Viruses and Bacteria

A. RNA viruses

1. carry RNA, usually 5 to 15 genes, + RNA dependent RNA polymerase
2. structure: RNA strand surrounded by coat proteins

3. ss RNA that serves as mRNA

a. pycornavirus: polio, rhinovirus (common cold),
b. togavirus: yellow fever, encephalitis, rubella
c. filoviruses: e.g. ebola (NCI web site)
d. retroviruses: RNA tumor viruses, have reverse transcriptase (RNA dependent DNA polymerase) and incorporate into host genome, e.g. HIV

4. ss RNA that serves as template for mRNA

a. rhabdovirus: rabies
b. paramyxovirus: measles, mumps
c. orthomyxovirus: influenza

5. ds RNA: reovirus - diarrhea viruses

B. DNA viruses

1. carry DNA, up to 100 genes, + DNA dependent DNA polymerase

2. ds Types

a. Papilloma virus: genital warts (can cause cervical cancer)
b. Adenovirus: respiratory diseases
c. Herpesvirus: Herpes simplex (cold sores), Herpes zoster (shingles)
d. Poxvirus: Variola (Smallpox)

3. ss types - parvovirus

4. T4-bacteriophage (dsDNA) structure

a. Head with DNA
b. Sheath surrounded by coat proteins
c. Tail fiber

II. Viral replication and virulence

A. Forms

1. Lytic phase - viruses infect and destroy cells
2. Lysogenic phase - host cell incorporates viral DNA
3. Temperate virus - go into inactive stage for a period of time - Herpes viruses become active under stress and produce cold sores, or shingles.

B. Evolution of virulence

1. Virulence should evolve depending on mode of transfer. If virus kills host before successfully infecting alternative host, that lineage of viruses will go extinct
2. Viruses which transfer between hosts are expected to exhibit high virulence, e.g. rabies is lethal to us, but it can move between species
3. Viruses which have persisted with a host population are expected to exhibit low virulence, e.g. colds are rarely lethal, but they don't infect other species
4. Predict that highly virulent viruses recently invaded a new host

i. HIV (human immunodeficiency virus) came from monkey and chimp SIV

ii. epidemic forms of influenza came from chickens or ducks. 1918 flu epidemic made 2 billion people sick and killed 40 million

5. Myxomatosis virus was used to kill rabbits in Australia, but then declined in virulence before the rabbit population was exterminated

C. Evolution of resistance to treatment

1. Viruses have high mutation rates, with RNA viruses (10-5 - 10-6) greater than DNA viruses (10-8 - 10-10) per nucleotide site/replication
2. Some viruses have "chromosomes," e.g. genome is divided into multiple pieces. When coinfection of a host cell occurs, new viruses can recombine, such as flu, which has 8 chromosomes
3. This means that viruses can evolve much faster than most hosts
4. HIV has the highest mutation rate ever recorded. HIV has repeatedly evolved resistance to AZT (azidothymidine) within individuals! AZT is a nucleotide analog which gets incorporated by reverse transcriptase, but stops transcription because AZT prevents the addition of another nucleotide.

III Darwinian medicine: Scientific American on Darwinian Medicine

A. Is fever adaptive? Possible hypotheses for fever:

1. Reducing fever helps stop viral infection if viral toxins raise body temperature to favor more rapid reproduction

2. High temperatures may interfere with viral growth or enhance immune response

B. Evidence

1. Taking fever reducing medicine did not help individuals that were infected with rhinovirus (cold virus)

2. Immune response of placebo group was stronger, suggesting anti-fever drugs interfere with immune response

IV. Bacterial diversity

A. Eubacteria - most have cell walls, but lack nuclei and organelles

1. Gram positive - thick layer of murein (peptidoglycan) outside plasma membrane

a. Actinomycetes - grow like fungi
b. Clostrids - Clostridium botulinum (causes botulism), another causes tetanus
c. Mycoplasmas - lack cell walls, form fruiting bodies like slime molds, some cause bacterial pneumonia, which often kills people with AIDS

2. Gram negative (have thin murein layer and outer layer of lipopolysaccarhides) - nonphotosythesizing

a. Myxobacteria
b. Rickettsias - typhus, Rocky Mtn spotted fever
c. Desulfovibrio
d. Spirochetes - syphilus, Lyme disease

3. Gram negative - photosynthesizing

a. purple nonsulfur, e.g. Escherichia coli, our symbiotic gut bacteria
b. rhodopseudomonas
c. Purple sulfur
d. cyanobacteria (blue-green algae): can fix C and N
e. Prochlorophytes
f. green sulfur (use H2S as electron donors)

4. cause many diseases: bubonic plague, cholera, diphtheria, syphilis, gonorrhea, leprosy, scarlet fever, tetanus, TB, whooping cough, meningitus, strep throat, staph infections

5. beneficial bacteria

a. nitrogen fixation
b. cellulose digestion - cattle and termites
c. blood digestion - leech and vampire bats
d. food preparation: yoghurt, cheese
e. antibiotics - tetracyclin, neomycin, aureomycin
f. DNA amplification - DNA polymerase from Thermus aquaticus

B. Archaebacteria - live in extreme environments. Evolved more recently than Eubacteria and share common ancestor with all eucaryotes.

1. Halophiles - high salt environments (> 25% NaCl), photosynthetic
2. Methanogenic - bogs and marshes, hydrothermal vents, source of all methane, including mammalian flatulence, use H2 gas to reduce CO2 and produce methane. 1.3 trillion cows produce 1 billion tons of methane/year!
3. Sulfur reducing - volcanos and hydrothermal vents
4. Thermoacidophilic - volcanos, hydrothermal vents, geysers

V Physiology

A. Reproduction

1. Cell division by fision, can reproduce every 20 min
2. Sporulation

B. Genetic exchange - not tied to reproduction

1. Conjugation - exchange DNA with a partner

a. occurs between different mating types
b. involves exchanging plasmids - circular DNA with a few functional genes
c. other genetic elements (e.g. viruses) can also move during conjugation

2. Transformation - pick up fragments of DNA from dead cells (necrophilic sex!)
3. Transduction - DNA fragments are carried by viruses between bacterial cells

C. Energy metabolism

1. anaerobic - can survive without oxygen, e.g. clostrids causing botulism
2. facultatively anaerobic
3. Autotrophic (generate energy )

a. photoautotrophs - fix CO2 to build organic (C) molecules
b. chemoautotrophs

i. nitrogen fixing - convert atmospheric N2 to nitrates or ammonia to nitrites and release them into the soil where they can be used by plants. Extremely important, some live in root nodules of legumes.

ii. some forms use hydrogen sulfide instead of water to make organic molecules, e.g. CO2 + 2H2S -> (CH2O)n + 2S

4. Heterotrophic (consume other organisms and act as decomposers)

a. photoheterotrophs - get energy from light, but carbon from other animals, e.g. purple nonsulfur bacteria
b. chemoheterotrophs - most bacteria

VI. Evolved human responses to minimizing bacterial toxins?

A. Spices in cooking

1. spicy foods occur in tropical regions where bacterial spoiling occurs rapidly

2. spicy foods inhibit growth of bacteria

B. Pregnancy sickness

1. first trimester fetuses are vulnerable to bacterial toxins associated with some plants
2. women often avoid eating foods with toxins to prevent pregnancy sickness