Lecture Notes: Chemical and Cellular Evolution PDF

BIO1202 – Genetics and Evolution Chemical and Cellular evolution Lecturer: Dr. Arianne-Elise Harris Chemical evolution The term “chemical evolution” was introduced by Melvin Calvin*. It refers to the synthesis of biochemically important molecules from smaller molecules and certain chemical elements...

BIO1202 – Genetics and Evolution Chemical and Cellular evolution Lecturer: Dr. Arianne-Elise Harris Chemical evolution The term “chemical evolution” was introduced by Melvin Calvin*. It refers to the synthesis of biochemically important molecules from smaller molecules and certain chemical elements Chemical evolution therefore describes chemical changes on the primitive Earth and gave rise to the first forms of life. * Melvin Calvin was a biochemist best known for unraveling the secrets of photosynthesis and explained it through the ‘Calvin cycle’. How did it all begin? It was assumed that smaller “building block” molecules were formed initially and through “polycondensation”, gave rise to macromolecules in later stages of development. Building block molecules were deemed molecules such as amino acids, fatty acids or nucleobases. They may have been synthesized in the atmosphere, hydrosphere or on the lithosphere of young Earth. Endogenous synthesis of CO, CO2, CH4, N20, NH3. Another theory proposes that these molecules may not have been formed on Earth but brought from outer space (within or outside our solar system) by meteorites / comets. Others suggest it could be the combination of the two processes. The BIG BANG All matter concentrated in a single mass and blew apart with a “big bang” A disk-shaped cloud of dust condensed and formed the Sun, and the peripheral matter formed its planets. Heat produced compaction, radiation and impacting meteorites melted Earth. Then, as the planet cooled, Earth’s layers formed and hot hydrogen gas made up the first atmosphere. Stages of chemical evolution: STAGE 1: the primitive environment… Let’s relate this back to our explosion of molecules and gases …. In the first stage, molecules in the primitive environment formed simple organic substances i.e amino acids. Russian scientist Aleksandr Ivanovich Oparin deemed these molecules hydrogen, ammonia, water vapour and methane. Oxygen was lacking, so Oparin proposed that ultraviolet radiation from the sun provided energy for the transformation of these molecules into organic molecules. this is called Abiogenesis This explanation was termed “Spontaneous synthesis” and could’ve only occurred in a primitive environment. STAGE 1– Enter Oxygen… Abiogenesis became impossible when cells began to photosynthesis and added oxygen to the atmosphere. O2 rising in the atmosphere formed the ozone layer which shielded Earth from ultraviolet radiation. The introduction of 02 created a newer version of Oparin’s hypothesis, which contended that the primitive atmosphere also contained carbon monoxide, carbon dioxide, nitrogen, hydrogen sulfide and hydrogen. Evidence to support this can be seen in present-day volcanoes. STAGE 1– Miller-Urey experiment… So is it true or not? Did life begin spontaneously? … In 1957, Stanley Miller and Harold Urey conducted a laboratory experiment to offer evidence that chemical evolution the way Oparin described it, actually occurred. They used: a warm flask (ocean), an “atmosphere” of: water, hydrogen, ammonia and methane. Sparks were discharged into the artificial atmosphere - representing lightning. A condenser was used to “cool” the atmosphere, creating rain that returned water and dissolved compounds back to the simulated ocean. Miller-Urey experiment cont’d… When Miller and Urey analyzed the contents of their solution after a week, they found various organic compounds ! Some compounds included amino acids that compose the proteins of living things. Their results gave credence to the idea that simple substances under warm, primordial seas, can give rise to the chemical building blocks of organisms. Their limitation? – They could not precisely reproduce the conditions of primitive Earth. So in the end, they demonstrated only the plausibility of the spontaneous synthesis of organic molecules. Fun fact: Many called their results “the primordial soup” STAGE 2 – Accumulation of organic molecules In the second stage, simple organic molecules formed and joined together into larger structures (proteins). The units are linked to each other by the process of dehydration synthesis – forming polymers. To prove this however, abiotic synthesis of polymers had to occur without assistance of enzymes. Additionally, these reactions give off water, thus would not occur spontaneously in a watery environment. STAGE 2 – Enter Sydney Fox… Sydney Fox of the University of Miami, suggested that waves or rain in the primitive environment could’ve provided enough energetic force through splashing organic monomers (the primordial soup) onto the hot, molten surface of young Earth. This would have allowed polymers to form abiotically. When Fox attempted this in his lab, he produced proteinoids – abiotically synthesized polypeptides ! STAGE 3 – Protobionts The next stage in chemical evolution suggests that polymers interacted with each other and organized into aggregates – known as protobionts. Protobionts are not capable of reproducing but had other characteristic of living things. Protobionts are described to have semipermeable and excitable membranes , similar to those found in modern day cells. STAGE 4 – Synthesis of RNA. In the final stage of chemical evolution, protobionts developed the ability to reproduce and pass genetic information from one generation to the next. Scientists theorize RNA to be the original hereditary molecule! In 1980, Thomas Cech and his associates at the University of Colorado discovered that RNA molecules can function as enzymes in cells. This meant that RNA could have replicated in prebiotic cells without using protein enzymes Through mutations and errors, variations of RNA molecules could have been produced during replication, thus introducing genetic diversity and variation amongst the cells So in a nutshell…. Given the four stages of chemical evolution: Primitive environment Polymer synthesis Protobiont synthesis RNA synthesis Natural selection, operating on the different RNAs would have brought about subsequent evolutionary development. This would’ve fostered the survival of RNA sequences best suited to environmental parameters i.e temperature, salt concentration etc. As protobionts grew and split, their RNA passed on to offspring and with time, a diversity of prokaryotic cells came into existence. Macromolecules and cellular evolution In the next timeline of evolution, we have the macromolecules. We’ve established that through a series of chemical reactions, the monomeric building blocks polymerize spontaneously under plausible primitive / prebiotic conditions A critical characteristic of macromolecules from which life evolved, is the ability to replicate itself. Only a macromolecule capable of directing the synthesis of new copies of itself would have been capable of reproduction and thus, evolution. There are two major classes of informational macromolecules in present-day: NUCLEIC ACIDS PROTEINS Only nucleic acids can direct their self-replication Nucleic acids Nucleic acids can serve as templates for synthesis because of specific base pairings between complementary nucleotides. A critical step in understanding molecular evolution was thus reached in 1980s, when Sid Altman and Tom Cech discovered that RNA is capable of catalyzing several chemical reactions, including the polymerization of nucleotides. RNA is thus uniquely able to serve as a template for and to catalyze it’s replication. Ordered interactions between RNA and amino acids then evolved into the present-day genetic code, and DNA eventually replaced RNA as the genetic material. The first cell Presumed to have arisen by the enclosure of self-replicating RNA in a membrane composed of phospholipids. Phospholipids are the basic components of all present-day biological membranes including present-day biological membranes. Phospholipid membranes are amphipathic molecules – one portion of the molecule is soluble in water and another is not. They have long, water-insoluble (hydrophobic) hydrocarbon chains joined in water-soluble (hydrophilic) head groups. When placed in water, phospholipids spontaneously aggregate into a bilayer with their phosphate-containing head groups on the outside in contact with water, and their tails on the inside in contact with each other The first cell The enclosure of self-replicating RNA and associated molecules in a phospholipid membrane would thus have maintained them as a unit, capable of self-reproduction and further evolution. Because cells originated in a sea of organic molecules, they were able to obtain food and energy directly from their environment. This is a self-limiting endeavor, so cells needed to evolve mechanisms for generating energy and synthesizing the molecules necessary for their replication. Thus began a controlled, semi-conservative metabolic energy pathway that uses Adenosine 5’-triphosphate (ATP) The mechanisms using ATP are thought to have evolved in 3 stages that correspond to glycolysis, photosynthesis and oxidative metabolism. Evolution through Glycolysis and Photosynthesis Glycolysis provided a mechanism by which the energy in preformed organic molecules (eg. glucose) could be converted to ATP. This ATP is then used as a source of energy to drive other metabolic reactions. The development of photosynthesis is generally thought to have been the next major evolutionary step – it allowed the cell to harness energy from sunlight, independent from the utilization of glucose. Evolution through Glycolysis and Photosynthesis The first photosynthetic bacteria, which evolved more than 3 billion years ago, probably utilized H2S to convert CO2 to organic molecules – a pathway still used by some bacteria present day. The use of H20 in photosynthetic reactions produces the by-product of free 02; this mechanism is thought to have been responsible for making 02 abundant in Earth’s atmosphere. The release of 02 as a consequence of photosynthesis changed the environment in which cells evolved, leading to the development of oxidative metabolism. Evolution through Oxidative metabolism There is debate on whether this came before or after photosynthetic reactions. Debates for oxidative metabolism BEFORE photosynthesis present that with the increase in atmospheric O2, a strong selective advantage was created for organisms capable of using 02 in energyproducing reactions. O2 is a highly reactive molecule, and oxidative metabolism as provided a mechanism for generating energy from organic molecules that is much more efficient than anaerobic glycolysis. Fun fact: the complete oxidative breakdown of glucose to CO2 and H20 yields energy equivalent to that of 36 to 38 molecules of ATP. This is in contrast to the 2 ATP formed by anaerobic glycolysis. Prokaryotes The first living things on Earth were the prokaryotic cells. They exist today as present-day bacteria. Prokaryote fossils were first found in 3.4 million-year-old rock in the southern part of Africa, and in even older rocks in Australia. Some were found to be photosynthetic! All forms of life are theorized to have evolved from the original prokaryotes ~ 3.5-4.0 billion years ago. Prokaryotes in the present day are divided into two groups: 1. ARCHAEBACTERIA and 2. EUBACTERIA. Archaebacteria Live in extreme environments and were most prevalent in primitive Earth. Thermoacidophiles – live in hot sulfur springs (~ 80C and pH value as low as 2). Eubacteria Include the common forms of present-day bacteria These are a large group of organisms that live in a wide of environments, including soil, water and other organisms. Eukaryotes Like prokaryotic cells, all eukaryotes are surrounded by plasma membranes and they contain ribosomes. Eukaryotes are more complex however because they contain a nucleus, a variety of cytoplasmic organelles and a cytoskeleton. The nucleus contains the genetic information of the cell and is organized in a linear way instead of free, circular DNA. The nucleus is the site of DNA replication and RNA synthesis; the translation of RNA into proteins takes place on ribosomes in the cytoplasm. Eukaryotes Eukaryotes are generally larger than prokaryotes and contain a variety of membrane-enclosed organelles (recall what these organelles are ?) Organelles provide compartments in which different metabolic activities are localized. This compartmentalization provided by cytoplasmic organelles is what allows eukaryotic cells to function efficiently. There are two organelles that are critical for energy metabolism and for the continuation of our exploration into cellular evolution: The Mitochondria The Chloroplast The Mitochondria and Chloroplast Mitochondria are found in almost all eukaryotic cells and are critical for energy metabolism. They form the sites for oxidative metabolism and are responsible for generating ATP from glucose. Chloroplasts are the sites of photosynthesis and are only found in plant cells and green algae. Lysosomes and peroxisomes work in conjunction with chloroplasts for digestion and various oxidative reactions respectively. Additionally most plant cells contain vacuoles. These perform a variety of functions including storage and digestion of both nutrients and waste molecules that come about through photosynthesis. N.B: Despite the illustration being green, the mitochondria is NOT in fact green. Mitochondria carry a orange-brown coloration due to the various chemicals composing them. The contain cytochrome C (green), flavin (yellow) and sulfuriron clusters (reddish-brown). The Endo-symbiotic theory It wouldn’t be an evolution lecture, if this theory doesn’t come up ! …. Eukaryotes developed at least 2.7 billion years ago – following from the 1.5 billion years of prokaryotic evolution. Studies DNA indicate that archaebacteria and eubacteria are as different to each other as they are to present day eukaryotes. This indicated a divergence of three lines of descent from a common ancestor – giving rise to archaebacteria, eubacteria and eukaryotes. Interestingly, archaebacterial genes are more similar to eukaryotes than eubacteria – indicating that archaebacteria and eukaryotes shared a common line of ancestry at some point ! This was explored through the ENDO-SYMBIOTIC THEORY aka endosymbiosis. The endo-symbiotic theory This theory is particularly well studied in support of information gained of mitochondria and chloroplasts – both of which are thought to have evolved from bacteria. Both are like bacteria in size, and like bacteria, reproduce by dividing in two. Both contain their own DNA – which encodes some of their components (recall slide 29). The Endo-symbiotic theory The accepted version of this theory states: 1. Mitochondria are thought to have evolved from aerobic bacteria and chloroplasts from photosynthetic bacteria. 2. The acquisition of aerobic bacteria would have been a natural selection process of some anaerobic cells to acquire the ability to carry out oxidative metabolism as the atmosphere became more 02 dense. 3. The acquisition of photosynthetic bacteria on the other hand, would have provided the nutritional independence to perform photosynthesis, utilizing the ultraviolet rays from the Earth’s sun. https://www.sciencephoto.com/media/516060/view/endosymbi otic-theory 4. Both associations were advantageous to their cellular partners and cells containing aerobic (mitochondria) and photosynthetic (chloroplasts) were selected for during evolution. 5. Through time, most genes in these original bacteria became incorporated into the nuclear genome of the cell, so few remains unique to the chloroplast and mitochondria DNA. Plants and animal cells today Continuing cell specialization and division of labour among cells has led to the complex and diverse life observed in modern day. Plants are composed of fewer cell types than animals, but each different kind of plant cell is specialized to perform specific tasks. Cells of plants are organized into three main tissue systems: ground tissue, dermal tissue and vascular tissue. Ground tissue: parenchyma cells (2 types: collenchyma & sclerenchyma) Dermal tissue: epidermal cells – protective coat and nutrient absorption Vascular tissue: xylem and phloem – transport of water and nutrients respectively. Plants and animal cells today Animal cells are considerably more diverse than plants. The human body, for example, is composed of more than 200 different kinds of cells. Animal cells are generally considered to components of five main types of tissues: Epithelial tissue – forms sheets that cover the surface of and line internal organs Connective tissue – constitutes formations of cartilage, adipose, bone etc. Blood – function in O2 transport, immunity and inflammatory reactions Nervous tissue – composed of nerve cells, neurons and are highly specialized for signal transmission throughout the body. Muscle – Force and movement, elasticity and structure, energy consumption and production. A partial list of literature sources used to compile notes and PowerPoint presentation (See Reading material for more) Calvin, M. (1969). Chemical evolution. Chemistry in Britain, 5(1), 22-28. Rauchfuss, H. (2008). Chemical evolution and the origin of life. Springer Science & Business Media. The Origin and Evolution of Cells - The Cell - NCBI Bookshelf https://www.ncbi.nlm.nih.gov/books/NBK9841/