1. Chapter 1 Cells and Genomes

2. Definition of Life Textbook definition -intricately organized chemical factories that take in matter from their surroundings and use these new materials to generate copies of themselves NASA definition - a self-sustained chemical system capable of undergoing Darwinian evolution

3. A few more definitions of life Version 1 - minimalist; life is a self-sufficient system maintained by replication and subject to change by mutation. Thus the simplest form of life is an assemblage of nucleic acids sustained by an external source of nutrients (to provide energy), its integrity preserved by the binding of biopolymers to a mineral surface Version 2 -posits a semipermeable barrier (a membrane) to maintain the integrity of a primitive living system Version 3 -requires the presence of the molecular machinery (proteins) to metabolize ingested nutrients. In this case, the monomers essential to the process of living are the products of metabolism; they are not provided by some external source

4. A simplified time flow of the origin of life Origin of Earth --------------------------------4.5 billion years ago Oldest rock ------------------------------------3.9 billion years ago Molecular evolution Transition to life First cell ----------------------------------------3.5 billion years ago 1. Life originated from inanimate matter as a spontaneous and continuous increase of molecular complexity. 2. The chemical process(es) of transition to life can be reproduced in the laboratory with the presently available chemical techniques and methods. 3. This can be implemented in a reasonable experimental time span.

5. An arbitrary scale of complexity towards the emergence of life The main assumption held by most scientists about the origin of life on earth is that life originated from inanimate matter through a spontaneous and gradual increase of molecular complexity Cells Metabolic networks Polymer complexes Macromolecules Biomonomers Molecules Atoms

6. Living organisms appear extraordinarily diverse, yet all living things are made of cells and these units of living matter all share the same machinery for their most basic functions Astonishing variety in individual particulars; astonishing constancy in fundamental mechanisms “What is true of E. coli is also true of the elephant” - Jacques Monod, 1971

7. Study of living organisms is closely tied with their origins - all living organisms are made of cells - all organisms and all cells descended from a common ancestor through evolution by natural selection - present day molecules are a rich source of information about the course of evolution

8. The universal features of cells on earth

9. Each species reproduces itself faithfully. This phenomenon of heredity is a central part of the definition of life.

10. All cells store their hereditary information in DNA

11. All cells replicate their DNA by templated polymerization

13. All cells transcribe portions of their hereditary information into RNA

16. All cells use proteins as catalysts

18. This feedback loop is the basis of the autocatalytic, self-reproducing behavior of living organisms

19. All cells translate RNA into protein in the same way

21. The fragment of genetic information corresponding to one protein is one gene

22. The consumption of free energy is fundamental to life

23. All cells function as biochemical factories dealing with the same basic molecular building blocks

24. All cells are enclosed in a plasma membrane across which nutrients and waste materials must pass

25. Membrane transport proteins

27. A living cell can exist with fewer than 500 genes

28. Proc Natl Acad Sci U S A. 2006 Jan 10;103(2):425-30.

29. Metabolic pathways and substrate transport mechanisms encoded by M. genitalium Glass, John I. et al. (2006) Proc. Natl. Aad. Sci. USA 103, 425-430

30. The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella Science 314:267 (2006)

34. Science 317: 632 – 638 (Aug 3, 2007)

35. July 2007 Better Biofuels Using synthetic biology, LS9 custom-makes hydrocarbons. By Neil Savage The U.S. Department of Energy has set a goal of replacing 30 percent of gasoline used in the United States with fuels from renewable biological sources by 2030. So it is hardly surprising that some biotech startup companies are positioning themselves to take advantage of an anticipated booming biofuels market. While much of the focus is on etha­nol, LS9 of San Carlos, CA, is using relatively new "synthetic biology" techniques to engineer bacteria that can make hydrocarbons for gasoline, diesel, and jet fuel. Hydrocarbon fuels are better suited than ethanol to existing infrastructure, and their manufacture would require less energy. LS9 is at a very early stage, but it has brought together leaders in synthetic biology and industrial biotech­ nology. The company is equipping microbes with gene pathways that play a role in energy storage in other microbes, plants, and even animals. Other startups, such as Amyris of Emeryville, CA, and SunEthanol of Amherst, MA, are also trying to use synthetic biology to develop biofuel­-producing microrganisms. LS9's microbes produce and excrete hydrocarbons that are useful as fuels, says Stephen del Cardayre, vice president for research and development. Now the company is working to customize the microbes' products and boost outputs. "We certainly have gone beyond what we think anybody else was even thinking of doing" in terms of producing hydrocarbons, says George Church, a geneticist at Harvard Medical School and an LS9 cofounder.