Prokaryotes Flashcards
How did early taxonomists classify species?
They classified all species as either plants or animals
What system has been adopted more recently for classifying species?
The three-domain system: Bacteria, Archaea, and Eukarya
What are the two domains of prokaryotes?
Bacteria and Archaea
What are the main three kingdoms included under the eukaryotic domain?
Fungi, Plantae and Animalia
What does the tree of life suggest about eukaryotes and archaea?
They are more closely related to each other than to bacteria
What is the tree of life based on?
It is largely based on rRNA, however, drawing the tree using genes other than rRNA reveals different relationships
Horizontal gene transfer
The movement of genes from one genome to another
How does horizontal gene transfer occur?
By exchanging of transposable elements and plasmids, viral infection, fusion of organisms, transformation
Can disparities in phylogenic trees be explained by the occurrence of horizontal gene transfer?
Yes some can - horizontal gene transfer has played a key role in the evolution of both prokaryotes and eukaryotes
What do some biologist argue about horizontal gene transfer and the tree of life?
They argue that horizontal gene transfer was so common that the early history of life should be represented as a tangled network of connected branches
Where can prokaryotes be found?
Wherever there there is life, they can thrive in habitats that are too cold, too hot, too salty, too acidic, or too alkaline for any eukaryote
Are prokaryotes important to our existence?
Yes - the vast majority of prokaryotes are essential for out existence
What kinds of materials do prokaryotes recycle?
They recycle carbon, nitrogen, and almost every chemical element, between organic mater and the soil, ocean, and atmosphere
Bacteria cells in/on the human body produce important vitamins, protect us from disease, and are integral to good health
How do Archaea differ from Bacteria?
In many key structural, biochemical, and physiological characteristics
Were mis-characterized as extremophiles since the first known archaea were found inhabiting extreme environments
Archaea dominate some of the largest habitats on Earth like ocean midwaters
Why are two prokaryotic domains recognized?
Because bacteria and archaea diverged so early in life and are so fundamentally different - both lack a membrane-bound nucleus but thats not a formal taxonomic classification, rather describes their appearance
Is the shared absence of a feature a good way to classify organisms together?
No - many microbiologists avoid and dislike the term “prokaryote” whose members share the absence of a nuclear membrane
What do most common prokaryotes look like?
Most are unicellular - some species may aggregate transiently - the most common shapes are spheres (cocci), rods (bacilli), and helices
What is an important feature of nearly all prokaryotic cells?
Their cell wall which maintains cell shape, provides physical protection, and prevents the cell from bursting in a hypotonic environment (one with a low solute concentration)
What are bacteria cell walls made up of?
A modified sugar polymer called peptidoglycan
What do the walls of archaea lack?
Peptidoglycan
Gram stain
A valuable traditional tool for classifying many bacterial species into groups based on differences in their cell wall composition
Gram-positive bacteria
Have simpler cell walls, with large amounts of peptidoglycans - they are broadly a phylogenetic group although some members of the tree grouping do not stain Gram-positive
Gram-negative bacteria
Have more complex cell walls and less peptidoglycan
- an outer membrane on the cell wall contains lipopolysaccharides, carbohydrates boned to lipids
- gram-negative bacteria are phylogenetically diverse
- generally more pathogenic and antibiotic-resistant
- can evade defense systems because they are often coated with a sticky slime layer
What do may antibiotics inhibit?
The synthesis of cross-links in peptidoglycan, preventing the formation of a functional wall, particularly in gram-positive species
What is the cell wall of many gram-negative bacteria covered by?
A capsule/sheath/glycocalyx - a sticky layer of polysaccharide or protein
What is slime for?
- Capsules adhere the cells to their substratum
- They glue together the cells of those prokaryotes that live as colonies
What is another way for prokaryotes to adhere to one another or to the substratum?
Surface appendages called fimbriae or pili
- fimbriae or pili can fasten pathogenic bacteria to the mucous membranes of its host
- some are specialized for holding two prokaryote cels together long enough to transfer DNA during conjugation
What is the most common method of movement for prokaryotes?
The action of flagella, scattered over the entire surface or concentrate at one or both ends - the flagella of prokaryotes differ in structure and function from those of eukaryotes
What do bacterial flagellum look like?
They are chains of globular proteins wound in a tight spiral (like a corkscrew) from a filament which is attached to another protein (the hook) and the basal apparatus
What is rotation of the filaments driven by?
The entry of protons into the cell through the basal apparatus after the protons have been actively transported by proton pumps in the plasma membrane, the electrical potential from charge separation provides
How did flagella most likely evolve?
Flagella likely evolved as existing proteins were added to an ancestral secretory system
Exaptation
Where structures adapted for one function take on new functions through descent with modification
What is another way that cells move around?
By secreting a jet of slimy threads that anchor the cell to the substratum - the cell glides along at the growing end of threads
How do flagellated cells move around in relatively uniform evironments?
They may wander randomly
How do flagellated cells move around in a heterogenous environment?
Many prokaryotes are capable of taxis, movement toward or away from a stimulus
- With chemotaxis, binding between receptor cells on the surface and specific substances results in movement towards the source (positive chemotaxis) or away (negative chemotaxis), requires a sort of molecular short term memory
Chemotaxis in bacteria
A biased random walk, where the bacteria alternates between runs and tumbles. Runs are straight and tumbles change the direction - better = more runs than tumbles, worse = more tumbles than runs
Are the cellular and genomic organization of prokaryotes and eukaryotes similar?
No - they are fundamentally different
Prokaryotic cells lack a nucleus enclosed by membranes, other internal compartments bounded by membranes and use infolded regions of the plasma membrane for many metabolic functions
Where is DNA typically concentrated?
As a snarl of fibers in the nucleoid region
What promotes genetic diversity in prokaryotes
Rapid reproduction , mutation, and genetic recombination
Prokaryotes have considerable genetic variation
What are some key features of prokaryote biology
They are small
They reproduce by binary fission
They have short generation times (fastest 20 min)
Transformation
A cell can absorb and integrate fragments of DNA from their environment
Allows considerable genetic transfer between prokaryotes, even across species lines
Uptake of foreign DNA from the surrounding environment
Transduction
Bacteriophage viruses transfer genes between prokaryotes
Phages can mistakenly package bacterial DNA and inject into new host upon infection
1. Phage infects bacterial donor cell that carries the A+ and B+ alleles
2. Phage DNA is replicated and phage proteins are synthesized
3. Fragment of bacterial DNA with A+ allele is packaged within a phage capsid
4. Phage with A+ allele infects bacterial recipient cell
5. Incorporation of phage DNA creates recombinant cell with genotype A+B-
Conjugation
One cell directly transfers genes to another cell
The process where genetic material is transferred between prokaryotic cells
In bacteria, the DNA transfer is always one way
The physical union of two bacterial cells, donor cell uses a hollow pillus to bridge the cells and passes DNA to recipient
F Factor in plasmids
Cells with F plasmid function are DNA donors during conjugation
Cells without F facter are DNA recipients during conjugation
Transferable during conjugation
F Factor in chromosomes
Cell with F factor are donors during conjugation
Callled Hfr (high frequency of recombination) cells
The recipient becomes a recombinant bacterium with DNA from two different cells
Binary fission
Synthesizing DNA almost continuously - how prokaryotes reproduce asexually
What is a particularly important source of genetic variation in prokaryotes?
Mutation - mutation rates are low but they accumulate rapidly because generation times are short and populations are large
Lenski’s laboratory evolution experiments
Used E. coli - determined that natural selection in bacteria can result in significant phenotypic changes as well (even in a “constant” environment)
Growth as applied to prokaryotes
Refers to multiplication of cells and population increases, rather than enlargement of individual cells
Conditions for optimal growth vary according to species
Variables: temperature, light levels, pH, salt concentrations, nutrient sources, etc.
Why is prokaryotic growth in the laboratory and in nature always checked at some point?
- The cells may exhaust some nutrient
- Alternatively, the colony poisons itself with an accumulation of metabolic waste
- in nature many populations near “steady state” where growth rate is about = death rate, often because of predators, viruses or competition
Endospores
specialized cells that remain dormant
Can survive extreme heat, cold, space travel, etc.
A capsule containing nucleus
Bacillus anthracis
The causative agent of anthrax
Example of a spore-forming bacterium “in the news”
2001 Anthrax mail attacks on Washington D.C.
Total damage exceeded $1 billion
Decontamination by fumigation with chlorine dioxide gas
Nobody was charged with the attack
What four groups can prokaryotes be grouped into?
Autotroph
- Photoautotroph
- Chemoautotroph
Heterotroph
- Photoheterotroph
- Chemoheterotroph
What are the majority of known prokaryotes?
Chemoheterotrophs
- includes decomposers that absorb dissolved nutrients or nutrients from nonliving organisms and parasites
- some have very exacting nutritional requirements, while others are less specific in their requirements
Parasites
Absorb nutrients from the body fluids of living hosts
Non-biodegradable
Commonly “man-made” like most plastics. Interestingly, some bacteria have evolved the ability to break down some plastics, slowly
What is another facet of nutritional diversity among prokaryotes
Accessing nitrogen, which is an essential component of proteins and nucleic acids
Nitrogen fixation
When bacteria convert N2 to NH4+, making atmospheric nitrogen available to other organisms for incorporation into organic molecules
Nitrifying bacteria
Bacteria that convert ammonium (NH4+) to nitrite (NO2-) and nitrate (NO3-)
- most of plants nitrogen uptake is via NO3- and NH4+ derived by bacterial activity
What is required for the oxidation of ammonia to nitrate?
Oxygen - bacterial activity in soil requires oxygen and stops in anaerobic or water-logged soils
Anaerobic
Conditions with no oxygen
Denitrifying bacteria
Can convert nitrate to nitrogen gas in anaerobic conditions
- plant-available nitrogen can be lost in anaerobic or water-logged soils
Obligate aerobes
Require oxygen
- e.g., Nitrifying bacteria, Mycobacterium tuberculosis
Facultative anaerobes
Can survive with or without oxygen
- e.g., Denitrifying bacteria, E. coli (gut organisms)
Obligate anaerobes
Poisoned by oxygen
- e.g., Clostridium perfringens (causes gangrene)
Rhizosphere
The layer of soil bound to the plant’s roots
Rhizobacteria
bacteria contained in the rhizosphere that act as decomposers and nitrogen-fixers
- produces hormones that stimulate plant growth
- produces antibiotics that protect roots from disease
- absorbs toxic metals or makes nutrients more available to roots
What are the most self-sufficient of all organisms?
Nitrogen fixing cyanobacteria - they require only light energy, CO2, N2, water and some minerals to grow
Heterocyst
nitrogen-fixing cells
Prokaryotic driven nitrogen fixation
Makes atmospheric nitrogen available to other organisms - without this process, global biomass, including human population, would “run down” due to denitrification and starvation for usable N
Trichodesmium cyanobacteria
Fix 50% of nitrogen in marine systems
Biofilms
Metabolic cooperation that occurs in surface-coating colonies
Bioremediation
The use of organisms to remove pollutants from the environment (prokaryotes are the principal agents in this)
What is the name Archaea?
A misnomer (a wrong or inaccurate use of a name or term)
Extreme thermophiles
Thrive in very hot environments
Extreme halophiles
Live in high saline environments
Methanogens
Strictly anaerobic, Archaea that live in swamps and marshes and produce methane as a waste product
Where does ~20% of US methane production come from?
Cows
What toxins do pathogenic prokaryotes typically release to cause diseases?
Exotoxins or endotoxins
Exotoxins
Cause disease even if the prokaryotes that produce them are not present
- Excreted, e.g., bacteria that cause botulism
Endotoxins
Released only when bacteria die and their cell walls break down
- Surface-associated, e.g., Salmonella
Do prokaryotes cause about half of all human infectious diseases?
Yes - e.g., Lyme disease is caused by the spirochete Borrelia burgdorferi
“Great Plate COunt Anomaly”
Conducted in 1959 by Jannasch and Jones
Culture methods and light microscopy gave different #’s
- discovered that the vast majority of prokaryotes are not culturable
What does sequencing of ribosomal RNA sequences reveal?
Taxa identity and relative abundance in samples
Marine virus “kill the winner” hypothesis
Once a seawater microbe becomes dominant, it’s high abundance increases its contact rate with viruses, leading to significant increases in infection and subsequent lysis, which then control its abundance. As a consequence, viruses may sustain a high population diversity among their hosts
Example of frequency-dependent selection
