Stereochemistry of a-Amino Acids
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Questions and Answers

What is the preferred stereochemistry of amino acids in natural proteins?

  • R-configuration
  • L-configuration (correct)
  • S-configuration
  • D-configuration
  • What is a consequence of the asymmetry of the surface of proteins?

  • Protein synthesis
  • Protein denaturation
  • Formation of asymmetric protein structures
  • Highly specific molecular recognition of binding targets (correct)
  • What role does the stereochemistry of amino acids play in protein structure?

  • Protein synthesis
  • Denaturation of proteins
  • Protein degradation
  • Formation of secondary structure (correct)
  • How are the 20 common amino acids classified?

    <p>By their side chains</p> Signup and view all the answers

    Where are hydrophobic amino acids usually found in a protein molecule?

    <p>In the core of the protein</p> Signup and view all the answers

    Which amino acid has a side chain that forms a covalent bond with the α-amino group?

    <p>Proline</p> Signup and view all the answers

    What is the term used to describe the specific arrangement of amino acids in a protein?

    <p>Secondary structure</p> Signup and view all the answers

    Why is the preference for L-amino acids in proteins significant?

    <p>It allows for the formation of asymmetric protein structures</p> Signup and view all the answers

    What is the direction of the hydrogen bonds in the alpha-helix with respect to the helix axis?

    <p>Almost parallel to the helix axis</p> Signup and view all the answers

    Which of the following types of secondary structures has a macrodipole moment?

    <p>Alpha-helix</p> Signup and view all the answers

    What is the characteristic of the side chains in an alpha-helix?

    <p>Side chains of similar polarity every 3–4 residues</p> Signup and view all the answers

    In a beta-sheet, where are the hydrogen bonds located?

    <p>Between adjacent chains</p> Signup and view all the answers

    What is the characteristic of the side chains in a beta-sheet?

    <p>Alternating polar and nonpolar side chains</p> Signup and view all the answers

    What is the direction of the side chains in an alpha-helix?

    <p>Away from the center of the helix</p> Signup and view all the answers

    What is the characteristic of the side chains in a beta-sheet?

    <p>Located on opposite faces of the sheet</p> Signup and view all the answers

    What is the handedness of the n = -3 helix?

    <p>Left-handed</p> Signup and view all the answers

    What is the primary structure of a protein?

    <p>The sequence of amino acid residues</p> Signup and view all the answers

    What is the outcome of strong mineral acid, such as 6 M HCl, on peptide bonds?

    <p>Cleaves all peptide bonds, including Asn and Gln amide bonds</p> Signup and view all the answers

    What is the role of proteolytic enzymes in peptide bond hydrolysis?

    <p>They cleave peptide bonds at specific sites</p> Signup and view all the answers

    What is the relationship between DNA sequence and protein sequence?

    <p>DNA sequence corresponds to protein sequence</p> Signup and view all the answers

    What is the central dogma in the context of gene expression?

    <p>DNA is transcribed into RNA and RNA is translated into protein</p> Signup and view all the answers

    What is a characteristic of proteins, such as insulin, after translation?

    <p>They undergo post-translational modification</p> Signup and view all the answers

    What is the reason for the slow rate of peptide bond hydrolysis in aqueous solutions at physiological pH and temperature?

    <p>The reaction is kinetically slow</p> Signup and view all the answers

    What is the outcome of using chemicals that cleave at specific sites, such as CNBr, on peptide bonds?

    <p>Cleaves only specific peptide bonds</p> Signup and view all the answers

    What is the main function of collagen in the body?

    <p>To form the matrix material in bone</p> Signup and view all the answers

    What is the characteristic of every third residue in collagen?

    <p>It is always a glycine</p> Signup and view all the answers

    What is the result of a deficiency in Vitamin C?

    <p>Weakened collagen fibers</p> Signup and view all the answers

    What is the repetitive motif in the sequence of collagen?

    <p>Gly–X–Y, where X is often proline and Y is proline or hydroxyproline</p> Signup and view all the answers

    What is the effect of cross-linking on collagen?

    <p>It makes collagen less elastic and more brittle</p> Signup and view all the answers

    What is the role of hydroxyproline and hydroxylysine in collagen?

    <p>They are present in the sequence of collagen</p> Signup and view all the answers

    What is the structure of the tropocollagen molecule?

    <p>A triple helix of three polypeptide chains</p> Signup and view all the answers

    What is the result of the oxidation of lysine side chains?

    <p>The formation of a cross-link</p> Signup and view all the answers

    What is the necessary condition for protein folding to occur?

    <p>The overall free energy change for folding must be negative.</p> Signup and view all the answers

    Which of the following factors contributes to the stability of the folded structure of a globular protein?

    <p>The interplay of the unfavorable conformational entropy change, the favorable enthalpy contribution, and the favorable entropy change arising from the burying of hydrophobic groups.</p> Signup and view all the answers

    What is the primary role of disulfide bonds in protein structure?

    <p>To stabilize the folded structure of proteins, particularly in proteins exported from cells.</p> Signup and view all the answers

    What is the typical timescale for the folding of globular proteins from their denatured conformations?

    <p>Less than a second</p> Signup and view all the answers

    What is NOT a characteristic of protein folding?

    <p>A completely random search through a vast conformational space.</p> Signup and view all the answers

    What is the environment inside most cells with respect to sulfhydryl groups?

    <p>Reducing</p> Signup and view all the answers

    What is the role of internal disulfide bonds in protein structure?

    <p>To stabilize the folded structure of proteins, particularly in proteins exported from cells.</p> Signup and view all the answers

    What is the significance of the rapid kinetics of protein folding?

    <p>It implies that protein folding is a highly coordinated process.</p> Signup and view all the answers

    Study Notes

    Stereochemistry of the α-Amino Acids

    • α-Amino acids' stereochemistry is designated as D- or L-, which is best visualized from its Fischer projection.
    • There is a preference for L-amino acids in proteins.
    • The preference for L-amino acids in natural proteins has two important consequences:
      • The surface of any given protein is asymmetric, which is the basis for the highly specific molecular recognition of binding targets by proteins.
      • The stereochemistry of the amino acids plays an important role in the formation of so-called "secondary structure" and thereby the overall structure of proteins.

    Properties of the Amino Acid Side Chains

    • The 20 common amino acids are classified by their side chains:
      • Aliphatic
      • Hydroxyl or sulfur-containing
      • Aromatic
      • Basic
      • Acidic and their amides
    • The more hydrophobic amino acids, such as isoleucine, are usually found within the core of a protein molecule, where they are shielded from water.
    • Proline is the only amino acid in which the side chain forms a covalent bond with the α–amino group.

    Peptides and the Peptide Bond

    • While hydrolysis of peptide bonds is thermodynamically favored in aqueous solutions, the reaction is exceedingly slow at physiological pH and temperature.
    • Peptide bond hydrolysis can be achieved by:
      • Strong mineral acid (e.g., 6 M HCl) cleaves all peptide bonds (including the Asn and Gln amide bonds).
      • Chemicals that cleave at specific sites (e.g., CNBr cleaves at Met).
      • Proteolytic enzymes (proteases) that cleave at specific sites.

    Proteins: Polypeptides of Defined Sequence

    • Every protein has a defined number and order of amino acid residues, referred to as the primary structure of the protein.
    • The primary structure of a protein corresponds to the DNA (gene) sequence.
    • The genetic code is responsible for the translation of DNA into protein.

    Post-translational Modification

    • Many proteins, such as insulin, undergo post-translational modification.

    Secondary Structure: Regular Ways to Fold the Polypeptide Chain

    • There are two main types of secondary structures:
      • The α-helix, where the hydrogen bonds are within a single polypeptide chain and are almost parallel to the helix axis.
      • The β-sheet, where the hydrogen bonds are between adjacent chains and are nearly perpendicular to the chains.
    • The 3₁₀ helix is less common than the α-helix.
    • Secondary structures can be amphiphilic (or amphipathic), displaying a predominantly hydrophobic face opposite a predominantly hydrophilic face.
    • The α-helix has side chains of similar polarity every 3–4 residues.
    • The β-strand has alternating polar and nonpolar side chains.

    Fibrous Proteins: Structural Materials of Cells

    • Collagen is a fibrous protein that forms the matrix material in bone, constitutes the major portion of tendons, and is an important constituent of skin.
    • The basic unit of the collagen fiber is the tropocollagen molecule, a triple helix of three polypeptide chains.
    • The chains wrap around each other in a right-handed sense, with hydrogen bonds between the chains.
    • Every third residue can be only glycine.
    • Hydroxyproline and hydroxylysine are present in collagen.
    • A repetitive motif in the sequence is of the form Gly–X–Y, where X is often proline and Y is proline or hydroxyproline.

    Scurvy and Collagen Weakening

    • Scurvy is a connective tissue disease caused by a deficiency in Vitamin C (ascorbic acid), leading to weakened collagen fibers.
    • The disease is caused by failure to hydroxylate prolines and lysines in collagen, resulting in less hydrogen bonding between the chains of tropocollagen.

    Cross-Linking in Collagen

    • Lysine side chains can oxidize to aldehyde derivatives, which can react with either a lysine residue or with one another to produce a cross-link.
    • This process continues through life, making the collagen steadily less elastic and more brittle.

    Factors Determining Secondary and Tertiary Structure

    • The stability of the folded structure of a globular protein depends on the interplay of three factors:
      • The unfavorable conformational entropy change, which favors the unfolded state.
      • The favorable enthalpy contribution arising from intramolecular interactions.
      • The favorable entropy change arising from the burying of hydrophobic groups within the molecule.
    • The role of disulfide bonds in stabilizing the folded structure.

    Dynamics of Globular Protein Structure

    • The folding of globular proteins from their denatured conformations is a remarkably rapid process, often complete in less than a second.
    • Protein folding is not a completely random search through a vast conformational space, but rather takes place through a series of intermediate states.

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    Description

    Learn about the stereochemistry of a-amino acids, including their designation as D- or L- and the preference for L-amino acids in proteins.

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