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BIOL-M 250 > Final Exam > Flashcards

Final Exam Flashcards

1
Q

Vibrio fischeri

A
  • “Milky seas”
  • Marine bacterium
  • Symbiosis with squid (stores v. fischeri “light organ” and feeds bacteria which emit light)
  • Luciferase enzyme (production regulated by quorum sensing)
  • Produces light only at high cell density
  • Quorum sensing

Advantage is to create counter-illumination (no shadow)

name hint–found in fish light organ

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2
Q

16S rRNA

A
  • Nucleic acid sequence
  • Found in all living things (used for comparison)
  • Part of ribosomes
  • Constant and highly variable regions

More similar 16S rRNA sequence = more similar bacteria

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3
Q

Consequences of 16S rRNA phylogeny

A
  • 5 kingdom tree became 3 kingdom tree
  • Scientists realized most biological diversity was in microscopic organisms
  • Photosynthesis evolved multiple times
  • Archaea were discovered
  • Facilitated/changed way bacteria were named
  • Enabled the field of microbial ecology
  • Gave strong support for endosymbiotic theory
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4
Q

Epulopiscium fischelsoni

A

-Found in gut of surgeon fish
-Visible to the naked eye, but still a bacteria!
-VERY unusual cell division, deviation from Binary Fission
> daughter cells grow inside mother cells
> mother cell is killed when daughters are released

name hint–found in fish gut

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5
Q

Escherichia coli

A

-E. coli (K12) most studied organism EVER, helpful gut microbe (no pili)
-E. coli (O157:H7) dangerous pathogen, phage infection introduces toxin and pilus on chromosome
^ identical 16S rRNA but chromosomes only 75% similar

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6
Q

Phage

A

Viruses (proteins and nucleic acids) that infect bacteria

Lysogeny strategy (in E. coli):

  • Inserts its genome into E. coli genome
  • Phage genes replicated by E. coli
  • E. coli now secretes Shiga toxin (damages human cells)
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7
Q

Shiga toxin

A

A/B toxin

Destroys eukaryotic ribosomes to kill host cell

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8
Q

Mycoplasma pneumoniae

A
  • Causes “walking pneumonia”
  • Among smallest bacteria
  • Uses cholesterol to buffer membrane fluidity
  • “Attachment organelle” that allows for Gliding motility

name hint–begins with “M” … think of Motility (Gliding)

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9
Q

Magnetospirillum magnetotactum

A
  • Contains magnetosomes (Storage granules of magnetite)
  • Uses magnetosomes to orient motility in a magnetic field
  • These magnetosomes are actually membrane invaginations
  • MamK filament organizes magnetosomes inside of cell

name hint–magneto for magnetosomes

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10
Q

Storage granules

A

1) Energy storage
2) Element storage
3) Damaged proteins

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11
Q

Mycobacterium tuberculosis

A
  • # 1 infectious bacterial pathogen (infects the lung)
  • Thick, waxy cuticle
  • Unusual capsule, two EPS layers with a unique waxy, mycolic acid lipid layer between them
  • Resistant to most everything, but grows VERY slowly
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12
Q

Extracellular polysaccharides (EPS)

A

Extra, non-essential, layers beyond the peptidoglycan

ex: Capsule, Slime layer

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13
Q

Caulobacter crescentus

A

-Asymmetric division (swimmer cell, stalked cell)
^ stalked cell produces multiple swimmers
-Grows in very dilute water
-World’s strongest glue “holdfast”

name hint–think of a crescent as asymmetrical

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14
Q

Deinococcus radiodurans

A

-Isolated from an irradiated can of meat
-Extremely radiation resistant
-Nucleoid is compacted into a “torus”
^ contains many copies of the chromosome to be able to quickly reassemble after radiation damage

name hint–radiodurans, relate to radiation

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15
Q

Radiation

A

Ionizes most common molecule in the cell (water), which then attacks the largest molecule in the cell

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16
Q

Bdellovibrio bacteriovorus

A
  • Intracellular predator of Gram Negative bacteria
  • Pulls itself into the periplasm with Type IV pili

1) Infects periplasm
2) Elongates and solidifies host outer membrane
3) Does not use binary fission, multiple simultaneous divisions
4) Host lysis and release

name hint–bacteriovor, think of preying on bacteria

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17
Q

Chlamydia trachomatis

A
  • Causes most common STD in the United States
  • Intracellular pathogen, grows inside human cells
  • Lacks FtsZ
  • Cannot make own ATP, steals energy from host

Alternates between two cell types, “elementary body” (EB) or dormant form and “reticulate body” (RB) or growing form

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18
Q

Cloistridium acetylbutylicum

A
  • Gram positive, soil bacterium
  • Can eat unusual substrates, dynamite (TNT)
  • Ferments sugars to acetone (gunpowder) and butanol (rubber/biofuel)
  • Possible biofuel source

name hint–creates acetone (acetyl) and butanol (butyl)

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19
Q

Fermentation

A

Strategy to burn excess NADH and restore the pool of NAD+, electrons dumped back onto the substrate

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20
Q

Geobacter metallireducens

A
  • Gram negative, soil bacteria
  • Consumes sugars, respires metals
  • Pili conduct electrons outside cell “nanowires”

Nanowire

  • allows respiration of insoluble metals
  • conductive pilis anchored in plasma membrane and part of the electron transport chain

name hint–think of “metallireducens” … respire metals

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21
Q

Respiration

A

Use of an electron transport chain to make proton motive force

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22
Q

Halobacterium salinarum

A

-Archaea
-Extremely halophilic, desiccation/radiation resistant
-Bacteriorhodopsin phototrophy
^ single proton pump directly coupled to light absorption (does not use Electron Transport Chain)
-requires photo-pigment cofactor, found in the human eye

name hint–halo- prefix (like salt)

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23
Q

Sinorhizobium meliloti

A
  • Soil bacterium, legume symbiont
  • Fixes nitrogen in plant nodules
  • Form symbioses with different bacteria
  • Plant gets nitrogen–bacterium gets carbon
  • Receives/sends signals to plant, infects through infection thread, forms bacteriods, make rhizopines (energy source) to feed bacterium on outside of plant
  • leghemoglobin–similar to hemoglobin, safely delivers bound oxygen to bacteroid. Controls oxygen so as not to destroy nitrogenase

name hint–“rhizo” for rhizopines (energy source) to feed bacterium on outside of plant

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24
Q

Rhizopines

A

An exotic carbon, nitrogen, and energy source that only the Sinorhizobium on the outside can eat

25
Q

Bacillus subtilis

A
  • Gram-positive soil bacterium
  • “industrial workhorse”–produces proteases, riboflavin, fungicide
  • powerful genetic system
  • “competent” takes up free DNA from the environment
  • regulates process of sporulation through a cascade of sigma factors

name hint–“sub”sets of sigma factors

26
Q

Alternative sigma factors

A

Different gene sets that can be expressed by changing sigma factors, a way of coordinately regulating hundreds of genes of like-function throughout the genome

27
Q

Bacillus subtilis sporulation

A

Mothercell develops a “forespore”

  • Metabolically dormant
  • Resistant to heat, desiccation, radiation
28
Q

Cascade of sigma factors

A
  • Starvation (sigma H)
  • Early forespore (sigma F)–compartment specific
  • Early mothercell (sigma E)
  • Late forespore (sigma G)
  • Late mothercell (sigma K)
29
Q

Fremyella diplosiphon

A
  • Cyanobacterium
  • Fixes carbon, fixes nitrogen

-Chromatic acclimation
> in green light, makes green absorbing pigment
> in red light, makes red absorbing pigment

-adjusts antenna proteins to match light color
(controlled by a two component system)
> does nothing in green light
> in red light…
phosphorylates RcaC, binds to DNA, activates red pigments, and represses green pigments

name hint–“fremyella” … free my ella, light (color)

30
Q

Pigment optimization

A

Fremyella sees different colored lights in water (like a prism), some colors penetrate farther than others

31
Q

Heterocysts

A

(Nitrogen fixing bacteria), fixes nitrogen and shares with chain

Specialized, differentiated, non-growing, O2 impermeable cell types found in cyanobacteria

32
Q

Agrobacterium tumefaciens

A
  • Plant pathogen, creates tumors or galls
  • Transfers Ti plasmid to plant by conjugation
  • Ti plasmid directs production of growth hormone and octopine synthesis

1) Transfers Ti plasmid to plant by conjugation
2) Ti plasmid recombined into plant chromosome
3) Plant expresses Ti genes (growth hormone + octopine)
4) Agrobacterium feeds on octopines !!!

33
Q

Borrelia burgdorferi

A

Tick-borne human pathogen, causes Lyme disease

  • Endo-flagellum rotates cell body to push through viscous environment
  • Requires no iron (Fe)
  • Has linear chromosome
34
Q

Myxococcus xanthus

A

Soil bacterium, mistaken for a eukaryote, exhibits gliding motility, makes antibiotics and anti-cancer drugs

Cooperative feeding–secretes digestive enzymes, shares nutrients from prey

  • Trail following (gliding motility)
  • Predation of other bacteria
  • Aggregation
  • Multicellular fruiting bodies
35
Q

Streptococcus pneumoniae

A
  • Gram Positive diplococci
  • Infects the lung
  • A secondary infection from the flu, causes most death
  • Com machinery
  • Antigenic variation, 90 different capsule structures

Variation–many different capsules to evade immune system
Mimicry–some capsules look like host cell sugars

36
Q

Griffith Transformation Experiment, 1928

A

No capsule - harmless
With capsule - virulent
Dead, with capsule - harmless
Dead capsule w/ live no capsule - virulent

Capsule is required for virulence

Capsule genes transferred to avirulent strain during co-infection by natural competence (transformation)
^ Found by Avery Experiment, 1930 (2 years later)

37
Q

Yersinia pestis

A
  • Causes Bubonic Plague
  • Carried between rodents and people by fleas
  • Variety of virulence factors on three different plasmids
  • Uses Type III secretion system (~10 toxins directly injected into host cell, antigens never exposed to immune system)
38
Q

Streptomyces coelicolor

A
  • Mistaken for a fungus
  • Gram Positive soil bacterium
  • Linear chromosome
  • Hyphal growth, rare cell division
  • Polyketide antibiotics (75% of world’s antibiotics)

1) Grows into substrate
2) During starvation it secretes antibiotics and hydrophobin
3) Grows into the air and forms chains of spores

39
Q

Problems with a linear chromosome

A

Discontinuous strand must continuously re-prime, no template DNA to re-prime the termini

Eukaryotes use Telomerase to extend the 3’ termini

Streptomyces have Tpg “Terminal proteins” covalently fused to ends of chromosomes, these proteins somehow fill in the DNA gap

40
Q

Polyketides

A

Look very complex but are actually variations on one another, related to fatty acid biosynthesis

41
Q

Polyketide biosynthesis

A

Large gene “island”, modular, a series of enzymes fused together, sequential stepwise reactions, enzymatic assembly line

42
Q

Novel antibiotic

A

Rearranging domains on synthase can produce new antibiotic structures

43
Q

Regulation and Resistance

A

Also encoded in “islands”

genetic regulators–control production of polyketide synthase

resistance genes–provide for resistance to the polyketide antibiotic being made

44
Q

Methanococcus jannaschii

A
  • Deep vent isolated
  • No pseudopeptidoglycan
  • Plasma membrane with an S-layer
  • Chemolithoautotroph, use Reverse TCA Cycle for carbon fixation
  • Methanogen

Methanogenesis–reduces CO2 to CH4 in multiple steps

Unusual cofactors, vitamins unique to archaea

45
Q

Volta Experiment

A

Alessandro Volta performed an experiment where he showed that gas from disturbed decaying plant matter was flammable

46
Q

Bacteria

A
  • Small
  • Lack organelles (membrane enclosed sub-compartment)
  • Have nucleoids (unlike a nucleus has no membrane)
  • Prokaryote
  • Single, circular chromosome
  • 70S ribosomes
  • Peptidoglycan
47
Q

4 requirements for microscopy

A

Magnification–relative increase in image size

Resolution–the ability to distinguish two points that are close together

Light Quality–sets limit of resolution

Contrast–the ability to detect objects against a background

48
Q

Classification strategies for bacteria

A
  1. ) ) Numerical Taxonomy (traits)
    2) DNA-DNA hybridization (genome comparison)
    3) Phylogenetics (molecular chronometer)
    4) Polyphasic approaches (combination)
    5) Naming by disease
49
Q

Special features of the Gram Negative envelope

A

1) Outer membrane
2) Lipopolysaccharide
3) Braun’s lipoprotein
4) Porins
5) Periplasm

50
Q

Binary Fission

A

Two identical daughter cells made from a single mother cell

51
Q

What conditions limit bacterial growth?

A
  1. Temperature
  2. Desiccation
  3. Oxygen
  4. Radiation
  5. Acidity
  6. Pressure
  7. Chemicals
  8. Nutrients
52
Q

Types of transport

A

Passive diffusion–Molecules pass directly through membrane, requires a gradient

Facilitated diffusion–Molecules pass through membrane
by way of proteins, requires a gradient

Primary Active transport–ATP is expended for proteins to pump solutes against a gradient. Can concentrate substrate.

Secondary Active transport–Diffusion of one molecule is used to pump another molecule against a gradient. Can concentrate substrate.

PTS transport–Energy is expended and substrate is
changed during transport. Can concentrate substrate.

53
Q

Protein Secretion Systems

A

1) Sec-dependent GENERALIZED Secretion (SEC)
2) Type II OUT Secretion
3) Type III Needle Complex secretion
4) Twin-Arginine Translocase (TAT)

54
Q

Chemoorganotrophy

A

Pentose Phosphate Pathway–rearranges sugar structure

Glycolysis (EMP or ED)–makes ATP from glucose

Electron Transport Chain–burns NADH to produce PMF

F1F0ATPase–makes ATP from PMF

TCA Cycle–makes NADH from pyruvate/acetyl-CoA

B-oxidation Pathway–makes NADH from fatty acids

55
Q

NADH, PMF, ATP

A

Electron Transport Chain – NADH > PMF
Reverse Electron Transport Chain – PMF > NADH

F1F0ATPase – PMF > ATP
Reverse F1F0ATPase – ATP > PMF

56
Q

Bacterial Translation

A
  1. Ribosome recognizes Shine-Dalgarno sequence
  2. Multiple initiating codons (AUG, UUG, GUG)
  3. formyl-Methionine
  4. Transcription and translation occur simultanteously
  5. Different ribosome structure 70S ribosomes/16S rRNA (Antibiotic sensitivity)
57
Q

Classes of RNA

A
  1. Message RNA (mRNA)
    Informational RNA. Has SD sequence. One specific mRNA for each protein to be translated.
  2. Transfer RNA (tRNA)
    Activates amino acids. Decodes mRNA. Shared pool. No SD or start codon.
  3. Ribosomal RNA (rRNA)
    Major structural and catalytic component of ribosomes. Shared pool. No SD or start codon.
58
Q

RNA biosynthesis (Transcription)

A
  1. Activation and polymerization of RNA nucleotides
    templated by DNA.
  2. Catalyzed by RNA polymerase.
  3. Transcriptional start = promoter
  4. Transcriptional stop = rho-independent terminator or rho-dependent terminator

BIOL-M 250 (11 decks)

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