ch2
How is a species defined in the bacterial classification system?
A species is defined loosely as a group of strains that share many common features while differing from most other bacterial strains.
Describe the various multicellular arrangements formed by some bacteria as a result of their cellular division.
Bacillus and streptococcus can form long chains of cells because they do not fully separate after cell division. Other bacteria, like staphylococci form clusters that look like bunches of grapes. Hyphae are long chains of cells formed by some bacteria that can rise above or penetrate below the main group of cells, not unlike strands of hair or tree roots. Cyanobacteria can form long, smooth chains of cells that are contained within a polysaccharide sheath.
2.6 Identify the taxonomic groups used to classify bacteria
Bacteria are classified using the same scheme as is used for plants and animals. Each species is defined by common features it shares with related bacteria. The highest taxonomic rank in the scheme is "Domain" (i.e. bacteria, archaea, or eukarya), followed by "Phylum", "Class", "Order", "Family", "Genus" and "Species."
2.5What are the roles of bacterial flagella and how do bacterial flagella differ from archaeal and eukaryal flagella?
Bacterial flagella are long appendages that help bacteria actively move through their environment. They provide the bacteria with the ability to move closer to or away from certain chemicals or conditions. Some bacteria require their flagella in order to cause disease. Flagella are used for motility both in liquid environments (swimming), or on surfaces (swarming). Archael flagella are similar in form to bacterial flagella but are not homologous when looking at the protein sequences of the various components nor are they similar with regard to how they assemble. Eukaryal flagella are composed of cytoplasmic microtubules and are quite distinct from the bacterial and archael flagella.
Speculate on some potential benefits to bacteria of biofilm formation.
Biofilms (covered more extensively in chapter 15) are surface associated communities of one or more species of bacteria.
Describe how chemoreceptors and flagella are involved in the process of chemotaxis
Chemoreceptors are proteins found in the bacterial plasma membrane that enable the bacteria to sense certain attractants or repellants. Once activated these receptors communicate with the flagella via cytoplasmic proteins to control whether the flagella should continue to propel the bacteria forward, or to reverse direction and cause the bacteria to tumble. By prolonging the periods of forward motion and reducing the amount of tumbling the bacterial cell can make a "random walk" toward (or away) from the particular nutrient (or toxin).
What are the most common bacterial shapes?
Common bacterial shapes include spherical (cocci), rods (bacilli), curved rods (vibrio) and spiral (spirilla). The terms in parentheses refer to the terms used by scientists to describe bacteria with these shapes.
What are inclusion bodies and what is their role in the bacterial cell?
Inclusion bodies are large granules that serve as storage of particular nutrients including carbon, nitrogen, or phosphorus.
What are the general size ranges of bacteria?
Most bacteria are between 0.5 μm and 5 μm in length or diameter. However some bacteria fall greatly outside of this general range.
What role do ParM proteins play in bacterial cell division?
ParM proteins helps copies of plasmid DNA molecules move to the opposite ends of the bacterial cell. In this way each newly formed cell inherits a copy of the plasmid after cell division.
Differentiate between the terms "pili" and "fimbriae."
Some scientists use the term "pili" exclusively for surface appendages that are involved in conjugal transfer of DNA, and "fimbriae" for all other surface appendages involved in adhesion, etc.
Describe the functions of the FtsZ protein and the Z-ring in bacterial cells.
The FtsZ protein is related to the eukaryal cytoskeleton protein tubulin. FtsZ protein monomers polymerize together to form a ring on the inner face of the cytoplasmic membrane at the point where the cell will divide. This ring interacts with membrane proteins that direct the synthesis of new cell wall. The FtsZ ring can contract, getting smaller through the release of FtsZ monomers, which in turn leads to the cell wall constricting at the point of cell division.
Differentiate between Gram-positive and Gram-negative bacterial cell envelopes.
The Gram-positive cell envelope primarily consists of a very thick cell wall (peptidoglycan). Intermingled with the peptidoglycan are other polymers including teichoic acids, anionic polymers that are either tethered to the cell membrane (lipoteichoic acids) or to the peptidoglycan (wall teichoic acids). In Gram-negative bacteria the peptidoglycan layer is quite thin compared to that of the Gram-positive bacteria. These bacteria instead possess an additional membrane outside of the layer of peptidoglycan (the outer membrane), which contains a unique type of lipid called lipopolysaccharide (LPS). The space bounded by the inner and outer membranes is called the "periplasm." The peptidoglycan layer is found in the periplasm.
2.3 How are cytoskeletal-like proteins involved in magnetotaxis?
The MamZ protein is similar to eukaryal actin and the MreB protein of bacteria. This protein has been found in filaments associated with magnetosomes (using a green fluorescent protein tagged version of the MamZ protein). Another protein, MamJ, may act as a tether that links magnetosomes to the MamZ filaments. Mutant Magnetospirillum bacteria that lack either the MamZ or MamJ proteins produce magnetosomes that fail to line up properly.`
What is the purpose of the MreB protein in bacteria?
The MreB protein is evolutionarily related to actin and it plays a role in defining the shape of non-spherical bacteria. MreB polymers form bands underlying the plasma membrane (in the cytosol) and appear to control or guide the synthesis of the cell wall to generate a cylindrical shaped cell.
Each bacterium's scientific name is binomial and based on which taxonomic categories?
The binomial name of a given bacteria is based on its genus and species. In the bacterial name Staphylococcus aureus, for example, Staphylococcus refers to the genus and aureus refers to the species.
Describe the structure and function of the bacterial cell wall.
The cell wall is a rigid structure that gives the bacterial cell its shape and protects the cell from both mechanical and osmotic lysis. It is a net-like structure composed of "peptidoglycan," a complex polymer composed of glycan (carbohydrate) strands made of repeats of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). Most NAM residues are attached to short "wall peptides" that can be crosslinked (by peptide bonds) to wall peptides contained on other NAM residues from other glycan strands, hence generating the net-like structure. In several bacteria (like E. coli) wall peptides are linked directly to one another, but in other species they are connected through a peptide interbridge. The amino acid composition of the wall and interbridge peptides can vary between bacterial species.
What characteristics are used to classify bacteria?
The classification of bacteria was difficult since many bacteria look similar on first glance under a microscope. Scientists have relied on shape, size, Gram stain morphology, and whether the bacteria had structures like pili or could generate spores. Scientists also have relied heavily on metabolic characteristics (like what nutrients the bacteria can or cannot grow on). Recently, however, scientists have started to rely more and more on DNA sequence data to classify bacteria.
What additional components are contained within the cytoplasm of bacterial cells?
The cytoplasm is an aqueous (water-based) mix of RNA (mRNA and tRNA), ribosomes, and proteins. Many of these proteins are enzymes that carry out metabolic functions while others serve structural purposes.
2.2What is the nucleoid and how is it different from the eukaryal nucleus?
The nucleoid is a large mass in the cell cytoplasm comprising the bacterial chromosome coated with various proteins and RNA molecules undergoing synthesis. Unlike the eukaryal nucleus, the nucleoid/bacterial chromosome is not bounded by its own membrane
Describe the strategies used by bacterial cells to package the large chromosome into a "manageable form."
The nucleoid is condensed into a manageable form by its interactions with positively charged ions, its association with positively charged proteins and the fact that it is supercoiled due to the action of various topoisomerases.
Describe the role of porins and TonB-dependent receptors in Gram-negative bacteria.
The outer membrane of Gram-negative bacteria presents a barrier to the transfer of nutrients and waste between the bacterial cell and the environment. To facilitate diffusion of these molecules, the outer membrane has proteins called "porins," which serve as channels that permit the diffusion of small molecules (generally less than 600 Da in size) across the membrane. Molecules that utilize porins to transit the membrane do so through passive diffusion. Some nutrients (like iron or vitamin B) have difficulty crossing the membrane or are present in very low concentrations in the environment. To ensure their uptake Gram-negative bacteria produce high affinity receptors on their surface that bind these nutrients and deliver them to the periplasm. This type of transport process is "active" instead of "passive" - it requires energy from the proton motive force to drive movement of the TonB protein to help pull the receptor and its target substrate into the periplasm.
2.4 What are the key components of the bacterial plasma membrane and what are its functions?
The plasma membrane is primarily a bilayer formed by a mixture of phospholipids and, in a small subset of bacterial species, cholesterol-like molecules called hopanoids. The lipid bilayer serves as a permeability barrier that prevents charged or large polar compounds from entering the cell. Small polar molecules (like water) and uncharged compounds (like CO2, O2 and N2) can diffuse freely across the membrane. Approximately half of the membrane is composed of protein. These proteins perform many functions including the transport of various molecules (nutrients or wastes) either into or out of the cell. Some membrane proteins form "secretion systems" (like the SecYEG channel) that are involved in the export of proteins from the cytoplasm to the outside of the cell. Other proteins are involved in sensory systems that can detect conditions present in the outside environment. Still others are involved in energy capture by creating gradients of ions or other components across the membrane while different proteins utilize this gradient to move the cell, transport molecules, or generate ATP.
What is the type III secretion pathway?
The type III secretion pathway enables the transport of proteins across the inner and outer membrane simultaneously. It is composed of several proteins that combine to make a structure that resembles a syringe that crosses both membranes and the peptidoglycan layer. Proteins synthesized in the cytoplasm enter a pore at the base of the syringe and are actively secreted into the environment or into another cell (a "host" cell). Type III secretion systems share considerable homology to the structures that make bacterial flagella.
Explain the processes of gliding motility and actin-based motility. Provide examples.
twiching motility occurs when bacteria employ pili (surface appendages) to grab onto a surface. The bacteria move by rapidly retracting the pili, which propels the bacteria forward. Gliding motility is defined as a type of motility where the bacteria move smoothly over a surface without using a flagella to propel them. How gliding motility occurs is poorly understood and not all gliding bacteria may use the same mechanism. Actin-based motility occurs when certain bacteria, like Listeria and Shigella, invade a eukaryal cell (for example an epithelial cell). After being taken up by the eukaryal cell (the host cell) the bacteria breaks out of the vacuole and enters the host cell cytoplasm. The bacteria is then able to polymerize host cell actin at one cell pole, which provides a force sufficient to move the bacteria through the cytoplasm. The force generated is sufficient to shoot the bacteria into a neighboring host cell, thereby allowing the bacteria to spread without being exposed to the outside environment.
