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Questions and Answers
What defines the chemical and structural properties of amino acids?
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?
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?
How many different amino acids are typically found in polypeptides?
- 15
- 10
- 25
- 20 (correct)
What type of bond connects the α-carboxylate of one amino acid to the α-amino group of another amino acid?
What type of bond connects the α-carboxylate of one amino acid to the α-amino group of another amino acid?
What is lost when NH3+ and COO- groups form a peptide bond?
What is lost when NH3+ and COO- groups form a peptide bond?
Which end of a polypeptide has the free positively charged amino terminus?
Which end of a polypeptide has the free positively charged amino terminus?
What do you call the repeating part of a polypeptide?
What do you call the repeating part of a polypeptide?
'Consists of a central α-carbon with attached amino group, carboxyl group and a hydrogen atom.' describes the ______ structure of an amino acid.
'Consists of a central α-carbon with attached amino group, carboxyl group and a hydrogen atom.' describes the ______ structure of an amino acid.
Which amino acids have unique Ramachandran plots?
Which amino acids have unique Ramachandran plots?
For which amino acid is the motion frozen in a pentapeptide except for the central residue?
For which amino acid is the motion frozen in a pentapeptide except for the central residue?
In an α helix, what is the linear distance per residue?
In an α helix, what is the linear distance per residue?
Which type of bond stabilizes local structural elements in secondary structures of proteins?
Which type of bond stabilizes local structural elements in secondary structures of proteins?
What pattern do the CO and NH groups form hydrogen bonds in an α helix?
What pattern do the CO and NH groups form hydrogen bonds in an α helix?
Which amino acid residues have all backbone CO and NH groups involved in hydrogen bonding in an α helix?
Which amino acid residues have all backbone CO and NH groups involved in hydrogen bonding in an α helix?
What is the structure of essentially all α helices found in proteins?
What is the structure of essentially all α helices found in proteins?
Which bond leads to changes in the φ value in a Ramachandran plot?
Which bond leads to changes in the φ value in a Ramachandran plot?
What are the backbone amide to carbonyl oxygen hydrogen bonds stabilized by in proteins?
What are the backbone amide to carbonyl oxygen hydrogen bonds stabilized by in proteins?
Why is glycine rarely found in α helices?
Why is glycine rarely found in α helices?
Which structural element can accommodate bulkier amino acid side chains?
Which structural element can accommodate bulkier amino acid side chains?
Why is proline not suitable for α helices?
Why is proline not suitable for α helices?
Which type of β-sheet is stabilized by hydrogen bonds between CO and NH groups of amino acids on adjacent strands?
Which type of β-sheet is stabilized by hydrogen bonds between CO and NH groups of amino acids on adjacent strands?
What kind of change in the polypeptide chain direction characterizes an abrupt (tight) reverse turn?
What kind of change in the polypeptide chain direction characterizes an abrupt (tight) reverse turn?
What contributes to the charge and hydrophobicity of a peptide structure?
What contributes to the charge and hydrophobicity of a peptide structure?
In which type of loop are i to i+3 hydrogen bonds commonly found?
In which type of loop are i to i+3 hydrogen bonds commonly found?
Why is there no free rotation about the peptide bond?
Why is there no free rotation about the peptide bond?
What is the distance between adjacent residues in a fully extended β-strand?
What is the distance between adjacent residues in a fully extended β-strand?
What type of secondary structure has side chains of adjacent amino acids pointing in opposite directions?
What type of secondary structure has side chains of adjacent amino acids pointing in opposite directions?
Which atoms lie in a plane due to the planarity of the peptide bond?
Which atoms lie in a plane due to the planarity of the peptide bond?
What stabilizes a parallel β-sheet structure?
What stabilizes a parallel β-sheet structure?
In what configuration are virtually all peptide bonds found in proteins?
In what configuration are virtually all peptide bonds found in proteins?
What distinguishes a mixed β-sheet from other structural elements?
What distinguishes a mixed β-sheet from other structural elements?
Which amino acid can have two different configurations for its peptide bond?
Which amino acid can have two different configurations for its peptide bond?
What determines the path of a polypeptide chain?
What determines the path of a polypeptide chain?
What does the Ramachandran plot illustrate?
What does the Ramachandran plot illustrate?
What is one critical property for consideration of higher-order protein structure as mentioned in the text?
What is one critical property for consideration of higher-order protein structure as mentioned in the text?
What attribute distinguishes proline from other amino acids regarding its peptide bond?
What attribute distinguishes proline from other amino acids regarding its peptide bond?
Flashcards
Amino acid properties
Amino acid properties
Determined by their unique side chains and central α-carbon atom.
Peptide bond
Peptide bond
Connects the α-carboxylate of one amino acid to the α-amino group of another.
Polypeptide ends and backbone
Polypeptide ends and backbone
Positively charged amino terminus at one end. Backbone is the repeating part.
Amino acids with unique Ramachandran plots
Amino acids with unique Ramachandran plots
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α-Helix rise per residue
α-Helix rise per residue
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Hydrogen bonds in protein structure
Hydrogen bonds in protein structure
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Hydrogen bond pattern in alpha helix
Hydrogen bond pattern in alpha helix
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Chirality of α helices
Chirality of α helices
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Ramachandran plot change
Ramachandran plot change
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Why glycine is rare in α helices
Why glycine is rare in α helices
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β-Pleated sheet advantage
β-Pleated sheet advantage
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Why proline is not in α helices
Why proline is not in α helices
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Antiparallel β-sheet stabilization
Antiparallel β-sheet stabilization
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β-turn
β-turn
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Source of peptide charge/hydrophobicity
Source of peptide charge/hydrophobicity
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Hydrogen bonds in β-hairpin loops
Hydrogen bonds in β-hairpin loops
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Rotation of peptides
Rotation of peptides
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Residue distance in β-strand
Residue distance in β-strand
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Side chain orientation in β-strand
Side chain orientation in β-strand
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Peptide bond planarity
Peptide bond planarity
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Parallel β-sheet stabilization
Parallel β-sheet stabilization
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Ramachandran plot
Ramachandran plot
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Critical property for higher-order structure
Critical property for higher-order structure
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Proline's unique peptide bond
Proline's unique peptide bond
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Determination of path of polypeptide chain
Determination of path of polypeptide chain
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What defines amino acids?
What defines amino acids?
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Alpha carbon attachments
Alpha carbon attachments
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Naturally occurring amino acids
Naturally occurring amino acids
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Amino acids in polypeptides
Amino acids in polypeptides
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Peptide bond formations
Peptide bond formations
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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.
