Biochemistry Chapter 4 Notes
Biochemistry Chapter 4 Notes Chem 3375
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This 4 page Class Notes was uploaded by Nancy Ly on Tuesday September 22, 2015. The Class Notes belongs to Chem 3375 at Texas State University taught by Dr. Kerwin in Fall 2015. Since its upload, it has received 42 views. For similar materials see Principles of Biochemistry in Chemistry at Texas State University.
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Date Created: 09/22/15
CHEM 3375 Principles of Biochemistry CHAPTER 4 READING LOG Amino Acids Before you read What is the purpose of reading this material The purpose of reading this material is to understand the general properties of amino acids and to identify all 20 amino acids by structure What do I already know about this topic 0 There are 20 amino acids 0 Names of the amino acids While you read Amino acids monomeric units of proteins at amino a primary amino group and a carboxylic acid group substituent on the same carbon atom Amphoteric substances that can act as either an acid or base can also be referred to as ampholytes Zwitterions dipolar ions molecules that bear charged groups of opposite polarity Peptide bond CO NH linkage Dipeptides tripeptides oligopeptides and polypeptides polymers composed of two three a few 3 10 and many amino acid residues also called peptide units Linear polymer each amino acid residue is linked to its neighbors in a head to tail fashion rather than forming branched chains R groups side chains of amino acids lsoelectric point pl the pH at which a molecule carries no net electric charge Nterminus amino terminus Cterminus carboxyl terminus Optically active rotate the plane of planepolarized light Asymmetric centers or chiral centers the central atoms Enantiomers molecules that are nonsuperimposable mirror images Dextrorotatory right rotation on the plane of planepolarized light clockwise Levorotatory left rotation on the plane of planepolarized light counterclockwise Polarimeter an instrument that can detect the rotation on the plane of plane polarized light Speci c rotation a quantitative measure of optical activity of the molecule Absolute con guration spatial arrangement Glyceraldehyde a molecule with one asymmetric center Stereoisomers optical isomers molecules with different con gurations about at least one of their chiral centers but are otherwise identical Diastereomers two optical isomers also called allo forms Meso form internally compensated two asymmetric centers in a molecule are mirror images of each other such molecules are superimposable on its mirror image and is therefore optically inactive CahnlngoldPrelog RS system the chiralities of compounds with multiple asymmetric centers can be unambiguously described R right L left Prochiral molecules that can be converted from achiral to chiral in a single step Racemic equal amounts of each member of an enantiomeric pair After you read The key points of this reading are A All proteins are composed of the standard 20 amino acids In a physiological pH range both the carboxylic acid and amino groups of at amino acids are completely ionized In solid state the a amino acids are zwitterionic because the basic amine group abstracts a proton from the nearby acidic carboxylic acid group Amino acids physical properties are characterized by ionic compounds Amino acids are more soluble in polar solvents than nonpolar solvents 01 amino acids polymerize through the elimination of a water molecule Proteins are molecules that consist of one or more polypeptide chains Polypeptides range in length from 40 to 34000 amino acid residues Polypeptides are linear polymers The various organisms on Earth collectively synthesize an enormous number of different protein molecules whose great range of physicochemical characteristics stem largely from the varied properties of the 20 39standard amino acids There are tree major types of amino acids 0 Those with nonpolar R groups 0 Those with uncharged polar R groups 0 Those with charged polar R groups Nine amino acids are classi ed as having nonpolar side chains 0 Glycine has the smallest possible side chain an H atom o Alanine valine leucine and isoleucine have aliphatic hydrocarbon side chains ranging in size from a methyl group for alanine to isomeric butyl groups for leucine and isoleucine o Methionine has a thiol ether side chain that resembles an nbutyl group in many of its physical properties 0 Proline a cyclic secondary amino acid has conformational constraints imposed by the cyclic nature of its pyrrolidine side chain 0 Phenylalnine has a phenyl moiety contains aromatic side chains 0 Tryptophan has in indole group contains aromatic side chains Six amino acids are classi ed as having uncharged polar side chains 0 Serine and threonine bear hydroxylic R groups of different sizes 0 Asparagine and glutamine have amidebearing side chains of different sizes both are respectively amides of aspartic acid and glutamic acid 0 Tyrosine has a phenolic group which together with the aromatic groups of phenylalanine and tryptophan accounts for most of the UV absorbance and uorescence exhibited by proteins 0 Cysteine has thiol group which forms a disul de bond to another cysteine residue through the oxidation of their thiol groups The disul de bond has a great importance in protein structure it can join separate polypeptide chains or crosslink two cysteines in the same chain Two disul delinked cysteines are referred to as the amino acid cystine Five amino acids have charged side chains 0 Lysine has a butylammonium side chain 0 Arginine has a guanidine group o Histidine carries an imidazolium moiety out of all the 20 q amino acids histidine with pKR 60 ionizes within the physiological pH range 0 Aspartic acid and glutamic acid negatively charged above pH 3 in their ionized state they are often referred to as aspartate and glutamate The 20 amino acids vary considerably in their physicochemical properties such as polarity acidity basicity aromaticity bulk conformational exibility ability to crosslink ability to hydrogen bond and chemical reactivity These several characteristics many of which are interrelated are largely responsible for proteins great range of properties HendersonHasselbalch equation A Z 6 0 4 4 pHpK10g 2 Amino acids never assume the neutral form in aqueous solution For a amino acids the application of the HendersonHasselbalch equation indicates that to a high degree of precision 1 pI pKipK 0 K and K are the dissociation constants of the two ionizations involving the neutral species 0 For monoamino monocarboxylic acids such as glycine K and K represent K1 and K2 0 For aspartic and glutamic acids K and K are K1 and KR o For arginine histidine and lysine the quantities are KR and K2 Optically active molecules have an asymmetry such that they are not superimposable on their mirror image in the same way that a left hand is not superimposable on its mirror image a right hand The COI atoms of all the amino acids with the exception of glycine are asymmetric centers Glycine which has two H atoms substituent to its Ccx atom it superimposable on its mirror image and is therefore not optically active Enantiomeric molecules are physically and chemically indistinguishable by most techniques 0 Only when probed asymmetrically for example by planepolarized light or by reactants that also contain chiral centers can they be distinguished andor differentially manipulated Speci c rotation 25 observed rotation degrees on D O 0 optical path length dm x concentration g c m3 b o 25 refers to the temperature at which polarimeter measurements are customarily made 0 D refers to the monochromatic light that is traditionally employed in polarimetry the Dline in the spectrum of sodium ln Fischer projections horizontal bonds extend above the plane of the paper and vertical bonds extend below the plane of the paper All a amino acids derived from proteins have the L stereochemical configuration Points of diastereomers o The Dallo and Lallo are mirror images of each other as are the D and L forms Neither allo form is symmetrically related to either of the D or L forms 0 Diastereomers are physically and chemically distinguishable from one another by ordinary means such as melting points spectra and chemical reactivity that is they are really different compounds in the usual sense The four groups surrounding a chiral center are ranked according to a speci c priority scheme atoms of higher atomic number bonded to a chiral center are ranked above those of lower atomic number Two chemically identical substituents to an otherwise chiral tetrahedral center are geometrically distinct that is the center has no rotational symmetry so that it can be unambiguously assigned left and right sides Planar objects with no rotational symmetry also have the property of prochirality If a trigonal carbon is facing the viewer such that the order of priority of its substituents decreases in a clockwise manner that face is designated as the re face The opposite face is designated as the siface The biosynthesis of a substance possessing asymmetric centers also invariably produces a pure stereoisomer Many drugs are chemically synthesized as racemic mixtures although only one enantiomer has biological activity B One topic I understood well is And classi cation and characteristics of the 20 amino acids C One topic I struggled with is The chirality Fischer projection and CahnlngoldPrelog system D These are the questions about C or another topic that I still have after reading the material How would you label a molecule in the RS system and the L and D system What is a method in order to identify the molecules as an RS system or L and D system I think that consulting these resources can help me answer these questions or get additional information on this topic The biochemistry textbook Online resources
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