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

Pre-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?

In-class notes:

• Photorespiration
  • Carbon dioxide (CO2) is split up to get oxygen (O2) and carbon (C). The carbon is used to make glucose, and the oxygen is toxic to an enzyme
  • is an example of a way in which the process isn't completely specific/specialized, and has included limitations, even through selection
  • evolution isn't perfect (and has limitations), and sometimes, these get papered over and the cell goes on living with them
  • in this case, the C4 cycle has developed to handle the limitation
• Linear Electron Chain
  • begins with photon from the sun (energy)
  • the chain of molecules that take the energy from the sun and pass it along
    • each stage uses what it can of the energy and passes the rest along
    • most of the energy ends up going to proton pumps with create ATP
• NADP is an electron carrier molecule

Q: How would this kind of system evolve? What kind of pressures must have existed?

• Photosynthesis is a pretty efficient process
  • however, it is less efficient than cellular respiration
  • and considerably less efficient than any process designed by humans (such as the internal combustion engine)
• Photosynthesis and cellular respiration aren't divorced processes
  • the plant uses its glucose (from photosynthesis) in the mitochondria, to create more ATP (when the sun isn't shining)
  • but animals get their glucose from what they eat, which is then used by the mitochondria
  • plants effectively store energy in glucose (ex. maple tree sap)
• Plants are net producers of oxygen, and net consumers of carbon dioxide
• Humans are net producers of carbon dioxide, and net consumers of oxygen
  • Earth's atmosphere is 78% nitrogen, 21% oxygen, and only 0.03% carbon dioxide

Computer security

• plants provide energy to almost everyone else, but why? why haven't they evolved to protect themselves from animals?
• animals prevent the plants from consuming everything
  • by themselves, the plants are unsustainable
  • they need someone to eat them
• so, might computer security be in need of a predator?
  • do we need to find some constant pressure to keep security on the path?
• How can we work out a system where the pressures create better, stronger systems?
  • i.e. one where evolution will take place
  • predation addresses material imbalances
  • what are the inputs and outputs of computer security?
    • on the internet, there seems to be a lot of information, but the challenge is in parsing it into wisdom