Chapter 1 -- Life. Chapter 2 -- Atoms, Molecules and Bonds. Chapter 3 -- Water

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1 Chapter 1 -- Life In the beginning... Molecular evolution Heirarchy and organization levels of organization Form follows function Language in science Cell and Molecular Biology -- Biology 20A Chapter Outlines -- part 1 -- Campbell, 5th Edition Chapter 2 -- Atoms, Molecules and Bonds Elements in Biology Nuclear composition Electron configuration quantum states, transitions Orbital theory valence shell periodic table noble gasses, octet rule Chemical bonding covalent, ionic, hydrogen bonds electronegativity molecular shape Chemical reactions equilibrium steady state Chapter 3 -- Water H-bond, polarity Properties cohesion adhesion high specific heat high heat of vaporization expanding on freezing solvent dissociation (ionization) ph, buffers

2 Chapter 4 -- Carbon Hydrocarbons Molecular shape orbital hybridization Isomers structural (positional) geometric stereo- Functional groups oxygen nitrogen others Ionization of organic acids Electronegativity, polarity, H-bonding Chapter 5 -- Macromolecules Assembly by elimination of water Monomers -- polymer Carbohydrates aldo- and ketochiral carbons and the number of isomers ring formation disaccharides, polysaccharides Lipids fatty acids and glycerol fats, unsaturation phospholipids steroids Proteins amino acid monomers zwitterion -- charged amino and carboxy groups at neutral ph side chains non-polar (greasy) polar charged polymerization -- peptide bond (elim. of water) functions storage information transfer transport mechanical work chemistry on other molecules (enzymes) higher order structure

3 primary structure -- order of amino acids along peptide backbone secondary structure -- α- helix, β-pleated sheet held together by H-bonds along peptide backbone tertiary structure -- folding of helices, sheets and random coil into globular shapes held together by side chains, mostly (and backbone, where applicable) hydrophobic interactions ionic interactions disulfide bonds H-bonds quaternary structure -- multiple separate subunits same forces as tertiary (disulfide rare) denaturation = unfolding Nucleic acids make up DNA (genes - info storage), and RNA (info transfer) in cell nucleotides sugar, base, phosphate sugar -- ribose, deoxyribose bases -- purines (A and G), pyrimidines (C and T or U) polymerization -- elimination of water primary structure = order of bases along strand secondary structure -- base pairing C-to-G, A-to-T (or -U) via H-bonds double helix -- right-handed helical turns unzips for copying or mrna synthesis antiparallel strands 5 to 3 direction of synthesis (and convention when writing sequences) Chapter 6 -- Metabolism Oxidation states Energy interconvertable potential, kinetic Thermodynamics 2 laws: Energy not destroyed; disorder (entropy) increases. Free energy G = H - T S Exergonic = spontaneous: G < 0 Endergonic = require E input: G > 0 Equilibrium: G = 0 Reactions contribution of concentration, K eq ATP synthesis, reaction coupling Enzymes activation energy induced fit regulation

4 Chapter 7 -- The Cell Prokaryotes no organelles cell wall Eukaryotes nucleus -- DNA storage, gene regulation, RNA synthesis ribosomes -- protein synthesis * endoplasmic reticulum (ER) rough with ribosomes -- hydrophobic protein synthesis, glycosylation for secretion smooth without ribosomes -- lipid synthesis; detox of drugs, poisons budding of vessicles * Golgi apparatus -- sorting and targetting of proteins, more budding of vessicles: cis, trans faces * lysosomes -- bag of enzymes, breakdown of food recycling of organelles programmed cell death: Apoptosis * vacuoles -- storage of plant proteins peroxysome -- detox of toxins by oxidation. accompanied by formation of hydrogen peroxide * = part of endomembrane system, buds off nuclear membrane Chapter 8 -- Membranes Structure fluid mosaic of embedded proteins in 2D Functions to separate compartments Properties diffusion osmosis facilitated diffusion active transport ion transport co-transport Chapter 9 -- Respiration Catabolism Redox reactions Glycolysis Fermentation Krebs (TCA) cycle Electron transport Reduction potential Proton pump Oxidative phosphorylation ATPase

5 Regulation Chapter Photosynthesis Similarities to respiration in reverse Location Light reactions pigments, metals and light membrane bound photosystems Z-scheme and non-cyclic electron flow proton pump (reprise) ATPase as in respiration NADPH Dark reactions (Calvin cycle) carbon fixation via Rubisco glyceraldehyde phosphate CO 2 regulation - photorespiration C 4 and CAM plants