BICH 410 1st Edition Final Exam Study Guide Format Study info on questions from previous tests Plenty of time do not rush Chapter 1 The Facts of Life I II III H O C and N make up 99 of atoms in the human body Why is this A Covalent bond formation by electron pairing and the stability and versatility of these products B What is bond energy i Energy required to break a bond H H H C C C and C O bonds have relatively high bond energies meaning they are very stable bonds Weak forces maintain biological structure and determine biomolecularinteractions A Weak forces are very important They may be weak but all of them working together can make for strong interactions B Weak forces restrict organisms to a narrow range of environmental conditions i Conditions such as pH temperature ii Very important for building proteins because they need to constantly be made and unmade which would be difficult with very strong bonds in place The last section of the chapter was about organelles in the cell which she did not stress She said that there probably wouldn t be a question from this section Spend your time studying other things Chapter 2 Water I Hydrophobic interactions are considered the secret of life what does hydrophobic mean A Water fearing i The way water interacts with things with hydrogen bonds and hydrophobic interactions is what makes life the way it is B Nonpolar solutes interact differently with water by organizing it i The H bond network of water reorganizes to accommodate the nonpolar solute ii This decreases entropy disorder because the system is becoming more ordered iii Amphiphilic molecules interact favorably with both polar and nonpolar environments Amphipathic molecules contain both polar and nonpolar groups These terms mean the same thing Example fatty acids alcohols iv Amphiphilic molecules in aqueous solution form MICELLES Keq H OH H20 pH log H pH pOH 14 Ka H A HA SUPER IMPORTANT Henderson Hasselbalch equation pH pKa log A HA C Buffers are solutions that resist changes in pH as acid and base are added i Most buffers consist of a weak acid and its conjugate base D Why is water so special i Very good solvent for ionic and polar solutes ii Poor solvent for nonpolar substances iii Hydrophobic interactions membranes form and the cellular nature of life is created iv High dielectric constant forms ions v High heat capacity enables temperature regulation https ecampusprod tamu edu bbcswebdav pid 1146621 dt content rid7408414 1 courses BICH 410 1511 M2 Water pdf important link to understand water if you are still confused Chapter 3 Thermodynamics I Terminology A The system the portion of the universe with which we are concerned eg the cell The surroundings everything else Isolated system cannot exchange matter or energy Closed system can exchange energy Open system can exchange either or both B Enthalpy H the total energy Free Energy G Theenergy available to dowork Entropy S Disorder A system s thermal energy that is unavailable for work C Standard state free energy change G is the value of delta G when temperature is 298 K pressure at 1 atm and concentrations at 1 M i Biochemical free energy change G has to be at a pH of 7 Equations G H T S G G RT ln C D A B Go RT lnK eq Very Important Concept If G 0 the reaction is at equilibrium If G 0 the reaction proceeds as written If G 0 the reaction proceeds in the opposite direction II Why are ATP and ADP such useful molecules A Large negative free energy change on hydrolysis is due to electrostatic repulsion oxygens with negative charge stabilization of products by ionization and resonance entropy factors i Hydrolysis relieves electrostatic repulsion and increases energy favorable Memorize this Make sure you know which form is more stable which is keto which is enol and that the process is called tautomerization How can reactions in cells run against their thermodynamic potential formation of ATP Reactions are driven in the thermodynamically unfavorabledirection via couplingwith highly favorable processes Also a very important reaction Example of coupling Chapter 4 Amino Acids I Structure and Properties A All contain a central tetrahedral carbon atom i There are 20 common amino acids each with a different R group or side chain ii They join to each other through peptide bonds via dehydration because water is released iii There are Non polar amino acids polar uncharged amino acids acidic amino acids basic amino acids There really isn t a way around this you have to memorize the 20 amino acids and their R groups B The alpha carboxyl always has a pKa of 2 and the alpha amino has a pKa of 9 i Some amino acids have R groups with pKas that also need to be memorized ii Aspartic Acid Asp D pKa carboxyl 3 9 iii Glutamic Acid Glu E pKa carboxyl 4 3 iv Histidine His H pKa imidazole 6 0 v Cysteine Cys C pKa sulfhydryl 8 3 vi Tyrosine Tyr Y pKa phenolic OH 10 1 vii Lysine Lys K pKa amino 10 5 viii Arginine Arg R pKa guanidino group 12 5 ix Serine Ser S pKa hydroxyl 13 x Threonine Thr T pKa hydroxyl 13 xi Average 2 9 and any pKas of the side groups to get pI xii Example 2 9 8 3 6 4 6 325 C All amino acids are chiral but glycine i L amino acids predominate in nature ii R S nomenclature is better esp for amino acids with 2 chiral centers D The chapter talks about NMR and different technologies but she said that this wouldn t be on the test E Peptide Bond i Found in the trans conformation ii Has partial 40 double bond character important iii Length of 0 133 nm which is longer than double bond but shorter than single iv the six atoms of the peptide bond group define a plane the amide plane Each unit of an amino acid is called a residue 2 residues dipeptide 3 residues tripeptide etc One polypeptide chain a monomeric protein More than one multimeric protein Homomultimer one kind of chain Heteromultimer two or more different chains F I Sequence of Amino Acids i Unique of every protein ii Is a form of genetic information iii Is read amino to carboxyl terminus Proteins A Protein structure i Primary 1 sequence Secondary 2 local structures H bonds Tertiary 3 overall 3 dimensional shape Quaternary 4 subunit organization ii Solubility is influenced by pH iii Know the purification steps in this figure iv Purification processes to know 1 Dialysis concentration 2 Ion exchange chromatography charge 3 Gel filtration chromatography size 4 SDS PAGE molecular weight 5 Affinity chromatography B Sequencing i Sanger sequenced the two chains of insulin ii Established that all