Review Questions Flashcards
Describe the two different forms of geologic evidence that supports microbial evolution. What are they? What do they support?
- Stromatolites-microbial mats consisting of layers of filamentous prokaryotes and trapped mineral. Evidence 3.5 bya mats comprised of green sulfure bacteria. 4.5 bya. fossil evidence of the prokaryotic life that remains today.
- Iron Banding in geological record
Visible iron banding around 2.5 bya. This shows the evolution of aerobic phototrophs that perform the following reaction:
02 + Fe2+ → iron oxide (2FeO3)
Slow accumulation of oxygen over time
Draw a Phylogenetic tree and label all the parts. Describe the significance of each of these labels.
Branch lengths=evolutionary time
What evidence supports the sub-surface hypothesis?
Hydrothermal springs provide not only a less hostile environment it also provides a steady supply of inorganic molecules (particularly H2 and H2S). Also, reduced compounds come in contact with more H2O and are thereby oxidized forming precipitates (mounds). The composition of the mounds (Fe-Mg silicates) reacted with minerals and H2 to form amino acids and sugars. A large amount of phosphate also exists in the ocean, leading presumably to ATP generation.
Flow of hydrogen and H2S from crust provided ED to power reduce promoting the development of pH gradients.
What are two hypotheses surrounding endosymbiosis?
- Hydrogen hypothesis: an archaeal cell engulfed an H2 producing bacteria. This evolutionarily became mitochondria in eukaryotic cells and led to the formation of the eukaryotic nucleus.
- Eukaryotic cells (with preexisting nucleus) engulfed aerobic and phototrophic bacteria which evolutionarily became mitochondria and chloroplasts respectively.
What is bootstrapping and how is it used?
Bootstrapping is the statistical analysis of the assigned topology. Re-sample the alignment 500-1000 times in order to see how many times the same topology is assigned. This helps determine how confident you are in your tree topology. If there is a high percentage of getting the same topology, there is higher confidence that the alignment is correct.
What is the difference between maximum likelihood and parsimony?
Parsimony only looks for the tree with the least amount of nucleotide changes (most parsimonious tree). Maximum likelihood looks at the probability of every nucleotide change that would occur. Many trees are created is then constructed based on which changes are statistically most likely to occur.
Compare photosynthesis in different anoxygenic phototrophs (Purple Bacteria, Green Sulfur Bacteria and Heliobacteria).
Purple bacteria use reverse electron flow to create the reducing power needed for photosynthesis. Green sulfur bacteria and heliobacteria do not use reverse electron flow, but instead funnel in electrons at higher energy states so the electron can directly be transferred to NAD+.
Explain PCR bias—(what is it and where does it come from)-remember four for FC
PCR bias is the skewing of the distribution of PCR products due to unequal amplification or cloning efficiency. PCR bias can come from a number of places in the PCR amplification including…
- mistakes by polymerase,
- chimeric sequences,
- certain sequences being amplified more than others,
- secondary structure,
- primers can miss some clades,
- target gene may not be ideal.
Describe the subsurface hypothesis for the origin of life. Why might it be more valid than the surface hypothesis?
- Life originated in hydrothermal vents
- Steady stream of nutrients (H2, H2S, etc.) from the hydrothermal vent.
- Clay and inorganic precipitates could form, which could lead to reactions that produce organic molecules.
- Earth’s early environment would have been too hot and too chaotic for inorganic and organic compounds to be stable, so the subsurface hypothesis makes more sense than the surface hypothesis.
Why is the 16S rRNA gene a good phylogenetic marker?
- It encodes the small subunit of the ribosome, which every prokaryote has.
- There are both highly conserved and variable regions (allows all to be targeted, but you can infer phylogeny based on the differences).
- Molecular clock property can be assumed.
- 16s is good enough to differentiate between different generations
In 454 pyrosequencing, how do they measure a base being added and it what cases is it not very effective?
We flow the nucleotides one by one over the plate. Pyrophosphate is released when a nucleotide is added, which is converted to ATP by sulfurylase for luciferase to create a photon of light. The light is measured via a CCD (charged coupled device) camera. This can be bad in homopolymer regions where multiple beams of light of the are measured and make bigger peaks, in which case it can be difficult to determine how many nucleotides of the same type were added. Its hard to differentiated between 4 blips of light and 5 blips of light.
Describe the process and general structures that accomplish electron transfer in cyclic photophosphorylation.
A chlorophyll (or bacteriochlorophyll) are excited by incoming light. This excites an electron which is passed to pheophytin then to an accessory protein such as ubiquinone which transports the proton/e- across the membrane to the cytocrome complex. The final step is the transfer of electrons from the cytochrome back to the chlorophyll molecule thus no electrons are extinguished from the process (cyclic).
Explain the significance of quinones in the purple phototrophic bacteria reaction center.
Accepts protons from bacteriopheophytin and shuttles the protons across the membrane in order to create a proton motive force which is needed for the production of ATP.
Briefly describe the 4 different methods of creating phylogenetic trees
- UPGMA - distance matrix method - assumes that the evolutionary rate is the same, comparing the differences between the sequences
- neighbor joining - compares base pair differences without assuming an equal rate of evolution
- parsimony - minimizes the amount of evolution and it takes the path of least resistance, oversimplifying the evolutionary path
- maximum likelihood - likelihood based of probability of which tree is most likely to be the proper phylogenetic tree.
What is syntrophy? Explain why it is important for the environment and what is unique about the energetic in syntrophs
Syntrophy: The cooperation of two or more organisms to anaerobically degrade a substance neither can degrade alone. The heart of syntrophy is interspecies H2 transfer. Syntrophy is characteristic of anoxic catabolism in which methanogenesis or acetogenesis are the terminal processes in the microbial ecosystem.
Syntrophs are key links in the anoxic portions of the carbon cycle. Syntrophs consume highly reduced fermentation products and release a key product for anaerobic H2 consumers. Without syntrophs, a bottleneck would develop in anoxic environments in which electron acceptors other than CO2 were limiting.
Energetically, syntrophs produce H2 from more electropositive E.D.s– this cannot occur without an energy input. Thus the reaction is coupled with an energetically favorable opposite reaction that consumes H2. Syntrophic bacteria strive on strive on a severely marginal energy gain.
Examples: Syntrophomonas, Syntrophobacter, Pelotomaculum, Syntrophus, Ethanol fermentation coupled to methanogenesis
