Total Expectations1. How does evolution of species through natural selection account for diversity of life? All species are related by common ancestry. Species evolve because of natural selection for variable heritable traits. “Selection” is when a trait leads to reproductive advantage: the trait’s fitness. Individuals do not adapt, species evolve.2. Contrast the miasma theory and germ theory. Specifically what evidence supportseach? Germ theory: in medicine, the theory that certain diseases are caused by the invasion of the body by microorganisms, organisms too small to be seen except through a microscope. Pasteur further demonstrated between 1860 and 1864 that fermentation and the growth of microorganisms in nutrient broths did not proceed by spontaneous generation. He exposed freshly boiled broth to air in vessels that contained a filter to stop all particles passing through to the growth medium: and even with no filter at all, with air being admitted via a long tortuous tube that would not pass dust particles. Nothing grew in the broths, therefore the living organisms that grew in such broths came from outside, as spores on dust, rather than being generated within the broth.Miasma theory: held that diseases such as cholera, chlamydia or the Black Death were caused by a miasma a noxious form of "bad air", also known as "night air". The theory held that the origin of epidemics was due to a miasma, emanating from rotting organic matter. Miasma explained why cholera and other diseases were epidemic in places where the water was undrained and very foul-smelling. The miasma theory was consistent with the observations that disease was associated with poor sanitation (and hence foul odours) and that sanitary improvements reduced disease.3. Propose a logical follow-up experiment given data supporting a hypothesis WHAT THE FUCK4. How does the long term e. coli growth experiment support the theory of evolution? The long-term evolution experiment was intended to provide experimental evidence for several of the central questions of evolutionary biology: how rates ofevolution vary over time; the extent to which evolutionary changes are repeatable in separate populations with identical environments; and the relationship betweenevolution at the phenotypic and genomic levels. All twelve of the experimental populations show an increase in cell size, and in many of the populations, a more rounded cell shape. This change was partly the result of a mutation that changed the expression of a gene for a penicillin binding protein, which allowed the mutant bacteria to outcompete ancestral bacteria under the conditions in the long-term evolution experiment. However, although this mutation increased fitness under these conditions, it also increased the bacteria's sensitivity to osmotic stress and decreased their ability to survive long periods in stationary phase cultures.5. Be able to describe the simple basis of evolution by natural selection as presented in class (this is a rephrasing of the preconditions for natural selection). All species are related by common ancestry. Species evolve because of natural selection for variable heritable traits. “Selection” is when a trait leads to reproductive advantage: the trait’s fitness. Individuals do not adapt, species evolve.6. Presented with the cholera toxicity pathway, predict what would happen if parts were manipulated (ions added outside, proteins removed or added etc.) WHAT THE FUCK (osmosis)7. What distinguishes a differentiated cell from a stem cell? (lecture) Stem cells have the potential to become any type of cell once they are further along in development. Differentiated cells, on the other hand, already have a set purpose and can only become one type of cell when they develop and mature.8. phosphorylation / kinase / phosphatase/ negative feedback/ positive feedback/ switches/ amplification/receptor/ kinase cascade / (reading/lecture) Phosphorylation: the addition of a phosphate group to a moleculeKinase: enzymes that activate or inactivate other proteins by adding a phosphate group to themPhosphatase: an enzyme that removes phosphate groups from cascade proteins are always present in the cellNegative feedback: A self-limiting, corrective response in which a deviation in some variable triggers responses aimed at returning the variable to normal.Positive feedback: A physiological mechanism in which a change in somevariable stimulates a response that increases the change. Relatively rare in organisms but is important in generation of the action potential.Switches: ex: GTPase where it is on or off depending on phosphateAmplification: takes hormones in miniscule concentrations but triggers a large response from cells.Receptor: a protein that changes its shape and activity after binding to a signalingmolecule.Kinase Cascade: GDP goes to GTP and when RAS is activated it triggers phosphorylation and activation of another protein. The phosphorylated protein then catalyzes the phosphorylation of other proteins which phosphorylate yet another population of proteins.9. What are the important parts of a signal transduction pathway? (reading) 10. How does blocking a receptor change a signaling pathway? (reading) Stops signal from being received.11. What is the significance of the hydrophobicity of a signal? A receptor? (reading) Ability of a signaling molecule to pass through lipid bilayers determines how a target cell recognizes it. Most lipid-soluble signaling molecules are able to diffuseacross the hydrophobic region of the plasma membrane and enter the cytoplasm of their target cells. Large or hydrophilic signaling molecules are lipid insoluble and do not cross the plasma membrane. Must be recognized at the cell surface12. How is the cAMP signal in dictyostelium analogous to a microphone’s job? (lecture) Just as a microphone takes a small sound and amplifies it into a louder one, cAMPtakes a single signal and amplifies it into several signals.13. How can the same signal evoke a variety of responses in different cells? (reading/lecture) Signals have different pathways which affect how the signal is expressed14. Concept of the second messenger (reading)Second messenger are a non-protein signaling molecule that elicits a response to the first messenger. They are effective because they are small and diffuse rapidly to spread the signal throughout the cell. In addition they can be produced quickly in large quantities. Because arrival of a