Topics for the first midterm: Chem142A (Kahn, Summer 2004) As a general rule, you are expected to know all the material that was covered in the lecture. The following list, organized by chapter numbers as in the 4th edition of the textbook, contains concepts that I think are especially important. I adopted it from last year’s lists. If you are using the 3rd edition of the textbook, you may want to check out the midterm guides I and II for the year 2003 in order to find which chapter covers which topic. Chapter 1. I expect you to have a good knowledge and/or understanding of nearly all the material from Chapter 1 of the 4th edition. 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. I expect that you know the function and basic properties of cell parts covered in the lecture. There were few we did not cover (e.g. peroxisomes, lysosomes, starch granules), I will not test you on these. Some 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 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 Golgi complex Flagella and pili Mitochondria Chloroplast (do not worry about fine structure - thylakoids, lumen) Vacuole Cytoskeleton: microtubules and actin filaments Evolution of eukaryotic cells VirusesCommon 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 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” hypothesis Chapter 2. You are expected to know everything from this chapter. While some of the material may seem like a review of your general chemistry, there chapter contains several difficult concepts, such as the role of entropy in hydrophobic effect. Problems from this chapter offer lots of 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 Osmosis, hypotonic and hypertonic solutions 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. 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 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 four ionizable groups Peptides, distinction between proteins and peptides Biological function of peptidesBiological 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 Approaches to peptide and protein sequencing 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: 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 Structure and shape of 310 helix Structures of parallel and antiparallel