Microbiology Exam 2 Cards 2

• Example of phototrophic archaea
• Has pigment becteriorhodopsin
• Appears purple: abosrbs green light and reflects blue and red
• Absorbs e- and shifts from cis to trans
• Going from trans to cis releases photon

• e- donor is H20
• Makes ATP to fix CO2, making glucose or sucrose in Dark Reaction

• P2 excites e- to split H20
• Drops in energy to P1
• NADP+ is the electron carrier

Chlorophylls and Accessory Pigments : Collect photons

• Rubisco binds CO2
• Large, slow enzyme: Can react with O2 or CO2
• 18 ATP required to fix 6 CO2 into glucose
• 12 NADPHs are also required

• Green & purple bacteria, Purple bacteria
• e- donor is H2S, Sulfide Ions, H2, or Ferrous Ions
• Chlorophylls absorb infrared light, less energy = less ATP
• Only one photosystem
• Slow growth

Nitrate -> Nitrite -> Nitric Oxide -> Nitrous Oxide -> N2

NH3 -> Nitrite -> Nitrate

• O2 is e- acceptor to oxidize nitrite
• Can perform nitrification under anoxic conditions. Has organelle to protect it from toxic byproduct

• N2 -> NH3
• Ammonia is then used to make amino acids

• Has a triple bond (980 kJ to make/break bond)
• Requires 6 e- to reduce

• Iron containing enzyme
• There are alternate forms of nitrogenase
• Dinitrogenase- enzyme w/ Moliptonone (Mo) cofactor
• Dinitrogenase reductase- Inactived by O2 so used only in anoxic envir.
• Not too specific, can break other triple bonds

• Anaerobic process (must be done in absense of oxygen)
• Can be performed by aerobes or anaerobes

• Found in root nodule, very low O2 concentration
• Both plant and bacteria secrete chemicals
• -Rhizobia factors make root hairs curl so that bacteria can penetrate
• -Plant factors cause bacteria to grow, nodule forms
• Bacteria then changes to bacterioid

• Bacterioid membrane is surrounded by symbiosome membrane
• Plant gets ammonia/amides, Bacteria gets sugars and organic acids
• Leghemoglobin (Lb) produced by plant keeps O2 levels low in infected area

Arise from a single cell

Populations of metabolically related organisms

Set of guilds that interact together

Communities of organisms + Their natural environment

Biologically and chemically mediated chemical transformations of elements

Physical habitat. Resources available for growth

Best conditions for fastest doubling time

• Small environments of microbes
• Ex. Bacillus = 3mm microenvironment

• Act as primary producers, consumers, decomposers, food
• Biochemical cycles, transform things from gas to mineral or vice versa

• Have resources for growth / prevent growth
• ex. fungicide to prevent fungal growth

Can not isolate all microbes. The ones we do isolate don't always act the same in lab setting (ex. lose capsule)

• 1. Streak plates to obtain single colonies
• 2. Agar shake- Can make agar, add sample, then place on more agar for anaerobes
• 3. Liquid Dilution- Successive dilutions until the last tube shows no growth (10 or fewer cells) = Most Probable Number

• 1. Microscopy - Gram stain should only show one type of cell
• 2. Look at colony characteristics
• 3. Growth in media in which cultures grow poorly and contaminants grow well (should be no growth)

Microbes don't get nearly as many nutrients in natural environment. Growth rate can be as low as 1% in natural environment what it is in lab setting

• 1. PCR and DGGE
• 2. Metagenomics
• 3. Staining Methods (Fluorescent, Viability, Fluorescent Antibody, GFP)

• DAPI- colors microbe blue by binding nucleic acid
• Acridine Orange- Also binds nucleic acid
• *Both fluoresce under UV
• **Problem- can't tell the difference between live and dead cells

• Depends on whether or not cytoplasmic membrane in intact
• 2 Dyes
• - Propidium Iodide- penetrates only cells w/o intact membrane
• - Green fluorescent dye- penetrates all cells
• **See mix of green and orange/red (Green=living cells)

• Antibody is used in place of a nucliec acid for dying
• Limited to specific strains or species (must be specific)

• Insert GFP into genome and add to natural population of microbe
• Reporter Gene- Used to tell if gene is transcribed
• Needs O2 to autofluoresce so useless in anoxic environment

• Nucleic acid probe (oligonucleotide is complimentary to a sequence in target gene OR RNA-hybridize)
• Tagged w/ fluorescent dye
• Fluoresces under microscope
• *Must use different nucleic acid prope to observe different species

• Beneficial relationship
• Cooperative transformation of one compound into a compound another organism needs

• Ex. Potists feed on bacteria
• Ex. Bacteria infect other bacteria

• One species benefits while harming another species non-specifically
• Ex. Streptomyces produce antibiotics to kill other microbes inhabiting soil

One species benefits while harming a specific host

Both species benefit through growth in proximity, however both species are easily separated to grow independently

because they secrete polysaccarides to encase cells

Most live at the surface but some can be found 4-5 km deep

• Contains rhizosphere
• Earliest stage of decomposition by fungi and bacteria so many nutrients available

Peat or top soil. Contains broken down organic material and minerals

Experience periods of H20 saturation from rain which leaches some nutrients, so has fewer microbes than O and A Horizons

Increasing proportion of minerals and rock fragments broken off from bedrock

• Microbes in crustal rocks (3 km deep)
• Energy source - radioactive decay of atoms including uranium
• Carbon source- Minerals

Protist that sucks nutrients out of fungal filaments

• -Create CO2 which becomes carbonic acid to disolve rock into mineral components of soil
• -Secrete organic acid
• -Decompose organisms

Marine ecosystem primary producers

Oligotrophic: Extremely low concentration of nutrients and orgnisms

• filamentous marine cyanobacteria in tropical and subtropical oceans
• Nitrogen Fixing

• Zooplankton- not many
• Phytoplankton (algae and protozoa)- 3,000-4,000
• Photosythetic bacteria- 100,000
• Heterotrophic bacteria- 1,000,000
• Viruses- 10,000,000

Light can reach organisms 100-200m in open ocean / 1m in coastal region

Where water column meets ocean floor and soil

Archaea usually found in extreme environments. Only become more numberous than bacteria in deep ocean (2,000 meters)

• Barotolerant- >3,000 m
• Barophilic- 4,000-6,000 m (grow optimally in high pressure)

• Proteins are folded in a way to minimilize effect of pressure
• Membrane is high in unsaturatated fatty acids
• Omph porins- play role in nutrient aquisition

Tube worm at thermal vent. No digestive tract but has blood vessels w/ oxygen. Trophosome (bacteria) uses oxygen to fix CO2, making organic compounds for the tube worm.

Even though organisms produce O2, this causes more heterotrophs to grow and consume it, making an anoxic environment

• Input of sewage causes spike in bacterial population
• There is a lag in algae/cyanobacteria growth but O2 will inc. when they do

• -microbial oxygen consuming property of a body of water
• -the amount of organic matter that can be oxidized by microorganisms
• *carbon and oxygen concentrations are inversely related in a freshwater environment

When microbe population is big enough to remove pollutants, but require a limiting nutrient

Add specific microbes to decompose specific pollutants

• 1. Toxicity of site
• 2. Initial levels of contaminant / microbes
• 3. Ability of contaminant to be biodegraded
• 4. Soil properties

All genes present in cell or virus

Transmit genetic material from parent to offspring

Genetic info transferred from one cell to another

Used smooth and rough streptococcus. Living rough cells took genetic info for capsule formation from dead smooth cells

Found that DNA was the source of info transmitted

480 proteins. Found this by using transposons to mutate genes and determine if they were essential.

RNA Polmyerase and Promotors (DNA sequence in front of gene to activate expression)

• In eukaryotic genes, 1 gene is generally used to make 1 protein
• In prokaryotic genes, many genes can follow the promotor and all be expressed into mRNA at same time

Region of promotor and genes

• Eukaryotes- 90% non-coding
• Prokaryotes- 15% non-coding

• 1. Has to remove introns (splicing)
• 2. Add poly A tail
• 3. Add 7-methylguanosine to 5' end (capping)

• Prokaryotes: 30S and 50S
• Eukaryotes: 40S and 80S

• Can code as few as 2-30 genes or as many as a few hundred
• Have genes that aren't necessary for living
• Can be used to clone genes

• 1. Antibiotic resistance gene (to select for transgenic bacteria)
• 2. Several unique restriction sites
• 3. Promotors for replication of DNA

• Can be interspecies or intraspecies
• 1. Transformation
• 2. Transduction
• 3. Conjugation

• Take in DNA from environment
• Must have DNA binding protein to bind single strand DNA
• If DNA is not integrated into host genome it will be broken down

• Genetic exchange mediated by a virus
• Bacteriophage gets copy of bacterial DNA, is replicated, and inserts bacterial DNA into next host cell (rather than virul DNA)

• dsDNA, circular or linear
• Episomes- plasmids that become integrated into the chromosome
• Curing- Eliminates plasmids in host cell using heat
• Can be passed via conjugation

• Donor= male / Recipient= female
• Must have cell to cell contact through pillus
• Transer single strand (not in circular form)
• Once one bacteria has plasmid, will eventually transfer to all others