Bioorganic Chemistry and the Origin of Life

Summary A challenging theme in bioorganic chemistry is the unification of established theories of biochemistry and organic chemistry to provide new patterns for interpretation and experimentation. Especially relevant examples of such interactions can be drawn from the field of enzyme catalysis and, in particular, the role of cofactors therein.Knowledge of the chemical mechanisms by which some of the cofactors function has progressed rapidly with the aid of studies of the cofactors themselves (or compounds of related structure, models) stripped of the accompanying apoenzyme. The striking successes in this field likely arise from a fundamental resemblance between bioorganic chemistry (especially coenzyme models) and chemical evolution before the appearance of coded polypeptide enzymes.     

From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection

It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.     

An Extended Model for the Evolution of Prebiotic Homochirality: A Bottom-Up Approach to the Origin of Life

A generalized autocatalytic model for chiral polymerization is investigated in detail. Apart from enantiomeric cross-inhibition, the model allows for the autogenic (non-catalytic) formation of left and right-handed monomers from a substrate with reaction rates epsilon L and epsilon R, respectively. The spatiotemporal evolution of the net chiral asymmetry is studied for models with several values of the maximum polymer length, N. For N = 2, we study the validity of the adiabatic approximation often cited in the literature. We show that the approximation obtains the correct equilibrium values of the net chirality, but fails to reproduce the short time behavior. We show also that the autogenic term in the full N = 2 model behaves as a control parameter in a chiral symmetry-breaking phase transition leading to full homochirality from racemic initial conditions. We study the dynamics of the N--> infinity model with symmetric (epsilon L = epsilon R) autogenic formation, showing that it only achieves homochirality for epsilon > epsilon c, where epsilon c is an N-dependent critical value. For epsilon 相似文献   

Question 1: Peptide Nucleic Acids and the Origin and Homochirality of Life

The possibilities of pseudo peptide DNA mimics like PNA (peptide nucleic acid) having a role for the prebiotic origin of life prior to an RNA world is discussed. In particular a scenario is proposed in which protocells with an achiral genetic material through several generations stepwise is converted into a chiral genetic material, e.g., by incorporation of RNA units. Provided that a sufficiently large sequence space is occupied, a selection process based on catalytic function in which a single cell (first common ancestor) has a definite evolutionary advantage, selection of this cell would by contingency also lock it into homochirality. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

Engine of Life and Big Bang of Evolution: A Personal Perspective

Photosystem II (PS II) is the engine for essentially all life on our planet and its beginning 2.5 billion years ago was the 'big bang of evolution.' It produces reducing equivalents for making organic compounds on an enormous scale and at the same time provides us with an oxygenic atmosphere and protection against UV radiation (in the form of the ozone layer). In 1967, when I began my career in photosynthesis research, little was known about PS II. The Z-scheme had been formulated [Hill and Bendall (1960) Nature 186: 136–137] and Boardman and Anderson [(1964) Nature 203: 166–167] had isolated PS II as a discrete biochemical entity. PS II was known not only to be the source of oxygen but of variable chlorophyll fluorescence [Duysens and Sweers (1963) In: Studies on Microalgae and Photosynthetic Bacteria, pp. 353–372. University of Tokyo Press, Tokyo] and delayed chlorophyll fluorescence [Arnold and Davidson (1954) J Gen Physiol 37: 677–684]. P680 had just been discovered [Döring et al. (1967) Z Naturforsch 22b: 639–644]. No wonder the 'black box of PS II' was described at that time by Bessel Kok and George Cheniae [Current Topics in Bioenergetics 1: 1–47 (1966)] as the 'inner sanctum of photosynthesis.' What a change in our level of understanding of PS II since then! The contributions of many talented scientists have unraveled the mechanisms and structural basis of PS II function and we are now very close to revealing the molecular details of the remarkable and thermodynamically demanding reaction which it catalyzes, namely the splitting of water into its elemental constituents. It has been a privilege to be involved in this journey.     

Comets: Chemistry and chemical evolution

Summary Lasting commitment to cosmic chemistry and an awareness of the fascinating role of comets in that study was a consequence of an association with Harold Urey early in my astronomical career. Urey's influence on cometary research spread as colleagues with whom I was associated, in turn, developed their own programs in cometary chemistry. One phase of the Chicago research shows that Whipple's icy nucleus would be below about 250 K. This property, combined with their small internal pressure, means cometary interiors remain essentially unchanged during their lifetime. Observations of cometary spectra indicate that they are rich in simple organic species. Experiments on comet-like ice mixture suggests that the extensive array of interstellar molecules also may be found in comets. The capture of cometary debris by the earth or the impact of comets would have been an early source of biochemically significant molecules. Recent hypotheses on radiogenic heating and melting of water ice in the central zone of nuclei do not seem consistent with recent observations or ideas of structure. Thus comets are not a likely place for life to develop.     

Origin of fatty acid synthesis: Thermodynamics and kinetics of reaction pathways

Summary The primitiveness of contemporary fatty acid biosynthesis was evaluated by using the thermodynamics and kinetics of its component reactions to estimate the extent of its dependence on powerful and selective catalysis by enzymes. Since this analysis indicated that the modern pathway is not primitive because it requires sophisticated enzymatic catalysis, we here propose an alternative pathway of primitive fatty acid synthesis that uses glycolaldehyde as a substrate. In contrast to the modern pathway, this primitive pathway is not dependent on an exogenous source of phosphoanhydride energy (ATP). Furthermore, the chemical spontaneity of its reactions suggests that it could have been readily catalyzed by the rudimentary biocatalysts available at an early stage in the origin of life.     

Vocabulary of Definitions of Life Suggests a Definition

Abstract

Analysis of the vocabulary of 123 tabulated definitions of life reveals nine groups of defining terms (definientia) of which the groups (self-)reproduction and evolution (variation) appear as the minimal set for a concise and inclusive definition: Life is self-reproduction with variations.     

A Universal Definition of Life: Autonomy and Open-Ended Evolution

Life is a complex phenomenon that not only requires individual self-producing and self-sustaining systems but also a historical-collective organization of those individual systems, which brings about characteristic evolutionary dynamics. On these lines, we propose to define universally living beings as autonomous systems with open-ended evolution capacities, and we claim that all such systems must have a semi-permeable active boundary (membrane), an energy transduction apparatus (set of energy currencies) and, at least, two types of functionally interdependent macromolecular components (catalysts and records). The latter is required to articulate a 'phenotype-genotype' decoupling that leads to a scenario where the global network of autonomous systems allows for an open-ended increase in the complexity of the individual agents. Thus, the basic-individual organization of biological systems depends critically on being instructed by patterns (informational records) whose generation and reliable transmission cannot be explained but take into account the complete historical network of relationships among those systems. We conclude that a proper definition of life should consider both levels, individual and collective: living systems cannot be fully constituted without being part of the evolutionary process of a whole ecosystem. Finally, we also discuss a few practical implications of the definition for different programs of research.     

中国植物区系中的特有性及其起源和分化

对中国植物区系中的239个特有属,分属67个科,进行了分析研究,列出了这些特有属在种子植物各个科的分布,现代地理分布范围。结果表明含特有属在10个以上的有5个科即Gesneriaceae,Compositae,Labiatae,Cruiciferae,Umbelliferae;其中以Gesneriaceae居榜首(27属),Compositae位居第二(20属),Labiatae有12属,居第三。含2属的科有15个,含1属的科有30个;其中Ginkgaceae,Davidiaceae,Eucommiaceae,Acanthochlamydaceae组成了中国植物区系最具古老性、特有性和代表性的4个单型科。在此基础上,从特有属在被子植物八纲系统各个纲的分布特点,以及在各个科组成和系统关系及已有地质、化石历史和系统学,形态,分子证据论述了这些特有属的起源、系统关系及在植物地理上的关系。在裸子植物中,特有属最为丰富,几乎皆是地质历史上北极-第三纪成分的残遗,起源时间较早,可追溯到白垩纪或更早。被子植物中,中国特有属存在于八纲被子植物的所有纲中,几乎在现代被子植物各个演化阶段均有古老残遗的特有类群存在,同时也不乏新特有类群尤其是在演化的高级阶段的类群。从起源上看,被子植物的古特有属主要发生于晚白垩纪和早第三纪,地质历史上大都占有广阔的分布区;新特有属多发生在新第三纪以后。其源头主要是北极第三纪、古热带第三纪(冈瓦纳第三纪)和古地中海第三纪的奇妙结合,不少类群是就地起源的;特有性是在第三纪中晚期以后北半球气候变迁,迁移途径(如北大西洋陆桥和白令陆桥)中断后形成的,这一时期是我国特有属形成发展的起始标志。     

A quantitative investigation of the chemical space surrounding amino acid alphabet formation

To date, explanations for the origin and emergence of the alphabet of amino acids encoded by the standard genetic code have been largely qualitative and speculative. Here, with the help of computational chemistry, we present the first quantitative exploration of nature's “choices” set against various models for plausible alternatives. Specifically, we consider the chemical space defined by three fundamental biophysical properties (size, charge, and hydrophobicity) to ask whether the amino acids that entered the genetic code exhibit a higher diversity than random samples of similar size drawn from several different definitions of amino acid possibility space.We found that in terms of the properties studied, the full, standard set of 20 biologically encoded amino acids is indeed significantly more diverse than an equivalently sized group drawn at random from the set of plausible, prebiotic alternatives (using the Murchison meteorite as a model for pre-biotic plausibility). However, when the set of possible amino acids is enlarged to include those that are produced by standard biosynthetic pathways (reflecting the widespread idea that many members of the standard alphabet were recruited in this way), then the genetically encoded amino acids can no longer be distinguished as more diverse than a random sample. Finally, if we turn to consider the overlap between biologically encoded amino acids and those that are prebiotically plausible, then we find that the biologically encoded subset are no more diverse as a group than would be expected from a random sample, unless the definition of “random sample” is adjusted to reflect possible prebiotic abundance (again, using the contents of the Murchison meteorite as our estimator). This final result is contingent on the accuracy of our computational estimates for amino acid properties, and prebiotic abundances, and an exploration of the likely effect of errors in our estimation reveals that our results should be treated with caution. We thus present this work as a first step in quantifying and thus testing various origin-of-life hypotheses regarding the origin and evolution of life's amino acid alphabet, and advocate the progress that would add valuable information in the future.     

Origin of life: Consideration of alternatives to proteins and nucleic acids

Summary Starting with relatively simple, non-hydrolyzable compounds in aqueous solution, entirely spontaneous condensations give rise to polymers that contain purines, pyrimidines, amino acids, coenzymes, lipid components and even phosphate. The presence of certain lipid micelles allows significant product formation at millimolar substrate concentrations. The first step involves formation of a Michael adduct from--unsaturated carbonyl compounds and various nucleophiles. Polymerization of these adducts occurs via sequential Knoevenagel condensations. All reactions take place readily at temperatures below 45°. The polymers can act as macromolecular catalysts as evidenced by hydrolytic activity. The purines and pyrimidines in the polymers appear to be capable of both base pairing and stacking interactions with ribonucleic acids. Specific examples of potential alternatives to base pairing are presented. These results are discussed from the standpoint of the spontaneous development of reproducing molecules. Proteins and nucleic acids may be evolutionary developments which have displaced earlier biopolymers.     

Life Cycle Perspectives to Achieve Business Benefits: From Concept to Technique

The purpose of this paper is to describe how one pollution prevention tool, life-cycle assessment, can be used to identify and manage environmental issues associated with product systems. Specifically, this paper will describe what life-cycle assessment is, determine the key players in its development and application, and present ideas on how life-cycle assessment can be used today. LCA provides a systematic means to broaden the perspective of a company's decisionmaking process to incorporate the consideration of energy and material use, transportation, post-customer use, and disposal, and the environmental releases associated with the product system. LCA provides a framework to achieve a better understanding of the trade-offs associated with specific change in a product, package, or process. This understanding lays the foundation for subsequent risk assessments and risk management efforts by decision-makers.     

The Big Bang, Superstring Theory and the origin of life on the Earth

This article examines the origin of life on Earth and its connection to the Superstring Theory, that attempts to explain all phenomena in the universe (Theory of Everything) and unify the four known forces and relativity and quantum theory. The four forces of gravity, electro-magnetism, strong and weak nuclear were all present and necessary for the origin of life on the Earth. It was the separation of the unified force into four singular forces that allowed the origin of life.     

Exploring the evolution of standard amino-acid alphabet: when genomics meets thermodynamics

One of the most intriguing aspects of life is that despite the diversified apparent shapes, similar building blocks and infrastructures, such as standard amino acids and canonical genetic codes, are shared by most life on Earth. Thus, it is challenging to explore: why nature just selects these building blocks and strategies from numerous candidates to construct life? Was this deterministic or fortuitous? Thanks to the rapid progress in genomics, bioinformatics and synthetic biology, more and more basic principles underlying life design and construction were disclosed in the past decade. However, since the origin of early life is substantially a chemical process, to understand the enigma of life origin, chemists' efforts can not be neglected. In this paper, we focus on the evolution of standard amino-acid alphabet and indicate that chemistry, especially thermodynamics, is indeed critical to understanding the forming mechanisms of amino-acid alphabet. It is revealed that nature prefers low free energy and thus ubiquitous (cheap) small amino acids when beginning to build life, which is compatible with many recent findings from genomics and bioinformatics.     

The origin of the biologically coded amino acids

Biology uses essentially 20 amino acids for its coded protein enzymes, representing a very small subset of the structurally possible set. Most models of the origin of life suggest organisms developed from environmentally available organic compounds. A variety of amino acids are easily produced under conditions which were believed to have existed on the primitive Earth or in the early solar nebula. The types of amino acids produced depend on the conditions which prevailed at the time of synthesis, which remain controversial. The selection of the biological set is likely due to chemical and early biological evolution acting on the environmentally available compounds based on their chemical properties. Once life arose, selection would have proceeded based on the functional utility of amino acids coupled with their accessibility by primitive metabolism and their compatibility with other biochemical processes. Some possible mechanisms by which the modern set of 20 amino acids was selected starting from prebiotic chemistry are discussed.     

中国栽培稻的起源与演化

中国栽培稻起源地主要有4种假说:华南起源说、云南起源说、长江中下游说和长江中游-淮河上游说。对其进行了简要概括,并进行评述:目前没有一种假说能完全符合水稻起源的4个条件,此外有些学者提出水稻的多起源中心;从分子生物学角度综述了栽培稻籼粳分化研究进展,主要有两个起源说:一源论和二次(或多次)起源论,大量研究支持籼稻和粳稻多起源论;从古DNA、水稻落粒性与驯化、植硅石等方面探讨栽培稻起源演化的研究方法。旨在能为水稻的起源演化研究提供有价值的参考。     

Hypothesized origin of microbial life in a prebiotic gel and the transition to a living biofilm and microbial mats

This article hypothesizes that the origin of the first microbial cell(s) occurred as a series of increasing levels of organization within a prebiotic gel attached to a mineral surface, which made the transition to a biofilm composed of the first cell(s) capable of growth and division. A gel microenvironment attached to a surface for the origin of life, and subsequent living cells offers numerous advantages. These include acting as a water and nutrient trap on a surface, physical protection as well as protection from UV radiation. The prebiotic gel and the living biofilm contained the necessary water, does not impede diffusion of molecules including gases, provides a structured gel microscopic location for biochemical interactions and polymerisation reactions, where the necessary molecules for life need to be present and not limiting. The composition of the first gel environment may have been an oily-water mixture (or the interface between an oily-water mixture) of microscopic dimensions, but large enough for the organization of the first cell(s). The living biofilm then made the evolutionary transition to a microbial mat.     

The Cold Origin of Life: B. Implications Based on Pyrimidines and Purines Produced From Frozen Ammonium Cyanide Solutions

A wide variety of pyrimidines and purineswere identified as products of a dilute frozen ammoniumcyanide solution that had been held at –78°C for 27 years.This demonstrates that both pyrimidines and purines couldhave been produced on the primitive earth in a short time byeutectic concentration of HCN, even though the concentrationof HCN in the primitive ocean may have been low. We suggestthat eutectic freezing is the most plausible demonstratedmechanism by which HCN polymerizations could have producedbiologically important prebiotic compounds.     

From Land to Water: the Origin of Whales, Dolphins, and Porpoises

Cetaceans (whales, dolphins, and porpoises) are an order of mammals that originated about 50 million years ago in the Eocene epoch. Even though all modern cetaceans are obligate aquatic mammals, early cetaceans were amphibious, and their ancestors were terrestrial artiodactyls, similar to small deer. The transition from land to water is documented by a series of intermediate fossils, many of which are known from India and Pakistan. We review raoellid artiodactyls, as well as the earliest families of cetaceans: pakicetids, ambulocetids, remingtonocetids, protocetids, and basilosaurids. We focus on the evolution of cetacean organ systems, as these document the transition from land to water in detail.