1. Chapter 1 Cells and Genomes

2. 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

3. The universal features of cells on earth

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

5. All cells store their hereditary information in DNA

6. All cells replicate their DNA by templated polymerization

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

11. All cells use proteins as catalysts

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

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

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

17. The consumption of free energy is fundamental to life

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

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

20. Membrane transport proteins

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

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

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

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

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

30. 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.