Biochem Exam 1 Review - Lecture notes Chapters 1-4 PDF

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Biochemistry (4610) Highlights of Key Points Keep in mind that you are expected to build on your knowledge and not forget the information after an exam. Chapters 1,2,3,5, 6.1-6.4 (Exam 1) Know the generalized cellular structures and their functions in eukaryotic and prokaryotic cells. Know the 1st and 2nd laws of thermodynamics. 1st Law: Energy is conserved 2nd Law: Spontaneous reactions tend toward more disorder Understand what is meant by enthalpy, entropy and Gibbs free energy and the equation relating them to each other and be able to solve for any of the variables. Enthalpy: ΔH – heat absorbed (+) / heat released (-) Entropy: ΔS – more disorder = + Gibbs free energy: ΔG = ΔH – TΔS (if ΔG is negative – spontaneous reaction) Know the equation relating ΔG, ΔGo , and product and reactant concentrations. ΔGo = ΔG @ 298K, 1atm, 1M ΔG = ΔGo + RTlnQ (Q = concentration) Be able to simplify and include Keq, when ΔG = 0. At equilibrium (ΔG = 0) Keq = e-(ΔGo/RT) ΔGo is exponentially related to Keq Understand Le Chatlier’s Principle, coupled reactions (Hess’ Law), know biochemical standard states and deviations from cellular conditions, and be able to interpret the significance of values for equilibrium constants or ΔG. (ex/ What is significance of Keq >1?) Le Chatlier’s Principle: balance – adjusts to new equilibrium in response to stress. Standard States = 298K, 1atm, 1M pH = 7 Understand the different types of intermolecular forces. H-bonds, London Dispersion, etc.

Thoroughly understand the chemical properties of water and its ability to act as a solvent. Water is composed of H-bonds – longer and not as strong as covalent bonds – short lived bonds – constantly forming and breaking. H20 minimizes temperature changes Polar and ionic substances dissolve in water. Thoroughly understand pH and the mechanism of buffers. (Know Henderson-Hasselbalch and that it derives from definition of KA) pH = -log[H+] pH > 7 is basic pH < 7 is acidic pH is property of solution and pKa is property of acid HH = pH = pKa + log[A-]/[HA] Buffers – solutions consisting of a weak acid and conjugate base which resist change in pH Buffering region - ±1 unit around pKa Know the significance of pKa and relationship to pH. If pH is above pKa – there is more conjugate base Be able to draw the structure of a nucleotide using any of the five standard bases.

Know the properties of the 20 “standard” amino acids, side chains, amino and carboxy termini, and determination of pI.

Know the 3 letter abbreviation for each amino acid. Amino acid structures will be provided on exam one.

Understand that there are other amino acids. Know the structure and properties of a peptide bond. The peptide bond is an amide bond – but good biochemists do not identify it as such

Know methods of protein purification and be able to apply the techniques to a mixture of proteins. (Chromatography methods, electrophoresis.)

Understand protein 1o, 2o, 3o, 4o structure.

Understand peptide bond and constraints. Peptide bonds are planar – rotate around one specific point Know the key features of and differences between fibrous and globular proteins. Fibrous proteins: long and elongated – water insoluble Globular proteins: spherical – water soluble Know the key features of 2o structures: α-helix, β-sheet. α-helix: right handed turn – like phone cord – 3.4 AAA to do complete turn – 1 AA reacts with 5 AA and 2 interacts with 6 … -- around 12 AA long and gly and pro don’t show up often β-helix: extended structure of amino acid chains bonded with each other -

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Antiparallel C N NC Parallel CN CN β-bends: 180-degree turn – gly and pro

Know what is meant by nonrepetitive structure, properties of β-bends. Nonrepetitive structure: can’t recognize and classify – not random Understand the trends of 3o structure of globular proteins, including location of amino acids. Considered supersecondary structures- recognizable pattern of two or more secondary structures

Understand that proteins are dynamic. Proteins can move and bend – change shape Understand the forces maintaining 3-D structure of proteins and the contributions of each. Noncovalent interactions Hydrophobic interactions – effect Hydrogen bonds Electrostatic interactions – van der waals and ion pairs Know what causes protein denaturation. Heat: disrupt noncovalent interactions pH extremes: decrease attractions, increase repulsions detergents organics Chaotropic agents: disrupt structure of water – disrupts hydrophobic interactions BE SURE YOU CAN EXPLAIN HYDROPHOBIC INTERACTIONS....