Handout

From Biolk483

//These notes are verbatim what Dr. Stillwell gave us on this first day because he wasn't sure he would be able to see well enough to write on the board. //Note: text in italics was extracted from class notes

• Biochemistry is the study of the molecular basis of life.
• This is not a simple problem but it is a solvable problem.
• The time will come when we know everything about life at the molecular level.
• When I was in graduate school, it was predicted that they were close to developing a computer simulation of the bacteria E. coli. And this was before the computer age. We are further from that goal now than we were then. The more we know the more we don't know.
• We will discuss structure, organization, and function of living matter in molecular terms.

Contents 1 Are we close? 2 What is the definition of life? 3 Thread of Life 4 Origin of Life

Are we close?

• We have now sequenced the entire human genome --3billion base pairs. That using the single letter cod would fill the entire Encyclopedia Britannica. Does this not tell us everything we need to know? No, the DNA sequence is static. It cannot address the question related to dynamic interactions.
• Static vs. Dynamic
  • Static is what is there.
  • Dynamic involves poorly understood molecular interactions.
• Questions need to be addressed --How does a seemingly random collection of inanimate molecules come together to give a dynamic living system?

What is the definition of life?

• It is a collection of properties.
• DOG, VIRUS, ROCK
  • If you started to take properties away from the dog eventually the dog would die and have no more life than a rock. Could you then take the properties that are removed from the dog and put them in the rock and make the rock live? If so what are these minimal properties for life?
• For most of history this question was easy --VITALISM (a basic difference between living and non-living: a vital spirit imparted by God
  • Vitalism is based on a spirit imparted by god. It cannot be isolated nor can it be studied. Therefore living and non-living entities are totally different. The concept of a spirit does not allow the study of life.
• This concept was challenged first by the German chemist Wohler in 1828.
  • He heated the inorganic rock ammonium cyanide and produced urea.
  • It was believed at the time that urea could only be made by a living kidney.
  • This was the beginning of modern biochemistry.
• A few years later in 1836 Schwann developed the cell theory that he published at age thirty. He received so much grief from the scientific community (read: chemists) that he quit science and never published again.
• Later in the 1800s Charles Darwin developed the concept of evolution. And modern biology was on its way.
• In the 1890's a branch of biology called synthetic biology was developed. Its leader was LeDuc who mixed solutions of different densities together and took pictures of them. They looked so much like living mushrooms that mycologists (those who study mushrooms) of the day actually placed these artifical mushrooms into biological classifications. Clearly they weren't living. This emphasized the importance between appearance and actual function.
• So is it appearance or substance? Substance, so we find a thread of life....

Thread of Life

• This is the biochemical theme that connects all living organisms. Biochemistry is more important than gross appearance. All cells that exist on planet Earth now or ever share the same basic biochemical themes.
  • They are more similar than different.
  • We want to understand the thing that makes us all similar.
• So viatalism was finally put to rest --or was it? Every so often vitalism which is based on faith reappears:
  • Creationism
  • Intelligent Design
• If vitalism, creationism and intelligent design were true there would be no point in studying biochemistry.

Origin of Life

• A major question today is "are we alone?" Does life exist anywhere else in the universe other than planet Earth?

Origin of the Universe	12-15 Billion years ago
Formation of Earth	4.5-4.6 BYA
Liquid Water Appears	~4.4 BYA
Chemical Evolution	4.0-4.4 BYA
Oldest Rock (Isua Greenland as far as man can go)	4.05 BYA
Oldest Microfossil (?)	4.0 BYA
First clear microfossil	3.5 BYA
Origin of Eukaryotes	2.0 BYA
Origin of multi-cellular organisms	~0.9 BYA

• Therefore life evolved between 4.4 and 3.5 BYA.
• We could be the left-overs of another planet
  • Pansperia: transfer of life between planets
• Once organic stuff was used up by single cell organisms, photosynthesis began and the oxygen output killed most everything. Somethings survived where there was no oxygen, some were adopted by organisms with photosynthetic abilities (i.e. the mitochondria).
• When a photosynthetic capable organism adopted an organism that could use oxygen, there became organisms that could use both and become multicellular.

• Question is there only one genesis or one genesis? Is life created easily or with great difficulty? Did life begin on earth or somewhere else and was spread to earth (panspermia)?
• Basic Assumptions:

1. Life on earth began from a single ancestral cell. If there were multiple origins there would be multiple biochemical themes.
2. All life in the universe will have principles similar to life on earth. Life will be based on C, H, O, N. The elemental composition of all parts of the universe are the same and is abundant in these elements.
3. Life is based on liquid water. Therefore NASA is looking for the appearance of water either in the present or the past on various planets and moons in our solar system. We cannot envision life without liquid water. If there is non-water-based life in the universe we would not recognize it as life.
4. Time domains we assume that basic biochemical events will occur on time scales similar to what they are on earth.
5. Reactions must be catalyzed so that all reactions occur within a similar time frame. (Need of enzymes.)
6. Information storage --need of nucleic acids or something similar.
7. Energy currency similar to ATP.
8. Need of barrier membrane for containment and separation; cell size is limited by rate of diffusion in water.
9. Biological polymers: proteins, nucleic acids, polysaccharides, "membranes" (in parentheses because it is not really a polymer)
10. Energetically open system need to bring in energy from the outside to maintain life.