BioSec 2012: Elizabeth

Elizabeth's BioSec Notes

(Organized by class dates) Brain dumps, class notes, useful insights, points of confusion, it's all here.

Jan 25

Class readings:

Chapter 2: Origins of Life
Chapter 3: Selection, Biodiversity, and Biosphere

In-class notes:

• Chemistry Review
  • energy difference between reactants and products in a chemical reaction
  • however, you need an input of energy to begin the reaction
• a catalyst changes (lowers the energy needed to reach the intermediate state, making the reaction more likely to take place
  • the catalyst is unchanged in the process
• Biological catalysts are enzymes (proteins) that hold the reactants and situate them in such a way that the reaction can happen more easily
  • enzymes move the reactants around
  • enzymes can have crystalline structure
• cell logic is built on pattern-matching
  • enzyme is looking for the reactants that fit its receptors
• ATP: Adenosine Triphosphate
  • energy carrier/source for cells
  • universal resource, used by all cells
• ADP: Adenosine Diphosphate
  • similar to ATP, but has one fewer phosphate group
  • has lower energy than ATP
  • the cell expends energy to turn it into ATP
  • then the cell breaks up the ATP to use the stored energy
• Eukaryotic cells vs. Prokaryotic cells
  • in eukaryotic cells, the genetic sequence isn't simply copied from DNA to RNA. Instead, parts of different sequences are picked and chosen and edited into proteins.
  • this means that a lot of the information in the DNA is there to control and regulate how parts are edited and assembled.
• Because of how evolution works (building on what already worked), understanding how a system works is equivalent to understanding its history, and why it is the way it is.
  • however, it can be hard to know where stuff came from, and what came first

Jan 27

Class readings:

Chapter 4: Energy and Enzymes
Chapter 5: Membranes and Transport

In-class notes:

• ATP provides the energy to shake things up, get things moving so that reactions can go
• Fluid Membrane Model: active transport
  • steric: does it fit through the transport channel?
  • charge: does it have the right charge?
  • selectively open: channels can be open or closed

• Chapter 6 (Cellular respiration) preview
• respiration = the process of getting oxygen into the cell
• glycolysis: ancient process to create ATP, doesn't involve oxygen
• Figure 6.5 - important diagram
  • glucose oxidation happens in steps so that more energy (ATP) can be harnessed and not lost as heat (wasted energy)
• there isn't anything particularly special about the molecules used in cellular respiration (glucose), but it is noteworthy that all eukaryotic cells use the same molecules and seem to be evolutionarily related
• look at the process/architecture of the Calvin and Krebs cycles

Feb 1

Class readings:

Chapter 6: Cellular Respiration
Chapter 7: Photosynthesis

In-class notes:

Both chapters address how cells make ATP and other byproducts.

• not a lot of discussion about how the two processes fit together (I mean, photosynthesis is the more important because it creates the glucose for cellular respiration to use?)
• much of the in-depth chemistry was confusing
• In Ch 7, I didn't fully understand the last section about photorespiration and how plants avoid it
  • what is the problem, really?
  • I understand that the C4 cycle resolves it

Possible application-y thoughts

• both photosynthesis and cellular respiration involve a lot of cyclical processes (like loops, I suppose) that transform one product into another
• the cellular structure model seems like it could be applied to computers (and is similar to what exists), but maybe the metaphor could be extended to be larger?
• what would ATP map to in the computer world? Information output?
• It seems that the processes are finely tuned so that most of the by-products (except energy lost in heat) get used - is there a moral in that story?