Introduction
This lecture presents a general overview of Biological Energy Conservation.
Living things succeed if they reproduce new generations. To do this they must have two main functions:
- a machinery to conserve and pass on the genetic information that codes the phenotype of the species, and
- an ability of individuals to survive long enough to reproduce.
The former function is the subject of one of the main revolutions of biology in the last half-century, the development of modern molecular genetics following the introduction of the Watson-Crick-Wilkinson-Franklin model of DNA in the mid 1950s, and the rich areas of new knowledge deriving from that.
For the latter function, a major component of success is the ability to extract energy from the environment in competion with other species. This has been the subject of a second revolution, - that associated with our understanding of metabolic energy conversion reactions. This followed the tracing of the pathways of cellular metabolism in the first half of the 20th century, the elucidation of the mechanism of substrate level oxidative phosphorylation, mainly by Efraim Racker, and the formulation of the chemiosmotic hypothesis to explain electron transfer linked oxidative or photosynthetic phosphorylation by Peter Mitchell, introduced in the early 1960s.
In this course, we will explore the evolution of the energy conversion apparatus, the mechanisms of energy conversion, and the physicochemical tools necessary for a deeper understanding of those mechanisms. The main emphasis will be on the major pathways for energy conversion, - photosynthesis and respiration, - with some consideration of the metabolic reactions that link these processes to the main biochemistry and physiology of the organism.
The molecular basis of energy transduction
The field of bioenergetics has seen an explosion of interest in the past two decades, because of the availability of structures for some of the protein complexes catalyzing the reactions of the major pathways. These have provided new insights into mechanism, and revealed some amazing molecular devices. Several of these have become the darlings of the biophysical community, because they provide rich possibilities for understanding processes fundamental to energy conversion, - the physical basis for the coupling mechanisms through which energy transduction occurs.
- The photochemical reaction centers of bacterial and green plant photosysnthesis have provided a playground for testing theories of electron transfer, in which the structures have provided details of distance and local milieu essential for an understanding of the factors that determine rates, as measured by ultra-fast spectroscopic approaches. The lessons from these model systems are already being applied widely to other electron transfer processes.
- Structures of light-harvesting complex have yielded new ideas and insights into excitation transfer processes and exciton energy funnelling.
- The structures of the ATP synthase complex have revealed the smallest turbine-driven motor, confirming ideas based on detailed analysis of data from earlier biochemical and biophysical approaches. This device promises to spawn a whole field of nanotechnology, in which the nanomotor is linked to machinery operating on a molecular scale.
- Structures for the respiratory complexes have opened new possibilities for understanding the coupling of electron transfer to proton pumping. The bc1 complex has revelaed a new mechanism for electron transfer over distance, - a movement of the mobile extrinsic domain of the iron sulfur protein through 25 nm, - and hinted at other dynamic features. Cytochrome oxidases are showing us novel mechanism for coupling electron transfer to local protonic potential, through deep proton wells into the catalytic core.
- Structures of bacteriorhodopsin have provided us with the most detailed dynamic picture of a photomolecular pump, in which protons activated through photoisomerization are switched between proton conduction pathways in and out of the protein.
Mitochondria, - their role in cell death and aging
Although an involvement of mitochondrial genetic defects in certain inherited diseases has long been studied, the medical world has woken to the importance of mitochondrial research because of a new understanding of the role of these organelles in two processes central to cellular metabolism and health. These are:
- The controlling function of mitochondrial integrity in apoptosis, - programmed cell death. The ability of the body to get rid of cells that go wrong is critical to control of cancer, and to the efficient recycling of macromolecular constituents. The mitochondria, through release of factors that turn on the cascade of reactions leading to apoptosis, are of central importance in determining how and when the cell recognizes that it's time to go.
- The role of the respiratory chain in generation of reactive oxygen species (ROS), - the main causal agents in DNA damage leading to cellular aging. Two of the main complexes of the respiratory chain, - Complex I, or NADH:ubiquinone oxidoreductase, and Complex III, or the bc1 complex, - are the main sites in the cell at which O2 is reduced to superoxide anion, the molecule from which the ROS are derived. Because mitochondria have a less efficient DNA repair mechanism than the nucleus, they are the main victims of this damage. As a consequence, your mitochondria become disfunctional as you age, resulting in loss of energy, and eventually death by "cellular suffocation". Your mitochondrial energy metabolism is essential for survival, but the mechanism has built-in this suicidal reaction. If nothing else kills you, your mitochondria will, - a classical "Catch-22" of cellular metabolism.
Photosynthesis, ecology and global warming
Photosynthesis provides the driving force for the biosphere, the source all the O2 we breath, and the main pathway for utilization of CO2, and its incorporation into food (if the importance of photosynthesis to the health of all living things were more generally appreciated, we would all be sun-worshipers). The worries about global warming have added a recent interest in the ecological importance of photosysnthesis. It has become clear that the increased productivity arising from increases CO2 levels represents one of the main mechanisms ameliorating global warming. Things are not getting bad quickly, because photosysnthesis has rallied to the cause.
All of the above are good reasons for a renewed interest in biological energy conversion. The important fact is that these processes are central to all living processes, and have been thoughout evolution. The invention of oxygenic photosynthesis, and the consequent development of an aerobic biosphere, and the adaptation of organsims to this potentially poisonous reagent through the invention of respiration, were crucial in the evolution of the eukaryotic cell, the modern biosphere, and its animal and plant inhabitants. You cannot understand biology if you don't understand biological energy conversion.
Evolution of the biosphere
Geological time
(From Introduction to Evolutionary Biology.)
Millions of years ago "Meter scale"
Preambrian Time (1 billion yrs = 1 m)
Archean Era 4600-2500 4.6-2.5 m
Proterozoic Era 2500-570 2.5-0.57 m
Phanerozoic Time
Paleozoic Era
Cambrian Period 570-505 57-50.5 cm
Ordovician Period 505-438 50.5-43.8 cm
Silurian Period 438-408 43.8-40.8 cm
Devonian Period 408-360 40.8-36 cm
Carboniferous Period 360-286 36-28.6 cm
Permian Period 286-245 28.6-24.5 cm
Mesozoic Era
Triassic Period 245-208 24.5-20.8 cm
Jurassic Period 208-144 20.8-14.4 cm
Cretaceous Period 144-66.4 14.4-6.64 cm
Cenozoic Era
Tertiary Period
Paleocene Epoch 66.4-57.8 6.64-5.78 cm
Eocene Epoch 57.8-38.6 5.78-3.86 cm
Oligocene Epoch 38.6-23.7 3.86-2.37 cm
Miocene Epoch 23.7-5.3 2.37-0.53 cm
Pliocene Epoch 5.3-1.6 0.53-0.16 cm
Quarternary Period
Pleistocene Epoch 1.6-0.01 1.6-0.01 mm
Holocene Epoch 0.01-0 10-0 µm
A brief history of the biosphere
Years ago "Meter scale" Event
4.5 billion 4.5 m Formation of solar system
4.1 billion 4.1 m Earliest evidence for a solid surface on earth
3.8 billion 3.8 m Oldest rocks in geological record
3.5 billion 3.5 m Stromatolites - fossil bacteria (cyanobacteria?)
2.2 billion 2.2 m Atmosphere became oxidizing (age of rust layer)
1.5-2 billion 1.5 m Eukaryote cell evolved
0.65-1 billion ~1 m First metazoans
650 million 65 cm Trilobites and similar fossils
250 million 25 cm First dinosaurs
150 million 15 cm First mammals
65 million 6.5 cm Last disosaurs
4.5 million 4.5 mm Hominids diverge from apes
1.5 million 1.5 mm Early man
10 thousand 10 µm Early civilization
70 years 70 nm A human life
Universal phylogeny
*** green bacteria
*******
* *** flavobacteria
BACTERIA *******
* ********* spirochetes
*************
* * ***** gram negative bacteria
* * ********
* * * ***** purple bacteria
* **** ***
* * *** eukaryotic mitochondria
****** *
* * * ***** gram positive bacteria
* * *********
* * ***** cyanobacteria
* * **** eukaryotic chloroplasts
************** *
* * *************************** deinococci
* *
* ******************************** thermotagales
*
****
* ARCHAEA *************** halophiles
* **********
* * *************** methanogens
* ********
* * ************************ methanogens
* **********
* * *
* * ******************************* thermophiles
* ****
* * *
* * **************************************** thermophiles
* *
*** **** choanoflagellates
* *****
* EUKARYOTES * **** animals
* *******
* * ******** fungi
* *******
* * ************** plants
* *****
* * ******************** ciliates
* *******
* * ************************ cellular slime molds
* ******
* * ****************************** flagellates
*********
*********************************** microsporidia
The major cycles of the biosphere
The biosphere is in a steady state in which the elements which make up living things are circulated through cycles of reactions, - synthesis to build up complex molecules, and degradation to break them down. Of these, the carbon cycle is the most prominent, but nitrogen, phosphorous, and sulfur cycles are also important. In the synthetic phase, photosynthesis in plants, algae and photosynthetic bacteria is used to build up complex molecules from simple ones, and in the degradative phase, animals break down complex molecules to their simple oxidized forms by respiration, and bacteria and fungi by fermentation and respiration.
The input of energy through photosynthesis generates biomass with an energy equivalent 10-30 times that involved in all anthropogenic processes. Since photosynthesis operates with a low efficiency (1-10%), the energy flux through photosynthesis is 100-1000 times all that associated with human activity.
The role of photosynthesis and bioenergetics in evolution.
Photosynthetic forms are found in almost all branches of the bacteria, but in none of the archaea. In contrast, although the early biosphere was anaerobic, electron transfer enzymes of the respiratory chain are found in both, and clearly have a common origin. The ATP synthase enzyme, which uses the H+ gradient generated by electron transfer to make ATP, also shows strong evidence for a common origin before the separation of the two main prokaryotic branches. It therefore seems likely that both these latter processes, and the chemiosmotic mechanism of energy transduction they catalyze, predate photosynthesis, so that the early stages of evolution were driven by exploiting the redox drop between H and CO2 (as in methanogenesis), the modest free energy gradients available from anaerobic fermentation, and electron from transfer to acceptors other than oxygen. It seems likely that photosynthesis evolved early in the bacteria, and that the exploitation of light as an energy source drove the diversification of species that led to the separation of the two main branches of the prokaryote world.
The major metabolic pathways
The evolution of the eukaryote cell involved metabolic diversification through exploitation of the combined metabolic potential of the ur-eukaryote and its symbiont partners.
Mitochondrial and chloroplasts
Mitochondrial are thought to have originated from a symbiotic association of a respiratory bacterium with a fermentative archaeal host. The record of this origin is clear in the DNA and protein synthetic apparatus of the mitochondrion, as the remnants of the apparatus needed for a free living cell. Similarly, the sequences of mitochindrial enzymes show a common origin with those of modern non-sulfur photosynthetic bacteria and the respiratory bacteria which developed from them.
Similarly, the chloroplast originated from a cyanobacterial symbiont, and the DNA, apparatus for protein sysnthesis, and sequence alignments, show similar evidence of its origin.
For both mitochondria and chloroplasts, the host cell has taken over much of the task of protein sysnthesis, and this has let to a redistribution of DNA to the nucleus, and the evolution of pathways for a traffic in protein across the membranes of the organelles. Possible advantages to this redistribution are:
- The host cell takes control of the organelle.
- The activities of the organelle can be fine-tuned by addition of regulatory subunits.
- The regulation allows for a better coordination of activities between the host and the organelle.
- The DNA in the host cell nucleus is protected from damage by free radicals generated by oxidative metabolism, because the repair mechanisms in the nucleus are better than in the organelle.
The eukaryote cell as a mirror of evolution.
The separate origins of the mitochondria (and chloroplast), and the host cell, are reflected not only in their DNA and protein synthetic apparatus, but also in their metabolic activities. Glycolysis in the cytoplasm reflects the fermentative life-style of the archaeal progenitor of the host; the aerobic metabolism and respiratory chain of the mitochondrion reflects its origin as a respiratory bacterium.
Useful Links
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Carbon cycle and Global Change
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©Copyright 1996,
Antony Crofts, University of Illinois at Urbana-Champaign,
a-crofts@uiuc.edu