08/29/06

From Biolk483

• SETI is the Search for Extra Terrestrial Intelligence; it is a distributed computing program that analyzes radio waves coming to earth from outer space
• Carl Sagen: spokesman for projects without much hope but great possibility

Contents 1 Life is Knowable: 2 Biochemical hierarchy: how things are put together at different levels 2.1 1. Environmental Precursors 2.2 2. Add Energy to get Organic Materials 2.2.1 1953 2.2.2 Carboxylic Acids and Amino Acids 2.3 3. Macromolecules 2.4 4. Organelle: membrane surrounded package 3 Composition of the Cell 4 Prokaryotes

Life is Knowable:

• about 16 chemical linkages make up all the chemicals in our body
• about 100k different molecules in the human body
• e.coli only has 6k molecules.
• These numbers aren't impossible. We can know everything about these properties.

Biochemical hierarchy: how things are put together at different levels

1. Environmental Precursors

• little things, < 200 Atomic Mass Units (AMU)
• CO, CO2, H2S, N2, NH2, etc.
• Na+, K+, Cl+, ions, etc.
• H20: most important of all molecules
  • 18 AMU
  • 1 liter = 1000g / 18 AMU = 55.5 Molarity
    • This means that interfacing with H20 must be done at very high Molarity
    • Most biochemical components have Molarities around 0.001M

2. Add Energy to get Organic Materials

• Types of energy that may have added to the environmental precursors to give organic materials:
  • Lightning, heat, radioactivity, magnatism, sonic booms, UV light, etc.

1953

• 1953: Stanley Miller did the primordial soup experiment:
  • This experiment involved cycling some a mixture of liquid and gas environmental precursors through a closed system with an electrical discharge.
  • He found that the clear solution slowly turned yellow, then orange, then red.
  • When he examined the solution he found dicarboxylic acids and amino acids (two very stable organic compounds).
  • This experiment first showed that organic materials could arise from simple environmental precursors.
• 1953: Watson and Crick found the double helix.
• 1953: Sanger sequences insulin
• These things are why 1953 was so important to biochemistry. And it was all possible because the manhattan project produced radioisotopes that are now used more than routinely in biochemistry experiments.

Carboxylic Acids and Amino Acids

• once organic molecules are evolving, then comes metabolic intermediates like pyruvate, citrit, small, <300 AMU; these are the simplest biochemical building blocks.
• these slightly larger molecules (relative to the environmental precursors) come along as this new organic material.
• They are able to polymerized, hence we have:
  • nucleotides polymerizing to make nucleic acids
  • saccahrides polymerizing to make polysaccharides
  • complex ligands forming membranes (but remember that membranes are NOT macromolecules)
  • amino acids polymerizing to make proteins
• example of size
  • amino acids: Alanine is 5 angstroms = 5 x10^-10 meters
  • lipids: phosphatidylcholine = 35 angstroms
• most biochemical macromolecules are 10^6 or 10^9 Angstroms
  • it is not by chance that a molecule in the body is this large; this is big hint that it is biochemically important.

3. Macromolecules

• Put together some macromolecules and we have a "supramacromoleclar assembly"
  • these assemblies are combinations of lipids, proteins, nucleic acis and sugars
  • these are around 10^9 angstrums
  • example: fatty acid synthase, which is 2.4 million AMU with 27 activities; Ribosomes: 4 million AMU

4. Organelle: membrane surrounded package

• only found in eukaryotes
• made up of supramolecular assemblies, macro molecules, polymers, etc.
• example: mitochondria
  • about as big as a prokaryote (indeed, believed to have once been a prokaryote)
  • about 20k angstroms
• this is as large as biochem goes
• so, not cells, tissue, organs, organisms, or ecosystems

Composition of the Cell

• we have 63 trillion cells
• percentage by weight breakdown:

Water	70-90%
Macromolecules	22%
Sugars	3%
Lipids	2%
Inorganic Ions	1%
Amino Acids and their precursors	0.4%
Nucleotides	0.4%
Other small molecules	0.2%

Prokaryotes

• note that we did lots of drawing of the cell with the different cell components (cell wall, nuclear zone, etc.). Exact positions were not noted but the list is important to know and general function.
• prokaryotes (proks) are small with no organelles
• E. coli are considered "the laboratory of biochemistry"
  • E. coli makes up 2/3 of fecal matter
  • they are easy to grow lots of
  • approximately 6000 molecules and 3000 proteins in E. coli
• Important elements of the prokaryote:
  • Cytosol
  • Ribosomes (found in all cells)
  • Nuclear zone; there is no nucleus in prokaryotes, and there is just a single chromosome.
  • Storage granules
  • Mesosome; vaginated, increases surface area.
    • The mesosome can be interpreted as a precursor to mitochondrial folds.
  • Cell wall: made up of murein (which is not the same as cellulose as seen in plants), the cell wall is static (no biochemical activity) and has big holes...anything can get through.
  • Plasma membrane: lipid bilayer, thin, impermeable, dynamic.
    • note that there are no covalent bonds in the membrane, hence it is not a polymer. It is only held together by the hydrophobic effect.