Improving our forum - suggestions & to-do list

Any ideas for making this better.

My initial thoughts
* Compile topic-specific reading lists (book-and-chapter or paper).  This would be ongoing and not just what was assigned the first time.

PHYSICAL PRINCIPLES OF CELL BOLOGY

This thread is meant to include key principles we have gleaned.

ENERGY STORAGE - The cell stores energy not by having "fuels" which are "burned" but rather by maintaining processes (reactions/flows) out of equilibrium.  A key example is that [ATP] is maintained much higher than the value to which it would equilibrate given the ADP and Pi in the cell.  ATP is an example of an 'activated carrier', but there are numerous others.  Besides carrier molecules, energy is also stored by out-of-equilibrium gradients across membranes -- such as of ions and protons. In fact, ATP synthesis is driven by non-equilibrium proton [H+] concentrations maintained across the appropriate membrane.

ENERGY TRANSDUCTION - Energy is regularly converted among different carriers and 'devices' in the cell.  A sequence of activated carriers with high-energy electrons create a proton gradient, which in turn is used to generate ATP.  The constant downhill flow of (free) energy - from original source (food or light) to cellular waste - keeps the cell operating in an orderly way.  The flow of energy provides the power for information to flow in a single direction -- e.g., from a signal outside the cell to the nucleus.

March 28, 2012 meeting

Mar 28, 2012 - First Meeting

A good mix of students, postdocs and faculty were in attendance.  The discussion covered both science and planning logistics, including the following:


Science

• The source of ATP's free energy is not intrinsic to the molecule but to the fact that the cell keeps the [ATP]/[ADP] ratio far from equilibrium.
• ATP synthesis is driven by a proton gradient across the mitochondrial inner membrane (in eukaryotes).
• Membrane-surrounded compartments are very useful for maintaining systems out of equilibrium
• The non-equilibrium nature of the cell provides directionality (effective non-reversibility) so that 'life can go on'.  For example, cells divide but don't combine!  We need to think about energy and information flow through cellular processes.
• Evolution provides a valuable perspective.  For example, when thinking about cellular energy sources (food), note that hydrocarbons and molecular oxygen (produced by cells) were not initially available on earth.  Fortunately, sunlight was around to get things started.
• Dan Zuckerman declared Franklin Harold's book (see references) to be essential reading.  It gives the big picture of cell biology and is incredibly well written.

Planning/Logistics

• Meet every two weeks during summer but once a month until classes end.
• Participants should bring in books of interest.  Dan Zuckerman brought a big stack (some in references).  Also mentioned were an astrobiology book and Kauffman's The Origins of Order.  Feel free to put additional info or suggestions as a comment.
• Start some kind of web forum (which is this!).  Everyone should feel free to add comments.

REFERENCES

A running list of valuable references (books, articles, links).  Let's use the [author-year] convention for citing in our discussions.

[Alberts-2002] B Alberts et al., Molecular Biology of the Cell, 4th edition (note there is a later edition) "Fat Alberts" or "Big Alberts"
[Alberts-2004] B Alberts et al., Essential Cell Biology, 2nd edition (simplified but still excellent version of Fat Alberts) "Baby Alberts"
[Alon-2007] Uri Alon, An Introduction to Systems Biology
[Berg-2002] JM Berg, et al., Biochemistry, 5th edition
[Harold-2001] FM Harold, The way of the cell
[Harris-1995] DA Harris, Bioenergetics at a glance
[Hill-1989] TL Hill, "Free energy transduction and biochemical cycle kinetics," Chapter 1.  This is a classic book, and chapter 1 is essential reading, nicely presented.  The rest of the book is more opaque.  Available cheaply in Dover edition.
[Nicholls-1992] DG Nichools and SJ Ferguson, Bioenergetics3

WELCOME

Biology for Physical Scientists ... If your eyes glaze over at cell-sigaling spiderwebs and you haven't learned too much biology from biophysics books, you may be in the right place.  Let's see whether we can leverage our knowledge of physical science to understand cell biology.

Regarding this blog...  Please post comments and corrections.  This will be most helpful to the group.  Many of you know a lot more than I do!  I will try to update my posts to reflect the wisdom of the group.

If you want to reach me, use the email ddmmzz AT pitt.edu (Dan Zuckerman).