Chemists & Biochemists
This is just a rough draft of the class web
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.
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
The course should provide a review of
some biochemical principles, along with some astronomy, earth history,
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
Class attendance is
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;
of the solar system.
Become familiar with the planets and major moons in our solar
Look at the atlas
the universe to see how our solar system fits into the galaxy.
Hubble extreme deep
field image can make you feel very small.
Tues Sept 3 Stars. What are
Read the star wiki page
and sun wiki page
Read the stellar evolution
Describing stars: apparent
magnitude and luminosity.
diagram (color vs luminosity diagram)
OBAFGKM stellar classification system
tutorial and questions
Measuring distances to stars:
main sequence fitting, Cepheid
Distances to many stars are known from the Hipparcos parallax
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
Water, and its properties.
What happens to G, K and M-type stars as they age?
of habitable zone migration during the lifetime of a star
Describe a star that will have planets for the longest habitable
Tues Sept 10 Telescopes. history of the telescope cartoon (PDF)
magazine adaptive optics (PDF) history of adaptive optics (PDF)
of large ground-based telescopes Hobby-Eberly telescope
space telescope wiki recent
adaptive optics article
Telescopes of the near future: Giant Magellan telescope
Large telescopes (PDF)
space telescope wiki Webb space telescope NASA page
Thur Sept 12 Introduction to extrasolar planets
(exoplanets) and their detection
Methods of detecting exoplanets:
Radial velocity method. radial velocity
Transit method transit
Transit timing variation transit
timing variation wiki
Detection of exoplanets by gravitational
Tues Sept 17
Papers from Science exoplanet feature (May 2013):
more introduction (PDF)
exoplanet habitability (PDF)
exoplanet properties (PDF)
planets of Kepler 62 (PDF)
space telescope wiki page
Nature paper Kepler-11 (PDF)
Gliese 581 wiki page
Gliese 667 wiki page
exoplanet survey satellite (TESS) will follow Kepler.
Thur Sept 19 Drake equation,
Sept 24 Mid-term
Thur Sept 26 If there
is life on Mars,
would it be? Overview of Mars.
Mars wiki page
climate of Mars
water on Mars
geology of Mars
Mars (wiki) Mars
lost much of its original atmosphere (Science Daily)
Science Laboratory: summary of important events
Tues Oct 1 How could life
survive on Mars?
of metabolism of earth's prokaryotes. What's universal to all
Thurs Oct 3 Life deep underground.
Metabolism of prokaryotes that live far
bacteria. Bold traveler paper (PDF)
supplementary material (PDF)
Deep subsurface life Science
Daily article and the associated Science paper (PDF)
paper on deep subsurface water (PDF)
Tues Oct 8 Acquiring carbon for
growth: Calvin cycle, reductive TCA cycle and Wood-Ljungdahl
Calvin cycle wiki
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,
would it be? How would it survive?
Life in deep oceans: photosynthesis
by green sulfur bacteria (PDF)
Photosynthesis using blackbody radiation. blackbody
spectrum of water.
Energy capture by bacteriorhodopsin. bacteriorhodopsin
Habitable moons as a place to find life: What are
properties of an
ideal habitable moon?
Tues Oct 15 Where else might there be life in
Where is there liquid water in our solar system?
What about tides as an energy source? tide
Thur Oct 17 Saturn's moons Titan and Enceladus.
Tues Oct 22 Mid-term
Thur Oct 24 Understanding ET life requires an
understanding of earth's life & its history.
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
Tues Oct 29 Origin of life & early
the Last Universal Common Ancestor (LUCA).
Lane LUCA paper (PDF)
Thur Oct 31 Origin of metabolism
early life papers:
Lane and Martin origins of membrane
Russell and Martin,
origin of cells (PDF)
Russell and Martin, vents (PDF)
Russell disequilibrium (PDF)
Origin of metabolism (PDF)
Early enzymes: Carbon fixation, nitrogen
ferredoxin, pyruvate synthase, electron transport
acetyl CoA synthase (PDF)
more acetyl CoA synthase (PDF)
corrin iron-sulfur protein (PDF)
Nitrogenase and nitrogen fixation
ATP synthase (PDF)
evolution of carbon fixation (PDF)
early carbon fixation (PDF)
hydrogenase wiki page
wiki page hydrogenases
Tues Nov 5 Origin of the genetic code, tRNA and
Thur Nov 7 Origin of
evolution of photosynthesis paper (PDF)
Evolution of the oxygen evolving complex
Evolution of Rubisco.
Tues Nov 12 Origin of eukaryotes and complex
carbon cycle, and the importance of plate
Thur Nov 14 Methane on Mars: What does
meteorites and panspermia.
Tues Nov 19 Mid-term
Thur Nov 21 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.
of an exoplanet (Science Daily, 11july2013)
exoplanet atmospheres (wiki)
atmosphere (Science Daily)
Thur Nov 28 Thanksgiving
Tues Dec 3 Rare
Thur Dec 5 Habitability of planets orbiting red
dwarfs, and 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.
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
C+ 77% to 80% ; C 73% to 77% ; C- 70 to
D+ 67% to 70% ; D 63% to 67% ; D- 60 to
F < 60 % of possible points
Incomplete grades will only be given in the case of truly extraordinary
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
along with your graded exam; include a brief written description of the
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
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
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
- 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
- Behavior Concerns Advice Line (BCAL):
- Information regarding emergency
evacuation routes and emergency procedures can be found at:
Science news at Science
Picture of the Day
Diagram of the electromagnetic
(EM) spectrum (PDF)
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
Chandra x-ray telescope and galactic center.
HW problem ideas:
Stars & planets:
How long would a transit of earth last, if seen by a
Detecting a Jupiter by radial velocity.
delta G and equilibrium
IR and photosynthesis
bacteriorhodopsin as a proton pump, powered by IR,
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
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
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
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