FA Study Guide - Qtr 01.pdf

BIOC 460/660 Study Guide Foundations of Biochemistry and Molecular Biology I Terminology is important in every science class, and there was a lot in this course. You should be sure that you are familiar with the importan...

BIOC 460/660 Study Guide Foundations of Biochemistry and Molecular Biology I Terminology is important in every science class, and there was a lot in this course. You should be sure that you are familiar with the important terms in the slides and in the chapters. Your familiarity with each term or concept should include: 1. What is the definition of the term? 2. How was this term used in the lecture? 3. How might this term be applicable to a potential problem or question? On the following pages is a list of things we covered in class, and besides terminology, these are some key ideas/concepts you should be familiar with: 1 BIOC 460/660 Study Guide Foundations of Biochemistry and Molecular Biology I Quarter #1: Foundations of Biochemistry, Bioenergetics/Thermodynamics, Water, and Amino Acids Biochemistry of Life - Features of living matter - Domains of life - Basic structure of cells and common components - Components of cells unique to bacteria, plants, and animals - Use of energy and carbon sources - Elements essential for life - Why carbon is so unique and critical to biochemistry - Common functional groups of biological molecules - cis vs. trans and stereospecificity of binding - Theory of life from simple molecules - RNA as an initial molecule and why important - Fidelity of information duplication and potential role of mutation - Organelles through endosymbiosis Thermodynamics - Living organisms must obey laws of thermodynamics - Transformation of energy from one form to another is key - Equilibrium vs. dynamic steady-state - Types of systems (and what kind of system living organisms are) - Catabolism vs. anabolism; what is metabolism? - Where energy for all life comes from and why - Gibbs free-energy - How entropy, enthalpy, and temperature affect free-energy - How temperature is always used in equations - Endergonic vs. exergonic and what this means for a reaction to occur - Equilibrium constant and how it is defined - How equilibrium constant is related to standard free-energy and actual free-energy - Relationship between K'eq and ΔG'o - Coupling reactions and why important - Free-energy vs. activation free-energy - Spontaneity vs. speed of reactions - How to speed reactions up and why do these speed them up - Biological catalysts - Pathways and regulation of catalysts Water - Why is it important for life? - Features of a water molecule (structure, dipoles) - How do water molecules interact with each other? - Characteristics of water compared to organic molecules - Why is ice less dense than water? - Why are hydrogen bonds important? 2 BIOC 460/660 Study Guide Foundations of Biochemistry and Molecular Biology I - Water as a solvent - Polar vs. nonpolar or hydrophilic vs. hydrophobic - Amphipathic - Types of noncovalent interactions - How are salts dissolved in water? - Differences between van der Waals interactions and hydrophobic effect - Why does the hydrophobic effect occur? - Why is the hydrophobic effect useful? - Colligative vs. noncolligative properties of water - Osmotic pressure and how it is calculated - Osmotic pressure in living cells and how environment affects this Ionization of Water, Dissociation of Weak Acids, and Buffers - Products from ionization of water - Direction of reaction and resulting Keq - Do free H+ ions ever exist in water? - What is proton hopping? - What is Kw? - How does this contribute to pH? - What is pH a measure of? - What units are used for ion concentrations in calculating pH? - Major difference between strong and weak acids - Ionization constant (or acid dissociation constant) of a weak acid? - Calculating pH of a weak acid - What is pKa? - What is a weak acid and conjugate base? - Buffering capacity of weak acid/conjugate base - Henderson-Hasselbalch equation o What does the Henderson-Hasselbalch equation relate? - Buffer systems in vivo Amino Acids, Peptides, and Proteins - Basic structure of an amino acid and attached groups - Structures of all the R-groups (i.e., know the structures of the 20 common amino acids) - Stereoisomer configuration of amino acids - Naming conventions of common amino acids - General classification of amino acids and important features/distinctions of each - Ionization of amino acids - What is a zwitterion and how does this apply to an amino acid? - Why aren't pKa values the same for the amino and carboxyl groups of different amino acids? - Isoelectric point (pI) - Buffering capacity of amino acids - Ionizable R-groups and calculating pI - Peptide bond formation and energetics of its formation/cleavage - Naming of peptides - Peptide functions - Polypeptides and other non-amino acid (non-protein) associations and attachments 3 BIOC 460/660 Study Guide Foundations of Biochemistry and Molecular Biology I - Uncommon amino acids (how do they arise and some functional significance) Protein Purification and Analysis - Properties of proteins making them conducive to separation - Column chromatography - Ion exchange chromatography - Size exclusion chromatography - Binding affinity chromatography - Electrophoresis - SDS-PAGE - Markers - Isoelectric focusing - 2D electrophoresis - Specific activity - Protein sequencing by Edman's degradation and MALDI-MS - Protein synthesis in vitro 4