Topics for the second midterm: Chem142A (Kahn, Summer 2009) You are expected to know all the material that was covered in the lecture. Most importantly: Chapter 4. The few important topics that we covered after the first midterm are: 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 Main differences between the α-helix and the 310 helix Structures of parallel and antiparallel β-sheets Ramachandran diagrams, know where the α-helix and β-sheets are Structure and function of fibrous proteins α-keratin, β-keratin, collagen, and silk fibroin Structure of amino acid proline, recognize hydroxylated prolines Biological function of vitamin C in formation of collagen Covalent cross-linking in keratin and collagen How are membraneous proteins unique Distinction about tertiary and quaternary structure in globular proteins Symmetry in oligomeric proteins The concept of protein motifs (but not all the structures / names) Protein folding and denaturation The importance of ribonuclease folding experiment Assisted folding (chaperones, chaperonins) Basic steps and main bottlenecks in NMR and X-ray crystallography Chapter 5. Please read pg 153-170 (pg 157-174 in 4th ed) to reinforce the concepts on protein function. 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 the textbook is. You are expected to know: Key concepts: ligand, binding site, etc Quantitative measures of interaction strength and rate; binding thermodynamics: free energy, enhalpy and entropy Graphical interpretation of binding isotherms Lock and key vs. induced fit model Protein flexibility and importance of induced fit (hexokinase example, see also http://www.chem.ucsb.edu/~molvisual/ABLE/induced_fit/) Oxygen-heme interactions Myoglobin: structure and function Hemoglobin: structure and function Oxygen binding to myoglobin, know the structure of histidine now Cooperativity in oxygen binding to hemoglobin T and R state in hemoglobin Role of F-helix in cooperativity of hemoglobin Heterotropic cooperativity, Bohr effect, 2,3-bisphosphoglycerate Transport of CO2 by hemoglobin Molecular origin of sickle cell anemiaCorrelations between sickle cell anemia and geographic location (latitude, altitude) Task of the immune system Humoral and cellular immune system Antigens and antigen presentation, MHC I and MHC II Different types of T cells B-lymphocytes and mechanism of antibody production General structure of antibodies: constant and variable regions Generation of soluble antibodies during humoral immune response Viruses that attack immune system: why HIV is so bad Examples of roles of motor proteins Role of kinesin, dynein, and microtubules in trafficking Structure and protein composition of the muscle tissue Molecular mechanism of the muscle contraction Role, and the general work mechanism of ATP synthase Chapter 7. Please know the names or structures of monosaccharides D-glyceraldehyde, D-dihydroxyacetone, ribose, glucose, galactose, mannose, and fructose; be able to recognize functional groups in various derivatives of carbohydrates. Some areas of special interest include: Functions of carbohydrates in living organisms Differences between aldoses and ketoses Open chain and ring structures of monosaccharides Isomerism, D,L nomenclature, epimers and anomers Recognize enantiomeric and diastereomeric pairs (e.g. erythrose and threose) Physical and optical properties of saccharides Spectropolarimetry as a method to study carbohydrates in solution Biologically important chemical reactions of saccharides Structure and function of disaccharides containing glucose and galactose (e.g. trehalose) Structure of polysaccharides starch, glycogen, cellulose, and chitin Physical properties of solutions of polysaccharides Glucogen’s role as a source of rapid energy source in animals General structure and function of peptidoglycan Biological role of lysozyme in animals How glycosylaminoglycans differ from simple polysaccharides Glycoproteins, the role of carbohydrates there Glycolipids, why some bacteria are gram-negative? General structure of proteoglycan and proteoglycan aggregates Structural difference between syndecans and glypicans Extracellular matrix, and processes involving its degradation Examples of biorecognition involving carbohydrates (e.g. influenza virus-cell interactions) Biosynthesis and degradation of proteoglycans Experimental approaches to study the sequence and structure of complex carbohydrates How to determine the composition of a complex carbohydrate How to determine which atoms form the glycosidic bonds in