This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Protein Structure Basics”.
1. The building blocks of proteins are ______ naturally occurring amino acids, small molecules that contain a free amino group (NH2) and a free carboxyl group (COOH).
a) ten
b) twenty
c) nine
d) nineteen
View Answer
Explanation: Both of these groups are linked to a central carbon (Cα), which is attached to hydrogen and a side chain group (R). Amino acids differ only by the side chain R group. The chemical reactivities of the R groups determine the specific properties of the amino acids. Amino acids can be grouped into several categories based on the chemical and physical properties of the side chains, such as size and affinity for water.
2. Within the hydrophobic set of amino acids, they can be further divided into aliphatic and aromatic.
a) True
b) False
View Answer
Explanation: Aliphatic side chains are linear hydrocarbon chains and aromatic side chains are cyclic rings. Within the hydrophilic set, amino acids can be subdivided into polar and charged. Charged amino acids can be either positively charged (basic) or negatively charged (acidic).
3. ______ the smallest amino acid, has a hydrogen atom as the R group.
a) valine
b) proline
c) Glycine
d) threonine
View Answer
Explanation: Of particular interest within the twenty amino acids are glycine and proline. It can therefore adopt more flexible conformations that are not possible for other amino acids. Proline is on the other extreme of flexibility. Its side chain forms a bond with its own backbone amino group, causing it to be cyclic. The cyclic conformation makes it very rigid, unable to occupy many of the main chain conformations adopted by other amino acids.
4. The peptide formation involves two amino acids covalently joined together between the carboxyl group of one amino acid and the amino group of another.
a) True
b) False
View Answer
Explanation: This reaction is a condensation reaction involving removal of elements of water from the two molecules. The resulting product is called a dipeptide. The newly formed covalent bond connecting the two amino acids is called a peptide bond. Once an amino acid is incorporated into a peptide, it becomes an amino acid residue. Multiple amino acids can be joined together to form a longer chain of amino acid polymer.
5. A linear polymer of more than fifty amino acid residues is referred to as a ________
a) dipeptide
b) oligopeptide
c) peptide
d) polypeptide
View Answer
Explanation: A polypeptide, also called a protein, has a well-defined three-dimensional arrangement. On the other hand, a polymer with fewer than fifty residues is usually called a peptide without a well-defined three-dimensional structure. The residues a peptide or polypeptide are numbered beginning with the residue containing the amino group, referred to as the N-terminus, and ending with the residue containing the carboxyl group, known as the C-terminus.
6. Which of the following is not correct?
a) The rigid double bond structure forces atoms associated with the peptide bond to lie in the same plane, called the dipeptide plane
b) A peptide bond is actually a partial double bond owing to shared electrons between
O=C–N atoms
c) Because of the planar nature of the peptide bond and the size of the R groups, there are considerable restrictions on the rotational freedom by the two bonded pairs of atoms around the peptide bond
d) The angle of rotation about the bond is referred to as the dihedral angle (also called the torsional angle)
View Answer
Explanation: The rigid double bond structure forces atoms associated with the peptide bond to lie in the same plane, called the peptide plane. For a peptide unit, the atoms linked to the peptide bond can be moved to a certain extent by the rotation of two bonds flanking the peptide bond.
7. Which of the following is not correct about the stabilizing Forces?
a) Protein structures from secondary to quaternary are maintained by noncovalent forces
b) They include electrostatic interactions but not van der Waals forces, and hydrogen bonding
c) Electrostatic interactions are a significant stabilizing force in a protein structure
d) Electrostatic interactions occur when excess negative charges in one region are neutralized by positive charges in another region
View Answer
Explanation: It includes electrostatic interactions, van der Waals forces, and hydrogen bonding. The result is the formation of salt bridges between oppositely charged residues. The electrostatic interactions can function within a relatively long range (15 Å). Hydrogen bonds are a particular type of electrostatic interactions similar to dipole–dipole interactions involving hydrogen from one residue and oxygen from another. Hydrogen bonds can occur between main chain atoms as well as side chain atoms.
8. Which of the following is not correct about the α-Helices?
a) An α-helix has a main chain backbone conformation that resembles a corkscrew
b) Nearly all known α-helices are right handed, exhibiting a leftward spiral form
c) Nearly all known α-helices are right handed, exhibiting a rightward spiral form
d) In right handed helix, there are 3.6 amino acids per helical turn
View Answer
Explanation: The structure is stabilized by hydrogen bonds formed between the main chain atoms of residues i and i + 4. The hydrogen bonds are nearly parallel with the helical axis. The average φ and ψ angles are 60◦ and 45◦, respectively, and are distributed in a narrowly defined region in the lower left region of a Ramachandran plot.
9. Which of the following is not correct about the β-sheet?
a) A β-sheet is a fully extended configuration built up from several spatially adjacent regions of a polypeptide chain
b) Each region involved in forming the β-sheet is a β-strand
c) The β-strand conformation is pleated with main chain backbone zigzagging and side chains positioned on same sides of the sheet
d) β-Strands are stabilized by hydrogen bonds between residues of adjacent strands
View Answer
Explanation: The β-strand conformation is pleated with main chain backbone zigzagging and side chains positioned alternately on opposite sides of the sheet. β-strands near the surface of the protein tend to show an alternating pattern of hydrophobic and hydrophilic regions, whereas strands buried at the core of a protein are nearly all hydrophobic. The β-strands can run in the same direction to form a parallel sheet or can run every other chain in reverse orientation to form an antiparallel sheet or a mixture of both.
10. Which of the following is not correct about the Coils and Loops?
a) They are regular structures
b) They are irregular structures
c) The loops are often characterized by sharp turns or hairpin-like structures
d) If the connecting regions are completely irregular, they belong to random coils
View Answer
Explanation: Residues in the loop or coil regions tend to be charged and polar and located on the surface of the protein structure. They are often the evolutionarily variable regions where mutations, deletions, and insertions frequently occur. They can be functionally significant because these locations are often the active sites of proteins.
11. Globular proteins are usually insoluble.
a) True
b) False
View Answer
Explanation: Globular proteins are usually soluble and surrounded by water molecules. They tend to have an overall compact structure of spherical shape with polar or hydrophilic residues on the surface and hydrophobic residues in the core. Such an arrangement is energetically favorable because it minimizes contacts with water by hydrophobic residues in the core and maximizes interactions with water by surface polar and charged residues. Common examples of globular proteins are enzymes, myoglobins, cytokines, and protein hormones.
12. Which of the following is not correct about the Integral Membrane Proteins?
a) Membrane proteins exist in lipid bilayers of cell membranes
b) The exterior of the proteins spanning the membrane must be very hydrophobic to be stable
c) The exterior of the proteins spanning the membrane must be very hydrophilic to be stable
d) Most typical transmembrane segments are α-helices
View Answer
Explanation: Because they are surrounded by lipids, the exterior of the proteins spanning the membrane must be very hydrophobic to be stable. Occasionally, for some bacterial periplasmic membrane proteins, they are composed of β-strands. The loops connecting these segments sometimes lie in the aqueous phase, in which they can be entirely hydrophilic.
13. Which of the following is not correct about the X-ray Crystallography?
a) In x-ray protein crystallography, proteins need to be grown into large crystals in which their positions are fixed in a repeated, ordered fashion
b) The protein crystals are illuminated with an intense x-ray beam
c) The x-rays are deflected by the electron clouds surrounding the atoms in the crystal producing a regular pattern of diffraction
d) The protein crystals are illuminated with an intense infrared beam
View Answer
Explanation: The diffraction pattern is composed of thousands of tiny spots recorded on a x-ray film.
The diffraction pattern can be converted into an electron density map using a mathematical procedure known as Fourier transform. To interpret a three-dimensional structure from two-dimensional electron density maps requires solving the phases in the diffraction data.
14. Which of the following is not correct about the NMR?
a) It stands for Nuclear Magnetic Resonance
b) NMR spectroscopy detects spinning patterns of atomic nuclei in a electric field
c) NMR spectroscopy detects spinning patterns of atomic nuclei in a magnetic field
d) Protein samples are labeled with radioisotopes such as 13C and 15N
View Answer
Explanation: Radiofrequency radiation is used to induce transitions between nuclear spin states in a magnetic field. Interactions between spinning isotope pairs produce radio signal peaks that correlate with the distances between them. By interpreting the signals observed using NMR, proximity between atoms can be determined.
15. One can search a structure in PDB using the four-letter code or keywords related to its annotation.
a) True
b) False
View Answer
Explanation: Each entry is given a unique code, PDB id, consisting of four characters of either letters A to Z or digits 0 to 9 such as 1LYZ and 4RCR. The identified structure can be viewed directly online or downloaded to a local computer for analysis.
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