Chapter 3AMINO ACIDS, PEPTIDES, AND PROTEINSLehninger Principles of Biochemistry, Fourth Edition
Mar. 06, 2007
2.1 Weak Interactions in Aqueous Systems
Hydrogen Bonding Gives Water Its Unusual Properties
Water Forms Hydrogen Bonds with Polar Solutes
Water Interacts Electrostatically with Charged Solutes
Entropy Increases as Crystalline Substances Dissolve
Nonpolar Gases Are Poorly Soluble in Water
Nonpolar Compounds Force Energetically Unfavorable Changes in the Structure of Water
van der Waals Interactions Are Weak Interatomic Attractions
Weak Interactions Are Crucial to Macromolecular Structure and Function
Solutes Affect the Colligative Properties of Aqueous Solutions
Amino Acids share common structural Features
Proteins are polymers of amino acids, with each amino acid residue joined to its neighbor by a specific type of covalent bond.
The a-carbon of AA is a chiral center. Molecules with a chiral center are optically active, they rotate plane-polarized light.
The additional carbons in an R group are designated b, g, d, e etc.
Carbon atoms are numbered from one end, giving priority to carbons with substitutions. containing atoms with the highest atomic numbers.
Absolute Configuration: D, L System
Enantiomers -nonsuperimposable mirror images of each other the two forms represent a class of stereoisomers.
The absolute configurations of simple sugars and amino acids are specified by the D, L system.
RS system is used in the systematic nomenclature of organic chemistry and describes more precisely the configuration of molecules with more than one chiral center.
Nearly all biological compounds with a chiral center occur naturally in only one stereoisomeric form, either D or L. The amino acid residues in protein molecules are exclusively L-stereoisomers. D-Amino acid residues have been found only in a few, generally small peptides, including some peptides of bacterial cell walls and certain peptide antibiotics.
Amino Acids Can Be Classified by R Group
Nonpolar, Alipatic R Groups
Glycine has the simplest structure, its very small side chain makes no real contribution to hydrophobic interactions
Methionine, one of two sulfur containing amino acids. has a nonpolar thioether group. First AA residue in translation of proteins
Alanine, Valine, Leucine, and Isoleucine could contribute to hydrophobic interaction.
The secondary amino (imino) group of Pro is held in a rigid conformation that reduces the structural flexibility of polypeptide regions containing proline.
Aromatic R Groups
Absorbance of UV by Aromatic Amino acids
All are relatively nonpolar (hydrophobic).
-OH group of throsine can form hydrogen bonds and are important functional group. Can be phosphorylated as well.
All can absorb UV light (280 nm), Tyrosine and Tryptophan are stronger than phenylalanine. Use for protein quantification.
Polar, Uncharged R Groups
Polar, Uncharged R Groups
The R groups of these amino acids are more soluble in water, or more hydrophilic, than those of the nonpolar amino acids, because they contain functional groups that form hydrogen bonds with water.
Serine and Threonine has –OH, which contribute to polarity, and could be phosophorelated.
Asparagine and Glutamine are the amides of Aspartate, and Glutamate, and are easily hydrolyzed by acid or base.
Cysteine is readily oxidized to form a covalently linked dimeric AA called cystine (disulfide bond).
The disulfide-linked residues are strongly hydrophobic (nonpolar). Disulfide bonds play a special role in the structures of many proteins by forming covalent links between parts of a protein molecule or between two different polypeptide chains.
Positively Charged (Basic) R Groups
Lysine has a second primary amino group at e position. Its R group has significant positive at pH=7.
Arginine has a positively charged guanidino group
Histidine a imidazole group, and is the only standard amino acid having an ionizable side chain with a pKa near neutrality. It serves as a proton donor/ acceptor in a enzyme-catalyzed reaction
Negatively Charged (Acidic) R Groups
Two amino acids having R groups with a net negative charge at pH=7 are asparate and glutamate, each of which has a second carboxyl group
Nonstandard Amino Acids - I
Nonstandard Amino Acids
Some 300 additional amino acids have been found in cells.
Are created by modification of standard residues already incorporated into a peptide.
4-hydroxyproline, a derivative of proline, isfound in plant cell wall protein, 5-hydroxylysine, derived from lysine, both are found in collagen.
6-N Methyllysine is a constituent of myosin.
G-carboxyglutamate, found in the blood-clotting protein prothrombin and Ca2+ binding protein.
Desmosine, derivative of four Lys residues, which is found in the elastin.
Selenocysteine is introduced during protein synthesis, and contains Selenium rather than sulfur of cysteine, derived from serine.
Nonstandard Amino Acids - II
Ornithine and citrulline are not constituents of proteins.
They are key intermediates (metabolites) in the biosynthesis of arginine and in the urea cycle.
Amino acids Can Act as Acids and Bases
Zwitterion (hybrid ion): dipolar ion, can act as either an acid (proton donor or a base (proton acceptor) - Amphoteric mater: ampholyte (amphoteric electrolytes)
Amino Acids Have Characteristic Titration Curves
The pKa is a measure of the tendency of a group to give up a proton, with the tendency decreasing tenfold as the pKa increases by on unit.
Titration Curves Predict the Electric Charge of Amino Acids
Isoelectric point (isoelectric pH): pI, The characteristic pH at which the net electric charge is zero.
Titration Curves of Glutamate
Titration Curves of Histidine
Effect of the Chemical Environment on pKa
Effect of the chemical environment on pKa
The perturbed pKa of glycine is caused by repulsion between the departing proton and the nearby positively charged amino group. The opposite charges on the resulting zwitterion are stabilizing, nudging the equilibrium farther to the right.
The electronegative oxygen atoms in the carboxyl groups, which tend to pull electrons toward them, increasing the amino group to give up a proton.
Formation of a Peptide Bond by Condensation
A few amino acids are joined - an oligopeptide.
Many amino acids are joined, - a polypeptide.
“Protein” and “polypeptide” are sometimes used interchangeably, molecules referred to as polypeptides generally have molecular weights below 10,000 (D), and those called proteins have higher molecular weights.
Peptides Can Be Distinguished by Their Ionization Behavior
The acid-base behavior of a peptide can be predicted from its free -amino and -carboxyl groups as well as the nature and number of its ionizable R groups.
Peptides have characteristic titration curves and a characteristic isoelectric pH (pI) at which they do not move in an electric field.
Biologically Active Peptides and Polypeptides Occur in a Vast Range of Sizes
Titin, a constituent of vertebrate muscle, which has 27,000 AAs, and M.W.=3,000,000.
Single peptide chain Vs. multisubunit protein: two or more polypeptide associated noncovalently.
The individual polypeptide chains in a multisubunit
protein may be identical or different. If at least two
are identical the protein is said to be oligomeric, and the identical units (consisting of one or more polypeptide chains) are referred to as protomers.
Ex. Hemoglobin- has four polypeptide subunits: two identical a chains and two identical b chains, all four held together by noncovalent interactions. Each subunit is paired in an identical way with a subunit within the structure of this multisubunit protein, so that hemoglobin can be considered either a tetramer of four polypeptide subunits or a dimer of ab protomers.
The average M.W. of AA= 110 (128-18)
Conjugated protein: Protein contains permanently associated chemical components: non AA part: Prosthetic group. Classified on the basis of the chemical nature of the prosthetic groups. i.e. lipoproteins, glycoproteins and metalloproteins
Levels of Structure in Protein
Primary: A description of all covalent bonds. The sequence of AA residues
Secondary: particularly stabl
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