Topics for the first midterm: Chem142A (Kahn, Summer 2005) You are expected to know all the material that was covered in the lecture. The following list, organized by textbook chapters, list concepts that I think are especially important. Chapter 1. I expect you to have a good knowledge and/or understanding of nearly all of the material in Chapter 1. Topics that we skipped and you are responsible for include the subcellular fractionation of tissues, the function of intermediate filaments, and the strength of covalent bonds. Know the function and basic properties of cell parts that we covered in the lecture. There were few we omitted (peroxisomes, lysosomes, and starch granules); I will not test you on these. Areas of special interest include: The science of biochemistry and its relations with other sciences Characteristic features of life Conditions that support life, extremophiles Chemical description of processes in living organisms Concepts of equilibrium and steady state Basic ideas of thermodynamics, equilibrium and kinetics Activation free energies vs. reaction free energies Organisms as energy transformers Ways to accelerate reactions, with the focus on catalysis Metabolic and signal transduction pathways Storage and transmission of genetic information Role of random mutations and natural selection in evolution Understand difference between selection and genetic engineering Classification of living organisms based on their metabolism Classification of living organisms based on similarities of genetic code Classification of living organisms into six kingdoms Differences in cell structure between bacteria, plant, and animal cells Life-functions of these cell types Cell wall and cell membrane Nucleus and nucleolus Cytoplasm Ribosomes and endoplasmic reticulum Flagella and pili Mitochondria and chloroplast (do not worry about fine structure - thylakoids, lumen) Vacuole Cytoskeleton: microtubules and actin filaments Evolution of eukaryotic cells Viruses Common functional groups Configurations and conformations R and S nomenclature Stereospecificity, three and four-point model in understanding it General types of chemical reactions, with simple examples Nucleophilic substitution reactions Addition-elimination reactions Acidity, basicity, nucleophilicity, and leaving group ability Macromolecules as polymers of monomeric subunits Know what proteins, DNA and polysaccharides are made of Structural hierarchy in cells Prebiotic evolution, “RNA world” hypothesisChapter 2. You are expected to know everything from this chapter. While some of the material may seem like a review of your general chemistry, the chapter contains several difficult concepts, such as the role of entropy in hydrophobic effect. Problems from this chapter offer opportunities for you to show your math skills. Yes, these are some formulas that you need to remember. At minimum, you should know how to write expressions for equilibrium constants, and be able to calculate the pH when you know the pKa and some concentrations. On the positive side, you do not have to remember pKa values of any of the compounds. I might ask on the exam about: Weak non-covalent interactions between molecules Electrostatic interactions vs. van der Waals interactions Entropy as a measure of disorder; hydrophobic effect All the interesting properties of water Ionization of water, ionic product Acids and bases, acid dissociation constant, pKa pH scale Titration and titration curves Buffer solutions Water as a reactant and living environment Calculations using equilibrium constant (remember, no “+” signs here) Calculations using Henderson–Hasselbalch equation Derivation of Henderson–Hasselbalch equation Chapter 3. All the material on pages 75-89 is important. Be familiar with the material on pages 89-110 to the extent that we covered in the lecture. Some areas of special interest include: Properties of amino acids, including chirality Structure and names of 20 common amino acids Recognition of less common amino acids Ionization properties of amino acids and peptides Titration curves, approximate pKa values, and the concept of pI Calculation of pI for systems with less than five ionizable groups Peptides, distinction between proteins and peptides Biological function of peptides Biological function of proteins Detection of amino acids, (ninhydrin, UV-spectrophotometry) Basic strategies for separation of peptides and proteins Basic strategies for analysis and characterization of peptides and proteins Three principles of chromatographic separation of proteins SDS PAGE and isoelectric focusing Chemical/enzymatic approaches to peptide and protein sequencing Applications of mass spectrometry to study peptides and proteins Chapter 4. The secondary structure of proteins and structure/function of fibrous proteins (pg. 116-132) will be covered. We briefly discussed X-ray diffraction and biomolecular NMR (pg.136-139) but I will not quiz you on details of these methods. Know all about: Distinction between conformation and configuration Forces that stabilize secondary and tertiary structures The peptide bond, and proline as a special residue Ramachandran diagrams Structure, shape, and dipole moment of alpha helix Structures of parallel and antiparallel β-sheets Structure and function of fibrous proteins α−keratin, collagen, and silk fibroin Biological function of vitamin C in formation of