Chapter 1 Pasteur s experiment o 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 generation o o o o Cell theory o Does not occur under normal lab conditions Apparently occurred at least once Addresses the formation of living cells from previously nonliving material Never been directly observed in natural setting Anton van Leeuwenhoek 1600s Developed more powerful microscopes First to describe the diversity of cells Chapter 2 Water and Carbon the Chemical Basis of Life Chemical Evolution Pattern component simple chemical compounds combined to form complex carbon containing substances that accumulated in the oceans 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 bonds Hypothesis Molecules with carbon carbon bonds will form Entropy decreased while potential energy increased o Water o Vital because it is an excellent solvent Both O H bonds are polar Partial charges Molecule is bent Partial charge sticks out away from partial charge Hydrogen bonding makes it possible for almost any charged or polar molecule to dissolve in water Hydrogen bonds are not as strong as ionic or covalent Downward pull due to surface hydrogen bonds with water molecules below them Water molecule at surface adhere to the glass resisting this pull o Water resists any force that increase its surface area Functional groups Surface tension Table 2 3 page 35 Amino Attract a proton Acts as a base Carbonyl Aldehydes Ketones Site of reactions that link these molecules into larger more complex cmpds Most likely to make covalent bonds Carboxyl Hydroxyl Phosphate Sulfhydryl Aldehydes ketones Act as an acid Lose a proton in solution Act as weak acid Highly polar Drop a proton Most likely to make hydrogen bonds O P bonds When broken release large amounts of energy Carry 2 negative charges Can form disulfide bonds Contribute to protein structure o o o o o o o o o o o o o Most likely to make covalent bonds or become protonated deprotonated Can t make covalent bonds with other molecules Methyls o Hydrolysis o Spontaneous o o o o o Involves an increase in entropy If entropy is increased If potential energy is decreased Require no input of energy delta G Exergonic Chemical reactions tend to speed up when the conc of the reactants is increased o Because the reactants will collide more frequently Chapter 3 Protein Structure Function Miller s experiment o o Chemical evolution occurs readily if simple molecules with high free energy are exposed to a source of kinetic energy Simulated the second stage in chemical evolution prebiotic soup Presence of amino acids supports Amino acids o o 20 different ones Form covalent bonds to NH2 the amino functional group COOH the carboxyl functional group H a hydrogen atom An R group side chain Polypeptides o o Peptide bonded backbone 3 key points R group orientation Directionality Flexibility 50 amino acids protein Proteins Crucial to most tasks required for cells to exist Catalysis Defense Movement Signaling Structure Transport Primary structure Unique sequence of amino acids Stabilized by peptide bonds Secondary structure Folding of polypeptide chains into regular structures Alpha helix Beta pleated sheet Stabilized by hydrogen bonding between atoms of the backbone o Tertiary structure Distinctive 3D shape of a polypeptide Hydrogen bonding Hydrophobic interactions Van der Waals interactions Covalent bonding Ionic bonding Depends on both primary and secondary structure Quaternary structure Combination of polypeptide subunits Van der Waals interactions Occur between side chains Enzymes o o o o o o o o o o o o o Bring reactants together in precise orientations Stabilize transition states Lower activation energies for reactions Speed up chemical reactions Have active sites Induced fit conformational change Enzyme catalysis 3 step process Initiation enzymes orient reactants precisely as they bind to specific locations within active site Transition state facilitation the act of binding induces the formation of transition state Termination reaction products have less affinity for the active site than the transition state does Binding ends enzyme returns to original conformation products are released o Enzyme cofactors o Enzyme regulation Metal ions or small organic molecules called coenzymes Required for enzymes to function normally Part of active site Competitive inhibition Allosteric regulation More products that compete for active site Bind at a location other than active site Does not affect active site directly Changes shape of enzyme to make the active site accessible or inaccessible Limits to the rate of catalysis o Substrate concentration Low speed of reaction increases in a linear way Intermediate increase in speed begins to slow High reaction rate plateaus at max speed o o pH levels temperature optimal temp and pH Chapter 4 Nucleic Acids the RNA World Nucleic acids made up of monomers called nucleotides 3 components to a nucleotide o o o Phosphate group Sugar Nitrogenous base Purines A G Pyrimidines G U T Uracil in ribonucleotides Thymine in deoxyribonucleotides o o Nucleotides polymerize to form nucleic acids Form covalent bonds Involves the formation of a covalent bond between the phosphate group of one nucleotide and the hydroxyl group of the sugar component of another nucleotide Condensation reaction Phosphodiester linkage Endergonic process Sugar phosphate backbone is directional o o o One end has an unlinked 5 carbon Other end has an unlinked 3 carbon 5 3 direction Bases added at the 3 end o o o o o o DNA Structure Function Primary structure 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 Sugar phosphate backbone created by phosphodiester linkages and a sequence of any four nitrogenous base Sugar is deoxyribose of purines of pyrimidines X ray crystallography o o DNA strands are antiparallel Twisted together to form a double helix Coiled sugar phosphate backbones on the outside spiral Nitrogenous bases on the inside Form purine pyrimidine pairs Allows hydrogen bonds to form between certain pairs DNA functions as