Biochemistry : Secondary Structure
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Example Questions
Example Question #1 : Protein Folding
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?
Two
Three
Four
Five
Six
Four
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 #2 : Secondary Structure
Which of the following best describes a characteristic of a protein motif?
A commonly occurring arrangement made up of multiple secondary structures
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 tertiary structures
A unique arrangement made up of tertiary structures found only in a single protein
A commonly occurring arrangement made up of multiple secondary structures
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 #1 : Secondary Structure
What type of bonds are the "backbone" of secondary protein structure?
Amide bonds
Amino acid bonds
Peptide bonds
Van der Waals interactions
Hydrogen bonds
Hydrogen bonds
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 #4 : Secondary Structure
Which of the following amino acids is least likely to be found in the middle of an alpha helix?
Methionine
Serine
Glutamic acid
Proline
Proline
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 #2 : Secondary Structure
The stabilization of secondary structure in polypeptides is conferred by which of the following?
Metal cations
Disulfide bonds
The R-groups of the amino acids
The amino acid backbones
The phosphate groups
The amino acid backbones
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 #11 : Protein Folding
Why are antiparallel beta sheets more stable than parallel beta sheets?
The antiparallel sheets are composed of more stable amino acids
There are more hydrophobic interactions between its amino acids
There are more covalent interactions between its amino acids
The hydrogen bonding angle is optimized by antiparallel sheets
The hydrogen bond angle is 150 degrees
The hydrogen bonding angle is optimized by antiparallel sheets
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 #51 : Protein Structure And Functions
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)?
1 and 5, so every 5 amino acids
1 and 6, so every 4 amino acids
1 and 6, so every 6 amino acids
1 and 4, so every 4 amino acids
1 and 3, so every 3 amino acids
1 and 4, so every 4 amino acids
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 #52 : Protein Structure And Functions
With respect to proteins, alpha structures are __________ and beta structures are __________.
helices . . . pleated sheets
left . . . right
L . . . D
parallel . . . antiparallel
primary . . . secondary
helices . . . pleated sheets
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 #1 : Secondary Structure
Which of the following amino acids is found in beta turns?
Histidine
Cysteine
Methionine
Glutamine
Proline
Proline
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 #10 : Secondary Structure
A(n) __________ is formed by antiparallel beta sheets, where the first and last strands are connected via hydrogen bonding.
beta barrel
alpha domain
Rossman fold
helix-turn-helix
beta barrel
All the answer choices are different examples of protein supersecondary structures. Beta barrels are commonly found in transmembrane porin proteins.
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