Topics for the second midterm: Chem142A (Kahn, Summer 2004) Chapter 4. The focus here is on the secondary structure of proteins. There is no need to know details of X-ray diffraction and biomolecular NMR (pg. 136-139). We will not cover protein motifs (pg 141-144). 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 of alpha helix Structures of parallel and antiparallel β-sheets Distinction about tertiary and quaternary structure in globular proteins Symmetry in oligomeric proteins Why membraneous proteins are unique Structure and function of fibrous proteins α−keratin, collagen, and silk fibroin Protein folding and denaturation Assisted folding (chaperones, chaperonins) Chapter 5. Material in the textbook from pg 157-174. You need to have an understanding of the immune system to the extent we covered in the lecture. The function of motor proteins will be covered; note that we were more detailed in the lecture than textbook is. You are expected to know: Key concepts: ligand, binding site, etc General themes: interactions and protein flexibility Quantitative measures of interaction Oxygen-heme interactions Myoglobin: structure and function Hemoglobin: structure and function Oxygen binding to myoglobin Cooperativity in oxygen binding to hemoglobin T and R state in hemoglobin Role of F-helix in cooperativity of hemoglobin Two models for cooperativity (no math) Heterotropic cooperativity, Bohr effect, 2,3-bisphosphoglycerate Transport of CO2 by hemoglobin Molecular origin of sickle cell anemia Task of the immune system Humoral and cellular immune system Antigens and antigen presentation, MHC Different types of T cells B-lymphocytes Generation of soluble antibodiesChapter 6. All the material will be covered. I might ask on the exam about: What enzymes are and why we need them How enzymes work Basic principles on how to derive kinetic equations Acid-base catalysis Covalent catalysis Role of metal ions in catalysis Importance of proximity and good orientation of reactants Ground state destabilization Transition state stabilization Induced fit Mechanism of chymotrypsin Mechanism of haloalkane dehalogenase Mechanism of alcohol dehydrogenase How to measure reaction rates Michaelis–Menten (steady state) kinetics The meaning of Vmax and Km in a simple one-substrate mechanism Two-substrate enzymes, sequential vs. Ping–Pong mechanism Regulation of enzyme activity, allosteric enzymes Reversible and irreversible enzyme inhibition Competitive inhibition, transition state analogs Uncompetitive inhibition Mixed inhibition Chapter 7. The focus here is at the properties and function of mono-, di-, and polysaccharides. There is lots of chemistry going on, and I expect that you know the reactions that are covered in the textbook and in the lecture. On the other hand, I do not expect you to know the names or structures of saccharides other than ribose, glucose, galactose, mannose, and fructose. You are not expected to know details about the function of glycoconjugates, lectins, and selectins. Some areas of special interest include: Differences between aldoses and ketoses Open chain and ring structures of monosaccharides Isomerism, D,L nomenclature, epimers and anomers Physical and optical properties of saccaharides Chemical reactions of saccharides Basic structure of disaccharides (e.g. compare maltose with trehhalose) Structure of polysaccharides starch, glycogen, and cellulose Different types of glycoconjugates Functions of saccharides in living organisms Experimental approaches to study the sequence and structure of