Topic 1

Question 1

Taxonomy:

Answer 1

Science of classifying/naming biological organisms

Question 2

Phylogeny:

Answer 2

Study of the evolutionary relationships between different organisms

Question 3

Each organism has two names:

Answer 3

The genus (more broad) and species (more specific)

Question 4

Scientific Names

Answer 4

• Species names (species/genus) italicized(or underlined - handwriting only)
• The genus is capitalized and species is lower case
• Higher taxa (family, class, order, phylum, kingdom) are not italicized. They are capitalized, through.
• After the first use in a manuscript, paper, or report, scientific names are abbreviated with the first letter of the genus plus the species name

Question 5

Subspecies:

Answer 5

Essentially just the next finer classification after species

Question 6

Biovar or biotype -

Answer 6

grouping based on physiological or biochemical

difference from other members of the species

Question 7

Serovar or serotype -

Answer 7

grouping based on surface antigens

Question 8

Phylogenetic trees

Answer 8

• Visual means of showing predicted
  evolutionary relationships between different organisms
• Evolutionary time goes from left(root) to right (modern lineages)
• Branches show evolutionary history
  unique to connecting lineages

Question 9

Determining phylogenetic relationships: comparing DNA sequences

Answer 9

• Over evolutionary time, DNA sequences change
• Comparing DNA sequences that are conserved amongst all organisms can be used to determine how closely related they are
• More differences in DNA sequence = more evolutionary distance
• Certain DNA sequences are better choices than others.Typically looking for highly conserved genes with a highly conserved function that accumulate mutations slowly over time.

Question 10

Determining phylogenetic relationships: SSU rRNA sequencing

Answer 10

• The ribosome is a conserved feature of all organisms of earth
• The ribosomal RNA (rRNA) of the small subunit (SSU) of the ribosome is commonly sequenced to infer phylogenetic relationships
• Variable regions useful for identifying relationships, conserved regions useful for PCR

Question 11

The Woese tree of life

Answer 11

- Universal tree of life based on nucleotide sequence similarity in
ribosomal RNA (rRNA) 

• Genealogy of all life on Earth
• Established the presence of three domains of life: Bacteria,Archaea, Eukarya

Question 12

16S rDNA to identify/classify bacteria

Answer 12

• Isolate genomic DNA (pure culture, environmental/clinical sample)
• Use PCR primers that bind highly conserved regions of 16S rDNA
• PCR amplify & sequence 16S rDNA. Align/analyze sequences

Question 13

Phylogenetic trees: Limitations

Answer 13

1. Horizontal gene transfer (HGT)

2. homologous recombination

Question 14

homologous recombination

Answer 14

DNA sequence of host genes can be replaced with that of homologous genes from another organism