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Study Guide for Examination I, Biology 122, Spring ‘16 The Scienctific Process Inductive, Deductive Logic Evolutionary Theory i. Evidence that lead Darwin to inductive reasoning concerning mechanisms of evolution ii. Modern evidence that supports the theory of Evolution iii. Homology vs Analogy in evolution (convergent evolution vs evolution by descent) Chemistry Basics Atomic structure, energy levels (shells), electron orbitals, electron configurations of atoms, covalent bonds Weak bonds (H bonds, ionic bonds, hydrophobic forces, Van der Waals attractions) Water chemistry (pH, h bonds, polar solvent characteristics, other water characteristics) Redox reactions Biomolecules Carbohydrates, Lipids, Nucleic Acids, Proteins Protein Structure (1o – 4o structure), main chain atoms and amino acid sidecahins Alpha helices, beta sheets, loops, turns as elements of 2o structure – h bonding of main chain atoms Weak bonds in providing protein 3o structure (hydrophobic, salt bridges [ionic bonds], H bonds, Van der Waals attractions Disuphide bridges (cysteine S-S bonds) Cell Structure, Cell Membranes Endomembrane system, nucleus, cytoskeleton, plasma membrane, mitochondria, chloroplasts Diffusion and osmosis, concentration gradients Mechanisms of Transport (active and passive), coupled transport, pumps, transporters, ion channels Lipid bilayers, fluid mosaic model of membranes Enzymes as Catalysts Active sites, cofactors, competitive vs non-competitive inhibition, allosteric regulation of activity, lowering of activation energy of reactions that they catalyze Energy, Thermodynamics 1st and 2nd laws of thermodynamics energy transfer, importance of ATP structure in serving as an energy currency molecule delta G0, delta G, and the importance of delta enthalpy (H) and delta entropy (S) in determining reaction spontaneity or non-sponteneity biological factors that make delta G different that delta G0 – the push-pull of biochemical pathways Biochemical Pathways Catabolism vs Anabolism Glycolysis, Cellular Respiration Stepwise oxidation of glucose = catabolism of glucose Phases of Glycolysis, products of Glycolysis, net yields of energy molecules – location of pathway Role of NAD+, NADH, FAD, FADH2 as electron carriers (redox reactions) Pyruvate oxidation under aerobic conditions, pyruvate fermentation under anaerobic conditions – net yields of important energy molecules – location of pathway Krebs (aka Citric Acid) Cycle, net yields of energy molecules – location of pathway Role of Coenzyme A (CoA) Substrate level phosphorylation of ADP to produce ATP Mitochondrial structure Electron transport chain (ETC), role of NADH, FADH2 in donating electrons to ETC, where located, function of ETC complexes and electron carriers, production of H+ gradient across inner mitochondrial membrane, net H+ pumping caused by electrons donated by NADH, FADH2, role of oxygen in ETC (1/2 O2 + e- + H+ >>> H2O) ATP Synthase – where located, structure, function in using H+ gradient to synthesize ATP (oxidative phosphorylation), net yield of ATP/turn of the rotor complex Overall balance sheet of ATP yield in Glycolysis + Pyruvate Oxidation + Krebs Cycle + Oxidative Phosphorylation Note Bene: if you study the cinelectures and use the links of various activities on the course syllabus and have paid attention and taken notes on our active learning exercises in class, you should obtain a good understanding of the above concepts. If you wish, you can review the end-of-chapter summaries in the Openstax text to see if you are comprehending the major concepts. If you are using the Openstax text exclusively instead of using the cinelectures, this is also a good idea. – I would suggest at least 5-6 hours of studying the course material for this exam.