Chapter 27 - Bacteria and Archaea

Question 1

What is a distinctive feature of prokaryotes?

Answer 1

They lack a nucleus

Question 2

What are the prokaryotic domains of microscopic organisms that cycle carbon but don’t produce or consume oxygen?

Answer 2

Bacteria and Archaea

Question 3

What is the basic organization of the cells of prokaryotes?

Answer 3

• No membrane-bound nucleus
• Not really any cell compartments
• Circular chromosomal DNA
• Sometimes circle plasmid DNA (replicate independent of cDNA)
• Plasma membrane and cell wall
• Ribosomes
• Cytoplasm

Question 4

What is an extra feature that photosynthetic bacteria carry?

Answer 4

Internal membranes, where light reactions take place

Question 5

What is the bacterial cell wall made of?

Answer 5

Peptidoglycan, made up of sugars and amino acids. Some bacteria have more layers of peptidoglycan than others, while others have those with outer layers of phospholipids

Question 6

True or False: Bacteria lack the cytoskeletal framework that organizes cytoplasm in eukaryotic cells

Answer 6

False: Bacteria do have internal scaffolding of proteins that determine shape and properties of proteins

Question 7

What is the typical size of a bacterial cell?

Answer 7

200-300 nm, with most being 1-2 micrometers

Question 8

What is the reason that bacterial cells are so small?

Answer 8

Diffusion - the net movement of molecules from a region of higher concentration to lower concentration. This is how photosynthetic bacteria get the CO2 they need, and how respiring bacteria take in molecules and oxygen.
Small cells have more surface area in proportion to its volume, so diffusing molecules don’t have to travel far to fill the cell - long filaments also facilitate diffusion

Question 9

Why are some cells a big bigger than the average bacterial cell? What is an example?

Answer 9

Thiomargarita namibiensis, but it cheats by the fact that 98% of its volume is taken up by a large vacuole, so the part that takes in the molecules from diffusion is a thin layer around the vacuole.

Question 10

What mechanisms in bacteria promote genetic diversity?

Answer 10

• Streamlined bacterial genome

- Can reproduce rapidly when nutrients required for growth are available in the local environment

Question 11

What is the difference in reproduction between bacteria and eukaryotic organisms?

Answer 11

Bacteria lack the sexual processes of eukaryotic organisms - they do NOT undergo meiosis and cell fusion

Question 12

How then do bacteria obtain new genes?

Answer 12

horizontal gene transfer - obtaining genes from distant relatives

1. conjugation - connect pilus tube for direct cell-to-cell transfer of plasmids (one way) Ex: genes that confer antibiotic resistance
2. transformation - DNA of dead bacterial cell released into environment and taken up by live bacterial cells (pneumonia)
3. transduction - by means of viruses - used in lab to introduce new genes into bacteria

Question 13

What are the benefits of horizontal gene transfer?

Answer 13

-allows bacterial cells to gain beneficial genes from organisms distributed throughout the bacterial domain
-give them highly efficient mechanisms to add or subtract genes in order to evolve and adapt
CONS include passing on antibiotic resistance between bacteria

Question 14

What are archaea and what are some of their qualities?

Answer 14

• they are prokaryotic - no membrane-bound nucleus, genes in single circular chromosome
• size in archaea limited by diffusion, utilize horizontal gene transfer

Question 15

What are the specific structures of Archaea?

Answer 15

• membranes are from lipids but they are different than bacterial and eukaryotic membranes
• diversity of molecules in cell walls, but no peptidoglycan
• DNA transcription employs RNA polymerase like eukaryotes, also translation more similar to eukaryotes
• most abundant organisms in the ocean

Question 16

What is the simple process of photosynthesis?

Answer 16

CO2 reduced to carbohydrates–>water oxidized to O2

-water is electron donor, O2 is the electron acceptor for oxidation

Question 17

Why is photosynthesis in photosynthetic eukaryotes considered “oxygenic”?

Answer 17

Because it is oxygen-producing - water is almost everywhere, and no other molecule is available to donate electrons

Question 18

True or False: All respiration in eukaryotic cells in aerobic

Answer 18

True. Eukaryotes utilize oxygen in respiration, since oxidation of carbohydrates generates the most energy above all other oxidants

Question 19

True or False: If oxygen and sunlight is limited or absent, there is no way for Bacteria and Archaea to participate in respiration and photosynthesis

Answer 19

False. In the absence of oxygen and sunlight, only Bacteria and Archaea can use alternative electron donors and acceptors

Question 20

Electron donors_______

Electron acceptors________

Answer 20

Electron donors reduce.

Electron acceptors oxidize.

Question 21

What makes Bacteria and Archaea essential to nature?

Answer 21

They gather carbon and harvest energy. They are the foundation of the carbon cycle.

Question 22

What is a microbial mat and how is it structured?

Answer 22

It is a carpet of densely packed communities of mostly bacteria and archaeans that grow where eukaryotes cannot.
Top surface: cyanobacteria uses water as electron donor - respires O2 to CO2 aerobically and carry out a carbon cycle
-O2 then slowly diffuses through the mat but become quickly depleted a few mmm into the mat, and there is also reduced sunlight
-CO2 continues to be reduced to carbohydrates by anoxygenic photosynthetic bacteria
-anaerobic respiration and fermentation support microbial populations in last layer

Question 23

How do anoxygenic bacteria function?

Answer 23

They are photosynthetic, absorbing sunlight by bacteriochlorophyll, but uses a single photosystem

Question 24

What is the difference between anoxygenic photosynthesis and oxygenic photosynthesis?

Answer 24

Anoxygenic photosynthesis only employs a single photosystem. This means they use other electron donors other than water, and do not release O2 as a byproduct. They are restricted to sunlit habitats where O2 is absent because their electron donors would themselves become oxidized.

Question 25

What are some electron donors of anoxygenic photosynthesis?

Answer 25

H2S, H2, Fe2+, Arsenite

Question 26

What is fermentation and how does it work?

Answer 26

It’s an alternative to cellular respiration as a way of extracting energy from organic molecules. Fermentation is only the partial oxidation of carbon compounds to molecules that are less oxidized than CO2. It does not require an external electron acceptor like CO2, but it does yield less energy than respiration.

Question 27

What are the details of fermentation and what organisms utilize it?

Answer 27

It plays an important role in O2 poor environments that are rich in organic matter. Often requires more than one organism, most present in bacteria in archaea, but is also used in a minor way by eukarya. Done by hetertrophs.

Question 28

True or False: Prokaryotic organisms are required to sustain Earth’s carbon cycle, while eukaryotic organisms are optional

Answer 28

True. Only prokaryotic heterotrophs can complete the recycling of organic carbon in oxygen poor environments such as in waters or sediments.

Question 29

Phototroph

Answer 29

organisms that gain energy from the sun

Question 30

Chemotroph

Answer 30

organisms that gain energy from chemical compounds

Question 31

Autotrophs

Answer 31

organisms that require CO2 or other inorganic molecules for energy

Question 32

Heterotrophs

Answer 32

organisms that require organic molecules for energy

Question 33

Photoheterotrophs

Answer 33

Organisms that use sunlight to make ATP, but rather than reducing CO2 to make organic molecules, they use carbon and other organic molecules from the environment. Examples include heliobacteria and green non sulfur bacteria.

Question 34

Chemoautotrophs

Answer 34

Organisms that gain carbon by reducing CO2 to form carbohydrates, but obtain energy from chemical reactions using inorganic molecules. (H2, H2S) Electron acceptor is most likely O2 or Nitrate. These organisms live on the edge between O2 rich and O2 poor environments because they need both oxidized and reduced molecules. Widespread among Bacteria and Archaea only.

Question 35

Name different ways that bacteria can be placed into phylogeny

Answer 35

1. culture morphology
2. nutrient assays
3. Gram stain
4. Gene sequencing
5. Molecular sequencing (rRNA genes)

Question 36

What is the current popular opinion on bacterial and archaea phylogeny?

Answer 36

The evolution of prokaryotes should not be viewed as a tree but a series of complicated and sometimes interlinked branches because of horizontal gene transfer

Question 37

What are the pros and cons of gene sequencing?

Answer 37

Pros: enabled us to discover sequences of countless bacteria that hadn’t been cultured in lab for morphological studies
Cons: There is a lot of horizontal gene transfer, which may distract from accurate or clean phylogenies - at least 85% of all genes in bacterial genomes have been transferred at least once

Question 38

Why is the analysis of rRNA genes useful in prokaryotic phylogenies?

Answer 38

It helps to identify bacteria because there is little rRNA gene transfer, but there are still jumps to be aware of.

Question 39

What exactly is a bacterial species?

Answer 39

BCS can’t be applied- so bacteria are classified according to rRNA - if their rRNA is more than 97% identical. They are also classified in terms of population-level processes - namely periodic selection

Question 40

What is periodic selection?

Answer 40

The episodic loss of diversity, when diversity gradually increases through time and then rapidly falls off with the emergence of a successful variant that outcompetes the rest. This is a useful way to define a single species.

Question 41

Proteobacteria

Answer 41

Most diverse of all bacterial groups. Defined largely by similarities in gene sequences of rRNA, and include many bacteria that are involved in the expanded carbon cycle and other biochem cycles. Ex: anoxygenic photosynthetic bacteria and chemoautotrophs
Most are involved in mutually beneficial relationships.

Question 42

Gram stain

Answer 42

A way of classifying bacteria discovered in 1884. Use violet dye that is retained by bacteria with thick peptidoglycan walls. These are “gram positive”

Question 43

What do gram positive bacteria indicate?

Answer 43

These are a pretty well-defined group of the bacterial tree.

Question 44

Cyanobacteria

Answer 44

A monophyletic group of bacteria that are all bacteria capable of oxygenic photosynthesis- very diverse group

Question 45

Purple bacteria

Answer 45

anoxygenic photosynthesizers that are photoautotrophic

Question 46

Green sulfur bacteria

Answer 46

gain electrons from hydrogen sulfide and deposit elemental sulfur on their walls - intolerant of oxygen gas. Found in hot springs.