27 Bacteria and Archaea Flashcards
What is a genus of microorganism that can tolerate wide salt ranges?
Halobacterium, which is actually a archaea
What is Halobacterium?
An archaea genus that can tolerate high levels of salt.
What is the basic premise of the the Gram stain?
It dies peptidoglycan as purple so that bacteria that have it on their plasma membrane can be distinguished from those who do not have it on their plasma membrane
How can bacteria be classed based on how they appear under a Gram stain?
‘Gram-positive bacteria’ and ‘Gram-negative bacteria’
What is the structure of gram-postive bacteria?
The differences lie in the plasma membrane. In Gram positive bacteria the plasma membrane is covered with an external layer of peptidoglycan, which acts a the cell wall.
What is peptidoglycan?
A polymer composed of sugars cross-linked with polypeptides
It is the primary component of bacterial cell walls.
What is the structure of a gram-negative bacteria?
They have a phospholipid membrane bilayer that acts as the plasma membrane.
External to this is a comparatively thin layer of peptidoglycan.
External to this is an outer membrane, which consists of a phospholipid membrane bilayer.
Note that the peptidoglycan layer and the external phospholipid membrane bilayer are collectively called the ‘cell wall.’
Generally speaking, are Gram-negative or Gram-positive bacteria more resistant to antibiotics? Why
Generally Gram-negative bacteria as many antibiotics work by inhibiting the peptidoglycan cross linking (this allows them to not affect human cells, which lack peptidoglycan)
What is the cell wall of a bacterium covered with?
Either a ‘slime layer’ or a ‘capsule’
What is a ’slime layer’?
An outer coating of a bacterium that is not dense or defined like a capsule
What is a ‘capsule’?
An outer coating of a bacterium that is very dense and defined, unlike a ’slime layer’
What can the slime coats/capsules of bacteria be covered with?
Fimbriae or pili
What is a pilus?
The singular form of pili
What are fimbriae?
Hairlike appendages that are shorter and more numerous than ‘pili’
What are ‘pili’?
Appendages that pull to cells together prior to horizontal gene transfer between bacteria.
They are longer but less numerous than fimbriae.
What is a taxis?
A directed movement toward or away from a stimulus.
What is a directed movement towards or away from a stimulus called?
A taxis
What is a positive taxis?
When the bacterium etc. moves towards a stimulus i.e. positive phototaxis towards light
What is the structure of a prokaryotic flagellum?
Embedded in the inner plasma membrane is a ‘motor’ which appears as a set of discs
In the centre of these disks is a ‘rod’ which extends outside the cell wall.
Just outside the cell wall the rod bends to form the ‘hook’. The ‘filament’ is the long trailing tail that extends form the hook
What is exaption?
When evolution repurposes features for other uses.
Where is the DNA of a bacterium located?
In a ’nucleoid’
What is a ’nucleoid’?
A region in a bacterium’s cytosol which holds the chromosome.
Note that it is not membrane bound and is thus loosely defined.
It appears lighter than surrounding areas in an electron microscope
What is a common way that bacteria tolerate changing environmental conditions i.e. periodic drought?
When they lack certain nutrients or during harsh conditions they can become dormant ‘endospores’
What are ‘endospores’?
A dormant form that many bacteria can assume when they lack certain nutrients or under harsh conditions.
The original cell produces a copy of its chromosome and surrounds it with a tough multilayered structure, forming the endospore.
Water is removed from the endospore, and its metabolism halts. The original cell then lyses, releasing the endospore.
When dehydrated they become active bacteria
Does meiosis occur in prokaryotes?
Nope
What are What is the ploidy of prokaryotes?
They are all haploid
What is ‘genetic recombination’?
The combination of DNA from two sources
How does ‘genetic recombination’ occur in eukaryotes?
With fertilisation and in meiosis (crossing over)
What is the combination of DNA form two sources called?
Genetic recombination
How does genetic recombination occur in prokaryotes?
Since they do not perform meiosis or fertilisation it only occurs in ‘horizontal gene transfer’
What are the basic methods of horizontal gene transfer?
Transformation, transduction, conjugation and plasmids
What is ’transformation’ as a method of horizontal gene transfer?
The genotype and possibly phenotype of a prokaryotic cell are altered by the uptake of foreign DNA from its surroundings.
For example transformation occurs when a nonpathogenic cell takes up a piece of DNA carrying the allele for pathogenicity and replaces its own allele with the foreign allele, an exchange of homologous DNA segments. The cell is now a recombinant.
What is ’transduction’ as a method of horizontal gene transfer?
Phages (bacteriophages = viruses that infect bacteria) carry prokaryotic genes from one host cell to another.
If some of this DNA is then incorporated into the recipient cell’s chromosome by DNA recombination, a recombinant cell is formed.
What is ’conjugation’ as a method of horizontal gene transfer?
DNA is transferred between two prokaryotic cells (usually of the same species) that are temporarily joined.
In bacteria, the DNA transfer is always one-way: One cell donates the DNA, and the other receives it.
The tow bacteria are held together by a pilus
What are ’plasmids’ as a method of horizontal gene transfer?
Plasmids are small sections of DNA. They can be transferred between bacteria in ‘horizontal gene transfer’
In what form of horizontal gene transfer are pili (singular: plies) involved?
Conjugation
How are certain forms of horizontal gene transfer regulated?
With the ‘F factor’
What are the forms of F factor?
It is just F factor if it exists in the bacterial chromosome.
If it is in its own plasmid it is the ‘F plasmid’
What forms of horizontal gene transfer does the F factor regulate?
Conjugation and Plasmid
How does the F factor regulate conjugation?
The F factor consist of genes needed for the formation of a pilus etc.
Cells that have the F factor are called HFR (high frequency recombinant) During conjugation they act as donors and transfer genetic information to the other bacterium.
Note that the HFR bacterium can transfer the F factor to the host F- bacterium, causing it to become F+ (HFR)
What does the ‘F’ in F factor stand for?
Fertility
What is a ‘F+’cell?
One with the F factor
What is a ‘F-‘ cell?
One without the F factor
What does ‘HFR’ refer to?
High frequency recombination.
It refers to a bacteria which has the F factor in its chromosome and thus is F+
How does can the F plasmid be transferred to another bacterium?
A cell carrying an F plasmid (an F+ cell) forms a mating bridge with an F– cell. One strand of the plasmid’s DNA breaks at one point.
Using the unbroken strand as a template, the cell synthesizes a new strand . Meanwhile, the broken strand peels off, and one end enters the F– cell. There synthesis of its complementary strand begins.
DNA replication continues in both donor and recipient cells, as the transferred plasmid strand moves farther into the recipient cell.
Once DNA transfer and synthesis are completed, the plasmid in the recipi- ent cell circularizes. Now both cells are F+ cells.
What are ‘resistance genes’?
Genes that confer resistance to an antibiotic
What are genes that confer resistance to an antibiotic called?
‘Resistance genes’
What are resistance genes in the form of plasmids called?
R plasmids
What are ‘R plasmids’?
Plasmids that carry ‘resistance genes’ i.e. antibacterial resistance
What are plasmids that carry resistance genes called?
R plasmids
How can organisms be grouped based on their type of respiration? (think deeper than aerobic/anaerobic)
Obligate aerobes, obligate anaerobes and facultative anaerobes
What are ‘obligate aerobes’?
Organisms that must use O2 for respiration and thus can not survive with out it
They can only perform aerobic respiration
What are ‘obligate aerobes’?
Organisms that can only perform anaerobic respiration.
They are often poisoned by O2 due to its reducing nature.
What are some typical electron acceptors used in anaerobic respiration?
Nitrates (NO3-) and Sulfate (SO4 2-)
What are ‘facultative anaerobes’?
Organisms that use oxygen for aerobic respiration when possible.
However they are also able to perform anaerobic respiration or fermentation when necessary in anaerobic conditions
What are organisms that only perform aerobic respiration called?
Obligate aerobes
What are organisms that only perform anaerobic respiration called?
Obligate anaerobes
What are organisms that can perform aerobic or anaerobic respiration called?
Facultative anaerobes
Which cells are notoriously facultative anaerobes in the human body?
Muscle cells
Based on the from of respiration they perform, how can muscle cells be classed?
Facultative anaerobes (they prefer to do aerobic, but can do anaerobic respiration if oxygen deprived)
What is it called when atmospheric nitrogen is converted into compounds?
Nitrogen fixation
What is nitrogen fixation?
When atmospheric nitrogen is converted into compounds i.e NH3
How can organisms be grouped based on nutritional modes?
Photoautotroph, chemoautotroph, photoheterotroph, chemoheterotroph
What are photoautrophs in terms of energy source and carbon source?
Energy Source: Light
Carbon Source: CO2, HCO3- etc.
What are chemoautotrophs in terms of energy source and carbon source?
Energy Source: Inorganic chemicals such as H2S, NH3 or Fe2+
Carbon Source:CO2, HCO3- etc.
What are photoheterotrophs in terms of energy source and carbon source?
Energy Source: Light
Carbon Source: Organic compounds
What are chemoheterotrophs in terms of energy source and carbon source?
Energy Source: Organic compounds i.e glucose
Carbon Source: Organic compounds
What are are some examples of photoautotrophs?
Photosynthetic prokaryotes (for example, cyanobacteria); plants; certain protists (for example, algae)
What are are some examples of chemoautotrophs?
Unique to certain prokaryotes (for example, Sulfolobus)
What are are some examples of photoheterotrophs?
Unique to certain aquatic and salt-loving prokaryotes (for example, Rhodobacter,
Chloroflexus)
What are are some examples of chemoheterotrophs?
Many prokaryotes (for example Clostridium) and protists; fungi; animals; some plants.
How do cyanobacteria perform nitrogen fixation?
Most cells in a filament carry out only photosynthesis, while a few specialized cells called heterocysts (sometimes called heterocytes) carry out only nitrogen fixation. Each heterocyst is surrounded by a thickened cell wall that restricts entry of O2 produced by neighboring photosynthetic cells. Intercellular connections allow heterocysts to transport fixed nitrogen to neighboring cells and to receive carbohydrates.
This is important as the O2 produced in photosynthesis inhibits the enzymes used for nitrogen fixation
What are the basic places ‘metabolic cooperation’ is seen?
Nitrogen fixation in cyanobacteria and in biofilms
What is ‘metabolic cooperation’
Cooperation between prokaryotic cells allows them to use environmental resources they could not use as individual cells.
What are heterocysts?
Specialised cyanobacteria that are specialised to perform nitrogen fixation.
Note that they are the same species as the other cyanobacteria they metabolically cooperate with.
What are biofilms?
Sheets of bacteria that metabolically cooperate.
What are archaea?
They are one of the three basic domains but and are most similar to bacteria.
What are the basic ways that archaea, bacteria and eukarya can be compared?
Structure, Chemical composition, genetics and tolerance
How do bacteria, archaea and eukarya compare in terms of structure?
Bacteria, Archaea, Eukarya
Nuclear envelope: absent, absent, present
Membrane-bound organelles: absent, absent, present
Circular chromosome: present, present, absent
How do bacteria, archaea and eukarya compare in terms of chemical composition?
Bacteria, Archaea, Eukarya
Peptidoglycan in cell wall: present, absent, absent
Membrane lipids: unbranched hydrocarbons, soem branched hydrocarbons, unbranched hydrocarbons
RNA polymerase: one kind, several kinds, several kinds.
How do bacteria, archaea and eukarya compare in terms of genetics?
Bacteria, Archaea, Eukarya
Initiator amino acid for protein synthesis: Formyl-methionine, methionine, methionine
Introns in genes: very rate, present in some, common
Histones associated with DNA: Absent, present in some species, present
How do bacteria, archaea and eukarya compare in terms of tolerance?
Bacteria, Archaea, Eukarya
Response to the antibiotics streptomycine and chloramphenicol: Growth inhibited, no effect, no effect
Growth at temperatures >100ºC: No, some species, no
What class of organism are all extremophiles?
Archaea
What are extremophiles?
Organisms (all archaea) that live in extreme environmental conditions
What are organisms that live in extreme environmental conditions called?
Extremophiles
What are the basic types of extremophiles?
Extreme halophiles and extreme thermophiles
What are extreme halophiles?
Those that live is extremely salty environments
What is the salinity of sea water?
3.5%
