microbio 2

Genetics 447 with Keating at Rutgers University - New Brunswick/Piscataway

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By: Angela Lin
Created: 2011-04-09
Size: 111 flashcards
Views: 45

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Woese and Fox

who looked at rRNA seq and suggested a new group archae

ribosomes

-mostly comprised of RNA

-not prone to rapid evolution, ribosomal seq conserved

methanogens

-O2 kills them

-unusual enzymes

-cell walls diff from other org

-rRNA seq were diff from bacteria and euk

3 phyla of archae and 1 proposed

1. euryarchaea

2. crenarchaeota

3. nanoarcheaota

4. korarchaeota

what kind of microbes are part of euryarchaea

methanogens, extreme halophiles

what kind microbes are part of crenarcheaota

thermophylea, hyperthermophylea

what kind microbes are part of nanoarcheaota

nanoarchaeum

-only genus with this phylum

what mircobe lives in assoc with ignococcus (hyperthermpphilic crenarchaeote), why?

nanoarchaeum

lacks genes for most enzymes so needs it for nutrients

what microbe has the smallest genome, how small?

nanoarcheaum, 4.9 x 10^5

characteristics of archae domain

1. stain both gram +/-

2. variety of shapes

3. 0.1 - 15 um diameter

4. binary fission, sometimes budding

5. physiology is diverse

6. (they are extremophiles)

extremophiles consists of: (6)

1. halophiles

2. psycrophiles (tolerate cold 0-20, 34% of prok biomass in caostal antartic surface water)

3. thermophiles (50-80)

4. hyperthermophiles (greater than 80)

5. barophiles (greater than 1 atm)

6. methanogens: produce methane gas and strict anaerobes

cell wall of archae

-no NAM (N-acetylnuramic acid)

-no D-amino acid

-resist attack by lysozymes and antibiotics because of above

gram pos archaea

single thick layer of thick wall

-pseudopeptidoglycan-pseudomurein

pseudomurein

-polymer of NAT instead of NAM

-B-1,3 glycosidic link b/w NAT and NAG

gram neg archaea

no outer mem

no peptidoglycan layer

protein or glycoprotein

20-40 nm thickness

S layer (hexagonal symmetry)

archaeal lipids

lack fatty acids

branched chain hydrocarbons

repeating isoprene

no hapanoids no sterols

isoprene chain in archaeal lipid

-hydrophobic

-internal in mem

-glycerol diether: 2 phytanyl (4 linked isoprenes) attached by ether linkages form bilayer because they 2 chains dont bond

-biphytanyl: phytanyl side chains from each glycerol are covalently bonded together producing diglycerol tetraether, monolayer (no gap)

genetic material of archaea

-single chromo

-circular DNA

-small genome

-few plasmids

-genome assoc with histones

What causes DNA stability in thermophiles

1. potassium cyclic 2,3-diphysphglyvocreate

2. reverse DNA gyrase

3. heat stable DNA binding proteins (Sac7d)

potassium cyclic 2,3-diphysphglyvocreate

salt

large amounts in cyto

prevents chemical damages

Reverse dna gyrase

unique for topoisomerase

-hyperthermophiles

-pos supercoils stabilize DNA

(normal DNA gtyrase in thermophiles introduces neg supercoils)

heat stable proteins

increase mp in DNA stability in thermophiles

-binds to minor groove of DNA

What causes lipid stability for hyperthermophiles

lipid monolayer: resists tendency of heat to pull it apar unlike non hyperthermophiles lipid bilayer

-diglycerol tetraether

thermoplasma

archaea

no cell wall

55 degrees

pH~2

cell mem comprised of lipoglycan (glycerol tetraether monolayer and mannose and glucose-->stablizes mem

upper temp limit of thermophiles

depends on stability of monomers

ex: ATP and NAD+ hydrolyze fast in vitro at 120 degrees, half life is less than 30 min, at 120 ATP is degraded instantly, 120 degrees is the upper limit to life above that momomers cannot survive

phylum euryarchaeota are what kind of philes

halophiles

inhabit higlhly saline env

natural salt lakes, solarsalt evaporation ponds, artificial saline habitats (surface on fish and meats)

very high salt requirement

maintaining osmotic balance in hypertonic env

halobacterium

-needs large amounts for sodium for growth because it stabilizes cell wal

-cell walll: glycoprotein, high content of aspartate and glutamate (acidic AA, neg charge, repel-->lysis)

-cell wall stabilized by Na by binding to outer surface of wall to maintain integrity, if not cell wall will break away and lysis

-high conc of na outside the cell creates plasmolysis, potassium is then pumped into cell until its higher then Na conc. this maintains positive h2o balance, K+ compatible solute

methanogens

strict anaerobes

found in rumen, intestinal tract, fresh water, and marine sediemnts

obtain E by methanogensis: converting, CO2, HCOO(formate), and CH3OH (methanol) forming methane (CH4) ormethane and CO2

methanogenesis practical importance: fuel, and E source

methanogenesis eco problem: methane can absorb infrared radiation-->green house gas

eukaryotes first appeared when

1.9-2.1 bya

what is the diff b/w euk cells to prok cells

mem bound nucleus

mem bound organelles

what kingdoms are in euk

1. fungi

2. protista

3. animal

4. plants

kingdom fungi

chemoheterotrophs

-saprophytes: digest dead organic matter and organic wastes

-parasites: nutrients from living org

kingdom protista

-great diversity

-some unicellular

-some colonial (loose assoc of cells, no differentiation, no specialization)

-nuclei & mem bound organelles

-groupings

groupings of protista

1. plant like protests (algae): chloroplasts, photosynthesis

2. fungus-like protests: water colds, slime molds

3. animal-like protests: protozoa

cell wall diff between 3 domains

B: peptidoglycan

A: lack peptidoglycan but may have many pseudopeptidoglycan

E: if present, cellulose or chitin, lack peptidoglycan

mem lipids diff between 3 domains

B: fatty acids bounded by ester links to glycerol, linear FA

A: no FA, phytanyl or biphytanyl instead, branched, bonded by ether links to glycerol

E: FA bonded by ester link to glycerol

RNA polymerase diff between 3 domains (transcription DNA-->RNA)

B: single type, 5 polypeptides (alpha, beta, betaprime, sigma, omega)

A: more complex, less than or equal to 8 polypeptides, more similar to the polymerase found in E

E: 3 RMA polymerase, major 10-12 polypeptides

protein synthesis diff between 3 domains

ribosomes similar in size b/w B and A

protein synth similar b/w A and E

B: rib size 70S, start codon AUG, tRNA with formylmethianine 9modified)

A: rib size 70S, start codon AUG, tRNA methianine (unmodified)

E: rib size 80S, start codon AUG, tRNA methianine unmodified

anaerobic prototzoa

1. diplomonads

2. parabasalids

diplomonads (anaerobic protozoa)

2 nuclei (equal size)

lack mit

lack hydrogenosomes

has mitosomes: derived from mit, double mem, mit-like proteins, func unclear

example of diplomonads

Giardia intestinalis

trophozoite stage: anterior rounded, posterior tapered point, 2 adhesive discs (attach to ep cells) , 2 nuclei, 4 pairs of flagella, 2 median bodies (support)

parasite: live sin SI duoderm and bile duct

binary longitudinal fission

adhesive discs attach the ep cells and could damage villi (lesions)

what is the pathology of diplomonads?

diarrhea, malabsorbtion of nutrients, inability to absorb fat soluble substances such as vitb12 and folate --> steatorrhea (fat in feces)

"back packers disease"

life cycle of giardia intestinalis

trophozoite passes thru SI and encysts in LI, cysts out of host, ingested by next host, cysts pass thru stomach and encysts in SI

parabasalids

parabasal body structural support for golgi body

lack mit

have hydrogenosome (degenerate mit, size of mit, no cristae: foldings of inner mem, oxidize pyruvate from glycolysis fermentation, end product is H2)

example of parabasalids

trichomonas vaginalis

reproductive tract in trich. vag.

female in vag and urethra

male in urethra, prostate, and seminal

what is the pathology of trich vag

male: asymtomatic

female: trich vaginitis

trich vaginitis

it feeds on lactic producing bacteria so raises the pH from 4-4.5 to 5-6

troph

inflammation of vaginal epithelium

tenderness, pain, itchym leucorrhea (increase production of mucus)

whats the tramission method trich, vag

no cysts

direct contact: sexual

Aerobic protozoa

1. Kinetoplastids

2. Amoebas

kinetoplastids

has kinetoplast (mass of DNA in mit)

habitat in aquatic feed on bacteria, some parasites

example of kinetoplast

trypanosoma brucei

tryp. brucei

african sleeping sickness

blood: invade CNS

causes inflammation of brain and spinal cord

amoeba

pseudopodia (extension of cells): motility and food acquisition

2 types of amoebas: testate (shell), naked

example of amoeba

eutamoeba histolytica

naked amoeba

human intestinal tract

amoebic dysentery

ulceration of intestinal tract (bloody diarrhea)

example of a testate amoeba

foraminifera

test made up of calcium carbonate

pores in test

forameus (little holes)

strands of cytoplam extend out of pores

locomotion

feeding

marine: uplift ex. White cliffs of dover, England

fungus-like protists

cellular slime molds

acellular slime molds

cellular slime molds

unicellular amoeboid cells

habitat in leaf litter of temperate forests

forage for prey primarily bacteria

resource depletion chemotactic signaling

causes cells to come together-->form slug

multicellular aggregate

slug moves around and produces spores-->disperse-->germinate-->new cell

acellular slime mold

plasmodium: multinucleate cytoplasm (1000s of diploid nuclei)

leaf litter of temperate forests

under resource depletion, stalked sporangia are produced

meiosis-->haploid spores-->disperse-->germinate-->grow and multiply-->haploid cells fuse-->diploid cell-->plasmodium

algae

red algae

diatoms

red algae

rhodophytes

marine

phototrophic chlorophyll a, phycobiliproteins, accessory pigments, pycoerytherin (red)

cell wall of red algae

cellulose fibers embedded in polymer matrix (glucose and galactose derivatives)

commercial uses: agar, carageenan (thickness in ice cream and dairy stuff))

diatoms

marine and aquatic

photosynthetic

frustule: cell wall (silica)

1000s of perferations

specialized pores secrete mucus so it can glide thru

frustule comprised of 2 overlapping vaves like pteri dish

growth and reproduction of diatoms

1. frustule rigid get to 2x thickness-->cell division

2. asexual: 2 valves are going to seperate

each valve become the larger half for the new cell

once ~1.3 max size cant divide-->die

3. sexual: environmental cues, N limitation, increase temp, increase lgiht,-->meiosis, all diatoms in pop produce gametes

fertilization-->zygote-->dev into spore-->grows and new shell

fungi

yeasts, unicellular org

example of yeast fungi

saccaromyces cerevisiae

cell division by budding, new cells form as outgrowths of parent cell, bud grows and spereates fmor parent

characteristics of viruses

small

not cells

genetic material DNA or RNA

invade susceptible host cells-display living properties

obligate intracellular parasites

do not grow and divide (replicate only inside living host cells, requires host cell machinery)

host cell dies-->tissue damage

components of viruses

capsid

envelope

virus Nucleic acids

DNA or RNA

info for replication

single strand or double

linear, circular, or segmented(several fragments of DNA/RNA)

capsid virus

protein coat, surrounds NA

gives it its shape

rolein attachment

capsomer: protein subunit that make sup capsid

envelope (outer mem) of virus

acquired from host mem

lipid bilayer mem outside the capsid

composition: det by substances that are present in host cell mem and viral NA

spikes (not all virus): glycoproteins, func is to attach to specific receptors that are on host cell

hemagglutination

spike bind virus to host RBA, RBA clump together (hemagglutinate) useful in ID

HA influenza hemagglutinanine

found on surface of influenza viruses

play a role in immune response

16 diff types: H1-H16

H1,H2,H3 in human influenza viruses

advantages to envelope

1. "hide" virus from host immune response

2. help virus infect new cells by fusion of the env with host cell mem

viral envelope can be easily damaged by:

increased temp

freezing and thawing

pH below 6 or above 8

lipid solvents and chemical disinfectants (chlorine, H2O2, phenol, sometimes either sensitive: good for ID)

nucleocapsid

genome + capsid

naked virus

only nucleo capsid, no env

enveloped virus

nucleocapsid and environment

virian

extracellular phase (not in host cell)

host range and specificity

-host range: spectrum of host a virus can infect

-some virus can infect bacteria, algae, fungi, protozoa, plant, inverts, verts

-most viruses are only limited to 1 hosr and in specific cells or tissues that it can infect

theories on the origins or viruses (3)

1. viruses and cellular organisms evolved together

2. reverse evolution (viruses were once cells and then they lost cell func, remained only the info for replication

3. evolved form cells they infect (plasmid: DNA mol found in bacterial cells, independently replicating, separate from main host chromosome, occur in DNA and RNA form)

T4 bacteriophage

double stranded DNA in head

tail surrounded by contractile sheath

base plate and tail fibers involved in binding phage to bacterial cell

lytic cycle (viral replication): 5 stages

1. attachment

2. penetration

3. synthesis of NA and proteins

4. assembly and packaging

5. release (lysis) of mature virian form host cell

attachment stage of lytic cycle

1. virian not motile (chance encounter to host cell)

2. attach to cell wall

3. tail fibers attach (reversible)

4. baseplate binds (irreversible)

penetration stage of lytic cycle

1. conformational chance in tail sheath: cyclander of 24 rings get wider and shorter

2. hollow tail push thru cell wall

3. DNA extruded from head thru tail into host cell infecting the cell

Synthesis of phage, NA, and proteins stage of the lytic cycle

1. T4 genome: early, middle, late proteins

2. T4 produce proteins that modifies the host RNA polymerase so that it recognizes different phage promotors to synthesize mRNA

3. early promotors can be read directly by host polymerase

early and middle proteins of T4 genome

enzymes involved in DNA replication and transcription

Late proteins of T4 genome

code for head and tail proteins that are needed for lysis

E. coli RNA polymerase begins synthesizing phage mRNA within 2 min. what do the early genes encode for? (virian gene)

-proteins that shut off host cell by degrading chromosome which stops host gene expression-->provides raw material

-proteins that covalently modify host RNA polymerase alpha subunit by viral enzyme catalyzing transfer of ADP-ribose group from NAD+ to the alpha subunit(aka ADP ribosylation) -->protein inactivation (in T4, it inhibits transcription of host genes promoting viral gene expression)

-proteins needed for phage DNA synthesis (5 min following infection)

what do middle genes encode for? (virian phage)

-another enzyme which catalyzes ADP-ribosylation of 2nd alpha subunit-->turns off some early T4 genes, RNA polymerase specificity changes recognizing middle promotors

-DNA replication

-HMC (hydroxymethylcytosine): the reason why viral DNA avoids attack form host cell

HMC (instead of cytosine)

protect T4 DNA from attack by host endonucleases bacterial defense mechanism(restriction enzymes would otherwise cleave viral DNA)

late mRNA direct synthesis by:

-phage structural proteins

-proteins that aid phage assembly without becoming phage structure

-proteins involved in cell lysis and phage release

when does late transcription begin in virian phage

12 min after infection

when does viral DNA synthesis begin

5 min after infection

when does lysis and release happen in virian phage

25 min after infection

how many structural proteins encode for baseplate

how many structural proteins encode for prohead (procapsid)

assembly in lytic cycle in virian phage

-late mRNA

-structural proteins

-self assembly

What aids in the assembling of prohead/procapsid?

scaffolding proteins

how does head and tail combine?

spontaneously, do not need protein

What kind of protein helps in DNA movement in and out of head?

portal protein

what is the order of self assembly?

1. base plate-->tail tub-->sheath-->prohead

2. tail fibers-->baseplate/tt/sh/ph

3. all of that-->DNA--> fully assembled virian

T4 lysozyme

attacks host cell wall peptidoglycan

holing: produce holes in host cell mem-->stopping respiration

lysogenic cycle (temperate phage)

multiply in vialytic cycle or enter latent state in host cell

prophage

-latent stage

-phage DNA integrate into host chromosome

-replicate along with host chromosome and passed onto daughter cells

-phage DNA repressed, most of genes not transcribed

-not a phage but has potential to produce phage

Lambda DNA (temprate phage)

-ds linear

-40 genes genome clustered according to function (1. head synth, 2. tail synth, 3. lysogeny and regulation, 4. DNA replication 5. cell lysis)

-cos site: 12 nucleotides of if single stranded at 5'

-uses E. coli ligase to real ends where single stranded cohesive ends base pair

lytic cycle of temperate phage

1. phage enters host--> circulation of phage chrmosome

2. transcription using host RNA polymerase ( poly binds to 2 promotors PL and PR and occurs in both directions--> different DNA strands)

3. 1st genes to be transcribed are regulatory proteins that control lytic cycle leftward (gene N) rightward (genes cro and CII)

these proteins control orderly sequence of protein synthesis

protein lambda repressor

-starts lysogenic cycle

-236 aa long

-binds to operate OL and OR (operator site on phage DNA regulates activity of group of genes with common promotor)

-RNA polymerase cant bind to promotors PL and PR anymore shuttin off transcription of all genes except for repressor

-repressor is synthesized continually in lysogen

About this deck

By: Angela Lin
Created: 2011-04-09
Size: 111 flashcards
Views: 45

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