Chapter 27 - Bacteria and Archaea Flashcards
What is a distinctive feature of prokaryotes?
They lack a nucleus
What are the prokaryotic domains of microscopic organisms that cycle carbon but don’t produce or consume oxygen?
Bacteria and Archaea
What is the basic organization of the cells of prokaryotes?
- 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
What is an extra feature that photosynthetic bacteria carry?
Internal membranes, where light reactions take place
What is the bacterial cell wall made of?
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
True or False: Bacteria lack the cytoskeletal framework that organizes cytoplasm in eukaryotic cells
False: Bacteria do have internal scaffolding of proteins that determine shape and properties of proteins
What is the typical size of a bacterial cell?
200-300 nm, with most being 1-2 micrometers
What is the reason that bacterial cells are so small?
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
Why are some cells a big bigger than the average bacterial cell? What is an example?
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.
What mechanisms in bacteria promote genetic diversity?
- Streamlined bacterial genome
- Can reproduce rapidly when nutrients required for growth are available in the local environment
What is the difference in reproduction between bacteria and eukaryotic organisms?
Bacteria lack the sexual processes of eukaryotic organisms - they do NOT undergo meiosis and cell fusion
How then do bacteria obtain new genes?
horizontal gene transfer - obtaining genes from distant relatives
- conjugation - connect pilus tube for direct cell-to-cell transfer of plasmids (one way) Ex: genes that confer antibiotic resistance
- transformation - DNA of dead bacterial cell released into environment and taken up by live bacterial cells (pneumonia)
- transduction - by means of viruses - used in lab to introduce new genes into bacteria
What are the benefits of horizontal gene transfer?
-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
What are archaea and what are some of their qualities?
- they are prokaryotic - no membrane-bound nucleus, genes in single circular chromosome
- size in archaea limited by diffusion, utilize horizontal gene transfer
What are the specific structures of Archaea?
- 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
What is the simple process of photosynthesis?
CO2 reduced to carbohydrates–>water oxidized to O2
-water is electron donor, O2 is the electron acceptor for oxidation
Why is photosynthesis in photosynthetic eukaryotes considered “oxygenic”?
Because it is oxygen-producing - water is almost everywhere, and no other molecule is available to donate electrons
True or False: All respiration in eukaryotic cells in aerobic
True. Eukaryotes utilize oxygen in respiration, since oxidation of carbohydrates generates the most energy above all other oxidants
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
False. In the absence of oxygen and sunlight, only Bacteria and Archaea can use alternative electron donors and acceptors
Electron donors_______
Electron acceptors________
Electron donors reduce.
Electron acceptors oxidize.
What makes Bacteria and Archaea essential to nature?
They gather carbon and harvest energy. They are the foundation of the carbon cycle.
What is a microbial mat and how is it structured?
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
How do anoxygenic bacteria function?
They are photosynthetic, absorbing sunlight by bacteriochlorophyll, but uses a single photosystem
What is the difference between anoxygenic photosynthesis and oxygenic photosynthesis?
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.
What are some electron donors of anoxygenic photosynthesis?
H2S, H2, Fe2+, Arsenite
What is fermentation and how does it work?
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.
What are the details of fermentation and what organisms utilize it?
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.
True or False: Prokaryotic organisms are required to sustain Earth’s carbon cycle, while eukaryotic organisms are optional
True. Only prokaryotic heterotrophs can complete the recycling of organic carbon in oxygen poor environments such as in waters or sediments.
Phototroph
organisms that gain energy from the sun
Chemotroph
organisms that gain energy from chemical compounds
Autotrophs
organisms that require CO2 or other inorganic molecules for energy
Heterotrophs
organisms that require organic molecules for energy
Photoheterotrophs
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.
Chemoautotrophs
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.
Name different ways that bacteria can be placed into phylogeny
- culture morphology
- nutrient assays
- Gram stain
- Gene sequencing
- Molecular sequencing (rRNA genes)
What is the current popular opinion on bacterial and archaea phylogeny?
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
What are the pros and cons of gene sequencing?
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
Why is the analysis of rRNA genes useful in prokaryotic phylogenies?
It helps to identify bacteria because there is little rRNA gene transfer, but there are still jumps to be aware of.
What exactly is a bacterial species?
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
What is periodic selection?
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.
Proteobacteria
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.
Gram stain
A way of classifying bacteria discovered in 1884. Use violet dye that is retained by bacteria with thick peptidoglycan walls. These are “gram positive”
What do gram positive bacteria indicate?
These are a pretty well-defined group of the bacterial tree.
Cyanobacteria
A monophyletic group of bacteria that are all bacteria capable of oxygenic photosynthesis- very diverse group
Purple bacteria
anoxygenic photosynthesizers that are photoautotrophic
Green sulfur bacteria
gain electrons from hydrogen sulfide and deposit elemental sulfur on their walls - intolerant of oxygen gas. Found in hot springs.
