MC1: The archaea

Question 1

In what type of conditions do archaea usually live?

Answer 1

Extreme conditions

Question 2

What are the three domains of life?

Answer 2

Bacteria, eukarya, archaea

Question 3

Who, in 1977, announced the discovery of archaea?

Answer 3

Carl Woese

Question 4

What did Carl Woese compare to discover the archaea?

Answer 4

Ribosomal RNA genes

Question 5

What was Carl Woese doing when he discovered archaea?

Answer 5

He was looking at how different bacteria were genetically releated

Question 6

Why are microbes harder to classify?

Answer 6

There is no fossil record of them

Question 7

Why did Carl Woese look at the 16S rRNA gene?

Answer 7

• Conserved
• Present in all organisms
• Not subject to horizontal gene transfer
• 16S rRNA is part of the small subunit of the bacterial ribosome (it stabilises it)
• The loops vary by species

Question 8

What were initially thought to be the three groups of archaea?

Answer 8

1. Methanogens
2. Halophiles
3. Hyperthermophiles

Question 9

Why were archaea initially viewed as exremophiles?

Answer 9

Because they had only been found living in harsh conditions such as hot springs and salt lakes

Question 10

Why is the view of archaea as extremophiles no longer valid?

Answer 10

They have since been found living in many habitats, including soils, oceans, marshlands, and the human colon, oral cavity, and skin

Question 11

Give examples of harsh conditions archaea can cope with. What are the names of organisms that can live in these conditions?

Answer 11

1. High salt concentrations
   Halophiles live in hypersaline environments such as salt lakes
2. Temperature
   Thermophiles live in hot springs where archaea grow optimally at >80°C; some can reproduce at 122°C
3. Acidic or alkaline conditions
   Acidophiles can grow at pH 0 (equivalent to thriving in 1.2M H₂SO₄)
   Alkaliphiles can grow at pH 11

Question 12

What is the role of uncultured archaea in deep-sea marine sediements?

Answer 12

Removal of methane via anaerobic oxidation of methane stored in these sediments

Question 13

What happens to methane at cold temperatures and high ocean pressure? What happens as oceans warm?

Answer 13

Methane combines with water into methane hydrate crystals

As oceans warm, this bubbles up, releasing more methane into the atmosphere

Question 14

How do archaea generate terrestrial methane?

Answer 14

They are present in rice paddies and in the guts of cattle

They generate approx. 10-25% of global methane emissions

Question 15

Are there any examples of archaeal pathogen or parasites?

Answer 15

No, but they are often mutualists or commensals

Question 16

What proportion of humans have methanogens in their guts? What ability does this give them?

Answer 16

50% – they can set fire to their farts!

Question 17

How are archaea exploited by humans?

Answer 17

• Methanogens are used in biogas production and sewage treatments
• Enzymes from thermophile archaea are exploited in biotechnology

Question 18

How are archaeal products used by humans?

Answer 18

• Pfu DNA polymerase from Pyrococcus furiosus allowed PCR to be used for DNA cloning which revolutionised molecular biology
  
  • It has superior thermostability and proofreading abilities to Taq DNA polymerase – Pfu possesses 3’→5’ proofreading abilities so errors in Pfu DNA polymerase-generated PCR fragments will have fewer errors than Taq-generated PCR ones
• Amylases and galactosidases that function at over 100°C allow food processing at high temperatures, e.g. the production of low lactose milk and whey
• Their stability makes their enzymes easier to use in structural biology so they are used as a proxy for protiens of interest

Question 19

What important role can archaea play in human disease treatment?

Answer 19

Archaeocins (a new class of antibiotics) differ in structure from bacterial antiiotics so may have novel forms of action

A few have been characterised but many more are believed to exist, especially within Holoarchaea and Sulfolobus

They may allow the creation of new selectable markers for use in archaeal molecular biology

Question 20

Do archaea have peptioglycan cell walls?

Answer 20

No

Question 21

What are the key differences between the cell walls of bacteria and archaea?

Answer 21

Arhcaeal cell walls are more chemically and structurally diverse

They are a semi-rigid lattice of pseudomurein, sugars, protiens, or glycoproteins

They do not contain peptidoglycan

Question 22

Compare bacterial flagella to archaeal flagella.

Answer 22

Bacterial: helical filaments that rotate to provie motility
Archaeal: similar but different in many ways and non-homologous

Bacterial: produced by the addition of flagellin subunits at the tip
Archaeal: produced by the addition of flagellin subunits at the base

Bacterial: thicker and hollow allowing flagellin subunits to pass through

Question 23

How are archaeal membranes different to bacterial and eukaryotic membranes?

Answer 23

1. Fatty acids
   B/E: fatty acids linked by ester bonds to a glycerol
   A: fatty acids linked by ether bonds to a glycerol
2. Side chains
   B/E: fatty acids
   A: branced isoprenes
3. Glycerol
   B/E: D-glycerol
   A: L-glycerol

Question 24

How does RNA polymerase differ between bacteria and archaea/eukaryotes?

Answer 24

Bacteria have simple RNAP consiting of four polypeptides

Archaea have multiple RNAPs and more than eight polypeptides

Eukaryotes have multiple RNAPs and 10-12 polypeptides, closer in size to archaea

Question 25

Differentiate between protein synthesis in archaea, bacteria, and eukaryotes.

Answer 25

• Various features of protein synthesis in archaea are similar to those of eukaryotes but not of bacteria
• Bacteria have an initiator tRNA that has a modified methionine
• Eukaryotes and archaea have an initiator tRNA with an unmodified methionine

Question 26

What energy sources do archaea and bacteria use?

Answer 26

• Organic compounds, e.g. sugars
• Ammonia
• Metal ions
• Hydrogen gas

Question 27

Has classical photosynthesis (using chlorophyll) been found in any archaea?

Answer 27

Nope