Amino Acids and Protein Structure
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Questions and Answers

What determines the tertiary structure of a polypeptide chain?

  • The sequence of amino acids
  • The pH of the solution
  • The temperature of the environment
  • The primary structure of the polypeptide chain (correct)

    • Why do glutamate, aspartate, histidine, lysine, or arginine disrupt the helix?

  • They are non-polar amino acids and form strong bonds.
  • They are non-polar amino acids and form weak bonds.
  • They are polar amino acids and form hydrogen bonds.
  • They are charged amino acids and form ionic bonds or repel each other electrostatically. (correct)

    • What is a characteristic of globular proteins in aqueous solutions?

  • They have a linear structure
  • They have a loose, open structure
  • They are always soluble in water
  • Their structure is compact, with a high-density of atoms in the core (correct)

    • What is the fundamental functional and three-dimensional structural unit of a polypeptide?

    <p>Protein domain</p> Signup and view all the answers

    What type of amino acids can interfere with the formation of the alpha helix?

    <p>Amino acids with bulky side chains</p> Signup and view all the answers

    What is true about the length of polypeptide chains and their domains?

    <p>Polypeptide chains with more than 200 amino acids often have multiple domains</p> Signup and view all the answers

    What is the location of hydrophobic side chains in globular proteins?

    <p>In the interior of the molecule</p> Signup and view all the answers

    What is the characteristic structure of the beta conformation?

    <p>A zigzag structure</p> Signup and view all the answers

    How are beta sheets often visualized in illustrations of protein structure?

    <p>As broad arrows</p> Signup and view all the answers

    Why do hydrophilic groups in the interior of globular proteins form hydrogen bonds or electrostatic interactions?

    <p>To eliminate the possibility of water molecules binding to these groups</p> Signup and view all the answers

    What is the core of a protein domain built from?

    <p>Combinations of super-secondary structural elements</p> Signup and view all the answers

    What is true about the folding of a peptide chain within a domain?

    <p>It occurs independently of folding in other domains</p> Signup and view all the answers

    What role do α-helix and β-sheet structures play in globular proteins?

    <p>They provide maximal hydrogen bonding for peptide bond components</p> Signup and view all the answers

    What is a key difference between alpha helices and beta sheets?

    <p>Beta sheets are composed of two or more peptide chains.</p> Signup and view all the answers

    What determines the unique three-dimensional structure of each polypeptide?

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

    What is the result of maximal hydrogen bonding in globular proteins?

    <p>The possibility of water molecules binding to hydrophilic groups is eliminated</p> Signup and view all the answers

    In what ways can beta strands be arranged in a beta sheet?

    <p>Antiparallel or parallel</p> Signup and view all the answers

    What are beta turns/loops typically found in?

    <p>Globular proteins</p> Signup and view all the answers

    What types of interactions cooperate in stabilizing the tertiary structures of globular proteins?

    <p>Different types of interactions, including covalent disulfide bonds, hydrophobic interactions, hydrogen bonds, and ionic interactions</p> Signup and view all the answers

    What is the function of beta turns/loops in proteins?

    <p>To connect successive runs of alpha helix or beta conformation</p> Signup and view all the answers

    What is the main characteristic of fibrous proteins?

    <p>Highly elongated protein molecules with a single type of secondary structure</p> Signup and view all the answers

    Which type of fibrous protein is characterized by being soft and flexible?

    <p>β Sheet</p> Signup and view all the answers

    What is the principal component of hair, nails, and wool?

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

    What is the structure of the α-keratin chain?

    <p>A left-handed helix</p> Signup and view all the answers

    What is the repeating pattern in each α-keratin chain?

    <p>7-residue repeat</p> Signup and view all the answers

    What is the characteristic of collagen molecules?

    <p>They are composed of three polypeptide chains</p> Signup and view all the answers

    What is the amino acid composition of collagen?

    <p>30% Gly and 15-30% Pro or Hyp</p> Signup and view all the answers

    What is a consequence of abnormal collagen synthesis or structure?

    <p>Dysfunction of cardiovascular organs</p> Signup and view all the answers

    What is the consequence of the accumulation of spontaneously aggregating proteins in neurodegenerative disorders?

    <p>Alzheimer disease</p> Signup and view all the answers

    What is the role of the prion protein (PrP) in transmissible spongiform encephalopathies (TSEs)?

    <p>Causative agent of TSEs</p> Signup and view all the answers

    What is the consequence of misfolding of transthyretin protein?

    <p>Irreversible tissue damage</p> Signup and view all the answers

    What is the function of transthyretin protein?

    <p>Carrying vitamin A and thyroxine</p> Signup and view all the answers

    What is the consequence of mutation in the gene coding for transthyretin?

    <p>Structural changes leading to misfolding</p> Signup and view all the answers

    What percentage of African Americans are carriers of the Val42Ile variant?

    <p>3-4%</p> Signup and view all the answers

    What is the prevalence of Transthyretin Amyloidosis cardiomyopathy (ATTR-CM) in patients with heart failure?

    <p>14%</p> Signup and view all the answers

    What is the characteristic of wild-type ATTR?

    <p>Present in 25% of patients over 80 years</p> Signup and view all the answers

    Study Notes

    Protein Structure

    • The helix structure of a protein can be disrupted by certain amino acids, such as glutamate, aspartate, histidine, lysine, or arginine, which are charged and can form ionic bonds or repel each other electrostatically.
    • Tryptophan, with its bulky side chains, or valine or isoleucine, which branch at the β-carbon, can also interfere with the formation of an α-helix if they are present in large numbers.

    β-Sheet

    • In the β conformation, the backbone of the polypeptide chain is extended into a zigzag rather than a helical structure.
    • The zigzag polypeptide chains can be arranged side by side to form a structure resembling a series of pleats.
    • Hydrogen bonds are formed between adjacent segments of the polypeptide chain.
    • β-strands are often visualized as broad arrows in illustrations of protein structure.
    • β-sheets are composed of two or more peptide chains (β-strands), or segments of polypeptide chains, which are almost fully extended.
    • In β-sheets, the hydrogen bonds are perpendicular to the polypeptide backbone.

    β-Bend/Turns

    • β-bends/turns are normally present in globular proteins.
    • Nearly 2/3 of the proteins in turns or loops are connecting elements that link successive runs of α-helix or β-conformation.
    • β-turns connect the ends of two adjacent segments of an antiparallel β-sheet.

    Fibrous Proteins

    • Fibrous proteins are highly elongated protein molecules whose shapes are dominated by a single type of secondary structure.
    • Examples of fibrous proteins include:
      • Coiled coil: Keratin (durable, insoluble, unreactive)
      • β sheet: Silk, fibroin of spider web (soft, flexible)
      • Triple helix: Collagen (strong, high tensile strength)

    Keratin

    • Keratin is the principal component of hair, nails, wool, horns, hooves, scales, feathers, and shells.
    • α-keratin is found in mammals, while β-keratin is found in birds and reptiles.
    • The α-keratin chain is an α-helix, and pairs of α-keratin chains are inter-wound to form a two-chain coiled coil.
    • Each α-keratin chain consists of ~310 residues having a 7-residue repeat, with residues a and d being nonpolar.

    Collagen

    • Collagen is a triple helix protein that contains three polypeptide chains.
    • Each chain is a left-handed helix (3 residues/turn), and the three helical chains are twisted together in a right-handed manner to form a superhelical structure.
    • Collagen has a distinctive amino acid composition, with 30% glycine and 15-30% proline or hydroxyproline.

    Collagen Disorders

    • Abnormal collagen synthesis or structure can cause diseases such as:
      • Cardiovascular disorders (aortic and arterial aneurysms and heart valve malfunction)
      • Bone disorders (fragility and easy fracturing)
      • Skin disorders (poor healing and unusual distensibility)
      • Joint disorders (hypermobility and arthritis)
      • Eye disorders (dislocation of the lens)
    • Examples of collagen disorders include:
      • Scurvy (vitamin C deficiency)

    Tertiary Structure of Globular Proteins

    • The primary structure of a polypeptide chain determines its tertiary structure.
    • Globular proteins have a compact, high-density structure with a high degree of close packing.
    • Hydrophobic side chains are buried in the interior, while hydrophilic groups are generally found on the surface of the molecule.
    • Hydrophilic groups in the interior of the polypeptide are involved in hydrogen bonds or electrostatic interactions.

    Protein Domains

    • Protein domains are the fundamental functional and three-dimensional structural units of a polypeptide.
    • Domains are modular units that are built from combinations of super-secondary structural elements (motifs).
    • Folding of the peptide chain within a domain usually occurs independently of folding in other domains.
    • Each domain has the characteristics of a small, compact globular protein that is structurally independent of the other domains in the polypeptide chain.

    Interactions Stabilizing Tertiary Structure

    • The unique three-dimensional structure of each polypeptide is determined by its amino acid sequence.
    • Interactions between the amino acid side chains guide the folding of the polypeptide to form a compact structure.
    • Different types of interactions cooperate in stabilizing the tertiary structures of globular proteins, including:
      • Covalent disulfide bonds
      • Hydrophobic interactions
      • Hydrogen bonds
      • Ionic interactions

    Protein Misfolding

    • Deposits of misfolded proteins are associated with a number of diseases, including amyloidoses.
    • The prion protein (PrP) has been implicated as the causative agent of transmissible spongiform encephalopathies (TSEs), including Creutzfeldt-Jakob disease in humans, scrapie in sheep, and bovine spongiform encephalopathy in cattle.

    Transthyretin Amyloidosis (ATTR)

    • ATTR occurs as a result of misfolding of the transthyretin protein produced by the liver.
    • The misfolded protein produces amyloid fibrils that can deposit in various tissues, causing irreversible damage.
    • Mutation in the gene coding for TTR can cause structural changes leading to misfolding (hATTR); normal aging process can render ATTR tetramer prone to misfolding (wATTR).
    • ATTR cardiomyopathy (ATTR-CM) is a systemic amyloidosis caused by the accumulation of transthyretin fibrils in the myocardium.

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    Description

    This quiz covers the effects of different amino acids on protein structure, including those that disrupt the alpha-helix and those that interfere with beta-sheet formation.

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