MBS326R exam 3

Proteobacteria

a domain of bacteria that includes medically and scientifically important species such as salmonella; includes gram negative; facultatively or obligately anaerobic, chemolithoautotrophic, and heterotrophic

nonproteobacteria

a group of bacteria that contain photosynthetic bacteria (photosynthesizing); includes gram positive and gram negative; photoautotrophs and chemoheterotrophs

hyperthermophiles (NON PROTEO GRAM NEGATIVE BACTERIA): aquifex pyrophilus

growth optimum 85 c; rod shaped bacteria; grows best in environments with low oxygen levels

hyperthermophiles (NON PROTEO GRAM NEGATIVE BACTERIA): thermotoga

grow at high temps; rod shaped, wrapped with an outer envelope, toga like structure; can grow on methanol and acetate

(NON PROTEO GRAM NEGATIVE BACTERIA): deinococcota

tough (resistant to drying out and radiation); can be spherical or rod shaped; stains as a gram positive (purple in color) but is gram negative due to second membrane

(NON PROTEO GRAM NEGATIVE BACTERIA): photosynthetic bacteria; cyano bacteria

carry out oxygenic photosynthesis; two photosystems; water as an electron donor; generates oxygen; largest and most diverse group of photosynthetic bacteria; light energy converted to chemical energy

(NON PROTEO GRAM NEGATIVE BACTERIA): photosynthetic bacteria; purple, green, and aerobic anoxygenic phototropic bacteria

carries out anoxygenic photosynthesis; one photosystem; alternate electron donor to water (H2 or H2S); live in environments where light is available and oxygen levels are low

(NON PROTEO GRAM NEGATIVE BACTERIA): bacteroidota

includes photolithoautotrophs and chemoheterotrophs; found in gut and oral cavity; up to 30% of human feces

(NON PROTEO GRAM NEGATIVE BACTERIA): fusobacterioa

includes photolithoautotrophs and chemoheterotrophs; found in gut and oral cavity; spindle shape; associated with infections and diseases in humans

(NON PROTEO GRAM NEGATIVE BACTERIA): chlamydiae

coccoid shape (spherical); non motile (can't move); obligate parasites; small genome so can't metabolize carbs or synthesize ATP or NAD

(NON PROTEO GRAM NEGATIVE BACTERIA): spirochaetota

chemoorganotropic bacteria (obtain energy by oxidizing organic compounds); periplasmic flagella; corkscrew like movement over surfaces

(PROTEOBACTERIA): alphaproteobacteria

oligotrophs (low nutrient environments); defined by relationships with nitrogen

example of alphaproteobacteria: rhodobacteria

uses light energy and has rs with nitrogen

(PROTEOBACTERIA): betaproteobacteria

oligotrophic soil bacteria; associated with ammonia oxidation; occupy diverse environments

1st example of betaproteobacteria: thiobacillus

soil, freshwater, and marine habitats; chemolithotrophs (oxidize sulfur compounds)

2nd example of betaproteobacteria: neisseria

non motile, aerobic, cocci; gonorrhea

3rd example of betaproteobacteria: bordetella

aerobic, motile, coccobacilli; chemoorganotrophs; whooping cough

(PROTEOBACTERIA): deltaproteobacteria

anaerobic: sulfur reduction, deep in soil

aerobic: not tied to sulfur; pathogens; related to soil

(PROTEOBACTERIA): gammaproteobacteria

largest bacterial class; based on metabolism and ecological niche; photoliths, enterics, pathogens

1st example of gammaproteobacteria: enterobacteriaceae

facultative anaerobes; chemoorganotrophs; found in soil environments where oxygen is limited

2nd example of gammaproteobacteria: pseudomonadales

motile; aerobic chemoorganotrophs; found anywhere; if you have infection it's most likely this

(PROTEOBACTERIA): epsilonproteobacteria

dealing with stomach/digestive tract

1st example of epsilonproteobacteria: campylobacter

can cause reproductive issues in cattle; can mimic host nerve cells to turn against host

2nd example of epsilonproteobacteria: helicobacter pylori

causes stomach ulcers and gastritis; microaerophile (can't grow under pH 4.5); produces enzymes that burn stomach lining

(FEATURE OF PROTEOBACTERIA): magnetotactic bacteria

means of navigation (Earth's magnetic field); occupy freshwater or marine sediments; highly motile

(GRAM POSITIVE BACTERIA): order actinomycetota

chemoorganotrops; facultative or strict anaerobes (require CO2); make hyphae

1st example of actinomycetota: bifidobacterium

human gut microflora; nonmotile, non sporing, and anaerobic

2nd example of actinomycetota: mycobacteriaceae

packed mycolic acids; hydrophobic and impenetrable to antibiotics bc of thick fat later

3rd example of actinomycetota: streptomycetales

hyphae help produce antibiotics and mineralization; largest bacterial genome

1st example of firmicutes: bacillus

endospore forming rods; produce antibiotics; motile with ton of flagella

2nd example of firmicutes: clostridiales

form heat resistant endospores; responsible for food spoilage; nerve related problems

1st example of cocci: staphylococcus

normal part of skin microflora; cause disease; bunch of circles together; facultative anaerobic, nonmotile

2nd example of cocci: enterococcaceae

normal part of gut microflora; can become opportunistic; round

3rd example of cocci: streptococcaceae

part of gut, respiratory, and mouth microflora; disease causing; grape like structures

baltimore classification system

A system used to classify viruses based upon their type of genome and replication strategy; 7 groups

DNA groups: dsDNA

+/- DNA transcribed to +mRNA, then translated to protein; +/- DNA replicates, then assembles into viral capsid

DNA groups: ssDNA

circular +DNA uses bacterial DNAP to synthesize +/- DNA via rolling circle replication; dsDNA then transcribed and translated to proteins to be assembled into viral structure; RCR turns dsDNA back into +DNA to be stored in capsid

RNA groups: dsRNA

+/- RNA transcribed to +mRNA, to be translated to protein; +mRNA also replicated to create +/- DNA to be assembled into virus; host cells lack the right polymerase so viruses bring in a RNA-dep RNAP which allows for completion of cycle

RNA groups: +RNA

+RNA can be translated right away to create virus; +RNA then replicates to make -RNA, replicating back to +RNA (to produce more copies of +RNA); what is made first is the RNA-dep RNAP to create the -RNA strand

-RNA

cannot serve as mRNA to make proteins since negative so must bring in a RNA-dep RNAP to make +RNA; -RNA is replicated into +RNA; then translated into protein and replicated back to -RNA to assemble into virus

retroviruses: +ssDNA-RT

+ssRNA is reverse transcribed into -DNA; reberse transcriptase converts ssDNA into dsDNA

retroviruses: dsDNA-RT

dsDNA is transcribed to ssRNA, then replicated to dsRNA; RT then converts dsRNA back into dsDNA and is then transcribed to mRNA

reverse transcriptase

lots of roles; is error prone with no proofreading abilities

T4 = virulent/lytic dsDNA phage

generalized transduction; produce virally encoded DNA-dep DNAP; attachment = phage long tail fiber contacts E coli's outer membrane

Lamba bacteriophage = temperate bacteriophage

specialized transduction; after infecting host can be either lytic or lysogenic cycle; linear dsDNA at the start then circularizes after injecting into host cytoplasm

Latent infection = lysogenic cycle

will occur if high levels of cll/clll; won't show symptoms right away

lytic infection

will occur if no high levels of cll/clll; could show symptoms right away

viruses

most are eukaryotic; can be enveloped or not

bacteriophage

infect bacteria

archaea

extremophiles; microbial dark matter (never been grown in lab)

methanogenesis

last step in anaerobic degradation of organic compounds; if no oxygen available churn out methane; consequence is too much methane

methanotrophs

solves problem of too much methane by oxidizing methane and turning to CO2

examples of archaea

thermoacidophiles, methanogens, haloarchaea

archaea structural adaptations

monolayer; ether stability

archaea metabolic adaptations

sulfur and methane

protista features

plasmalemma (cell membrane); vacuoles; cilia/flagella; free living and in freshwater; grow in environments where oxygen is limited

prions

made from spontaneous generation of mutant protein form; cause neurodegenerative disease; cause proteins to misfold

eukaryotic microorganisms

need certain conditions to survive; include protists and fungi

what differs between eukaryotic cells

cell wall.

plant cells have cellulose and fungal cells have chitin

eukaryotic cells common features

larger than bacterial and archaeal cells; diverse to adapt to environments; cell wall composition is diverse

encystment

formation of dormant cysts in harsh conditions

excystment

escape from cyst in good conditions

trophozoites

actively growing and replicating protists

the protists: plant like protists

possess chlorophyll, perform photosynthesis, and contribute to carbon fixation

examples: diatoms, euglenozoa, chloroplastida

the protists: fungi like protists

decompose organic material, reproduce with spore formation and form multicellular structures

examples: myxogastria (acellular slime molds) and dictyostelia (cellular slime molds)

the protists: animal like protists

differ in terms of motility (pseudopods, cilia, flagellum)

examples: amoebozoa (important in terms of ecological relationships)

fungal groups

decompose organic matter

fermentation, antibiotics

fungal groups: zoosporic fungi

produce motile spores; must infect host cells to complete life cycle; polar tube for host invasion

fungal groups: zygomycetous group

alternative mechanisms of spore dispersal; sexual reproduction occurs when environmental conditions are not favorable; free living and parasitic

fungal groups: dikarya group

most diverse fungal group; may be filamentous or unicellular; always without flagella

fungal groups: dikarya: ascomycota

create tiny spores inside sacs called asci; found in freshwater, marine and terrestrial habitats

white nose syndrome: white hyphae will grow around bat muzzles

fungal groups: dikarya: basidiomycota

club fungi; saprophytes decay plant matter

innate immunity

first line of defense; resistance to any foreign microbe; general mechanisms such as skin, mucus

acquired immunity

if innate system cannot find foreign microbe, this comes into play; tailored to specific foreign microbe; has memory (effectiveness increases on repeated exposure)

antigens

any substance recognized by the immune system; enables immune system to rid the host of foreign invadors

barriers in innate resistance: skin

mechanical barrier to microbial invasion

barriers in innate resistance: mucosal membranes

protective covering that resists penetration and traps microbial invaders

complement system

barrier breached through damage (e.g. cut yourself) turn to complement system. triggers inflammation and recruits WBC; lysing microbial cell membranes; opsonization (tagging microbe for destruction)

"knockout blow"

bone marrow - B cells

originate and develop in bone marrow; await introduction to the antigen to which they will make targeted antibody

thymus - T cells

mature T cells enter bloodstream where they await activation by innate immune cells

mast cells

specialized tissue cells that trigger local inflammatory reactions and are responsible for many allergic symptoms

dendritic cells

in the tissues; responsible for processing foreign matter and presenting it to lymphocytes

natural killer cells and innate lymphocytes

do not express antigen specific receptors; innate response, no memory

endocytosis/phagocytosis

process by which phagocytic cells recognize and kill cellular microbes

recognition of microbe by phagocyte: opsonin dependent

protein coated

recognition of microbe by phagocyte: opsonin independent

microbe associated molecular patterns

inflammation

defense reaction to tissue energy

acute inflammation is immediate response of body to injury

cardinal signs of inflammation

redness, warmth, pain, swelling

granuloma

when phagocytic cells can't destroy pathogen and mass of cells formed in attempt (basically if infection isn't dealt with)

characteristics of adaptive immunity

1. discrimination: between non self and self

2. specificity - activated T and B lymphocytes respond to specific non self antigens

types of adaptive immunity: antibody mediated (humoral)

B cells act and circulate antibodies that bind toxins to destroy them

types of adaptive immunity: cell mediated (cellular)

T cells attack target cells infected with intracellular pathogens

can be CTL or CD8+

recognition of foreignness: endogenous antigen protein

class 1 binds to peptides by sampling proteins in cytoplasm

recognition of foreignness: exogenous antigen processing

class 2 binds fragments that come from antigens outside cell and present to T helper cells

CTLS: effector cells

go to work

CTLS: memory cells

sleep

B cell biology

become plasma cell once activated; made out of membrane bound antibodies

antibodies

don't kill a pathogen but can mess with it's ability (to replicate, etc)

four polypeptide chains: constant C regions

sequence does not vary

four polypeptide chains: constant V regions

form antigen binding sites