Biochemistry and Astrobiology, CH391L

Biochemistry and Astrobiology - CH391L - Spring 2012

Instructor: David W. Hoffman, Associate Professor, Dept of Chemistry & Biochemistry
Office hours: Monday noon-1 pm, Thursday 2-3 pm, or by appointment, in Welch 4.230C.
Email: dhoffman@mail.utexas.edu
Class meeting: Tuesday & Thursday at 11 am, in Welch 4.224
Class unique number: 52530

Class web page:   http://hoffman.cm.utexas.edu/courses/index_ab_sp12.html

Teaching Assistant: Cassidy Terrell (graduate student in biochemistry).
T.A.'s office hours: Tuesday 2-3 pm in Welch 5.262.
   or make an appointment by email to Cassidy at: crterrell@mail.utexas.edu

Rationale and description. The past decade has brought remarkable discoveries that demonstrate the extreme conditions under which life can exist. In parallel, earth-based observations and unmanned probes have provided new information regarding past and present conditions elsewhere in our solar system. During the next decade, there will be a vigorous search for the signs of extraterrestrial life, inside and outside our own solar system. An aim of this course is to provide the scientific background necessary to understand the strategies and observational tools that may be used in this search. The course should provide a review of some biochemical principles, along with some astronomy, earth history, and chemistry.

Organization. The course will be based on readings, class notes, and student-led in-class presentations. Grades will be based on 2 mid-term exams, homework assignments, an in-class presentation, and a final exam. Class attendance is expected.

Schedule for Spring 2012 (30 classes total)

Tues Jan 17    Introduction: Where are we, and how did we get here?
       solar system wiki    astrobiology primer (PDF) astrobiology wiki
       class notes (PDF)    class 1 notes (PPT) link to atlas of the universe

Thur Jan 19    Stars and elements.
       class notes (PDF) class notes (PPT)
       Read pages 741-747 in the astrobiology primer.
   Also, look at the stellar evolution wiki.
       HW questions #1 and #2 are due next Thursday (the questions are in the class notes).

Tues Jan 24    Finding exoplanets: Direct imaging methods. Radial velocity methods.
       Science magazine's history of the telescope cartoon (PDF)
       Science magazine's article on future big telescopes (PDF)
       detection of an exoplanet by the radial velocity method (PDF)
       class notes (PDF) class notes (PPT)
       homework (PDF) (Magrathea, radial velocity, transits) due the same day as exam 1

Thur Jan 26    Finding exoplanets II: Transit methods.
       class notes (PDF) class notes (PPT)
       link to NASA Kepler home page
       2011 Nature paper about Kepler-11 (PDF)
       link to exoplanet wiki page
       some study questions to do (PDF), mostly on units and solar system

Tues Jan 31    Interstellar medium. Water in our solar system. Tides.
       class notes (PDF) class notes (PPT)
At this point, you should have read sections 1 & 2 of the astrobiology primer (PDF):
      Section 1 is "Stellar Formation and Evolution"
      Section 2 is "Planetary Formation and Evolution"

Thur Feb 2 Making ATP. Bold Traveler bacteria.
   class notes (PDF) class notes (PPT)
   Science paper, Bold Traveler (PDF)

Tues Feb 7      Earth's orbital cycles. Milankovitch cycles.
   class notes (PDF) class notes (PPT)
       I think the Milankovich cycle wiki page is worth reading.

Thur Feb 9    Bacteria/archaea/eukaryotes.
       class notes (PDF) class notes (PPT)

Tues Feb 14    Early life, origin of ribosome.
   class notes (PDF) class notes (PPT)

       homework #3 (one page, PDF)    due the same day as exam #1

Thur Feb 16    mid-term exam #1

Tues Feb 21 Early life, life origins topics.
   class notes (PDF) class notes (PPT)
       M. Russell paper, origin of autotrophs at white smokers (PDF)

Thur Feb 23     Oxygen in the atmosphere.
   class notes (PDF) class notes (PPT)
       paper on "oxygen catastrophy" (PDF)

Tues Feb 28     Detecting life on exoplanets. More metabolism comments.
   class notes (PDF) class notes (PPT)

Thur Mar 1       Photosynthesis topics
   class notes (PDF) class notes (PPT)
       Blankenship (PDF)    Bjorn & Govindjee (PDF)

Tues Mar 6      Moons of Saturn.
   class notes (PDF) class notes (PPT)
       I thought the Titan wiki page (and links therein) is very good.

Thur Mar 8      Mars and methane.    class notes (PDF) class notes (PPT)
       link to article at NASA web site

March 10-18    Spring break

Tues Mar 20    Origin of eukaryotes. some notes (PDF)

Thur Mar 22    Rare earth hypothesis. Rare earth notes (PDF)

Tues Mar 27    mid-term exam #2

Thur Mar 29    Ken Bolster. Fermi Paradox and the Great Filter.
              Fermi Paradox slides (ppt)     questions to think about (PDF)

                        Mark Bradley. Global climate change.
                        Mark's slides (pptx)

Tues Apr 3    Will Montgomery and Neil Williams.
                         Space exploration and terra-forming.
                         Will and Neil's slides (pptx)

Thur Apr 5       Rachel Whittaker. Evolution of the atmosphere. Rachel's slides (pptx)
                         Josh Bryant. The Wood-Ljungdahl pathway for carbon fixation.
                         Josh's slides (PDF)

                         homework due April 19 (PDF)

Tues Apr 10 Dustin Holden. Mass spectrometry on the Mars Science Lab.
                         Dustin's slides (pptx)
                         Michael Ledbetter. Possible chemistry for life.    Micheael's slides (pptx)

Thur Apr 12    Manish Patel. Methanogens: How they work, and where to find them.
                         Manish's slides (ppt)
                         Sameer Prakash. slides (pptx)

Tues Apr 17    Nik Savage, Sarah Moench. Permian-Triassic extinction event.
                         Nik and Sarah's P-T extinction slides (pptx)

Thur Apr 19     Christina Davis, Katie Peth. Cretaceous-Tertiary (K-T) extinction event.
       Christina and Katie's K-T extinction slides (ppt)

Tues Apr 24    Jeff Li. Cambrian explosion. Jeff's slides (pptx)
Liz Gratton. RNA world hypothesis. Liz's slides (pptx)

Thur Apr 26    Eric Jones. Earth extremophiles that could survive in ET environments.
                          John Lin. Panspermia. John and Eric's slides (pptx)

Tues May 1     Sodium-dependent ATPase.
                          class notes (PDF) class notes (PPT)    Na dependent ATPase paper (PDF)

Thur May 3     Michelle Tran.   David Hoffman.
                  class notes (PDF) class notes (PPT)

Final exam: Covers the entire course. The final exam schedule is set by the registrar's office.
The final exam is scheduled for Monday, May 14, 9 am to noon.

Grading: Graded homeworks, midterm exams, final exam.

Your grade will be based on the total points you earn on mid-term exams, graded homeworks, and a final exam, divided by the number of possible points. Expect grades to be as follows:

   A    92 % of possible points ; A- 90% of possible points
   B+ 87% to 90% ; B 83% to 87% ; B- 80 to 83 %
   C+ 77% to 80% ; C 73% to 77% ; C- 70 to 73 %
   D+ 67% to 70% ; D 63% to 67% ; D- 60 to 63 %
   F   < 60 % of possible points

Students with disabilities may request appropriate academic accommodations from the Division of Diversity and Community Engagement, Services for Students with Disabilities, 471-6259.

Miscellaneous web links.

Daily science news: Science Daily   Astronomy Picture of the Day
The excellent History of Climate Change page at the American Institute of Physics site.