Question 1

In the microarray shown in the textbook (p. 414), the cDNAs were labeled with red and green fluorescent tags. Why do some spots on the microarray emit yellow light?

Accepted Answer

When both red and green cDNAs hybridize to the same spot on a microarray, the combined fluorescence appears yellow due to the additive color mixing of red and green light.

Question 2

Which technique can most accurately quantify RNA and determine levels of gene expression?

Accepted Answer

RNA-seq is the most accurate technique for quantifying RNA and determining levels of gene expression because it directly sequences the RNA in a sample, allowing for a precise measurement of gene expression levels.

Question 3

What can be removed from pre-mRNA during alternative splicing?

Accepted Answer

During alternative splicing, both exons and introns can be removed to produce different mRNA variants from the same pre-mRNA transcript.

Question 4

RNAi is commonly used in which experimental strategy?

Accepted Answer

RNAi (RNA interference) is a biological process used to silence or reduce the expression of specific genes, effectively "knocking down" their activity.

Question 5

A researcher wants to investigate the function of a gene without permanently altering the gene's function or activity. Which experimental approach should she choose?

Accepted Answer

Gene knockdown is the appropriate choice because it allows for the temporary reduction in the expression of a gene, enabling the study of its function without permanently altering the gene's function or activity.

Question 6

During DNA sequence annotation, which feature is not identified?

Accepted Answer

Protein interactions are not typically identified during DNA sequence annotation. DNA sequence annotation focuses on identifying and mapping regions of the genome that encode for proteins (protein-coding genes), noncoding RNA genes, origins of replication, and pseudogenes, rather than detailing interactions between proteins. Protein interactions are usually studied in the context of proteomics or functional genomics, not during the initial DNA sequence annotation process.

Question 7

Microarrays let us identify which DNA sequences are present in a particular cell type under certain conditions. How can microarrays help us understand cellular functions?

Accepted Answer

Microarrays are used to identify which genes are being expressed at a particular time in a cell, providing insights into the cell's function and how it responds to different conditions.

Question 8

The study of gene function by observing changes in phenotype is termed _____.

Accepted Answer

Phenomics is the study of phenomes—the physical and biochemical traits of organisms—as they change in response to genetic mutation and environmental influences. It involves observing changes in phenotype to understand gene function.

Question 9

Through a sequence similarity search, a researcher identifies a gene whose predicted protein product has a putative function of a photosynthesis-enhancing enzyme. Which experimental method could be performed to verify this function?

Accepted Answer

The answer of Through a sequence similarity search, a researcher...

Question 10

Which eukaryotic organelle(s) contain its/their own DNA?

Accepted Answer

Mitochondria and chloroplasts both contain their own DNA, which allows them to replicate independently of the cell's nucleus. This is a key piece of evidence supporting the endosymbiotic theory, which suggests that these organelles were once independent prokaryotic organisms.

Question 11

Which field of study applies mathematics and computer science to gain information from biological data, such as data related to gene structure and function?

Accepted Answer

Bioinformatics is the field that applies mathematics and computer science to analyze and interpret biological data, including information related to gene structure and function.

Question 12

Many cancers can be identified based on microarray analysis of _____.

Accepted Answer

Signature genes are often used in microarray analysis to identify various types of cancers because these genes have expression patterns that are unique or significantly altered in cancerous cells compared to normal cells.

Question 13

A(n) _____ has a DNA sequence similar to a functional gene, but has been mutated so that it no longer produces a functional gene product.

Accepted Answer

Pseudogenes are sequences of DNA that are similar to functional genes but have been mutated in such a way that they no longer produce a functional product. They can arise through processes such as gene duplication followed by mutation that disrupts the gene's function.

Question 14

Protein-coding ORFs are easier to identify in which type of organism?

Accepted Answer

Prokaryotes have few or no introns, making their protein-coding ORFs easier to identify compared to eukaryotes, which often contain numerous introns within their genes.

Question 15

RNA-seq (whole-transcriptome sequencing) _____.

Accepted Answer

RNA-seq identifies and quantifies RNA transcripts in a sample, providing insights into the transcriptome of an organism at a given time. It is not limited to identifying only 100 sequences at a time, nor is it a hybridization technique or being replaced by DNA microarrays. While it can be used in cancer research, stating it as the most common method for identifying cancer genes is too specific and overlooks its broad applications.

Question 16

What is directly sequenced in RNA-seq?

Accepted Answer

The answer of What is directly sequenced in RNA-seq?
...

Question 17

A gene encoding a subunit of hemoglobin in humans is found to be homologous to a gene in chimpanzees. The homologous gene in chimpanzees likely _____.

Accepted Answer

Homologous genes in different species often encode proteins that perform similar functions. Since the gene in humans encodes a subunit of hemoglobin, the homologous gene in chimpanzees is likely to encode the same or a very similar hemoglobin subunit, given the close evolutionary relationship between humans and chimpanzees.

Question 18

A sequence similarity search reveals that a candidate gene's sequence has a partial match to a known gene's sequence. What does this most likely indicate?

Accepted Answer

A partial match in a sequence similarity search suggests that the candidate gene may share a specific protein domain with the known gene, indicating a possible functional or structural similarity at the domain level, rather than implying identical genes or proteins.

Question 19

Which organism has the largest number of protein-coding genes?

Accepted Answer

Oryza sativa (rice) has the largest number of protein-coding genes among the options listed, with over 50,000 genes.

Question 20

A researcher obtains the results of his RNA-seq analysis. Several transcripts are listed as being derived from the same gene. How is this possible?

Accepted Answer

Alternative splicing allows for different transcripts to be created from the same gene sequence by including or excluding certain exons, leading to multiple mRNA variants from a single gene.

Quiz 19: Genomes and Proteomes

In the microarray shown in the textbook (p. 414) , the cDNAs were labeled with red and green fluorescent tags. Why do some spots on the microarray emit yellow light?