MS130 - Biology
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Pete Markiewicz

Week 02

More on "generation debt"
http://www.csmonitor.com/2006/0111/p13s02-wmgn.html

Students suffocate under loans, unwise credit card purchases
http://www.usatoday.com/money/perfi/general/2006-02-22-student-loans-usat_x.htm

Student financial burden about to get worse
http://www.latimes.com/news/nationworld/nation/la-na-collegedebt5mar05,1,6485004.story?track=rss

Youth does much worse than older Americans during current economic recovery
http://www.msnbc.msn.com/id/11943055/

A family oddity becomes the norm (closer parent/child attachments)
"...Nearly 19 million adults between the ages of 18 and 34 still live at home, the US Census reports - a 48 percent increase since 1970..."
http://www.csmonitor.com/2006/0322/p14s01-cogn.html 

Web Links - Biomolecules, Energy, Cells, Microbes, Cell-Computer Analogy

THE ORIGIN OF LIFE

"...In some worlds there is no Sun and Moon, in others they are larger than in our own world, and in others, mor numerous...In some parts there are more worlds, in others fewer, some are increasing, some at their height, some decreasing; in some parts they are arising, in others failing. They are destroyed by collision with one another...There are some worlds devoid of living creatures or plants or any moisture..."

-Democritus, 460-470BC

• Archean Landscape
  Picture of Earth 4 billion years ago
  
   
• Basic material of life (CHON)
  • Carbon - forms backbone of bio-molecules
  • Hydrogen - part of carbon-bearing molecules, energy transfer
  • Nitrogen - forms part of protein structure
  • Oxygen - part of carbon-bearing molecules, energy transfer
     
• Origin of life (attempts to re-create early Earth conditions)
  The Miller-Urey experiment
  http://www.bioteach.ubc.ca/Biodiversity/origin/
  

Result: biomolecules found in living things today can be made by non-living processes

Origin of life research inspires Exobiology - possiblity of life on other planets

• Resources
  • The Astrobiology Web
  • Exoplanets (lists all planets found around other stars to date)
  • The search for small (Earth-sized) planets
  • Astrobiology Magazine
  • NASA Astrobiology Institute

BIOMOLECULES

"..Bio-molecules are, communication webs created by the intercommunication of atoms of oxygen, hydrogen, nitrogen, carbon and phosphorous. The intercommunication of these elements in highly complex patterns results in molecular replication (memory)..."

• Structure is directly or indirectly specified by genetic information in DNA
• Assembled from CHON and trace elements
• Extremely complex structures
• Structure creates function - "nanomachines"

Interactive Biomolecule tutorials (3D structure visualization)
http://www.umass.edu/microbio/chime/

DNA - the cell's "data storage system"

Sample DNA Structure
http://cmgm.stanford.edu/biochem/biochem201/Slides/DNA%20Structure/003%20Watson%20Crick%20B%20DNA.JPG
 

DNA fragment (side viewO	DNA looking down the strand

• 3D animation of DNA "Double helix" structure
  http://www.ebi.ac.uk/2can/tutorials/structure/#
• DNA bases
  http://img.sparknotes.com/figures/7/749a4182b7527e44d289a612e420f40c/dna_bases.gif
• DNA code
  http://www.biophysik.uni-bremen.de/radmacher/biophyvorlesung/data02/dna_code.jpg
  
• DNA sequence mapped to genes (like files on computer hard drive)}
  http://genetics.med.harvard.edu/~seidman/cg3/artemis/artemis_screen2.gif
• The human genome database
  http://gdbwww.gdb.org/
  Celera genomics - finished the human genome first
  http://www.celera.com
• DNA->RNA->Amino acids into Protein
  http://cellbio.utmb.edu/cellbio/ribosome.htm
• Individual amino acids
  http://www.agen.ufl.edu/~chyn/age2062/lect/lect_02/3_19b.gif
• Database of sequenced DNA genomes from various living organisms
  http://www.cbs.dtu.dk/services/GenomeAtlas/
• RNA structure database
  http://www.rnabase.org/

Proteins - the cell's "nanomachines"

• Protein structures - 3D rotating model of a small protein
  http://www.nyu.edu/pages/mathmol/txtbk2/topic2.htm
  
  
  Example for Casein (a major milk protein)
  
   
• RCSB Protein Databank
  http://www.rcsb.org/pdb/
• Chimera - protein modeling software
  http://www.cgl.ucsf.edu/chimera/

Lipids - create the cell membrane ("bag")
http://io.uwinnipeg.ca/~simmons/1115/cm1503/plasmamembrane.htm

Individual lipid (fat) molecules in bilayer	How lipids and proteins form cell membrane

HOW BIOMOLECULES CREATE THE LIVING STATE
THE CELL-COMPUTER/ROBOT ANALOGY

The modern view of life is similar to a computer connected to robot arms, with software specifying the construction of said computer and robots. The nanocomputer/nano-robot system can therefore assemble copies of itself. In other words, life reduces to molecules in organized motion.

Why James Watson and Francis Crick are famous? They figured out DNA structure out on assumption that DNA was a "data storage" molecule in the early 1950s)
http://library.thinkquest.org/20830/Textbook/HistoryofDNAResearch.htm
http://www.ocean.udel.edu/extreme2004/genomics/dnahistory.html
 

Detailed cell-computer analogy

Example of cell-computer components

Space-filling model of proteins "reading" DNA like hard drive "heads" reading hard drive
Ku protein, "cradles" DNA during repair of broken strands
http://www.hhmi.org/news/goldbergj.html

The Ribosome - the "industrial robot" that assembles proteins according to the code specified by DNA

http://www.mun.ca/biology/scarr/4241F2_ribosome.jpg
 

Space-filling model of ribosome with the three t-RNA molecules in plac

http://www.lbl.gov/Science-Articles/Archive/ribosome-crystallography.html

• Nanotechnology - attempt to buil artificial "molecular machines" emulating DNA, protein, lipids, etc
  Nanotube modeler software - http://www.jcrystal.com/products/wincnt/

ENERGY PROCESSING IN LIVING THINGS

The living world is solar-powered. Plants and other autotrophs use solar energy to manufacture bio-molecules. Animals and plants then break down these bio-molecules, releasing energy to power the living machinery

Energy and metabolism in living and other systems

• Energy Conversion Table
• http://www.wiredwales.com/info/c_factor/energy.htm
  • Watts = ((watt-hour = kilogram-calorie / 0.08605) / 24 hours)
  • Humans run at ~200 watts, brain at 25 watts
  • 1 horsepower = 746 watts (140,000 watts driving on freeway)
  • Personal computers use 400-1,000 watts
  • Blow-dryer - up to 3,000 watts

• Description of energy, entropy, metabolism
  http://arnica.csustan.edu/Biol1010/energy/energy.htm
• Substrate-level phosphorylation (Fermentation, glycolysis) - does not need oxygen

  C6H12O6	---------->	CO2, 2ATP + NADH+
  		2% efficiency

• Photosynthesis and Respiration - use oxygen, much more energy released

  Photosynthesis	---------->	11% efficiency
  Heat + 36 ATP + 6 CO2 + 6 H20		C6H12O6 + 6 O2
  38% efficiency	<-----------	Respiration
  Note: solar cells are typically 1% efficient, but may reach 30% in theory

   

ATP - the "energy" molecule of the cell and F0/F1 ATPase - the "engine" of life

Schematic	Space-filling model

How energy is created to create ATP

• Types of energy processing in living things
  • Photoautotroph - uses solar energy to manufacture organic compounds from inorganic molecules (carbon, hydrogen, nitrogen, oxygen)
  • Chemoautotroph - uses chemical energy to manufacture organic compounds (e.g. reduced sulfur compounds at deep-ocean geothermal vents
  • Heterotroph - breaks down organic compounds from other organisms for energy and to build its own bio-molecules

1. Photosynthesis - use of solar energy to generate chemical gradients to operate ATPase

Structure of the chlorophyll molecule
A nano-scale solar cell used by photoautotroph cells to capture solar energy and convert it into electrical power (creates electrical gradients to make ATPase operate, assembles bio-molecules from CHON. Has a Magnesium atom at center of structure. NOTE - embedded in a complex structure of proteins

3D rotating model of chlorophyll
http://www.public.asu.edu/~jpbirk/3dstruct/chlorophyll.htm

Schematic of chlorophyll molecules in protein complex embedded in cell or chloroplast memberane
http://www.blc.arizona.edu/courses/181summer/graphics/graphics%20lect9/Life7e-Fig-08-07-0%20molecular%20structure%20of%20chlorophyll.jpg

Photosynthesis "Dark reactions" - generate bio-molecules from ATP

• Why plants appear green (chlorophyll and other pigments absorb red and blue light)
  
  (from: http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPS.html )
   

2. Substrate-level phosphorylation - A series of enzymes couple sugar breakdown to ATP synthesis. Also called "fermentation" or "glycolysis". Low efficiency, does not need oxygen.

3. Oxidative respiration - breakdown of organic molecules generates chemical potential to drive ATPases (similar to chlorophyll system). Requires oxygen.

Heat + 36 ATP + 6 CO2 + 6 H20		C6H12O6 + 6 O2
38% efficiency	<-----------	Respiration

How ATP is created by photosynthesis and respiration

• ATP is synthesized by F0/F1 ATPase or similar protein complexes during photosynthesis and respiration (a 50-100Hz rotary engine powered by electrical potential on two sides of lipid bilayer membrane
  http://www.mrc-dunn.cam.ac.uk/research/atpase.html
   
   
• Schematic of F0/F1 operation
  http://www.rit.edu/~gtfsbi/IntroBiol/images/CH07/figure-07-13-2.jpg
  
   

  Schematic showing that F0/F1 ATPase rotates to assemble/disassemble ATP molecules.	Another schematic or the rotary operation of the F0/F1 ATPase
  Another diagram of the F0 rotary engine powering the ATP synthesis operation	Space-filling model of F0/F1 ATPase protein

Breakdown of ATP "high energy" bonds provides power to other cellular systems
 

Example of mechanical process powered by ATP binding to protein - the molecular "rotor" in prokaryote flagella
http://199.17.130.29/berg/ILLUST/flagella.JPG

EVOLUTION OF METABOLISM DURING THE HISTORY OF LIFE

Oxygen was a deadly poison for early life, but required for more complex life chemical reactions
http://www.astrobio.net/news/modules.php?op=modload&name=News&file=article&sid=1910&mode=thread&order=0&thold=0

When oxygenic photosynthesis evolved is not clear, but geochemical data suggest that between about 2.3 and 2.2.billion years ago, there was sufficient oxygen in the atmosphere to permit an ozone layer to form. That singular event appears to have precipitated a massive increase in genome and metabolic complexity.
Credit: Science.

Bio-energy compared to energy from oil

A barrel of oil contains the equivalent of almost 25,000 hours of human labor.

"...Even at today's prices, a dime buys enough electricity to lift a pickup truck 500 feet in the air. A gallon of gasoline contains as much energy as that expended riding a bicycle across the United States or hiking 300 miles across Arizona..." - Matt Simons

"With high energy consumption goes a high standard of living. Thus the enormous fossil fuel energy which we in this country control feeds machines which make each of us master of an army of mechanical slaves. Man's muscle power is rated at 35 watts continuously,''little more than you are working, but you have got to sleep, 'or one-twentieth horsepower. Machines therefore furnish every American industrial worker with energy equivalent to that of 244 men, while at least 2,000 men push his automobile along the road, and his family is supplied with 33 faithful household helpers. Each locomotive engineer controls energy equivalent to that of 100,000 men; each jet pilot of 700,000 men. Truly, the humblest American enjoys the services of more slaves than were once owned by the richest nobles, and lives better than most ancient kings. In retrospect, and despite wars, revolutions, and disasters, the hundred years just gone by may well seem like a Golden Age.'' - Hyman Rickover in 1957

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