Topics for the first midterm: Chem142A (Kahn, Fall 2007) You are expected to know all the material that was covered in the lecture. Below is a lists of concepts that I think are especially important. Chapter 1. I expect you to have a good knowledge and/or understanding of nearly all the material from Chapter 1. Few topics that we skipped and you are not expected to know are 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 (e.g. peroxisomes, 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 Concept of non-equilibrium and steady state Basic ideas of thermodynamics, equilibrium and kinetics Activation free energies vs. reaction free energies Organisms are energy transformers Ways to accelerate reactions, with 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 the 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 Flagella and pili Mitochondria Chloroplast (do not worry about the fine structure - thylakoids, lumen) Vacuole in plants Cytoskeleton: microtubules and actin filaments Evolution of eukaryotic cells Viruses Common functional groups Configurations and conformations (small molecules as well as proteins) Stereospecificity, the three-point model in understanding it General types of chemical reactions, with simple examples Nucleophilic substitution reactions Addition-elimination reactions Acidity, basicity, nucleophilicity, and the 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: Types of 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, calculation of pH of a solution of strong or weak acids Titration and titration curves Buffer solutions, calculation of pH in buffer solutions Water as a reactant and living environment Calculations using equilibrium constant (remember, no “+” signs here) Calculations using Henderson–Hasselbalch equation Chapter 3. All the material on pages 75-89 is important. You should 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 common amino acids (except proline, arginine, histidine) Recognition of some 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 functions of peptides Biological functions of proteins Detection of amino acids, (ninhydrin, PITC, UV-spectrophotometry) Strategies for separation of peptides and proteins 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 first mid-term focuses at the secondary structure of proteins (pg 116-125. There is no need to know details of X-ray diffraction and biomolecular NMR (pg. 178-181). Make sure that you know all about: Forces that stabilize secondary and tertiary structures The peptide bond, and proline as a special residue Definition of φ and ψ angles in peptides The importance of steric bumping in secondary structure Structure, shape, and dipole moment of alpha helix Structures of parallel and antiparallel β-sheets Ramachandran diagrams, know where the α-helix and β-sheets