just coincidence (long sequence with no codons that happens to have a start)

Answer 3

You compare it to other genomes and check whether its conserved in terms of evolution, you may find that it lines up with other previously discovered exons

Question 4

CDNA

Answer 4

DNA copy that is complementary to an mRNA strand, this meaning it differs from the original because it wont contain introns, regulatory regions, promoters, etc, strictly the coding region but in DNA form

Question 5

EST

Answer 5

Expressed sequence tag, when scientists were poor they couldn’t sequence a whole gene for its cDNA so they only did the ends

Question 6

CDNAs and ORFs that are part of potential genes

Answer 6

If you can find a cDNA that matches the ORF youre looking at, thats strong evidence that its an actual gene
Why: ORFs that are suspected of being genes are defined as have a start codon and no stop for a while, this would be an exon, and cDNA contains only exons, and we only get cDNA from mRNAs, and those are translated aka its a real coding gene, so if the exon you found matches an exon in a soon-to-be translated transcript, its likely a real gene

Question 7

Are all exons translated

Answer 7

No, not those from the UTRs, so not all exons are actually protein-encoding

Question 8

Comparative genomics

Answer 8

Studying the genome and comparing it to that of other species to find evolutionarily similar genes or similar regulatory sequences, not only to identify them but you can also see how important they are, the more conserved the more likely they’re important
You can also compare sequences within an organism or individuals within the same species (evaluating different phenotypes)

Question 9

How can you test whether a sequence is actually a regulatory sequence

Answer 9

You clone it and associate it to a reporter gene in a bacterial cell and see if its capable of promoting transcription of this reporter gene

Question 10

Synteny

Answer 10

The idea that the genes in human and mouse occur in the same order (ish) and the same chromosome, so its the same general arrangement of info