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Which of the following is most unstable condition in protein folding? (1) Non-polar side chain exposed to outside (2) Polar side chain present in core of protein (3) Non polar side chains in core of protein (4) Polar amino acids exposed to outsid

Understanding Stability and Instability in Protein Folding

Which one of the following is the most appropriate statement regarding folded proteins? (1) Charged amino acid side chains are always buried. (2) Charged amino acid side chains are seldom buried. (3) Non-polar amino acid side chains are seldom buried. (4) Tyrosine residues are always buried.

Protein Folding and Amino Acid Side Chain Distribution

Which of the following is most unstable condition in protein folding? (1) Non-polar side chain exposed to outside (2) Polar side chain present in core of protein (3) Non polar side chains in core of protein (4) Polar amino acids exposed to outsid

Protein Folding: Favorable and Unfavorable Interactions

The following observations are made on a 30-residue polypeptide (a) Unordered structure is observed in water but a helical conformation is observed in medium of low dielectric constant. (b)The peptide is resistant to degradation by proteases. (c) Red blood cells are lysed by the peptide. (d) β-mercaptoethanol has no effect on peptide structure. Which of the following statements can be correctly attributed to the above observations? (1)The peptide is entirely composed of D-amino acids and is amphipathic. (2)The peptide is entirely composed of L-amino acids and is not amphipathic. (3)The peptide is rich in disulphide bonds between D-cysteines. (4)The peptide is entirely composed of L –aromatic amino acids.

Structural and Functional Analysis of a 30-Residue Polypeptide

Following are statements related to peptide/protein conformation. A. The circular dichroism spectra of collagen and a protein in α-helical conformation will be identical. B. The allowed region for the dihedral angles ϕ, Ψ in Gly, spans a large area in the Ramachandran map. This can be drastically reduced by substituting the two hydrogens with methyl groups. C. Proline has high frequency of occurrence in β- turns. D. In a β-hairpin structure, the dihedral angles ϕ, Ψ of amino acids flanking the β-turn region will be 600, -300, respectively.

Understanding Protein Conformation: Circular Dichroism, Ramachandran Map, and β-Turns

Which statement is correct for globular proteins? (1) Always contain only α helix (2) Always contain only β sheets (3) Contains more reverse turns (4) Contains α helix, β sheets and reverse turns

Structure and Characteristics of Globular Proteins

A. L-threonine and L-allo-threonine interact identically with plane polarized light. B. van der Waals’ interactions are always attractive. C. Poly (pro) ll-helix is not stabilized by intermolecular hydrogen bonds. D. The folding of a protein is associated with an overall positive change in free energy and negative change in entropy. E. Lysine acetylation on histone is associated with loosening of the histone complex from DNA.

Understanding Protein Folding, van der Waals Interactions,

β-α-β motif is composed of two beta strands joined by an alpha helix through connecting loops. This motif is known for (1) ligand binding (2) stereological hindrance in binding of ligand (3) catalytic center (4) transmembrane domain

The β-α-β Motif: Structure, Function, and Role in Ligand Binding

Following statements are made related to protein structure A. The hydrogen bonding patterns between the CO and NH groups are n → n +3 in α-helix; n → n + 4 in 310 helix and n → n + 5 in π helix. B. In a ß turn, there are 10 atoms between the hydrogen bond donor and acceptor. C. In a 𝛾 tum, there are 6 atoms between the hydrogen bond donor and acceptor. D. Parallel sheets have evenly spaced hydrogen bonds, which bridge the strands at an angle.

Hydrogen Bonding in Alpha-Helices, Beta-Turns, and Beta-Sheets

Phosphorylation of ADP to ATP occurs through energy metabolism, comprising oxidative phosphorylation or substrate level phosphorylation or photo- phosphorylation (in plants). ATP can also be formed from ADP through the action of adenylate kinase. Crystal structure determination of adenylate kinase shows that the C-terminal region has the sequence – val-asp-asp-val-phe-ser-gln-val-cys-thr-his-leu-asp-thr- leu-lys. What can be a possible conformation of the sequence? (1) A helix that is not amphipathic (2) Amphipathic helix (3) Leucine zipper helix (4) Beta helix

Structural Analysis of Adenylate Kinase

A protein has 30% alanine. If all the alanines are replaced by glycines, (1) helical content will increase. (2) ß-sheet content will increase. (3) there will be no change in conformation (4) the alanine-substituted protein will be less structured than the parent protein.

Impact of Alanine-to-Glycine Substitution on Protein Structure

Which is correct for α-helix of a protein (1) It has H-bonding in two or more parallel running chains (2) There is intra-chain H-bonding in single helix (3) No H- bonding is seen (4) is a tertiary structure

Alpha-Helix in Protein Structure: Hydrogen Bonding and Stability

The following statements describe the propensity and role of amino acids in the secondary structure of proteins A. Alanine has a high frequency of occurrence in α- helices B. Proline has a high frequency of occurrence in α- helices C. The 𝛘 does not affect the helix propensity of serine, threonine and valine D. Peptide bonds involving ‘N’ of proline may display cis-trans isomerism

Understanding Amino Acid Propensity in Protein Secondary Structure

How long should it take the polypeptide backbone of a 6-residue, 10-residue, 15-residue and 20- residue folding nucleus to explore all its possible conformations? Assume that the polypeptide backbone randomly reorients every 10-13 seconds (s). (1) 10-7s, 10-3s, 102 s, 107 s, respectively (2) 10-1Os, 10-6s, 103 s, 1010 s, respectively (3) 10-5s, 10-2s, 10s, 103s, respectively (4) 1s, 10s, 100s, 107s, respectively

Time Required for a Polypeptide Backbone to Explore All Possible Conformations

Consider a 51-residue long protein containing only 100 bonds about which rotation can occur. Assume that 3 orientations per bond are possible. Based on these assumptions, how many conformations will be possible for this protein? (1) 3100 (2) 1003 (3) 351 (4) 51 x 100 x 3

Estimating Possible Conformations of a 51-Residue Protein

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Determining the Length of an α-Helical Section in a Membrane

Indicate which one of the following statements about nucleic acids and protein structures is correct. (1) Hydrogen bonding between the bases in the major and minor grooves of DNA is absent (2) Both uracil and thymine have a methyl group but at different positions. (3) The backbone dihedral angles of α-helices and ß- sheets are very similar. Only the hydrogen bonding pattern is different. (4) A ß-turn is formed by four amino acids. The type of ß-turn is determined by the dihedral angles of the second and third amino acid.

Understanding Nucleic Acid and Protein Structures:

The following statements were made to describe a typical collagen structure. A. Collagen has a triple-helical domain structure which consists of three distinct α-chains. B. The collagen triple helix is stabilized by isoprenyl bonds. C. Each α-chain has a left-handed polyproline ll-type helix. D. Each α-chain is composed of multiple triplet sequences of Gly-Y-Z in which Y is commonly proline and Z is usually hydroxyproline. Which one of the following options has all correct statements?

Collagen: Triple Helix, Amino Acid Composition, and Stability

Following are statements on ß-turns: A. All the 20 coded amino acids have equal propensity to form ß -turns. B. Pro cannot occur in ß-turns. C. Pro-Gly sequence strongly favours ß-turns. D. In Asn-Gly ß-turns, Asn can have positive ϕ,Ψ values. Choose the combination with all correct statements

Beta-Turns in Proteins: Structure

In a 30-residue peptide, the dihedral angles φ/Ψ have been determined by one or more methods. When their values are examined in the Ramachandran plot, it is (1) not possible for φ/ Ψ values to be distributed in the helical as well as beta sheet region. (2) possible that the φ/ Ψ values are all in the helical region although circular dichroism spectral studies indicate beta sheet conformation. (3) possible to conclude that the peptide is composed of entirely D-amino acids. (4) not possible to conclude if the peptide is entirely helical or entirely in beta sheet conformation.

Ramachandran Plot and Protein Conformation Analysis

$The exact backbone dihedral angles in a folded protein can be obtained by (1) deconvolution of its circular dichroism spectra obtained at different pH and temperature (2) estimating the number of protons that exchange with deuterium on treating the protein with D2O (3) forming fibres of the protein and analyzing the fibre diffraction pattern (4) analysis of the crystal structure of the protein obtained by X-ray diffraction at high resolutions$

Determining Backbone Dihedral Angles in Folded Proteins

The following are four statements on the peptides/proteins conformation: A. Glycine has a largest area of conformationally allowed space in the Ramachandran plot of Φ and Ψ B. A 20-residue peptide that is acetylated at the N-terminus and amidated at the C- terminus has Φ = -600 (±5), Ψ = -300(±5) for all the residues. It can be concluded that conformation of the peptide is helix-turn-strand C. The allowed values of Φ, Ψ for amino acids in a protein are not valid for short peptide D. A peptide Acetyl-A1 – A2 -A3 -A4-CONH2 (A-A4 are amino acids) adopts well defined ß-turn. The dihedral angles of A2 and A3 determined the type of ß- turn Choose the combination of correct statements.

Protein Structure and Ramachandran Plot Analysis

Given below are statements related to protein structures: A. The dihedral angles of an amino acid X in Acetyl-x- N-Methyl amide in the Ramachandran plot, occur in very small but equal areas in the left and right quadrants. It can be concluded that X is not one of the 20-coded amino acids. B. The dihedral angles of a 20-residue peptide are represented in the Ramachandran plot. It is possible to conclude that the peptide does not have a proline. C. Two proteins can have a similar fold even if they do not share significant similarity in their primary structure. D. On denaturation of a protein by urea, the interactions that would be disrupted are ionic bonds and van der Waal’s interaction but not disulfide bonds. Choose the combination with ALL CORRECT answers:

Protein Structures: Ramachandran Plot and Structural Stability

The hemagglutinin protein in influenza virus contains a long α-helix, with 53 residues. Which of the following correctly describes the attributes of this α helix? (1) The length is 75.6 Å, 14 turns, total of 102 Hydrogen bonds (2) The length is 106 Å, 14 turns, total of 106 Hydrogen bonds (3) The length is 75.6Å, 14 turns, total of 104 Hydrogen bonds (4) The length is 75.6Å, 10 turns, total of 102 Hydrogen bonds

Structure of Hemagglutinin α-Helix in Influenza Virus

How many hydrogen bonds involving the backbone CO and NH can be observed in an a-helix consisting of 15 amino acid residues? (1) 10 (2) 11 (3) 12 (4) 13

Hydrogen Bonding in an α-Helix of 15 Amino Acids

An α-helix in a peptide or protein is characterized by hydrogen bonds and characteristic dihedral angles. Choose the right combination. (1) Hydrogen bonding between the amide CO of residue i and amide NH of residue i + 4. Dihedral angles in the region φ = -500, Ψ = -600 (2) Hydrogen bonding between the amide NH of residue i and amide CO of residue i + 4. Dihedral angles in the region of φ = -500, Ψ = -60. (3) Hydrogen bonding between the amide CO of residue i and amide NH of residue i + 4. Dihedral angles in the region of φ = -500, Ψ = +60. (4) Hydrogen bonding between the amide CO of residue i and amide NH of residue 1 + 3. Dihedral angles in the region of φ = -500, Ψ = -60

Dihedral Angles and Hydrogen Bonding in α-Helices

In an alpha helical polypeptide, the backbone hydrogen bonds are between (1) NH of n and CO of n + 4 amino acids (2) CO of n and NH of n + 3 amino acids (3) CO of n and NH of n + 4 amino acids (4) NH of n and CO of n + 3 amino acids

Hydrogen Bonding Pattern in α-Helical Polypeptides

The position of collagen triple helix in Ramachandran plot is at- (1) Top Left (2) Top right (3) Bottom right (4) Bottom left

Collagen Triple Helix Position in the Ramachandran Plot

Acetyl-(Ala)18-CONH2 exists in α-helical conformation in solution. Most of the backbone dihedral angles (φ, Ψ) will be. (1) -600, -300 (2) 600,300 (3) -600 ,-300 (50%) and 600, 300 (50%) (4) -800, 1200

Dihedral Angles (ϕ, Ψ) in α-Helical Peptides: Acetyl-(Ala)18-CONH2

Which one of the statements on protein conformation, detailed below is INCORRECT? (1) L- amino acids can occur in Type l’ ß- turns where ϕ, Ψ are positive (2) A peptide rich in proline is unlikely to adopt α- helical structure (3) Proline residues have high propensity to occur in ß- turns (4) The dihedral angles ϕ, Ψ of amino acids in unfolded proteins are exclusively positive

Understanding Dihedral Angles and Secondary Structures

ϕ and Ψ values for right handed a helix of L-amino acid are expected to be (1) ϕ Negative, Ψ negative (2) ϕ Negative, Ψ positive (3) ϕ Positive, Ψ negative (4) ϕ Positive, Ψ positive

ϕ and Ψ Angles in Right-Handed α-Helices of L-Amino Acids

Which one of the following statements on protein conformation is NOT true? (1) Dihedral angles of side-chains in amino acids are depicted in the Ramachandran plot. (2) Infrared spectroscopy can be used to deduce hydrogen bonding in peptides. (3) Three dimensional structures of protein composed of 100 amino acids can be obtained by nuclear magnetic resonance spectroscopy (4) Globular proteins have α-helical and ß- sheet components

Understanding Protein Conformation: Key Facts

The regions of phi, psi space occupied by well characterized protein secondary structures are marked on a Ramachandran plot as shown above. Which of the following statements is CORRECT? Secondary Structure Regions in the Ramachandran Plot Secondary Structure Regions in the Ramachandran Plot (1) A- right handed α helix, B- ß strand, C- left handed α helix, D- collagen, (2) A- ß strand, B- right handed α helix, C- left handed α helix, D- collagen, (3) A- collagen, B- right handed α helix, C- left handed α helix, D- ß strand,

Secondary Structure Regions in the Ramachandran Plot

he Ramachandran plot graphically shows which combination of torsional angles phi (φ) and psi (Ψ) of amino acid residues contained in a peptide are possible. Examination of the plot below shows that only certain regions of the conformational space are permissible. Why are all the theoretical combinations of φ and Ψ not possible?

Restrictions in the Ramachandran Plot

Choose the correct statement about peptides in Ramchandran plot. (1) Peptides that are unstructured will have all the backbone dihedral angles in the disallowed regions. (2) It is not possible to conclude whether two peptide adopts entirely helix or entirely beta sheet confirmation. (3) The occurrence of beta turn conformation formation in a peptide can be deduced.

Understanding Peptides in the Ramachandran Plot

If the pyrollidine ring of proline is reduced to a linear to a linear form, the new amino acid will have (1) constrained ϕ than proline (2) constrained Ψ than proline (3) relaxed ϕ than proline (4) unaffected ϕ and Ψ

Effect of Pyrrolidine Ring Reduction in Proline on ϕ and Ψ Angles

The ϕ and Ψ values of a ß-strand composed of all D- amino acids will mainly occupy which quadrant in the Ramachandran plot? (1) upper left (2) upper right (3) lower left (4) lower right

Ramachandran Plot Quadrant for β-Strands of D-Amino Acids

The area of allowed regions in the Ramachandran map will be least for (1) Gly (2) L—Ala (3) L-Pro (4) α-methyl L-Valine

Which Amino Acid Has Least Allowed Region in Ramachandran Map

On a Ramachandran plot – glycine, L-Ala and L-Pro were plotted. Which statement is correct? (1) L-alanine will occupy greatest area (2) All amino acids will occupy same area (3) L-alanine and glycine will occupy similar area (4) Smallest are would be occupied by L-Proline

Ramachandran Plot: Understanding Glycine, L-Alanine & L-Proline

n the diagram for peptide shown below, angle ϕ represents bonds between Understanding Phi (ϕ) and Psi (ψ) Angles in Peptides Understanding Phi (ϕ) and Psi (ψ) Angles in Peptides (1) N – C’ (2) C’ – C (3) C – O (4) N – H

Understanding Phi (ϕ) and Psi (ψ) Angles in Peptides

The peptide unit (Cα – C’O – NH – Cα) is planer due to (1) restriction around Cα – C’ bond (2) restriction around C’ – N bond (3) restriction around N – Cα bond (4) hydrogen bonding between carbonyl oxygen and imino hydrogen of the peptide backbone

Understanding the Planarity of the Peptide Bond

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