Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

1. CHEME 355 Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216. “The first pillar of life is a Program. By program I mean an organized plan that describes both the ingredients themselves and the kinetics of the interactions among ingredients as the living system persists through time. For the living systems we observe on Earth, this program is implemented by the DNA that encodes the genes of Earth's organisms and that is replicated from generation to generation, with small changes but always with the overall plan intact. The genes in turn encode for chemicals--the proteins, nucleic acids, etc.--that carry out the reactions in living systems. It is in the DNA that the program is summarized and maintained for life on Earth.”

2. “The second pillar of life is IMPROVISATION. Because a living system will inevitably be a small fraction of the larger universe in which it lives, it will not be able to control all the changes and vicissitudes of its environment, so it must have some way to change its program. If, for example, a warm period changes to an ice age so that the program is less effective, the system will need to change its program to survive. In our current living systems, such changes can be achieved by a process of mutation plus selection that allows programs to be optimized for new environmental challenges that are to be faced.” CHEME 355 Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

3. “The third of the pillars of life is COMPARTMENTALIZATION. All the organisms that we consider living are confined to a limited volume, surrounded by a surface that we call a membrane or skin that keeps the ingredients in a defined volume and keeps deleterious chemicals--toxic or diluting--on the outside. Moreover, as organisms become large, they are divided into smaller compartments, which we call cells (or organs, that is, groups of cells), in order to centralize and specialize certain functions within the larger organism.” CHEME 355 Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

4. CHEME 355 Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216. “The fourth pillar of life is ENERGY. Life as we know it involves movement--of chemicals, of the body, of components of the body--and a system with net movement cannot be in equilibrium. It must be an open and, in this case, metabolizing system. Many chemical reactions are going on inside the cell, and molecules are coming in from the outer environment--O2, CO2, metals, etc. The organism's system is parsimonious; many of the chemicals are recycled multiple times in an organism's lifetime (CO2, for example, is consumed in photosynthesis and then produced by oxidation in the system), but originally they enter the living system from the outside, so thermodynamicists call this an open system. Because of the many reactions and the fact that there is some gain of entropy (the mechanical analogy would be friction), there must be a compensation to keep the system going and that compensation requires a continuous source of energy. The major source of energy in Earth's biosphere is the Sun--although life on Earth gets a little energy from other sources such as the internal heat of the Earth--so the system can continue indefinitely by cleverly recycling chemicals as long as it has the added energy of the Sun to compensate for its entropy changes.”

5. “The fifth pillar is REGENERATION. Another system for regeneration is the constant resynthesis of the constituents of the living system that are subject to wear and tear. For example, the heart muscle of a normal human beats 60 times a minute--3600 times an hour, 1,314,000 times a year, 91,980,000 times a lifetime. No man-made material has been found that would not fatigue and collapse under such use, which is why artificial hearts have such a short utilization span. The living system, however, continually resynthesizes and replaces its heart muscle proteins as they suffer degradation; the body does the same for other constituents--its lung sacs, kidney proteins, brain synapses, etc.” CHEME 355 Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

6. CHEME 355 Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216. “The sixth pillar is ADAPTABILITY. Improvisation is a form of adaptability, but is too slow for many of the environmental hazards that a living organism must face. For example, a human that puts a hand into a fire has a painful experience that might be selected against in evolution--but the individual needs to withdraw his hand from the fire immediately to live appropriately thereafter. That behavioral response to pain (a reflex) is essential to survival and is a fundamental response of living systems that we call feedback.”

7. “Finally, and far from the least, is the seventh pillar, SECLUSION. By seclusion, in this context, I mean something rather like privacy in the social world of our universe.” CHEME 355 Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216.

8. CHEME 355 Koshland, D.E. (2002) The seven pillars of life. Science 295: 2215-2216. “At the present time the way in which mutation and selection (survival of the fittest) has worked over evolutionary time no longer seems to apply to Homo sapiens. We have become more compassionate, less demanding. Perhaps a newer approach--longer life and deliberate changes in the program by a supreme council of wise Solomons--could be substituted for the cruder survival-of-the-fittest scenario. I do not necessarily advocate such a drastic change in the current mechanism of improvisation, which has served us well over the centuries, but am only pointing out that there is the possibility to change particular mechanisms as long as we maintain the pillars.”

9. CHEME 355 Engineering/Technology "All around I see evidence of the impact of science on society. This is so obvious and so well known that little more remains to be said about it. Science and the technologies it has spawned form the basis of all human activity, from the houses that we live in, the food that we eat, the cars that we drive, to the electronic gadgetry in almost every home that we use to remain informed and entertained.” Brenner, S. (1998) The impact of science on society. Science 282: 1411-1412.

10. CHEME 355 Genotype - Phenotype Correlation The April 1998 issue of Life magazine ran a cover story, complete with a double-helix spanning the length of the page, boldly titled "Were You Born That Way?" The subtitle left no doubt about the answer: "Personality, temperament, even life choices. New studies show it's mostly in your genes.” Allen, G.E. (2001) Is a new eugenics afoot? Science 294: 59-61.

11. Phenotype. In the mid-1800s, a monk named Gregor Mendel, working in Brno in the Czech Republic, observed that the offspring of certain plants had physical characteristics similar to the physical characteristics of the plants' parents or ancestors. Mendel set out to examine and quantify the physical traits in pea plants (because of their speedy reproductive cycles) in an attempt to predict the traits that would occur in future generations. Mendel counted many thousands of instances of seven different traits, including plant height, flower color and position, seed color and shape, and pod color and shape, and concluded that certain particles or "factors" were being transmitted from parent to offspring and so on, thus providing a connection from one generation to the next. Mendel suggested that these factors were directly responsible for physical traits. His interpretation of the experimental data further suggested that each individual had not one, but two factors for each trait, and that these factors interacted to produce the final physical characteristics of the individual. CHEME 355 Geneticist: A gene is a trait

12. CHEME 355 Systems Biologist: A gene is a component in a network of reciprocal interactions between cells and environment

13. CHEME 355 Evolutionary Biologist: A gene is an agent of change

14. CHEME 355 It is sequencing the genomes of other animals to help biologists better understand the construction of the human genome. These genome databases are new frameworks for organizing all biological and medical knowledge, much as the periodic table of elements organizes all of chemistry. Humans have far fewer genes than was generally expected to be the case. The fruit fly has almost 14,000 genes, the roundworm 19,000, and humans only 30,000 or so.

15. CHEME 355 About the only thing humans have in common with mice is that we are fellow mammals. Yet, of the 26,000 confirmed human genes, only 300 had no counterpart in the mouse. On this basis, the chimpanzee, our closest relative, is expected to have essentially the same set of genes as humans.

16. CHEME 355 Pathologist: A gene is a mutation

17. CHEME 355 Gerontologist: Aging may be caused by genes wearing out

18. Recombinant DNA Technology. A plasmid and the gene of interest are both cut with the same restriction endonuclease. The plasmid and gene now have complementary "sticky ends." They are incubated with DNA ligase, which reforms the two pieces as recombinant DNA. Recombinant DNA is allowed to transform a bacterial culture, which is then exposed to antibiotics. All the cells except those which have been encoded by the plasmid DNA recombinant are killed, leaving a cell culture containing the desired recombinant DNA. DNA cloning allows a copy of any specific part of a DNA (or RNA) sequence to be selected among many others and produced in an unlimited amount. This technique is the first stage of most of the genetic engineering experiments: production of DNA libraries, PCR, DNA sequencing, et al. CHEME 355 Biotechnology: A Gene is a Product to Manufacture at Scale

19. CHEME 355 Intellectual Property A gene is a proprietary product (research university)

20. CHEME 355 Society A gene is a political issue

21. Genetic flow of information CHEME 355

22. CHEME 355 Technological advances The preceding fifty years has been a time of rapid and profound technological change. Elucidation of the genetic flow of biological information (i.e. information flow from DNA to RNA to protein) has provided for: development of recombinant DNA technology rise of molecular cell biology advent of intellectual property (in biology and medicine) development of the biotechnology industry development of transgenic technologies (including human gene therapy) elucidation of the modern definition of stem cells advent of mammalian cloning technology

23. CHEME 355 The Requirements of Genetic Material Once it had been accepted that there was genetic transmission of traits, the search began for the factor that carried the information. It was established that the following characteristics were required of genetic material: It must be able to replicate, in order to be in each cell of a growing organism. It must be able to control expression of traits: traits are determined by the enzymes and proteins that act within us; these proteins are determined by their sequences; therefore, the genetic material must be able to encode the sequence of proteins.

24. Avery, Macleod, McCarty Proof linking chromosomes and traits Chromosomes Technology Miescher Griffith Mendel 1940 1943 1860 1900 Watson, Crick, Wilkins, Franklin Hershey, Chase Chargoff 1952 1953 CHEME 355 The Search for Genetic Material

25. CHEME 355 • Hereditary Material is Bound on Chromosomes • At the turn of the century, two developments in technology allowed scientists to observe material inside the cell nucleus: the construction of increasingly powerful microscopes and the discovery of dyes or stains that selectively colored the various components of the cell. Long, thin, rod-like structures, which tended to become colored when the cell was treated with certain stains, called chromosomeswere observed in the nucleus. • In addition: • The number of chromosomes in any cell appeared to double immediately prior to mitosis. • Germ cells appeared to have exactly half of the number of chromosomes found in somatic cells. • The fertilization of an egg with a sperm cell produces a diploid cell called a zygote, which has the same number of chromosomes as the somatic cells of that organism.

26. CHEME 355 Proof that the chromosomes were Mendel's hereditary factors did not come until 1905. Microscopic observations discovered the sex chromosomes. These chromosomes were named "X" and "Y." Gender was shown to be the direct result of a specific combination of chromosomal material, and sex became the first phenotype (physical characteristic) to be assigned a chromosomal location - specifically the X and Y chromosomes. Quantitative analysis of chromosomes showed a composition of about 40% DNA and 60% protein. At first, it seemed that protein must be responsible for carrying hereditary information, since not only is protein present in larger quantities than DNA, but protein molecules are composed of twenty different subunits while DNA molecules are composed of only four. It seemed clear that a protein molecule could encode not only more information, but a greater variety of information, because it possessed a substantially larger collection of ingredients with which to work.

27. The Transforming Principle - DNA Might be the Genetic Material DNA was first identified in 1868 by Friedrich Miescher, a Swiss biologist. He called the substance nuclein, noted the presence of phosphorous, and separated the substance into a basic part (which we now know is DNA) and an acidic part (a class of acidic proteins that bind to basic DNA). In 1943, Oswald Avery, Colin Macleod, and Maclyn McCarty, at the Rockefeller Institute, discovered that different strains of the bacterium Strepotococcus pneumonae could have different effects on a mouse. One virulent strain could kill an injected mouse, and another avirulent strain had no effect. CHEME 355 DNA is the genetic material, Avery et al. 1943

28. CHEME 355 DNA is the genetic material, transfection

29. CHEME 355 DNA is the genetic material, mutation

30. CHEME 355 Genetic flow of information is carried out inside of cells

31. CHEME 355 Genetic flow of information is carried out inside of cells

32. CHEME 355 Chromosomal defects; point mutations

33. CHEME 355 Genotype-phenotype

34. CHEME 355 Post-mortem x-ray OI type II OSTEOGENESIS IMPERFECTA Definition Clinical syndromes Demographics Prominent phenotype - bone weakness - abnormal mineralization Likely candidate for mutation? Type I collagen!

35. CHEME 355 Collagen structure & biosynthesis / biomineralization Structure Biosynthesis

36. CHEME 355 Initial Studies Penttinen, R.P., Lichtenstein, J.R., Martin, G.R., and McKusick, V.A. (1975) Abnormal collagen metabolism in cultured cells in osteogenesis imperfecta. Proc Natl Acad Sci U S A 72:586. Barsh, G.S., and Byers, P.H.(1981) Reduced secretion of structurally abnormal type I procollagen in a form of osteogenesis imperfecta. Proc Natl Acad Sci U S A 78:5142. Barsh, G.S., David, K.E., and Byers, PH. (1982) Type I osteogenesis imperfecta: a nonfunctional allele for pro alpha 1 (I) chains of type I procollagen. Proc Natl Acad Sci U S A 79:3838. Chu, M.L., Williams, C.J., Pepe, G., Hirsch, J.L., Prockop, D.J., Ramirez, F. (1983) Internal deletion in a collagen gene in a perinatal lethal form of osteogenesis imperfecta. Nature 304:78.

37. Two Classes of Mutation Structural and Null CHEME 355

38. Gly Asp • Glycine mutations are the most common structural mutations • Gly - X - Y - Gly - X - Y • Ala, Asp, Arg, Ser, Cyc, Trp, Val, Tyr, Term Asp Gly G A T C G A T C Gly Gly Gly Gly CHEME 355 Normal Abnormal

39. CHEME 355 Inheritance patterns New Accident

40. OI IV OI II CHEME 355 Inheritance patterns Somatic Mosaicism

41. OI II OI II CHEME 355 Inheritance patterns Gonadal Mosaicism

42. Gly Asp ? G A T C G A T C Post-mortem x-ray image CHEME 355