BCHS 3304 Exam 2

Local spatial alignment of amino acid backbone without regard to side chains is the _____ of proteins.

• Primary structure

• Secondary structure

• Tertiary structure

• Quaternary structure

• None of the above

Answer explanation

The secondary structure of proteins refers to local spatial arrangements of the amino acid backbone, such as alpha helices and beta sheets, without considering the side chains.

In right handed α-Helix, a hydrogen bond may be found between the C=O of the 5th residue and the N-H of the _____ residue.

• 7th

• 8th

• 9th

• 10th

• 11th

Answer explanation

In a right-handed α-helix, hydrogen bonds form between the C=O of one residue and the N-H of another. The 5th residue forms a bond with the N-H of the 9th residue, making 9th the correct answer.

A β-turn takes a minimum of _____ residues

• 3

• 4

• 5

• 6

• 7

Answer explanation

A β-turn requires a minimum of 4 residues to form the necessary hydrogen bonds and structural conformation, making 4 the correct answer.

The torsion angle between Cα and N on an amide plane is called the _____ angle.

• Δ

• μ

• Ф

• ψ

• ξ

Answer explanation

The torsion angle between Cα and N in an amide plane is referred to as the Ф (phi) angle. This angle is crucial in determining the conformation of proteins and peptides.

The Ф and ψ angle combination for right-handed α-helix is most likely____

• -57, -47

• -119, 113

• -139, 135

• -49, -26

• -51, 153

Answer explanation

The Ф and ψ angles for a right-handed α-helix are typically around -57° and -47°, respectively. This combination allows for the optimal hydrogen bonding and stability of the helical structure.

The Ф and ψ angle combination for antiparallel β sheet is most likely____

• -57, -47

• -119, 113

• -139, 135

• -49, -26

• -51, 153

Answer explanation

The Ф and ψ angles for antiparallel β sheets are typically around -139° and 135°, which corresponds to the correct answer choice. This configuration allows for optimal hydrogen bonding between strands.

In a protein, the most conformationally restricted amino acid is ______; the least conformationally restricted is ______.

• Trp, Gly

• Met, Cys

• Pro, Gly

• Ile, Ala

• Ala, Pro

Answer explanation

Proline (Pro) is the most conformationally restricted amino acid due to its cyclic structure, limiting its backbone flexibility. Glycine (Gly), with its small side chain, is the least restricted, allowing for greater conformational freedom.

Which of the following has (have) both a favorable hydrogen bonding pattern and Ф and ψ values that fall within the allowed Ramachandran conformational regions?

• α helix

• collagen helix

• β sheet

• all of the above

• none of the above

Answer explanation

All options (α helix, collagen helix, β sheet) exhibit favorable hydrogen bonding and have Ф and ψ values within the allowed Ramachandran regions, making 'all of the above' the correct choice.

Which one of these characteristics is not true for the α helix?

• There are 3.6 amino acids per turn.

• There is a requirement for glycine every third amino acid residue.

• A hydrogen bond forms between the carbonyl oxygen of the n th amino acid residue and the -NH group of the (n + 4) th amino acid residue.

• Proline is typically not found in the α helix.

• It is right-handed.

Answer explanation

The statement about glycine is incorrect; while glycine can be present, it is not a requirement for every third residue in the α helix. The other characteristics listed are true for the α helix.

Myosin and a-keratin have coiled coil structure, and the amino acid sequences of them often show 7-residue pseudo repeats. In the following section of the coiled coil structure, residues a, d, a’, d’ are often _____

• hydrophobic

• hydrophilic

• positively charged

• negatively charged

Answer explanation

In coiled coil structures like myosin and a-keratin, the residues at positions a and d are typically hydrophobic. This arrangement helps stabilize the coiled coil by promoting interactions between the hydrophobic regions.