Biochemistry : Secondary Structure

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #11 : Secondary Structure

What is the only level of protein structure that does not involve covalent bonding?

Possible Answers:

Primary structure

Secondary structure

Quaternary structure

Tertiary structure

Correct answer:

Secondary structure

Explanation:

Covalent bonding is when two nonmetals share electrons in order to form a bond. This type of bonding can be observed in the primary (peptide bonds), tertiary (disulfide bonds), and quaternary (disulfide bonds) levels of protein structure. The secondary structure of proteins only uses hydrogen bonding as the folding force.

Example Question #61 : Protein Structure And Functions

What is the hydrogen bonding pattern within an alpha helix?

Possible Answers:

Lone pair on C=O of residue i to hydrogen on N-H of residue i+4.

Hydrogen of N-H of residue i to hydrogen on N-H of residue i+4.

Lone pair on C=O of residue i to hydrogen on N-H of residue i+3.

Hydrogen of N-H of residue i to hydrogen on N-H of residue i+3.

Lone pair on C=O of residue i to hydrogen on N-H of residue i+2.

Correct answer:

Lone pair on C=O of residue i to hydrogen on N-H of residue i+4.

Explanation:

Within an alpha helix, the structure is stabilized by hydrogen bonding between the lone pair on a carbonyl oxygen to a hydrogen of an amino backbone group. Remember, hydrogen bonding must occur between a lone pair of an electronegative atom and a hydrogen connected to an electronegative atom. Two of the answer choices suggest that the hydrogen bonding occurs between two hydrogen atoms, which is not possible.

Finally, the alpha helix contains 3.6 residues per turn. As such, the correct answer is "Lone pair on C=O of residue i to hydrogen on N-H of residue i+4."

Example Question #11 : Secondary Structure

Which of the following choices correctly describes the relative orientation of side chains within an alpha helix?

Possible Answers:

None of these

The side chains point "in" and "back" relative to the turns of the helix.

The side chains point "in" and "forward" relative to the turns of the helix.

The side chains point "out" and "forward" relative to the turns of the helix.

The side chains point "out" and "back" relative to the turns of the helix.

Correct answer:

The side chains point "out" and "back" relative to the turns of the helix.

Explanation:

The side chains of the amino acid residues within an alpha helix point "out" and "back" relative to the turns of the helix. Despite differing polarity's of side chains, this pattern holds true. This first reason this pattern is important is in order to minimize steric hindrance. Finally, this pattern allows for a maximization of hydrogen bonding between the side chains and the backbone amides.

Example Question #11 : Secondary Structure

Which of the following best describes how the large and branched side chains are organized within a beta-sheet?

Possible Answers:

They organize parallel to each other in consecutive polypeptide chains.

They are kept far apart from each other.

None of these

They alternate every other residue.

They are kept near each other.

Correct answer:

They are kept far apart from each other.

Explanation:

Large side chains have increased Van der Waals interactions repelling each other, which is unfavorable. To minimize this steric clash, these residues must be kept far apart, and "They are kept far apart from each other." is the correct answer.

Large residues being near each other in a beta sheet would be very unfavorable. If these large residues alternated in a "every other" manner, they would still be relatively close to each other. Finally, if these residues were kept parallel to each other, they would be on different. But these chains would still be in close proximity to each other, and unfavorable interactions would occur.

Example Question #61 : Macromolecule Structures And Functions

What is percent composition of alpha helix, beta sheet, and irregular structure within a typical protein?

Possible Answers:

Alpa helix: 25%

Beta sheet: 50%

Irregular structure: 25%

Alpa helix: 33%

Beta sheet: 33%

Irregular structure: 33%

Alpa helix: 50%

Beta sheet: 25%

Irregular structure: 25%

Alpa helix: 49.5%

Beta sheet: 49.5%

Irregular structure: 1%

Alpa helix: 25%

Beta sheet: 25%

Irregular structure: 50%

Correct answer:

Alpa helix: 33%

Beta sheet: 33%

Irregular structure: 33%

Explanation:

The two most common secondary structures within a protein are alpha helixes, and beta-sheets. However, remember that there are multiple types of alpha helixes and beta-sheets, and all have slightly different properties. Overall, alpha helixes and beta sheets are in approximately equal amounts.

Anything not regarded as an alpha helix or a beta sheet is typically referred to as a "irregular structure". This can include random coilcoil structures, Beta-hairpin turns, in addition to a seemingly infinite number of unnamed structures. Overall, there is as much irregular structure as beta sheet and alpha helix within a protein, and the correct answer is 33% for all three.

Example Question #12 : Secondary Structure

Referring to the secondary structure of proteins, proline is necessary for which of the following?

Possible Answers:

For the beta bend of antiparallel beta sheets

For the hydrogen bonding, stabilizing antiparallel beta sheet

For hydrogen bonding interactions in alpha helices

For proper polypeptide chain subunit interactions

The beta bend needed for parallel beta sheet secondary structures 

Correct answer:

The beta bend needed for parallel beta sheet secondary structures 

Explanation:

Proline is necessary for the beta bend (along with a glycine). This beta bend is needed for the polypeptide to turn 180 degrees and come back to form a parallel beta sheet. Proline disrupts the hydrogen bonding of alpha helices, and is not needed for antiparallel beta sheets, since there is no beta turn required. 

Example Question #13 : Secondary Structure

How many amino acids are per turn in an alpha helix secondary structure?

Possible Answers:

1.8

0.4

3.6

7.2

10.4

Correct answer:

3.6

Explanation:

Polypeptide chains in proteins fold to attain a more compact secondary structure. The two forms of secondary structures are alpha helices and beta sheets. Amino acids that are separated by three or four residues in a polypeptide chain within a secondary alpha helix structure are spatially close and can form hydrogen bonds. 

Example Question #11 : Secondary Structure

The alpha helix is a type of secondary protein conformation. Which of the following amino acids can interfere the most with the formation of an alpha helix?

Possible Answers:

Threonine

Histidine

Proline

Arginine

Lysine

Correct answer:

Proline

Explanation:

Secondary structures in proteins consist of alpha helices and beta sheets. Proline has an additional amino group that interferes with the formation of an alpha helix. Amino acids such as lysine and arginine can form ionic bonds due to their charges. Other amino acids, like isoleucine, tryptophan, or valine disrupt the helix due to big side chains. However, amongst the amino acid mentioned in the answers, proline has the most disruptive effect.

Example Question #11 : Secondary Structure

Which of the following are true of beta bends in protein structures?

I. Beta bends are secondary protein structures.

II. Beta bends consist of sequences of four amino acids.

III. In beta bends amino acids proline and glycine are common.

IV. Hydrogen and ionic bonds stabilize beta bends.

Possible Answers:

I, II, III, and IV

I and IV

I, II, and IV

II and III

I, II, and III

Correct answer:

I, II, III, and IV

Explanation:

Beta bends are part of secondary protein structures. They serve as a link between alpha helices and beta sheets. Beta bends are composed of proline and glycine, amino acids that usually are not found in alpha helices.

Example Question #12 : Secondary Structure

Which of the following statements are true about motifs in a protein structure?

I. The most common motif is beta-alpha-beta, when an alpha helix connects two parallel strands of a beta sheet.

II. Motifs are usually composed of more than one form of secondary structure.

III. Motifs are supersecondary structures.

IV. Motifs are combinations of alpha helices and beta sheets.

Possible Answers:

I, II, III, and IV 

III and IV

I, II, and III

III only

I and II

Correct answer:

I, II, III, and IV 

Explanation:

Motifs are supersecondary protein structures. Motifs are combinations of secondary structures such as alpha helices and beta sheets.The beta-alpha-beta and the beta hairpin motifs are some of the most common.

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