bioc nucleic acids lec 2

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Questions and Answers

What two dihedral angles are essential for describing the backbone conformation of a protein?

Omega and Delta

Gamma and Sigma

Alpha and Beta

Phi and Psi (correct)

Which of the following areas on a Ramachandran plot indicates minimal strain and van der Waals clashing?

Red areas

Green areas (correct)

Blue areas

Yellow areas

What is the relationship between positive phi values and backbone conformations?

They promote H-bonding interactions.

They are largely disallowed. (correct)

They enhance amino acid stability.

They are commonly found in proteins.

How do observed conformations in proteins typically compare to allowed areas in Ramachandran plots?

They are a compromise between stability and strain. Signup and view all the answers

What does the dihedral angle phi (φ) measure?

The angle between carbonyl carbon groups Signup and view all the answers

What major protein secondary structures are most residues involved in forming?

α-helices and β-strands Signup and view all the answers

What describes the dihedral angle defined as omega (Ω) in protein structure?

Angle between C of the previous residue and nitrogen of this residue Signup and view all the answers

Which statement about the stability of peptide bonds is accurate?

Trans peptide bonds are more stable than cis by around 20 kJ/mol Signup and view all the answers

What is the average ratio of amino acids that adopt a cis configuration when not followed by proline?

1 in 3000 Signup and view all the answers

What geometric arrangement is preferred for the omega angle in peptide bonds?

180° Signup and view all the answers

Why are cis peptide bonds much less stable than trans peptide bonds, except when proline is involved?

Cis bonds create steric clashes with side chains Signup and view all the answers

What role does proline play in peptide bond configuration?

Proline more readily adopts cis configuration Signup and view all the answers

What factor primarily dictates the conformation of protein backbones?

The specific angles defined by bonds connecting residues Signup and view all the answers

What is the primary characteristic of proline that limits its flexibility compared to other amino acids?

The presence of an imine ring Signup and view all the answers

What defines the conformational flexibility of glycine among amino acids?

It has no sidechain and lacks steric hindrance Signup and view all the answers

What is the relationship between the φ and ψ angles in an extended conformation of a peptide?

φ = -ψ Signup and view all the answers

Which statement best describes secondary structure elements in proteins?

They consist of repeated interactions between similar types of residues. Signup and view all the answers

What is the typical number of residues per turn in an α-helix?

3.6 residues Signup and view all the answers

Which of the following describes the hydrogen bonding in an α-helix?

The carbonyl oxygen of each residue H-bonds with the NH of the residue 4 residues C-terminal. Signup and view all the answers

What is the result of minimizing conformational strain in proteins?

Attainment of a minimal energy state for the backbone Signup and view all the answers

What are the favored regions of the Ramachandran plot primarily indicative of?

Specific secondary structures in proteins Signup and view all the answers

Which of the following statements about hydrogen bonds in proteins is true?

Optimal hydrogen bonding geometry is crucial for favorable conformations. Signup and view all the answers

Which amino acids are most strongly favored to form α-helices?

Methionine, Alanine, and other linear residues Signup and view all the answers

What is the primary factor stabilizing β-sheets in protein structure?

Hydrophobic interactions Signup and view all the answers

Which amino acids are preferred at the N-terminus of α-helices and the C-terminus of β-strands?

Aspartic acid, Asparagine, Serine Signup and view all the answers

What role does Proline play in protein structure?

It breaks the hydrogen bonding pattern, favoring loops Signup and view all the answers

What is the significance of the P(α) value in the Chou & Fasman prediction algorithm?

It quantifies the preference of a residue to form α-helices Signup and view all the answers

Which of the following amino acids would most likely favor β-strands?

Valine Signup and view all the answers

Which of the following correctly describes the overall findings of Chou & Fasman's algorithm?

It uses information from known structures to derive preferences for structural predictions. Signup and view all the answers

What type of amino acids are most likely to interfere with the packing of side chains in α-helices?

Long hydrophilic residues Signup and view all the answers

What stabilizes the α-helix structure in proteins?

Hydrogen bonds and van der Waals contacts Signup and view all the answers

Which statement is true regarding the handedness of helices?

Right-handed helices are the standard configuration in proteins Signup and view all the answers

What is the backbone geometry preference of parallel and antiparallel β-sheets?

Each type prefers slightly different backbone geometries Signup and view all the answers

In which structure do polyproline II helices primarily appear?

As a stable conformation in proline-rich proteins Signup and view all the answers

What is the nature of β-turns in protein structures?

They consist of four residues stabilized by main chain hydrogen bonds Signup and view all the answers

Why do loops in protein structures exhibit a wide range of conformations?

They lack a regular inbuilt set of H-bond interactions Signup and view all the answers

How do polyproline I helices differ from polyproline II helices?

Polyproline I helices are left-handed and all-cis Signup and view all the answers

What characteristic distinguishes loops from other secondary structural elements in proteins?

Loops can adopt almost any conformation due to local interactions Signup and view all the answers

What stabilizes the structure of PPII helices?

Hydrogen bonds between adjacent PPII helices Signup and view all the answers

What role do β-sheets play in protein structure?

They consist of hydrogen bonds that stabilize the structure Signup and view all the answers

Which of the following best describes the role of hydrogen bonds in loops?

Loops make hydrogen bonds wherever possible within the protein structure Signup and view all the answers

What percentage of protein residues do loops generally comprise?

30% Signup and view all the answers

In terms of residue preferences, why do loop residues have varied conformations?

Residues can adopt conformations minimizing steric clashes Signup and view all the answers

What interaction is crucial for stabilizing the structure of the Rossmann fold domain?

Hydrogen bonds between β-strands Signup and view all the answers

Study Notes

Protein Backbone Conformation

Three bonds join each Cα to the next Cα.
The conformation of the protein backbone is described by three angles per residue: omega (Ω), phi (Φ), and psi (Ψ).

Dihedral Angles

The dihedral angle is the angle between two planes, formed by four atoms (A-B-C-D).
Measured clockwise.
The omega angle (Ω) is the dihedral angle between the carbonyl carbon of the previous residue and the nitrogen of the current residue.
The omega angle is typically near 180° due to the resonance stabilization of the peptide bond creating partial double bond character.

Proline’s Impact on Peptide Bond Conformation

Proline residues more readily adopt the cis conformation due to steric clashes in the trans conformation.
About 5.4% of Xaa-Pro peptides are cis, compared to 0.03% of other amino acids.

Phi & Psi Angles & Ramachandran Plots

Phi (φ) is the dihedral angle between the N-Cα and Cα-CO bonds, measured clockwise.
Psi (ψ) is the dihedral angle between the Cα-CO and CO-N bonds, measured clockwise.
The Ramachandran plot illustrates the allowed combinations of phi and psi angles, highlighting regions with low strain and optimal hydrogen bonding.
Each amino acid has its own Ramachandran plot, with variations in allowed conformations due to side chain characteristics.
Glycine, with only a hydrogen side chain, exhibits greater flexibility due to fewer steric constraints.
Proline's ring structure restricts its phi angle, limiting conformational flexibility.

Common Protein Secondary Structures

Secondary structures are runs of residues in (near) identical conformations, stabilized by repeated patterns of hydrogen bonds.
The extended conformation occurs when phi ≈ -psi, creating a maximally extended polypeptide chain.
The alpha-helix is a common secondary structure, characterized by a repeating pattern of hydrogen bonds between residues four residues apart.
Alpha-helices are right-handed and stabilized by hydrogen bonds, tight packing, and minimal backbone strain.
Beta-sheets consist of extended strands of polypeptide chains that can be parallel, anti-parallel, or mixed.
Beta-sheets are stabilized by main chain hydrogen bonds between adjacent strands.
Polyproline II helices are right-handed, with three residues per turn and no internal hydrogen bonds.
Polyproline II helices are commonly found in proline-rich regions and are important for protein interactions.

Loops

Loops are irregular and flexible connections between secondary structural elements.
Loops are stabilized by interactions with other protein structures, water molecules, and side chains.
Loops exhibit significant conformational diversity, playing critical roles in protein function.

Side Chain Conformations (Rotamers)

Side chains adopt specific conformations (rotamers) to minimize steric clashes.
Rotamers are influenced by the chemical nature and size of the side chain, with smaller and less branched side chains exhibiting fewer rotamers.

Amino Acid Preferences for Secondary Structure

Alpha-helices favor linear amino acids that pack closely.
Beta-sheets favor large, nonpolar amino acids and beta-branched amino acids.
Proline disrupts the hydrogen bonding pattern of both alpha-helices and beta-sheets.

Predicting Secondary Structure

Chou & Fasman developed an algorithm to predict secondary structure based on the amino acid sequence.
The algorithm uses tables of amino acid preferences for alpha-helices, beta-sheets, and turns, derived from analyzing existing protein structures.

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bioc nucleic acids