Astrobiology for Chemists & Biochemists

This is just a rough draft of the class web page.

CH364F (unique no. #####) and CH391L (unique no. #####). 

Instructor:  David W. Hoffman, Associate Professor, Dept of Chemistry & Biochemistry
Office hours:  To be determined, or by appointment, in Welch 4.230C.
Class meeting:  Tuesday & Thursday

Course 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.  The course is intended for students who are pursuing a degree in chemistry or biochemistry.  Prerequisites: Organic chemistry (CH310M, 318M, 320M or 328M) and at least one semester of biochemistry.

Class web page:  

Textbook:  There will assigned readings from various sources.   

Class attendance is expected. 

Exams will be given during the regular class time.


Thur Aug 29    Course organization.  Where are we, and how did we get here?
                         Read the solar system wiki page  and follow the links to the planet pages; also formation of the solar system.
                         Become familiar with the planets and major moons in our solar system. 
                         Look at the atlas of the universe  to see how our solar system fits into the galaxy.
                         The Hubble extreme deep field image can make you feel very small.                                

Tues Sept 3      Stars.  What are they?
                         Read the star wiki page  and  sun wiki page before class.
                         Read the  stellar evolution wiki page. 

                         Describing stars: apparent magnitude, absolute magnitude and luminosity.  
                         Hertzsprung-Russell diagram (color vs luminosity diagram)   
                         the OBAFGKM stellar classification system  
                         luminosity tutorial and questions 
                         Measuring distances to stars:  stellar parallax, main sequence fitting,  Cepheid variable stars
                         Distances to many stars are known from the Hipparcos parallax data. 
                         The Gaia satellite should expand on the Hipparcos measurements:  Gaia satellite overviewGaia satellite wiki
                         Also, for very long distances: type Ia supernovas, red shift, other methods.   

Thur Sept 8      Water and the circumstellar habitable zone.
                         Water, and its properties.                  
                         What happens to G, K and M-type stars as they age? 
                         Animation of habitable zone migration during the lifetime of a star 
                         Describe a star that will have planets for the longest habitable lifetime.
Tues Sept 10    Telescopes.  history of the telescope cartoon (PDF) 
                         Time magazine adaptive optics (PDF)    history of adaptive optics (PDF) 
                         List of large ground-based telescopes   Hobby-Eberly telescope 
                         Hubble space telescope wiki   recent adaptive optics article  

                         Telescopes of the near future:  Giant Magellan telescope    Large telescopes (PDF) 
                         Webb space telescope wiki    Webb space telescope NASA page 
Thur Sept 12    Introduction to extrasolar planets (exoplanets) and their detection
                         exoplanet wiki    exoplanet detection wiki  
                         Methods of detecting exoplanets:
                                 Radial velocity method.  radial velocity wiki   Doppler spectroscopy wiki   Radial velocity animation      
                                 Transit method   transit method wiki  
                                 Transit timing variation  transit timing variation wiki
                                 Detection of exoplanets by astrometry                
                                 Detection of exoplanets by gravitational microlensing  

Tues Sept 17    Papers from Science exoplanet feature (May 2013):
                                 introduction (PDF) 
                                 more introduction (PDF) 
                                 exoplanet habitability (PDF) 
                                 exoplanet properties (PDF) 
                                 planets of Kepler 62 (PDF) 
                                 glossary (PDF) 
                         Kepler space telescope wiki page  
                         MEarth transit detection project 
                         Nature paper Kepler-11 (PDF) 
                         Gliese 581 wiki page    Gliese 667 wiki page  
                         The transiting exoplanet survey satellite (TESS)  will follow Kepler.
Thur Sept 19    Drake equation, Fermi paradox         
Tues Sept 24    Mid-term exam #1 

Thur Sept 26    If there is life on Mars, where would it be?  Overview of Mars. 
                         Mars wiki page   climate of Mars (wiki)   water on Mars   geology of Mars 
                         atmosphere of Mars (wiki)    Mars lost much of its original atmosphere (Science Daily)     
                         Mars Science Laboratory 
                         Mars Science Laboratory: summary of important events 

Tues Oct 1       How could life survive on Mars? 
                         Review of metabolism of earth's prokaryotes.  What's universal to all known life?
Thurs Oct 3      Life deep underground.
                         Metabolism of prokaryotes that live far below earth's surface.
                         Uranium powered bacteria.  Bold traveler paper (PDF)   supplementary material (PDF)      
                         Deep subsurface life  Science Daily article  and the associated  Science paper (PDF) 
                         Nature paper on deep subsurface water (PDF)    
Tues Oct 8       Acquiring carbon for growth: Calvin cycle, reductive TCA cycle and Wood-Ljungdahl pathway.
                         Calvin cycle wiki 
                         reductive TCA cycle wiki   reductive TCA cycle paper (PDF)                         
                         Wood-Ljungdahl pathway (PDF)
Thur Oct 10     Introduction to Europa.  Europa wiki page  
                         If there is life on Europa, where would it be?  How would it survive?   
                         Life in deep oceans:  photosynthesis by green sulfur bacteria (PDF) 
                         Photosynthesis using blackbody radiation.  blackbody radiation calculator 
                         Absorption spectrum of water.  
                         Energy capture by bacteriorhodopsin.   bacteriorhodopsin (PDF)    
                         Habitable moons as a place to find life: What are the properties of an ideal habitable moon?  

Tues Oct 15     Where else might there be life in our solar system?  
                         Where is there liquid water in our solar system?
                         What about tides as an energy source?   tide wiki page   tidal bulge simulator  
Thur Oct 17     Saturn's moons Titan and Enceladus.

Tues Oct 22     Mid-term exam #2.

Thur Oct 24     Understanding ET life requires an understanding of earth's life & its history.
                        earth history wiki    evolutionary history of earth's life wiki   timeline of human evolution wiki
                        Earth's O2 atmosphere.   Abelson's oxygen paper (PDF) 
                        Requirements for an O2 atmosphere. 
Tues Oct 29     Origin of life & early life topics.  
                         Features of the Last Universal Common Ancestor (LUCA).
                         Lane LUCA paper (PDF)    LUCA wiki page   

Thur Oct 31     Origin of metabolism and early life papers:
                               Lane and Martin origins of membrane energetics (PDF) 
                               Russell and Martin, origin of cells (PDF) 
                               Russell and Martin, vents (PDF)  
                               Russell disequilibrium (PDF) 
                               Origin of metabolism (PDF) 
                        Early enzymes:  Carbon fixation, nitrogen fixation, ferredoxin, pyruvate synthase, electron transport chain.                   
                               acetyl CoA synthase (PDF)     more acetyl CoA synthase (PDF) 
                               corrin iron-sulfur protein (PDF)      
                               Nitrogenase and nitrogen fixation        
                               pyruvate synthase 
                               sodium ATP synthase (PDF)        
                               evolution of carbon fixation (PDF) 
                               early carbon fixation (PDF)                             
                               hydrogenase wiki page    methanogen wiki page   hydrogenases of methanogens (PDF)          
Tues Nov 5    Origin of the genetic code, tRNA and translation.          

Thur Nov 7    Origin of photosynthesis.
                               Blankenship's evolution of photosynthesis paper (PDF)
                               Evolution of the oxygen evolving complex    
                               Evolution of Rubisco.
Tues Nov 12   Origin of eukaryotes and complex life. 
                               Hydrogen hypothesis.   
                        Earth's carbon cycle, and the importance of plate tectonics.

Thur Nov 14   Methane on Mars:  What does it mean?
                        Mars meteorites and panspermia.
Tues Nov 19   Mid-term exam #3
Thur Nov 21   Milankovitch cycles.  Milankovitch cycle wiki page 
                        Climate change.  Anoxic oceans. 
                        Greenhouse effect.   greenhouse effect wiki page   runaway greenhouse effect (PDF) 
Tues Nov 26   Spectroscopy of exoplanet atmospheres and surfaces.     
                        Spectrum of an exoplanet (Science Daily, 11july2013)         
                        exoplanet atmospheres (wiki)      exoplanet atmosphere (Science Daily) 

Thur Nov 28     Thanksgiving holiday
Tues Dec 3     Rare earth hypothesis.                       

Thur Dec 5     Habitability of planets orbiting red dwarfs, brown dwarfs, and rogue planets.     
                       Barnard's star      rogue planet letter to nature (PDF)                
Final exam:  Covers the entire course, and is required.  The date and time are set by the UT Registrar.
Grading:  Midterm exams are 100 pts each; the final exam will be 150 pts.
Your grade will be based on the total points you earn on the midterm exams, plus the final exam. 
The final exam is required.  Grades will 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
   Incomplete grades will only be given in the case of truly extraordinary circumstances.

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

Notice regarding accommodations for religious holidays:  “By UT Austin policy, you must notify me of your pending absence at least fourteen days prior to the date of observance of a religious holy day.  If you must miss a class, an examination, a work assignment, or a project in order to observe a religious holy day, you will be given an opportunity to complete the missed work within a reasonable time after the absence.”

Regarding exam regrades:  I you believe there has been an error in grading your exam, I am willing to consider re-grade requests. Submit regrade requests in writing along with your graded exam; include a brief written description of the grading error.  Re-grade requests should be submitted within one week of when the exam is returned.

UT Policy on Scholastic Dishonesty:  In promoting a high standard of academic integrity, the University broadly defines scholastic dishonesty—basically, all conduct that violates this standard, including any act designed to give an unfair or undeserved academic advantage, such as falsifying academic records, cheating, plagiarism, unauthorized collaboration, collusion, misrepresenting facts (e.g., providing false information to postpone an exam, obtain an extended deadline for an assignment, or even gain an unearned financial benefit). Any other acts (or attempted acts) that violate the basic standard of academic integrity (e.g., multiple submissions—submitting essentially the same written assignment for two courses without authorization to do so).  Several types of scholastic dishonesty—unauthorized collaboration, plagiarism, and multiple submissions—are discussed in more detail on this Web site to correct common misperceptions about these particular offenses and suggest ways to avoid committing them.  For the University’s official definition of scholastic dishonesty, see  Section 11-802, Institutional Rules on Student Services and Activities

Recommendations regarding emergency evacuation from the Office of Campus Safety and Security, 512-471-5767, :
    -  Occupants of buildings on The University of Texas at Austin campus are required to evacuate buildings when a fire alarm is activated. Alarm activation or announcement requires exiting and assembling outside.
    -  Familiarize yourself with all exit doors of each classroom and building you may occupy.  Remember that the nearest exit door may not be the one you used when entering the building.
    -  Students requiring assistance in evacuation shall inform their instructor in writing during the first week of class.
    -  In the event of an evacuation, follow the instruction of faculty or class instructors.
    -  Do not re-enter a building unless given instructions by the following: Austin Fire Department, The University of Texas at Austin Police Department, or Fire Prevention Services office.
    -  Behavior Concerns Advice Line (BCAL):  512-232-5050
    -  Information regarding emergency evacuation routes and emergency procedures can be found at:

Miscellaneous stuff: 
   Science news at  Science Daily 
   Astronomy Picture of the Day 
   Diagram of the electromagnetic (EM) spectrum (PDF)  
   Some excellent animations 

          The astrobiology primer (PDF)  provides a general introduction to astrobiology.  Its from 2006,
                         so its not entirely up-to-date, but is certainly worth reading.

Positive thought:  If you can't fix all the world's problems, at least try to make it a slightly better place, one day at a time, one person at a time, every day.

Other possible topics:

Origin and evolution of the genetic code.
Origin and evolution of the ribosome and translation.
Composition of exoplanets.  Gleise 436b 
Evolution of archaeal membranes (PDF) 
resurrecting ancient proteins (PDF) 
Battling entropy.

Chandra x-ray telescope and galactic center.

HW problem ideas:

Stars & planets:
    How long would a transit of earth last, if seen by a distant observer?
    Detecting a Jupiter by radial velocity.
    delta G and equilibrium
    membrane transport
    IR and photosynthesis
    bacteriorhodopsin as a proton pump, powered by IR, in a rock.
         converting thermal energy to chemical energy to information.

what's the maximum pH gradient that can be established by capturing the energy of an IR photon?

transits => planet size
radial velocity => planet mass

Rossman fold, NADH oxidation, enzyme mechanism of a dehydrogenase.
describe an ideal habitable moon (mass, distance to star, distance to planet)

Origin of life:

Useful links, images and ideas:

Getting around the tidal locking problem in M & K-type stars:
    A tidally-locked planet in habitable zone, with large tidally-locked moon in 24 hour orbit.
    Star rises and sets every day on the tidally locked moon.
    Tidal flexing keeps moon geologically active (see Io, for example).

Mars Science Laboratory wiki page

New Horizons probe arrives at Pluto on July 14, 2015  

Kepler's laws of planetary motions

atmospheres of planets in our solar system

calculating temperature of a planet (use greenhouse effect, albedo

What is the (approximate) minimum radial velocity that is currently detectable by HARPS? 
What is the maximum radial velocity of an earth-size planet orbiting
      within the habitable zone of a K-type star? 
What is the maximum radial velocity of a "super earth" with 4x earth's mass, orbiting a star
      with 80% of the sun's mass?

global warming art dot com