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Week 1 Notes

by: Raquel Notetaker

Week 1 Notes BIOL 1010

Raquel Notetaker
GPA 3.5
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Evolution: Origins of life: the RNA world What is life
Introduction to Biology
Class Notes




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This 11 page Class Notes was uploaded by Raquel Notetaker on Sunday February 7, 2016. The Class Notes belongs to BIOL 1010 at Rensselaer Polytechnic Institute taught by in Spring 2016. Since its upload, it has received 20 views. For similar materials see Introduction to Biology in Biology at Rensselaer Polytechnic Institute.


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Date Created: 02/07/16
Introductory Biology How did life arise? Ingredients for the origins of life 1. Basic elements & basic organic compounds 2. Complex biomolecule(s) capable of replication 3. A membrane enclosure 4. Selection & evolutionary change Were building blocks of life present? 1. All elements are forged in the interior of stars- when a star explodes in a supernova elements blasted into space 2. Many carbon-based molecules including CN, CH3, CO, CO2, amino acids and precursors of nucleotides brought to Earth by asteroids and comets. 3. Early oceans were a chemical factory for rich array of organic molecules Most common elements in living organisms?  Carbon  Oxygen  Hydrogen  Nitrogen  Calcium  Phosphorous  Potassium  Sulfur Formation of Solar System, Earth and Life  Our solar system formed about 4.5-4.6 billion years ago  The Earth’s surface had cooled sufficiently for oceans to form by 4.0 billion years ago  The first fossil evidence of life is about 3.7-3.8 billion years old Stanley Miller Experiments 1953, 23 year old Stanley Miler sets up an experiment to mimic early Earth environment in a flask. The flask contained water vapor, H2, CH4 and NH3. For energy he used heat and a sparking device to mimic the lightning. After a week, he found specific organic compounds, amino acids, the building blocks for proteins. Organic Compounds Hydrogen and other elements covalently bond to carbon to form:  Carbohydrates  Lipids  Proteins  Nucleic Acids Ingredients for the Origin of Life 1. Basic elements and basic organic compounds 2. Complex biomolecules capable of replication Was RNA the original self-replicating molecule?  Ancient viruses use RNA as genetic material, not DNA. Some are still common such as influenzas and hepatitis C  Further evidence lies in diverse role of RNA in all modern cells and discovery of catalytic functions.  Only RNA can initiate DNA replication  RNA regulates gene expression, repairs genes, caries genetic information from DNA to ribosomes.  Ribosome, an ancient molecular complex that assembles proteins is made of RNA + protein. The RNA is part of the catalytic site for peptide bond formation “DNA needed to make proteins but proteins needed to make DNA”  Proteins known as enzymes catalyze reactions essential to cell’s survival  Proteins were thought to be the only biological molecules capable of catalysis  Ribozymes: Catalytic functions discovered  Altman and Cech (1982) discovered RNAs can act as catalysts for chemical reactions. These catalytic RNAs are known as ribozymes  Certain ribozymes called RNA replicates were also found to catalyze their own synthesis RNA World G C  All these lines of evidence suggest use of RNA by early T life forms for genes and replication preceded proteins and DNA  Later more stable and efficient molecules such as DNA and proteins evolved and replaced much of RNA’s functionality RNA World Proto-cell Ingredients for the origin of life 1. Basic elements and basic organic compounds 2. Complex biomolecules capable of replication 3. A membrane enclosure 4. Selection and evolutionary change Lipid Bilayer  Natural bilayers are made of phospholipids having a hydrophilic head and two hydrophobic tails  When exposed to H2) spontaneously form a two-layered sheet with tails pointing toward the center  The cell membrane of all living organism are made of a lipid bilayer, as are membranes surrounding nucleus and other sub-cellular structures Formation of the protocell  Self-assembly of membrane  Permeability of membrane  Division of the protocell How do protocells evolve?  Protocells encapsulated with higher RNA content outcompete protocells with no or little RNA o They may grow by stealing membrane  RNAs must ne replicases and mutation rate will generate better versions and enhance competition with other protocells  Merging with other protocells can bring RNA with other capabilities into the protocell Proto-Cell Competition and Evolution  Replication of RNA molecules within protocell creates osmotic gradient  Cell membrane stretches- grabs fatty acids from membranes of cells with lower RNA replication rates and hence lower osmotic gradients  Via this process cells with higher rates of RNA synthesis divide and grow faster than other cell types- eventually outcompete and take over  Competitive vesicle growth could have played role in emergence of Darwinian evolution at one gene-one cell level Emergent properties Why is the whole greater than the sum of its parts? Emergent properties: From elements to an ionic moleculs  Common table salt  Chemical formula is NaCl  Or salt is one atom of Na+ and one of Cl- Physical Properties of Na+ and Cl-  Properties of Na+ at room temperature o Solid o Molecular weight: 23 o Melting point: +98 C o Boiling point: +883 C  Properties of Cl- at room temperature o Gas, dimer cl2 o Molecular weight: 35 o Melting point: -101 C o Boiling point: -34 C Emergent properties of NaCl  Properties of sodium chloride  Molecular weight: 58 (predictable)  Melting point: +800 C  Boiling point: +1465 C  Na Cl will be a solid at room temperature  Only the molecular weight was predictable from the physical properties of Na+ and Cl- What are emergent properties that add up to the basics for a protocell?  Atoms formed  Atoms combined to make precursor molecules  Precursors form into macromolecules (RNA) and structures (membranes)  Primitive RNAs develop replicase and catalytic activities  Protocells form by primitive membranes enclosing RNAs and other macromolecules Emergence is a property of living and nonliving systems  Emergence of order and self organization in non living systems and living systems are similar  Both depend on energy flows that maintain the systems far from thermodynamic equilibrium  Emergence of self organized chemical systems at some critical density of organic molecules and intermediate levels of energy may have laid foundation for the origin of life  So understanding emergence in simple systems may provide clues to how lifeless molecules led to living cells Emergent Properties- Nonliving systems Belousov-Zhabotinsky s e l i t r a Emergence in non-living systems  Why do ripples emerge in sand? What’s the mechanism? ooCritical mass of interacting sand particles orConstant intermediate energy input e Energy Input b m u N  Self-organized, emergent phenomena seem to defy the Second Law of Thermodynamics which states that inevitably everything in the universe becomes less ordered  “In a system, a process can occur only if it increases the total entropy of the efficient. Some energy is always lost as heatthe processes are never 100%  Entropy is a measure of a system’s degree of organization o High ordered systems have low entropy o Disorganized systems have high entropy Entropy Driven Reactions  If a reaction spontaneous due to a large positive increase in entropy it’s said to be entropy driven  drivenn folding and formation of lipid bilayers are spontaneous and entropy  Both result in decreased entropy of solute but increased entropy of water  They are spontaneous processes Emergent Properties- Living Systems The giant ant hill or the school of fish shown here are visible patterns that are generated by the individual actions of organisms and cannot be said in themselves to by the purpose of any individual A map of protein interactions or food relationships in the environment is an abstract and complex result of biological phenomena, quite incidental to the phenomena themselves Living Systems  One of the most important books in biology  Laid foundations for molecular biology and understanding of DNA and the gene  Life could be understood in terms of laws of physics and chemistry  Pointed out life did not violate the 2ndlaw of thermodynamics  To maintain itself and escape the inevitable dissolution demanded by the 2 nd law, life constantly takes in energy from environment  ‘Living matter evades decay to thermodynamic equilibrium by having a metabolism Life as an Emergent Property  Life is the ultimate emergent property  Life arose as inexorable sequence of emergent evens, each the inevitable consequence of interactions amongst carbon-based molecules  Universe may be organized such that life spontaneously emerges given appropriate conditions and sufficient time Life in a test tube  2002- complete functioning virus created from commercially available ingredients  Synthesized 5386 base DNA chain in test tube  2003- Venter predicts “first living cell” will be synthesized within 5 years Definition of life?  “Localized molecular assemblages that regenerate, replicate, and build new functionality through evolution”  “Transition to life arises when heritable information takes control of thermodynamic self-assembly, energy transduction, and replication”  “Living organisms are open systems that are far from thermodynamic equilibrium. They depend on a constant inflow of energy which they utilize to sustain themselves and make copies of themselves using hereditary information stored in DNA. All living organisms are subject to natural selection and hence evolve and change over time” Simplest known bacteria  Carsonella ruddii  182 genes 159,662 base pairs  Obligate endosymbionts with aphids


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