MCQ Bank

Protein secondary structure is predicted from the primary amino acid sequence. The primary sequence determines the local structural tendencies that lead to structures such as alpha helices and beta sheets.

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Q31

Alu fragment is ……………… bp long repeated fragment

A) 800
B) 300
C) 500
D) 400

AI Explanation

An Alu element is a short interspersed nuclear element (SINE) of approximately 300 base pairs in length. Alu sequences are highly repeated throughout the human genome.

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Q32

which algorithm is used for finding the shortest superstring of a substring/read of genome?

A) Superstring Problem Algorithm
B) Shortest Superstring Problem Algorithm
C) String finding Algorithm
D) Shortest read Algorithm

AI Explanation

The Shortest Superstring Problem addresses how to reconstruct a shortest sequence containing all given reads or substrings. It is relevant to genome assembly because overlapping sequencing reads can be combined into a larger sequence.

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Q33

In smith and waterman algorithm the initial matrix is created with _____ columns and _____ rows.

A) M+1 and N+1
B) M+1 and N
C) M and N+1
D) M and N

AI Explanation

The Smith-Waterman dynamic programming matrix includes an initial row and column for the empty prefixes of the two sequences. Therefore, for sequences of lengths M and N, the matrix has M+1 columns and N+1 rows.

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Q34

Which of the following is un true regarding Chou–Fasman methods?

A) First-generation method
B) Developed in the 1970s,
C) Suffer from the fact that the prediction rules are somewhat arbitrary
D) Based on single sequence statistics with clear relation to known protein-folding theories

AI Explanation

The Chou-Fasman method is a first-generation prediction method developed in the 1970s and is based largely on statistical propensities from known protein structures. It does not have a clear direct relationship to established protein-folding theories, making this statement untrue.

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Q35

The most frequent N-terminal ions of peptide are called _____.

A) b-ions
B) y-ions
C) a-ions
D) z-ions

AI Explanation

In peptide mass spectrometry, b-ions are the characteristic N-terminal fragment ions. They retain the N-terminal portion of the peptide after fragmentation.

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Q36

Find the lexicographic order of {TAT, ATG, TGG, GGT, GTG, TGC}.

A) TAT, TGC, TGG, GTG, GGT, ATG
B) ATG, GTG, TAT, GGT, TGC, TGG
C) ATG, GGT, GTG, TAT, TGC, TGG
D) TGG, TGC, TAT, GTG, GGT, ATG

AI Explanation

Lexicographic ordering arranges strings according to alphabetical order of their characters. Using A < G < T, the sequences sort as ATG, GGT, GTG, TAT, TGC, TGG.

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Q37

The first step of Needleman-wunsch algorithm is to ______.

A) Matrix filling with the appropriate scores
B) Traceback the sequences for a suitable alignment
C) Initialization of matrix with gap penalty
D) Initialization of a matrix with zero’s

AI Explanation

The Needleman-Wunsch algorithm begins by initializing the dynamic programming matrix, including the first row and column with cumulative gap penalties. The matrix is then filled with alignment scores followed by traceback.

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Q38

Steps of mass spectrometry involves ______.

A) Protein --> Peptide --> small fragmentation --> measure mass
B) Peptide --> small fragmentation --> measure mass
C) Protein --> small fragmentation --> measure mass
D) Small fragmentation --> Peptide --> Proteins --> measure mass

AI Explanation

In mass spectrometry-based peptide sequencing, a peptide is fragmented into smaller ions and their mass-to-charge ratios are measured. These fragment masses provide information about the peptide sequence.

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Q39

BAC stands for …………………..

A) None of the above
B) Bacterial artifact chromosome
C) Blood alcohol concentration
D) Bacterial artificial chromosome

AI Explanation

BAC stands for Bacterial Artificial Chromosome. BACs are cloning vectors derived from bacterial plasmids and are used to maintain relatively large DNA fragments.

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Q40

Which computational approach is used for the modified protein identification.

A) Dynamic Programming
B) Exhaustive search
C) Brute force
D) Divide and conquer

AI Explanation

Modified protein identification can require searching through possible peptide modifications and matching them against observed spectra. An exhaustive search systematically evaluates the possible modified forms to identify the best match.

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Q41

For aligning closely related sequence which alignment method is suitable.

A) Global Alignment
B) Multiple Sequence Alignment
C) Pairwise Alignment
D) Local Alignment

AI Explanation

Global alignment is suitable for closely related sequences of similar length because it aligns the sequences across their entire lengths. It is commonly implemented using the Needleman-Wunsch algorithm.

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Q42

If L = 3 and s = TATGGTGC, then spectrum (s, L) will be ______.

A) {TAT, ATG, TGG, GGT}
B) {TAT, ATG, TGG, GGT, ATG, GGT, TGC}
C) {TAT, ATG, TGG, GGT, GTG, TGC}
D) {TAT, ATG, TGG, GGT, GTG}

AI Explanation

For L = 3, the spectrum contains every consecutive substring of length three from TATGGTGC. These are TAT, ATG, TGG, GGT, GTG, and TGC, giving option C.

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Q43

The most frequent C-terminal ions of peptide are called _____.

A) a-ions
B) b-ions
C) y-ions
D) z-ions

AI Explanation

In peptide mass spectrometry, y-ions are the characteristic C-terminal fragment ions. They retain the C-terminal portion of the peptide after fragmentation.

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Q44

In Human Genome Project ______ nucleotide's were sequenced.

A) 4 Billion
B) 2 Billion
C) 3 Billion
D) 1 Billion

AI Explanation

The Human Genome Project determined the sequence of approximately 3 billion nucleotide bases in the human genome. This reference sequence provided a foundation for studying human genes and genomic variation.

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Q45

Glutamine (GLU) is most likely to found in _____.

A) Coils
B) Turns
C) Helices
D) Beta Sheets

AI Explanation

Glutamine (Gln) has a relatively high propensity to occur in alpha helices. Its polar amide side chain can participate in hydrogen bonding that supports helical structure.

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Q46

…….. Percent of Human genome has repeated elements

A) 50
B) 80
C) 30
D) 20

AI Explanation

Approximately 50% of the human genome consists of repeated or repetitive elements. These include transposable elements and other types of repetitive DNA sequences.

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Q47

Splicesome complex contain more than …………….. proteins

A) 500
B) 100
C) 200
D) 50

AI Explanation

The spliceosome is a large RNA-protein complex involved in pre-mRNA splicing. It contains more than 100 proteins along with small nuclear RNAs and associated components.

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Q48

________ size probes will be used to identify the fragments that are needs to be sequence in sequencing by hybridization process.

A) 8 – 32 nts
B) 32 – 60 nts
C) 100 – 500 nts
D) 2 – 8 nts

AI Explanation

Sequencing by hybridization uses short oligonucleotide probes to identify DNA fragments through complementary base pairing. Probes in the range of about 8–32 nucleotides are commonly used in this approach.

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Q49

_______ determines the protein structure.

A) Amino Acid
B) Nucleotides
C) DNA
D) RNA

AI Explanation

The amino acid sequence, or primary structure, is the fundamental determinant of a protein's three-dimensional structure. The sequence influences the folding and interactions that produce the final protein structure.