BIO 440 Midterm Functional Genomics 2025 Fall B-
Arizona State |2025-2026|
BIO 440: Functional Genomics (2022 Fall - B) - Midterm Examination
Section I: Foundational Concepts & Central Dogma (Questions 1-15)
1. What is the primary distinction between "structural genomics" and "functional
genomics"?
A) Structural genomics focuses on DNA, while functional genomics focuses on RNA.
B) Structural genomics aims to determine the 3D structure of genomes, while functional
genomics aims to understand gene function and interaction.
C) Structural genomics studies prokaryotes, while functional genomics studies eukaryotes.
D) Structural genomics uses only computational methods, while functional genomics uses
only experimental methods.
Answer: B
Rationale: Structural genomics is focused on the physical structure of the genome and its
products (e.g., sequencing, physical mapping). Functional genomics aims to use this
structural data to understand the dynamic aspects of gene function, regulation, and
interaction on a genome-wide scale.
2. Which of the following best describes the "Central Dogma" of molecular biology?
A) RNA can be reverse transcribed into DNA, which is then translated into protein.
B) Genetic information flows from DNA to RNA via transcription, and from RNA to protein via
translation.
C) Proteins are the only molecules capable of catalyzing chemical reactions in the cell.
D) The sequence of a protein determines the sequence of DNA from which it was coded.
Answer: B
Rationale: The Central Dogma, as proposed by Francis Crick, describes the fundamental flow
of genetic information. While exceptions like reverse transcription exist, the core principle is
that DNA is transcribed to RNA, which is then translated to produce proteins.
3. A mutation occurs in a protein-coding gene that changes a codon from UAC (Tyrosine) to
UAU (Tyrosine). What type of mutation is this?
A) Missense mutation
, B) Nonsense mutation
C) Frameshift mutation
D) Silent mutation
Answer: D
Rationale: Because both UAC and UAU code for the same amino acid (Tyrosine), the protein
sequence remains unchanged. This is a silent mutation, often possible due to the
degeneracy of the genetic code.
4. Which of the following high-throughput technologies is most directly used to quantify
the complete set of mRNA transcripts present in a cell at a specific moment?
A) ChIP-Seq
B) RNA-Seq
C) Yeast Two-Hybrid screening
D) Bisulfite sequencing
Answer: B
Rationale: RNA-Sequencing (RNA-Seq) uses next-generation sequencing to determine the
identity and quantity of every RNA molecule in a sample. This provides a snapshot of the
transcriptome, revealing which genes are active and their expression levels.
5. What is the primary role of the enzyme helicase in DNA replication?
A) To synthesize new DNA strands by adding nucleotides.
B) To glue Okazaki fragments together on the lagging strand.
C) To unwind the double helix by breaking hydrogen bonds between base pairs.
D) To add a short RNA primer to initiate replication.
Answer: C
Rationale: DNA helicase is a motor protein that uses ATP hydrolysis to separate the two
complementary strands of the DNA double helix. This creates the replication fork, allowing
other enzymes like DNA polymerase to access the single-stranded templates.
6. Which of the following experimental approaches would be most suitable for identifying
the specific binding sites of a transcription factor across the entire genome?
A) RNA interference (RNAi)
B) Mass spectrometry
C) Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq)
D) Microarray analysis
Answer: C
Rationale: ChIP-Seq combines chromatin immunoprecipitation (ChIP) with high-throughput
sequencing. An antibody specific to the transcription factor of interest is used to pull down
the DNA fragments it is bound to. These fragments are then sequenced and mapped to the
genome to identify binding sites.
Arizona State |2025-2026|
BIO 440: Functional Genomics (2022 Fall - B) - Midterm Examination
Section I: Foundational Concepts & Central Dogma (Questions 1-15)
1. What is the primary distinction between "structural genomics" and "functional
genomics"?
A) Structural genomics focuses on DNA, while functional genomics focuses on RNA.
B) Structural genomics aims to determine the 3D structure of genomes, while functional
genomics aims to understand gene function and interaction.
C) Structural genomics studies prokaryotes, while functional genomics studies eukaryotes.
D) Structural genomics uses only computational methods, while functional genomics uses
only experimental methods.
Answer: B
Rationale: Structural genomics is focused on the physical structure of the genome and its
products (e.g., sequencing, physical mapping). Functional genomics aims to use this
structural data to understand the dynamic aspects of gene function, regulation, and
interaction on a genome-wide scale.
2. Which of the following best describes the "Central Dogma" of molecular biology?
A) RNA can be reverse transcribed into DNA, which is then translated into protein.
B) Genetic information flows from DNA to RNA via transcription, and from RNA to protein via
translation.
C) Proteins are the only molecules capable of catalyzing chemical reactions in the cell.
D) The sequence of a protein determines the sequence of DNA from which it was coded.
Answer: B
Rationale: The Central Dogma, as proposed by Francis Crick, describes the fundamental flow
of genetic information. While exceptions like reverse transcription exist, the core principle is
that DNA is transcribed to RNA, which is then translated to produce proteins.
3. A mutation occurs in a protein-coding gene that changes a codon from UAC (Tyrosine) to
UAU (Tyrosine). What type of mutation is this?
A) Missense mutation
, B) Nonsense mutation
C) Frameshift mutation
D) Silent mutation
Answer: D
Rationale: Because both UAC and UAU code for the same amino acid (Tyrosine), the protein
sequence remains unchanged. This is a silent mutation, often possible due to the
degeneracy of the genetic code.
4. Which of the following high-throughput technologies is most directly used to quantify
the complete set of mRNA transcripts present in a cell at a specific moment?
A) ChIP-Seq
B) RNA-Seq
C) Yeast Two-Hybrid screening
D) Bisulfite sequencing
Answer: B
Rationale: RNA-Sequencing (RNA-Seq) uses next-generation sequencing to determine the
identity and quantity of every RNA molecule in a sample. This provides a snapshot of the
transcriptome, revealing which genes are active and their expression levels.
5. What is the primary role of the enzyme helicase in DNA replication?
A) To synthesize new DNA strands by adding nucleotides.
B) To glue Okazaki fragments together on the lagging strand.
C) To unwind the double helix by breaking hydrogen bonds between base pairs.
D) To add a short RNA primer to initiate replication.
Answer: C
Rationale: DNA helicase is a motor protein that uses ATP hydrolysis to separate the two
complementary strands of the DNA double helix. This creates the replication fork, allowing
other enzymes like DNA polymerase to access the single-stranded templates.
6. Which of the following experimental approaches would be most suitable for identifying
the specific binding sites of a transcription factor across the entire genome?
A) RNA interference (RNAi)
B) Mass spectrometry
C) Chromatin Immunoprecipitation followed by sequencing (ChIP-Seq)
D) Microarray analysis
Answer: C
Rationale: ChIP-Seq combines chromatin immunoprecipitation (ChIP) with high-throughput
sequencing. An antibody specific to the transcription factor of interest is used to pull down
the DNA fragments it is bound to. These fragments are then sequenced and mapped to the
genome to identify binding sites.
