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.
Email: dhoffman@mail.utexas.edu
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: http://hoffman.cm.utexas.edu/courses/index_ab_f13.html
Textbook: There will
assigned readings from various
sources.
Class attendance is
expected.
Exams will be given during the
regular class time.
Schedule
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 overview, Gaia 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)
Ferredoxin
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,
http://www.utexas.edu/diversity/ddce/ssd/
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, http://www.utexas.edu/safety/ :
- 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:
www.utexas.edu/emergency
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.
Metabolism:
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