BIOL 213 1st Edition Lecture 5Outline of Last Lecture II. MolarityA. DefinitionB. Tips on how to do the molarity problems III. Acids, Bases and pHa.Definitions of acid and baseb.Ionization of water; Kw c.Tips on how to do problems involving pHd.BuffersIV. Review of the most common chemical groups in biological moleculesa. A list, their formulas, a unique characteristic, and where they’re commonly foundV. Macromoleculesa. “Monomers” of allb. Condensation reactionVI. Polysaccharidesa. Descriptioni. Major functionsb. Structurei. How the flipping of an –O and –OH can change the sugarc. Glucose i. Alpha and betaVII. Lipidsa. Descriptioni. Ester linkageb. Basic structurei. Hydrophobic and hydrophilic partsii. Saturated vs Unsaturatedc. Propertiesd. Two main different kinds covered in lecturei. Triacylglycerolii. Phospholipid1. PhosphatidylserineVIII. Cholesterola. Basic structureb. Main functionsThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.i. Hormones IX. Proteinsa. Descriptioni. Major functionsb. Amino Acidsi. Structureii. Classification (nonpolar, charged, or uncharged polar)iii. We need to be able toOutline of Current Lecture I. A protein’s function is linked to its structureII. Overview of the levels of protein structureIII. Primary structurea. Amino acid sequenceIV. Secondary structurea. α helices b. β sheets i. antiparallelii. parallelV. Tertiary structurea. Interaction of α helices and β sheetsVI. Quaternary structurea. Multiple polypeptide subunitsi. Identicalii. DifferentVII. Protein foldinga. Defects lead to diseasesVIII. Enzymesa. Lower activation energyCurrent LectureI. A proteins function is linked to its structurea. Why we need to know this:i. So that we can understand how enzymes work1. Enzymes are very structure specific because they have to bind to the right substrate in order to catalyze the right reactionii. To understand how drugs affect proteins1. How they can bind to the proteins to create different results/functions of the proteiniii. To understand diseases like Alzheimer’s1. Which are caused by misfolded proteinsiv. To understand the molecular basis of many areas of biology1. To understand molecular biology is to understand proteinsb. Proteins can bind to other molecules (ligands)i. The proteins structure determines the1. Affinity (tightness) of the bond2. Specificity of the bonda. One protein won’t bond to just any ligand, the structures have to be compatible3. Binding sitea. Where the two bind togetherII. Overview of the levels of protein structurea. Primaryi. Determined by the sequence of amino acidsb. Secondaryi. These are the little folds within a polypeptideii. Main shapes: α helices and β sheetsc. Tertiaryi. This is the entire chain folding up on itself, becoming globular d. Quaternaryi. Multiple polypeptide chains bind together to create a functional protein III. Primary structurea. Determined by the sequence of amino acidsb. Amino acids are held together by covalent bonds (peptide bonds) between the amine and carboxyl groupi. Via condensation reactionc. This sequence ultimately determines the final structure of the proteind. Sickle cell anemia is an example of how an incorrect primary structure can lead to a diseasei. Only one amino acid is different between normal and sickle red blood cellse. This is the reason why proteins have structural polarity – because structure is super importantIV. Secondary Structurea. These make the protein more stableb. Each is composed of hydrogen bonding between the –H of the amino group and the =O of the carbonyl group (formerly the carboxyl group) on two amino acidsi. The carboxyl group is now carbonyl because the –OH was removed in the condensation reaction, all that’s left is C=O, which is indeed carbonylii. Side chains are not involved in the bonding of secondary structurec. α helicesi. When the =O is bonded to an –H four amino acids awayii. This results in a helical shape which makes a complete turn every 3.6 amino acidsiii. Side chains can influence the position of the protein in the cell1. Hydrophobic α helix can be in the cell membranea. The side chains point outward in an α helixb. If each side chain of a group of amino acids is hydrophobic,this α helix will move to a nonpolar place, like the lipid bilayer!i. The helix fits nicely between the phospholipidsc. This is the basis for many proteins embedded in the bilayer2. Amphipathic coiled-coila. If a strip of side chains down two α helices is hydrophobic,the two will coil together so that the hydrophobic region ofeach is on the inside of the coilb. This can also be reversed so that if a hydrophilic strip is on each and the helix is in a hydrophobic region, the two helices will coil so that the hydrophilic region is inside the coili. This is generally less common because most of a cell is aqueousd. β sheetsi. This is the hydrogen bonding of the –H and =O of amino acids so that the polypeptides are stretched out, resulting in a pleated shapeii. At each of the bends, the side chains of the amino acids point outiii. Antiparallel β sheet1. This is when the polypeptide is in a winding-like shape2. It curves around so that each section of the polypeptide is runningin the opposite direction of at least one of the sections to the side of itiv. Parallel β sheets1. This is when the polypeptide is in a loop-like shape, but not an α helix!2. It loops around so that each section of the polypeptide is running in the same direction as at least of the sections to the side of itv. The strands of polypeptide in a β sheet do not have to be consecutive1. A part of the polypeptide chain can start a β sheet, then go loop around for a while, maybe make some α helices or do something else random, then come line back up with the piece of the β sheetpiece, bonding to it through hydrogen bonds, making it larger2. Then it could go wander around a little more, then line back up the β sheet, bonding to it through hydrogen bonds, making it larger3. Then it might wind back and forth for a while, adding several antiparallel sections to the β sheetvi. As opposed to an α helix, in which a decent amount of consecutive polypeptide has to be involved in the same helixV. Tertiary Structurea. This is the interaction of the α helices and β sheets to form a larger polypeptide domainb. The helices and sheets bond together via noncovalent