Amino Acid Polarity

8 Key excerpts on "Amino Acid Polarity"

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  eBook - ePub

  Biochemistry

  • Donald Voet, Judith G. Voet(Authors)
  • 2021(Publication Date)
  • Wiley

    (Publisher)

  dipolar ions. The zwitterionic character of the α-amino acids has been established by several methods including spectroscopic measurements and X-ray crystal structure determinations (in the solid state the α-amino acids are zwitterionic because the basic amine group abstracts a proton from the nearby acidic carboxylic acid group). Because amino acids are zwitterions, their physical properties are characteristic of ionic compounds. For instance, most α-amino acids have melting points near 300°C, whereas their nonionic derivatives usually melt around 100°C. Furthermore, amino acids, like other ionic compounds, are more soluble in polar solvents than in nonpolar solvents. Indeed, most α-amino acids are very soluble in water but are largely insoluble in most organic solvents.

  B. Peptide Bonds

  The α-amino acids polymerize, at least conceptually, through the elimination of a water molecule as is indicated in Fig. 3-3 . The resulting CO—NH linkage, which was independently characterized in 1902 by Emil Fischer and Franz Hofmeister, is known as a peptide bond. Polymers composed of two, three, a few (3–10), and many amino acid residues (alternatively called peptide units) are known, respectively, as dipeptides, tripeptides, oligopeptides, and polypeptides. These substances, however, are often referred to simply as “peptides.” Proteins are molecules that consist of one or more polypeptide chains. These polypeptides range in length from ∼40 to ∼34,000 amino acid residues (although few have more than 1500 residues) and, since the average mass of an amino acid residue is ∼110 D, have molecular masses that range from ∼40 to over ∼3700 kD.

  Figure 3-3

  Condensation of two α-amino acids to form a dipeptide. The peptide bond is shown in red.

  Polypeptides are linear polymers

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  Voet's Principles of Biochemistry

  • Donald Voet, Judith G. Voet, Charlotte W. Pratt(Authors)
  • 2018(Publication Date)
  • Wiley

    (Publisher)

  • The pK values of the ionizable groups of amino acids may be altered when the amino acid is part of a polypeptide. 2 Stereochemistry • Amino acids are chiral molecules. Only L-amino acids occur in pro- teins (some bacterial peptides contain D-amino acids). 3 Amino Acid Derivatives • Amino acids may be covalently modified after they have been incor- porated into a polypeptide. • Individual amino acids and their derivatives have diverse physiologi- cal functions. NH CH SH CH O C CH 2 CH 2 CH 2 CH 2 NH O C 2 H 3 N + COO – COO – NH CH S CH O C CH 2 CH 2 CH 2 S CH 2 CH 2 NH O C H 3 N + COO – COO – NH CH CH O C CH 2 CH 2 CH 2 NH O C H 3 N + COO – COO – Glutathione (GSH) (-Glutamylcysteinylglycine) 2 1 O 2 H 2 O Glutathione disulfide (GSSG) REVIEW QUESTIONS 1 List some covalent modifications of amino acids in proteins. 2 Cover the labels in Figs. 4-14 and 4-15 and identify each parent amino acid and the type of chemical modification that has occurred. 3 Discuss important functions of amino acid derivatives. 95 KEY TERMS protein 80 α-amino acid 81 α carbon 81 R group 81 zwitterion 84 condensation reaction 84 peptide bond 84 dipeptide 84 tripeptide 84 oligopeptide 84 polypeptide 84 residue 84 N-terminus 84 C-terminus 84 pI 86 optical activity 88 polarimeter 88 chiral center 89 chirality 89 enantiomers 89 absolute configuration 89 Fischer convention 89 stereoisomers 89 levorotatory 89 dextrorotatory 89 Fischer projection 89 Cahn–Ingold–Prelog (RS) system 90 racemic mixture 90 peptidase 90 neurotransmitter 93 isopeptide bond 94 PROBLEMS EXERCISES 1. Identify the amino acids that differ from each other by a single methyl or methylene group. 2. The 20 standard amino acids are called α-amino acids. Certain β and γ amino acids are found in nature. Draw the structure of β-alanine (3-amino-n-propionate) and γ-aminobutyric acid. 3. Glutamate, a 5-carbon amino acid, is the precursor of three other amino acids that contain a 5-carbon chain.

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  Textbook of Biochemistry with Clinical Correlations

  • Thomas M. Devlin(Author)
  • 2015(Publication Date)
  • Wiley-Liss

    (Publisher)

  J. Biochem. 97:175, 1979; and from Nozaki, Y., and Tanford, C., J. Biol. Chem. 246:2211, 1971. CHAPTER 3 PROTEINS I: COMPOSITION AND STRUCTURE • 89 charge within the nonpolar interior in stabilizing protein conformation or participation in catalysis. Transmembrane proteins reverse the positioning of their side-chain polarity from that of water-soluble globular proteins. Within the membrane, these proteins often position hydrophobic side chains on the outside and ionic groups on the inside to provide binding interactions and to form ion channels (p. 477). Amino Acids Undergo a Variety of Chemical Reactions Amino acids in proteins react with a variety of reagents that may be used to investigate the function of specific side chains. Some common chemical reactions are presented in Table 3.7. Reagents that modify acid side chains have been synthesized to bind to specific sites in a protein’s structure, such as the substrate-binding site. The strategy is to model the structural features of the enzyme’s natural substrate into the modifying reagent. The reagent binds to the active site like the natural substrate and reacts with a specific side chain. This identifies the modified amino acid as being located in the substrate-binding site and helps identify its role in catalysis.

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  Chemical and Functional Properties of Food Proteins

  • Zdzislaw E. Sikorski(Author)
  • 2001(Publication Date)
  • CRC Press

    (Publisher)

  The presence of a majority of hydrophobic amino acids in the interior and exposition of hydrophilic ones at the surface of the molecule is a common feature of all known three-dimensional structures of globular proteins. How-ever, the ion pairs between basic and acidic amino acid residues can be found inside, and clusters of hydrophobic residues can be found at the surface of protein molecules. The latter are often involved in interactions stabilizing the quaternary structure of oligomeric proteins. Proteins embedded in biological membranes are especially rich in hydrophobic amino acids, especially in their fragments traversing the membrane. 3.6. PROTEINS IN SOLUTION Due to the large size of protein molecules, at least some of them do not form true solutions but rather form aqueous colloidal systems, especially at high solute concentration. Solubility of a given protein is strongly dependent on its molecular structure, especially on the relative content of hydrophobic and hydrophilic amino acids. It also depends on the properties of the solvent, temperature, pH, and ionic strength. Solubility of globular proteins generally increases with temperature up to around 40°C and then rapidly decreases, lead-ing to protein denaturation and eventual formation of a precipitate. However, solubility of some fibrous proteins, which are practically insoluble at ambient temperature, also increases on heating above 40°C. Conversion of collagen suspension into gelatin may serve as a good example of such phenomenon. The pH-dependence of protein solubility is the consequence of its polyionic character. Each protein molecule contains (besides the N-terminal a-amino- and the C-terminal a-carboxyl-) a number of ionizable functional groups in side chains of their constitutive amino acids, including -COOH of Asp and Glu, protonated e-amino of Lys and guanidyl of Arg, -OH of Tyr, -SH of Cys, imidazole of His, and phosphate in phosphoproteins.

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  Biochemistry

  An Integrative Approach

  • John T. Tansey(Author)
  • 2019(Publication Date)
  • Wiley

    (Publisher)

  tyrosine at pH 8.0 9. Tyrosine is generally listed as a polar amino acid. How else could this amino acid be categorized? 10. Which amino acids have aromatic side chains? Recall from or- ganic chemistry that organic molecules follow Huckle’s rule (the 4n + 2 rule). Show that each of the proposed aromatic amino acids follows this rule. 11. Which amino acids absorb in the UV? Why do other amino acids not absorb in the UV? 12. Based on the properties of the side chain, which amino acid would you predict to be most soluble in water? Least soluble in water? 13. Selenocysteine and selenomethionine are alternative amino acids found in some organisms. Examine the periodic table. How would the chemistry of these seleno amino acids compare to sulfur- or oxygen- containing amino acids? 3.2 Proteins Are Polymers of Amino Acids 14. With few exceptions, such as proline, how is it that most amino acids can form either an α helix structure or a β sheet structure? 15. How many different ways can the 20 common amino acids com- bine to form a protein 450 amino acids long? 16. The average mass of an amino acid in a protein is 110 g/mol. Dividing the mass of titin (3,816 kDa) by the number of amino acids (34,350) does not give the exact figure of 110. Why? 17. How could the alteration of a protein sequence lead to a change in the location of a protein in the cell? 18. Recently, there have been reports of college students being di- agnosed with scurvy. What is scurvy, and how is it treated? Why do most Americans not get scurvy, and why might these college students have developed it? 19. ATP is usually the source of the phosphate in biochemical re- actions, such as phosphorylation of proteins. Why is this the case? Could other molecules serve as the source? Which of the phosphates on ATP is the source of the phosphate? Why, in terms of energy and of equilibrium, does ATP have this role? 20. Cation-π interactions are predicted from electrostatics.

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  Principles of Biochemistry

  • Donald Voet, Charlotte W. Pratt, Judith G. Voet(Authors)
  • 2014(Publication Date)
  • Wiley

    (Publisher)

  2 Stereochemistry K E Y C O N C E P T S • Amino acids and many other biological compounds are chiral molecules whose configurations can be depicted by Fischer projections. • The amino acids in proteins all have the L stereochemical configuration. With the exception of glycine, all the amino acids recovered from polypep- tides are optically active; that is, they rotate the plane of polarized light. The direction and angle of rotation can be measured using an instrument known as a polarimeter (Fig. 4-9). Optically active molecules are asymmetric; that is, they are not superimpos- able on their mirror image in the same way that a left hand is not superim- posable on its mirror image, a right hand. This situation is characteristic of e 84 C H E C K P O I N T • Draw a generic amino acid and identify the  carbon and its substituents. • Draw the structures of the 20 standard amino acids and give their one- and three- letter abbreviations. • Draw a Cys–Gly–Asn tripeptide. Identify the peptide bond and the N- and C-termini, and determine the peptide’s net charge at neutral pH. • Classify the 20 standard amino acids by polarity, structure, type of functional group, and acid–base properties. • Why do the pK values of ionizable groups differ between free amino acids and amino acid residues in polypeptides? FIG. 4-8 Greek nomenclature for amino acids. The carbon atoms are assigned sequential letters in the Greek alphabet, beginning with the carbon next to the carbonyl group. FIG. 4-9 Diagram of a polarimeter. This device is used to measure optical rotation. H 2 C β H 2 C γ H 2 C δ H 2 C ε Glu Lys H NH NH + C α C O 3 H 2 C β H 2 C γ COO – H NH C α C O Analyzer (can be rotated) Degree scale (fixed) Polarimeter tube Fixed polarizer Light source Plane of polarization of the emerging light is not the same as that of the entering polarized light. Optically active substance in solution in the tube causes the plane of the polarized light to rotate. + +90° –90° 180° 0° –

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  Introduction to General, Organic, and Biochemistry

  • Morris Hein, Scott Pattison, Susan Arena, Leo R. Best(Authors)
  • 2014(Publication Date)
  • Wiley

    (Publisher)

  KEY TERMS simple protein conjugated protein KEY TERMS alpha (a) amino acid essential amino acids D-amino acids L-amino acids amphoteric or amphiprotic zwitterion isoelectric point electrophoresis More Practice? Try Paired Exercises 31–32. C H A P T E R 2 9 R E V I E W 790 CHAPTER 29 Amino Acids, Polypeptides, and Proteins • Ten of the common amino acids are essential amino acids because they are needed for good health and cannot be synthesized in the human body. • Dietary protein is classified as either complete or incomplete. • Complete dietary protein provides all the essential amino acids. • Incomplete dietary protein does not provide all the essential amino acids. • The a-carbon is chiral for all the common amino acids but one (glycine). • When shown in a Fischer projection formula the carboxyl group is at the top and the R group is at the bottom of the structure: • L-amino acids have the amine group on the left side of the a-carbon. • D-amino acids have the amine group on the right side of the a-carbon. • Only L-amino acids are found in proteins. • Amino acids are amphoteric (or amphiprotic) because they can react either as an acid or as a base. • In neutral solutions, amino acids form dipolar ions called zwitterions. • When amino acids have a net charge, they will migrate toward either the positive or negative electrode in an electrolytic cell. • An amino acid’s charge depends on pH. • The pH at which an amino acid has no overall charge (and will not migrate in an electrolytic cell) is called the isoelectric point. • Basic amino acids have isoelectric points from 7.8 to 10.8, neutral amino acids have isoelectric points from 4.8 to 6.3, and acidic amino acids have isoelectric points from 2.8 to 3.3. 29.3 FORMATION OF POLYPEPTIDES • An amide bond is formed when a carboxyl group on one amino acid reacts with the a-amine group of a second amino acid to eliminate water. • This amide bond links amino acids together and is termed a peptide linkage or peptide bond.

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  Chemistry, 5th Edition

  • Allan Blackman, Steven E. Bottle, Siegbert Schmid, Mauro Mocerino, Uta Wille(Authors)
  • 2022(Publication Date)
  • Wiley

    (Publisher)

  Negative ions pass through the column as they are not held strongly. purified negative ions aspartic acid (at pH 3.25) lysine (at pH 3.25) – + + H 3 N NH 3 OOC – – + COO O O NH 3 1264 Chemistry Sequence analysis Once the amino acid composition of a polypeptide has been determined, the next step is to determine the order in which the amino acids are joined in the polypeptide chain. The most common sequencing strategy is to cleave the polypeptide at specific peptide bonds, determine the sequence of each fragment, and then match overlapping fragments to arrive at the sequence of the polypeptide. 24.5 Three-dimensional shapes of polypeptides and proteins LEARNING OBJECTIVE 24.5 Explain the functional importance of the three-dimensional shape of proteins. Many of the properties of polypeptides and proteins are governed by the precise three-dimensional shape of these complex molecules. The complexity of the shape arises from the nature of the peptide bond. Geometry of a peptide bond FIGURE 24.14 Planarity of a peptide bond. All of the atoms shown (C, O, N and H) lie in the same plane. Bond angles around the carbonyl carbon atom and the amide nitrogen atom are approximately 120°. N C H O C α C α 118.5° 121.5° 120.0° In the late 1930s, Linus Pauling (1901– 1994; Nobel Prize in chemistry, 1954) began a series of studies aimed at deter- mining the geometry of a peptide bond. One of his first discoveries was that a peptide bond is planar. As shown in figure 24.14, the four atoms of a peptide bond and the two -carbon atoms joined to it all lie in the same plane. Had you been asked in the chap- ter on chemical bonding and molecular structure to describe the geometry of a peptide bond, you probably would have predicted bond angles of 120° around the carbonyl carbon atom and 109.5° around the amide nitrogen atom. This prediction agrees with the observed bond angles of approximately 120° around the carbonyl carbon atom.

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