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 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 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 equation
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