bio Flashcards
What is the definition of Bioinformatics?
a) The sum of the computational approaches to analyze, manage, and
store biological data.
b) The study of animal behavior
c) The study of geological formations
d) All of the above
Answer: a
Which of the following is NOT a part of Bioinformatics?
a) Analyzing genomes
b) Analyzing proteomes
c) Studying animal behavior
d) Three-dimensional modeling of biomolecules and biological systems
Answer: c
Computational biology requires clever algorithms to:
a) Find interesting patterns
b) Visualize vast collections of data
c) Predict missing or hard-to-observe features
d) All of the above
Answer: d
Data types of Bioinformatics include:
a) DNA sequences
b) RNA sequences
c) Protein sequences
d) Lipid sequences
e) All of the above
Answer: (e)
Which of the following are ways to find genes?
a) Search for sequence of DNA similar to known gene
b) Search the genome sequence for patterns of letters that “look like
genes”
c) Both a and b
d) None of the above
Answer: c
Sequence alignment aims to identify important sequences by finding
conserved regions.
a) True
b) False
Answer: a
Sequence alignment aims to find genes similar to known genes.
a) True
b) False
Answer: a
What are nucleotides composed of?
a) A nitrogenous base, a five-carbon sugar, and a phosphate
b) A nitrogenous base, a six-carbon sugar, and a phosphate
c) A nitrogenous base, a four-carbon sugar, and a phosphate
d) A nitrogenous base, a three-carbon sugar, and a phosphate
Answer: a
What is the primary function of nucleotides in metabolism?
a) Providing chemical energy
b) Providing structural support
c) Serving as cofactors of enzymatic reactions
d) Acting as food additives
Answer: a
Which nucleotide is used in place of thymine in RNA?
a) Guanine
b) Adenine
c) Cytosine
d) Uracil
Answer: d
………. can fold upon itself,sometimes forming bonds between
two of the same nucleotide, and can also be used for structural
elements in the cell.
a) DNA
b) RNA
c) Both a and b
d) None of the above
Answer: c
In the central dogma of biology:
a) DNA encodes genes, most of which encode for proteins via the
genetic code
b) Proteins perform much of the work of the cell.
c) RNA acts as an intermediate step
d) All of the above
Answer: d
DNA makes RNA and RNA makes protein.
a) True
b) False
Answer: a
DNA encodes genes, most of which encode for proteins via the
genetic code.
a) True
b) False
Answer: a
Which of the following is the genetic code?
a) The set of rules used by a cell to interpret the nucleotide sequence
within a molecule of mRNA
b) The sequence of amino acids in a protein
c) The process of DNA replication
d) The arrangement of nucleotides in a DNA molecule
Answer: a
What is meant by redundancy in the genetic code?
a) Each amino acid is specified by only one mRNA codon
b) Most amino acids are specified by more than one mRNA codon
c) Each codon specifies multiple amino acids
d) There is no redundancy in the genetic code
Answer: b
………. is a molecular process that copies genetic information into
nearly identical RNA molecules while ………. is a process that
converts RNA to proteins.
a) Translation, Transcription
b) Translation, Translation
c) Transcription, Translation
d) Transcription, Transcription
Answer: c
How do you convert RNA to a protein?
a) Map codons to amino acids using the genetic code chart.
b) Perform reverse transcription to convert RNA back to DNA
c) Use RNA to directly assemble amino acids into proteins
d) All of the above
Answer: a
What is the role of ribosomes in translation?
a) Ribosomes synthesize mRNA
b) Ribosomes read the genetic code and assemble amino acids into
proteins c) Ribosomes generate DNA
d) Ribosomes replicate tRNA molecules
Answer: b
What molecules surround ribosomes during translation?
a) Messenger RNA (mRNA)
b) DNA
c) Transfer RNA (tRNA)
d) Ribosomal RNA (rRNA
Answer: c
Transfer RNA(tRNA) molecule consists of two distinct ends that bind
to:
a) A specific amino acid
b) A specific codon in the mRNA sequence
c) Both a and b
d) None of the above
Answer: c
What is the function of transfer RNA (tRNA) during translation?
a) tRNA binds to a specific codon in the mRNA sequence and
assembles amino acids
b) tRNA generates mRNA
c) tRNA synthesizes ribosomes
d) tRNA replicates DNA
Answer: a
How many distinct phases are involved in translation?
a) One
b) Two
c) Three
d) Four
Answer: c
Sequence alignment aims to understand evolutionary relationships
and distances between sequences.
a) True
b) False
Answer: a
What are the three phases of translation?
a) Start, middle, end
b) Initiation, transcription, termination
c) Initiation, elongation, termination
d) DNA binding, mRNA synthesis, protein assembly
Answer: c
What is a polysome?
a) A single ribosome translating a single mRNA molecule
b) Multiple ribosomes translating multiple mRNA molecules
c) Multiple ribosomes translating a single mRNA molecule
d) A protein involved in mRNA synthesis
Answer: c
What happens at the start of the initiation phase of translation?
a) The ribosome attaches to the tRNA strand
b) The ribosome attaches to the mRNA strand and locates the start
codon
c) The mRNA attaches to the tRNA strand
d) The mRNA is transcribed into DNA
Answer: b
What is the start codon for translation?
a) UUU
b) AUG
c) GGG
d) CCC
Answer: b
During elongation in translation, what happens when the ribosome
shifts to the next codon on the mRNA?
a) The ribosome releases the mRNA
b) The corresponding tRNA binds to the codon
c) The mRNA is transcribed into DNA
d) The ribosome releases the tRNA
Answer: b
What happens to the first tRNA molecule during elongation in
translation?
a) It remains bound to the mRNA
b) It is released from the ribosome
c) It attaches to the ribosome
d) It is transcribed into DNA
Answer: b
What signals the end of the genetic message in translation?
a) Start codon
b) Termination
c) Stop codon
d) Initiation
Answer: c
What signals the start of the genetic message in translation?
a) Start codon
b) Elongation
c) Stop codon
d) Initiation
Answer: a
What do the start and stop codons signal?
a) Initiation and Elongation
b) Initiation and Termination
c) Start and Stop codon
d) None of the Above
Answer: c
What is often required for proteins after translation?
a) Transcription
b) Post-translational modification
c) DNA replication
d) mRNA processing
Answer: b
What is one example of post-translational modification?
a) Transcription
b) Translation
c) Proteolysis
d) mRNA splicing
Answer: c
What is usually the first amino acid excised during proteolysis?
a) Methionine
b) Phenylalanine
c) Leucine
d) Tryptophan
Answer: a
What are some functions performed by proteins after translation?
a) Catalyzing biochemical reactions, DNA replication, and transcription
b) mRNA splicing, DNA replication, and mRNA processing
c) Catalyzing biochemical reactions, providing structural support for
the cell, and creating channels through the cell membrane
d) Transcription, translation, and mRNA splicing
Answer: c
Which of the following databases contains primarily protein
sequences?
a) GenBank
b) UniProt
c) PubMed
d) NCBI
Answer: d
Which of the following databases contain primarily nucleotide
sequences?
a) GenBank
b) UniProt
c) PubMed
d) PDB
Answer: a
Sequence alignment is a vital step in genome assembly, and other
sequence analysis tasks.
a) True
b) False
Answer: a
Sequence alignment aims to provide hints about protein structure
and function.
a) True
b) False
Answer: a
………. is a nucleotide or amino-acid sequence pattern that is
widespread and usually assumed to be related to biological function
of the macromolecule.
a) Motif
b) Genome
c) BLAST
d) GenBank
Answer: a
………. is a database of protein families and domains.
a) Motif
b) Genome
c) BLAST
d) PROSITE
Answer: d
………. is an organism’s complete set of genetic information.
a) Motif
b) Genome
c) BLAST
d) PROSITE
Answer: b
………. is a comprehensive public database of nucleotide sequences.
a) Motif
b) Genome
c) GenBank
d) PROSITE
Answer: c
………. is a text-based, bioinformatic data format used to store
nucleotide or amino acid sequences.
a) Motif
b) Genome
c) GenBank
d) FASTA
Answer: d
………. is a suite of programs used to generate alignments between a
nucleotide or protein sequence.
a) BLAST
b) Genome
c) GenBank
d) FASTA
Answer: a
………. refers to the process of searching for similarities or patterns
within biological sequences, such as DNA, RNA, or protein
sequences.
a) BLAST
b) Genome
c) Pattern Matching
d) FASTA
Answer: c
What is the primary purpose of the Z algorithm?
a) Sorting integers
b) String searching and pattern matching
c) Graph traversal
d) Encryption
Answer: b
What data structure is constructed by the Z algorithm for a given
string?
a) Binary search tree
b) Z-array
c) Hash table
d) Linked list
Answer: b
What does a Z-value at index ‘i’ in the Z-array represent?
a) Length of the longest prefix of the string
b) Length of the longest suffix of the string
c) Length of the longest substring starting from position ‘i’ that is also
a prefix of the string
d) Index of the character ‘i’ in the string
Answer: c
In what context is the Z algorithm particularly efficient?
a) Short patterns and long text strings
b) Long patterns and short text strings
c) Sorting integers
d) Encryption and decryption
Answer: b
Which algorithm is conceptually similar to the Z algorithm in string
matching efficiency?
a) QuickSort
b) BubbleSort
c) Knuth-Morris-Pratt (KMP) algorithm
d) Depth-First Search (DFS)
Answer: c
Where can the Z algorithm find applications?
a) Image processing
b) Bioinformatics
c) Real-time operating systems
d) Compiler design
Answer: b
Which step is NOT part of the Z algorithm’s process?
a) Constructing the Z-array
b) Calculating Z-values
c) Constructing a suffix tree
d) Pattern matching using Z-values
Answer: c
Consider the string P = “ababababc”. What is the value of Zi(P) for
i=5?
a)1
b) 2
c) 3
d) 4
Answer: d
Consider the string P = “abcabcabc”. What is the value of Zi(P) for
i=3?
a)3
b) 6
c) 9
d) 0
Answer: a
Consider the string P = “abababcababababc”. What is the Z-box at
index i=7?
a)”ababc”
b) “abababc”
c) “bababab”
d) No Z-box at i=7
Answer: b
In Bioinformatics, how is the Z algorithm applied?
a) Identifying gene mutations in DNA sequences
b) Searching for specific protein motifs in amino acid sequences
c) Analyzing metabolic pathways in cells
d) Classifying species based on morphological traits
Answer: b
Which of the following scenarios best illustrates the practical use of
the Z algorithm?
a) Searching for a word in a text document
b) Sorting a list of integers in ascending order
c) Analyzing stock market trends
d) Identifying repeated patterns in genomic sequences
Answer: d
What is the time complexity of the Z algorithm for pattern matching
in a text of length ‘n’ with a pattern of length ‘m’?
a) O(n)
b) O(m)
c) O(n + m)
d) O(n * m)
Answer: c
In the KMP algorithm, what data structure is preprocessed to aid in
pattern matching?
a) Stack
b) Queue
c) Prefix function (also known as failure function)
d) Heap
Answer: c
What is the key idea behind the KMP algorithm’s efficiency in string
matching?
a) It uses divide and conquer techniques
b) It preprocesses the pattern to skip unnecessary comparisons
during matching
c) It uses hashing to quickly compare patterns
d) It converts strings into numerical representations
Answer: b
What is the time complexity of the Knuth-Morris-Pratt (KMP)
algorithm for pattern matching in a text of length ‘n’ with a pattern of
length ‘m’?
a) O(n)
b) O(m)
c) O(n + m)
d) O(n * m)
Answer: c
What is the prefix function (failure function) in the KMP algorithm
compute?
a) The length of the pattern
b) The number of matches in the text
c) The longest proper suffix that is also a prefix of the pattern
d) The longest proper prefix that is also a suffix of the pattern
Answer: c
Consider the string P = “abababcababababc”. What is the value of
spmi(P) for i=8?
a) 3
b) 6
c) 8
d) 9
Answer: c
Given the string P = “abcdabcyabcdabcy”, what is the spmi(P) for
i=12?
a) 3
b) 4
c) 8
d) 12
Answer: b
What is a key feature of the Boyer-Moore algorithm that contributes
to its efficiency in string matching?
a) It uses dynamic programming
b) It preprocesses the pattern to skip unnecessary comparisons
c) It relies on hash tables for pattern storage
d) It has a time complexity of O(n*m)
Answer: b
In the Boyer-Moore algorithm, what does the “bad character rule”
refer to?
a) Preprocessing the pattern to identify potential matches
b) Skipping comparisons by identifying mismatches based on
characters in the text
c) Using a hash table to store character positions
d) Sorting characters in the pattern for faster matching
Answer: b
How does the Boyer-Moore algorithm handle the “good suffix rule” in
string matching?
a) By preprocessing the pattern to identify good suffixes
b) By using dynamic programming for suffix matching
c) By shifting the pattern based on the last occurrence of a
mismatched character
d) By comparing suffixes of the pattern with the text for matches
Answer: c
What is the time complexity of the Boyer-Moore algorithm in the
worst-case scenario for pattern matching?
a) O(n)
b) O(m)
c) O(n + m)
d) O(n * m)
Answer: a
In Boyer-Moore’s “bad character rule,” what does the algorithm
prioritize when encountering a mismatch between the pattern and
text?
a) Matches in the pattern
b) Matches in the text
c) The last occurrence of the mismatched character in the pattern
d) The first occurrence of the mismatched character in the text
Answer: c
Consider the string P = “abracadabra” and the character ‘a’. What is
R4(‘a’)?
a) 1
b) 2
c) 3
d) 4
Answer: b
Consider the string P = “abracadabra” and the index i=7. What is L(7)
for this string?
a) 1
b) 4
c) 7
d) 0
Answer: b
Consider the string P = “abracadabra” and the index i=5. What is L(5)
for this string?
a) 1
b) 4
c) 7
d) 0
Answer: b
Given the string P = “mississippi” and the index i=9. What is l(9) for
this string?
a) 0
b) 2
c) 4
d) 6
Answer: c
For the string P = “algorithm” and the index j=5. What is Nj(P) for this
string?
a) 1
b) 3
c) 5
d) 8
Answer: d
Consider the string P = “banana” and the index i=3. What is L(3) for
this string?
a) 1
b) 2
c) 3
d) 0
Answer: d
What is the primary advantage of the Rabin-Karp algorithm for string
matching?
a) It uses dynamic programming techniques
b) It has a time complexity of O(n*m)
c) It utilizes hashing for pattern matching
d) It requires preprocessing of the pattern
Answer: c
In the Rabin-Karp algorithm, what is the purpose of using hashing?
a) To store character positions in a hash table
b) To compare characters sequentially in the text
c) To quickly compare patterns using their hash values
d) To determine the length of the pattern
Answer: c
What data structure is central to the Shift-And algorithm for pattern
matching?
a) Hash table
b) Trie
c) Bitmask
d) Stack
Answer: c
How does the Shift-And algorithm process patterns for matching?
a) It compares characters sequentially
b) It converts patterns to numerical values
c) It uses bitwise operations on a mask
d) It sorts characters in the pattern
Answer: c
In string algorithms that use characters as digits, what is the purpose
of computing a prime number ‘p’?
a) To represent the length of the text string
b) To compute hash values of substrings efficiently
c) To convert characters to numerical values
d) To determine the length of the pattern
Answer: b
When computing a prime number ‘p’ for hashing, what properties
should ‘p’ ideally possess?
a) It should be divisible by all characters in the alphabet
b) It should be close to the length of the text string
c) It should be large and randomly chosen
d) It should be a perfect square
Answer: c
In string algorithms, what is the purpose of computing the value ‘ts’
for the text string?
a) To represent the total number of characters in the text string
b) To store the hash value of the entire text string
c) To encode characters into numerical values
d) To determine the length of the pattern
Answer: b
How does the choice of ‘p’ affect the hashing process in string
algorithms?
a) It influences the speed of hashing but not the accuracy
b) It affects the distribution of hash values and collision probabilities
c) It determines the size of the hash table
d) It has no impact on hashing
Answer: b
In the context of representing strings as numbers in base d, if the
alphabet size |∑| = 10 (0 to 9), what is the base ‘d’ for this scenario?
a) Base 8
b) Base 10
c) Base 16
d) Base 20
Answer: b
When a string represents a number in base d, how does the length of
the string affect the magnitude of the represented number?
a) Longer strings represent smaller numbers
b) Shorter strings represent larger numbers
c) Length of the string does not affect the magnitude
d) It depends on the specific characters in the string
Answer: c
Using Horner’s rule, compute the numerical value 𝑝p for the string
“648237”.
a) 648237
b) 327846
c) 236478
d) 836824
Answer: b
After performing a “left shift” operation on the string “123456”, what
is the resulting string?
a) 123457
b) 234561
c) 234567
d) 345612
Answer: c
After performing a “left shift” operation on the string “123456”, what
is the resulting string?
a) 123457
b) 234561
c) 234567
d) 345612
Answer: c
What is the worst-case runtime complexity of the Rabin-Karp
algorithm with explicit matching?
a) O(1)
b) O(n)
c) O(m)
d) O(mn)
Answer: d
In the Shift-And algorithm, what is the impact on time and space
complexity if the length of pattern ∣𝑃∣∣P∣ in bits is less than or equal
to the computer word size?
a) Time complexity becomes O(|T|) and space complexity becomes
O(|P|).
b) Time complexity becomes O(|P| × |T|) and space complexity
becomes O(|P|).
c) Time complexity becomes O(|T|) and space complexity becomes
O(|T|).
d) Time complexity becomes O(|P| × |T|) and space complexity
becomes O(|T|).
Answer: a
What is dynamic programming primarily used for in algorithmic
problems?
a) Solving problems recursively
b) Finding optimal solutions to problems by breaking them into
smaller subproblems
c) Implementing algorithms with low time complexity
d) Sorting data efficiently
Answer: b
What is the main idea behind dynamic programming?
a) Breaking down a problem into smaller overlapping subproblems
b) Using randomization for faster computation
c) Solving problems using a divide-and-conquer approach
d) Storing solutions in a hash table
Answer: a
In dynamic programming, what is memoization used for?
a) Storing previously computed solutions to avoid redundant
computations
b) Generating random numbers for algorithmic problems
c) Sorting data efficiently
d) Dividing problems into smaller subproblems
Answer: a
What is the time complexity of a dynamic programming solution that
solves a problem with 𝑛n subproblems, each taking 𝑂(𝑘)O(k) time to
solve?
a) O(n)
b) O(nlogn)
c) O(k)
d) O(nk)
Answer: d
What is the key difference between dynamic programming and
greedy algorithms?
a) Dynamic programming focuses on optimizing local choices, while
greedy algorithms make globally optimal choices at each step.
b) Greedy algorithms use memoization, while dynamic programming
uses recursion.
c) Dynamic programming always guarantees the optimal solution,
while greedy algorithms may not.
d) Greedy algorithms are more efficient than dynamic programming
for solving complex problems.
Answer: a
What is the purpose of the “bottom-up” approach in dynamic
programming?
a) It involves starting from the largest subproblem and breaking it
down into smaller subproblems.
b) It uses recursion to solve subproblems and then combines their
solutions.
c) It iteratively solves subproblems from the smallest to the largest,
avoiding redundant computations.
d) It focuses on storing solutions in a hash table for quick access.
Answer: c
What is the purpose of defining overlapping subproblems in dynamic
programming?
a) To create more complex subproblems for efficient computation
b) To reduce the number of subproblems
c) To identify subproblems that share common solutions to avoid
redundant computation
d) To increase the time complexity of the algorithm
Answer: c
