Chapter 21 Flashcards
Antigen
Substances that stimulate antibody production by the immune system.
Bioremediation
Applications of chemical and biological knowledge to decontaminate polluted environments.
Archaea aka Archaebacteria
One of two domains of prokaryotes; archaeans have some unique molecular and biochemical traits, but they also share some traits with Bacteria and other traits with Eukarya.
Bacteria
One of the two domains of prokaryotes; collectively, bacteria are the most metabolically diverse organisms.
Eukarya
The domain that includes all eukaryotes, organisms that contain a membrane-bound nucleus within each of their cells; all protists, plants, fungi, and animals.
What are the three domains of living organisms?
- Archaea (Archaebacteria) - prokaryotes
- Bacteria - prokaryotes
- Eukarya - eukaryotes
Biomass
The dry weight of biological material per unit area or volume of habitat.
Eukaryote
Organism in which the DNA is enclosed in a nucleus.
Prokaryote
Organism in which the DNA is suspended in the cell interior without separation from other cellular components by a discrete membrane.
Identify the structural features of organelles and cell walls that distinguish prokaryotes from eukaryotes.
- Prokaryotes have a nucoleoid rather than a nucleus.
- Prokaryotes do not have anything equivalent to the mitochondria, endoplasmic reticulum, or Golgi complex found in eukaryotes. With few exceptions, the reactions carried out by these organelles in eukaryotes are distributed between the cytoplasmic solution and the plasma membrane in prokaryotes.
- Both have flagella but they are different in structure and pattern of movement.
Nucleoid
The central region of a prokaryotic cell with no boundary membrane separating it from the cytoplasm, where DNA replication and RNA transcription occur.
What are the common shapes of prokaryotes?
- Spiral (spirilla)
- Spherical (cocci; coccoid)
- Cylindrical (rods; bacilli)
- Square
Draw a Bacterial Cell
Describe the general structure of prokaryotic cells.
- Cell Wall
- Plasma Membrane
- Cytoplasm
- Most consist of a single, circular DNA molecule.
- Plasmids
- Ribosomes
- Capsule
- Flagella
- Pili
Plasmid
A DNA molecule in the cytoplasm of certain prokaryotes, which often contains genes with functions that supplement those in the nucleoid and which can replicate independently of the nucleoid DNA and be passed along during cell division.
Generally contain genes for nonessential but beneficial functions such as antibiotic resistance.
Cell Wall
A rigid external layer of material surrounding the plasma membrane of cells in plants, fungi, bacteria, and some protists, providing cell protection and support.
Cytoplasm
All parts of the cell that surround the central nuclear or nucleoid region.
Plasma Membrane
The outer limit of the cytoplasm responsible for the regulation of substances moving into and out of cells.
Ribosome
A ribonucleoprotein particle that carries out protein synthesis by translating mRNA into chains of amino acids.
Messenger RNA (mRNA)
An RNA molecule that serves as a template for protein synthesis.
Amino Acid
A molecule that contains both an amino and a carboxyl group.
Ribonucleic Acid (RNA)
A polymer assembled from repeating nucleotide monomers in which the five-carbon sugar is ribose. Cellular RNAs are mRNA (which is translated to produce a polypeptide), tRNA (which brings an amino acid to the ribosome for assembly into a polypeptide during translation), and rRNA (which is a structural component of ribosomes). The genetic material of some viruses is RNA.
Amino Group
Group that acts as an organic base, consisting of a nitrogen atom bonded on one side to two hydrogen atoms and on the other side to a carbon chain.
Peptidoglycan
A polymeric substance formed from a polysaccharide backbone tied together by short polypeptides, which is the primary structural molecule of bacterial cell walls.
Gram Stain Procedure
A procedure of staining bacteria to distinguish between types of bacteria with different cell wall compositions.
Cells are first stained with crystal violet, rinsed with ethanol, and then counterstained with safranin. Some cells retain the crystal violet and thus appear purple when viewed under the microscope; these are termed Gram-positive cells. In other bacteria, ethanol washes the crystal violet out of the cells, which are colourless until counterstained with safranin; these Gram-negative cells appear pink under the microscope.
Explain the differences between Gram positive and Gram negative bacteria.
Gram-positive bacteria have cell walls composed almost entirely of a single, relatively thick peptidoglycan layer.
The cell wall of Gram-negative bacteria has two distinct layers: a thin peptidoglycan layer just outside the plasma membrane and an outer membrane external to the peptidoglycan layer. This outer membrane contains lipopolysaccharides (LPS) and thus is very different from the plasma membrane. The outer membrane protects Gram-negative bacteria from potentially harmful substances in the environment.
Outer Membrane
In Gram-negative bacteria, an additional boundary membrane that covers the peptidoglycan layer of the cell wall.
Lipopolysaccharide (LPS)
A large molecule that consists of a lipid and a carbohydrate joined by a covalent bond.
Gram-negative
Describing bacteria that do not retain the stain used in the Gram stain procedure.
Gram-positive
Describing bacteria that appear purple when stained using the Gram stain technique.
Capsule
An external layer of sticky or slimy polysaccharides coating the cell wall in many prokaryotes.
Polysaccharide
Chain with more than 10 linked monosaccharide subunits.
Monosaccharide
The smallest carbohydrates, containing three to seven carbon atoms.
Flagellum (plural, Flagella)
A long, threadlike, cellular appendage responsible for movement; found in both prokaryotes and eukaryotes, but with different structures and modes of locomotion.
Pilus (plural, Pili)
A hair or hairlike appendage on the surface of a prokaryote.
Describe prokaryotic flagella.
They are made of rigid helical proteins and rotate much like the propeller of a boat
Sex Pilus
Pili that not only allows bacterial cells to adhere to each other but also acts as a conduit for the transfer of plasmids from one cell to another.
Photoautotroph
A photosynthetic organism that uses light as its energy source and carbon dioxide as its carbon source.
Chemoheterotroph
An organism that oxidizes organic molecules as an energy source and obtains carbon in organic form.
What modes of nutrition are found only in prokaryotes?
Photoheterotrophs
Chemoautotrophs
Photoheterotroph
An organism that uses light as the ultimate energy source but obtains carbon in organic form rather than as carbon dioxide.
Chemoautotrophs
aka
Lithotrophs
aka
Chemolithotrophs
An organism that obtains energy by oxidizing inorganic substances such as hydrogen, iron, sulphur, ammonia, nitrites, and nitrates and uses carbon dioxide as a carbon source.
Aerobe
An organism that requires oxygen for cellular respiration.
Cellular Respiration
The process by which energy-rich molecules are broken down to produce energy in the form of ATP.
Obligate Aerobe
A microorganism that uses oxygen for cellular respiration and requires oxygen in its surroundings to support growth.
Obligate Anaerobe
A microorganism that cannot use oxygen and can grow only in the absence of oxygen.
Faculative Anaerobe
An organism that can live in the presence or absence of oxygen, using oxygen when it is present and living by fermentation under anaerobic conditions.
Anaerobic Respiration
The process by which molecules are oxidized to produce ATP via an electron transport chain and ATP synthase, but unlike aerobic respiration, oxygen is not the final electron acceptor.
What is oxygen’s involvement in aerobic respiration?
We breathe oxygen to provide the final electron acceptor for the electrons we remove from our food and pass down an electron transport chain to make ATP via aerobic respiration.
Nitrogen Cycle
A biogeochemical cycle that moves nitrogen between the huge atmospheric pool of gaseous molecular nitrogen and several much smaller pools of nitrogen-containing compounds in soils, marine and freshwater ecosystems, and living organisms.
Biogeochemical Cycle
Any of several global processes in which a nutrient circulates between the abiotic environment and living organisms.
Nitrogen Fixation
A metabolic process in which certain bacteria and cyanobacteria convert molecular nitrogen into ammonia and ammonium ions, forms usable by plants.
Describe the great biochemical versatility of prokaryotes and their role in biogeochemical cycles.
The ability of prokaryotes to metabolize such a wide range of substrates makes them key players in the life-sustaining recycling of elements such as carbon, oxygen, and nitrogen, among others.
Nitrification
The conversion of ammonium (NH4+) to nitrate (NO3-). This is carried out in two steps by two types of nitrifying bacteria present in soil and water, one of which converts ammonium to nitrite (NO2-), and the other converts nitrite to nitrate. Nitrate is then taken up by plants and fungi and incorporated into their organic molecules.
How do prokaryotes reproduce?
In prokaryotes, asexual reproduction is the normal mode of reproduction. In this process, a parent cell divides by binary fission into two daughter cells that are exact genetic copies of the parent.
Endotoxin
A lipopolysaccharide released from the outer membrane of the cell wall when a bacterium dies and lyses.
Exotoxin
A toxic protein that leaks from or is secreted from a bacterium and interferes with the biochemical processes of body cells in various ways.
Lipopolysaccharide
A large molecule that consists of a lipid and a carbohydrate joined by a covalent bond.
Lysed
Refers to a cell that has ruptured or undergone lysis.
Binary Fission
Prokaryotic cell division—splitting or dividing into two parts.
Outline various mechanisms of resistance to antibiotics in bacteria.
Some bacteria are able to pump antibiotics out of the cell using membrane-bound pumps.
They can also produce molecules that bind to the antibiotic or enzymes that break down the antibiotic, rendering it ineffective against its target.
Alternatively, a simple mutation can result in a change in the structure of the antibiotic’s target, so that the antibiotic cannot bind to it.
Horizontal gene transfer.
Finally, bacteria can develop new enzymes or pathways that are not inhibited by the antibiotic.
Identify various human practices that promote the development of bacterial resistance to antibiotics.
The practice of adding low levels of antibiotics to animal feed is another example of human practice that promotes the development of antibiotic-resistant genes in bacteria.
Antibiotic
A natural or synthetic substance that kills or inhibits the growth of bacteria and other microorganisms.
Biofilm
A microbial community consisting of a complex aggregation of microorganisms attached to a surface and surrounded by a film of polymers.
Slime Layer
A coat typically composed of polysaccharides that is loosely associated with bacterial cells.
Quorum Sensing
The use of signalling molecules by prokaryotes to communicate and to coordinate their behaviour.
How does a biofilm form?
Imagine a surface, such as a rock in a stream, over which water is flowing. Due to the nutrients in the water, the surface rapidly becomes coated with polymeric organic molecules, such as polysaccharides or glycoproteins. Once the surface is conditioned with organic molecules, free prokaryotes attach in a reversible manner in a matter of seconds (step 1).
If the cells remain attached, the association may become irreversible (step 2), at which point, the prokaryotes grow and divide on the surface (step 3).
Next, the physiology of the cells changes, and they begin to secrete extracellular polymeric substances (EPS), a slimy, glue- like substance similar to the molecules found in bacterial capsules. EPS extends between cells in the mixture, forming a matrix that binds cells to each other and anchors the complex to the surface, thereby establishing the biofilm (step 4).
The slime layer entraps a variety of materials, such as dead cells and insoluble minerals. The physiological change accompanying the formation of a biofilm results from marked changes in a prokaryote’s gene expression pattern—in effect, the prokaryotes in a biofilm become very different organisms. Over time, other organisms are attracted to and join the biofilm; depending on the environment, these may include other bacterial species, algae, fungi, or protozoa producing diverse microbial communities (step 5).
What are the 6 particularly important evolutionary branches of bacteria?
Proteobacteria, green bacteria, cyanobacteria, Gram-positive bacteria, spirochetes, and chlamydias.
Describe the major characters of proteobacteria.
Gramnegative.
Purple colour comes form their photosynthetic pigment, a type of chlorophyll disctinct from that of plants.
Many present-day species are photoautotrophs (the purple sulphur bacteria) or photoheterotrophs (the purple nonsulphur bacteria), or chemoheterotrophs.
Among the chemoheterotrophs classified with the proteobacteria are E. coli, plant pathogenic bacteria, and bacteria that cause human diseases such as bubonic plague, gonorrhea, and various forms of gastroenteritis and dysentery. The proteobacteria also include both free-living and symbiotic nitrogen- fixing bacteria.
Describe the major character of Green Bacteria.
Photosynthetic, green, gramnegative bacteria.
Do not produce oxygen as a byproduct of photosyntheis.
Are photoautotrophs and photoheterotrophs.
Describe the major characters of cyanobacteria.
Gram-negative.
Photoautotrophs.
Blue-green in colour.
Carry out photosynthesis by the same pathways and using the same chlorophyll as eukaryotic algae and plants. Like plants and algae, they release oxygen as a by-product of photosynthesis.
Help fix nitrogen into organic compounds in aquatic habitats and as symbiotic partners with fungi in lichens.
Describe the major characters of gram-positive bacteria.
Chemoheterotrophs.
Some cause human diseaseases, other perform lactic acid fermentation in food.
Describe the major characters of spirochetes.
Have helically spiralled flagella embedded in their cytoplasm, causing the cells to move in a twisting, corkscrew pattern. Their corkscrew movements enable them to move in viscous environments such as mud and sewage, where they are common. Some spirochetes are harmless inhabitants of the human mouth; another species, Treponema pallidum, is the cause of syphilis. Termites have symbiotic spirochetes in their intestines that enable them to digest cellulose.
Describe the major characters of chlamydias.
These bacteria are unusual because although they are Gram-negative and have cell walls with an outer membrane, they lack peptidoglycan.
All the known chlamydias are intracellular parasites that cause various diseases in animals.
One bacterium of this group, Chlamydia trachomatis, is responsible for one of the most common sexually transmitted infections of the urinary and reproductive tracts of humans and also causes trachoma, an infection of the cornea that is the leading cause of blindness in humans.
Identify the major characters of Archaea.
The lipid molecules in archaeal plasma membranes are unlike those in the plasma membranes of all other organisms: there is a different linkage between glycerol and the hydrophobic tails, and the tails are isoprenes rather than fatty acids. Also, some lipids have polar head groups at both ends. These unique lipids are more resistant to disruption, making the plasma membranes better suited to extreme environments. Similarly, the unique cell walls of Archaea are more resistant to extremes than those of bacteria; some Archaea can even survive being boiled in strong detergents!
Chemoautotrophs or chemoheterotrophs.
None known as pathogens.
What are the three evolutionary branches of Archaea?
Euryarchaeota
Crenarchaeota
Korarchaeota
Euryarchaeota
A major group of the domain Archaea, members of which are found in different extreme environments. They include methanogens, extreme halophiles, and some extreme thermophiles.
Crenarchaeota
A major group of the domain Archaea, separated from the other archaeans based mainly on rRNA sequences.
Group includes most of the extreme thermophiles as while as psychrophiles.
Korarchaeota
A group of Archaea recognized solely on the basis of rRNA coding sequences in DNA taken from environmental samples.
This group has been recognized solely on the basis of DNA samples obtained from marine and terrestrial hydrothermal environments. To date, no members of this group have been isolated and cultivated in the lab, and nothing is known about their physiology. Molecular data indicate that they are the oldest archaeal lineage.
Methanogens
Methanogens (methane generators) live in low-oxygen environments and represent about one half of all known species of Archaea.
They are obligate anaerobes that live in the anoxic (oxygen-lacking) sediments of swamps, lakes, marshes, and sewage works, as well as in more moderate environments, such as the rumen of cattle and sheep, the large intestine of dogs and humans, and the hindguts of insects such as termites and cockroaches.
They generate energy by converting various substrates such as carbon dioxide and hydrogen gas or acetate into methane gas, which is released into the atmosphere.
Halophiles
Halophiles are salt-loving organisms.
Extreme halophilic Archaea live in highly saline environments such as the Dead Sea and on foods preserved by salting.
They require a minimum NaCl concentration of about 1.5 M (about 9% solution) to survive and can live in a fully saturated solution (5.5 M, or 32%).
Most are aerobic chemoheterotrophs, which obtain energy from sugars, alcohols, and amino acids using pathways similar to those of bacteria.
Many extreme halophiles use light as a secondary energy source, supplementing the oxidations that are their primary source of energy.
Extreme Thermophiles
Extreme thermophiles live in extremely hot environments such as hot springs and ocean floor hydrothermal vents.
Their optimal temperature range for growth is 70°C to 95°C, close to the boiling point of water. By comparison, no eukaryotic organism is known to live at a temperature higher than 60°C.
Some extreme thermophiles are members of the Euryarchaeota, but most belong to the Crenarchaeota.
Psychrophile
An archaean or bacterium that grows optimally at temperatures in the range of -10°C to -20°C.
