LS 2 Chapters 2 & 3

Life Science 2 Textbook: Purves, Orians, and Heller, Life, The Science of Biology, 8th edition. Sinauer Associates, Inc.; Sunderland, Freeman and co. Chapter 2: Chemistry of Life 2.1 All is matter composed of atoms: proton and neutron in a nucleus; electrons orbiting in shells Element: pure substance containing 1 kind of atom (H, C, N, O, etc) molecule = group of elements electron (e-): first shell (2e-), second shell (8e-), etc e- farther away from nucleus ( higher energy level 2.2 chemical bond: attractive force linking 2 atoms together in molecule 1. covalent bond: 2 atoms share 1 or more e- pairs ( both stable; very strong bond 2. ionic bond: e- transfer; attraction between ions with opposite charges compound: molecule of atoms of 2 or more elements bonded together 2 atoms with close electronegativities (EN) = nonpolar covalent bond; e- shared equally 2 atoms with different e-negativies = polar covalent bond; e- shared unequally e- go toward the more EN atom: i.e., H2O ( O has negative dipole moment and H has positive ( opposite charges are separated ion: atom that gains or loses an e-; can interact with polar molecules (i.e., NaCl in H2O) Molecules polar: hydrophilic; ionic/polar dissolve in water because of H-bonds nonpolar: hydrophobic; hydrophobic interactions between nonpolar substances = Van der Waals forces amphipathic: both; interact with anything Hydrogen bonds: interaction btwn 2 molecules (not atoms); i.e., O of H2O is attracted to H of another H2O) 2.4 Water (the solvent of life) - each molecule forms H bonds with 4 other molecules the 4 bonds increase the space H2O molecule take up ( H2O expands when freezing; ice < dense than H2O Solid: molecule held rigidly by H bonds Liquid: H bonds break and form constantly Gas: doesn?t form H bonds Cohesion: water molecules resist coming apart when under tension can travel against gravity (i.e., from roots to leaves) stick together on another surface surface tension: water molecule on surface are H-bonded to other water molecules below living organisms are >70% water by weight solution = substance (solute) dissolved in liquid (solvent) if water is the solvent ( aqueous solution Quantitative analysis: measures concentrations [ ]s mole concept: mole = amount of substance in grams whose weight is equal to its molecular weight molarity (M), mol/L Acids and Bases acids release H+ in water; bases accept H+ or release OH- strong acids: complete reaction (HCl); release lots of H+ weak acids: some original acid remains (-COOH) strong bases: ionize completely; OH- absorb H+ to produce H2O weak bases: HCO3-, NH3, -NH2 ionization of strong acids or bases = irreversible acid: H donor; base: H acceptor pH scale: measure of [H+]; 1-14 ( acid to base log [H+] = pH of a solution pH = 7 ( [H+] = 1x10^7 M Chapter 3: Macromolecules and the Origin of Life 3.1 monomers covalent bonding ( polymers large polymers = macromolecules polymers vs. monomers: proteins ( 20 amino acids carbohydrates ( glucose, fructose, galactose lipids ( fatty acids and glycerol nucleic acid ( nucleotides functions related to shape and chemical properties of the monomers some functions: energy storage, structural support, transport, protection/defense, metabolism regulation, heredity, movement/growth monomers ( polymers by condensation rxns: loss of H2O polymers ( monomers by hydrolysis rxns: gain of H2O 3.2 Proteins: structural support, protect, transport, catalyze, regulate; polymers of amino acids amino acids: carboxyl group and amino group attached to the same alpha carbon both acids and bases: carboxyl lost H, amino group gains H also attached to alpha carbon: H, side chain (R group) only L amino acids found in proteins (not D) 20 amino acids distinguished by their R groups 5 have hydrophilic R (e- charged) 5 have polar, uncharged R 7 have nonpolar, hydrophobic R cysteine: terminal disulfide (-S-S-) glycine: H = the R group proline: modified amino group covalent bonding with R; a ring amino acid polymerization carboxyl group reacts with amino group ( condensation rxn ( peptide bond, which is inflexible Primary structure: sequence of amino acids in a polypeptide chain ?N-C-C-?N from amino group, alpha carbon, C from carboxyl group (repeating) amino acid monomers are joined, forming polypeptide chains determined by covalent bonds contains all the info needed for unique shape of proteins Secondary structure: consists of repeated spatial patterns in different regions of a polypeptide chain; 2 types, determined by H bonding between amino acids making up the primary structure (how R?s interact) 1. alpha helix: right handed coil forming H bonds between N-H and C=O R extends outward Common in keratin (hair) 2. Beta pleated sheet: formed from 2 or more polypeptide chains that are almost completely extended and aligned stabilized by H bond btwn N-H on 1 chain and C=O on other chain alpha and beta can exist in same polypeptide chain Tertiary structure: chain bonding and folded back and forth ( 3D chape; interactions between R groups 1. covalent disulfide bridges: btwn cysteine groups 2. hydrophobic R?s: clump together, away from H2O ( fold 3. Van der waals: stabilize interactions btwn hydrophobic R?s 4. ionic bonds: + and ? charged R?s, away from H2O ( salt bridges 5. H bond: btwn R?s stabilizes folds Quaternary structure: ways that 2 or more polypeptide chains (subunits) bind/interact forces holding subunits together, how units shift not all proteins have H >1 tertiary structures interacting why we need proteins enzymes need certain surface shapes to bind substrates; expedite chemical rxns carrier proteins: on cell membrane; allow substances to enter chemical signals bind to proteins on cell membrane native proteins: functional, has tertiary structure denatured proteins: loss of tertiary structure; caused by changes in pH, temperature, [salts]; different proteins function under different conditions; disrupt H bond/ionic attraction ( repulsion The 20 amino acids Positively charged, hydrophilic: arginine, histidine, lysine Negatively charged, hydrophilic: aspartic acid, glutamic acid Polar, uncharged: serine, threonine, asparagines, glutamine, tyrosine Nonpolar, hydrophobic: alanine, isoleucine, leucine, methionine, phenylalanine, tryptophan, valine Special: cysteine, glycine, proline ( -SH, -H, ring, respectively how are proteins different from other macromolecules? ( go thru modifications; largest number of macromolecules 3.3 Carbohydrates (H-C-OH); Source of quick energy usable by body tissues; structural; Energy storage and transport molecules Monosaccharides: monomers (glucose, fructose) Many covalently bonded (glycosidic linkages) = di/oglio/polysaccharides Most are D isomers (not L) Disaccharides: 2 monosaccharides joined by glycosidic linkages; i.e., maltose = 2 glucoses Ogliosaccharides: several monosaccharides often have additional functional groups often covalently bonded to proteins/lipids on outer cell surface ( recognition signals Polysaccharides: giant polymers of monosaccharides Starch: glucose; binds with water; plants store sugar in this form Glycogen: glucose; animal livers/muscles Cellulose: plant cell walls; structure material chemically modified carbs addition of functional groups chitin: exoskeleton of insects; derivative of glucosamine 3.4 Lipids Insoluble in water because nonpolar, covalent bonds Aggregate away from water, attract each other: additive van der waals forces Functions: energy storage, cell membrane, capture light energy, hormones, vitamins, thermal insulation, electrical insulation of nerves, water repellency fats/oils = triglycerides = 3 fatty acids and 1 glycerol; carboxyl terminal of fatty acid bonds with ?OH of glycerol in an ester linkage formed by condensation rxn saturated fatty acid: all single C-C; rigid, straight unsaturated fatty acid: 1 or more C=C; kinks ( not packaged tightly; monosaturated; 2 or more = polyunsaturated phospholipids: lipids with phosphate group, which is negatively charged ( attracted to water, hydrophilic; forms bilayer of cell membranes nontriglycerides carotenoids: vitamin A steroids: multiple rings sharing C?s cholestrol: membranes testosterone, vitamin D2, cortisol vitamins: vitamin A, D, E, K; acquire from diet waxes: ester link between saturated fatty acid and saturated alcohol 3.5 Nucleic Acids (DNA and RNA); polymer of nucleotides Storage, transmission, genetic info DNA encodes hereditary info, used to specify amino acid sequence of proteins by RNA intermediate Info ( DNA ( RNA ( proteins Nucleotides: pentose sugar, phosphate, nitrogenous base N base: pyrimidine ring or purine fused ring Sugar of DNA and RNA: deoxyribose and ribose, respectively Nucleotides joined by phosphodiester link between sugar and phosphates; additive H bonds stabilize molecule RNA: one polynucleotide chain; DNA: 2 chains 4 N bases purines: adenine (A) and guanine (G) pyrimidines: cytosine (C) and thymine (T, in DNA) and uracil (U, in RNA) pairsL A-T, C-G, A-U nucleotides with other functions: ATP (adenosine triphosphate): energy transducer in biochemical rxns GTP (guanosine triphosphate): powers protein synthesis Camp (cyclic AMP): hormone action, transfer info by nervous system