Prokaryotes & Viruses

1. Prokaryotes & Viruses Chapter 16

2. Early Earth • Earth is about 4.6 billion years old • Fossils resembling photosynthetic prokaryotes have been found in dome shaped rocks called stromatolites, date back to 3.5 billion year ago.

3. Origin of Organic Molecules • In 1953, Miller & Urey designed an experiment to simulate conditions on early Earth • Under many different conditions this basic set up has produced all 20 amino acids, several sugars, lipids, the nitrogenous bases found in DNA & RNA and ATP • Solutions of amino acids and dropped them onto the surface of hot sand, clay or rocks has resulted in the formation of polypeptides

4. The RNA World • A characteristic of life is the process of inheritance, which is based on molecules that can copy themselves. DNA  RNA  Protein • How did this information flow originate? • A popular hypothesis is that genes were originally short strands of RNA capable of replicating without enzymes • Scientists have observed RNA molecules copying themselves in solutions containing nucleotides without enzymes or cells present • During the “RNA world”, RNA might have stored genetic information in addition to directing protein synthesis

5. Formation of Pre-Cells • Experiments have shown that polypeptides can form microscopic fluid-filled spheres. • If certain kinds of lipids are in the solution selectively permeable membranes will form. • These “molecular packages” are referred to as pre-cells

6. Hypothetical 4-Stage Sequence for Origin of Life • Small organic molecules formed from simpler inorganic molecules • These small molecules joined into more complex ones • Molecules that could copy themselves provided a basis for inheritance of molecular information • These molecules became packaged within membranes and separated from their surroundings

7. Archaea v. Bacteria • “archaea” is derived from the Greek work for ancient • Exist in harsh habitats resembling conditions of early Earth • They are referred to as “Extremophiles” • Thermophiles • Halophiles • anaerobic • Believed to be as closely related to eukaryotes as they are to bacteria • Contain different information in their nucleic acids • RNA polymerases differ • Lack introns • Susceptible to antibiotics that do not affect archaea • Contain peptidoglycan in their cell walls

8. Phylogenic Tree of the Three Domains

9. Structure & Function of Bacteria: Shape • Cocci – spherical • Bacilli – rod-shaped • Spirilla – spiral shaped

10. Structure & Function of Bacteria: Cell Wall • Gram + (purple stain): thick layer of peptidoglycan • Gram – (pink stain): thinner layer of peptidglycan with outer membrane

11. Structure & Function of Bacteria: Motility • Flagellum • Pilli • Slime secretion

12. Bacterial Reproduction Binary fission: DNA is copied and moved to opposite ends of the cell as the cell divides; occurs almost continuously. • Rapid reproduction rate, many can divide within 20 minute • Results in a colony of cells that are clones (unless mutations occur)

13. Genetic Variation • Despite reproducing asexually, bacteria are able to obtain genetic variation through conjugation • Two bacterial cells temporarily join and exchange plasmid DNA; does not need to occur between cells of the same species/strain

14. Endospores • Allow bacteria to survive periods of very harsh conditions by going into a dormant endospore form • After copying DNA, one copy is surrounded by a thick protective coat and the outer cell disintegrates • Often able to survive for years in this state, when conditions are more favorable, the endospores will absorb water and grow again.

15. Modes of Nutrition

16. The Oxygen Revolution • The evolution of photosynthetic cyanobacteria resulted in the presence of free oxygen in oceans, lakes & the atmosphere • This oxygen was toxic to many existing organisms because it attacks the bonds of organic molecules & many went extinct • Some were not exposed to oxygen and remained anaerobic; their descendants still exist in similar environments today • A small number were able to use the oxygen in the extraction of energy from food, their descendents are the wide variety of aerobic organisms in existence today

17. Beneficial Uses of Bacteria • Chemical recycling: • Decomposers: replenish soil nutrients and release CO2 back to the atmosphere • Nitrogen fixing bacteria: convert nitrogen gas in the atmosphere to an organic form usable by other organisms for nucleotide and amino acid formation • Bioremediation: • Sewage treatment: decompose organic matter in sewage sludge • Oil spill clean-up: genetically modified digest oil • Clean old mining sites: detoxify by extracting lead & mercury • Medicine/Pharmaceuticals: • Produce desired gene products: insulin, HGH • Probiotics: restore beneficical intestinal bacteria • Food: • Cheese • Yogurt

18. Viruses & Bacteriophage: The Boundary of Life • All living things share 8 characteristics. Viruses do not meet all of these characteristics. • Viruses attack eukaryotic cells and Bacteriophages attack prokaryotic cells. • Viruses and phages are capable of reproducing at a very rapid rate, but only in a host cell. • Viruses are responsible for many diseases and can be found everywhere.

19. Viral Structure

20. Viruses & Disease • Method of causing disease is very different from that of bacteria • Therefore methods for treatment & prevention differ from methods for bacteria • Antibiotics will not work on viruses because they target specific not found in viruses or host cells • Damage or prevent formation of bacterial cell wall • Some examples of viral diseases include: Influenza (RNA) Polio (RNA) Common cold (RNA) Hepatitis (DNA) Measles (RNA) Herpes (DNA) Mumps (RNA) Smallpox (DNA) AIDS (RNA) Rabies (RNA)

21. Viral Infection • Viruses and bacteriophages invade cells and use the host cell's machinery to synthesize more of their own macromolecules. • Once inside the host the bacteriophage or virus may go into two reproductive cycles: • Lytic cycle: destroying the host cell during reproduction. • Lysogenic Cycle – a parasitic type of partnership with the cell

22. Lytic Cycle & Lysogenic Cycle

23. Viruses are host specific – a protein on the surface of the virus has a shape that matches a molecule in the plasma membrane of its host, allowing the virus to lock onto the host cell.

24. Proviruses A provirus is a DNA virus that has been inserted into a host cell chromosome.

25. Retroviruses & HIV • Retroviruses reverse the normal DNA to RNA to protein flow • In RNA viruses, the RNA nucleotide will be translated • Reverse transcriptase catalyzes the synthesis of DNA from an RNA template, the DNA intermingles with host DNA as a provirus making it difficult to detect

26. Prions • Proteins that cause several diseases of the brain: Mad cow disease, Kuro, Creutzfeldt-Jacob disease (CJD) & Scrapie (in sheep) • Only infectious agent that do not contain genetic material • Normal form play important roles in brain function such as helping nerve cells communicate • Abnormal prions destroy the brain • Three ways to acquire abnormal prions: • Infection with abnormal prions • Inherited genes that give rise to abnormal prions • Spontaneous genetic mutations that give rise to abnormal prions

27. Viroids • Small strands of RNA rather than strands of protein. • Smaller than the strands of genetic info in viruses and contain no protein coat. • Replicated using host cell machinery, like viruses • Cause plant diseases: potato spindle tuber, avocado sunblotch, chrysanthemum stunt, and chrysanthemum chlorotic mottle

28. Immune Response

30. HIV doesn’t target just any cell, it goes right for the cells that want to kill it. “Helper" T cells are HIV's primary target. These cells help direct the immune system's response to various pathogens. HIV undermines the body's ability to protect against disease by depleting T cells thus destroying the immune system. The virus can infect 10 billion cells a day, yet only about 1.8 billion can be replaced daily.

31. Defense Against Viral Diseases

32. From HIV to AIDS • During first few years (7-10) after HIV infection, person is usually asymptomatic. • During the symptomatic phase, the body has insufficient numbers of T-Cells (from normal 800-1200 /mm3 to 200/ mm3 ) to mount an immune response against infections. • Chronic diarrhea, minor mouth infections, night sweats, headache & fatigue are common • At the point when the body is unable to fight off infections, a person is said to have the disease AIDS. (Generally when count drops below 200 /mm3 ) • It is not the virus or the disease that ultimately kills a person; it is the inability to fight off something as minor as the common cold.

33. AIDS: The Global Epidemic • Around 2.6 million people became infected with HIV in 2009. • Sub-Saharan Africa has been the hardest hit by the epidemic. In 2009 over two-thirds of AIDS deaths were in this region