Presentation on theme: "Chapter 3 The Origin of Molecules and the Nature of Life"— Presentation transcript:
1 Chapter 3 The Origin of Molecules and the Nature of Life Figure CO: Hot thermal spring
2 Overview of Molecular Evolution Natural preconditionsLaboratory reproductionOnly on Earth? Elsewhere?Specific locations?RNA, DNA, proteins“organic” moleculesLife = organisms?
3 Prerequisites for the Origin of Molecules Our Sun and the Earth’s orbit (Goldilocks zone)Sun provides steady radiant energyEarth’s nearly circular orbit provides a relatively constant input of light energy(Goldilocks zones)
4 Figure 01: Various Molecules Observed in Molecular Clouds within Our Galaxy There is also much water, H2O, in the universe.Adapted from Buhl, D., Origins of Life 5 (1974):
5 Prerequisites for the Origin of Molecules ChemicalsEarth is chemically diverse, in part because it is part of young solar systemCarbon – an element well suited to be the structural basis of lifeWaterHydrogen and OxygenUniversal solventNitrogen, Sulfur, Phosphate, Iron, etc.
6 Elements Found on Earth 92 occur naturally in nature24 occur naturally in the bodythe most common: H, C, O, Nvital elements for life
7 The Origin of LifeThis is the cover of the first English edition (1938) of the pioneering work of the biochemist Aleksandr Ivanovich Oparin ( ), published in Russian in 1924 (in English in 1936)Oparin elaborated, within the framework of Darwinism, the first successful scientific approach to the problem of the origin of life, modernizing the old spontaneous generation controversy as a new hypothesis of Biogenesis (Abiogenesis)
8 Oparin’s The Origin of Life Oparin’s book stands out as a milestone in science because no one had given serious thought to the problem of the origin of life after Louis Pasteur concluded in 1864 that life always came from pre-existing lifeTo account for life on the Earth, several leading scientists even proposed that the first forms of life were delivered to the Earth from elsewhere (panspermia), but Oparin’s basic premise was that living systems must have arisen from non-living chemicals on the early Earth
9 John Burdon Sanderson [J.B.S.] Haldane (1892-1964) British contemporary of Oparin who independently proposed (1928) a similar hypothesis that conditions on the primitive Earth favored chemical reactions that synthesized organic compounds from inorganic precursors: biopoiesisHaldane had also suggested that the earth's pre-biotic oceans – very different from their modern counterparts – would have formed a "hot dilute soup" in which organic compounds, the building blocks of life, could have formed – the “primordial organic soup” of early oceans, tidal pools or warm ponds
10 J.B.S. Haldane "Theories have four stages of acceptance. i) this is worthless nonsense;ii) this is an interesting, but perverse, point of view,iii) this is true, but quite unimportant;iv) I always said so.““J.B.S. Haldane was perhaps the most brilliant science populariser of his generation.” Arthur C. Clarke
11 Harold Urey & Stanley Miller In 1953, Harold C. Urey and his graduate student, Stanley L. Miller, at the University of Chicago conducted experiments that simulated hypothetical conditions present on the early Earth and test for the occurrence of chemical evolution
12 “Life” Sparked in Test Tubes: The Miller-Urey Experiments Heated water, simulating vulcanism, produced water vapor circulating through the closed system of glass chambersMiller and Urey placed gases into the upper chamber thought to be present in Earth’s early reducing atmosphere, and applied a repeating spark to simulate lightning
13 “Life” Sparked in Test Tubes: The Miller-Urey Experiments Condensers cooled the gases and vapors, causing molecular reaction products to collect in the waterSamples were taken from this water over the next week and analyzedMany simple and some surprisingly complex organic molecules were recovered
14 Miller-Urey ProductsAmong the organic molecules formed were amino acids, basic building blocks of proteinSubsequent follow-up trials, by many other biologists, using various combinations of “primitive atmospheres,” produced even more complex organic compoundsSugars, lipids, and some of the building blocks for nucleic acids were also formed
15 Sidney Walter Fox ( )In 1958 Fox and Kaoru Harada reported that heating dry amino acid mixtures to 180oC produced polymers resembling proteinsThe dry heat actually melted the amino acids and baked out water molecules so that chemical bonds formed that linked the amino acids together into polymers they called thermal condensation products, or proteinoids
16 Sidney Walter Fox ( )In the 1960s, Fox and his collaborators found that under certain conditions proteinoids assembled into microscopic spherical balls, which they referred to as proteinoid microspheresThese were similar to the coacervate described by Oparin, and the fact that they were composed of amino acid polymers made them a more attractive model of a prebiotic protocell than the mixture of gelatin and gum arabic that Oparin had studiedFurthermore, dry heat seemed to be a very plausible energy source for driving condensation reactions
17 Chemical Development of Prebiotic Organic Compounds - How? coacervate dropletsOther simulation experiments can generate building blocks from the primordial soupMiller and Urey formed amino acidsGaseous H2, CH4 (methane), NH3(ammonia), H2O(steam)Sparks (simulate atmospheric lightning)Oparin and Fox formed protobionts, proteinoids, & microspheres (also called coacervate droplets)These molecular collections mimic cell behavior, but are non-living
18 Replicating the Production of the First Molecules in the Laboratory Miller-Urey type experiments continue to be carried out to this day, using a variety of ingredients and experimental conditionsEvolution of carbon-based molecules was not as unlikely an event as had previously been thought
19 Possible Sites for the Origin of the First Molecules on Earth Hydrothermal ventsThermophilic (heat-loving) organismsVolcanoesSponge-like minerals (zeolites) that can retain and catalyze organic compoundsClaysLayered clays served as polymerizing templates
20 Chemical Development of Prebiotic Organic Compounds -How? Bada and Miller's “sub-ice organic gazpacho” theory (ice as a catalyst for abiosynthesis reactions)Amino acids of extraterrestrial originCarbonaceous chondrite meteorites contain organic compounds, amino acids, fatty acids, etc.Murchison Meteorite, Australia (L) and Allende Meteorite (~2 tons), Mexico (R)
21 What Came Next From the Primordial Organic Soup? Phospholipids (of an appropriate length) can spontaneously form lipid bilayers, a basic component of the cell membrane.The polymerization of nucleotides into random autocatalytic RNA molecules might have resulted in self-replicating ribozymes (RNA world hypothesis).Natural Selection pressures for catalytic efficiency and diversity result in ribozymes which catalyse peptidyl transfer (hence formation of small proteins), since oligopeptides complex with RNA to form better catalysts. Thus the first ribosome is born, and protein synthesis becomes more prevalent.Proteins outcompete ribozymes in catalytic ability, and therefore become the dominant biopolymer. Nucleic acids are restricted to predominantly genomic use.
22 Increased Complexity of Organic Molecules - How? Amino acids are monomersMonomers must peptide bond to form proteinsThis requires an input of energy and removal of waterHow could this occur?Evaporation?Tidal pools?Freezing?Chemical dehydration?Bonding to charged mineral surfaces?Clays? Pyrites?
23 Biopoesis AgainBiologist John Desmond Bernal ( ) coined the term Biopoesis for this process, and suggested that there were a number of clearly defined "stages" that could be recognized in explaining the origin of life in the 1960s.Stage 1: The origin of biological monomersStage 2: The origin of biological polymersStage 3: The evolution from molecules to cellBernal suggested that evolution (natural selection) may have commenced early, some time between Stage 1 and 2.
25 BiopoesisAbiogenesis/Biopoesis remains an exciting area for current research
26 DNA, RNA and ProteinsThree fundamental classes of molecules are associated with modern lifeReplication, transcription, translationFigure 03: DNA replicates and information is transferred from DNA to RNA to protein
27 The mystery: which came first, DNA, RNA, or protein? Figure 02: Mutual Dependence of Information Carried by Nucleotide SequencesThe mystery: which came first, DNA, RNA, or protein?
28 Which of These Molecules Evolved First: DNA, RNA or Protein? DNA First? (“DNA World”)Protein synthesis depends on the prior existence of RNA and DNA.Proteins First? (“Protein World”)Some amino acid polypeptides form without DNA.RNA First? (“RNA World”)RNA could catalyze chemical reactions and replicate
29 History of Chemistry for the Origin of Life The RNA World refers to a hypothetical stage in the origin of life on Earth
30 It Was a Small RNA World After All The phrase "The RNA World" was coined by Walter Gilbert in 1986 in a commentary on the then recent observations of the catalytic properties of various RNAsHowever, the idea of independent RNA life is older and can be found in Carl Woese's book The Genetic Code (1967)Five years earlier, the molecular biologist Alexander Rich, of the Massachusetts Institute of Technology, had posited much the same idea in an article
31 The RNA WorldDuring the time of the RNA World, proteins were not yet engaged in biochemical reactionsRNA carried out both the information storage task of genetic information and the full range of catalytic roles necessary in a very primitive self-replicating systemLater RNA catalyzed the formation of DNA
33 Quick ReviewWere there other early lifeforms with other molecular mechanisms of inheritance beyond the “RNA world?”Who knows?Perhaps finding life elsewhere in the universe will demonstrate them?Nucleic AcidsDNA ReplicationRNAsTranscriptionTranslation
34 Nucleic Acids DNA is the genetic material made of 4 building blocks – nucleotidesadenine (A), guanine (G), cytosine (C), thymine (T)A-T, C-G in the chaindouble helix modeldouble stranded DNARNA carries hereditary information from nuclear DNA to the cytoplasm (inside cells)uracil (U) replaces Tsingle stranded RNAComplimentaryBase-Pairing
36 DNA Forms a Template for Its Semiconservative Replication
37 DNA Replication semi-conservative helicase – unwinds DNA DNA polymerasesone strand is the templatebuilds a complementary strandbases pair with hydrogen bondsA-TC-G
38 DNA Replication Enzymes DNA Primase, DNA Replicase, DNA Polymerase III, DNA Polymerase I(DNA Polymerse II is a repair enzyme)
39 DNA Replication in a Bacterium The circular bacterial DNA begins replication at a single site, the replication originReplication proceeds out in both directions, until copies of each strand of DNA are produced
40 Information Transfer— DNA to RNA to Protein DNA triplets transcribed to produce complementary codon triplets in mRNAEach mRNA codon triplet specifies a particular amino acidSequentially, codon by codon, the mRNA is a blueprint used in translation to produce a particular protein molecule
41 Three RNAs in Protein Synthesis Different types of RNA play a different role in the synthesis of protein.mRNArRNAtRNA
42 Two Stage Protein Synthesis Transcription (in nucleus*)DNA – gene blue printtriplet code - 3 bases/AAtemplateexons - expressedintrons – excisedRNA – tools for protein synthesismRNAtRNArRNATranslation (in cytoplasm)Ribosomecodons are read to build a primary protein structure* No nucleus in the prokaryotes
47 In Organisms, Information Flows from DNA to RNA to Proteins The Central DogmaOf Molecular BiologyThe Genetic CodeIsUniversalandRedundantUnambiguous
48 The Genetic CodeThe code is universal because it specifies the same 20 amino acids in all organisms with only few exceptionsThe code is redundant because there are multiple codons which code for the same AAThe code is unambiguous because any one codon codes for only one amino acidThe code is a triplet code because 3 bases represent a single AA in a codon
49 The Lac OperonThe Lac Operon is a classic example of negative feedback gene regulation in prokaryotes
50 The Lac OperonWhen lactose is absent then there is very little Lac enzyme production (the operator has LacI repressor bound to it)When lactose is present but a preferred carbon source (like glucose) is also present then a small amount of enzyme is produced (LacI is not bound to the operator)
51 The Lac OperonWhen lactose is the favored carbon source (e.g., in the absence of glucose) cAMP-CAP binds upstream of the promoter at a specific siteThis allows the RNA polymerase to bind to the promoter and Lac enzyme production is maximized
52 Why The Lac Operon? Consider mice : life span perhaps 2 years Mouse pups weaned at 3 weeksIn optimal growth conditions E. coli will divide every 30 minutes3 weeks is at best, 1008 E. coli generations2 years is at best, E. coli generations
53 Molecules and Life What is Life? Associated with DNA, RNA and proteins DNA as the central molecule of life – hereditable information; Carbon -- structural, physiological and metabolicOrganic molecules can be formed abioticallyDid life begin with molecules around 4.5 Bya, with cells 3.5 to 3.8 Bya, or with the first proto-organisms at some point in between?
54 What are the Properties of Life? Organization: Composed of one or more cells, the basic unit of life.Metabolism: Transform energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism) to generate useful energy.Homeostasis: Regulation of the internal environment to maintain a relatively constant state.Growth: Maintain a higher rate of anabolism than catabolism to increase size and complexity and repair damage to the cell or organism.Adaptation: The ability to change over time in response to the environment. Individuals develop and populations evolve.Response to stimuli: A change in activity (metabolism, behavior, etc.) appropriate to the change in the environment which was the stimulus.Reproduction: The ability to produce new individual organisms, either asexually, or sexually.
55 Living SystemsThe Central Dogma: DNA RNA Protein explains how life on earth today, and since the RNA World was replaced by the DNA World, manages to achieve those seven fundamental propertiesFigure 03: DNA replicates and information is transferred from DNA to RNA to protein
56 Enzyme Action and Regulation 4/15/2017Enzyme Action and RegulationEnzymes are protein catalystsEnzymes are key products of the genetic blueprints for living systemsAgain, it is thanks to enzymes that living systems achieve the seven fundamental properties of life