Lecture 4

Question 1

Why do we use ribosomal RNA for phylogenetic clasiffication?

Answer 1

• Because it is essential and has not changed over time (conserved)
• Large allowing for non lethal mutations to accumulate

Question 2

Rule of parsimony

Answer 2

the sequence of evolutionary fchange is the one involving the fewest changes (mutations)

Question 3

Limits of using 16s RNA?

Answer 3

1) most orgs have more than one RNA gene
2) horizontal gene transfer can change RNA
3) only single gene considered

Question 4

DNA hybridization

Answer 4

isolating dna from two orgs and letting it reanneal together. the more cross hybridization, the more relatedness

Question 5

How is agrose gel made?

Answer 5

Using red algae you heat and allow H bonds between strands of agar to bind

Question 6

Reotation

Answer 6

The way that DNA fragments migrate through the gel (hermal motion of very long linear, entangled macromolecules in polymer melts or concentrated polymer solutions. Derived from the word reptile, reptation suggests the movement of entangled polymer chains as being analogous to snakes slithering through one another)

Question 7

Dideoxy sequencing

Answer 7

looks at chain termination to figure out base sequences

Question 8

Limitations of dideoxy

Answer 8

1) depends on ability to distinguish between one base additions
2) works by chaing termination
3) Tedious

Question 9

Pyrosequencing

Answer 9

looking at the light produced everytime a DNA is added to a strand using dNTP’s in the wells and looking at light emittion

Question 10

Parallel sequencing

Answer 10

Sequencing all DNA at one time and looking at contig alignment

Question 11

MLST

Answer 11

Multi locus sequencing use to sequence the uculturable looking at relatedness in large groups of bacteria