BCH 380 1st Edition Exam 1 Study Guide Lectures 1 11 Chapters 1 4 6 8 Chapter 1 Biochemistry and the Union of Life I Molecular Constituents Class 1 Protein 2 Carbohydrate 3 Lipid 4 Nucleic Acid Monomers Amino Acids Monosaccharide Fatty Acid Nucleoside Polymer Peptide Polysaccharide Triacylglycerol DNA RNA Bonding stereochemistry is important Function follows form Have directionality N terminus to C terminus II Prokaryotes vs Eukaryotes Eukaryotes are much more compartmentalized with membrane bound organelles such as a nucleus mitochondria etc III Eukaryote Organelles and Functions Chapter 2 Water and the Four Weak Forces I II III Water solvent of life Have nonbinding electrons on same side Has a dipole due to the big difference in electronegativity between H and O as well as its geometry Polar and uncharged The water dipole allows one water to weakly interact with other water molecules hydrogen bond The Four Weak Forces allows for 3D structure recycling of monomers and reversibility 1 Hydrogen bonds a hydrogen bond donor D is a polarized hydrogen a hydrogen bond acceptor A is a lone pair of electrons The higher electronegative atom pulls the electron cloud towards itself resulting in a partial charge and giving it a dipole Draw bond using dashed lines Example includes water interacting with other water moleculeso Hydrogen Donor lone pair of electrons on Oxygen acceptor 2 Van Der Waals Interactions bring two atoms together to induce dipole Weakest of all weak forces but can be somewhat strong in aggregate Every atom has Van Der Waals interactions due to their electron clouds Van Der Waals Contact Distance the distance two atoms need to be apart to achieve their sweet spot between attraction and repulsion from one another 3 Hydrophobic Interactions interactions between nonpolar molecules waterhating Nonpolar parts away from water usually inside Important translational force in protein folding Gain more energy through more Hydrogen bond formation of water increases entropy of system 4 Electrostatic Ionic Interactions Atoms with opposite charges attract Can include hydrogen bonds and Van der Waals interactions because all include charge differences except electrostatic interactions include coulombic interactions formal charge differences Salt NaCl in water IV Each ion of the solid crystal becomes surrounded by water molecules with the negative end of the water molecules approaching closest to the positive sodium ions and the positive end of the water molecules surrounding the negative chloride ions The water molecules pull these ions one by one away from the rest of the crystal Why Hydrocarbons don t dissolve in water Hydrocarbons are nonpolar The C H bond has no dipole because they share their electrons equally V Acid Base Chemistry Equilibrium Constant Kw o Kw 1x10 14 M Ka equilibrium constant for an acid o HA H Ao Ka H A HA o Larger stronger acid smaller weaker acid Kb equilibrium constant for a weak base o B H2O BH OHo Kb BH OH B pH log H pOH log OH pOH pH 14 V Buffers Henderson Hasselbalch Equation o pH pKa log A HA Know when to use this equation and when to use Ka or Kb equations Be able to do titration problems Chapter 3 Amino Acids I 20 Amino Acids Know how to draw all but Trp Arg and His but recognize them and their 1 and 3 letter abbreviations II Enantiomers mirror images non superimposable a Fischer Projection OH or NH3 on left L or right D Glyceraldehyde CHO CHO HO C H H C COO CH2OH CH2OH L glyceraldehyde OH D glyceraldehyde NH III 3 C H COO COOH3N COO H H C R NH3 III R R H NH3 R Amino Acid Stereochemistry R S o R clockwise o S Counterclockwise naturally occurring Prioritize atoms and assign direction lowest priority goes behind the H 1 Compare the atomic number Z of the atoms directly attached to the stereocenter the group having the atom of higher atomic number receives higher priority 2 If there is a tie we must consider the atoms at distance 2 from the stereocenter as a list is made for each group of the atoms bonded to the one directly attached to the stereocenter Each list is arranged in order of decreasing atomic number Then the lists are compared atom by atom at the earliest difference the group containing the atom of higheratomic number receives higher priority 3 If there is still a tie each atom in each of the two lists is replaced with a sub list of the other atoms bonded to it at distance 3 from the stereocenter the sublists are arranged indecreasing order of atomic number and the entire structure is again compared atom by atom This process is repeated each time with atoms one bond farther from the stereocenter until the tie is broken Priority Order for amino acids except when use cycsteine 1 NH3 group 1 2 COO 1 NH3 NH3 2 R COO 3 2 R amino acid OOC R 3 S amino acid 3 R IV Acid Base Properties of Amino Acids if pH 10 everything that can be deprotonated will be if pH 10 everything will be protonated a Zwitterionic Form Blue on chart Zwitterionic Form 0 charge b pI pI pKax pKay 2 where pKax and pKay are pKa s on either side of 0 charge How to find pI 1 Draw fully protonated molecule 2 Deprotonate completely carboxylic acids first one in R group first then the one on the amino acid Amine from amino acid second 3 Write the charges of each step that was deprotonated 4 Write the pKa of each step 5 Find the two pKas on either side of the 0 charge step use these in the equation pI pKax pKay 2 ifpI 6 then there are lots of acidic side chains in protein ifpI 6 then lots of basic side chains c Cysteine disulfide bonds be able to draw Chapter 4 Protein Structure I II III 1 2 Peptide Bond link amino acids amide bond Amino N terminus to C terminus Normally trans oriented Think of peptide bond as if it is in its resonance form with a double bond no rotation and sp2 hybridized Peptide Protein Nomenclature Dipeptide dodecapeptide 2 amino acids 12 amino acids Polypeptide full length polypeptide Multiple polypeptides interacting together o Greek letters e g a2b2 o Hompolymer Heteropolymeretc o Homodimer heterotrimeretc Difference between polypeptide and protein o Polypeptide may or may not be active component o protein implies native form Conformation overall 3D architecture of a protein Domain part of a polypeptide chian that could fold and possibly function on its own Potentially multiple domains per polypeptide multiple functions per polypeptide Holenzyme complete and catalytically active protein Apoenzyme protein missing a cofactor to make it catalytically active The Four