BISC 499Special Topics

Origin of Life and Synthetic Biology

Units: 2

Fall 2018, Wed, Time:12 Noon-1:50PM

Location: RRI, room 121

Instructor: John Tower, PhD

Office: RRI 219C

Office Hours:Tues 10-11:50

Contact Info:Email (preferred method for contact)

Emails typically returned within 48hrs.

Phone 213-740-5384

Course Description

The question of how life first arose from inorganic materials has long fascinated scientists and the public. Both theoretical studies and laboratory research have provided insight into possible pathways for the evolution of the first cells. One hypothesis is that early life was RNA-based, potentially including self-replicating RNA molecules. More recently, scientists have attempted to create life in the laboratory, and have begun to engineer cells with properties not normally found in nature (synthetic biology) – for example, expanded genetic codes and novel amino acids. This class will include presentation and discussion of classic and recent papers from the primary research literature, as well as lectures by Dr. Tower and guest lecturers. The course is designed for undergraduates and beginning graduate students with previous coursework covering basic molecular biology and biochemistry. Each student will be responsible for presenting a paper to the class and leading the discussion. Topics will include:

- Generation of organic molecules from inorganic chemicals

- Comet and asteroid seeding of the earth

- Replicators and the primordial soup

- Origin of cells

- Synthetic biology – designer genomes and cells

Learning Objectives

Students are expected to gain an understanding of the basic concepts and the state of the field for origin of life and synthetic biology. Students will gain practical experience in critically evaluating primary research papers, and in presenting primary research papers to the class.

Syllabus for COURSE ID, Page 1 of 5

Recommended Preparation: BISC 220Lg or BISC 221Lg, BISC 320L, BISC 325 and BISC 330L.

Syllabus for COURSE ID, Page 1 of 5

Course Notes

Copies of lecture slides, discussion papers, background readings and other class information will be posted on Blackboard.

Required Readings and Supplementary Materials

Required readings and supplementary materials will be posted on Blackboard.

Description and Assessment of Assignments

Paper presentation (60%):will involve presenting a primary research paper to the class using PowerPoint format. Presentations will be graded on organization, background research, clarity of presentation, and reponses to class questions. Class participation (15%): is based on asking questions and participating in discussion during paper presentations. Questions (20%):each student will submit2 written questions about the paper to be presented and these will be collected and graded. Final exam (5%): students will be required to write a briefparagraph describing what they have learned about one of the course topics (origin of life or synthetic biology).

Grading Breakdown

Including the above detailed assignments, how will students be graded overall? Participation should be no more than 15%, unless justified for a higher amount. All must total 100%.

AssignmentPoints% of Grade

Paper presentation6060

Class participation1515

Questions2020

Final exam55

Total100100

Grading Scale (Example)

Course final grades will be determined using the following scale

A95-100

A-90-94

B+87-89

B83-86

B-80-82

C+77-79

C73-76

C-70-72

D+67-69

D63-66

D-60-62

F59 and below

Assignment Submission Policy

Each student must bring two written questions about the discussion paper to each class. The written questions will be collected at the beginning of class.

Grading Timeline

Grades for questions and paper presentations will be available on Blackboard by the next class meeting.

Additional Policies

Attendance at each class is expected. Missed classes will result in loss of questions points and class participation points for that class meeting.

Course Schedule: A Weekly Breakdown

Topics/Daily Activities / Readings and Homework / Deliverable/ Due Dates
Week 1
/ Over-view of origin of life. Student sign-up for paper presentation dates. / Background reading: Breaker&Joyce 2014 The Expanding View of RNA and DNA Function. Chemistry & Biology 21:1059-1065 / None
Week 2
/ The spark of life: The Miller-Urey experiments create organic molecules from inorganic materials /
Discussion papers: Miller 1953 A Production of Amino Acids Under Possible Primitive Earth Conditions. Science 117:528-529.
Miller & Urey 1959 Organic Compound Synthesis on the Primitive Earth. Science 130:245-251. /
2 questions re discussion papers due beginning of class
Week 3
/ Ancient aliens: The Murchison meteorite and seeding of earth from space / News article:
Discussion paper: Koga&Naraoka 2017 A new family of extraterrestrial amino acids in the Murchison meteorite. Scientific Reports 7:636 / 2 questions re discussion paper due beginning of class
Week 4
/ Whats so hot about thermal vents? / News article: Ghose2013 Origin of Life: Did a Simple Pump Drive
the Process? Live Science
News article: Lane & Page 2009 How life evolved: 10 steps to the first cells. New Scientist
Discussion paper: Lane & Martin 2012 The Origin of Membrane Bioenergetics Cell 151:1406-1416 / 2 questions re discussion paper due beginning of class
Week 5
/ Geology meets microsopy: The fossil record for cells / News article: Ghosh 2017 Earliest evidence of life on Earth 'found'. BBC Science & Environment.
Discussion paper: Dodd et al 2017 Evidence for early life in Earth’s oldest hydrothermal vent precipitates. Nature 543:60-65 / 2 questions re discussion paper due beginning of class
Week 6
/ Protocells: Formation of the first micelles and cells / Background reading: Schrum et al 2010 The Origins of Cellular Life. CSH PerspectBiol2:a002212
Discussion paper: Zhu&Szostak 2009 Coupled Growth and Division of Model Protocell Membranes. JACS 131:5705-5713 / 2 questions re discussion paper due beginning of class
Week 7
/ Sticking together: Non-enzymatic RNA replication / Discussion paper: Prywes et al 2016 Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides. eLife5:e17756 / 2 questions re discussion paper due beginning of class
Week 8
/ Molding life from clay: Surface effects on polymerization / Discussion paper: Ferris & Ertem1993 Montmorillonite Catalysis of RNA Oligomer Formation in Aqueous Solution. A Model for the Prebiotic Formation of RNA. JACS 115:12270-122275. / 2 questions re discussion paper due beginning of class
Week 9
/ Activating the monomers: diamidophosphate (DAP) phosphorylation of building blocks / News article: Scientists Find Potential “Missing Link” in Chemistry That Led to Life on Earth 2017 Scripps Res Inst
Discussion paper: Gibard et al 2018 Phosphorylation, oligomerization and self-assembly in water under potential
prebiotic conditions. Nature Chemistry 10:212-217. / 2 questions re discussion paper due beginning of class
Week 10
/ Self-splicing introns: The first ribozyme / Background reading: Cech 1990 Self-Splicing of Group I Introns. Ann Rev Biochem 59:543-68.
Discussion paper: Kruger et al 1982 Self-Splicing RNA: Autoexcision and Autocyclization of the Ribosomal RNA Intervening Sequence of Tetrahymena. Cell 31:147-157. / 2 questions re discussion paper due beginning of class
Week 11
/ RNA replicators in the lab – RNA-Catalyzed RNA
Polymerization / Background reading: Breaker&Joyce 2014 The Expanding View of RNA and DNA Function. Chemistry & Biology 21:1059-1065
Discussion paper: Johnston et al 2001 RNA-Catalyzed RNA Polymerization: Accurate andGeneral RNA-Templated Primer
Extension. Science 292:1319-1325 / 2 questions re discussion paper due beginning of class
Week 12
/ RNA replicators in the lab – self-replicating RNA / Discssion paper: Lincoln & Joyce 2009 Self-Sustained Replication of an RNA Enzyme. Science 323:1229-1232 / 2 questions re discussion paper due beginning of class
Week 13
/ Synthetic genomes / Discussion paper: Gibson et al 2010 Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329:52-56 / 2 questions re discussion paper due beginning of class

Week 14

/ Synthetic cells / Discussion paper: Kurihara et al 2015 A recursive vesicle-based model protocell with a primitive model cell cycle. Nature Comm 6:8352 / 2 questions re discussion paper due beginning of class

Week 15

/ Expanded genetic code / Background reading: Chin 2017 Expanding and reprogramming the genetic code. Nature 550:53-60
Discussion paper: Zhang et al 2017 A semi-synthetic organism that stores and retrieves increased genetic information. Nature 551:644-647 / 2 questions re discussion paper due beginning of class

FINAL

/ Final exam / Students will be asked to write a brief narratie paragraph describing what new they have learned about one of the course topics (Origin or life or Synthetic biology) / Date: For the date and time of the final for this class, consult the USC Schedule of Classes atclasses.usc.edu.

Statement on Academic Conduct and Support Systems

Academic Conduct:

Plagiarism – presenting someone else’s ideas as your own, either verbatim or recast in your own words – is a serious academic offense with serious consequences. Please familiarize yourself with the discussion of plagiarism inSCampusin Part B, Section 11, “Behavior Violating University Standards”policy.usc.edu/scampus-part-b. Other forms of academic dishonesty are equally unacceptable. See additional information inSCampusand university policies on scientific misconduct,

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