Protein Structure and Function
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Protein Structure and Function

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Questions and Answers

What type of secondary structure is primarily formed by keratin?

  • β sheets
  • α helices (correct)
  • Random coils
  • Triple helices

    • What role do disulfide bonds play in proteins?

  • They transport oxygen
  • They provide energy to the protein
  • They stabilize protein structure (correct)
  • They assist in DNA replication

    • In Anfinsen's experiment, what was concluded about protein structure?

  • Only disulfide bonds determine structure
  • The primary sequence determines the final structure (correct)
  • Proteins can fold without any sequence information
  • Structure is independent of primary sequence

    • Which protein is primarily responsible for oxygen transport?

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

    What proteins are involved in transporting cholesterol in the body?

    <p>Apolipoproteins and HDL</p> Signup and view all the answers

    What is the main function of myoglobin in the body?

    <p>Store oxygen</p> Signup and view all the answers

    Which type of protein structure do β sheets belong to?

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

    What is the relationship between myoglobin and hemoglobin?

    <p>Myoglobin stores oxygen, while hemoglobin transports it</p> Signup and view all the answers

    What is the primary role of proteins within a cell?

    <p>Act as the workhorses of the cell</p> Signup and view all the answers

    What does a pKa value indicate about a group in relation to pH?

    <p>The pH at which the group is 50% protonated</p> Signup and view all the answers

    When are groups primarily protonated?

    <p>When the ambient pH is less than their pKa</p> Signup and view all the answers

    What structural feature accounts for peptide bonds maintaining a planar configuration?

    <p>They possess a resonance structure</p> Signup and view all the answers

    What form of amino acids are found in all life on Earth, apart from glycine (G)?

    <p>Levorotary (L) form</p> Signup and view all the answers

    Which level of protein structural organization refers to the amino acid sequence?

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

    Under what condition do disulfide bonds typically form?

    <p>In oxidizing environments</p> Signup and view all the answers

    In protein structure, what does the term 'dihedral angle' refer to?

    <p>The angle between the two planes formed by four atoms</p> Signup and view all the answers

    What is the main characteristic of Van der Waals forces?

    <p>They are very weak and influence hydrophobic interactions</p> Signup and view all the answers

    What is the typical length of a hydrogen bond?

    <p>1.6 - 2.0 Ångstrom</p> Signup and view all the answers

    What is the typical value of the dihedral angle Ω in peptide bonds?

    <p>Always 0 or +180 degrees</p> Signup and view all the answers

    Which structure encompasses multiple subunits folded into a complex?

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

    What role do reducing agents play in laboratory protocols concerning disulfide bonds?

    <p>They prevent oxidation of disulfide bonds</p> Signup and view all the answers

    What is the significance of the dihedral angles Φ and Ψ in polypeptides?

    <p>They influence the overall stability and conformation</p> Signup and view all the answers

    Which structural motifs are well-represented when plotting dihedral angles Φ against Ψ?

    <p>Alpha-helices, beta-sheets, and Lα structures</p> Signup and view all the answers

    What allows proline to have a unique twist in the peptide bond configuration?

    <p>Its cyclic structure</p> Signup and view all the answers

    What characterizes the secondary structure of proteins?

    <p>Includes both α-helices and β-sheets</p> Signup and view all the answers

    How many residues are involved in one complete turn of an α-helix?

    <p>3.6 residues</p> Signup and view all the answers

    What percentage of β-sheets are typically found in a mixed parallel and anti-parallel configuration?

    <p>20%</p> Signup and view all the answers

    What is the primary structural level of protein organization?

    <p>Amino acid sequence</p> Signup and view all the answers

    Which statement about α-helices is true?

    <p>They can contain both hydrophobic and hydrophilic residues on one side</p> Signup and view all the answers

    What term refers to the structural organization level involving multiple subunits?

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

    What is the distance between consecutive rungs of an α-helix turns?

    <p>5.4 Å</p> Signup and view all the answers

    Which of the following describes the pleated nature of β-sheets?

    <p>They are not flat but exhibit a pleated formation</p> Signup and view all the answers

    What is the main characteristic of hemoglobin's affinity for oxygen at low pH?

    <p>It releases oxygen into the tissue.</p> Signup and view all the answers

    How does the structure of hemoglobin affect its function?

    <p>It exhibits a sigmoidal saturation curve.</p> Signup and view all the answers

    What happens to oxygen binding in hemoglobin when oxygen pressure increases?

    <p>Hemoglobin binds more oxygen.</p> Signup and view all the answers

    What term is used to describe hemoglobin when it is bound to oxygen?

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

    Which of the following statements is true about myoglobin and hemoglobin?

    <p>Both proteins have similar amino acid sequences.</p> Signup and view all the answers

    What role do prolines play in the structure of myoglobin?

    <p>They prevent oxidation of Fe(II) to Fe(III).</p> Signup and view all the answers

    According to Le Chatelier’s principle, how does low pH affect hemoglobin's behavior?

    <p>It shifts equilibrium towards weaker acids.</p> Signup and view all the answers

    What is the significance of the first crystal structures of myoglobin and hemoglobin being solved?

    <p>It provided insights into how oxygen is transported in blood.</p> Signup and view all the answers

    Study Notes

    Protein Structure and Function

    • Proteins are essential components of cells; their shapes, functions, and responses to the environment determine cellular behavior.

    Review of Basic Concepts

    • The pKa of a group is the pH at which it is 50% protonated.
    • A group is primarily protonated at pH values lower than its pKa.
    • Carboxylic acids are considered acidic due to their low pKa, meaning they are deprotonated at neutral pH.
    • Basic groups have a high pKa.
    • Elements towards the upper right of the periodic table are more electronegative.
    • Peptide bonds form via dehydration reactions and have a partial double bond character, contributing to their planar nature.
    • Cysteines can be oxidized to form disulfide bonds - a process favored in oxidizing environments, such as the extracellular space; reducing environments, like the cytosol, prevent disulfide bond formation.
    • Hydrogen bonds have lengths between 1.6 and 2.0 Angstroms.
    • Van der Waals forces between nonpolar groups are weak; the aggregation of hydrophobic domains in proteins is driven primarily by entropy of water molecules, not by Van der Waals forces.
    • All amino acids, except glycine, are chiral and exist in the levorotary (L) form in all known life.

    Levels of Structural Organization

    • Proteins have four levels of structural organization:
      • Primary: Amino acid sequence
      • Secondary: Alpha-helices, beta-sheets, and loops
      • Tertiary: Entire polypeptide chain, bundles of helices and sheets, domains
      • Quaternary: Multiple subunits folded into a complex

    Amino Acids

    • Dihedral angle: The spatial arrangement of amino acids is defined by three dihedral angles:
      • Φ (phi): angle along the N-Cα bond
      • Ψ (psi): angle along the Cα-C bond
      • Ω (omega): angle along the C-N bond

    Peptide Bond

    • Dihedral angles in a polypeptide:
      • The Ω angle is always 0 or +180 degrees.
      • Analyzing Φ and Ψ angles reveals preferred conformations:
        • Alpha-helix combinations
        • Beta-sheet configurations
        • A less common structure called Lα (left-handed alpha-helices)
      • The trans conformation of Ω is favored due to steric hindrance between consecutive side chains.
      • Proline's unique structure allows for a cis conformation because it is anchored to the backbone.

    Secondary Structure

    • α-helix:

      • Forms due to hydrogen bonding between the backbone NH and C=O groups.
      • Contains 3.6 residues per turn, with each residue spanning 100 degrees of rotation.
      • Consecutive α-helix turns are separated by 5.4 Angstroms.
      • Almost exclusively right-handed.
      • Amphipathic helices have hydrophobic residues on one side and hydrophilic residues on the other.
      • Fully buried helices consist of hydrophobic residues, and fully exposed helices are composed of hydrophilic residues.

    • β-sheet:

      • Also forms through hydrogen bonds between backbone NH and C=O groups.
      • All potential hydrogen bonds are satisfied, except for the flanking strands at the sheet ends.
      • About 20% of beta-sheets are mixed parallel and anti-parallel, the other 80% are purely one type or the other.
      • β-sheets are not flat, but pleated.

    Disulfide Bonds

    • Ribonuclease:

      • Contains disulfide bonds.
      • Illustrates Anfinsen's experiment, which suggested that primary sequence determines structure (current understanding is more nuanced).

    • Insulin:

      • Also contains disulfide bonds.

    • Immunoglobulins:

      • Chains are held together by disulfide bonds.

    Protein Carriers

    • Cholesterol:

      • Transported by high-density lipoprotein (HDL) and low-density lipoprotein (LDL) particles.
      • Apolipoproteins within these particles play a crucial role.

    • Solute Lipid Carriers (SLC family):

      • Transport carboxylic acids and small molecules.

    • Myoglobin (Mb) and Hemoglobin (Hb):

      • Transport oxygen.

    Hemoglobin

    • Oxygen-carrying team:

      • Hemoglobin: carries oxygen (transport function).
      • Myoglobin: stores oxygen (repository function).

    • Saturation curves:

      • Myoglobin: exhibits a parabolic curve, indicating simple binding.
      • Hemoglobin: displays a sigmoidal (S-shaped) curve, reflecting cooperative binding between heme units in the tetrameric structure.

    • Hemoglobin and oxygen:

      • Hemoglobin's affinity for oxygen increases with rising oxygen pressure.
      • Oxyhemoglobin: Hemoglobin with bound oxygen.
      • Deoxyhemoglobin: Hemoglobin without bound oxygen.
      • HbO2 is a stronger acid than Hb.
      • In acidic environments, Le Chatelier's principle dictates that the equilibrium shifts towards the weaker acid (Hb), releasing oxygen - an adaptation crucial for oxygen delivery to tissues with high oxygen consumption.

    • Crystal structures:

      • X-ray diffraction structures solved by Perutz and Kendrew (1961 Nobel Prize).
      • Myoglobin (Mb): contains seven helical chains, with heme nestled in the middle, secured by histidines; prolines create bends between helices.
      • Hemoglobin (Hb): similar amino acid sequence to Mb; its structure prevents oxidation of Fe(II) to Fe(III), which would render the molecule incapable of binding oxygen.

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    Description

    This quiz explores the fundamental concepts of protein structure and function, including key principles like pKa, peptide bonds, and molecular interactions. Understand how proteins interact within cellular environments and the significance of structural features in their functionality. Test your knowledge on the essential roles that proteins play in biological systems.

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