BCH 380 1st EditionExam# 1 Study Guide: Lectures: 1 – 11 Chapters 1-4,6-8Chapter 1: Biochemistry and the Union of LifeI. Molecular Constituents:Class Monomers Polymer1. Protein Amino Acids Peptide2. Carbohydrate Monosaccharide Polysaccharide3. Lipid Fatty Acid Triacylglycerol4. Nucleic Acid Nucleoside DNA/RNA- Bonding/stereochemistry is important- “Function follows form”- Have directionality N-terminus to C-terminusII. 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 ForcesI. 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 bondII. The Four Weak Forces- allows for 3D structure, recycling of monomers and reversibility1. 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 molecules-o Hydrogen =Donor, lone pair of electrons on Oxygen=acceptor2. 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 (water-hating)- 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 system4. 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). III. Salt (NaCl) in water:- 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, awayfrom the rest of the crystal.IV. 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: Kwo Kw= 1x10^-14 M- Ka: equilibrium constant for an acido HA H+ + A-o Ka= [H+][A-]/[HA]o Larger #= stronger acid, smaller #= weaker acid- Kb: equilibrium constant for a weak baseo B + H2O BH+ + OH-o Kb: [BH+][OH-]/[B]- pH= -log[H+]- pOH=-log[OH-]- pOH + pH=14V. Buffers- Henderson Hasselbalch Equation:o pH=pKa+ log [A-]/[HA]** Know when to use this equation andwhen to use Ka or Kb equations.** Be able to do titration problemsChapter 3: Amino AcidsI. 20 Amino Acids: Know how to draw all but Trp, Arg and His (but recognize them) and their 1 and 3 letter abbreviationsII. Enantiomers: mirror images- non superimposable a. Fischer Projection: OH or NH3 on left(L) or right(D):III.III. Amino Acid Stereochemistry: (R/S)o R= clockwiseo 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-listof the other atoms bonded to it (at distance 3 from the stereocenter), the sub-lists 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 2. COO- 3. R groupCOO-HNH3RCOO-NH3HRCH3N HCOO-RCH NH3COO-RCHO HCHOCH2OHCH OHCHOCH2OHGlyceraldehydeL-glyceraldehydeD-glyceraldehydeNH3COO-RNH3R-OOC123123R- amino acidS- amino acidIV. Acid/Base Properties of Amino Acids:*if pH> 10, everything that can be deprotonated will be*if pH<10, everything will be protonateda. Zwitterionic Form:Blue on chart: Zwitterionic Form= 0 chargeb. pIpI = pKax + pKay/2 where pKaxand pKay are pKa’s on either side of 0 chargeHow to find pI:1. Draw fully protonated molecule2. Deprotonate completely -carboxylic acids first (one in R-group first, then the one on the amino acid)-Amine from amino acid second3. Write the charges of each step that was deprotonated4. 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 chainsc. Cysteine disulfide bonds: (be able to draw)Chapter 4: Protein StructureI. 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 hybridizedII. Peptide/Protein Nomenclature- Dipeptide=>dodecapeptide: 2 amino acids=> 12 amino acids- Polypeptide: full length polypeptide- Multiple polypeptides interacting togethero Greek letters (e.g. a2b2)o Hompolymer/Heteropolymeretco Homodimer/heterotrimeretc- Difference between polypeptide and protein?o Polypeptide may or may not be active componento “protein” implies native form- Conformation: overall 3D architecture of a protein- Domain: part of a polypeptide chian that could fold and