Chemistry 153A8/07/06Handout #1Dr. Robert ClubbRm. 656 Boyer HallOffice Hours: M 2-3PMR [email protected] of Course•Introduction to biomolecular building blocks of cells.•Structure and function of proteins.•Proteins as enzymes.•Introduction to the basic metabolic reactionsused to extract energy from food.All cells (prokaryotic and eukaryotic) are constructed from the same basic components Plasma membraneAmino Acids (153A ~3 weeks) Sugars (153A ~1 week)Lipids (153A ~1 week)Nucleotides (153B, Transformation, synthesis, Expression Genetic material)Cells constructed from polymers of components**except lipids, which generally are monomeric153A (~4weeks)Core set of reactions utilized by organotrophs totransform free energy from complex molecules (food) intouseful chemical energy (ATP)153CPROTEINSHumans (~30,000 distinct proteins)Draft of Human Genome (2001)Functions:Catalyze reactions (enzymes)AntibodiesSignaling moleculesCell surface receptorsRegulate gene expressionStructural roleetc…….Proteins are formed by amino acidsAmino acids(20 different types)20 N= Number of possible distinct amino acidsequences if the chain is constructedfrom the 20 common amino acids andit has a length of N amino acids.For a sequence where N=8ProteinThe Basic Amino AcidCarboxyl GroupAmine groupVariable side chain that distinguishes the different amino acids from one anotherAlpha carbonExample of an amino acid (Alanine)R == Methyl groupThe Alpha Carbon is a Chiral CenterReview of stereoisomers (page 57-60)Chiral Center (tetrahedral carbon withfour different substituents attached to it) also called an assymmetric center Chiral molecules can not be superimposed about upon theirmirror image.Achiral Centers (tetrahedral carbon with three or lessdissimilar substituents). Also called a symmetric center.These centers can be superimposed onto their mirror imagemirrorThe stereoisomers of alpha carbon centersEnantiomers: pairs stereoisomers that are mirror images of each other. ( a special type of stereoisomer)Stereoisomers: the order of bonding is the same, but the spatial arrangementamong the atoms differs.Chiral centerAchiral centerEnantiomersDiastereomers: pair of stereoisomers that are not mirror images of each otherNumber of stereoisomers in a molecule depends on the number of chiral centers.# of stereoisomers = 2 N, where N is the number of chiral centers.# of enantiomers = 2 N-1, where N is the number of chiral centers.They have same physical properties (melting points, densities etc.). However, they rotate polarized light differentlyHave distinct physical properties.Nomenclature for Stereochemistry(a) Absolute Configuration(b) RS SystemTwo ways to describe the same thingFischer Projection DrawingIn nature the alpha carbons in amino acids are almost exclusively the L stereoisomer(A) Absolute Configuration(b) RS Nomenclature-SH > -OCH2 > -OH > -NH2 > -COOH > -CH2OH > -CH3 > -H( 1 ) ---------------------> ( 4 )11223344HCH3CO2-NH3+Amino Acids with more than one chiral centerIsoleucine ThreonineEnantiomersDiastereomersAcid-base review: page 60 - 69Amino Acids are zwitterionic at neutral pHZwitterions: contain charged groups of opposite polarityPopulations of the four ionization states of an α-amino acidTitration CurvesIonizable groups act to buffer the solution Titration experiment: add increments of NaOH to solution of anamino acid and then measure pHCH3COOH + -OH CH3OO- + H2OTitration curve for the amino acid glycineGlycinepK1= 2.34 pK2= 9.60pI (Isoelectric point): pH at which the compound has no net chargepI = 0.5 * (pK1+ pK2)Table 5-1The 20 Common Amino AcidsHydropathy index: Measure of the tendency of an amino acid to be in an aqueous environment.(-) tend to soluble in water; (+) tend to insoluble in waterAMINO ACIDS ARE BROADLY CLASSIFIED BASEDON THE IDENDITY OF THEIR SIDE CHAIN(1) NON-POLAR (aliphatic and aromatic)(2) POLAR CHARGED (positively and negatively)(3) POLAR UNCHARGEDPolymers of amino acids:Peptides, Polypeptides and ProteinsPeptide BondAmino Acid polymers have distinct ends(N-terminal) (C-terminal)Peptide bonds are planarResonance structureTrans peptide bondNomenclatureNCProtein: ~ > 40 amino acids are linked by peptide bonds. The amino acids typically form a defined and order three-dimensional structure.Peptide (oligopeptide): A few amino acids are linked bypeptide bondsPolypeptide: Many amino acids are linked by peptide bonds.Amino acid in a peptide linked chain is also called a “residue”DefinitionsNaming small peptidesAlanylglutamylglycyllysineThe tetrapetideGlycineLysineGlutamic acidAlanineThe Vast Majority of Interesting Amino AcidPolymers are Proteins (>~40 residues)Each protein has a distinct order and composition of amino acidsProteins with different biological functionsThe side chains of these amino acids tend to be insoluble in water.2ndchiral centerTypes of amino acids: Non-PolarImino acid(non-polar incontext of protein chain)Indole ringHydroxyl group favorable interacts with water.pKa ~ 10TYR –OH + -OH TYR—O - + H2ONon-polar cont…Aromatic…Amino Acids that are charged at neutral pHPositively charged (also called “Basic” amino acids)pKR~ 10.5 pKR~ 12.5Primary amineGuanidinogroupArginine amino acids have multiple resonance structuresTypes of amino acids: Polar ChargedPositively charged (continued)Imidazole ringpKR~ 6.0HistidineTypes of amino acids: Polar ChargedNegatively charged (also called “Acidic” amino acids)Example: (Glutamate)Aspartate (Aspartic Acid) Glutamate (Glutamic Acid)(hydrophilic)Types of amino acids: Polar ChargedSulfhydrylpKR~ 8Amide versions ofglutamate and aspartate(hydrophilic)Types of amino acids: Polar UnchargedCYSTEINE AMINO ACIDS CAN FORM DISULFIDE BONDSReduced form Oxidized form[O2]½O2+ 2H+ 2e- H2ODIFFERENT WAYS TO REPRESENTPROTEIN STRUCTUREAll atoms as spheresJust the backbone atoms as a tubeJust the backbone atoms, drawn to emphasize particular types of secondary structure No defined secondary structureα-helixβ-sheetMost proteins are water soluble and globularPrimarily non-polar side chains are located at the center of the protein.They are not in contact with the solvent.Amino acid side chains protrude from the surface and are primarily polar charged and polar uncharged amino acids. They interact with the water surrounding the protein. CORESURFACEHow are Three-Dimensional Structures of Proteins Determined?(1) X-ray
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