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Week 2 Notes

by: Raquel Notetaker

Week 2 Notes BIOL 1010

Raquel Notetaker
GPA 3.5

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Evolution: What is Life? Evolution of Cellular Life
Introduction to Biology
Class Notes
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This 13 page Class Notes was uploaded by Raquel Notetaker on Monday February 8, 2016. The Class Notes belongs to BIOL 1010 at Rensselaer Polytechnic Institute taught by in Spring 2016. Since its upload, it has received 19 views. For similar materials see Introduction to Biology in Biology at Rensselaer Polytechnic Institute.


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Date Created: 02/08/16
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 The Evolution of Cellular Life  The three major domains of the living world  Bacteria and archaebacterial lumped together until Woese defined Archaea (1968) Universal Features of Cellular Life All extant cells:  Enclosed by a membrane  Store hereditary information in DNA  Replicate there DNA using the same basic mechanism  Use RNA for transcription of DNA  Translate RNA into protein via tRNA and ribosomes  Use proteins as catalysts  Use ATP for free energy Prokaryotic cell Eukaryotic cell: Animal Eukaryotic cell: Plant Cells are complex systems  500 common cellular metabolic reactions with many interconnections  Most free living Archaea and Eukacteria have 1000-4--- genes  Eucaryotes have more genes and variety of organelles: mitochondria Cell types at different time periods  Hadian period led to possibility of protocells- 4 billion years ago  Prokaryotic (most likely bacterial domain)- 3.5 billion years ago fossil, but possible start at 3.8 billion years ago. Conditions were anaerobic on Earth Next up- Archaea  Extremely small archaea isolated from acid mine drainage in California  Archean are thought to arise slightly after bacteria- about 3.5 billion years ago This is about all that happened for approximately the next 1 billion year  Beginning of anaerobic bacterial photosynthesis about 3.2 billion years ago  Aquifex is an example of a living fossil. It has cyclic photosynthesis and is an extremophile growing at 95C An early non-oxygenic form of photosynthesis Some microorganisms shifted to photoautotrophic mechanism using sun as energy source. Slightly altered pigments, originally used to help early cells avoid excessive heat (hydrothermal vents), converted to photo-acceptors this occurred 3 billion years ago- cyclic photosynthesis. Photosynthetiic bacteria-cyanobacteria  Prior to exygenic photosynthesis there were photosynthetic bacteria  In modern photosynthesis, oxygen is utilized as a terminal electron acceptor. Earliest bacteria used other electron acceptors  Cyanobacterial lineage began with cyclic photosynthesis over 3 billion years ago and increased in diversity and importance along with ability to use non- cyclic photosynthesis Stromatolites and ancient photosynthetic bacteria  To the left are ancient stromatolite fossils where mats of cyanobacterial cells were flattened and compressed by dissolved minerals and sediments to give stratified appearance  To the left are modern stromatolites found in Australia, thought to be similar to those of 3 to 3.5 billion years ago Photosynthesis and oxygen  No oxygen early because there was no source. Oxygen is highly reactive  Development of oxygenic or non-cyclic photosynthesis (2.5 billion years ago) led to slow increase of oxygen present in the atmosphere. This was the start of the Proterozoic Period  Detect oxygen by presence of iron and sulfur oxidized compounds (seen in fossil deposits) Cyanobacteria Evolved Ability to Split H2O  Apart from Cyanobacteria, Photosystems I and II never found together in same bacteria  How did they evolve in Cyanobacteria?  Photosystem I first o Employed light energy to drive existing pathways o Used primitive porphyrin molecules to capture photons  Those genes duplicated and Photosystem II evolved- with a new form of chlorophyll that was a powerful oxidant and could split water  At some point I and II were coupled together successfully Banded Iron Formation  Over next 1.5 billion years O2 levels in the atmosphere slowly increased  When oxygen reached about 15 percent of atmosphere, reacted with iron to form iron oxides  Layers of iron oxide 1000s of meters thick on bottom of ocean  Aerobic respiration became dominant form of metabolism amongst Eubacteria  Anaerobes retreated to marginal environments Modern photosynthesis Chloroplast  Chromosome: circular, naked DNA  Ribosomes: 70s, synthesizes its own proteins  Grows divides and duplicates its DNA  Eukaryotic cell without chloroplast cannot make chloroplast  Wo membranes: inter membrane, ¾ protein, synthesizes ATP using light energy (photosynthesis) 2 Photosystems connected by electron transport chain- generated ATP and NADPH Photosynthesis Transformed the Planet  O2 energizes almost all existing life  Without O2 no multicellular planes and animals  Hence no complex food chains and ecosystems  Without O2 no ozone layer and no oceans  Earth would be like Mars- dry, red, no blue sky When were the first eukaryotes formed?  The lineage is ancient but hard to find during the early prokaryotic period. Not much difference in size from prokaryotes  Evidence of eukaryotic lipids in rocks dated 2.8 billion years ago  But first in fossil record come around 2.1 billion years ago, possibly acritarch Endosymbiont hypothesis  Increase in eukaryotic cell size was enhanced by compartmentalization and presence of endosymbionts 1-1.2 billion years ago  The symbiosis started from an interaction between a more primitive eukaryotic cell and an aerobic bacterium  Interaction may have been parasitism of a eukaryote by a prokaryote or eating of a prokaryote by a eukaryote  In either mechanism, over time the prokaryote evolved to become a mitochondrion or a chloroplast Major Events in the History of Life Pre and Post Cambrian Evolution Glacial Deposits Overlain by Carbonates  Layers of glacial deposits world-wide 750-600 million years ago  Evidence indicates that entire Earth froze for millions of years  Mass extinction took place  Life clung to existence around volcanoes and open ice at equator The Oxygen Revolution  High concentrations of O2 didn’t reach deep sea until about 600 million years ago  Until then deep ocean lacked O2 because of freezing  Not enough O2 to support larger, more complex animals  First Ediacara appear < 5 million years after oxygen level reached 15% of todays  O2 levels continued to rise during pre-Cambrian and Cambrian allowing even larger species to evolve Single Celled to Multicellular  Single cells are highly successful and still comprised of 50% of total biomass on Earth  So why proceed further or what is the advantage of multicellularity? o Collaboration and division of labor allows new resource exploitation Prokaryotic multicellularity  Formation of loose assocations or colonies of single cells  Myxobacteria as an example- live in soil on insoluble organic molecules but form loose clusters of cells that release digestive enzymes that makes it possible to digest the organic matter Ediacaran Fauna: 600-520 million years ago  Discovered in 1946 in southeast Australia- subsequently in Canada and Namibia  Fossils represent the most ancient complex organisms on Earth  Origin and subsequent evolution of many Ediacaran groups remains an enigma Major Events in the History of Life Discovering a Missing Link The Tiktaalik- could live in the sea but also on land


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