Introduction to Molecular Biophysics

Jack A. Tuszynski, Michal Kurzynski

• Publisher: CRC Press
• Year: 2003
• eBook ISBN: 9781135517731
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Molecular Biology
• Index: Biological Sciences

Molecular biophysics is a rapidly growing field of research that plays an important role in elucidating the mysteries of life's molecules and their assemblies, as well as the relationship between their structure and function. Introduction to Molecular Biophysics fills an existing gap in the literature on this subject by providing the reader with th

1

Origins and Evolution of Life

1.1Initiation

Planet Earth was formed about 4.6 billion years ago as a result of accretions (inelastic collisions and agglomerations) of larger and larger rocky fragments formed gradually from the dust component of the gaseous dusty cloud that was the original matter of the Solar System. The Great Bombardment ended only 3.9 billion years ago when a stream of meteorites falling onto the surface of the newly formed planet reached a more or less constant intensity. The first well preserved petrified microstamps of relatively highly organized living organisms similar to today’s cyanobacteria emerged about 3.5 billion years ago (Schopf, 1999), so life on Earth must have developed within the relatively short span of a few hundred million years.

Rejecting the hypothesis of an extraterrestrial origin of life, not so much for rational as for emotional reasons, we have to answer the question of the origins of the simplest elements of living organisms: amino acids, simple sugars (monosaccharides) and nitrogenous bases. Three equally probable hypotheses have been put forward to explain their appearance (Orgel, 1998). According to the first and the oldest theory, these compounds resulted from electric discharges and ultraviolet irradiation of the primary Earth atmosphere containing mostly CO₂ (as the atmospheres of Mars and Venus do today), H₂O, and strongly reducing gases (CH₄, NH₃, and H₂S). According to the second hypothesis, the basic components of living organisms were formed in space outside the orbits of large planets and transferred to the Earth’s surface via collisions with comets and indirectly via carbon chondrites. The third hypothesis is that these compounds appeared at the oceanic rifts where the new Earth’s crust was formed and where water overheated to 400°C containing strongly reducing FeS, H₂, and H₂S met cool water containing CO₂.

The origin issue is still open and all three hypotheses have been seriously criticized. First, the primary Earth atmosphere might not have been reducing strongly enough. Second, organic compounds from outer space may have deteriorated while passing through the Earth’s atmosphere. Third, the reduction of CO₂ in oceanic rifts requires nontrivial catalysts.

The three most important characteristics of life that distinguish it from other natural phenomena were expressed by Charles Darwin, whose theory of evolution is so crucial to modern biology (Dawkins, 1986). Taking into account the achievements of post Darwinian genetics and biochemistry, we define life as a process characterized by continuous (1) reproduction, (2) variability, and (3) selection (survival of the fittest). An individual must have a replicable and modifiable program, proper metabolism (a mechanism of matter and energy conversion), and capability of self-organization to maintain life.

FIGURE 1.1
Processing genetic information. (a) The classical dogma. The information is carried by DNA which undergoes replication during biological reproduction and transcription into RNA when it is to be expressed; gene expression consists of translation of the information written in RNA onto a particular protein structure. (b) Modern version of the classical dogma. RNA can be replicated and transcribed in the opposite direction into DNA. Proteins also can carry information as is assumed to occur in prion diseases.

The emergence of molecular biology in the 1950s answered many questions about the structures and functioning of the three most important classes of biological macromolecules: DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and proteins. However, in the attempts to develop a possible scenario of evolution from small organic particles to large biomolecules, a classical chicken-and-egg question was encountered: what appeared first? The DNA that carried the coded information on enzymatic proteins controlling the physiological processes that determined the fitness of an individual or the proteins that enabled the replication of DNA, its transcription into RNA, and the translation of certain sequences of amino acids into new proteins? See Figure 1.1a for illustration.

This question was resolved in the 1970s as a result of the evolutionary experimentation in Manfred Eigen’s laboratory (Biebricher and Gardiner, 1997). The primary macromolecular system undergoing Darwin’s evolution may have been RNA. Singlestranded RNA is not only the information carrier, program, or genotype. Because of a specific spatial structure, RNA is also an object of selection or a phenotype. Equipped with the concept of a hypercycle (Eigen and Schuster, 1977) and inspired by Sol Spigelman, Eigen used virial RNA replicase (Figure 1.1b), a protein, to produce new generations of RNA in vitro. The complementary RNA could polymerize spontaneously, without replicase, using the matrix of the already existing RNA as a template. Consequently, we can imagine a very early “RNA world” composed only of nucleotides, their phosphates, and their polymers — subject to Darwinian evolution, and thus alive based on the definition adopted (Gesteland et al., 1999).

A number of facts support the RNA world concept. Nucleotide triphosphates are highly effective sources of free energy. They fulfill this function as relicts in most chemical reactions of contemporary metabolism (Stryer, 1995). Dinucleotides act as cofactors in many protein enzymes. In fact, RNA molecules can serve as enzymes (Cech, 1986) and scientists now commonly talk about ribozymes. Contemporary ribosomes translating information from RNA onto a protein structure (see Figure 1.1a) fulfill their catalytic functions due to their ribosomal RNA content rather than their protein components (Ramakrishnan and White, 1998).

We have known for a number of years now about the reverse transcriptase that transcribes information from RNA onto DNA (Figure 1.1b). It also appears that RNA may be a primary structure and DNA a secondary one since modern organisms synthesize deoxyribonucleotides from ribonucleotides.

1.2Machinery of prokaryotic cells

The smallest present-day system thought to possess the key function of a living organism, namely reproduction, is a cell. A sharp distinction exists between simple prokaryotic cells (that do not have nuclei) and far more complex eukaryotic cells (with well defined nuclei). Evidence points to an earlier evolution of prokaryotic cells. Eukaryotic cells are believed to have resulted from mergers of two or more specialized prokaryotic cells. Unfortunately, little is known about the origins of prokaryotic cells. The scenario below is only an attempt to describe some key functional elements of the apparatus possessed by all prokaryotic cells and is not a serious effort to reconstruct the history of life on Earth.

The world of competing RNA molecules must have eventually reached a point where a dearth of the only building materials, nucleotides triphosphate, was created. Molecules that could obtain adequate supplies of building materials gained an evo...

Table of contents

• Cover
• Half Title
• Series Page
• Title Page
• Copyright Page
• Preface
• Contributor
• Contents
• 1 Origins and Evolution of Life
• 2 Structures of Biomolecules
• 3 Dynamics of Biomolecules
• 4 Structure of a Biological Cell
• 5 Nonequilibrium Thermodynamics and Biochemical Reactions
• 6 Molecular Biological Machines
• 7 Nerve Cells
• 8 Tissue and Organ Biophysics
• 9 Biological Self-Regulation and Self-Organization
• 10 Epilogue: Toward New Physics and New Biology
• Random Walks and Diffusion
• Models of Phase Transitions and Criticality
• Foundations of Nonlinear Physics
• Master Equations
• Author Index
• Subject Index