1. Taxonomy, Viruses, and Bacteria Fill-In Notes Taxonomy= Science of classification Carolus Linnaeus - Discovered our current classification system-based on physical characteristics How to classify: Use phylogenetic branching trees to show evolutionary relationships Use physical characteristics to group organisms

2. Levels of Organization: Gray Wolf example Kingdom: Animalia Phylum: Chordata Class: Mammalia Order: Carnivora Family: Canidae Genus: Canis Species: lupis Can remember the levels with the sentence: KING PHILLIP CAME OVER FOR GOOD SPAGHETTI

3. There are 6 kingdoms: Animalia, Plantae, Fungi, Protista, Eubacteria, Archaebacteria (Eu and Archaea used to be Kingdom Monera and then it split) Above the 6 kingdoms, there are 3 domains: Bacteria, Archaea and Eukarya Genus and species names are the two word names we give to organisms = binomial nomenclature (bi = two; nomial = name; nomen = naming; cloture = system) Ex: Homo sapiens, Escherichia coli, Armadillidium vulgare First word is Genus (is capitalized) Second word is species (not capitalized) BOTH are written in italics or underlined

4. Pathogen: Agent that can cause disease General Characteristics of Viruses Not considered to be alive because they are not cells and cannot perform any functions on their own. They have NO organelles and cannot use energy to build PROTEINS. A virus MUST enter a host cell in order to reproduce.

5. Virus Structure Figure 1.1: General virus structure

6. 1.All viruses have a capsid or head region that contains its genetic material. The capsid is made of proteins. 2. Some viruses have an envelope surrounding their capsid. This allows viruses to penetrate host cells through membrane fusion. 3. The virus's genetic material rests inside the capsid; that material can be either DNA, RNA, or even in some cases a limited number of enzymes. The type of genetic material a virus contains is used in classification as there are DNA viruses like herpes and the RNA viruses like HIV and flu. 4. In addition to the head region, some viruses have a tail region. The tail aids in binding to the surface of the host cell and in the introduction of virus genetic material to the host cell.

7. -Virus "Life" Cycles Figure1.2: Generalized Replication of Viruses

8. 1. All viruses share 6 basic steps in their replication cycles. These are: attachment, penetration, uncoating, replication, assembly and release 2. Lytic phase –virus particles infect the cell and replicate immediately 3. Lysogenic phase-viral genetic material enter the host cell, become incorporated in the cell and lies dormant (asleep). Gets passed on and reproduce and then will bust out of the cell in the lytic cycle (herpes). 4. Smaller than viruses are viroids = cause disease in plants = tobacco mosaic virus 5. Smaller than viroids are prions = made only of proteins that can cause other proteins to fold the wrong way so the protein does not function correctly. 6. List of viruses: cold, flu, herpes, HIV, Ebola, chickenpox, measles, mumps, rabies, smallpox, yellow fever, hepatitis

9. General Characteristics of Bacteria -Are prokaryotic cells (pro- means NO nucleus) -Structure

10. Roles of Bacteria a. Are cause of diseases. b. Most are beneficial to other organisms. c. Can be photoautotrophs = nitrogen fixing bacteria making nitrogen available to the roots of plants. d. Other bacteria are saprophytes, breaking down dead organic material. e. Others live symbiotically in the digestive tracts of other organisms to help with digestion.

11. f.Reproduce by binary fission not mitosis. In this process, the genetic material is replicated, and the two copies move to separate regions. Next, the plasma membrane pinches inward, producing two equal daughter cells. Takes place every 20 minutes. g. List of bacteria: acne, strep throat, E. coli, Salmonella, tuberculosis, syphilis, typhus, tetanus, tooth decay, bubonic plague, some types of pneumonia, bronchitis, good bacteria in your intestines and on your skin, helps make yogurt, pickles

12. Eubacteria Figure1.4: Common shapes of eubacteria -Shape Eubacteria are often classified by their shape. They fall into three main shape categories. round = cocci; rod= bacilli; spiral =spirilla.

13. Archaebacteria Characteristics 1. The name "archaebacteria," with its prefix meaning "ancient," suggests that this is an extremely old group but this is not the case. 2. The fact that most of these Monerans live in extremely hostile, extreme environments like deep in ocean, soil 3. Can be aerobic (oxygenated) conditions or anaerobic (non-oxygenated) conditions or facultative anaerobes (both conditions). 4. Have different types of proteins in their cell walls to make them Gram + or Gram -

14. Vaccinations Characteristics for vaccinations against BACTERIA. 1. Contains the pathogens or their toxins in a harmless form. 2. Treated w/ chemicals or heat, or genetically engineered 3. Dead bacteria cannot cause disease 4. Stimulate immune system to defend against the bacteria Ex: DPT shot (diphtheria, pertussis and tetanus)

15. Characteristics for vaccinations against VIRUSES. 1. Contains viruses made harmless by treatment w/ chemicals or by genetic engineering 2. Stimulates immune system to create defenses against the harmful form of a virus 3. Vaccination only works when the proteins on the virus don’t change Ex: smallpox, chickenpox, measles, and polio virus – same surface protein each generation Ex: HIV, cold viruses, flu viruses have surface proteins that change vaccine for an old coat would not recognize a new coat HIV changes the most rapidly

16. Antibiotics Characteristics Antibiotics are antibacterial drugs… do NOT work on viruses Examples: Penicillin, tetracycline, and streptomycin May prevent bacteria from making cell walls Definitely over prescribed Our immune system can fight off some of the lesser bacterial infections (given time!)

17. -Super Bacteria (ex: MRSA= super staph infection) Resistant to antibiotics Mutations occur randomly Get variations of bacteria that can resist an antibiotic Failure to take antibiotics as prescribed Weak bacteria are killed first, stronger bacteria survive