Microbiology Exam 1

Front 1

requirements/basis for life

Back 1

1) metabolism

-all living cells must be able to do glycolysis

2) reproduction

3) respond & adapt to external environment

4) growth

5) genetic variation & evolution

6) homeostasis (maintaining internal metabolism)

Front 2

1) what macromolecules can catalyze rxns?

2) first genetic info?

3) genetic info in all living cells?

4) can fermentation occur in the presence of oxygen?

5) which macromolecules can be used as source of energy?

-rank highest to lowest energy

-which is the PREFERRED energy source?

6) ALL living cells have..?

Back 2

1) proteins AND nucleic acids (RNA- ribozyme)

2) RNA

3) DNA

4) yes

5) carbs (polysaccharides), proteins (polypeptides), lipids

-HIGH --> LOW E: lipid > carbs > protein

-PREFERRED: carbohydrates (easier to break down than lipid)

6) 1) plasma membrane, 2) cytoplasm, 3) DNA, 4) ribosomes

Front 3

Microbes

-biogeochemical cycling

-biofilm

Back 3

forms of life too small to see w naked eye (bacteria, archaea, fungi, algae, protists, slime mold--viruses studied too)

-help in biogeochemical cycling (inorganic molecules are cycled to organic & back again--ex. nitrogen fixation, denitrification)

-live in biofilms (diverse groups w many dif members forming a microbial community & ecosystem--ex. microbes in intestines, slime on rocks, plaques on teeth, mold growths)

Front 4

1) Pasteur

2) Koch

3) Lister

Back 4

1) -disproved spontaneous generation theory

-pasteurization (using gentle heat to reduce # of microbes in food)

2) -determined Bacillus anthracis & Mycobacterium tuberculosis were causes of anthrax & tb

-"Koch's postulates" allowed others to determine which microbes caused disease

3) use of antiseptics / practices infection control

Front 5

first documented vaccine

Back 5

Smallpox

Front 6

Bacteria shapes

Back 6

-vibrio: comma-shaped

-pleomorphic: varied shapes, constantly changing--usually LACKS a cell wall

Front 7

Bacteria:

1) Thiomargarita namibiensis

2) mycoplasma sp.

Back 7

1) largest known species (700 um)

2) one of smallest species (0.2 um), lacks cell wall --> more pathogenic (harder to recognize)

Front 8

Bacteria cytoplasm components

Back 8

1) *DNA nucleoid: chromo (DNA + proteins) & replication machinery

-chromosome packaging proteins

-DNA & RNA synthesis enzymes

-Regulatory factors

-ribosomes

-plasmids

2) enzymes involved in breaking down substrates

3) *inclusion bodies: compact of same molecule

-*sulfur globules: energy source

-*poly-B-hydroxybutyrate: carbon & E source

4) *gas vesicles: buoyancy (usually for water dwelling photo synth bacteria--ex. cyanobact)

5)* Magnetosomes (magnetite): orienting cell--help find low oxygen areas

6) *Carboxysomes: location of carbon fixation rxns (contains rubisco enzymes --> photo synth)

7) *Cytoskeletal structures: FtsZ & MreB (cell division proteins)

Front 9

Bacteria cell components

-cell envelope

Back 9

1) cytoplasm (+ all components)

2) nuclear envelope

-plasma membrane

-cell wall

-outer membrane (sometimes, Gram neg)

Front 10

hopanoids

Back 10

sterols in plasma membrane that help w stability across temperature ranges

Front 11

transport across plasma membrane:

-diffuse

-osmosis:

-facilitated diffusion

-active transport

-cotransport

-ATP-binding cassette (ABC) transporter

Back 11

-diffuse: small (CO2 & O2) & nonpolar/hydrophobic molecules (benzene)

-osmosis: flow of water across PM from low [solute] / high [water]--> high [solute] / low [water]

-facilitated diffusion: protein channel to move particles with its conc gradient, no ATP used--only certain molecules can move through specific channel (aquaporin protein channel: H2O)

-active transport: use ATP to move AGAINST gradient

-cotrans: symport (same direction), antiport (opposite)

-ABC: ATP + Solute-binding protein (SBP) w solute --> shape change in channel --> solute moves across, SBP released --> ATP to ADP --> channel closes

Front 12

Bacteria plasma membrane

Back 12

-electron transport chain (create proton motive force --> ATP)---used for respiration or photo synth, used to derive energy for motion (flagella)

-*pigments for photosynth

-sensory proteins (detect env changes, alter gene exp)

Front 13

Bacteria cell wall

-composition

-function

-degradation

-antibiotic resistance

Back 13

-comp: cross linked strands of peptidoglycan: N-acetylglucosamine (NAG) & N-acetylmuramic acid (NAM)

-funct: protection from osmotic lysis

-degrad:

naturally- lysozyme

artificially- B-lactam antibiotics (prevent crosslink formation NAM-NAM)

-antibiotic resist: B-lactamase destroys B-lactam ring struct

Front 14

*Gram positive

1) stain

2) composition

3) unique char.s

4) penicillin/antibiotics

Back 14

1)purple (primary stain)

2)- THICK outer layer of peptidoglycan (40-80% dry weight of cell, ~40 nm)

-narrow periplasmic space (space btw cell wall & plasma memb)

-lacks outer membrane

3) -large pores throughout peptide matrix

-teichoic acids (negatively charged) in peptidog--ONLY in gram POS

-ENDOSPORE FORMATION

4) penicillin antibiotic effective ONLY against gram POS

Front 15

*Gram negative

1) stain

2) comp

3) unique char.s

4) penicillin/antibiotics

Back 15

1) pink (counter stain)

2) -THIN layer of peptidoglycan (5% dry weight of cell, ~2 nm)

-periplasmic space of varying width

-OUTER MEMBRANE composed of lipopolysaccharide (LPS)

3) -LPS can be harmful: ENDOTOXINS (Lipid A) --> inflammatory resp, outer side chain of polysaccharides (carbs) can vary & be changed to evade host immune resp.

-porin & TonB proteins in outer membrane: transfer molecules to periplasmic space

4) antibiotic/penicillin resistant

Front 16

Gram stain

1) primary stain

2) mordant

3) decolorizer

4) counterstain

Back 16

1) primary stain: crystal violet

2) mordant: iodine (form complex w crystal violet)

3) decolorizer: alcohol (ethanol)

-shrinks large pores in Gram + --> lock in crystal violet stain

-strip away some LPS in Gram(-) --> lose crystal violet stain

4) counterstain: Safarin

Front 17

Bacterial flagella

1) composition

2) flagellar movement

3) non-flagellar movement

Back 17

1) comp:

-filament (made of flagellin proteins)

-hook: protein, connects filament to basal body

-basal body: disc structure, produces torque on filament --> turn like propeller

2) -run: directional movement (ccw spin)

-tumble: random movement (cw spin)

3) -gliding motility: smooth sliding

-twitching motility (type 4 PILI): jerky

Front 18

Outside bacterial cell

-Surface arrays (S-layers)

Back 18

1) flagella & type 4 pili --> motility

2) fimbrae/adhesive pili (protein for attaching to surfaces) --> adherence

3) sex pili --> conjugation

4) capsules (thick layer of polysacch surrounding some cells) --> adhesion, defense against host immune, protection from drying out/dessication, formation of biofilm

5) Surface arrays (S-layers) (crystalline array of interlocking proteins) --> protection/armor in some gram pos & neg back

Front 19

*Endospore

-structure

Back 19

-survival structure formed through sporulation when cell growth stops due to harsh conditions, forms within & at expense of vegetative cell

-ONLY PRESENT in some Gram POSITIVE bacteria (bacillus & Clostridium sp.)

-highly differentiated cells resistant to heat, chemicals & radiation --> can survive indefinitely

-structure: diplicolonic acid & lots of Ca2+ (stabilize DNA, heat resistance), core of small acid soluble proteins (carbon & energy source during germination)

-"dormant" stage (low metabolic activity)

Front 20

Germination

Back 20

-occurs when environment becomes favorable again

-endospore transforms into vegetative cell (layers of the endospore break down)

-vegetative cell: reproductive structure--genetically identical to endospore, just dif structure

-vegetative cell formed by germination is identical (same genetic info) as the vegetative cell that made the endospore

Front 21

sporulation & germination

Back 21

[stressful cond]

-->---SPORULATION--->>>

vegetative cell endospore

(reprod struct) (surival struct)

<<<---GERMINATION---<--

[favorable cond]

Front 22

*Biofilm

-matrix

-benefits

-formation

Back 22

assemblage of bacterial cells adhered to a living or nonliving surface enclosed in an adhesive matrix excreted by the cells

-matrix: mix of polysacch (carbs)

-benefits: trap nutrients for microbial growth, defense, favorable niche, metabolic coop between species

-formation: homoserine lactones --> intracellular signaling/ communication (quorum sensing)

Front 23

1) under what conditions would you expect a capsule to form--ideal or stressed?

2) which will trigger sporulation? a) put veg cell in boiling water, b) expose veg cell to deadly chems, c) put veg cell in nutrient poor env?

Back 23

1) ideal -- lots of h20 & polysacch.

2) C (nutrient poor env) -- a & b will kill cell

Front 24

Euk. nucleus

-nucleolus

Back 24

nucleus: double membrane struct cont. linear chromosomes; site of replication & transcription (DNA --> RNA)

-nucleolus: non-membrane bound, within nucleus, ribosome synth.

Front 25

mitochondria & chloroplasts

Back 25

BOTH:

-use ETC to prod ATP (chemiosmosis)

-both are semiautonomous (used to be organisms & were engulfed --> support for endosymbiotic theory)

-has own DNA & can replicate indep

CHLORO:

-unique to photosynth organisms (algae)

-use the ATP they produce to fix carbon into organic compounds

MITO:

-NOT all eukaryotes have a mito--some have a hydrogenosome

Front 26

plasma membrane

-sterol in euk PM

Back 26

-sterol for stability: cholesterol

(in (some) bacteria: hopanoids)

-LESS proteins in memo than in bacterial plasma memo (lower protein abundance than in bacteria PM)

Front 27

Motility

Back 27

flagella AND cilia (unique to euk domain)

-flagella: longer, usually only 1 or 2, bigger movement/wave-like

-cilia: smaller, usually have many, smaller movement/rowing movement

Front 28

Fungi

Back 28

-model org: Saccharomyces cerevisiae (type of yeast)

-metabolism: heterotrophic

-cell wall: chitin

-motility: non-motile

-other: used in beer, bread, wine

Front 29

Protozoa (protists)

-model org:

-metabolism:

-cell wall:

-motility:

-other:

Back 29

-model org: Giardia lamblia

-metabolism: varied (most hetero, some phototrophic)

-cell wall: LACKS (none)

-motility: varied (flagella, cilia, other)

-other: Giardia LACKS a mitochondria (has a mitosome), is genetically old/not evolved & causes human DISEASE

Front 30

*Slime molds

-metabolism:

-cell wall:

-motility:

-other:

Back 30

-metabolism: heterotrophic

-cell wall: LACKS (none)

-motility: amoeboid (psuedopods)

-other: some can fuse many cells to form continuous MULTINUCLEATE giant cell; model for studying ecology, motility & cell-cell comm

Front 31

Algae

-model org

-metabolism:

-cell wall:

-motility:

-other:

Back 31

-model org: Chlamydomonas reinharatii

-metabolism: phototrophic (photosynthetic)

-cell wall: cellulose

-motility: flagella (2) or non-motile

-other: single or multi-cellular

Front 32

Endosymbiotic theory

Back 32

euk microbes arose by: one primitive microbe ingested another, forming a symbiosis & one inside became dependent

-evidence of mito & choloplast:

1) both resemble bact in size & shape

2) double membranes consistent w ingestion

3) each has own DNA & DNA seq more similar to bacteria DNA than to euk.

-mitochondria DNA --> proteobacteria

-chloroplast -> Cyanobacteria

Front 33

Beneficial roles of euk. microbes

Back 33

1)many are primary producers

-some algae produce large amounts of oxygen thru photo synth.

2)some are biodegraders (recycle nutrients)

-some can degrade cellulose

Front 34

*Eukarya organelles (10)

Back 34

1) nucleus: contains most of cell's DNA, site of transcription

2) mitochondrion: energy production

3) chloroplast: photosynthesis

4) rough ER: site of translation & protein folding; (has ribosomes on surface)

5) smooth ER

6) Golgi apparatus: modifies, sorts & transports proteins

7) Vacuole: storage & structure

8) Lysosome: digestion of macromolecules (cont. digestive enzymes)

9) Peroxisome: breakdown of fatty acids (cont. oxidative enzymes like catalase & oxidase)

10) hydrogenosome: production of H2 & ATP (has double membrane, remnant of mito, found in amitochondriacs)

Front 35

*Archaea shapes

Back 35

-rectangular (Thermoproteus sp.)

-irregular (Sulfolobus sp.)

Front 36

*Archaea cytoplasm

Back 36

-DNA + histones (single, circular chromo)

-inclusion bodies (gas vacuoles)

Front 37

*Archaea plasma membrane

Back 37

-unique to this domain!

-MONO or bilayer

-ETHER linkages (instead of Ester) hold phospholipids together

Front 38

*Archaea cell wall

Back 38

psuedomurein/psuedopeptidoglycan in some

-NAG + NAT

-N-acetyltalosaminuronic acid (NAT) instead of NAM like in bacteria

-B-1,3 glycosidic linkage (instead of 1,4 like in bacteria peptidoglycan) --> LYSOZYME is INEFFECTIVE against archaea

Front 39

*Archaea cell surface

Back 39

1) S-layer (layer of identical armor like subunits): protection from predation/viruses & adhesion

2) some form cannulae (hollow glycoprotein tubes that link cells together to form complex network)

3) flagella

-sim to bacteria: rotate to move

-different: thinner, comp of 2+ versions of flagellin protein, grow from base (not tip_

Front 40

Archaea phyla

Back 40

Crenarchaeota, Euryarchaeota, Korarchaeota, Nanoarchaeota

Front 41

Crenarchaeota

-*adaptations for survival

Back 41

-(hyper)thermophiles (greater than 50 C or 80 C)

-mesophiles (15-40 C): biogeochem cycling

-psychrophiles (less than 15 C): biogeochem cycling

-acidophiles

-barophiles

*adaptations for survival:

-lipid monolayers

-more alpha-helical regions in proteins

-more side chain interactions in proteins

-strong chaperone protein complexes

-thermostable DNA-binding proteins

Front 42

*Euryarchaeota

Back 42

1) Methanogens: reduce CO2 w H2 --> produce methane (CH4) & H20

-use energy produced to fix carbon

-ANAEROBES

-found in human gut, termite gut, swamp sediment, ruminants

2) Halophiles (Halobacterium salinaru): require NaCl (salt) conc greater than 1.5 M

-Great Salt Lake, Dead Sea: between 5 & 34% salinity

-maintain high K+ conc to offset high extracellular Na+ conc (protein channel, can pump K+ in when needed)

-high GC conc --> prevent DNA denaturing; highly acidic proteins that remain stable in salty env -> prevent potein denaturing

-produce energy through odd form of

PHOTOTROPHY (don't use chlorophyll or ETC--use bacteriorhodopsin to harness light E & generate proton motive force to make ATP)

-bacteriorhodopsin give off reddish hue

Front 43

Korarchaeota

Back 43

unculturable, not yet cultivated

-hyperthermophiles (detected from 16S rRNA)

Front 44

Nanoarchaeota

Back 44

-Nanoarchaeum equitas

-one of smallest organisms on earth (*1% of the volume of E. Coli)

-symbiots/parasites of crenarchaeota species

-from hydrothermal vents/hot springs (thermophiles)

Front 45

virus structure/size

Back 45

size: 10-100 nm

-exceptions: megavirus & mimivirus (euk. amoeba viruses)

structure:

-ss or ds RNA or DNA

-capsid (comp of capsomere proteins); capsid + genome = nucleocapsid

-envelopes (plasma memo around capsid--synth by host cell)

Front 46

envelopes

Back 46

animal viruses usually enveloped (acquired thru budding)

bacteria viruses usually naked

Front 47

viral replication cycle

Back 47

1) adhere to host cell (stick to specific receptors)

2) penetrate (get into cell) & uncut (release genome)

3) express genes to make proteins (synthesis)

4) replicate genome (synthesis)

5) assembly (put everything together) & exit (get new virus particles out)

-animals: ENTIRE virus (capsid, genome & env) enter

-bacteria: only GENOME enters

Front 48

virus names based on

Back 48

-location discovered

-disease caused

-organisms they infect

-appearance

Front 49

virus classification systems

Back 49

-International Committee on Taxonomy of Viruses (ICTV): complex criteria

-*Baltimore classification system: based on genome, sep into 7 classes

Front 50

viroids

Back 50

-NOT viruses

-naked ss circular RNA (no capsid)

-internal complementarity

-small

-resistant to ribonucleases

-plant disease

Front 51

satellite virus

Back 51

-require helper virus for replication

-carry own capsid gene

-ex. Hep D

Front 52

satellite RNAs

Back 52

-require helper virus for replication

-require capsid protein from helper virus

Front 53

prion

Back 53

-proteinaceous infectious particles

-JUST PROTEIN (no nucleic acids, genes, etc)

-revolve around protein conformation changes from normal to abnormal

-resistant

-cause spongiform encephalopathies (ex. mad cow)