Microbio Quiz 2 Study Sheet

Ester-link = bacteria, eukarya

Ether-link = archaea
Archae cannot do chlorophyll-based photosynthesis
Eukarya has whip-like flagella mechanism
Bacteria and archaea use rotation

Bacteria are sensitive to chloramphenicol, streptomycin, kanamycin,

and penicillin
Archaea and eukaryotes are not

Archaea similarities to eukaryotes

- Presence of introns
- RNA polymerase has TBP (TATA-binding protein) and TFB
(transcription factor B)
- Presence of histone homologs
- Presence of reverse gyrase is unique to archaea
o Reverse gyrase topoisomerase that twists DNA the other
way
 - Archaea have positive supercoils (bacteria and eukaryotes have
negative)
o Positive supercoils allow hyperthermophiles to resist high
temperatures

Archaea similarities to bacteria

- Circular genome
- Gene size and density
- Presence of operons

- Eukaryotes single gene monocistronic RNA

- Prokaryotes operon polycistronic RNA

- Esters hydrolyze more rapidly

- Methanogenesis only occurs in archaea, but not all archaea are
methanogenic
- Peptidoglycan helps resist osmotic stress doesnt exist in
archaea
- Archaea informational genes are similar to eukaryotes
- Archaea operational genes are similar to bacteria

- Pure ATP during glycolysis!

Different cell walls:

- Peptidoglycan: Bacteria
o Polysaccharide composed of two sugar derivatives (beta-1,
4 linkage) and a few amino acids repeating structure
called the glycan tetrapeptide
N-acetylglucosamine
N-acetylmuramic acid
o Strong due to cross-linking of double bonds
o Penicillin prevents biosynthesis
o Lysozyme destroys
- Pseudopeptidoglycan/ Pseudomurein: Archaea
 o Lysozyme cannot break the beta-1, 3 bonds
o N-acetyltalosaminuronic acid instead of the other one
- S layer: Archaea = most common, and some Bacteria
o Interlocking molecules of protein or glycoprotein
o Outermost layer
o Protection from osmotic lysis

Main takeaway: antibiotics and lysozyme that target peptidoglycan

cannot affect archaea since it doesnt have peptidoglycan

Gram (-) = single-layer

Gram (+) = at least two layers

In the archaeal metabolic pathway, glucose is catabolized by several

variants of the ED (Entner-Doudoroff) and EMP (Embden-
Meyerhoff-Parnas) pathways that rarely occur in bacteria.
- EMP = glycolysis
- Bacteria use phosphorylated intermediates and invest ATP

Methanogenesis is unique to archaea.

Archaea are the most ecologically diverse of the three domains

- Psychrophiles = cold
- Hyperthermophiles = hot
- Halophiles = high salt
- Acidophiles = acidic
- Methanogens = produce methane in anoxic conditions
- Also abundant in moderate habitats such as open ocean, soil,
and surface of plant roots
Euryarchaeota shows a greater range of metabolism
- Methanogens, halophiles, acidophiles, alkalinophiles
- Broad-ranging archaea
- Dominated by methanogens (syntrophs)
o All are poisoned by molecular O2 and therefore require
complete anaerobiosis
o Major substrates and reactions include:

- Methanosaeta form filaments during anaerobic digestion

o Traps bacteria into residual sludge
- Halophiles main inhabitants of high-salt environments are
members of the class Haloarchaea
o Their photo-pigments color salterns, which are used for salt
production
o Most are colored red by Bacterioruberin, which protects
them from light
o Halophilic archaea require at least 1.5M NaCl (up to 7x
seawater)
Adapt to high external NaCl by maintaining high
intracellular KCl
High-GC-content DNA and acidic proteins
o Important in proving chemiosmotic theory
o Haloarchaea are generally mesophilic
Can be neutralophilic or alkalinophilic
o Light driven proton pumps (rhodopsins)
 - Acidophiles
o Thermoplasmatales
Include acidophiles (as well as thermophiles)
Have no cell walls and no S-layers
Glycolipids help add maintenance to cell
membrane
o Thermoplasma acidophilum
Metabolism is based on S respiration of organic
molecules
o Ferroplasma species
Oxidize sulfur to sulfuric acid
Generate pH values of zero
Crenarchaeota shows a wider range of temperature
- Hyperthermophiles, thermophiles, mesophiles, and psychrophiles
- Scalloped archaea because often irregular in shape due to lipid
- All crenarchaeotes synthesize a distinctive tetraether lipid, called
crenarchaeol

-This compound forms monolayers, which contribute to its

stability in the heat
- Basophilic hyperthermophiles
o Grow near hydrothermal vents on the ocean floor
Pyrodictium abyssi
Pyrodictium occultum
o Because high pressure in deep water keeps it from boiling
o Also include mesophiles and psychrophiles
Thaumarchaeota important ammonium oxidizers

- Hydrogen based metabolism was indication that the 1st

metabolism to evolve on Earth was derived from a H-based
economy

Common traits of Bacteria

- Their central apparatus of gene expression:
o RNA polymerase
o Ribosomal RNAs
o Translation factors
- Underlies the selective activity of antibiotics
- Most bacterial cells possess cell walls made of peptidoglycan
o Another target for antibiotics

- The best characterized phylum is proteo-bacteria (divided into 6

different subphyla)
- Many phyla have few cultured representatives
Planctomycetes perform anaerobic ammonia oxidation/ nutrient
cycling
- A lot of invaginations in their membranes

Gram-positive bacteria
- Two distinct phylogenetic branches
o Phylum Firmicutes
Low-GC species
Bacillales
Genus Bacillus large rod-shaped cells
Sporosarcina only cocci to form endospores
o Vegetative cells develop inert endospores
in times of starvation and stress
B. anthracis
B. thuringiensis
B. subtilis
Clostridiales: genus Clostridium
Endospore swells, forming a drumstick
o C. botulinum
Botox is used to relax muscle
spasms
o C. tetani
o C. difficile
Important opportunistic pathogen
in the gut
Unusual Clostridiales: Epulopiscium fishelsoni
o HUGE (can be seen with the naked eye)
o Grows in GI tract of surgeonfish
o Gives live birth to two internal offspring
A derivation of the sporulation
program
Daughter cells emerge from
mother cell as it disintegrates and
dies
o Cells undergo no binary fission
 o Extreme polyploidy more than two
homologous sets of chromosomes

Non-spore-forming Firmicutes
Listeria monocytogenes
o Facultative anaerobic rod
o Causes gastroenteritis
o Actin propulsion system

Lactic acid bacteria preserve food by lowering

pH
o Food producers: ferment sugars, produce
lactic acid (gave rise to the world)
Lactococcus
Lactobacillus
Leuconostoc
Staphylococcus
o Facultative anaerobes
 More related to bacillus and listeria
Some are tetraploid
Do have respiratory chain
o Cocci in clusters
o S. auerus MRSA
Streptococcus also able to ferment and
produce lactic acid
o Aerotolerants dont need oxygen, but
arent poisoned by it either
No respiratory chain
o Cocci in chains
o S. pneumoniae
o S. pyogenes
Tenericutes
Mollicutes
o Completely lost their cell wall and S-layer
o Best known genus is Mycoplasma
Causes pneumonia and meningitis
Fried egg shaped colonies
require sterols for cell membrane
rigidity; some have lipogycans
Pleomorphic so small it can pass
through filters
o Phylum Actinobacteria
High-GC species
Actinomycetes an order in the Phylum
Actinobacteria
Streptomyces: antibiotic producers and
pathogens
Process of spore production is different from
Bacillus
o Long hyphae that become sectated =
intricate shapes
 Nonmycelial Actinobacteria
Mycobacterium
o Rod-shaped cells
o Have thick cell walls with mycolic acids
and phenolic glycolipids
Acid group instead of glycerol
Lipids are bound to carbons, not esters
Difficult to treat because they have
(in addition to thick peptidoglycan
wall) an outer lipid layer that is well
developed
o Replicate every 20 hours (slow and hard
to kill)
M. tuberculosis - TB
M. leprae - Leprosy
M. smegmatis harmless
commensal of humans
- Both groups have thick cell walls that retain the Gram stain
crystal violet
o Walls are reinforced by teichoic acids stabilize outer
membrane
- The average GC content is 40%
o When you plot GC, you get a hump at 40% and 65%
- Gram stain penetrates into cytoplasm and is retained there
- Thick peptidoglycan layer = retains it enough for us to visualize
it
Gram-negative bacteria
- Bacteriodetes
o Major gut commensal/ mutalist
o Shingobacteriales produce immunomodulatory
sphingolipids
Lipids are not linked by glycerol (sphingosene
instead)
Sphingolipids found in our gut too, so we study this
organism to learn how to modulate human immune
system
o Degrade complex polysaccharides
o Distantly related to proteo-bacteria
- Proteobacteria: metabolically diverse
o Traits are not phylogenetically conserved because of the so
many subdivisions

o
o Alpha-proteobacteria
Photoheterotrophs
Genetically unicellular
Perform photosynthesis or use carbon
Rhodobacter sphaeroides
o Grows in soil and water
Oligotrophs
Adapted to very low nutrient concentrations
Caulobater crescentus
Pelagibacter ubique (most abundant species on
Earth)
o Originally known for 16s sequence
o Smallest genome we know of (1.5
megabases)
Methylotrophs
Oxidize single-carbon compounds
Methylobacterium
Endosymbionts
N-fixers and plant roots
 Rhizobium and Sinorhizobium
Rickettsias
Intracellular pathogens
o Grows inside a vacuole inside of cells
Clade includes mitochondria
Rickettsia rickettsi
o Causes Rocky Mountain spotted fever
o Spread by ticks
o Gamma-proteobacteria
Pseudomonadales
P. aeruginosa (opportunistic)
Colonizes lung and causes chronic infection
Very resistant
Vibrionales
V. cholera
Most common infection transmitted by a
phage that infects it
Enterobacteriales
Facultatively aerobic
Can ferment rapidly on carbohydrates
o (Hetero-fermentation = number of
different byproducts) this is how they
are identified
o Many are commensal and dont do us
any harm
Escherichia coli
o Some strains grow normally in the
intestine
o Others, such as E. coli O157:H7, cause
serious illness, especially in children
Salmonella
o Delta & Epsilon proteobacteria
Myxococcus xanthus

Bdellovibrio bacteriovorans

Hellicobacter pilori
Gram-negative cell envelopes
- Thin layer of peptidoglycan
- Outer layer = primary contact surface, not completely
impermeable
o Small molecules pass through quite well
- Production of enterotoxin release of compounds into blood-
stream (associated with toxic shock)
- As volume of a bacterium increases, the ratio of surface area to
volume decreases
o Invaginated membranes or DNA in the periphery can help
overcome these setbacks
o Difficult for larger bacteria to live in a diffusion-
dependent environment
- The cell membrane defines the existence of the cell
o Anchors are important for stabilizing structures such as
flagella and pilli (important for cell-to-cell and surface
attachment)
o Critical: energy conservation when you have charge or
pH separation, you have a battery that you can use to
produce ATP
Membrane constituents
- Approximately equal parts of phospholipids and proteins
- Phospholipids: glycerol with ester links to two fatty acids and a
phosphoryl head group
o May have different side chain
- Archaea have L-glycerol while others have D-glycerol
- Components: length, decrease of saturation, and head-groups
- Membrane proteins functions:
o Structural support
o Detection of environmental signals
o Secretion of virulence factors and communication signals
o Ion transport and energy production/ storage
o *** Have hydrophilic and hydrophobic regions that lock the
protein in the membrane

Polar molecules and charged molecules require transport through

specific protein transporters

- Nutrient acquisition: facilitated diffusion

- Active transport requires energy
o Can be from another solutes concentration gradient

o Active transport: ABC transporters

The largest family of energy-driven transport
systems is the ATP-binding-cassette superfamily
In all three domains
Nutrient uptake
Multidrug efflux pumps (drug)
o Cancer cells have highly up-regulated
drug efflux pumps
Energy is coming from concentration gradients
 - Group translocation
o The group translocators are modular
o Net energy transfer is coming from PEP (a much more
energetic phosphate bond than ATP)
Transfers the phosphate bond to a number of carriers
that eventually gets donated to the incoming sugar
Changes the chemical by doing that
Taking advantage of the concentration gradient
o We dont actually have high levels of un-phosphorylated
sugars in the cells, they are phosphorylated as they enter
so that they dont go back across the transporter
o High sugar means low water availability

Membrane associated structures: curli, fimbriae, pilli, and flagella

- Curli are secreted as monomers and they polymerize outside the
cell
- Twitching and gliding motility happens on surfaces, while flagella
motility happens in fluids
- Curli are good at sticking to surfaces (so are polysaccharides)
- Different genes are controlling these processes and both
structures (such as curli) and polysaccharides (such as
cellulose) assist in attachment to the surface
o These structures are important in biofilm formation
and host interaction

How do cells grow in nature?

- In nature, many bacteria form specialized, surface-attached
communities called biofilms
 o When they grow together, that prevents diffusion, which
decreases the waste that leaves the environment
o Diffusion is very important for bringing in nutrients and
carrying away waste
o Need to modify metabolism to allow survival in the biofilm
Length of carbon chain can change
- Quorum sensing: expression of biofilm determinants
o Surface structures: hold fasts, Flagella, pili, fimbriae, curli
o Extracellular polymeric substances: slime, cellulose,
DNA, pNAG, alginate
o Surfactants: Rhamnolipids, surfactin
Keep liquid flowing through the channels so that
bacteria can get the nutrients that they need
delivered
- Pili, curli, holdfasts, and polysaccharides all contribute to biofilm
development
o Microcolonies is where we start to see a limit to diffusion
o Bacteria start to have different behavior; become
anaerobic

Gram (+) peptide pheromones (molecules) are predominant quorum

sensing molecules [polypeptides]
Gram (-) homoserine lactones are the predominant quorum sensing
molecules
- The length of the carbon chain is fairly species specific
Flagella critical in allowing microorganisms to chase after nutrients,
avoid predation, and move out of toxic environment
- Tumble-and-run = gaging where they are (run in favorable and
tumble in unfavorable)
- In bacteria, it is proton motor force that moves the flagella
o Rotation is expensive
Biosynthesis and function:
- A lot of stability = rings are stabilizing the torque
- Grows from base and is assembles from the inside, but
polymerizes towards the outside

Biomineralization:
- Carbonate minerals: usually extracellular and may serve as
ballast
o Helps them orient location
- Magnetosomes: membrane-embedded crystals of Fe3O4 fixation
o Orient the swimming of magnetotactic bacteria
o Chemotaxism moving towards food
o By lining with the poles, they are able to orient themselves
depth-wise in aquatic environment
o They use these to find anaerobic conditions since oxygen
poisons nitrogen fixation

Storage granules (store energy)

 - Polyphosphate
- Glycogen
- Polyhydroxyalkanoates
- Sulfur

- Cells store food, avoid toxic environment, and get nutrients using
all these structures!

- Carboxysome = stores sensitive enzymes (those sensitive to

oxygen)
o So that Carbon fixation can occur
o Limits diffusion of oxygen and increases concentration of
CO2

- Fungi need lower amount of nitrogen than bacteria

- Protein makes up the greatest amount of the cell by mass

Organisms can be phototrophs but still get their carbon from organic
compounds