BCH 380 1st EditionExam # 1 Study Guide Lectures: 1 - 14Lecture 1 (January 14)NO NOTES – went over syllabus Lecture 2 (January 16)6 abundant elements: C, N, O, P, S, H5 essential ions: Na, Mg, K, Ca, ClBiomolecules- What property unites H, O, C, and N and renders these atoms so appropriate to the chemistry of life?o Can form covalent bonds by e- pair sharings- Under more biological conditions, carboxylic acids exist as carboxylate anions - Under most biological conditions, amines exist as ammonium ionsMajor theme of Biological Macromolecules:- Nucleic acids (DNA, RNA) – polymers of nucleotides- Proteins (polypeptides) – a polymer of amino acidsProperties of Biomolecules:- Macromolecules and their building block have a “sense” or directionalityo Are informationalo Have 3D architecture- Most important building block used to make proteinso Dipeptide: 2 amino acids in a peptide bond- Representations of the structure of ribose, a sugar, is also an important biological building blocko Glucose and cellulose Lecture 3 (January 21)The Solvent Properties of Water Derive for its polar nature- The ratio of polar to nonpolar groups in a molecule affects its solubility in water- Nonpolar molecules are not soluble in water and are hydrophobicSodium Diodecyl Sulfate (SDS) – synthetic detergent- Molecules like SDS, which are polar on one end, and nonpolar at the other, are known asamphiphilic or amphipathic molecules - They can self associate to form detergent monlayers or micellesAmphipathic Molecules in Water- Monolayer and MicelleVander Waals Interactions- The electron clouds surrounding neighboring atoms can become synchronized with interacting oscillating dipoles- This attractive force is known as the Vander Waals Interactiono Relatively weak and falls quickly with distance Hydrophobic EffectNonpolar Solutes Order Water- Formation of a clathrate structure by water molecules surrounding a hydrophobic solute- The increased order in water structure is not energetically favorable (decreased entropy)Hydrophobic Interactions- Nonpolar solute “organizes” water- The H-bonds networkNoncovalent Interactions in Biomolecules- Charge-charge, H-bonds, and Van der Waals interactionsLecture 4 (January 22)Buffers- Solutions that can resist changes in pH- Most consist of a weak acid and its conjugate base - In graphs, flat points are where acid = conjugate baseChapter 3 – Amino AcidsAmino Acids- Has a carboxylate group, an amino acid group, a hydrogen atom, and a side chain- pH 7- There are 20 common, genetically encoded amino acids used by organisms- L-serine and D-serine. Common amino acids have the L (life) Configuration* Memorize the structures of 20 amino acidsLecture 5 (January 26)Oxidation of cystein:- When oxidation links the sulfhydryl groups of cystein molecules, the resulting compoundis a disulfide called cystine- Disulfide bonds generally found only in extracellular proteins- The cytosol and nucleus of the cell are reducing environments where disulfide bonds arenot formed* Make a connection between structure and the hydrophobic or hydrohpillic components- The peak of absorbance for most proteins peak at 280nm- most absorbance is present because presence of typtophan and tyrosine residues in the proteinLecture 6 (January 28)Ionization of amino acids- At basic pH, it is present as the anion, completely deprotonated- As protons are added, the pH is decreased by the addition of an acid, the amino group will become protonated forming a zwitterion (have both – and + charge)Henderson-HasselbackpH =pKa + log[PA]/[PD]Ionization of amino side chains- Negative charge is delocalizedPeptide bond between amino acids- The structure of the peptide linkage can be viewed as the product of a condensation reaction- The result is a dipeptide, in which amino acids are linked by peptide bonds Proteins separated in an SDS-phyacrylamide gel- Top stained proteins after separationo The high molecular weight proteins are at the top of the gelo Relationship between molecular weight and how far it travels in the gelLecture 7 (January 30)Can we take polypeptides apart into their individual amino acids? – Yes* Know that when a PTA derivative is and that proteins can be chemically sequenced from N-terminus one residue at a time- The N-terminal residue of a polypeptide chain reacts with phenylisothiosyanate to give a phenylthiocarbomoyl-peptide- Treating this derivative with trifluoroacetic acid releases an anilinothiazolinone derivative of theN-terminal amino acid residue- The limit on Edman sequencing a large protein, you need cleavage if you have pure protein in significant amountso Thus, before sequencing a large protein, you need to cleave it into smaller peptideso Also need to reduce all of the disulfide bondsSequences of DNA & Proteins- The amino acid sequence of a protein can also be deduced from the sequence of nucleotides in the sequence of nucleotides in the corresponding gene- Hydrophobic residue = blue- Polar residues = redLevels of Protein Structure:- Primary- Secondary- Tertiary- Quaternary Lecture 8 (February 2)Structures of proteins: - Primary- Secondary- Tertiary- QuaternaryHow are the 3D structures of proteins determined?- X-ray crystallography  protein concentrated in a crystal- Multidimensional NMR  protein concentrated in a solutionBovine Ribonuclease- Ribonuclease A is a secreted enzyme that hydrolyzes RNA during digestion- Bovine ribonuclease A NMR structure- Figure combines a set of very similar structures that satisfy the data on atomic interactions- Only the backbone of the polypeptide chain is shownResonance Structure of peptide bond- In this resonance form, the peptide bond is shown as a single C-N bond- In this resonance form, there is a double bond- The actual structure is best represented as a hybrid of the 2 resonance forms in which electrons are delocalized over the carbonyl oxygen, the carbonyl carbon, and the amide nitrogen- A peptide group consists of the N-H and the C=O groups involve in formation of the peptide bond, as well as the alpha carbon on each side of the peptide bond- Rotation around the N-C alpha and C alpha-C bonds that link peptide groups in a polypeptide chain can lead to crash b/t atomsRamachandran Plot- Plotting the rotations and when crashes b/t atoms occur- Observed phi and psi values in known structures are plottedThe Apha Helix - In the right handed helix, the backbone turns in a clockwise direction when viewed along the axis from either