Protein Structure: Primary and Secondary
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What is the primary structure of a protein?

  • The pattern of hydrogen bonds between amino acids
  • The overall shape of a protein
  • The specific 3D conformation of a protein
  • The sequence of amino acids in a polypeptide chain (correct)

    • What type of bonds are involved in the formation of α-helices?

  • Ionic bonds between amino acids
  • Hydrogen bonds between amino acids that are far apart
  • Covalent bonds between amino acids
  • Hydrogen bonds between amino acids that are near each other (correct)

    • What is the direction of the hydrogen bonds in an α-helix?

  • There are no hydrogen bonds in an α-helix
  • Perpendicular to the axis of the helix
  • Parallel to the axis of the helix (correct)
  • At an angle to the axis of the helix

    • What type of structure is characterized by extended 'flat' sheets?

    <p>β-sheet</p> Signup and view all the answers

    What are the two bonds that have free rotation in a protein?

    <p>Bond between α-carbon and amino nitrogen, and bond between carboxyl carbon and peptide bond</p> Signup and view all the answers

    In an α-helix, which amino acid is the C=O group of one amino acid bonded to?

    <p>The N-H group of an amino acid that is four down the chain</p> Signup and view all the answers

    What happens to hemoglobin in the lungs?

    <p>It releases CO2 and binds oxygen</p> Signup and view all the answers

    What level of protein structure involves local conformations maintained by extensive hydrogen bonding?

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

    What is the term for the sequence of amino acids in a polypeptide chain?

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

    What is the effect of 2,3BPG on hemoglobin?

    <p>Decreases the affinity of hemoglobin for oxygen</p> Signup and view all the answers

    What type of structure is characterized by a regular pattern of hydrogen bonds between the amide N-H and C=O groups of amino acids?

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

    What is the primary method used to determine the structure of proteins?

    <p>All of the above</p> Signup and view all the answers

    What is denaturation of proteins?

    <p>The loss of the structural order of a protein</p> Signup and view all the answers

    What is the direction of the hydrogen bonds in a β-sheet?

    <p>Perpendicular to the sheet</p> Signup and view all the answers

    What is the cause of denaturation of proteins?

    <p>pH changes, mercaptoethanol, detergent, heat, and urea/guanidine</p> Signup and view all the answers

    What is the result of errors in protein folding?

    <p>Diseases such as Alzheimer’s and Diabetes type 2</p> Signup and view all the answers

    What is the role of molecular chaperones?

    <p>To restore proteins that have become misfolded</p> Signup and view all the answers

    What is the term for the third phase of proteins?

    <p>Molten globule</p> Signup and view all the answers

    What is the characteristic of a molten globule?

    <p>It has a native-like secondary structure content</p> Signup and view all the answers

    What is the effect of hydrophobic interactions on protein folding?

    <p>It decreases the entropy of the system</p> Signup and view all the answers

    What is the turn repeat distance of an α-helix structure?

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

    Which amino acid creates a bend in an α-helix structure due to its cyclic structure and lack of N-H for hydrogen bonding?

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

    What type of protein structure has polypeptide chains organized approximately parallel along a single axis?

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

    What is the primary force stabilizing a completely folded and compacted polypeptide chain?

    <p>Interactions of amino acid side chains in non-neighboring regions</p> Signup and view all the answers

    What is the quaternary structure of hemoglobin?

    <p>Four polypeptide chains</p> Signup and view all the answers

    What is the primary function of globular proteins?

    <p>Water solubility</p> Signup and view all the answers

    What is the result of the Bohr effect on hemoglobin?

    <p>Decreased oxygen binding affinity</p> Signup and view all the answers

    What is the typical shape of a globular protein?

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

    What type of bonds are involved in the stabilization of the tertiary structure?

    <p>Non-covalent bonds</p> Signup and view all the answers

    What is the main difference between myoglobin and hemoglobin?

    <p>Number of subunits</p> Signup and view all the answers

    What is the primary structure of a protein composed of?

    <p>A sequence of amino acids in a polypeptide chain</p> Signup and view all the answers

    What type of hydrogen bonds are involved in the formation of secondary structures in proteins?

    <p>Hydrogen bonds between the amide N-H and C=O groups of amino acids</p> Signup and view all the answers

    What is the characteristic of α-helices in proteins?

    <p>They are formed by a regular pattern of hydrogen bonds between amino acids</p> Signup and view all the answers

    What is the direction of the hydrogen bonds in an α-helix relative to the axis of the helix?

    <p>Parallel to the axis of the helix</p> Signup and view all the answers

    What level of protein structure is characterized by local conformations maintained by hydrogen bonding?

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

    What is the characteristic of β-sheets in proteins?

    <p>They are extended 'flat' sheets of amino acids</p> Signup and view all the answers

    Which two bonds have free rotation in a protein?

    <p>The bond between the α-carbon and amino nitrogen and the bond between the α-carbon and carboxyl carbon</p> Signup and view all the answers

    What is the relationship between the C=O group of one amino acid and the N-H group of another amino acid in an α-helix?

    <p>They are hydrogen bonded</p> Signup and view all the answers

    What is the characteristic of the primary structure of a protein?

    <p>It is a linear sequence of amino acids from the N-terminal to the C-terminal end</p> Signup and view all the answers

    What is the relationship between the amino acids in a protein?

    <p>They are linked by covalent bonds</p> Signup and view all the answers

    What is the purpose of the hydrogen bonds in an α-helix?

    <p>To stabilize the polypeptide chain in a helical structure</p> Signup and view all the answers

    Why does proline create a bend in an α-helix structure?

    <p>Due to its cyclic structure and lack of N-H for hydrogen bonding</p> Signup and view all the answers

    What is the characteristic of a β-pleated sheet?

    <p>Polypeptide chains lie adjacent to each other in a sheet-like structure</p> Signup and view all the answers

    What is the function of globular proteins?

    <p>To be soluble in water and salt solutions</p> Signup and view all the answers

    What is the difference between myoglobin and hemoglobin?

    <p>Hemoglobin has a quaternary structure, while myoglobin does not</p> Signup and view all the answers

    What is the effect of the Bohr effect on hemoglobin?

    <p>It decreases the binding of oxygen to hemoglobin</p> Signup and view all the answers

    What is the turn repeat distance of an α-helix?

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

    What type of interaction is involved in the stabilization of the tertiary structure?

    <p>All of the above</p> Signup and view all the answers

    What is the characteristic of fibrous proteins?

    <p>They are insoluble in water and salt solutions</p> Signup and view all the answers

    What is the quaternary structure of a protein?

    <p>The association of polypeptide chains</p> Signup and view all the answers

    What is the function of 2,3BPG in hemoglobin?

    <p>To raise the P50 for deoxy-Hb</p> Signup and view all the answers

    What causes denaturation of proteins?

    <p>pH changes, mercaptoethanol, detergent, heat, and urea/guanidine</p> Signup and view all the answers

    What is the result of errors in protein folding?

    <p>Diseases such as Alzheimer's and Diabetes type 2</p> Signup and view all the answers

    What is the role of molecular chaperones?

    <p>To guide misfolded regions back into place</p> Signup and view all the answers

    What is the characteristic of a molten globule?

    <p>Native-like secondary structure content but without the tightly packed protein interior</p> Signup and view all the answers

    What is the primary method used to determine the structure of proteins?

    <p>All of the above</p> Signup and view all the answers

    What is the hydrophobic effect in protein folding?

    <p>Non-polar species in water reduce entropy</p> Signup and view all the answers

    What happens to hemoglobin in the lungs?

    <p>It releases both CO2 and H+ and binds oxygen</p> Signup and view all the answers

    What is the function of denaturation of proteins?

    <p>To lose the structural order that gives a protein its biological activity</p> Signup and view all the answers

    What is the role of hemoglobin in the lungs?

    <p>To release both CO2 and H+ and bind oxygen</p> Signup and view all the answers

    Study Notes

    Primary Structure

    • The primary structure of a protein refers to the sequence of amino acids in a polypeptide chain, read from the N-terminal end to the C-terminal end.
    • It is the linear amino acid sequence from N- to C-terminal end.

    Secondary Structure

    • The secondary structure of a protein refers to local conformations, maintained by extensive H-bonding that involves components of the peptide bond.
    • There are two major kinds of secondary structures found in proteins: α-helices and β-sheets.
    • α-helix: a helical structure formed by a regular pattern of hydrogen bonds between the amide N-H and C=O groups of amino acids that are near each other in the primary sequence.
    • In an α-helix, the C=O of one amino acid is hydrogen bonded to the N-H of an amino acid that is four down the chain.
    • The pattern of H-bonds pulls the polypeptide chain into a helical structure, with each turn containing 3.6 amino acids.
    • The turn repeat distance is 5.4Å (1 Å = 0.1 nm).
    • Factors that can disrupt an α-helix include proline, strong electrostatic repulsion, and steric crowding.
    • β-pleated sheet: a sheet-like structure formed by polypeptide chains lying adjacent to one another, with hydrogen bonds forming between the backbone of sheets.
    • R groups alternate, first above and then below the plane, and extend above and below the plane of the sheet.

    Super-Secondary Structures

    • Examples of super-secondary structures include β-α-β, α-α, β-meander, Greek key, and β-barrels.
    • Two ways to represent protein structures are space-filling models and ribbon structures.

    Tertiary Structure

    • The tertiary structure of a protein describes the completely folded and compacted polypeptide chain.
    • It is stabilized by interactions of amino acid side chains in non-neighboring regions of the polypeptide chain.
    • There are several types of tertiary structures, including globular and fibrous proteins.
    • Globular proteins are often approximated as spheres, tend to be water soluble, and have polar side chains on the exterior and non-polar side chains inside.
    • Fibrous proteins are often strong, insoluble, and have structural roles, with examples including keratin and collagen.

    Tertiary Structure Forces

    • Non-covalent forces that stabilize tertiary structures include H-bonding, electrostatic interactions, and hydrophobic interactions.
    • Covalent forces include disulfide bonds.

    Quaternary Structure

    • The quaternary structure of a protein refers to the association of multiple polypeptide chains.
    • Examples include hemoglobin, which has four sub-units labeled α and β.
    • Hemoglobin exhibits cooperativity, and the binding of oxygen is affected by pH and CO2 levels.

    Comparison of Hemoglobin and Myoglobin

    • Myoglobin is found in muscle and tissue, has no quaternary structure, and binds one oxygen molecule.
    • Hemoglobin is found in blood, has a quaternary structure, and binds four oxygen molecules.

    The Bohr Effect

    • The Bohr effect refers to the decrease in oxygen binding affinity of hemoglobin in response to increased CO2 and H+ levels.
    • In actively metabolizing tissue, hemoglobin releases oxygen and binds CO2 and H+.
    • In the lungs, hemoglobin releases CO2 and H+ and binds oxygen.

    Structure Determination

    • Methods of protein structure determination include X-ray diffraction of protein crystals, multi-dimensional nuclear magnetic resonance of proteins in solutions and membranes, and cryo-electron microscopy.

    Denaturation of Proteins

    • Denaturation refers to the loss of structural order that gives a protein its biological activity.
    • Causes of denaturation include pH changes, mercaptoethanol, detergent, heat, and urea/guanidine.
    • Denaturation may or may not be reversible, and errors in folding can contribute to diseases.

    Protein Folding

    • The hydrophobic effect refers to the reduction of entropy as non-polar species in water reduce entropy.
    • Globular proteins have hydrophobic residues inside, and membrane proteins have hydrophobic residues in the membrane interior.
    • Protein folding chaperones are part of a quality control system that aims to ensure proper protein folding or restore proteins that have become misfolded.

    Molten Globule

    • A molten globule is a third phase of proteins, characterized by a native-like secondary structure content but without the tightly packed protein interior.
    • It was first found in cytochrome c under low pH and high salt concentration.

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    Description

    Test your knowledge of protein structure, including the primary structure of amino acid sequences and secondary structures such as alpha-helices and beta-sheets. Learn about the different types of protein conformations and how they are maintained.

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