Prokaryotes

1. Prokaryotes • Bacteria were first discovered in the late 1600’s by Antony van Leeuwenhoek, using the microscope he invented. • The first recorded observation were of the bacteria found in the dental plaque of two old men who never cleaned their teeth.

2. Prokaryote Introduction • Prokaryotes are much more diverse in both habitat and metabolism than the eukaryotes. • However, prokaryotes are not very diverse in body shape or size. Much of their classification into different species is done by examining their internal biochemistry and their DNA. • Nearly all prokaryotes are single-celled. Differentiation into different cell types almost never occurs in prokaryotes. • Two major groups: the Eubacteria (sometimes just called Bacteria) and the Archaea (or Archaebacteria). Very different genetically.

3. Prokaryote Structure • Prokaryotes are simple cells. The DNA is loose in the cytoplasm—there is no separate nucleus. The ribosomes are also in the cytoplasm. In prokaryotes, transcription (synthesis of RNA) and translation (synthesis of proteins) occurs simultaneously. • The cell is surrounded by a membrane, but there are no internal membranes. • Outside the membrane is a cell wall, and sometimes an outer capsule which can have structures projecting form it. • Bacteria move using flagella: whip-like hairs similar to the flagellum of a sperm cell.

4. Bacterial Reproduction • Bacteria reproduce by the process of binary fission. The circular chromosome replicates its DNA. Then, the cell splits into 2 halves, each containing a single chromosome • No spindle apparatus (as exists in eukaryotic mitosis and meiosis).

5. Growth of Bacteria • Under ideal conditions, bacteria grow very rapidly: some double in number every 20 minutes. • Doubling in number: 1-2-4-8-16-… is exponential growth. It starts off slowly, but once going the number of bacteria increase very rapidly • Usually some nutrient runs short, or waste material builds up, and growth ceases. Eventually a die-off occurs, reducing the number of live bacteria.

6. Genetic Exchange in Bacteria • Bacteria don’t have sexes or a regular genetic exchange every generation the way most eukaryotes do. • However, there are several means of sharing DNA between individuals, even if they are not of the same species. • Conjugation is one such mechanism: the donor bacteria grows tubes that project from its surface to the surface of a recipient. A copy of the chromosomal DNA travels through this tube into the recipient, where it become incorporated into the recipient’s genome.

7. Bacterial Morphology • Bacteria only take a few basic shapes, which are found in many different groups. Bacterial cells don’t have internal cytoskeletons, so their shapes can’t be very elaborate. • Shape: coccus (spheres) and bacillus (rods). Spirillum (spiral) is less common. • Aggregation of cells: single cells, pairs (diplo), chains (strepto), clusters (staphylo). • Thus we have types such as diplococcus (pair of spheres) and streptobacillus (chain of rods).

8. Gram Stain • A major distinction between groups of bacteria is based on the Gram stain. In this method, bacteria are treated with the dye “crystal violet”, then washed. Often a second stain, “safranin” is applies to make the unstained bacteria visible. • Gram stain causes bacteria with a lot of peptidoglycan and very little lipid in their cells walls to stain purple. The presence or absence of peptidoglycan is a fundamental biochemical difference between groups of bacteria

9. Metabolic Diversity • Bacteria show far more metabolic diversity than eukaryotes • General classification, based on carbon (food) source and energy source. • autotroph vs. heterotroph. Autotrophs make their own food from non-organic sources (usually carbon dioxide). Heterotrophs use organic compounds from other organisms. • phototroph vs. chemotroph. Phototrophs get their energy from sunlight. Chemotrophs get their energy from chemical compounds. • Photoautotrophs get energy from sunlight and synthesize their own food from scratch, like green plants. • Photoheterotrophs ( a rare category) get energy from sunlight but need organic compounds made by other organisms. • Chemoautotrophs get energy from chemicals such as hydrogen gas, hydrogen sulfide or ammonia, and they use carbon dioxide as the raw material for their organic compounds. • Chemoheterotrophs get both energy and organic compounds from other organisms. We are chemoheterotrophs.

10. Relationship to Oxygen • For more than half of Earth’s history, oxygen wasn’t present in the atmosphere. Many bacteria evolved under anaerobic conditions. • Classification: • strict aerobes (need oxygen to survive) • strict anaerobes (killed by oxygen) • aerotolerant (don’t use oxygen, but survive it). • facultative anaerobes (use oxygen when it is present, but live anaerobically when oxygen is absent).

11. Spores • Some bacteria can form very tough spores, which are metabolically inactive and can survive a long time under very harsh conditions. • Allegedly, some bacterial spores that were embedded in amber for 25 million years have been revived. Others, trapped in salt deposits for up to 250 million years, have also been revived. These experiments are viewed skeptically by many scientists. • “Extraordinary claims demand extraordinary proof” • Spores can also survive very high or low temperatures and high UV radiation for extended periods. • Panspermia: the idea that life got started on Earth due to bacterial spores that drifted in from another solar system. (However, it still had to start somewhere!).

12. Archaea • Sometimes called “Archaebacteria” • Genetically as different from Eubacteria as we are. • One distinguishing characteristic: cell membranes don’t contain fatty acids, but instead use branched molecules called isoprenes. • Three main type: methanogens, extreme halophiles, extreme thermophiles.

13. Methanogens • Methanogens: convert hydrogen and carbon dioxide into methane to generate energy anaerobically. Methanogens are obligate anaerobes: they are killed by oxygen. • Methanogens digest cellulose in cow and termite guts. Each cow belches 50 liters of methane a day. A major greenhouse gas. • Methanogens are also in swamps, wetlands, and garbage dumps.

14. Halophiles • Extreme halophiles. Grow in very salty conditions. Colorful bacteria in seawater evaporation beds, Great Salt Lake. • Mostly aerobic metabolism. • Some have a form of photosynthesis that uses bacteriorhodopsin, a pigment very similar to the rhodopsin pigment in our eyes. It is also called “purple membrane protein”

15. Thermophiles • Extreme thermophiles. Live at very high temperatures: ocean hydrothermal vents (up to 113o C, which would be boiling except for the high pressure under the ocean), hot springs in Yellowstone National Park. • Use sulfur to generate energy just like we use oxygen: donate electrons to sulfur to create hydrogen sulfide. Some generate sulfuric acid instead—they live at very low pHs.

16. Eubacteria • The most common types of bacteria • Many categories: we will just look at a few of them. • Enteric bacteria live in the digestive tracts of animals. Enterics are facultative anaerobes. Best known example: Escherichia coli (E. coli), found in the human gut and also used as a common experimental organism in the lab. Most E. coli strains are harmless, but a few pathogenic (disease-causing) strains exist, causing food poisoning. A common source is ground meat, but it gets on unwashed vegetables as well. • Related enteric bacteria: Salmonella, Shigella. Cause food poisoning. Chickens carry Salmonella in their guts instead of E. coli.

17. Pyogenic Cocci • Pyogenic cocci. “Pyogenic” means “pus-forming”. These bacteria produce many of the worse infections. • Staphylococcus aureus and Neisseria gonorrheae are 2 examples: Staphylococcus produces pneumonia, toxic shock syndrome, strep throat, meninginitis, and various skin diseases, such as impetigo. Neisseria produces gonorrhea, a common sexually transmitted disease • Staphylococcus bacteria normally live on the skin and body cavities. Only occasionally cause disease. • Some strains of Staphylococcus are resistant to all known antibiotics.

18. Endospore-forming Bacteria • Most of these are in the genus Bacillus (named after their normal shape). • Their spores are very resistant to environmental conditions, and may survive millions of years before they revive. • Anthrax is caused by a Bacillus species. Also is this family are the bacteria that cause botulism (a very bad form of food poisoning) and tetanus (lockjaw--the muscles go rigid).

19. Rickettsia and Chlamydia • These bacteria are intracellular parasites of eukaryotic cells. They can’t survive outside a cell. Sometimes they have very reduced genomes: they rely on host genes for critical functions. • Rickettsia live in the gut linings of insects, and they infect mammals through mosquito and tick bites. They cause diseases like Rocky Mountain spotted fever, typhus, and Q fever. • Chlamydia infections are the most common sexually transmitted disease in the US.

20. Nitrifying and Nitrogen-fixing Bacteria • All proteins contain much nitrogen. The atmosphere is 80% nitrogen. However, we can’t directly use atmospheric nitrogen, because it is in the wrong form: N2. We need it in the ammonia form: NH3. • Nitrogen fixing bacteria are able to do this conversion. Most of them live in root nodules of certain plants, the legumes, such as alfalfa and soybeans. Farmers plant these crops to enrich their soil by naturally adding ammonia to it. • The nitrogen-fixing bacteria live in the soil and invade the nodules of young plants. • The nitrogen-fixing enzymes are poisoned by oxygen. The root nodules function to keep oxygen away from the bacteria. • Plants also need nitrogen in the form of nitrate, NO3. Nitrifying bacteria convert ammonia into nitrate.

21. Cyanobacteria • A major group of photosynthetic bacteria • The oceans contain large amounts of cyanobacteria (called plankton), that produce much of Earth’s oxygen. • Cyanobacteria are the source of chloroplasts in plant cells. They also have a symbiotic relationship in lichens: a fungus and a cyanobacteria provide each other with shelter and food from photosynthesis. • Cyanobacteria form cell walls to fossilize—among the oldest forms of life known. • Some have cell differentiation: they form filaments in which some cells become “heterocysts”, heavily walled cells that perform nitrogen fixation for the other cells in the filament.