Protein Structure and Peptide Bonds

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Questions and Answers

Which of the following statements about peptide bonds is correct?

Peptide bonds are always found in the trans conformation. (correct)

Peptide bonds have resonance structures that contribute to their stability. (correct)

Peptide bonds are completely flexible and rotate freely.

Cis configurations of peptide bonds are more common in proteins.

What amino acids are known to disrupt helical structures within proteins?

Cysteine and Alanine

Aspartic acid and Glutamic acid

Serine and Threonine

Glycine and Proline (correct)

What characteristic is typical of a β-turn in protein structure?

It is stabilized solely by covalent bonds.

It always involves hydrophobic interactions.

It forms a continuous helical structure.

It typically involves four amino acids. (correct)

Which non-covalent interaction is primarily responsible for the stability of secondary structures like α-helices and β-sheets?

Hydrogen bonds Signup and view all the answers

What information does a Ramachandran diagram typically convey?

It indicates allowable angles for phi and psi in protein backbones. Signup and view all the answers

What type of interaction is primarily responsible for the stabilization of α-helices?

Hydrogen bonds Signup and view all the answers

Which type of β sheet conformation has greater stability?

Antiparallel Signup and view all the answers

What is the diameter range of the outer structure of an α-helix with side chains?

10 – 12 Å Signup and view all the answers

Which of the following statements about β strands is true?

They are an extended conformation of polypeptides. Signup and view all the answers

What determines whether a polypeptide sequence can adopt a stable α-helix or β sheet structure?

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

What characterizes the primary structure of a protein?

Sequence of amino acids in a protein Signup and view all the answers

Which of the following interactions contribute to the tertiary structure of a protein?

Ionic interactions and hydrogen bonds Signup and view all the answers

Why do peptide bonds exhibit partial double bond character?

Due to resonance Signup and view all the answers

Which configuration of the peptide bond is more stable?

Trans configuration Signup and view all the answers

What primarily drives the folding of proteins into their functional structures?

Maximizing favorable non-covalent interactions Signup and view all the answers

What is the impact of resonance on peptide bonds?

It makes the bond rigid and nearly planar Signup and view all the answers

How are secondary structures defined in proteins?

Local folding of the backbone atoms Signup and view all the answers

What is the primary reason less than 1% of peptide bonds involving Pro are in the trans configuration?

Proline has a unique side chain structure Signup and view all the answers

Which amino acid is considered a strong helix former?

Alanine Signup and view all the answers

What is the primary reason proline is considered a helix breaker?

It cannot donate a hydrogen bond in an alpha helix. Signup and view all the answers

What characteristic of glycine limits its incorporation into helices?

It has large conformational flexibility. Signup and view all the answers

What defines a β turn in a polypeptide chain?

A 180-degree turn across four amino acids. Signup and view all the answers

In Type I β turns, which amino acid is often found at position AA2 to introduce a kink?

Proline Signup and view all the answers

What is the main difference between Type I and Type II β turns?

The orientation of the carbonyl oxygen of AA2 differs. Signup and view all the answers

Which amino acid is often found at position AA3 in Type II β turns due to steric hindrance?

Glycine Signup and view all the answers

Which of these structures contributes to the tertiary structure of proteins?

Alpha helices, beta strands, and turns Signup and view all the answers

What is the main exception to the cis and trans orientation of peptide bonds?

Proline Signup and view all the answers

Which angles are associated with the backbone of a polypeptide chain?

Phi (ϕ) and Psi (ψ) Signup and view all the answers

What do favorable phi (ϕ) angles minimize?

Repulsion between R-group and C=O Signup and view all the answers

Which feature of the Ramachandran plot indicates favorable or permitted phi and psi angles?

Blue-shaded regions Signup and view all the answers

What characterizes the alpha helix structure?

Right-handed and 3.6 residues per turn Signup and view all the answers

What does the helical wheel represent in alpha helices?

The 3D arrangement of side chains Signup and view all the answers

Which of the following secondary structures is characterized by a left-handed twist?

Collagen helix Signup and view all the answers

Which of the following is true regarding the peptide bond in proteins?

It is rigid and planar. Signup and view all the answers

Which dihedral angle is associated with the rotation around the Cα-N bond?

Phi (ϕ) Signup and view all the answers

Which secondary structure is represented with a characteristic hydrogen bonding pattern and is stable due to these interactions?

Alpha helix Signup and view all the answers

Study Notes

Protein Structure Levels

Primary Structure: Amino acid sequence of a polypeptide chain
Secondary Structure: Local folding of the polypeptide backbone, forming distinct shapes like alpha helices and beta sheets
Tertiary Structure: 3D arrangement of an entire polypeptide chain, including the interactions between side chains
Quaternary Structure: The arrangement of multiple polypeptide chains, forming a protein complex

Peptide Bond Properties

Peptide bonds have partial double bond character due to resonance, making them rigid and nearly planar
The trans configuration of the peptide bond is more stable than cis, due to reduced steric clashes between side chains
Proline is an exception, with a significant proportion of its peptide bonds in the cis configuration

Dihedral Angles

Phi (φ): Rotation around the N-Cα bond
Psi (ψ): Rotation around the Cα-C bond

Ramachandran Plot

Depicts the allowed combinations of phi and psi angles in a polypeptide chain
Favourable angles are determined by steric clashes and hydrogen bonding interactions
Allows prediction of secondary structure based on the distribution of phi and psi angles within the plot

Alpha Helix

Right-handed helical structure with 3.6 amino acids per turn
Stabilized by hydrogen bonds between the carbonyl oxygen of residue n and the amide hydrogen of residue n+4
Side chains point outward and downward from the helix

Beta Sheets

Formed by hydrogen bonding between extended polypeptide segments called beta strands
Can be parallel (strands run in the same direction) or antiparallel (strands run in opposite directions)
Antiparallel beta sheets are more stable than parallel due to optimal hydrogen bonding geometry

Turns and Loops

Connect and stabilize various secondary structures
Beta turns are the simplest, comprising four amino acids and causing a 180-degree turn in polypeptide direction
Type I and Type II beta turns differ in the orientation of the carbonyl group of the second amino acid in the turn
Type II turns often have glycine at position 3 due to reduced steric clashing

Secondary Structure Propensity

Not all amino acids are equally likely to form alpha helices or beta sheets
Small hydrophobic residues like alanine favor helix formation
Proline disrupts both helices and beta sheets due to its rigid cyclic structure
Glycine is also disfavored in helices because its high flexibility makes incorporation entropically unfavorable

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Description

This quiz explores the four levels of protein structure, including primary, secondary, tertiary, and quaternary formations. Additionally, it covers peptide bond properties, dihedral angles, and the significance of the Ramachandran plot in understanding protein conformation. Test your understanding of these essential concepts in protein chemistry!