BMB 401 Study Guide for Exam 1 (Lectures 1-14) You should focus your attention on understanding/knowing the following topics: Introduction • Biochemistry describes the molecular basis of life • The three major conceptual parts of Biochemistry revolve around structure, energy, and information. • Weak, non-covalent interactions are very important in biology • Know the characteristics of van der Waals, electrostatic, ionic, hydrogen bonding interactions Water • Know the basic characteristics of the water molecule • Polar vs. non-polar solvation • Water ionization equilibrium • Definition of pH • Strong vs. weak electrolytes • Ka and pKa • Calculation of pH for a certain amount of weak acid/base in pure water • Henderson-Hasselbalch equation • Calculation of pH for solution with weak acid after adding strong base (or weak base with strong acid) • Calculation of amount of dissociated acid (base) after adding strong base at given pH (or weak base with strong acid) • Titration curve • Buffer properties of weak acids/bases, biological buffers Thermodynamics • Potential vs. kinetic energy • Isolated vs. closed vs. open systems • First law of thermodynamics, exchange of energy with environment • Enthalpy • Entropy • Second law of thermodynamics • Free energy • Entropy-enthalpy balance • Conditions for equilibrium • Standard state free energy • Calculation of free energy changes at different concentrations • Calculation of free energy changes at different pH• Characteristics of biological high energy compounds • Transfer reactions (group, proton, electron) • Coupling of reactions • Redox reactions Amino acids • Basic chemistry of an amino acid (C-alpha, H, side chain, amino group, carboxyl group) • L- vs. D- amino acids • Ionization equilibrium of amino acids (termini and side chains, dominant charge states under biological conditions, pH near 7) • Amino acids: names, three-letter and one-letter abbreviations, recognize molecular structures, know characteristics (polar, non-polar, basic, acidic) • Know what is special about glycine, proline, cysteine, histidine • Peptide bond and formation of peptides • N- vs. C-termini • Torsional flexibility of peptide backbone: φ, ψ, ω torsion angles, trans/cis isomerization Proteins: Primary Structure • Sequence-structure-function paradigm • Structural hierarchy (primary, secondary, tertiary, quaternary) • Globular vs. fibrous vs. membrane proteins • Prosthetic groups and chemical modifications • Meaning of homolog, paralog, ortholog, analog • Homology modeling • Sequence conservation and evolution Proteins: 3D Structure • Ramachandran map (φ−ψ map) • Secondary structure elements • Stabilization of alpha-helix • Beta strands and sheets • Turns and loops • Secondary structure from sequence: I,i+4 pattern for helix; alternating pattern for beta sheet with equal distribution of hydrophobic residues (parallel) vs. preference for one side (antiparallel); PG in turns; high charge/low hydrophobicity in loops or disordered peptides • Hydrophobic effect, arrangement of non-polar amino acids in globular and membrane proteins • Protein folding via folding funnel • Protein domains fold independently• Protein misfolding diseases • Disordered peptides/proteins • Oligomerization into quaternary structures Enzymes • Role of enzymes (accelerate reactions, allow reactions to take place in biological environment, create reaction cascades, allow only specific reactions, facilitate coupling of reactions, allow for regulation) • Enzymes lower transition state energy but do not change equilibrium • Most favorable binding to transition state vs. binding of reactants • Enzyme cofactors • Meaning of holoenzyme and apoenzyme • Lock-and-key vs. induced fit mechanisms Enzyme Kinetics • Reaction velocity as a function of reactant concentration for catalyzed and uncatalyzed reactions • Dissociation constant Kd • Key assumptions of Michaelis-Menten kinetics • Michaelis-Menten rate equation • Meaning of Michaelis constant • Approximation of Michaelis-Menten kinetics at low substrate concentration • Meaning of diffusion-limited reactions. • Lineweaver-Burk plot Enzyme Inhibition • Reversible vs. irreversible inhibition • Characteristics of competitive, non-competitive, uncompetitive inhibition • Lineweaver-Burk plots in the presence of inhibitors and how to tell what type of inhibitor is present Enzyme Regulation • Different possibilities for how enzyme activity can be regulated • Proenzymes (zymogens) • Kinases/phosphatases • Allosteric inhibition and activation • Binding cooperativity • Hill
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