Introduction to Synthetic Biology

1. Introduction to Synthetic Biology x23 Series Herbert Sauro http://sys-bio.org/bioencseee-423523486586-in-2013/

2. Syllabus Week 1/2: Essential Molecular Biology and Introduction a) What is life?b) Evolutionary time scalec) DNA, RNA and proteinsd) The cellular contexte) Engineering DNAf) What is Synthetic Biology?g) Applications and ethical issues Week 3: Modeling Synthetic Circuits a) The need for modeling in synthetic biologyb) Stochastic and deterministic modelsc) Models of gene regulatory networksd) Software and modeling techniquese) Example simulations

3. Syllabus Week 4/5: Synthetic Biology Circuits a) Basic circuit, repression and activationb) Feed-forward circuitsc) Switchesd) Oscillatorse) Logic gates Week 6/7: Assembling a System: case study to build a working system a) Design objectiveb) The componentsc) The simulationd) DNA assembly methodse) Testing

4. Syllabus Week 8: Components and Standardization a) Standards in Engineeringb) The need for standards in synthetic biologyc) Examples of existing standards, biobricks, SBOL, Registry, GenBank, etcd) Variety of components used in synthetic biology Week 9: Practical Issues in Creating Devices a) Computer aided design and workflowsb) Orthogonality, Robustness, Tunability, Compatibility, Fan-Out, Signal Impedancec) Noise in biological systems Week 10:

5. What is Life? Traditional View (Wikipedia): • The ability to move; plants turn toward light, sponges' collar cells' flagella turn round, fungi (exc. the little pot fungi, which have flagellate spores) and bacteria without locomotory apparatuses... huh. • The ability to respire, turning nutrients into energy. For life on Earth, this process is glycolysis, and the storage of energy is maintained by ATP. • Sensitivity to the outside world, and an ability to react. Lions maul you if you poke them with a stick, plants will grow their roots out, E. coli bacteria will change direction toward sugar and away from acid. • Growth is self-explanatory; seeds or spores turn into plants or fungi or whatever, cute babies turn into annoying teenagers, bacteria... huh. • Reproduction is also self-explanatory; amoebae undergo mitosis, plants release pollen to fertilise other plants, bacteria divide, mules and sterile humans... huh. • Respiration generates waste, which is excreted or otherwise removed from the organism. Diffusion is a legitimate way to do this. • To meet the above characteristics, the organism needs nutrition. Even plants are going to need water and minerals.

6. What is Life? Modern View: • “self-sustaining chemical system capable of Darwinian evolution.” : Carl Sagan, Bruce Jokosky • “self-sustaining system capable of Darwinian evolution.”

7. Minimal Life Form

8. Timeline 4.54 3.8 3.5 2.4 1.8 0.6 Billions of Years Humans Multicellular Organisms First Life Oxygen in Atmosphere Blue-green Algae Formation of Earth Eukaryotic Cells

9. Timeline }

11. Typical Bacterium

12. Typical Animal Cell

13. Typical Plant Cell

14. Eulena: Protist

15. Amoeba:Protist

16. Paramecium: Protist

17. Characteristics of Earth Life • Liquid/Gel state • Chemistry • Massively Parallel

18. Molecules • Small molecules • Source of energy or material, structural components, signal transmission, building blocks of macromolecules • Water, sugars, fatty acids, amino acids, nucleotides • Proteins • Main building blocks and functional molecules of the cell • Structure, catalysis of chemical reactions, signal transduction, communication with extracellular environment

19. Molcules • DNA • Storage and reproduction of information • RNA • Intermediary molecule between DNA and protein

20. Central Dogma • Sequence of nucleotides • Backbone is composed of sugars, linked to each other via phosphate bonds • Each sugar is linked to a base • Adenine (A), Thymine(T), Guanine (G), Cytosine (C)

21. The Double Helix • DNA is generally found in a double strand form • A and T, C and G form hydrogen bonds • Two strands with complementary sequences run in opposite directions • 5’ A-T-C-T-G-A 3’ • 3’ T-A-G-A-C-T 5’ • They are coiled around one another • to form double helix structure

22. Genomes

23. RNA • RNA is made of ribonucleic acids instead of deoxyribonucleic acids (as in DNA) • RNA is single-stranded • In RNA sequences, Thymine (T) is replaced by Uracil (U) • mRNA carries the message from genome to proteins • tRNA acts in translation of biological macromolecules from the language of nucleic acids to amino acids

24. Proteins • Proteins are chains of amino acids connected by peptide bonds • Often called a polypeptide sequence • There are 20 different types of amino acid molecules (each amino acid in the chain is commonly referred to as a residue) • Proteins carry out most of the tasks essential for life • Structural proteins: Basic building blocks • Enzymes: Catalyze chemical reactions that enable the mechanism transform forms of matter and energy to one another (metabolism) • Transcription factors: Genetic regulation, i.e., control of which protein will be synthesized to what extent

25. Amino Acids

26. 20 Amino Acids

27. Protein Structure

28. Protein Stucture

29. Size Variation http://www.rcsb.org/pdb/education_discussion/molecule_of_the_month/poster_quickref.pdf