BIOPS Weds 4/18/2012 meeting
Here was the original plan:
Topic: Comparative energy production in bacteria, plants, animals (roughly)
Reading (see References):
- Mid-level (start here): Baby Alberts [Alberts-2004] Ch 14 or Berg [Berg-2002] Ch 18.
- Does anyone have a recommendation for bacteria? Ch 14 of Harris [Harris-1995] has some info.
- Most technical: Your favorite bioenergetics book, perhaps [Harris-1995] DA Harris, Bioenergetics at a glance or [Nicholls-1992] DG Nichools and SJ Ferguson, Bioenergetics. Any biochemistry book will have chapters on oxidative phosphorylation, photosynthesis, etc -- e.g., [Berg-2002]. Also fat Alberts [Alberts-2002] Ch 14.
- General: Keep on reading Harold, Way of the Cell
Here is a summary of what we discussed. (Those who attended were rewarded with fresh donuts from Peace, Love, & Little Donuts!)
In common among all cell types
- Use of ATP as primary energy currency
- ATP produced by F1F0ATPase (most cells)
- ATP synthesis driven by proton gradient (difference in proton concentrations) across a membrane
- Proton gradient produced by redox processes starting from ‘high energy electron’ carriers
- Use of ‘activated carriers’ (see below), which are molecules that store free energy under cellular conditions
Differences among cell types
- Mechanisms for pumping protons
- Carriers of high-energy electrons
- Krebs/citric acid cycle produces electron carriers to maximize energy extraction from glucose
- Original source of energy – bacteria are much more flexible in getting food
- Light, for plants and photosynthetic bacteria
- Hydrocarbons, for animal cells (originally produced by other cells)
- Other sources for extreme-philes??
- Aerobic respiration, where molecular oxygen is the ultimate receptor of high-energy electrons, is much more efficient than anaerobic respiration.
Activated carriers (common among cell types)
Definition:
a “kinetically stable” molecule (reactant) that is out of equilibrium with
respect to a reaction it can undergo to form product(s); examples: ATP → ADP +
Pi, NADH → NAD+ + e-; the carrier is out of equilibrium in that there is a
dearth of product relative to reactant compared to what would hold in equilibrium under cellular conditions; cell
maintains ‘activation’ of the carrier by continually producing it and limiting
the overall amount reacting by the amount of catalyst (enzyme) available. See Berg p. 383, 386]
- ATP (and perhaps other carriers) not only is kinetically stable for a long time (days) but is highly activated (stores a lot of free energy, being far from equilibrium) when both ATP and ADP are at similar concentrations. See Harris p. 20.
- Components of the redox chain can be considered activated carriers, wherein typical reactions involve the gain/loss of protons and electrons
- In eukaryotic cells, both sugars and fats are converted to the common activated carrier acetyl CoA, which is used to drive the citric acid cycle and ultimately the proton gradient.
Proton pumping (common among cell types)
We
reviewed several mechanisms of proton pumping across membrane. All are driven by a net flow of electrons
from higher to lower free energy.
Terminology here is non-standard.
See section “electron-transport chains and proton pumping” in Ch. 14 of
baby Alberts.
- Implicit/virtual proton pumping. A trans-membrane protein catalyzes two nearly simultaneous reactions at its two ends. At one end, a carrier is catalyzed to release a proton and electron. The proton is released into solution and the electron is ‘conducted’ by tunneling through the protein. At the other end, the electron joins with a proton from solution and attaches to a different (lower free energy) carrier. See Harris Ch. 24.
- Looping. Quinone/quinol (Q/QH2) species are mobile within the membrane and can shuttle protons from one side to the other using redox reactions similar to those just described. Q species must loop back and forth. See Harris Ch 24.
- Direct proton pumping via alternating access mechanism. See Harris Ch 25.
