November 21 Notes

Why do bacteria "want" to take up DNA from the environment??
*In environmentally stressful situations (ex. CHANGE in environment), bacteria are more likely to take up DNA
*genetic exchange (esp. transformation) is more likely in more genetically variable populations

II. Conjucation-DNA donor and reciient are both alive, and fairly closely related
*Gram-negative bacteria
**PILIN= protein that makes pilus
i) F+ bacteria have pilin
ii) bacteria without pilin plasmid=F- (recipient)
iii)F+ bacteria uses pilus to attatch to and pull close to F- bacteria. F+ then copies plasmid and sends copy to F- through merged cell envelopes
iv) now both donor and recipient are F+!!
*Gram-positive bacteria
i) at high population densities, pheromone is secreted. Pheromone attracts bacteria to eachother causing clumping of the bacteria

*Virion=a single virus particle
*capsid= protein coat surrounding a virus

Danya Hangman

I. Classification of viruses – based on host cell:
- Ex. Bacteriophages  infect bacteria; enterovirus  infect digestive tract cells
- Even within a particular host organism, particular viruses only infect certain host cell types
o Ex. HIV only infects tiny subset of human immune system cells (CD4+ T-cells)
a. Viruses have narrow host ranges
i. Implications for disease eradications
1. What traits must a disease have for it to be potentially eradicable
a. Be completely dependent on a human host for reproduction
b. Must have way of preventing new infections (ie vaccine)
c. Must have a way of knowing who has disease
II. Virus structure
a. Nucleic acid (NOTE: some viruses have RNA genomes, not DNA ones)
i. Virus genomes come in a variety of sizes but most genomes are smaller than bacterial
1. Ex. Picornaviruses polio (RNA) – 3000 bps with 3 genes
2. Poxviruses  smallpox, cowpox (RNA)– 300,000 bps, 300 genes
3. Because of programmed ribosomal frameshifting, may have more genes than usually assumed in viral genomes
ii. Viroid: self-replicating double stranded DNA circle; loop of self-replicating DNA
1. Ex: hepatitis D
b. Protein coat
i. Capsid: protein coat surrounding a virus
ii. Capsomeres: repeating protein subunits that make up capsid
1. Interactions between capsomeres determine shape of virus
iii. Virus shapes: viruses come in a limited range of shapes. Why?
1. Polyhedral: like a soccer ball: lots of faces of 3-D object all faces identical shape
2. Helical:tube shape from capsomerers wrapping around each other like a telephone cord
3. Complex: polyhedron attached to helices
a. Only infect bacteria
c. Enveloped viruses also have a membrane, derived from host cell membrane (Note: enveloped viruses only infect eukaryotic cells)
Examples: HIV, Flu, Herpes family herpes simplex I, chickenpox, STD herpes
d. Glycoproteins: attach membrane to capsid of enveloped viruses
i. Allow virus to attach to a host cell
ii. Part of envelope virus we have immune response against
e. Virion: singular virus particle

III. Viral Replication
a. Attachment/ adsorption
i. Virus bumps randomly into potential host cell in ~1:104 bumps, virion will transiently stick to surface of host cell
ii. IF viral surface proteins are the right shape to interact with the cell surface receptors, a tighter junction between virus and host cell forms
iii. If tight junction forms, cell engulfs virion
iv. If envelop virus, its membrane fuses with new host membrane
v. If not enveloped virus, virion just engulfed by host cell, brought into cell’s lysosome
vi. In case of complex shape bacteriophage, virus attaches to receptors on bacterial surface, injects DNA into bacteria
b. Penetration/ decoating
i. Lysosome of cell contains digestive enzymes at low pH, so lysosome breaks down capsid proteins – frees viral nucleic acid to be copied by host cell


Why are viruses specific to particular host cells?
- Only some kinds of cells have correct surface proteins for viral proteins to attach to
b. Penetration/ decoating
i. Lysosome of cell contains digestive enzymes at low pH, so lysosome breaks down capsid proteins – frees viral nucleic acid to be copied by host cell
c. Viral nucleic acids copied by host cell enzymes, etc.
i. DNA viruses: have DNA genomes
1. Ex. Smallpox, human papilloma virus
2. Host cell’s DNA polymerase copies viral DNA
ii. RNA viruses: have RNA genomes
1. Ex. Flu,
2. No living thing has enzyme that copies RNA  RNA
3. Have RNA replicase: specific enzyme that copies RNA RNA
a. First step in copying RNA: translation of RNA replicase gene by host cell’s ribosomes, and RNA
iii. Retroviruses: have RNA genomes
1. RNA  DNA copy via reverse transcriptase: enzyme specific to retroviruses
2. DNA copy becomes part of host cell DNA
3. DNA  RNA via RNA polymerase
d. Synthesis of viral proteins
i. Virus uses host RNA polymerase, ribosomes, tRNA, and amino acids to make its capsomeres, glycoproteins, other viral- specific proteins
ii. Ex: HIV host cell = CD4+T-cells, a kind of immune cell
iii. Ex: polio host cell = intestinal epithelia; motor neurons
e. Assembly of new virions
i. Once you have all the bits, new virions spontaneously self-assemble
ii. Wimmer (2003) synthesized polio genomes  took RNA polio genome  put in host cell, got new virions (Can viruses be eradicated?)
f. Release of new virions from host cell
i. Lysis of host cell: host cell blows up, releases new virions into environment (uncommon)
ii. Budding from host cell: enveloped viruses use glycoproteins to wrap selves in host cell membrane, tear free (Does not kill host cell)

a permann

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