MCB 102 Spring 2015 Midterm #1 7:00-9:00 PM Monday Feb. 23. Study Guide

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1 MCB 102 Spring 2015 Midterm #1 7:00-9:00 PM Monday Feb. 23 Study Guide Last name: A-C: 145 Dwinelle D-Z: Wheeler Auditorium In case of unexpected overcrowding, we may ask students to move to their non-assigned location. This is unlikely to happen. DSP: Individually notified of arrangements. Contact your GSI if you have not yet made arrangements for your exam. Calculators and other electronics Will be strictly prohibited in the exam. The exam will be designed so that you will not need them. What to bring Bring your Cal Student (picture) ID card. IDs will be checked when exams are turned in. The exam is closed-book and closed-notes. The only items you are allowed to bring to your seat during the test are writing implements (pens, pencils, erasers) and your test paper. Scratch papers are not allowed. The exam paper will have adequate working space. If you bring a backpack, briefcase, satchel, gym bag, purse, bookbag, etc. with you to the examination room, you will be required to leave it (and all of your class notes, study sheets, textbooks, etc.) at the front or sides of the room before the test commences and during the test. During examinations, you are not allowed to wear, or to bring to your seat, any headgear (hats, baseball caps, visors, berets, etc., except for head gear worn for religious reasons, e.g. yarmulkes, hijabs or turbans). No breaks are permitted. If you need to leave the room, you will be required to turn in your exam first. The only exception is if you have a letter from DSP that specifically states that you are permitted a break as part of your accommodation. Seating: The exam will be help in two large lecture halls with enough room to spread out. Do not sit directly next to, in front of, or behind someone else. Time limits will be strictly observed. When time is called, put your pen or pencil away immediately and line up with your ID in hand to turn in your exam. If you continue to work after time is called you may get a zero on the exam.

2 You are permitted to use a pencil but note from the course policies: Midterm exams written in pencil or erasable ink will NOT be eligible for any type of re-grading. Bring a pen to sign the cover page of your exam in ink. Once again: Calculators and other electronics Will be strictly prohibited in the exam. The exam will be designed so that you will not need them. Exams will be returned in your assigned discussion section Please remember to write your section number on the exam. Midterm #1 study tips The first midterm will cover the following topics: Fundamental forces and water Van der Waals Hydrogen bonding Electrostatics Hydrophobic effect Ionization of water and buffers Henderson-Hasselbach equation (any buffer calculations will be simple enough to do without a calculator) Amino acids One and three letter codes pka values of the seven readily titratable side-chains (rounded to one digit) Structures (be able to draw them, including hydrogens, and taking ph into account) Chirality Unusual amino acid properties, i.e. above ph 10, Lys acts like a hydrophobic side chains; the flatness of Arg is important, not just its positive charge; aromatic residues have a small partial negative charge at the ring center; etc. Cys oxidation Proteins Nature of peptide bonds Be able to draw the peptide bond and short polypeptide structures with sidechains, from scratch pi computation Analysis by SDS-PAGE and western blotting. Theory and practice. Use of reducing agents General concepts of mass spec. (You will not be asked to assign spectra.) Purification by ion exchange and size exclusion chromatography.

3 Quantitation by Bradford and UV absorbance (simple calculations doable by hand) Protein Structure Phi, psi angles- definition- be prepared to draw them on a diagram Cis and trans peptide bonds Ramachandran plot- be prepared to sketch it and/or identify regions of interest Alpha helices Beta strands, sheets, and turns Amino acid preferences to form helices, strands, and turns Faces of alpha helices Handedness of alpha helices Unusual roles of prolines and glycines Disulfide bonding Protein folding: the Anfinsen experiment, folding pathways, fundamental forces Denaturation of proteins Protein function Hyperbolic and sigmoidal binding curves and equations Be prepared to hand-draw curves highlighting main features Meaning of cooperativity Meaning of K a, K d, k 1, k -1 Myoglobin and hemoglobin Relating structure to binding Relating oxygen binding to physiology of exercise and altitude adaptation Role of heme and iron and relationship to protein structure Role of subunit interfaces and quaternary structure Connection between multiple subunits, multiple binding sites, and cooperativity How do fundamental forces, ph, and amino acid properties affect enzyme catalysis? Enzymes Main characteristics of enzyme catalysis Magnitude of rate accelerations Origin of rate acceleration in transition state stabilization Secondary factors contributing to rate acceleration Relationship of binding and catalysis Relationship of ground and transition states Michaelis-Menten equation and meaning of k 2, k cat, K m, V max, and k cat /K m Covalent catalysis Structural enzyme mechanisms Perturbed pka values Serine protease triad and oxyanion hole Electron pushing pathway of chymotrypsin Substrate binding pockets of chymotrypsin, trypsin, and elastase

4 Think about how ph changes and amino acid properties relate to enzyme mechanism Enzyme inhibition and activation Competitive, uncompetitive, mixed, and non-competitive inhibition Allosteric inhibition Cooperativity in enzymes Zymogen activation Enzyme degradation, ubiquitination, and the proteasome Synthetic enzyme inhibitors in medicine and research Transition state analogs Covalent inhibitors Specific and non-specific inhibitors Enzyme phosphorylation Carbohydrates You will not need to draw sugar structures from scratch You should be able to redraw a structure provided to you, say to convert a linear structure in Fischer projection to a ring diagram. Determine if a sugar is D or L Know the concept of epimers. You do not need to memorize the names and structures of the epimers of the five and six-carbon aldoses and ketoses. Aldoses vs. ketoses Pentoses vs. hexoses Pyranoses and furanoses Alpha and beta anomers Polysaccharides, reducing and non-reducing ends, glycosidic bonds Numbering of carbon atoms in sugars Protein modification by O- and N-linked sugars Nucleic Acids Bases, Nucleosides and Nucleotides: Definitions. You should be able to draw the nucleotides and their numbering systems. Sugar puckering definition and recognize the type of puckering. Polynucleotides Base pairing schemes. You should be able to draw the base pairs from memory DNA structure Alternative double stranded structures of DNA and their characteristic structural parameters Optical properties of DNA and how they can be used Thermodynamic stability of Nucleic acids Thermal melting of double stranded nucleic acids Doty-Marmur relation Lipids

5 Be prepared to draw structures of the glycerol phospholipid and sphingolipid backbones Be able to draw the structures of these common headgroups: choline, ethanolamine, serine, and inositol. Given a backbone drawing, be able to complete a drawing of one the abovementioned lipids. Know the charges at neutral ph on the common headgroups listed above Know how to label atoms in acyl tails of lipids Saturated, unsaturated, cis and trans fatty acids and acyl groups Recognize the structures of cholesterol, testosterone and estradiol Major lipid modification of proteins Remember the names and definition of lauric, myristic, palmitic, stearic, palmitoleic, oleic, and arachidonic acids. Assigned reading Not more than 10% of the points of the midterm will pertain mainly to the readingonly (not lecture/discussion) material. This works out to 8 points maximum out of the 85 total. Keratin, collagen, antibodies, chaperones, and prions are examples of potential topics.