Ramachandran Plot MCQ: Amino Acids Quiz and Flashcards

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Questions and Answers

What defines the chemical and structural properties of amino acids?

Amino group

Carboxyl group

Hydrogen atom

R-group (side chain) (correct)

Which stereochemistry configuration are most naturally occurring L amino acids found in?

S-configuration (correct)

R-configuration

No specific configuration

Mixture of R and S configurations

How many different amino acids are typically found in polypeptides?

20 (correct)

What type of bond connects the α-carboxylate of one amino acid to the α-amino group of another amino acid?

Peptide bond Signup and view all the answers

What is lost when NH3+ and COO- groups form a peptide bond?

Charges on NH3+ and COO- groups Signup and view all the answers

Which end of a polypeptide has the free positively charged amino terminus?

N-terminus Signup and view all the answers

What do you call the repeating part of a polypeptide?

Main chain or backbone Signup and view all the answers

'Consists of a central α-carbon with attached amino group, carboxyl group and a hydrogen atom.' describes the ______ structure of an amino acid.

Primary Signup and view all the answers

Which amino acids have unique Ramachandran plots?

Glycine and Proline Signup and view all the answers

For which amino acid is the motion frozen in a pentapeptide except for the central residue?

Alanine Signup and view all the answers

In an α helix, what is the linear distance per residue?

1.5 Å Signup and view all the answers

Which type of bond stabilizes local structural elements in secondary structures of proteins?

Hydrogen bonds Signup and view all the answers

What pattern do the CO and NH groups form hydrogen bonds in an α helix?

i to i+4 pattern Signup and view all the answers

Which amino acid residues have all backbone CO and NH groups involved in hydrogen bonding in an α helix?

Only those near the ends Signup and view all the answers

What is the structure of essentially all α helices found in proteins?

Right-handed Signup and view all the answers

Which bond leads to changes in the φ value in a Ramachandran plot?

$N-C_α$ bond Signup and view all the answers

What are the backbone amide to carbonyl oxygen hydrogen bonds stabilized by in proteins?

$CO$ groups to $NH_2$ groups Signup and view all the answers

Why is glycine rarely found in α helices?

It is entropically unfavorable to constrain in an α helix. Signup and view all the answers

Which structural element can accommodate bulkier amino acid side chains?

β-strands Signup and view all the answers

Why is proline not suitable for α helices?

It lacks an NH group to serve as a hydrogen bond donor. Signup and view all the answers

Which type of β-sheet is stabilized by hydrogen bonds between CO and NH groups of amino acids on adjacent strands?

Antiparallel β-sheet Signup and view all the answers

What kind of change in the polypeptide chain direction characterizes an abrupt (tight) reverse turn?

180° turn Signup and view all the answers

What contributes to the charge and hydrophobicity of a peptide structure?

Free R-groups Signup and view all the answers

In which type of loop are i to i+3 hydrogen bonds commonly found?

Reverse Turn loops Signup and view all the answers

Why is there no free rotation about the peptide bond?

Due to resonance stabilization Signup and view all the answers

What is the distance between adjacent residues in a fully extended β-strand?

3.5 Å Signup and view all the answers

What type of secondary structure has side chains of adjacent amino acids pointing in opposite directions?

β-strand Signup and view all the answers

Which atoms lie in a plane due to the planarity of the peptide bond?

Cα, C, O, N, H, and Cα Signup and view all the answers

What stabilizes a parallel β-sheet structure?

Inter-strand amide N to carbonyl O hydrogen bonds Signup and view all the answers

In what configuration are virtually all peptide bonds found in proteins?

Trans Signup and view all the answers

What distinguishes a mixed β-sheet from other structural elements?

It consists of multiple β-strands. Signup and view all the answers

Which amino acid can have two different configurations for its peptide bond?

Proline Signup and view all the answers

What determines the path of a polypeptide chain?

$\phi$ and $\psi$ angles Signup and view all the answers

What does the Ramachandran plot illustrate?

$\phi$ and $\psi$ angle combinations that are allowed and favorable Signup and view all the answers

What is one critical property for consideration of higher-order protein structure as mentioned in the text?

Planarity of peptide bonds. Signup and view all the answers

What attribute distinguishes proline from other amino acids regarding its peptide bond?

It can be found in either orientation when following another amino acid. Signup and view all the answers

Study Notes

Amino Acid Structure and Properties

The chemical and structural properties of amino acids are defined by their unique side chains and central α-carbon atom.
Most naturally occurring L amino acids are found in the S-stereochemistry configuration.

Polypeptide Composition and Bonds

Typically, 20 different amino acids are found in polypeptides.
A peptide bond connects the α-carboxylate of one amino acid to the α-amino group of another amino acid.
The formation of a peptide bond results in the loss of NH3+ and COO- groups.

Polypeptide Structure and Ends

The free positively charged amino terminus is located at the N-terminus of a polypeptide.
The repeating part of a polypeptide is called the backbone.
The central α-carbon atom of an amino acid has attached amino, carboxyl, and hydrogen groups.

Unique Amino Acid Properties

Glycine and proline have unique Ramachandran plots.
In a pentapeptide, the motion of all residues is frozen except for the central residue, except for glycine.

α-Helix Structure

The linear distance per residue in an α helix is approximately 0.15 nm.
Hydrogen bonds between CO and NH groups stabilize local structural elements in secondary structures of proteins.
In an α helix, the CO and NH groups form hydrogen bonds in a clockwise pattern.
All backbone CO and NH groups of alanine, leucine, and arginine residues are involved in hydrogen bonding in an α helix.
Essentially all α helices found in proteins have a right-handed structure.
The φ value in a Ramachandran plot can change due to the peptide bond.
Backbone amide to carbonyl oxygen hydrogen bonds are stabilized by the planarity of the peptide bond in proteins.

Other Secondary Structures

Glycine is rarely found in α helices due to its small size and lack of steric hindrance.
The β-pleated sheet structure can accommodate bulkier amino acid side chains.
Proline is not suitable for α helices due to its rigid, non-planar structure.
Antiparallel β-sheets are stabilized by hydrogen bonds between CO and NH groups of amino acids on adjacent strands.
An abrupt (tight) reverse turn in the polypeptide chain direction characterizes a β-turn.

Polypeptide Chain Properties

The charge and hydrophobicity of a peptide structure are contributed by the amino acid side chains.
i to i+3 hydrogen bonds are commonly found in β-hairpin loops.
There is no free rotation about the peptide bond due to its planarity.
The distance between adjacent residues in a fully extended β-strand is approximately 0.35 nm.
In a β-strand, the side chains of adjacent amino acids point in opposite directions.
The peptide bond is planar, with the atoms lying in a plane.
Parallel β-sheet structures are stabilized by hydrogen bonds between CO and NH groups of amino acids on adjacent strands.

Ramachandran Plot and Higher-Order Structure

The Ramachandran plot illustrates the possible conformations of a polypeptide chain.
The critical property for consideration of higher-order protein structure is the path of a polypeptide chain.
Proline is distinguished from other amino acids by its ability to have two different configurations for its peptide bond.
The attribute that distinguishes proline from other amino acids regarding its peptide bond is the lack of a hydrogen atom on its α-carbon atom.
The path of a polypeptide chain is determined by the amino acid sequence and the interactions between amino acid side chains.

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Description

Test your knowledge on Ramachandran plots and amino acids, including the unique plots for glycine and proline, as well as the rotations about N-Cα and Cα-C bonds for alanine residues in pentapeptides. Explore how peptide bonds affect the conformation of proteins.

Ramachandran Plots and Amino Acids Quiz

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