Module 3: Archaea

Question 1

Euryarchaeota

Answer 1

contains the methanogens

Question 2

Crenarchaeota

Answer 2

extremophiles
high temperature, high acidity (acidophiles), high salinity, or high pressure (barophiles)
modified proteins that contain more alpha helices
use of amino acids that encourage salt bridges and, specifically, side chain interactions

Question 3

Thaumarchaeota

Answer 3

most abundant organism on earth
low temperature
oxidize ammonia

Question 4

Nanoarchaeota

Answer 4

Nanoarchaeum equitans

is a symbiont that associates with Ignicoccus

Question 5

How are amino acids different between mesophiles and extremophiles

Answer 5

increased proportions of arginines and tyrosines

fewer cysteines and serines

Question 6

How were archaea first discovered and by whom

Answer 6

Carl Woese & George Fox in 1970’s
distinct rRNA sequences
Karl Stetter discovered Ignicoccus and Nanoarhcaeota, thinking they were bacteria

Question 7

key differences and similarities between archaea and bacteria

Answer 7

differences:
no methane producing bacteria
RNA polymerase
no nucleosome

same
size: approx. 0.5-5 microns
shapes: coccus, rod-like, spiral
mRNA, tRNA, ribosomes and DNA
inclusion bodies: gas vessicles
single circular chromosome
absent of a membrane-bound nucleus

Question 8

Key differences and similarities between archaea and eukaryotes

Answer 8

same:
RNA polymerase
histone proteins
package DNA in a nucleosome

Question 9

Differences in histones of archaea and eukaryotes

Answer 9

Eukarya: histone octamer interacts with approxiamtely 160bp of DNA
Archaea: histone tetramer interacts with approximately 60bp of DNA

Question 10

What group of archaea are associated with methanogenesis

Answer 10

methanothermobacter
methanosarcina
methanocaldococcus
methanococcus

Question 11

major phyla of the archaea and describe their common characteristics

Answer 11

crenarchaeota - extremophiles
euyarchaeota - methanogens
korarchaeota - uncultured archaea
nanoarchaeota - only nanoarchaeum which is symbiont with ignicoccus
thaumarchaeota - oxidize ammonia

Question 12

describe the shapes of cells found within the archaea

Answer 12

Typically 0.5-5 microns in diameter

Coccus, rod-like, spiral, pleiomorphic

Question 13

explain how Haloquadratum walsbyi tolerates high salinity

Answer 13

square-shaped
very high surface:volume ratio
increased biphytanyl in plasma membrane

Question 14

list three types of methanogens based on their growth substrate

Answer 14

hydrogenoclastic - break down hydrogen
Acetoclastic - break down acetate
Methylotrophic - break down one carbon compounds

Question 15

explain where you would find methanogens and why

Answer 15

anoxic environments - landfills, large intestines, sediments, waste water sludge, rice paddies, hydrothermal vents, cecum, rumen, termites
inhibited by oxygen
require carbon dioxide and hydrogen - end products of fermentation

Question 16

describe why the relationship between Nanoarchaeum and Ignicoccus is “bizarre.”

Answer 16

Ignicoccus:
ATP production in the periplasm
Nanoarchaeum:
does not contain any metabolic genes - including not being able to make its own membrane (lipid production), ATP production, amino acid production, nucleotide production
IS able to produce an S-layer, which protects Ignicoccus too

Question 17

Cytoplasmic membrane of archaea compared to bacteria

Answer 17

Head group:
A - glycerol 1-phosphate
B - glycerol 3-phosphate

Tails:
A - phytanyl chains
B - fatty acid hydrophobic

Attachment:
A - Ether group
B - Ester group

Question 18

Cell Wall differences

Answer 18

B:
beta 1-4, glycosidic linkages
NAMs
Presence of D-isomer amino acids

A:
beta 1-3, glycosidic linkages
NATs - not susceptible to lysozymes
No D-amino acids in the cell wall, only L-isomers

Question 19

Flagella of Archaea compared to Bacteria

Answer 19

B:
hollow tube
flagellin subunits pass through to grow through the tip
single flagellin protein

A:
solid
builds from base, like hair
multiple flagellin protein types