bimm 120 -- final

in regard to symbiosis, define the following?

1. mutualism

2. commensalism

3. parasitism

1. mutualism: both benefit

2. commensalism: one benefits, other unaffected

3. parasitism: one harmed

in regards to origin of human microbiome, what was the original hypothesis of the origin but what has been evidently found? what does this indicate?

• hypothesis: sterile womb

• actual: womb x sterile

  • bacteria in umbilical cord blood, amniotic fluid, fetal membrane

  • no inflammation

• indicate: infant incorporate initial microbiome before birth; birth/feeding add onto

in regards to microbial transmission from mom to child, where does the mother’s mouth/intestine/vagina bacteria end up in the child?

• mouth → amniotic fluid

  • transmitted via bloodstream

• Intestine/oral → meconium (baby first poo)

  • meconium contain enterobacteriaceae + lactic acid bacteria

  • vagina/bloodstream → womb

• vagina

  • during pregnancy, vagina microbiome ↑ lactobacillus (acidic pH)

  • vaginal microbiome differs btwn dif ethnicities

what is the meconium? what is it indicative of?

• meconium: first bowel movement of newborn

  • means body = functioning

what is jimenez et al study do to the meconium? what did they find?

• 21 newborn meconium samples

  • found not sterile

• e. faecium → orally pregnant mice

  • e. faecium found in meconium

are bacteria pH sensitive? what pH are human symbiotic bacteria? molds/yeasts?

yes; human symbiotic/pathogenic = 6.5-7.5 pH; molds/yeasts = 4-6 pH

how does the vaginal pH change? what does that do?

• acidic pH (<4); prevents candida albicans growth (> 4-4.5 pH) → prevents UTI

• pH < 4 → ↑ lactobacilius (pregnant woman)

what expt did dominguez-bello et all study in terms of newborns and delivery? what was their findings? conclusion?

• study: 16 rDNA sequencing study microbiome newborns; vag delivery/c-section

  • tried to restore microbime

• found: c-section → mom skin microbiome; vaginal → mom vag

  • after 1 yr, microbiomes converge

• conclusion: mode of delivery shape acquired/initial newborn microbiota composition

what 2 types of bacteria do vaginal born babies have?

• lactobacillus; digest lactose (milk sugar)

• bifidobacterium; prebiotic in breast milk break down human oligosaccharaies → short chain fattty acids → baby uses

what 1 type of bacteria do c-section born babies have? how long does it take to appear?

• bacteroidetes; 6mo

what does breast milk contain and what does it do to bifidobacteria?

• breast milk has urea — bifidobacterium → nitrogen → baby uses

what is the first milk the mother makes called? what is it rich in?

• Colostrum; rich in urea + milk oligosaccarides

  • maturing babies: colostrum ↑ urea

what bacteria gets transferred from mom breast skin to the newborn?

• sebaceous skin → breast milk

  • staphylococcus, corynebacteria, propionibacteria

what bacteria gets transferred from mom breast milk to the newborn?

• mammary gland (lymph circulation) → baby oral cavity

  • streptococcus, staphylococcus, serratia, lactococcus

after how long after birth does vaginally and c-sectoin newborn’s microbiomes converge? why does it take this long?

• 1 year; starts differently

• 1 year bc start eating solid foods

what 2 bacteria dominate the adult gut?

1. bacteroidetes

2. firmicutes phyla

what are the 3 roles of microbiomes?

1. first line of defense

2. immune system educator

3. metabolism

what happens if baby is given honey? what is in honey that causes this?

• clostridium botulinum → infant botulism

• honey: endospores → germinate intestine and crease hypErtonic environ

  • c. botulinum toxin —| muscle contract → flaccid paralysis

• baby small microbiome + x bile = x fight

what do normal microbiota produce to kill other bacteria?

bacteriocins

what 2 strategies have pathogens evolved to overcome normal microbiota?

1. use other nutrients

2. use other niches (via virulent factors)

what 2 things does the normal microbiota produce to protect itself from pathogens?

1. Iga (antibodies)

2. mucus; protect intestine from pathogens + used as carbon source by gluconate

what differs btwn germ free mice and regular mice? how can this be restored? waht recognizes these restoration factors? what do they trigger?

• germ free mice = thinner mucus layer

  • restore: ↑ LPS + peptidoglycan (PGN)

    • TLRs (toll-like- receptors)

    • activate immune system

waht is the order of the central dogma?

DNA → RNA → protein

how are genes expressed in bacteria?

1. alter DNA seq

2. transcription intiation

3. control mRNA stability

4. translation control

5. sense environment

   • quorum sensing

   • 2 component signal transduction

what are constitutive genes? inducible genes>

1. constitutive genes: housekeeping genes; always on (ie. glycolysis proteins)

2. inducible: only need in certain environments (ie. B-galactosidase, sporulation enzymes)

   • ↑ nucleotides in space: ↓ RNA pol bind

is lactose and glucose mono/disaccharides? what is prefered by e.coli?

• lactose: disaccharides

• glucose: monosaccharides

  • fewer steps to break down, e.coli prefer

what is an operon? promoter?

• operon: DNA segment w several genes controlled by promoter

• promoter: where RNA pol will bind (-35/-10)

operon + promoter share same region → crucial for lac operon expression

what are the 5 parts on lac operon? waht do the 3 code for?

lacl: lac repressor (not part of lacO)

→ bind/loop DNA → prevent RNA pol bind x access promoter

promoter

lacO: operator

3 genes

1. lacZ: B-galactosidase (lactose → 2 glucose)

2. lacY: lactose permease (lactose entry)

3. lacA: galactoside transcetylase (lactose isomers)

will the distuption of one gene on lac operon affect the others? why? what does this allow?

• each gene own start/stop site

• polycistronic pre-mRNA

  (— trans splicing → monocistronic mRNA)

• allows ↑ diversity/gene expression

how does lacI work in terms of repression? (-)

• lacl → lactose repressor

• binds to operator; bends DNA into loop

  • RNA pol x bind to promoter; prevent lacO operation

what represses the repressor of lacO?

• allolactose bind to repressor — conformational change → repressor cant repress operator

  • lacO transcribed

what repression is responsible for lacO prioritizing glucose > lactose when both are present?

• glucose = monosaccharide

• catabolite repression: regulation of transcription by repressors/activators

  • induces diauxic growth

what is diauxic growth? why does a lag occur?

• diauxic growth: biphasic growth pattern

  • both availble, glucose > lactose pref

• lag occurs after glucose used up to switch to lactose

  • CAP/CRP; catabolite activator protein

    • activated by cAMP (upstream RNA pol)

what regulates cAMP levels?

• ↑ PEP & sugar phosphotransferase system & AC: ↑ cAMP

  • glycolysis → PEP → pyruvate

  • (glucose present) PEP transfer phosphoryl group → new glucose molecule

• AC active = little/x glucose

what regulates CAP activity? what does CAP do?

• CAP: bends DNA allow spacer to ↑ -10 region + RNA pol binding

• ↑ cAMP; ↑ CAP activity; ↑ lacO

  • little/no glucose = AC active

  • AC + PEP = ↑ cAMP: ↑ CAP

• high glucose + CAP inactive (no cAMP)

what happens to lacO if there is no lactose present?

• no allolactose made

if ↑↑↑ glucose, ↓ cAMP, x lactose, will lacO be activated?

• no lactose: no allolactose to stop lacI repressor (no matter glucose levels)

• high glucose: AC inactive = ↓ cAMP = ↓ CAP

• no gene expression (x B-galactadase)

if ↓↓↓ glucose, ↑↑↑ cAMP, x lactose, will lacO be activated?

• no lactose: no allolactose to stop lacI repressor (no matter glucose levels)

• low glucose: AC active = ↑ cAMP = ↑ CAP

• no gene expression

if ↓ glucose, ↑↑↑ cAMP, yes lactose, will lacO be activated?

• yes lactose: allolactose stop lacI repressor

• low glucose: AC active = ↑ cAMP = ↑ CAP

• high gene expression

who discovered the first antibiotic? which was it? are they naturally producing?

• fleming → penicillin (mold)

• antibiotics: chemical compounds naturally produces by bacteria/fungi to compete other microorganisms

  • have selective toxicity

what is selective toxicity? what 2 groups could antibiotics be?

• ability of drug kill/inhibit pathogen wo affect host

  • -static: inhibit growth

  • -cidal: kill bacteria

• antibiotics: broad/narrow spectrum

what class of antibiotics degrade cell wall? how is this selectively toxic?

• b-lactam antibiotics

  • ↓ peptidoglycan crosslinking

    • aka transpeptidation (x cell wall synthesis)

• animals x have cell wall; gram(+) only

what are the 4 phases of the growth curve in a close system batch culture? where would penicillin be best adminstered?

1. lag phase (adjust environ./slow)

2. exponential phase (rapid/shortest gen time)

3. stationary phase (slowing growth/↓ nutrient)

4. death phase

• exponential/log phase

what are sites of protein synthesis? what are the 2 subunits? what is the difference btwn bacteria/euk rRNA? what are the 2 subunits composed of?

• bacterial ribosomes

• 2 subunits of protein + rRNA

• 70s ribosome: bacteria rRNA smaller/less dense than euk

  • 30s small subunit = 16s rRNA

  • 50s large subunit = 23S 5S

• macrolides, chloramphenicol, aminoglycosides/tetracyclines —| ribosome function

what subunits are the 70S and 80S euk ribosomes made of?

• 70S = 50+30

• 80S = 60+40

what are the 3 types of antibiotics that target bacterial ribosomes?

1. macrolides: —| peptide transfer (bind 50S)

   • block elongation (x work Gram(-))

2. chloramphenicol: —| peptide bond (23S rNA)

   • cause aplastic anemia: ↓ RBC/leukocytes → bone destruction

3. aminoglycosides/tetracyclines —| tRNA bind w mRNA (bind 16s rRNA)

   • broad spectrum; bind Ca2+/teeth color

what are the 3 methods to measure antibiotic susceptibility?

1. kirby-bauer disk diffusion

   • largest diameter of growth inhibition

   • x tell bacteriostatic/cidal; shows MIC

2. epsilometer test (e-test)

3. dilution susceptibility test

   • lowest conc browth wo growth = MIC

   • that tube transfered n cultivated to test bacteriostatic/cidal

   • not info on MLC

how do antibiotics at baby affect microbiome?

• ↑ anitbiotics: ↓ diversity: ↑ allergies/disease

• human microbiota x recover from antibiotic treatment

what are 4 ways bacteria develop resistance?

1. enzymes modify drug → destory/inactivate

2. alter binding target of drug

3. prevent drug entry

4. pump drug out

waht are the differences btwn viruses and bacteriophages?

viruses:

1. protein coat/capsid → dif shapes

2. classfification on nucleic acid present

   • contain DNA or RNA

3. enclosed by evelope (lipid) + spikes

4. infect specific cell type in one host

bateriophages:

1. DNA or RNA

2. life cycle regulation (repressor/activator)

3. lysis (lysins, holins: hole for phage escape)

4. x envelope virsus, x enter cell (only inject DNA/RNA)

5. well cahractertized genes

waht 5 things contribute to antibiotic resistance?

1. long term us eof single antibiotic

2. Widespread use

3. intact antibiotics in environ

4. clinical dosage > MIC

5. dif tissue/organ have ↑ inhibitatory conc

• HGT (?) + anti.res. = naturally occuring

why was antibiotic resisitance found in the cave>

• mutations = random

• cave: ↓ resources: ↑ microbiome competition

  • antibiotics: ↑ survival

howw can fight antibiotic resistance? waht study with mice and what bacteria dound this?

• fecal transplantation: restore normal gut microbiome (efficient probiotics)

• (relman) c.difficile infected mice treated w cultured species from curative pssg → cured

who discovered bacteriophages?

• felix d’herelle + frederick twort

  • bacteriophages found had bactericidal effect

• d’herelle use phage cure cholera

what was the plaque assay (d’herelle)?

• measure virus infectivity; similar to disk diffusion

• each plaque = infection from single virus particle

waht are the 4 types of bacteriophages? can they penetrate Gram(+)/(-) bacteria?

1. caudovirales (tailed)

2. siphoviridae (long, noncntractile tails)

3. myoviridae (contractil tail w sheath/cen tube)

4. podoviridae (short, noncontraile tails)

• flagellum/tail fiber allow to bind + inject DNA

• penetrate both Gram (+)/(-)

waht are the 4 steps a bacteriophage can penetrate gram(+)/(-)?

1. attatch to cell (tail fiber)

2. fiber retract + tail core (GP5) contact w cell wall

3. lysozyme-like enzyme froms small pore in peptidoglycan

4. tail sheath contrails + viral DNA enter cytoplasm

what 2 types of bacteriophages are there?

• lytic phage: kills cell (more common)

• temperate phage: lysogeny

  • parasitism/no viral reproduction/no death

benefits of phage therapy over anitbiotics?

phages jsut kill one species/strain

waht are teh physical/chemical requirements for growth?

physical:

• temperature, pH, osmotic pressure

chemcial requirements

• carbon, nitrogen, sulfur, phosphorous

• trace elements

• oxygen

waht is the use of chemicals for growth? waht 2 types of chemicals? what are the organisms called when they use those?

chemotrophy

• organic chemicals (glucose, acetate)

  • chemo-organo-trophs

• inorganic chemicals (H2, H2S, Fe2+, NH4+)

  • chemo-litho-trophs

waht is the use of light for growth? waht are those organisms called?

phototrophy

• phototrophs

how did primirive cells metabolize on the early life on earth? where did oxygen come from

• earth = anoxic (x oxygen)

• anaeorbic metabolism; prolly chemolithotrophic

• co2 → carbon | H2 → energy

• primitive ATPase = proton motive force

• 2.7 bya cyanobacteria emerged O2 production

• 4.2 bya: great oxidation event (↑ O2 levels)

  • oxygen became best e- acceptor

what does the krebs cycle produce? what is it considered? what are the products?

• ½ glucose → 2 CO2 + 3 NADH + 1 FADH2 + 1 GTP

• amphibolic: includes both catabolism/anabolism

how many ATPs are produces per 1 glucose in eukaryotes?

1 glucose → 38 ATP

• 1 NADH: 3 ATPs

• FADH2: 2 ATPs

where is the ETC located in eukaryotes? bacteria?

• eukaryotes: mitochondria

• bacteria: plasma membrane

protons pumped across the membrane in the ETC allow for what 3 things? (proton motor force)

• to produce ATP

• to spin flagella (movement); w MOT protein

• assist nutrient transport

how does the ATP synthase work as the protons move? what reaction occurs? is this reversible?

• enzyme used to make ATP

• as protons move in, gamma + epsilon subunits rotate → change active site

  • Pi + ADP → ATP (ccw)

• this process is reversible*

  *fermetative bacteria ATPase can only move one direction (ie. clostridium difficile)

in anaerobic respiration, what is the final electron acceptor in the ETC? how much energy does it yeild?

• not oxygen; prolly nitrate, sulfate, carbonate

• anaerobic < aerobic

in the eukaryote ETC, what are great electron donors? electron acceptor?

• e- donor: NAD+/NADH

• e- acceptor: oxygen

is the intestine strictly anaerobic? what keeps oxygen low in the intestinal lumen?

• gastrointestinal tract mucosa (intestinal villi): capillaries: ↑ oxygen than intestinal lumen

• facultative anaerobes choose to use oxygen so obligate anaerobes can survive

what 2 main bacterial phyla dominate gut microbiome?

1. firmicutes

2. bacteriodetes

how does immigration associate with gut microbiome?

• ↑ length US immigration: ↓ diverse gut microbiome: ↑ bacteroides: ↓ prevotella

  • bacteroides: sugar food breakdown

  • prevotella: plant breakdown