T4 - Genome: ds linear DNA

Capsid made up of proteins

Collar

Tail Sheeth

Tail fibers

Endplate

Others - envelopes made of lipids capture from host membrane, contain viral spike glycoproteins

lamba - Genome: ds linear DNA with cohesive end to circularize once in host

capsid

non-contractile tail

T4 - Lipopolysaccharides

Lamda - Outer membrane proteins PORIN

others - techoic acids, flagella, and pili

tail fibers interact with host receptors

Lysosome  break down cell wall or form the pores in the membrane to pass genome through

M13  injects linear ssDNA that circularizes in host

ssDNA serves as template for dsDNA in host

dsDNA makes more ssDNA that will leave to infect other cells w/o host death or new phages

Diluted phage with an MOI of .1 is mixed with e.coli and agar, serial dilutions, pour into petri dish with agar, incubate @ 37C, plaques form with infected cells lysing

cells infected = # of phages

                      phages/ml

Lytic Cycle

   _

\_/   

 y=# of phages

Concentration drops due to increased infection

-eclipse period host cells making new phages

rise period - lysing occurs increasing extra cellular concentration

 -flattens out as lysing completes

lytic cycle intemperate

contractile tail

170 genes

binds to lipopolysaccharide on host membrane

2 min: early mRNA synthesis via viral sigma factor and host RNA polymerase, hijacking of host replication enzymes arrest of host gene expression,host dna degrade for nucleotides to build phage dna

-linear genome is circulary permuted, replicated into concatmers= linear dsDNA 6-10 genomes ligated by homologous recombination(attached at overlaps yzabc+abcdef=yzabcdef) with 3% terminal redundancy = 103% original genome (DabcD) via cleavage and removal

3 min: phage dna replicated

5 min: late rna made using viral sigma factor, code for capsid, tail, baseplate, Lysosoes that degrade cell wall, Holin to put holes in mebrane

12 min: head and tails made

 13 min: heads filled

15 min: virions formed

22 mins: lysis

Restriction endonucleases- destroy injected viral dna

T4 counteracts by CH2OH like methylation of dna

lysogenic or temperate-> prophage -> only one lysogenic virus per cell

48.5 kb w/ 50 genes

inject DNA into cell, DNA circularizes

IF MOI is high than CI>Cro lysgogeny = too many phages

 If MOI is low than CI<Cro Lytic = not enough phages

High MOI:

-high CII that can't be broken down fast enough by FtsH which binds to Pre -> production of CI and CIII, CIII is made degrading Ftsh increasing amount of CII

-CI(lamda repessor) binds to operators 1 and 2 on OL and OR @PR/L and represses transcription of all other phage genes blocks cro attachment but leads to exprespression of Prm,

-Prm maintain lysogeny

attP site on viral DNA recombines with attB site on host DNA mediated by viral integrase between glacatose and biotin operons

DNA damage -> SOS response-> CI cleaves itself->increased Cro->xis operon encodes excisionase, exicis and integ excise viral dna

Low MOI:

 CII hydrolized by FtsH causes no CI production, no Prm production (lysogeny)

-Cro outcompetes CI for OR/L and PR/L

PR/L code for lytic cycle

 CIII-OL(123PL)-CI-OR(123PR & PRM)-Cro-Pre-CII

Lysogenic Cycle when virus dna is excises imprecisly, new virus dna has some host dna attached and not compelte virus dna, infects new host via lysogenic cycle, new host has both viral and host 1 dna

rolling circle

 Triggered by gene O

start at ori site

continuous replication to many copies

concatenated -2 combined to 1

cutting at cos site

- Symbiosis: living together
- Commensalism: one benefits, the other is not
affected
- Mutualism: both organisms benefit
- Parasitism: one benefits, the other is harmed

 - ectoparasties: Organsims that live on host surface

- endoparasites: Organism that live on the inside of host

- Infection: pathenogenisis, a pathogen grows and multiplies within or on another organism

Step 1: Attach and Invade host tissues

Step 2: Suppress host defenses

Step 3: Acquire nutrients from host

Step 4: Propagate

Step 5: Transmit to a new host

2 types of pathogens

Spread of pathogens

Primary pathogens: Have ability to penetrate host defense and cause disease in healthy hosts

Opportunistic: Cause disease in compromised hosts, have latent state that cannot be found in culture

Spread of:

- direct: host to host

-vectors: host to carrier to new host carrier usually insect

-fomites: host to inanimate object to new host

-resivoir: organism that carriers the pathogen but doesn't suffer

Virulence: quantitative measure of the pathogenicity - the relative ability of a pathogen to cause damage on a host

LD = # of organisms to kill host

Virulence factors: Individual characteristics of a pathogen that allow it to invade hosts and cause disease

Hypersensitivty - an exaggerated host immune response that damages tissue

Pathogenicty Islands: Large Segments of DNA that carry multiple virulence genes,
lower G+C content, tRNA facilitates integration,

 Horizontally Transfered,

Flanked by bacteriophage or transposon-related sequences

A mobile DNA element in plasmid or chromosome

captures and collects gene cassettes confering antibiotic resistance

Responsible for super bug

Contains integrase and att sites similiar to those in bacteriophages

Exotoxins: proteins released in the surroundings of the pathogen via protein secretion systems

Endotoxins: Structural components of GRAM NEGATIVE bacteria that are not secreted, Lipid A of LPS,  activates inflammatory response, causes toxic shock=overactivated immune system

1) Membrane Leakage by forming pores,

-Hemolytic alpha toxin pores in red blood cells

2)Cleaves 28s RNA inhibitng host protein synthesis, targets ribosomes, stops translation

3)Activate secondary messange pathways  which affects cGMP production -> cAMP causing no Na uptake and release of Cl- and H2O

4) Overactivate host immune system causing toxic shock

5) Proteases cleave host proteins ex: tetanus toxin cleaves components in nerve transmission

B consist of 5 subunits that form a pore which allows entry to subunit A which is toxin

Cholera toxin: Vibrio cholerae

Shinga Toxin

Labile Toxin: Escherichia Coli

Athrax Toxin

Toxin A1 subunit A2 subunit B subunit

Goal: Ribosylates the host G protein to over-activate cAMP production leads to CL, K, and H2O out of the cell

1) Binds to GM1 Receptor

2) Toxin is endocytosed

3) Phagosome is taken to ER

4) A1 removed and exported through ER to Cytoplasm

5) A1 attaches host ADP to host G protein that regulates adenylate cyclase NAD->NAm

6)ATP->cAMP

7)CAMP increases = ion transport increase

– Protective antigen (PA): seven PA subunits form a pore in the cell membrane to deliver the toxic factors

– Edema factor (EF): an adenylate cyclase  binds to calmodium, raises cAMP levels

Causes fluid secretion, tissue swelling

– Lethal factor (LF): a protease cleaves protein kinases – blocks signaling transduction no 2nd msngr cascades, Blocks immune system from fighting the infection

1) PA is made as a single peptide

2) Binds to surface, Human protease cleaves it

3)  Sevev PA autoassemble to form pore

4) EF or LF binds to rings and brought into cell by endocytosis

5)EF or LF are expelled through PA pore

Type III and IV: virulence-associated secretion systems
 Encode pili connecting pathogens and hosts
Interkingdom transfer

Redirect host signaling for benefit

Gram Positive

Design: Beta barrel channel in outer membrane, ToIC outer membrane channel & alpha helix tunnel in periplasm, HlyD periplasmic protein for membrane fusion, HlyB inner membrane, ATP inds to ABC site on HlyB via ATP hydrolysis in cytosol

1-step, secretes unfolded proteins

Secretes hemolysin alpha toxin

Gram Negative, ecoli & salmonella

Injects type 3 effectors directly into host cell

Salmonella: 13 toxins, actin causes endocytosis of bacterophage

causes expression of alternate sigma factor of host cell which is tricked into reading a salm. regulon thats coded like host's

effector proteins ->cdc42->JNK->gene expression->cytokines, Cl-, and H2O leave cell

Secretes DNA and Proteins

can extend and retract for mobility

used for conjugation, DNA uptake and release, effector translocators

releases pertussis toxin

Group Translocation

Siderophores, hormones, ice nucleation

 how ecoli uptakes iron

1) E.coli synthesizes and secretes an iron-binding siderophore called enterochilin that binds to Fe3+

2) FepA MSP on outer membrane transports compound into periplasm

3)FepB binds to compound acts as ABC transport to MSP FepG|D (2 parts left and right of MSP)

4) ATP binds to FepC on both FepG|D, ATP->ADP+P, ABC transport occur, compound brought into cytoplasm

5) Fe3+ seperated from enterochilin, Fe3+ -> Fe2+ to keep gradient

Broad- effective against many species

narrow- effective against few or a single species

Cidal - Kills cells - batericides and fungicides

static- ihibits growth of cells without killing them - reversible

MIC - minimum inhibitory concentration - lowest dose of an antiobiotic that prevents growth

MLC - Minimun lethal concentration - lowest dose that kills pathogen

Culture in diff concentrations lowest no growth is MIC, innoculate no growths, bacteria will start to grow, lowest no growth is MLC

Small Clear zone = HIGH MIC = resistant bact

Large Clear Zone = LOW MIC = sensitive bact

antibiotics are secondary metabolites

-prevent growth of competitors

polyketide antibiotics are synthesized in modular fashion via many enzymes

-make enzymes to disable antibiotic within cell

Penicilin

Beta-lactam  binds to penicillin-binding proteins in bact. membrane, inhibits peptidoglycan cross linking by catalyzing polymerization of peptidoglycan, cell lysis

Resistance by bacteria that secret beta-lactamase which hydrolyse beta-lactam

Ampicillin - can penetrate outer membrane on gram negative, given with clavulanic acid=beta lactamse inhibitor

Methicillin - MRSA strains, resistant to beta-lactamase

Quinolones: cidal, inhibits DNA gyrase and topoimerase thereby prvent relief of supercoiling and DNA seperation ie replication

Rifampin: cidal, Bind to RNA polymerase and blocks transcription, liver damage and orange body fluids

30s inhibitors:

Streptomycin: cidal, binds to 16S rRNA changing the shape of 30S inducing misreads

Tetracycline: static, broad spectrum, binds to A site and blocks incoming tRNA, effective aganst all, stains teeth

50s inhibitors:

Erythromycin: static, binds to 50S and prevents ribosomal movement along the mRNA

Chloraphenicol: static, inhibits peptidyl transferase activity prevent formation of peptide bonds in 50s

Gramicidin: cidal, forms ion channel in cell membrane, cell cannot maintain pmf

Platensimycin: cidal, blocks fatty acid synthesis in gram positive bact, no membrane

Efflux: exports drugs faster than it comes in, works for several antibiotics

Degrdation: Beta-lactamase

Modification: alter antibiotic so it cant function

Alternatio of target receptor: MRSA

Antibiotics act on fungal-specific cell structures

Sterols (cell membrane): imidazole-containing antifungal agents inhibit sterol synthesis – disrupt fungal membrane

Chitin (cell wall): chitinase

Efficient detoxification system in fungi to inactivate many drugs means Repeated applications of antifungal agents

– Protease inhibitors: against virus-specific enzymes

Reverse transcriptase: only in RNA virus

RNA-directed RNA polymerase (RDRP)

HIV protease – cocktail therapy

– Interferons: Natural proteins produced by host
immune system

Usually respond to the presence of double stranded RNA – anti-viral proteins

–  Inhibiting DNA synthesis affects virus more than host
– Acyclovir: blocks DNA synthesis
– Ribavirin: Lowers fidelity of viral RNA polymerase, Mutation rate is so high that virus cannot make functional progeny

Inhibitors of viral life cycle
– Amantadine inhibits viral uncoating, Prevents entry of virus into host cell

– Zanamivir blocks release of mature viral particles

used by early cell with onyl RNA

• Splices introns
• Regulates gene expression
• Synthesizes proteins
– RNA performs major functions in ribosomes
• Self-replication
• Help with protein folding – chaperone

– Secondary structure of RNA is important for its enzymatic activity

Molecular clock: temporal information contained in a sequence
A molecule whose sequence can be used as a measure of evolutionary distance

Criteria for chronometer
– Universal molecule found in all organisms
– Has conserved functions in all organisms
– Must be able to align molecules to determine genetic relatedness
– Constant substitution rate – sequence divergence proportional to time (slow evolving)
– Strictly vertical transferred
– 16s and 18s rRNA, cytochrome C, ATP synthase

Chloroplast: cyanobacteria
Mitochondria: rickettsia (proteobacteria)

-double membrane

-endosymbiotic => reductive evolution

-circular chromosome

-prokaryotic ribosomes 70s

Characterizes isolates of the same bacterial species

Based on DNA sequences of multiple (usually seven) housekeeping genes. – subspecies classification

Cyanobacteria – Fungi Interactions = Lichens

Pioneer biota – primary colonizer for soilless
surfaces

- Fungus provides shelter, water and minerals

Cyanobacteria generate organic carbon and fix atmospheric nitrogen

rhizosphere- zone around plant roots

-majority of microorganisms

-root exudation provides nutirents

Rhizobia – Legume Interactions =Nodulation

very species specfic, signal exchange initiates nodulation, Rhizobia enter root cortical cells through infection threads, become bacteroids within vacuole-like symbiosome

bacteriods=irregular shapes with no cell wall

- Plants provide carbon source and shelter
-Rhizobia fix atmospheric nitrogen to ammonia and provide it to the plants
- A major source of available nitrogen

Ectomycorrhizae - colonize surface of rootlets, Extended hyphae increase root surface area

 Endomycorrhizae - enter plant cell, captures and draws in nutrients

-Plants provide sugars

-Mycorrhizae provide P, Zn and Cu; and increase surface area or root system

- Greatly enhance water and nutrients uptake, Some plants are mycorrhizae obligate