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8/30/21 - Integrate Biology Chapter 1 Section 1- Section 1.1: Thermodynamics ● Living things can capture energy from environment and dissolve energy into heat more effectively than just a clump of carbon atoms ● Earliest forms of life evolved to manipulate thermodynamics to enable their bioenergetics, metabolism, and structure ● Lot of theories and experiments about how such highly organized life arose from random molecule assortments ● All organisms require order of cells (organelle, cells, tissues, organs, organ systems, organisms, populations, communities, ecosystem, and biosphere) but different cells in differing organisms function differently ● Organisms adapt to energy resources available in the environment; energy used to perform chemical reactions (metabolism) Section 1.2: Laws of Thermodynamics ● Thermodynamics is study of energy and its transformations; intersection between physics and chemistry ● Determines energy exchanged in a system and ability of the energy to perform work ● Energy conversion/processing is controlled by thermodynamics and two fundamental laws ● 1st law: energy can only be transferred or transformed. NOT created or destroyed ● 2nd law: every spontaneous reaction increases the entropy of the universe ○ Energy disperses, and systems dissolve into chaos. The more disordered something is, the more entropic we consider it. Entropy is a measure of the disorder of the universe ● Life is collection of organized molecules that can metabolize, grow, reproduce, responde, and evolve (controlled all by thermodynamics) ● Chemical reactions necessary to break/form bonds making up an organism is dependent on the energy sources available (1st) and whether the reaction can occur without any energy input (spontaneous, 2nd) ● Thermodynamics determines which rxns can provide energy for life and which can’t Section 1.3: Key Thermodynamic Concepts ● System: region being studied ● Surroundings: rest of the universe ● Enthalpy: organisms where temperature and pressure are constant, total energy of system is determined by enthalpy ○ Includes energy that can do work and energy that is due to disorder and can’t do work ● Change in enthalpy for a chemical reaction is enthalpy of final state minus enthalpy of initial state ○ ΔH = H final state, products - H initial state, reactants
● Positive ΔH indicates products have more enthalpy (energy) than reactants; energy was added; reactions are endo thermic because heat EN ters the system ● Negative ΔH indicates products have less enthalpy (energy) than react; energy was removed; reactions are exo thermic because heat EX its system ● Free energy (G): energy in system used to do work; availability of free energy might be due to change in potential energy (height) or change in chemical energy (bonds) ○ ΔG = G final state, products - G initial state, reactants ● If the reactants and products include more than one molecule, such as A + B → C + D, free energy could be written as ΔG = GC + GD – GA – GB ● Positive ΔG indicates products have more free energy than reactants; energy was added; end ergonic because free energy EN ters ● Negative ΔG indicates products have less free energy than reactants; energy was ex ergonic because free energy EX its ● Entropy (S): measure of disorder in a system; related to ways of arranging a system ○ Knocking something over causes things to scatter and increases disorder ○ More gas = more disorder ○ Melting ice is more disorder ● ΔS = S final state, products - S initial state, reactants ● Positive ΔS is more disordered ● Negative ΔS is less disordered Section 1.4: The Thermodynamic Equations and Laws Used in Biological Systems ● 1st law: relationship between enthalpy, free energy, and entropy ● First law of thermodynamics = total energy is conserved; with constant temperature and pressure, the equation looks something like ○ ΔH = ΔG + T ΔS ○ Where ΔH is the change in enthalpy, ΔG is the energy that can perform work, T is the absolute temperature in Kelvin (K), and ΔS is the change in entropy. ● Total energy of the system is a result of chemical work that occurs plus heat that increases the disorder ○ No work/no change in disorder = no change in energy ○ Adding energy = some does work and some is lost as heat ● Energy must be balanced in a system and flow from one type to another ● To change the energy of a system you have to put energy in ● 2nd law: disorder (entropy) of the universe is increasing; spontaneous processes increase disorder by releasing energy; non spontaneous processes also increase disorder by relying on external energy to run ○ Energy is transferred inefficiently so heat lost to the universe also helps increase disorder ● Gibbs free energy is used to determine whether the rxn is spontaneous in forward or reverse direction
Section 1.6: Implications of the Second Law ● Universe is the ultimate closed system ● 2nd law states entropy of a closed system (universe) must increase ○ For processes to occur that result in decrease in entropy on a local scale, must be compensated by increase in entropy somewhere else in the universe ○ Organisms are an example of ^ this trade-off ○ Subsections of the universe can decrease in entropy and become ordered but the rest of the universe must then increase in entropy to balance the decrease ● Sun is a supplier of this entropy ○ As sun burns and gives off energy, the entropy increases ○ Of all energy the sun showers over earth, small portion is used by life to create its order ○ Solar energy is used inefficiently by organisms ○ Wasted as heat energy that spreads out to increase the entropy of universe ○ Heat lost in energy conversions and chemical rxns balances the decrease in entropy due to life on earth ● Sun is a massive source of energy and thus, entropy ● Order of life is contingent upon sunlight energy sinks on earth ○ Processes creating this order also releases unusable heat energy into the universe ○ Heat/energy released counterbalances order created on earth ○ Difference between a cluster of carbon and organism is latter can capture energy from environment and dissipate energy as heat much more effectively ● 2nd law is one of the few definite laws that guide how energy is processed and which reactions can occur
○ Overall increase does not prevent localized decreases in entropy Section 1.7: Summary ● Life exists by converting available energy into usable energy to perform chemical reactions and physical work ● Processes that characterize life are: order, stimuli sensitivity, reproduction, growth, development, homeostasis and energy processing ● Every rxn facilitating these processes is contingent on energy processing and laws of thermodynamics ● First law regulates energy conservation and second law regulates whether a rxn can happen ● Complexity of life does not defy the Second law because order in an organism’s system comes with a price: energy lost as heat ● Unusable energy is released into universe and increases disorder/entropy of universe ● Organisms adapted to energy resources available in their environment ● Processes occuring in our body and to the existence of life on the planet can be understood by applying thermodynamics and math 9/3/ Class Notes: Lesson 3 Thermodynamics and Entropy GAE Recap ● Laws of physics ○ Conservation of matter: we don’t create out of nowhere ○ Conservation of energy (thermodynamics) ● Open vs closed systems: organisms ○ Open system: stuff can go in and out ○ Closed system: nothing goes in or out ● Open vs closed systems: cells ○ Nutrients energy and oxygen going in ○ Waste CO 2 heat going out ● Open vs closed systems: Earth ○ Light in, heat out ○ Energy arrives on earth, is transformed by life, and then flows out again ● Sources of biological energy: lightning, light, chemical energy (ATP) , thermal energy ● What ATP is used for: ○ Active transport ○ Movement within the cell ○ Metabolism ○ Cell division ● Organisms can do chemical work and physical work ● Chemical work to generate high energy molecules (Ex) ○ Metabolite: any molecule transformed in a metabolic rxn
○ Can never convert all the initial energy into work ○ Some energy is lost as heat, increasing disorder, TdeltaS ● Delta G is energy available to do work ● Organisms will always release heat, increasing disorder of surroundings and hence universe ○ Delta S has to be greater than 0 ● ΔH = ΔG + TΔS ○ For closed system, ΔH = 0 ○ ΔG = -TΔS ○ Spontaneous reaction must obey this relationship and so ΔG< ● For spontaneous reaction ΔG< ○ ΔG = Gfinal - Ginitial < ○ Free energy of initial state > final state ○ Reactants have more energy than products ● For closed system, a spontaneous reaction will obey ΔG < ○ Free energy of initial state > free energy of final state ○ Reactants have more energy than products ● If a reaction is not spontaneous, it can become spontaneous if it incorporates another high energy reactant ○ It can become spontaneous it if incorporates another high energy reactant (ATP) ● Conclusions from 2nd law, ΔG < ○ Spontaneous reactions (no additional energy) proceed in the direction that reduces free energy (useful energy available to do chemical work) ○ OR ○ In biological systems, spontaneous bioenergetic and metabolic reactions tend to proceed in direction that releases unusable heat into environment ● Although many reactions are exergonic, they don’t all happen spontaneously ○ Activation energy: energy needed to initiate the rxn to begin with ● Metabolism: the role of catalysts ○ Potential biocatalysis: inorganic catalysts, enzymes with metallic ion cofactors, enzymes lacking cofactors ○ Life’s challenge is to transform available molecules into useful molecules at right sites and times ○ Genome encodes the enzymes for meeting this challenge ● Plausible evolutionary scenario ○ Metallic ions/complexes were used as catalysts for most metabolic rxns in early protolife ○ Evolutionary relics: metallic cofactors at active sites of many enzymes of ancient origin ○ Most enzymes of more recent origin use only amino acids in their active sites
Section 3: Implications of 2nd law ● For a spontaneous process, the universe is getting more disordered over time ● For a physical system, when there is no chemical reaction, the entropy of the universe is increasing ○ ΔSunierse > 0 ○ Entropy is measure of disorder ○ Things that can lead to disorder are movement and mixing ● If there's no change in G, then ΔH = TΔS ○ Entropy correlates with heat loss in biological systems ○ Heat goes to increasing disorder of surroundings ● Organisms can use entropy increases in their surroundings and hence the universe to drive biological order, in particular “self-assembly” ● Membranes are composed of phospholipids ○ Hydrophilic head group and hydrophobic tails ○ Polar head group is charged phosphate ○ Tails are fatty acids ○ Amphipathic ● Why do these form lipid bilayers spontaneously ○ Lipid molecules in aqueous solution are surrounded by ordered arrays of water molecules ○ When lipids assemble, water is released, entropy is increased, and assembly is favored ● Self assembly forms bilayer that is charged outside (close to polar water molecules) and hydrophobic inside ● First membranes -- the separation of life from non-life ○ Hydrophobic interactions: drive formation of lipid vesicles for bounding early life forms ○ Spontaneous local order maximizes universal disorder ● “Hydrophobic interactions” ○ Non-polar molecules tend to neither attract or repel each other ○ Polar water molecules attract or repel one another ○ Polar and/or charged molecules tend to squeeze hydrophobic regions together ● Protein folding Polypeptide Adjacent water molecules Unfolded state Various configurations with exposed hydrophobic amino acids (intermediate S) Ice-like shells around exposed hydrophobic amino acids (low S) Folded state Active protein with Water molecules freely
○ Sequences that are NOT under selection change more quickly ■ Introns ■ 3rd positions of DNA sequence (don’t affect protein sequence) ○ Sequences that are selected change more slowly ■ Exons ■ Protein sequences ● Some sequences are very strongly selected to stay the same ○ Exonic DNA that specifies amino acids (1st and 2nd positions of codon) ○ Certain proteins that are critical to organismal function ■ Histones ■ Ribosomal RNA ● Rate of sequence change depends on balance between mutation and selection (fast to slow) ○ Change in mtDNA >>> nuclear DNA ○ Change in intros > coding sequence ○ Change of 3rd position of a codon > 1st and 2nd positions ○ Highly constrained genes ● In comparing closely related species, need enough sequence differences to compare ● Comparing distantly related species, need sequences that change some but not too much ● Section 2: Carl Woese’s Tree Prokaryote phylogeny ● Woese’s interest ○ Identify the eukaryote ancestor ○ Understand prokaryotic evolution ○ Determine the ancestral gene families ● Problem: Morphologies of prokaryotes are very similar ○ No characters for determining phylogenetic relationships ○ Had to await molecular revolution of 70s ● Woese chose rRNA as his molecular of choice ○ Critical for translating mRNA into protein ■ All organisms have it so no lateral gene transfer
○ Many critical domains that must fit together with 2 other rRNA subunits and 49 different ribosomal proteins ■ Strong selection so slow mutation rate ■ Good molecular clock for deep evolutionary times ● Carl Woese discovered Archaea Section 3: Rooting the Tree ● Problem is that in building the tree, there is no way to know which of the lineages came first (Eubacteria, Eukaryotes, ArchaeBacteria) ● Limits to molecular data ○ Determines organismal similarity ○ No temporal order -- can’t tell which came first ○ Need additional information -- where is root of the tree? ○ ● Fossil record sometimes provides context to determine the ancestor/outgroup ● Fossil record can help ○ In the example, jawless fish occurred first in the fossil record ○ Lineage is ancestral and so the outgroup to the other two ○ ○ ● But there isn’t much fossil record for prokaryotes/Three possible relationships depending on rooting of tree
○ Thermotolerant genes nearly identical ○ Hints that all is not so simple ● Likely because of horizontal/lateral gene transfer ○ Vertical gene transfer: the transmission of DNA from parent to progeny ○ Lateral gene transfer: the transmission of DNA between unrelated organisms ● rRNA sequence model of universal tree of life ○ rRNA tree ■ Assumes VGT ■ Predicts LUCA ○ rRNA tree is probably close to the true phylogeny of the major lineages of post-LUCA (Last Universal Common Ancestor) organisms ○ But some genes do undergo lateral transfer ● Whole genome model of universal tree of life ○ Recent LGT of physiological and metabolic genes that give selective advantage ○ Post-LUCAC (Last Universal Common Ancestral Community) - divergence of distinct lineages with differing levels of LGT ○ Very early/Pre-LUCAC - interacting community of self replicating organisms with lots of LGT → very rapid evolution ● One very special lateral gene transfer event: two domains of life merge to make eukarya through “ring” of life ○ Bacteria that became mitochondria was an a-proteobacteria ● Archaean ancestor of eukaryotes from Asgard lineage of archaeans ● New data from spring 2017 suggests ancestor of eukaryotes is Heimdallarchaeota ● Perhaps there are just two domains of life, but we’ll keep the three domain for now ○ Key Ideas ● Molecular sequence can be used to build phylogenetic trees ● Woese used rRNA to build tree of life 9/13/21: Class Notes - The Origin and Evolution of Life: A Product of Cosmic, Planetary, and Biological Processes Section 1: The “Mother” of all questions ● Cosmos formed 15 BYa + Earth formed ~4.5 BYa at just the right distance from sun
● Prebiotic earth: chemicals formed in the ocean and their complexity increased ● Evolution of early life: microbial organisms as early as 3.5 BYa and multicellular organisms by 1-1.5 BYa ● Evolution of more advanced life: more complex life forms arose 570-540 MYa and animals/plants/aquatic origins/terrestrial invasion around 441-416 MYa Section 2: Hypotheses ● Why is it hard to answer how life began on Earth? ○ Earliest steps in life’s evolution can no longer be observed ○ Even simplest extant life forms are complex ○ Unclear what molecules (DNA/RNA/proteins) were used to store information ● What is necessary for life? ○ Ability to metabolize and make energy available to do biological work ○ Ability to pass down genetic information ○ Cells to contain genetic information and metabolic enzymes ● Hypothesis 1: Metabolism first (importance of early atmosphere) ○ Oparin and Haldane suggested ordered set of chemical reactions was beginning of life ○ Life seeded by hydrothermal vents ○ Testing the iron - sulfur world hypothesis ■ Thermal vents are high temp and high pressure ■ Mineral clusters drive generation of complex organic molecules (pyruvic acid/nucleotides/peptides) ■ Laboratory experiments have demonstrated that steps in citric acid cycle can occur ○ Speculative “evidence” for early metabolism and iron-sulfur world ■ Metal atoms form the core for key enzymes ■ Cytochrome C: Cu and Fe ■ Nitrogenase: Fe and Mo ○ Thermophilic archaea and bacteria are closest to the root of tree of life ● Hypothesis 2: Information first ○ Organism can not evolve without a way to pass on information ○ Without information to provide consistency, “organisms” change at random ○ Life begins with inheritance and the passing of information ○ Why do organisms need to store information? ■ Store info on how to interact/survive in their environment (code for set of enzymes) ■ Pass information from one generation/cell to another (improve their survival) (genetic materials - DNA/RNA) ■ Use a genetic code to interpret genetic information to produce enzymes ○ Information flow is similar to most present day organisms
○ Inherent redundancy (double stranded) ○ Not autocatalytic ● Why is RNA less stable? ○ Single stranded (more prone to errors) ○ No redundancy ○ Ribose is more reactive ○ Autocatalytic ● DNA RNA Protein Can replicate Yes Yes No Stability More Less Much more Errors Fewer More Fewer Redundancy Double strand No No Act as enzyme No Yes Yes ● RNA can be an enzyme ○ Tom Cech’s lab studied RNA splicing in Tetrahymena ○ RNA acted to splice itself - no protein needed ● RNA at the heart of mRNA translation ● Primitive genetic material: rNA is first information storage system in organisms -- “RNA world” ○ RNA carries genetic information ○ RNA can catalyze reactions (like proteins) ○ Selection will favor variants with effective replication Section 4: Key ingredients - Incrediblists vs Inevitablists ● Key elements of life ○ Abiotic synthesis: make small organic molecules (amino acids and nucleotides) from inorganic ones ○ Join these building blocks into macromolecules (proteins, DNA/RNA) ○ Spontaneous organization (from protobionts: earliest cells) ○ Self-replication (make copies of self for inheritance) ● Chemical evolution proposed by Oparin - Haldane (‘20s) ○ Early earth’s atmosphere did not have oxygen ○ Simple molecules (H 2 , N 2 , CO 2 ) react to produce small organic compounds (H 2 CO, HCN) ○ Small organics react to form key building blocks (amino acids → proteins, nucleotides → nucleic acids, sugars → complex carbohydrates) ● Where did simplest organic molecules come from?
○ Cold source ■ Miller and Urey (‘50s) simulated conditions of early Earth ■ Inorganic molecules + energy → organic compounds ○ Hot source ■ Organic molecules could be made near the high temperature thermal vents on ocean floor ○ Out of this world source ■ Organic molecules may arrive on meteors ■ Murchison asteroid (1969) - had 6 AA and amphipathic lipids ● How do we get from simple to complex molecules? ○ May have happened on an inorganic substrate where metal ions can catalyze reactions ● Spontaneous organization ○ Hydrophobic interactions of amphipathic lipids ○ Biological “local” order at expense of universal disorder ● Protobionts : aggregations of abiotically produced molecules ○ Proto- first ○ -biont discreet unit of living matter ○ Inside proto-cell can maintain unique chemistry ● Self Reflection ○ RNA 1st DNA 2nd Stability Less More Catalyze reactions including replication? Yes No Proteins req’d for information transfer? No Yes Section 5: Alternative scenarios ● Alkaline hydrothermal vents are cooler than hot smokers ● Chemistry happened in porous rocks where “cells” are spaces lined with FeS ● Pores in rocks can act as cells enabling key chemicals to accumulate to higher concentrations ● Opportunity for important chemistry ○ Natural proton gradient: alkaline effluent inside rock; acidic water in ocean (dissolved CO 2 ) ○ Early “cells” can take advantage of proton gradients: Evolution of ATP synthase to convert the energy of moving protons into ATP; ATP synthase is shared by all of life and arose just once
● Some things to explains: differences in cell membrane and cell wall ○ ● Some things to explain: differences ○ ● Evolution of DNA world in “rockio” ● Evolution of free living cells ○ Evolved biochemical reactions to generate lipids/cell walls ○ Then organisms became free living ● Caveats ○ One scenario for how life could have evolved on earth ○ Seems plausible and scientists are working hard to test the individual steps with several key steps shown possible ○ BUT… more work is needed to further test this hypothesis ● Key questions from Lecture: ○ Do you think metabolism or information was the key first step to life? ○ What are some of the key ingredients for life? ○ How do either version of the tree of life (three domain vs ring of life) help explain the sequence of events that led to eukaryotes? 9/15/21: Class Notes - Prokaryotic Diversity Section 1: Why do we care Prokaryotes: Two domains of life ● Dominant: 90% of Earth’s biomass ● Extreme: Live in all possible habitats ● Versatile: Capable of all forms of bioenergetics
● Supportive: Recent and ancient symbiosis; Nutrient cycling in biogeochemical cycles ● Destructive: Major cause of disease Prokaryotic gene structure ● Operon: a sequence of DNA encoding a polycistronic RNA for synthesizing 2- proteins having related functions ● Basic elements ○ Regulator: encodes repressor ○ Promoter: binding site for RNA polymerase ○ Operator: binding site for repressor (blocks RNA polymerase) ○ Structural genes : open reading frames encoding proteins acting in the same process ● Inducible operon: lactose transport and metabolism Prokaryotic cell structure Major characteristics of 3 domains of life Bacteria Archaea Eukarya Nucleus No No Yes Chromosome (C) One circular C with 1 origin of DNA replication One circular C with 1-3 origins Several to many linear C with multiple origins Organelles No No Yes Growth forms Most unicellular, some multicellular All unicellular Many unicellular, many multicellular Reproduction Binary fission Binary fission Often sexual Lipid structure Glycerol bonded to unbranched fatty acids via ester links Glycerol bonded to branched lipids via ether links Glycerol bonded to unbranched fatty acids via ester links Cell wall polymers Peptidoglycan Wide variation, no peptidoglycan If present, chitin or cellulose
