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Biology and the Tree of Life a. Themes. All living things: i. Aquire and use energy ii. Are made up of cells iii. Process information iv. Replicate v. Evolve as populations b. Theory: Explanation for general class of phenomena. i. First part describes, second part describes mechanism c. Robert Hooke invented the microscope. d. Anton Van Leeowenhoek sampled pond water e. Cell: a highly organized compartment bound by a thin, flexible membrane. f. Rudolph Virchow state all cells come from pre-existing cells. g. Louis Pasteur tested this via flask experiemtn h. Consequences of cell theory i. All species share a common ancestor ii. Cells in a multicellular organism arise from one cell i. Two conditions of Natural Slection i. Variety in heritable traits ii. Traits have different success rates j. Natural selection acts on an individual; Evolution acts on a population k. Fitness: ability of individual to produce offspring. l. Adaptation: Trait that increases fitness m. Three fundamental groups (domains): Eukarya, Archaea, and Bacteria. i. Bacteria and Archaea are prokaryotes. n. Hypothesis must be tested rigorously. o. Experiments test single, well defined behavior Water and Carbon: The Chemical Bases of Life. a. Theories have pattern and process components. b. Chemical evolution: complex molecules made from simpler molecules and sons radiation. How life came from non-life. Made molecule that could self replicate. c. In atoms important to life, the outermost shell is not full d. Electronegativity: O>>N>C=H e. Nonpolar bonds have more potential energy f. Earths Ancient Atmosphere: CH4, NH3, H2O, CO2, N2 g. Most critical chemical evolution and reactions happened in aqueous solution h. Water: Because of hydrogen bonds, it: i. Is an excellent solvent ii. Experiences cohesion (molecules sticking together) iii. Experiences adhesion (molecules sticking to unlike molecules) iv. Denser as liquid that solid (in liquid, hydrogen bonds are constantly being broken and reformed) v. Has a high specific heat vi. Has a high heat of vaporization

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vii. Protected early molecules in chemical evolution i. Water can act both as an acid and as a base. j. pH= -log[H+] [H+]=10-pH k. Buffers reduce change in pH. They are typically weak acids l. Chemical evolution reactions occurred in: i. Atmosphere ii. Deep-sea vents. Hot and rich in metals m. Energy is the capacity to do work or supply heat. Potential/Kinetic n. KE of molecular motion=thermal energy o. First Law of Thermodynamics: Energy cannot be created or destroyed p. Formeldahyde (H2CO) and Hydrogen Cyanide (HCN), are key intermediates in creation of larger, more complex molecules. q. Reactions are spontaneous is: i. Products have a lower PE ii. Products have more entropy r. Gibbs free energy: G=H-TS i. G<0. Reaction is spontaneous and exergonic ii. G>0. Reaction is nonspontaneous and endergonic iii. G=0. Reaction is at equlibrim s. Second Law of Thermodynamics: entropy of the universe always increases. t. Photons can break electrons off of molecules and make highly reactive free radicals i. Energy of sunlight converted to chemical energy u. Carbon is the most versatile atom (Has a valence of 4) v. Formeldahyde + Heat acetaldehyde (has C-C bond) w. Carbon normally is just a skeleton of molecules . The reactivity of molecules come from functional groups. x. Functional Groups i. Amino: NH2. Amines. Acts as base (accepts proton) ii. Carbonyl: CO. Aldehydes/Ketones. React to produce larger molecules iii. Carboxyl: HCO2. Carboxylic acids. Act as acids (lose protons) iv. Hydroxyl: OH. Alcohols. Polar. (More stable + weak acid) v. Phosphate: PO4. Organic phosphates. Breaking O-P bond leads to big release of energy vi. Sulfhydryl: SH. Thiols. Disulfide bridges in proteins help maintain tertiary strucuture. Protein Structure and Function a. H2CO/HCN Organic Monomers Organic Polymers Self Replicating b. Stanley Miller: Experiment of Early Earths atmosphere. CH4, NH3, H2, Spark Amino Acids c. Polymerization: Endergonic and nonsponatenous d. Peptide bond: C-N. Very stable (almost double bond) e. Polypeptides go from amino exposed end carboxyl exposed end i. N-terminus C-terminus

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ii. Peptide bond cant rotate, but single bonds on either side can iii. Oligopeptide: <50 amino acids. iv. Proteins: >50 amino acids f. Proteins function in: catalysis, defense, movement, structure, signaling, transport. g. Protein structure: i. Primary: Amino Acid Sequence ii. Secondary: Hydrogen bonding in backbone between carbonyl O and amino H. (Alpha helices/Beta pleated sheets) iii. Tertiary: Side-chain interactions. Hydrogen bonds, Van der Waals, Hydrophobic interactions, Covalent Bonding (S-S), Ionic (acidbase) iv. Quaternary: 2+ polypeptides h. Folding is sponatenous. i. Enzymes: Catalysts that work by lowering the activation energy of a reaction. i. 3 Steps 1. Initiation 2. Transition-State Faciliation 3. Termination j. Emil Fischer: Lock and Key Model Nucleic Acids and the RNA World a. Biologists widely believe life started w/ RNA. b. Ribose has OH on 2 carbon of the pentose, Deoxyribose has H. i. The OH makes Ribose more reactive c. Cytosine, Uracil, and Thymine are pyrimidines (1!) d. Adenine and Guanine are purines (2!) e. A nucleotide has not been observed as forming during chemical evolution f. Polymerization: Phosphate on the 5 carbon of one nucleotide links to the hydroxyl on the 3 carbon of another nucleotide. Called phosphodiester linkage i. ALWAYS WRITTEN 5 3 ii. Polymerized as tri-phosphate activated phosphorylated. 1. Clay sized mineral particles in chemical evolution. g. Secondary structure formed by Hydrogen bonding between nitrogenous bases. h. Chargaff: Purines = Pyrimadines i. Rosalind Franklin and Maurice Wilksons: X-ray Crystallography. DNA is helical. j. Watson and Crick: DNA is double stranded and anti-parallel. Adenine bonds with thymine and cytosine bonds with guanine. i. Complementary base pairs. ii. Double helix iii. Major Groove exposes nitrogenous bases iv. Minor Groove only exposes the backbone k. DNAs primary structure gives a template for replication

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i. DNA doesnt self-replicate. Very stable. l. RNA can have up to four levels of structure i. Extra OH makes it more reactive ii. Complementary bonds on same strand. Produces unique structures like the hairpin. iii. Tertiary: Secondary structures fold into complicated shapes iv. Quaternary: Holds different RNA strands together. m. RNA is not as diverse and proteins, but more diverse than DNA. n. Sidney Altman and Thomas Cech discovered ribozymes in cells today. Introduction to Carbohydrates a. (CH2O)n b. Carbonyl, several OHs, and several C-H bonds. i. Aldehyde: Carbonyl on end ii. Ketose: Carbonyl in middle c. Monosaccharides likely to form rings in aqueous solution i. 1 Carbon bonds with 5 hydroxyl ii. Alpha: Hydroxyl below plane iii. Beta: Hydroxyl above plane d. Polymerization between two hydroxyl groups: glycosidic linkage. i. Alpha/Beta refers to 1 Carbon ONLY. e. Starch: Alpha glucose. Helix i. Amylose: Unbranced (only alpha 1,4) ii. Amylopectin: Branched (alpha 1,4 and alpha 1,6) f. Glycogen: Alpha glucose. i. More branched. (alpha 1,6 every 10 monosaccarides) g. Cellulose: Beta 1,4 glucose i. Alternating structure gives way to hydrogen bonding between strands. h. Chitin: Beta 1,4 N acetyl glucosamine. (NAc) i. Alternating structure gives way to hydrogen bonding between strands i. Peptidoglycan: Beta 1,4 N acetyl muramic acid and N acetyl glucosamine. i. N acetyl muramic acid has four amino acids. Peptide bonds. j. Polysaccharides probably had no role in origin of life i. Polymerization occurs only with help of enzymes, no replication, no catalytic functions. k. Carbohydrates provide raw carbon skeleton for more complex molecules. l. Structurally support cell. m. Key role in cell-cell recognition i. Glycoproteins form sugar coating. n. Energy storage: Photosynthesis reduces CO2 into (CH2O)n. i. Higher potential energy in C-C and C-H bonds than in C-O bonds. Greater free energy. ii. Fats have 2X the energy because of more C-H bonds instead of COH bonds o. Phosphorylase breaks down glycogen.

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p. Amylases break down starch q. CH2O + O2 + P CO2 + H2O + ATP Lipids a. Enclose RNA (chemical evolution) in membrane i. Separates life from non-life ii. Condenses chemicals (more efficient) b. Largely nonpolar and hydrophobic i. Mostly hydrocarbons c. Characterized by solubility i. Fats: Glycerol and 3 fatty acids 1. Ester linkage between hydroxyl of glycerol and hydroxyl of carboxyl on fatty acid. 2. Not a polymer ii. Steroids: 4-ring structure w/ R-group. 1. Hydrophilic hydroxyl on ring and hydrophobic hydrocarbon tail. iii. Phospholipid: Glycerol linked to phosphate and 2 chains of either isoprene or two fatty acids. d. Plasma membrane: Phospholipid bilayer. i. Amphipathic e. Micelle: Tiny droplet of phospholipids short chains. (short chains) f. Phospholipid bilayers: 2 sheet align. (long chains) i. Spontaneous drop in PE g. Liposome: Artificial membrane-bound vesicles h. Permeability=function of fluidity i. Higher the permeability= Higher the fluidity ii. Permeability decreases at lower temperatures and higher pressures i. Plasma membranes are selectively permeable. i. Small nonpolar> small polar> large polar> ions j. MEMBRANES ARE DYNAMIC k. Diffusion: movement of solutes down concentration gradient i. High concentration low concentration l. Osmosis: Diffusion of Water. i. High concentration low concentration m. Hypotonic: More solute n. Hypertonic: Less solute o. Isotonic: Same solute i. All are relative.