Lecture 5/6: taxonomic history

Question 1

what are the 3 steps in PCR and what is each step for?

Answer 1

1. denaturation (96 C): heat the reaction strongly to separate/denature the DNA strands. product will be a ssDNA template that can be used in the next step.
2. Annealing (55-65 C): Cool the reaction so that the primers can bind to their complementary sequences on the single-stranded template DNA.
3. extension (72 C). Raise the reaction temperatures so Taq polymerase extends the primers, synthesizing new strands of DNA.

Question 2

what is Monera?

Answer 2

• a concept that originated by Haeckel in the mid-19th century for microbes that were not protists.
• referred to as ‘bacteria’, rarely as ‘eubacteria’
• the concept of what a bacterium is, but was proved to define in a taxonomically-sound fashion.

Question 3

in 1977, what did Woese propose?

Answer 3

there were two types of bacteria:

• eubacteria
• Archaebacteria (a new group proposed by Woese).

Question 4

classical microbial taxonomy was based upon morphology and physiology, which are not optimal criteria on their own, but were the best available at the time.

This changed when?

Answer 4

in 1977 when Woese based phylogenetic analysis on ribosomal RNA.

Question 5

what was believed int he prokaryotic theory?

Answer 5

• there is no such thing as prokaryotes, it was a dream by Haeckel but it was disproven.
• in taxonomy, all levels need to be equal. We want to compare all organisms at the same level.

THEREFORE,

• the term prokaryotes is used as an adjective for organisms with no true nucleus.
• it infers that all prokaryotes are related. but they are not.
  prokaryotes are named as such because they do not have a true nucleus, but, they are not all related.

Question 6

what was the Monera supposed to be comprised of?

Answer 6

the bacteria and archaea

Question 7

what is the definition of a prokaryote

Answer 7

• a prokaryote is an artificial taxonomy with an artificial definition.
• they are not eukaryotes, no membrane-bound nucleus (true nucleus)
• BUT IN TAXONOMY YOU NEED UNIFYING DEFINITIONS
• therefore, not having a true nucleus does not give us the right to use the definition of prokaryote in taxonomy.
• the term should not be used at all because it is confusing now.