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Download Review Sheet Exam 1 C483 Spring 2014
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Review Sheet Exam 1 C483 Spring 2014 This sheet is intended as a study aid, not a comprehensive list of everything we covered. This sheet hits the highlights. General- The exam will be based largely on homework and discussion section problems. If you can do these problems, you will do fine on the exam. Many of these problems will be used verbatim, or be very similar to the exam problems. You are responsible for all the material covered in lecture, or assigned in the book, unless I stated otherwise. Please note that all during the semester I directed you in class about which topics would be emphasized and which deemphasized. I will never tell you that you don’t need to know something- on the other hand, the exam will stress fundamentals and things that were covered in class and in the homework. Chapter 1- This chapter largely summarized concepts we have been using throughout the course. Please note specific emphasis on functional groups- particularly phosphate esters and anhydrides and questions related to them. Please also note discussion of sugars, amino acids and the derivation of the D and L nomenclature. Please also note discussion of other biological components, such as lipids, detergents, and assemblies, such as micelles. Topics to knowReaction rates Thermodynamics Equilibrium Constants Activation Energy The scale of cell components (pp 24 and 25) Chapter 2- Water- This chapter should also have been substantially review. It covers the basic forces associated with water-water association, the dissolution of solutes in water, and solubility generally. These topics are the same as those we used to discuss protein structure and folding. Topics to knowPolarity of water Electrostatic forces Hydrogen bonds and the factors that affect them Diffusion Osmotic pressure Hydrophobic effects All noncovalent interactions Ionization of water pH Weak Acids (you should know the general pKa’s of most common acids and conjugate acids- i.e. carboxylates, phosphates, alkyl ammonium, etc.) Titration curves and buffers Henderson-Hasselbach equation and its use. Chapter 3- amino acids and protein structure. We explored the structure and side chain variation of the twenty common amino acids, as well as a number of modified amino acids and some amino acids that do not occur in proteins. You must know the structures of all these amino acids, as well as associated nomenclature (one and three letter, as well as full names). You should be familiar with the properties of side chains and approximate pKa’s. You should also understand the relation of amino acids to basic metabolites where this was covered (e.g. alpha ketoacids). Understand protein analytical techniques (purification schemes and analysis of amino acid content and sequencing). Topics to know Amino acid structure Categorization based on side chain Side chain properties, including pKa Titration curves Amino acid modifications Nonproteinacious amino acids of importance (e.g. ornithine) Peptide bond Analytical techniques- sequencing, chromatography (4 types), amino acid composition, molecular weight determination. Chapter 4- Understand the nature of the peptide bond and its role in protein structure. Cis-trans isomerization. Phi and psi angles and the Ramachandran plot are also important. Understand the hierarchy of protein structure (primary-secondary-tertiary-quaternary). Understand basic motifs of protein structure and the forces that govern them. Be familiar with supersecondary structures. Be conversant with the various methods of depicting protein structures. Understand domains and the assembly of secondary and supersecondary structures into tertiary structures. Understand covalent crosslinking in proteins and higher order assembly and the benefits to be derived from higher order structure. Recognize repeating motifs in protein structures. Understand the basics of protein-protein association and protein denaturation and renaturation. Understand the basic structure and function of collagen, myoglobin, hemoglobin, and antibodies. Understand cooperativity and allosteric regulation in hemoglobin and its physiological relevance. Topics to know Hierarchy of protein structure Methods for determining structure (x-ray vs. NMR) Conformation of the peptide backbone (amide bond and phi, psi angles) Ramachandran plots and which amino acids are disfavored in helices and why Cis/trans isomerization Alpha helix and its properties Beta strand and its association to beta sheet Loops and turn Common supersecondary structures Domains Quaternary structure Protein-protein interactions Denaturation and renaturation of proteins Structure and function of collagen, myoglobin, hemoglobin, and antibodies Cooperativity and allosteric regulation T to R interconversions and their effect on binding isotherms Ch 5- Be conversant with the basic types of enzymes (yes, you have to know this). Understand saturation kinetics and basic way in which enzyme kinetics is done. The Michaelis-Menten equation, its derivation and the assumption made to derive it. Basic kinetic constants. Association and dissociation constants. Lineweaver Burk plots. All types of inhibition and the graphical form of Lineweaver Burk plots that show inhibition. Inhibition constants. Enzyme regulation and covalent modification/regulation. Topics to know Six classes of enzymes and what they do Basic enzyme kinetics and how they are measured. Saturation kinetics Michaelis-Menten equation and its derivation. The meaning of kcat and Km. Lineweaver Burk plots Competitive, uncompetitive and noncompetitive inhibition Covalent inhibition Allostery and enzyme regulation Regulation by covalent modification