Biochemistry : Secondary Structure

Study concepts, example questions & explanations for Biochemistry

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Example Questions

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Example Question #64 : Biochemistry

An alpha-helix is formed by hydrogen bonding between the hydrogen of an amine group and the backbone carbonyl group how many amino acids upstream of it?

Possible Answers:

Five

Two

Four

Six

Three

Correct answer:

Four

Explanation:

Alpha-helices are formed by hydrogen bonding involving an alpha carbon-bound amine group's hydrogen and the carbonyl group attached to the amino acid four amino acids upstream.

Example Question #65 : Biochemistry

Which of the following best describes a characteristic of a protein motif?

Possible Answers:

A unique arrangement made up of secondary structures found only in a single protein

A family of proteins with similar functions

A commonly occurring arrangement made up of multiple secondary structures

A unique arrangement made up of tertiary structures found only in a single protein

A commonly occurring arrangement made up of tertiary structures

Correct answer:

A commonly occurring arrangement made up of multiple secondary structures

Explanation:

A protein motif (aka supersecondary structure) is a defined arrangement of secondary structures within a protein. It is commonly occurring enough to have an identified structure. An example would be the beta-alpha-beta loop. While the arrangement is made up of secondary structure, the overall motif itself can be considered supersecondary or possibly even tertiary, though its components are secondary structures. Motif's do not necessarily have a defined function across different proteins. Protein domains on the other hand, do.

Example Question #66 : Biochemistry

What type of bonds are the "backbone" of secondary protein structure?

Possible Answers:

Amino acid bonds

Hydrogen bonds

Van der Waals interactions

Peptide bonds

Amide bonds

Correct answer:

Hydrogen bonds

Explanation:

Hydrogen bonds stabilize interactions among the amide and carboxyl groups in the main chain of the polypeptide. These interactions may induce the formation of alpha-helices and/or beta-pleated sheets.

Example Question #11 : Protein Folding

Which of the following amino acids is least likely to be found in the middle of an alpha helix?

Possible Answers:

Proline

Methionine

Glutamic acid

Serine

Correct answer:

Proline

Explanation:

Proline is bound to two alkyl groups thus giving it a planar configuration, giving the nitrogen only the ability to accept hydrogen bonds not donate them. While this is not a problem at the beginning of an alpha helix this can disturb the bonds if place further down the chain. Thus proline is often referred to as the "alpha helix buster."

Example Question #12 : Protein Folding

The stabilization of secondary structure in polypeptides is conferred by which of the following?

Possible Answers:

Metal cations

The R-groups of the amino acids

Disulfide bonds

The amino acid backbones

The phosphate groups

Correct answer:

The amino acid backbones

Explanation:

Alpha helices and beta sheet, the dominant secondary structural motifs in polypeptides are formed by hydrogen bonds between the carbonyl and amino groups of the amino acid backbone.

Example Question #69 : Biochemistry

Why are antiparallel beta sheets more stable than parallel beta sheets? 

Possible Answers:

The antiparallel sheets are composed of more stable amino acids

The hydrogen bonding angle is optimized by antiparallel sheets

The hydrogen bond angle is 150 degrees

There are more covalent interactions between its amino acids

There are more hydrophobic interactions between its amino acids

Correct answer:

The hydrogen bonding angle is optimized by antiparallel sheets

Explanation:

In an antiparallel beta sheet, the hydrogen bonding angle is 180 degrees and optimal; this is the most stable angle. In parallel sheets, it is a less stable 150 degrees. Whether a sheet is parallel or antiparallel does not tell us anything about what amino acids it is composed of, so each of the other answers is incorrect.

Example Question #70 : Biochemistry

In a sequence of amino acids within an alpha helix, between which amino acids in the sequence does hydrogen bonding occur (i.e. every how many amino acids)?

Possible Answers:

1 and 3, so every 3 amino acids

1 and 5, so every 5 amino acids

1 and 4, so every 4 amino acids

1 and 6, so every 4 amino acids

1 and 6, so every 6 amino acids

Correct answer:

1 and 4, so every 4 amino acids

Explanation:

In an alpha helix, hydrogen bonding occurs every four amino acids, starting from the 1st binding to the 4th in the sequence; the 2nd amino acid binds to the 6th, the 3rd to the 7th, and so on. 

Example Question #53 : Macromolecule Structures And Functions

With respect to proteins, alpha structures are __________ and beta structures are __________.

Possible Answers:

L . . . D

primary . . . secondary

parallel . . . antiparallel

left . . . right

helices . . . pleated sheets

Correct answer:

helices . . . pleated sheets

Explanation:

Alpha helices and beta pleated sheets are two forms of secondary structure. Alpha helices can be either right handed (counterclockwise) or left handed (clockwise). Beta pleated sheets can be either parallel (amino and carbonyl groups do not line up) or anti parallel (amino and carbonyl groups line up). 

Example Question #54 : Macromolecule Structures And Functions

Which of the following amino acids is found in beta turns?

Possible Answers:

Histidine 

Cysteine

Glutamine

Methionine

Proline

Correct answer:

Proline

Explanation:

Glycine and proline are the two amino acids that are found in beta turns. These 180 degree turns are composed of four total amino acids. 

Example Question #55 : Macromolecule Structures And Functions

A(n) __________ is formed by antiparallel beta sheets, where the first and last strands are connected via hydrogen bonding.

Possible Answers:

Rossman fold

beta barrel

helix-turn-helix

alpha domain

Correct answer:

beta barrel

Explanation:

All the answer choices are different examples of protein supersecondary structures. Beta barrels are commonly found in transmembrane porin proteins.

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