Biological Molecules Polymers Know that only a small subset of the known elements are found in living systems o Know the most abundant C N O H Know that living organisms are o Closely related to organic carbon based chemistry Be able to recognize common functional groups in biological molecules Know the four major types of biomolecules and their general structures o Amino acids o Carbohydrates o Nucleotides o Lipids o Proteins Know the three types of polymers Polymers of amino acids joined by peptide bonds o Nucleic acids DNA and RNA o Polysaccharides Polymers of nucleotides joined by phosphodiester bonds Polymers of carbohydrates joined by glycosidic bonds Know which type of biological molecule does not form polymers and why Energy Metabolism G J mol Know the definition Gibbs free energy o Energy relevant to biochemical Understand the principle of enthalpy systems H J mol and how it relates to G o Heat content of system J K mol and how it relates to G Understand the principle of entropy S o Measure of the dispersion of the o Measure of disorder or energy of the system randomness Understand how temperature T K o Absolute temperature in Kelvin relates to entropy and G Know the equation G H o Under what conditions T S and how to use it appropriately would G always be a negative value o Given that building living systems results in a decrease in entropy what makes life possible from a thermodynamic perspective Know the principle of spontaneity and how it relates to G o G 0 nonspontaneous or endergonic o G 0 spontaneous or exergonic o Measure of equilibrium NOT speed o Be able to recognize or determine if a reaction or process is spontaneous reactions Understand the principle of coupling o Spontaneous biochemical involve oxidations and reductions reactions can be coupled with unfavorable reactions to net negative change in free energy Know that many biochemical reactions o Compounds are oxidized when electrons are extracted o Compounds are reduced when electrons are accepted o These are called redox reactions because both occur simultaneously oxidations and reductions of carbon and other compounds Metabolic reactions are catalyzed by o Know how to recognize enzymes o Mostly protein some RNA Domains of Life Know the three domains of life o How are they classified based on rRNA sequence Know what defines prokaryotes o Lack nucleus and internal o Archaea organelles Often inhabit extreme Similar in structure to environments bacteria o Bacteria Know what defines eukaryotes o Most often larger than prokaryotic cells o Contain nucleus and intracellular compartments Include microbes and macroscopic plants and animals o o Unicellular or multicellular Water Intermolecular water Understand the basic principles of Understand the basic principles of covalent bonds hydrogen bonds o Electronegative element covalently bonded to H atom and electrostatically attracted to 2nd H atom o What contributes to a strong H bond versus a weak one Understand the molecular structure of o What makes it a polar molecule Understand the formation of H bonds o What contributes to the surface in water in liquid and solid form tension of water Ionic bonds Be able to recognize H bond donors Know the relative strengths of the and acceptors different types of bonds o H bonds o o Covalent bonds o van der Waals dipole dipole and London dispersion forces intermolecular interactions involved for a given compound Know how to rank melting or boiling points of compounds Be able to determine the type of o Based on nature and strength of intermolecular forces Understand concept of dielectric constant o Measure of polarity Hydrophobic Effect Understand the principles of the hydrophobic effect Based mainly on changes in entropy How this drives spontaneous associations based on polarity How lipids can associate as micelles or membranes and what determines the nature of their association in an aqueous environment Benefits of lipid associations into membranes What types of molecules can pass thru the lipid bilayer Acid Base Chemistry Movement of protons in water Principles of spontaneous dissociation of water o Ionization constant of water Understand principles of pH scale and Be able to use ionization constant of water to determine concentration of either H or OH how to determine pH from H and vice versa dissociation constant and pK value Understand concept of acid o pH at which group is ionized o Be able to calculate pKa from Ka and vice versa Be able to recognize a weak acid conjugate base pair and distinguish between them charged or uncharged at given pH Be able to determine if group will be o Based on pK value Be able to use Henderson Hasselbach equation in acid base chemistry problems acid or base to water Understand effects of adding weak o Only partial dissociation Understand effect of adding strong to weak acid and strong to weak base Understand principles of buffers o Effective buffering range o How to determine pK value from titration curve Understand concepts of pH homeostasis o Principles of buffering with o How this works to help kidney bicarbonate and CO2 perform buffering function Principles of Buffers Amino Acids Peptide Bonds and L designations Understand the distinction between a protein and a polypeptide Understand the basic structure of an amino acid and the designations for the fundamental chemical groups o Know the significance of the D Know the names structures 3 letter and single letter abbreviations of the 20 common amino acids o Know how to classify them as hydrophobic polar uncharged or polar charged groups present o Know the types of functional Know where hydrophobic hydrophilic residues might be found in various types of proteins Know the formation and structure of peptide bonds o Dehydration of carboxy and amine groups o Side chains in trans conformation o Know that a peptide bond has resonance and the significance of this Shorter bond length Very stable No free rotation about C Atoms are very polar and Know how pH relates to pK of ionizable N bond tend to form H bonds groups on proteins o Know how to predict overall charge on peptide at given pH number of and charges o Know that pK s of carboxy and amine termini are 1 pH unit closer to neutral in peptide compared to those of free amino acid o Know what the pI is and its significance with regard to proteins o Know how local environment can affect pK values of amino acid side chains Primary Secondary Protein Structure Know the four levels of protein