Chapter 1- Pasteur’s experimento if he would have warmed the broth instead of boiled it: Cells would have appeared in both flasks Just warming the broth would not have killed any pre-existing organisms ,nor would it have allowed water vapor to become trapped in the swan neck- Spontaneous generationo Does not occur under normal lab conditionso Apparently occurred at least onceo Addresses the formation of living cells from previously nonliving materialo Never been directly observed in natural setting- Cell theoryo Anton van Leeuwenhoek (1600s) Developed more powerful microscopes First to describe the diversity of cellsChapter 2 – Water and Carbon: the Chemical Basis of Life- Chemical Evolutiono Pattern component – simple chemical compounds combined to form complex carbon-containing substances that accumulated in the oceanso Process component – complex carbon-containing compounds formed because energy in sunlight and extremely hot water was converted to chemical energy in the form of new chemical bondso Hypothesis: Molecules with carbon-carbon bonds will formo Entropy decreased while potential energy increased- Watero Vital because it is an excellent solvent Both O-H bonds are polarPartial charges Molecule is bentPartial – charge sticks out away from partial + chargeo Hydrogen bonding makes it possible for almost any charged or polar molecule to dissolve in watero Hydrogen bonds are not as strong as ionic or covalento Downward pull due to surface hydrogen bonds with water molecules below them Water molecule at surface adhere to the glass, resisting this pullo Water resists any force that increase its surface area Surface tension- Functional groupso Table 2.3 (page 35)o Amino Attract a proton Acts as a baseo Carbonyl Aldehydes Ketones Site of reactions that link these molecules into larger, more complex cmpds Most likely to make covalent bondsAldehydes & ketoneso Carboxyl  Act as an acid Lose a proton in solutiono Hydroxyl Act as weak acid Highly polar Drop a proton Most likely to make hydrogen bondso Phosphate O-P bondsWhen broken, release large amounts of energyCarry 2 negative chargeso Sulfhydryl Can form disulfide bondsContribute to protein structure Most likely to make covalent bonds or become protonated/deprotonated- Methylso Can’t make covalent bonds with other molecules- Hydrolysiso Involves an increase in entropy- Spontaneouso If entropy is increasedo If potential energy is decreasedo Require no input of energyo – delta Go Exergonic- Chemical reactions tend to speed up when the conc. of the reactants is increasedo Because the reactants will collide more frequentlyChapter 3 – Protein Structure & Function- Miller’s experimento Chemical evolution occurs readily if simple molecules with high free energy are exposed to a source of kinetic energyo Simulated the second stage in chemical evolution: prebiotic soupPresence of amino acids supports- Amino acidso 20 different oneso Form covalent bonds to:NH2 – the amino functional groupCOOH – the carboxyl functional groupH – a hydrogen atomAn “R” group – side chain- Polypeptideso Peptide-bonded backboneo 3 key pointsR-group orientationDirectionalityFlexibilityo 50+ amino acids = protein- Proteinso Crucial to most tasks required for cells to existCatalysisDefenseMovementSignalingStructureTransporto Primary structureUnique sequence of amino acidsStabilized by peptide bondso Secondary structureFolding of polypeptide chains into regular structuresAlpha helixBeta-pleated sheetStabilized by hydrogen bonding between atoms of the backboneo Tertiary structureDistinctive 3D shape of a polypeptideHydrogen bondingHydrophobic interactionsVan der Waals interactionsCovalent bondingIonic bondingDepends on both primary and secondary structureo Quaternary structureCombination of polypeptide subunits- Van der Waals interactionso Occur between side chains- Enzymeso Bring reactants together in precise orientationso Stabilize transition stateso Lower activation energies for reactionso Speed up chemical reactionso Have active siteso Induced fit – conformational changeo Enzyme catalysis 3 step process:Initiation – enzymes orient reactants precisely as they bind to specific locations within active siteTransition state facilitation – the act of binding induces the formation of transition stateTermination – reaction products have less affinity for the active site than the transition state does. Binding ends, enzyme returns to original conformation, products are releasedo Enzyme cofactorsMetal ions or small organic molecules called coenzymesRequired for enzymes to function normallyPart of active siteo Enzyme regulationCompetitive inhibitionMore products that compete for active siteAllosteric regulationBind at a location other than active siteDoes not affect active site directlyChanges shape of enzyme to make the active site accessible or inaccessible- Limits to the rate of catalysiso Substrate concentrationLow – speed of reaction increases in a linear wayIntermediate – increase in speed begins to slowHigh – reaction rate plateaus at max speedo pH levelso temperatureoptimal temp and pHChapter 4 – Nucleic Acids & the RNA World- Nucleic acids: made up of monomers called nucleotides- 3 components to a nucleotide:o Phosphate groupo Sugaro Nitrogenous base Purines (A, G) Pyrimidines (G, U, T)Uracil in ribonucleotidesThymine in deoxyribonucleotides- Nucleotides polymerize to form nucleic acidso Form covalent bondso Involves the formation of a covalent bond between the phosphate group of one nucleotide and the hydroxyl group of the sugar component of another nucleotideo Condensation reactiono Phosphodiester linkageo Endergonic process- Sugar-phosphate backbone is directionalo One end has an unlinked 5’ carbono Other end has an unlinked 3’ carbono 5’ -----> 3’ directiono Bases added at the 3’ end - DNA Structure & Functiono Primary structure Sugar-phosphate backbone created by phosphodiester linkages and a sequence of any four nitrogenous base Sugar is deoxyriboseo Secondary structure Consists of two antiparallel strands twisted into a double helix Stabilized by hydrophobic interactions Formed by hydrogen bonding between nitrogenous bases Watson and Crick model# of purines = # of pyrimidinesX-ray crystallographyo DNA strands are antiparallelo Twisted together to form a double helix Coiled sugar-phosphate backbones on