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 know-
Reaction 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 know-
Polarity 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