This set of Biochemistry Multiple Choice Questions & Answers (MCQs) focuses on “Protein Secondary

Structure”.

1. Which of the following does not affect the stability of an α-helix?

a) Electrostatic repulsion

b) Bulkiness

c) Interaction between R groups spaced three residues apart

d) Occurrence of alanine and glycine residues

View Answer

Answer: d

Explanation: The occurrence of Proline and Glycine residues affect the stability of an α-helix.

2. Which of the following is not true about secondary protein structure?

a) The hydrophilic/hydrophobic character of amino acid residues is important to secondary structure

b) The ability of peptide bonds to form intramolecular hydrogen bonds is important to secondary
structure

c) The alpha helix, beta pleated sheet and beta turns are examples of protein secondary structure

d) The steric influence of amino acid residues is important to secondary structure

View Answer

Answer: a

Explanation: The hydrophilic/hydrophobic character of amino acid residues is important to protein

tertiary structure rather than to secondary structure. In secondary structure, it is the steric size of the
residues that is important and residues are positioned to minimize interactions between each other and
the peptide chain.

3. β-pleated sheets are the examples of _________

a) Primary structure

b) Secondary structure

c) Tertiary structure

d) Quaternary structure
View Answer

Answer: b

Explanation: Secondary structure of proteins is of two forms α-helix and β-pleated structures.

4. A coiled peptide chain held in place by hydrogen bonding between peptide bonds in the same chain
is?

a) Primary structure

b) α-helix

c) β-pleated sheets

d) Tertiary structure

View Answer

Answer: b

Explanation: A coiled peptide chain held in place by hydrogen bonding between peptide bonds in the
same chain is α helix.

5. A structure that has hydrogen bonds between polypeptide chains arranged side by side is?

a) Primary structure

b) α-helix

c) β-pleated sheets

d) Tertiary structure

View Answer

Answer: c

Explanation: A structure that has hydrogen bonds between polypeptide chains arranged side by side is
β-pleated sheets.

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6. Which of the following are known as helix breakers?

a) Proline and glycine

b) Isoleucine and leucine

c) Valine

d) Threonine

View Answer

Answer: a

Explanation: Proline and glycine are known as helix breakers as they disrupt the regularity of the alpha
helical backbone conformation.

7. Which of the following is false about NMR spectroscopy?

a) NMR is an abbreviated form of Nuclear Magnetic Resonance

b) The intramolecular magnetic field around an atom in a molecule changes the resonance frequency
giving structural information about the atom

c) The intermolecular magnetic field around an atom in a molecule changes the resonance frequency
giving structural information about the atom

d) It is a technique that exploits magnetic properties of atomic nuclei

View Answer

Answer: c

Explanation: The intramolecular magnetic field around an atom in a molecule changes the resonance
frequency giving structural information about the atom.

8. Which of the statements is false about multiple sequence alignment?

a) Both protein and nucleic acid secondary structures can be used

b) More useful in RNA

c) These alignments can be made more accurate by the inclusion of secondary structure information

d) A significant increase in accuracy

View Answer

Answer: b

Explanation: Less useful in RNA. This is because base pairing is highly conserved than sequence.

9. Secondary structure is defined by _________

a) Hydrogen bonding
b) Vander Waals forces

c) Covalent bonding

d) Ionic bonding

View Answer

Answer: a

Explanation: Hydrogen bonding is present between the amine hydrogen and carbonyl oxygen atoms in
the peptide backbone.

10. Which of the following is a false statement?

a) α-Keratin is α helical

b) Collagen is α helical

c) Hemoglobin has a quaternary structure

d) α-Keratin is β pleated structure

View Answer

Answer: d

Explanation: Fibrous structural protein, α-Keratin is α helical.

1. The formation of _____ is determined by ______ interactions, whereas the formation of ____ is
strongly influenced by ______ interactions.

a) α-helices, long-range, α-helices, short-range

b) α-helices, long-range, β-strands, short-range

c) α-helices, short-range, β-strands, long-range

d) β-strands, short-range, β-strands, long-range

View Answer

Answer: c

Explanation: Protein secondary structure prediction with high accuracy is not a trivial ask. It remained a
very difficult problem for decades. This is because protein secondary structure elements are context
dependent. The formation of α-helices is determined by short-range interactions, whereas the
formation of β-strands is strongly influenced by long-range interactions. Prediction for long-range
interactions is theoretically difficult. After more than three decades of effort, prediction accuracies have
only been improved from about 50% to about 75%.

2. The secondary structure prediction methods can be either ab initio based, which make use of single
sequence information only, or homology based, which makes use of multiple sequence alignment
information.

a) True

b) False

View Answer

Answer: a

Explanation: The ab initio methods, which belong to early generation methods, predict secondary
structures based on statistical calculations of the residues of a single query sequence. The homology-
based methods do not rely on statistics of residues of a single sequence, but on common secondary
structural patterns conserved among multiple homologous sequences.

3. Which of the following is untrue regarding Ab Initio–Based Methods?

a) This type of method predicts the secondary structure based on a single query sequence

b) This type of method predicts the secondary structure based on a multiple query sequence

c) It measures the relative propensity of each amino acid belonging to a certain secondary structure
element

d) The propensity scores are derived from known crystal structures

View Answer

Answer: b

Explanation: Examples of ab initio prediction are the Chou–Fasman and Garnier, Osguthorpe, Robson
(GOR) methods. The ab initio methods were developed in the 1970s when protein structural data were
very limited. The statistics derived from the limited data sets can therefore be rather inaccurate.
However, the methods are simple enough that they are often used to illustrate the basics of secondary
structure prediction.

4. The Chou–Fasman algorithm determines the propensity or intrinsic tendency of each residue to be in
the helix, strand, and β-turn conformation using observed frequencies found in protein crystal
structures.

a) True
b) False

View Answer

Answer: a

Explanation: It determines the propensity or intrinsic tendency of each residue using observed
frequencies found in protein crystal structures (conformational values for coils are not considered). For
example, it is known that alanine, glutamic acid, and methionine are commonly found in α-helices,
whereas glycine and proline are much less likely to be found in such structures.

5. The GOR method is based on the “propensity” of each residue to be in one of the two conformational
states, helix (H), strand(E).

a) True

b) False

View Answer

Answer: b

Explanation: The GOR method is based on the “propensity” of each residue to be in one of the two
conformational states, helix (H), strand(E), turn(T), and coil (C). However, instead of using the propensity
value from a single residue to predict a conformational state, it takes short-range interactions of
neighboring residues into account.

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6. Which of the following is untrue regarding Chou–Fasman and GOR methods?

a) Both are the first-generation methods

b) They are developed in the 1970s,

c) They suffer from the fact that the prediction rules are somewhat arbitrary

d) They are based on single sequence statistics with clear relation to known protein-folding theories

View Answer

Answer: d

Explanation: They are based on single sequence statistics without clear relation to known protein-folding
theories. The predictions solely rely on local sequence information and fail to take into account long
range interactions. A Chou-Fasman–based prediction does not even consider the short-range
environmental information.

7. Which of the following is untrue regarding Homology-Based Methods?

a) The third generation of algorithms was developed in the late 1990s

b) They were developed by making use of evolutionary information

c) This type of method uses the ab initio secondary structure prediction of individual sequences only

d) This type of method combines the ab initio secondary structure prediction of individual sequences
and alignment information from multiple homologous sequences (>35% identity)

View Answer

Answer: c

Explanation: The idea behind this approach is that close protein homologs should adopt the same
secondary and tertiary structure. When each individual sequence is predicted for secondary structure
using a method similar to the GOR method, errors and variations may occur. However, evolutionary
conservation dictates that there should be no major variations for their secondary structure elements.

8. Because residues in the same aligned position are assumed to have the same secondary structure, any
inconsistencies or errors in prediction of individual sequences can be corrected using a majority rule.

a) True

b) False

View Answer

Answer: a

Explanation: By aligning multiple sequences, information of positional conservation is revealed. This

homology based method has helped improve the prediction accuracy by another 10% over the second-
generation methods.

9. Which of the following is untrue regarding Prediction with Neural Networks?

a) The third-generation prediction algorithms extensively apply sophisticated neural networks

b) It is used to analyze substitution patterns in multiple sequence alignments

c) It is not a machine learning process

d) It requires a structure of multiple layers of interconnected variables or nodes

View Answer
Answer: c

Explanation: A neural network is a machine learning process that requires a structure of multiple layers
of interconnected variables or nodes. In secondary structure prediction, the input is an amino acid
sequence and the output is the probability of a residue to adopt a particular structure.

10. Which of the following is untrue regarding Prediction with Neural Networks?

a) It has to be first trained by sequences with known structures

b) Between input and output are many connected hidden layers

c) Between the connected hidden layers the machine learning takes place to adjust the mathematical
weights of internal connections

d) It doesn’t have to be first trained by sequences with known structures

View Answer

Answer: d

Explanation: The neural network has to be first trained by sequences with known structures so it can
recognize the amino acid patterns and their relationships with known structures. During this process,
the weight functions in hidden layers are optimized so they can relate input to output correctly. When
the sufficiently trained network processes an unknown sequence, it applies the rules learned in training
to recognize particular structural patterns.

11. Which of the following is untrue regarding Prediction with Neural Networks?

a) When multiple sequence alignments and neural networks are combined, the result is further
improved accuracy

b) A neural network is trained by a single sequence

c) A neural network is trained by a sequence profile derived from the multiple sequence alignment

d) When the sufficiently trained network processes an unknown sequence, it applies the rules learned in
training to recognize particular structural patterns

View Answer

Answer: b

Explanation: A neural network is trained not by a single sequence but by a sequence profile derived from
the multiple sequence alignment. This combined approach has been shown to improve the accuracy to
above 75%, which is a breakthrough in secondary structure prediction. The improvement mainly comes
from enhanced secondary structure signals through consensus drawing. The following lists several
frequently used third generation prediction algorithms available as web servers.
12. Which of the following is untrue regarding PHD?

a) It stands for Profile network from Heidelberg

b) It is a web-based program that combines neural network only

c) It first performs a BLASTP of the query sequence against a non redundant protein sequence database

d) In initial steps it finds a set of homologous sequences, which are aligned with the MAXHOM program
(a weighted dynamic programming algorithm performing global alignment)

View Answer

Answer: b

Explanation: It is a web-based program that combines neural network with multiple sequence
alignment. After the initial steps, the resulting alignment in the form of a profile is fed into a neural
network that contains three hidden layers. The first hidden layer makes raw prediction based on the
multiple sequence alignment by sliding a window of thirteen positions.

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

Answer: b

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
Answer: a

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

Answer: c

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

Answer: a

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

Answer: d

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.

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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

Answer: a

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

Answer: b

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

Answer: b

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

Answer: c
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

Answer: a

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

Answer: b

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

Answer: c

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

Answer: d

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

Answer: b
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

Answer: a

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.