Study Guide for Exam 1 on Principles of Organismal Biology | BSCI 207, Study notes of Biology

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Lecture 1- Thermodynamics  all organisms have common physiochemical principles  they all have a common ancestor (LUCA) and all like is related  unique evolutionary histories Thermodynamics Pre-requisites for Organisms Energy for Free Bioenergetics Molecules for Free Metabolism Order for Free Structure Variation Evolution  Origin of Life- the earliest protolife o Metabolic reactions with in an enclosed regionconsequences  Separation of life and environment  Gradients of molecules across membrane  Different molecules and energy sources in protolife o Early life forms had to  Harness physiochemical processes  Evolved hereditary molecules to relay the solutions to next generation  Evolution allows the new organisms to better adapt to the solutions  Thermodynamics- study of energy transformations o system- area of interest o surroundings- rest of universe o closed vs. open  closed- don’t share energy with the surroundings  open- share energy w/ the surroundings o example: cellular respiration  energy into cell in form of light  transformed into ATP energy  waste CO2 is released  Thermodynamic Definition of an Organism (open system) o Consume high quality free energy o Release low quality free energy (heat) o Maintain ordered structures at the cist of decreased universal disorder  In organisms MOLECULES carry out all energy transformations  Organisms set up electrochemical gradients across membranes o Transport energy o Electron gradient- a difference of concentration charge across a membrane o Transport ions/ transforming gradients == ATP and vice versa  Enthalpy (H)—total energy of a system including chemical bond energy, phase, concentration, and order  First Law of Thermodynamic (ΔH)H) o Energy is neither created nor destroyed o However, it can be transformed into another type o ENERGY IS FOR FREE!!  Photosynthesis (electromagnetic light E)Chemical E and Heat E (organic molecules)  Respiration (Chemical E organic molecules) Chemical E ATP and Heat E  LIFES CHALLENGE transform available energy into useful form at the right times and right sights  Energy and reactions flow in a certain way—many are no reversible  Enthalpy and Work o H==G+TS  H- enthalpy  G- free energy in a system that’s available to do work  T- Temperature  S- Entropy—energy unavailable to do work, the disorder in a system  Second Law of Thermodynamics o All processes proceed in the direction the reduces the free E available to do work o Spontaneous G1>G2 and ΔG<0G<0 o All processes proceed in the direction that increases entropy, increase the energy unavailable to do work o Spontaneous S1>S2 or ΔG<0S>0 o Entropy is always increased  Spontaneous processes (ΔG<0G<0) o Occur if:  Products have lower potential energy than their reactants  Example: o Slide (high E, potential E) lose energy to friction, soil, air, etc.  less energy o Reaction decreased available energy and increased unavailable energy  When product molecules are less ordered than reactants  Example: o Wood is structured but when burned that molecules are freer and less structured  Follow the Heat!! o Heat- increase random molecular movement lowers the quality of useful energy Lecture 3- Information and Entropy  Information- reduction of uncertainty  Information Theory o Stability- constancy of conformation content o Fidelity- accuracy of information readout, how faithfully info is read o Entropy- degradation of info content, increase of randomness o Redundancy- number of info copies, increase the ability to maintain long term stability  Information Flow “Central Dogma”Central Dogma” o DNARNAproteins  Mutations is the equivalent of entropy  What was the first info system like??  What is Life o Genetic information is encoded in molecular structure o Genetic material is an “aperiodic crystal”  Not predicable , a level of variation  The variation allows to code different pieces of info  Variation in coding allows transmission of many different info o DNA=crystal!!!  Primitive Genetic Material- which was used?? o Inorganic crystals vs. nucleic acids o Inorganic crystals  High stability between generations (little entropy)  Very unlikely to change ions, shapes, etc.  Poor fidelity of crystal growth with in generations  Info gets distorted when growing new crystals o Nucleic Acid  Modest stability between generations (more entropy)  Mutations in reproduction  Poor fidelity with reading errors and mutations from generation to generations o Inorganic crystals are much better info store so it was once believed:  Silicon based life forms  C and Si have similar valence properties  Highly stable  Really abundant  However  Variability is good!!  Ability to evolve and adapt with variation  Silicon and inorganic cannot adapt or change, nucleic acids respond to selection !!!! o Sloppy info storing = good = pathway to evolve  Primitive Genetic Material = DNA vs. RNA o DNA- more stable, less error prone, not autocatalytic, double strand o RNA- less stable, more error prone, no redundancy, single strand, autocatalytic  RNA World o RNA probably first because autocatalytic and variation is very high so evolution towards those with effective replication processes o Boundary is helpful and protects from surroundings and controls access to info  They are very ordered  Lipids spontaneously form boundaries in h2o (phospholipids structures)  They are spontaneous= thermodynamically favored life takes advantage of it!!  Order from non- order o Hydrophobic interaction  Monolayers and bilayers form spontaneously  Spontaneous biological order at expensive of universal disorder o Self folder polypeptides  Assembly is spontaneous  Primitive Organisms o high quality energy taken in a release low quality energy o adaptive info storage system o take advantage of spontaneous rxns to increase universal disorder Lecture 4- Unity and Diversity of Life  organisms exploit many physiochemical processes o spontaneous reactions (thermodynamic) o moderately stable information storage to allow for adaptation o diffusion along gradients and evolve transport systems where diffusion ineffective  History matters- innovations produced by early life forms retained and enhanced later organisms  Phylogenies o Representation of relationship between organisms  Understanding for unity of life  Evolutionary innovations o Similarities (primitive, convergent, derived)  Primitive similarities  Single origin in distant ancestor and doesn’t imply close relationships  Homologous structures for example  Convergent similarities  Independent origins- doesn’t imply close relationship  Analogues structures  Derived Similarities  Single origin in relatively recent common ancestor  Implies close relationship  Phylogenies- 3 basic methods o Evolutionary taxonomy  Degree and timing of divergence  How dis-similar, how large the differences are, (degree)  How recent they shared an ancestor  Can be subjective  Is degree or timing more important in a specific group o Phenetics  Based ONLY on degree of divergence  Less subjective than evolutionary taxonomy  Makes no evolutionary assumptions (homology and analogy are equally important)  Strong correlation between level of similarity and relatedness o Cladistics  Based ONLY on timing of divergence  Based on synapomorhies  Less subjective than evolutionary taxonomy  Assumes evolutionary relationships and ignores analogies  2 types of homologous traits