Protein Structure: Primary and Secondary
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Questions and Answers

What does the 1° structure of a protein refer to?

  • The quaternary structure of a protein
  • The local conformations of a protein
  • The sequence of amino acids in a polypeptide chain (correct)
  • The 3D conformation of a protein
  • What type of bonds are involved in the formation of α-helices?

  • Ionic bonds
  • Disulfide bonds
  • Hydrogen bonds (correct)
  • Peptide bonds
  • Which of the following is a characteristic of α-helices?

  • Random coil structure
  • Helical structure (correct)
  • β-turns
  • Extended flat sheets
  • What is the direction of the hydrogen bonds in an α-helix?

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

    Which two bonds have free rotation in a protein?

    <p>Bonds between α-carbon and amino nitrogen, and bonds between α-carbon and carboxyl carbon</p> Signup and view all the answers

    What is the type of structure that involves extended, flat sheets?

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

    How many amino acids down the chain does the C=O of one amino acid hydrogen bond to in an α-helix?

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

    What is the average number of amino acids in each turn of the α-helix?

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

    What is the secondary structure element that involves a regular pattern of hydrogen bonds between amide N-H and C=O groups?

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

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

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

    What is the main difference between globular and fibrous proteins?

    <p>Globular proteins are soluble in water, while fibrous proteins are not</p> Signup and view all the answers

    What is the term for the local conformations maintained by extensive hydrogen bonding in a protein?

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

    Which of the following is NOT a type of secondary structure?

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

    What is the term for the association of polypeptide chains?

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

    What is the effect of the presence of BPG on hemoglobin's affinity for oxygen?

    <p>It decreases the affinity</p> Signup and view all the answers

    What is the purpose of hemoglobin in the blood?

    <p>To transport oxygen from the lungs to the tissues</p> Signup and view all the answers

    What is the main cause of denaturation?

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

    What is the result of heat-induced denaturation of proteins?

    <p>Exposure of nonpolar segments to aqueous solvent</p> Signup and view all the answers

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

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

    What is the term for the change in the oxygen binding behavior of hemoglobin in response to changes in pH and CO2 levels?

    <p>Bohr effect</p> Signup and view all the answers

    What is the function of molecular chaperones?

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

    What is the term for the structure of a protein that has a native-like secondary structure content but without tightly packed protein interior?

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

    What is the main difference between the oxygen binding curves of myoglobin and hemoglobin?

    <p>Myoglobin has a hyperbolic curve, while hemoglobin has a sigmoidal curve</p> Signup and view all the answers

    What is the function of the R groups in the α-helix structure?

    <p>They project outward from the α-helix</p> Signup and view all the answers

    What is the main role of hydrophobic effect in protein folding?

    <p>To reduce entropy</p> Signup and view all the answers

    Why do globular proteins tend to have a higher proportion of polar side chains on the outside?

    <p>To interact with the aqueous environment</p> Signup and view all the answers

    What is the consequence 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 location of hydrophobic residues in globular proteins?

    <p>Inside the protein</p> Signup and view all the answers

    What is the role of chaperones in protein folding?

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

    What is the strategy used by chaperones to guide misfolded regions back into place?

    <p>A variety of strategies</p> Signup and view all the answers

    What refers to the linear amino acid sequence from the N-terminal end to the C-terminal end?

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

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

    <p>Hydrogen bonds</p> Signup and view all the answers

    What is the characteristic of α-helices in terms of hydrogen bonding?

    <p>Hydrogen bonds are parallel to the axis</p> Signup and view all the answers

    Which bonds have free rotation in a protein?

    <p>Both A and B</p> Signup and view all the answers

    What is the term for local conformations maintained by extensive hydrogen bonding in a protein?

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

    What type of structure involves extended, flat sheets?

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

    What is the consequence of errors in protein folding?

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

    How many amino acids down the chain does the C=O of one amino acid hydrogen bond to in an α-helix?

    <p>4</p> Signup and view all the answers

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

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

    What is the secondary structure element that involves a regular pattern of hydrogen bonds between amide N-H and C=O groups?

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

    What is the main reason for the decrease in hemoglobin's affinity for oxygen in the presence of BPG?

    <p>Changes in side chain electrostatics</p> Signup and view all the answers

    Which technique is used to study protein structure in solutions and membranes?

    <p>Multi-dimensional nuclear magnetic resonance</p> Signup and view all the answers

    What is the consequence of heat-induced denaturation of proteins?

    <p>Exposure of nonpolar segments to aqueous solvent</p> Signup and view all the answers

    What is the role of molecular chaperones in protein folding?

    <p>To ensure proper protein folding</p> Signup and view all the answers

    What is the cause of denaturation due to urea and guanidine?

    <p>Disruption of H-bonds</p> Signup and view all the answers

    What is the location of hydrophobic residues in membrane proteins?

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

    What is the effect of mercaptoethanol on protein structure?

    <p>Breakage of S-S bonds</p> Signup and view all the answers

    What is the result of errors in protein folding?

    <p>Decreased biological activity</p> Signup and view all the answers

    What is the main role of the hydrophobic effect in protein folding?

    <p>To reduce entropy in water</p> Signup and view all the answers

    What is the strategy used by chaperones to guide misfolded regions back into place?

    <p>Variety of strategies</p> Signup and view all the answers

    What is the primary reason for the disruption of an α-helix by proline?

    <p>The restricted rotation due to its cyclic structure</p> Signup and view all the answers

    What is the characteristic of the side chains in a globular protein?

    <p>They are predominantly polar and located outside the protein</p> Signup and view all the answers

    What is the effect of the proximity of several side chains of like charge on the α-helix structure?

    <p>It disrupts the α-helix due to electrostatic repulsion</p> Signup and view all the answers

    What is the characteristic of the polypeptide chain in a β-pleated sheet?

    <p>It lies adjacent to one another in a sheet-like structure</p> Signup and view all the answers

    What is the role of hydrogen bonding in the formation of an α-helix?

    <p>It forms a hydrogen bond between the N-H and C=O groups</p> Signup and view all the answers

    What is the primary function of hemoglobin in the blood?

    <p>To transport oxygen from the lungs to the tissues</p> Signup and view all the answers

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

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

    What is the characteristic of the quaternary structure of hemoglobin?

    <p>It consists of multiple polypeptide chains</p> Signup and view all the answers

    What is the primary difference between the oxygen binding behavior of myoglobin and hemoglobin?

    <p>Hemoglobin exhibits cooperativity, while myoglobin does not</p> Signup and view all the answers

    What is the characteristic of fibrous proteins?

    <p>They are insoluble in water and have a fibrous structure</p> Signup and view all the answers

    What is maintained by extensive H-bonding that involves components of the peptide bond in a protein?

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

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

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

    Which bonds in a protein have free rotation?

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

    What type of structure is characterized by extended, flat sheets?

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

    What is the sequence of amino acids in a polypeptide chain referred to as?

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

    What is the characteristic of secondary structures in proteins?

    <p>Maintained by extensive H-bonding</p> Signup and view all the answers

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

    <p>From C=O of one amino acid to N-H of an amino acid that is four down the chain</p> Signup and view all the answers

    What type of protein structure involves local conformations maintained by extensive H-bonding?

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

    Which of the following is a characteristic of α-helices in proteins?

    <p>Helical, coiled</p> Signup and view all the answers

    What is the role of hydrogen bonding in the formation of α-helices?

    <p>To maintain the helical structure</p> Signup and view all the answers

    What is the primary cause of denaturation due to pH changes?

    <p>Changes in side chain electrostatics</p> Signup and view all the answers

    What is the role of molecular chaperones in protein folding?

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

    What is the effect of mercaptoethanol on protein structure?

    <p>Reduces S-S bonds</p> Signup and view all the answers

    What is the characteristic of the molten globule state?

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

    What is the primary reason for the presence of hydrophobic residues inside globular proteins?

    <p>To reduce entropy in the presence of water</p> Signup and view all the answers

    What is the effect of heat on protein structure?

    <p>Causes disruptive vibrations</p> Signup and view all the answers

    What is the role of cryo-electron microscopy in protein structure determination?

    <p>To study protein structure using complex computational processing algorithms</p> Signup and view all the answers

    What is the primary cause of denaturation due to urea and guanidine?

    <p>Disruption of H-bonds</p> Signup and view all the answers

    What is the characteristic of protein denaturation?

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

    What is the strategy used by chaperones to guide misfolded regions back into place?

    <p>Using a variety of strategies to guide misfolded regions</p> Signup and view all the answers

    What is the approximate distance between each turn of an α-helix?

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

    What is the main reason for the formation of a β-pleated sheet?

    <p>Hydrogen bonding between the backbone of sheets</p> Signup and view all the answers

    What is the characteristic of fibrous proteins?

    <p>They are insoluble in water and have a strong structure</p> Signup and view all the answers

    What is the term for the interaction between amino acid side chains in non-neighboring regions of the polypeptide chain?

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

    What is the function of hemoglobin in the lungs?

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

    What is the effect of BPG on hemoglobin's affinity for oxygen?

    <p>It decreases the affinity for oxygen</p> Signup and view all the answers

    What is the characteristic of the side chains in a globular protein?

    <p>Mostly polar on the outside and non-polar on the inside</p> Signup and view all the answers

    What is the term for the completely folded and compacted polypeptide chain?

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

    What is the role of proline in an α-helix?

    <p>It creates a bend in the α-helix</p> Signup and view all the answers

    What is the characteristic of the oxygen-binding curve of hemoglobin?

    <p>It is sigmoidal</p> Signup and view all the answers

    Study Notes

    Protein Structure Fundamentals

    • 1° structure of a protein refers to its linear amino acid sequence from the N-terminal to the C-terminal end.
    • Local conformations in proteins are maintained by extensive hydrogen bonding, particularly in secondary structures.
    • Free rotation occurs around the peptide bonds and the bonds involving the side chain, allowing flexibility.

    α-Helices

    • α-Helices consist of hydrogen bonds between the amide N-H group of one amino acid and the C=O group of another, typically four residues away.
    • Each turn of an α-helix contains approximately 3.6 amino acids.
    • The hydrogen bonds in α-helices run parallel to the helix axis.
    • Proline introduces a bend in the α-helix because of its rigid structure and inability to adopt a helical conformation.
    • The presence of like-charged side chains nearby may destabilize the α-helix due to repulsion.

    β-Pleated Sheets

    • β-Pleated sheets are characterized by extended, flat structures maintained by hydrogen bonding between strands.
    • In β-sheets, hydrogen bonds can connect distant parts of the polypeptide chain, contributing to stability.

    Protein Classes

    • Globular proteins tend to have polar side chains on the exterior for interaction with the aqueous environment, while hydrophobic residues are tucked inside.
    • Fibrous proteins typically provide structural support and have elongated shapes.

    Hemoglobin and BPG Interaction

    • Hemoglobin's primary function is gas transport, specifically oxygen delivery to tissues and CO2 transport from tissues back to the lungs.
    • 2,3-BPG lowers hemoglobin's affinity for oxygen, facilitating oxygen release in tissues.
    • Hemoglobin also exhibits the Bohr effect, which describes the change in oxygen binding in response to pH and CO2 concentration shifts.

    Protein Denaturation

    • Denaturation results from factors like heat, pH shifts, and chemical agents (urea, guanidine) that disrupt hydrogen bonding and protein structure.
    • Heat-induced denaturation leads to unfolding, loss of function, and potential aggregation.
    • Mercaptoethanol disrupts disulfide bonds, further altering protein conformation.

    Role of Molecular Chaperones

    • Chaperones assist protein folding by preventing misfolding and aggregation, guiding misfolded regions back into proper conformation.
    • Chaperones can recognize and bind to exposed hydrophobic regions on nascent or misfolded proteins.

    Structural Features and Techniques

    • Cryo-electron microscopy aids in protein structure determination by providing high-resolution images of proteins in their native states.
    • The molten globule state describes a partially folded state of proteins that retains some secondary structure but lacks a compact interior.

    Summary of Key Characteristics

    • Secondary structures, including α-helices and β-sheets, rely on hydrogen bonds and specific amino acid interactions for stability.
    • The arrangement and characteristics of amino acid side chains contribute significantly to protein functionality and structure.
    • The overall structure of proteins influences their biological activity, interaction with other molecules, and response to environmental changes.

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    Test your knowledge of protein structure, including the primary sequence of amino acids and secondary structures like alpha helices and beta sheets.

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