MICI2100 1.2

Question 1

Define phylogeny

Answer 1

the evolutionary relationship between organisms.

Question 2

name the three domains in Woese & Fox’s Tree of life

Answer 2

Archaea, Bacteria, Eukarya

Question 3

Genome organization of Archaea

Answer 3

prokaryotic (lack nucleus)

Question 4

membrane composition Archaea

Answer 4

branched hydrocarbon chains attached to glycerol by ETHER linkages (ether linkages more stable than ester, therefore can withstand more harsh environments)

Question 5

cell walls of archaea

Answer 5

unique, they LACK peptidoglycan

Question 6

antibiotic sensitivy of archaea

Answer 6

not sensitive.

Question 7

DNA packaging of archaea

Answer 7

histones

Question 8

motility of archaea

Answer 8

archaella rotate – flagella are solid

Question 9

examples of organisms in archaea domain

Answer 9

methanogens, extreme halophiles, and hyperthermophiles

Question 10

genome organization of Bacteria

Answer 10

prokaryotic – lacks nucleus

Question 11

membrane composition of bacteria

Answer 11

unbranched fatty acid chains attached to glycerol by ESTER linkages

Question 12

cell walls of bacteria

Answer 12

peptidoglycan

Question 13

antibiotic sensitivity of bacteria

Answer 13

unique

Question 14

DNA packaging of bacteria

Answer 14

nucleoid-associated proteins (NAPs)

Question 15

motility of bacteria

Answer 15

flagella rotate

Question 16

examples of organisms in bacteria domain

Answer 16

gram+ bacteria, gram- bacteria, mycobacteria, mycoplasma, cyanobacteria

Question 17

genome organization of eukarya

Answer 17

eukaryotic –has nucleus

Question 18

membrane composition of eukarya

Answer 18

unbranched fatty acid chains attached to glycerol by ESTER linkages

Question 19

cell walls of eukarya

Answer 19

LACK peptidoglycan

Question 20

antibiotic sensitivity of eukarya

Answer 20

NOT sensitive

Question 21

DNA packaging of eukarya

Answer 21

histones

Question 22

motility of eukarya

Answer 22

flagella whip

Question 23

examples of organisms in domain of eukarya

Answer 23

the four kingdoms - animalia, fungim plantae, protista

Question 24

the tree of life has changed overtime, give rundown of stages of the tree stage 1

Answer 24

Carl Linnaeus - developed a new way to categorize plants and animals – separated all living things he could SEE (plants and animals)

Question 25

the tree of life has changed overtime, give rundown of stages of the tree stage 2

Answer 25

Ernst Haeckel -- proposed four kingdoms (animals, plants, protists, and monera. monera included all bacteria (were prokaryotic) -- protists were all organisms that were not animals, plants, or fungi.

Question 26

the tree of life has changed overtime, give rundown of stages of the tree stage 3

Answer 26

Robert Whittaker -- added a fifth kingdom -- fungi. --fungi is a distinct branch of eukaryotes since the behaviours and appearances differ so much from protists.

Question 27

what differences did Woese and Fox concentrate on to differentiate the domains

Answer 27

the differences in the sequences of nucleotides in the ribosomal RNAs of any organism.

Question 28

basic description of horizontall gene transfer

Answer 28

the transfer of genes from one organism to another

Question 29

basic description of vertical gene transfer

Answer 29

gene transfer from parent to offspring

Question 30

give an example of a horizontal gene transfer given proteobacteria and fungi

Answer 30

an operon involved in siderophore biosynthesis was acquired from proteobacteria into a group of closely related yeasts. the genes qwere altered over the time they were resident in the yeasts, and were found to be expressed. their gene products were functional siderophores which are membrane ion transporters. Yeasts that were not able to transport iron across their membrane can now do so because of this operon.

Question 31

why did Woese and Fox choose rRNA

Answer 31

they chose it because they hypothesized that it would be very slow to evolve -- that the species would not easily tolerate mutations in this gene.

Question 32

the ribosome is an intricate machine -- main responsibility

Answer 32

responsible for translating mRNA to protein. (protein synthesis)

Question 33

basic structure of ribosome

Answer 33

2 subunits -- one small and one large and one 16S rRNA 16S folds into 3D shape bound by proteins to form the 30S ribosomal unit small subunit = 30S -- made up of 16S rRNA and 21 proteins large subunit = 50S -- two rRNA peices (5S and 23S rRNA) and 31 proteins 30S + 50S = 70S -- complete ribosome.

Question 34

similarities and differences between eubacteria and archaea -- small subunit assembly

Answer 34

similar - have the same sedimentation coefficient (30S) diff - more proteins bound to the archaeal subunit. (3v2) -- these archaeal proteins have sequence similarity to proteins found in similar roles in the eukaryotic small subunit -- makes archaeal enzyme more similar to eukaryotic than prokaryotic ribosome.

Question 35

similarities and differences between archaea and bacteria large subunit

Answer 35

sedimentation coefficient is similar for bacteria and archaea but larger for eukarya -- accessory proteins are VERY similar between archaea and eukarya -- evidence that archaea are closer evolutionary to eukaryotes than to prookaryotes (bacteria)

Question 36

how to identify new form of life using rRNA and DNA

Answer 36

- obtain a sample of organism. - isolate the DNA - use specific primers and PCR to amplify ribosomal DNA gene sequences - give to sequencing gurus - they will read chromatograms - and given this data can compare DNA sequence obtained to known ribosomal DNA sequences and place on tree where you see fit.