Exam Prep Mic Bio

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Phylogenetics

  • show the evolutionary relationships among various biological species or entities
  • one tree contains only species believed to have common ancestry
  • nodes
  • common ancestry
  • rooting your tree
  • 3 possible phytogenetic trees can be made froma character atrix that examines 3 characteristics

levels of organization

  • principals of self organization
  • every level of organization may have its own reliable rules and behaviour that mediate phenotypic expression
  • these self organizing principals can be used to predict outcomes in the phenotype but must be approached holistically considering all the processes at each level of organization
  • framing, contextualizing
  • over emphasis of DNA as an explanation for phenotypic expression
  • non genetic phenomenon that occurs at different levels of organization is more deterministic of phenotypic expression
  • DNA is the only known example of hereditary reproduction that uses a blue print everything else happens without a plan yet the absence of a plan does not mean the absence of rules, order or patterns.
  • no linear relationship between number of genes and number of cells
  • changes in cellular behaviour
  • changes perforate into higher levels of organization

Mapping Genotype to Phenotype

  • genotype - genetic make up of an organism
  • phenoype physical and observable characteristics of an organism
  • how do you get from genotype to phenotype
  • how do you take the linear base sequence of DNA and turn it into a 3 dimensional organism?
  • levels of organization
  • "genes for" concept - the shopping gene - who would you evaluate this statement
  • importance of environment - social factors
  • a localized DNA change is easily traced to its effects on to the phenotype but phenotypic changes cannot be predicted
  • this is because self organizing cause changes that occur when there is a basic problem with the protein

tool kit

  • tool kit - most organisms have the same tools or genes they just use them in different ways to do different things
  • Darwin - we are similar because of hereditary but we are different because of mutations
  • human genome project shows humans have virtually the same kinds of genes as other species
  • The way we think and our capabilities are certainly unique
  • the brain - a lesson in parsimony - who could we make such a complex brain was so little stuff
  • humans use vastly more cell organization - coordination
  • if an electric current passes then a stable synapse connection is created - stabilized by use
  • why is it difficult to predict a phenotype based on a genotype
  • examples - environment - temperature in butterflies - changes wing pigmentation
  • similar in catalytic sequence/ binding site
  • the human genome were suppose to be all the instructions for how to build a human
  • now we find out the set of instructions is the same instructions for every living animal
  • the idea of a toolkit has been reinforced
  • what is different is how we use the tools that makes us unique
  • there are 100 - 150 basic atoms in the world
  • combinations, patterns,
  • if these patterns are timed in space you can get even more
  • 22 fundamental amino acids
  • 3 subatomic particles

conclusion

  • underscore the importance of environment and context
  • gene content is mutable and changeable depending on context
  • although everything is context specific if you properly factor in levels of organization you can take elements that are out of context and artificially introduce them with positive results
  • for example you can usually take a limb gene from a mouse and save a fruit fly

Environment as a selection pressure

  • often the predominant influence on phenotypi expression
  • just because we have the genes does not mean they will translate to our phenotype
  • as information is passed from one level of organization to another complex polygenic mechanisms of inheretance become highly seneisitve to environmental changes
  • common environmental selection pressures included predetors, food sources and terrain

convergent evolution

  • every level of organization has its own rules
  • factors independently derived numerous times (bird and bat wings)
  • to many gains of logic
  • parsimony - simplest solution is the most likely
  • convergent evolution - two things that look quite similar but have independent origins - independently derived - at two different times - not ancestral
  • the forearm is ancestral - the wings are convergent or independently derived

Symbiotic cooperation

  • nodules on the roots of plants
  • clover -
  • what is great about nitrogen fixing?
  • proteins need amino acids and nitrogen is essential to amino acid construction
  • humans get nitrogen by eating plants
  • plants extract nitrogen from the air (80% nitrogen) by a synergistic relationship with bacteria
  • it exchanges sugar for nitrogen
  • forest fire rebirths are characterized by large growth of alder species which have increased ability to nitrogen fix
  • alfalfa is planted after a cash crop to re-nitroginate the soil

complexity theory

  • the whole is greater than the sum of its parts
  • humpty dumpty
  • it is not just content but conditions and arrangements
  • relationship between phenotype and genotype
  • content vs. organization
  • it is not the types of molecules but how they interact

four processes that facilitate emergent properties

  1. division
  2. movement
  3. apoptosis
  4. growth

example: the sun

  • mass determines the trajectory of the earths rotation not the content of the earth
  • Sub atomic particles are colourless until combined in atoms to produce colour
  • even though the power grid is man made there are unexplainable fluctuations that reinforce each other
  • in contrast with the reductionist view
  • taking it apart can often ruin the phenomenon you are trying to study
  • important for determining how you get phenotype from genotype
  • it must be how constitutent parts are used
  • interactions are the root of emergent properties

RNA World

1. in contrast with Central Dogma

  • there are times when the arrows move in the opposite direction
  • reverse transcription rna changes dna

before DNA

  • viruses are RNA
  • they preceeded the DNA world

4 types of RNA

  • RNA -
  • Rrna - ribosome - place where protein is made
  • Mrna - sits in the ribosome
  • Trna - hooks the amino acids together

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