Biophysics 354
Lecture 1



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:

  1. a machinery to conserve and pass on the genetic information that codes the phenotype of the species, and
  2. 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.

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:

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 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.

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    ©Copyright 1996, Antony Crofts, University of Illinois at Urbana-Champaign, a-crofts@uiuc.edu