Biochemistry Chapter 6 Quiz: Protein Structure

Questions and Answers

What is the typical repeat distance of strands in a β sheet?

6.5 A◦

7.0 A◦ (correct)

5.1 A◦

6.0 A◦

What characterizes the connection of parallel strands in β sheets?

They require a slight left-handed twist.

They require an extensive crossover connection. (correct)

They are linked by simple loops.

They are connected by a hydrogen bond network.

Which of the following describes the arrangement of polypeptide changes in reverse turns or β bends?

They commonly occur in the interior of proteins.

They usually involve four successive amino acid residues. (correct)

They consist of a 160° flip between residues.

They typically involve six successive amino acid residues.

What is the repeat distance for an α helix in a pair?

5.4 A◦ Signup and view all the answers

What defines the primary structure of α keratin?

The sequence and composition of nonpolar residues. Signup and view all the answers

How are the polypeptide chains in collagen characterized?

They consist of three intertwined chains. Signup and view all the answers

What is the structure formed by two staggered rows of head-to-tail associated coiled coils?

Protofilament Signup and view all the answers

Which of the following is true about the α keratin assembly?

The helices are inclined about 18° relative to one another. Signup and view all the answers

What is the major component of connective tissues like bones and cartilage?

Collagen Signup and view all the answers

In the coiled coil structure of α keratin, what is the predominant characteristic of residues a and d?

They are predominantly nonpolar. Signup and view all the answers

What is the molecular mass of collagen typically measured at?

285 kDa Signup and view all the answers

Which enzyme is responsible for converting proline residues to hydroxyprolyl in collagen?

Prolyl hydroxylase Signup and view all the answers

What is the primary dietary deficiency that leads to scurvy?

Vitamin C Signup and view all the answers

Which of the following best describes the structural arrangement of collagen?

Right-handed superhelical structure formed from left-handed polypeptides Signup and view all the answers

Which amino acid comprises nearly one third of the residues in collagen?

Glycine Signup and view all the answers

What is a β bulge in the context of protein secondary structure?

An extra residue not hydrogen bonded to a neighboring strand Signup and view all the answers

How does the amino acid sequence affect protein secondary structure?

It can distort the regular conformations of secondary elements. Signup and view all the answers

According to the analysis by Chou and Fasman, what is true about certain residues in protein structures?

They can break or disrupt other secondary structures. Signup and view all the answers

What percentage range does proline and its hydroxy derivatives constitute in collagen?

15-30% Signup and view all the answers

What may cause an initial and final turn to frequently deviate from its ideal conformation in an α-helix?

Variations in amino acid sequence Signup and view all the answers

What characterizes the primary structure of a protein?

The unique sequence of amino acids Signup and view all the answers

Which structure of a protein is involved in interactions between side chains?

Tertiary structure Signup and view all the answers

What describes the secondary structure of a protein?

It involves local spatial arrangements such as coils and folds Signup and view all the answers

What is the significance of peptide bonds in protein structure?

They provide rigidity and planar characteristics Signup and view all the answers

In terms of torsion angles, what is the conformation when the polypeptide chain is fully extended?

Both Φ and ψ are 180° Signup and view all the answers

What is the primary purpose of the Ramachandran diagram?

To indicate allowed conformations of polypeptides Signup and view all the answers

What defines the quaternary structure of a protein?

The spatial arrangement of multiple polypeptide chains Signup and view all the answers

Which residues are exceptions to the sterically allowed angles shown in the Ramachandran diagram?

Glycine and Proline Signup and view all the answers

What can cause steric interference in peptide groups?

Close proximity of amide hydrogen and carbonyl oxygen Signup and view all the answers

What is the helical conformation of the α Helix in terms of residues per turn?

3.6 residues per turn Signup and view all the answers

What type of bonds primarily hold the secondary structure of proteins together?

Hydrogen bonds between backbone atoms Signup and view all the answers

In which type of β sheet do the hydrogen-bonded polypeptide chains run in opposite directions?

Antiparallel β sheet Signup and view all the answers

Which statement accurately describes the torsion angles of a polypeptide backbone?

They represent rotations around peptide bonds Signup and view all the answers

Which of the following describes the rigid structure of the peptide group?

It has about 40% double bond character due to resonance Signup and view all the answers

What is the pitch of the α Helix?

5.4 A° Signup and view all the answers

What characterizes the side chains in β sheets?

They alternate above and below the plane of the sheet Signup and view all the answers

What is indicated by the dashed lines in the α Helix structure?

Hydrogen bonds between distant residues Signup and view all the answers

Which type of β sheet has a rippled or pleated appearance?

Pleated β sheet Signup and view all the answers

Which statement about the α Helix is NOT true?

It can have varying Φ and ψ angles based on side chain interactions. Signup and view all the answers

Who was one of the early discoverers of the α Helix structure?

Linus Pauling Signup and view all the answers

Study Notes

Levels of Protein Structure

Primary Structure: Linear sequence of amino acids in a protein.
Secondary Structure: Local spatial arrangement of polypeptide backbone; characterized by coils and folds.
Tertiary Structure: Three-dimensional configuration of an entire polypeptide, including side chains.
Quaternary Structure: Spatial arrangement of multiple polypeptide chains, also known as subunits.

Peptide Bonds and Backbone Structure

Peptide bonds connect amino acids, featuring ~40% double bond character due to resonance, resulting in rigid, planar structures.
Peptide groups predominantly assume trans conformation, keeping successive Cα atoms on opposite sides of the peptide bond.

Torsion Angles and Ramachandran Diagram

Backbone conformation described by torsion angles (Φ and ψ), both defined as 180° in fully extended conformation.
The Ramachandran diagram displays allowed conformations of polypeptides; blue regions indicate sterically allowed angles, while green denotes more crowded limits.

Regular Secondary Structures

Alpha Helix: Discovered by Linus Pauling, consists of 3.6 residues per turn with a favorable hydrogen-bonding pattern. Angles Φ = -57° and ψ = -47°, with a pitch of 5.4 Å.
Beta Sheets: Composed of extended polypeptide chains, featuring hydrogen bonding between neighboring strands. Divided into antiparallel (chains run in opposite directions) and parallel (chains run in the same direction).

Structural Features of Beta Sheets

Beta sheets exhibit a rippled or pleated appearance. Side chains extend perpendicularly to the sheet, with alternating R groups on opposite sides.
Each strand has a two-residue repeat distance of 7.0 Å.

Coiled Coil Structure

Alpha Keratin: Found in hair, nails, and skin, characterized by a coiled coil assembly due to the arrangement of nonpolar residues. The helices align to create a dimeric coiled coil structure.

Collagen Structure

Collagen: Most abundant vertebrate protein; strong fibers in connective tissues (bones, skin, blood vessels).
Composed of three polypeptide chains, with significant glycine content (~33%), as well as proline and hydroxyproline.
Collagen forms a triple helix structure, twisted to achieve a right-handed superhelical formation.

Vitamin C and Prolyl Hydroxylase

Proline residues in collagen are converted to hydroxyprolyl through a reaction requiring ascorbic acid (Vitamin C).
A deficiency in Vitamin C leads to scurvy, a disease affecting collagen stability.

Influence of Sequence on Secondary Structure

Amino acid sequence variations can distort ideal secondary structural conformations, resulting in occurrences like β bulges.
Research by Chou and Fasman reveals certain residues favor specific secondary structures while disrupting others, assisting in predicting protein secondary structures based on amino acid sequences.

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Description

Test your knowledge on the three-dimensional structure of proteins in this Chapter 6 quiz. Explore the primary, secondary, and tertiary structures of polypeptides, along with the concept of protein subunits. Perfect for students looking to deepen their understanding of protein biochemistry.