Question 1

What is proteomics?

Accepted Answer

Proteomics is the study of the entire set of proteins produced by an organism or system, which includes their structures, functions, and interactions. Option B accurately describes this definition. Option A describes genomics, while option C refers to proteome functional analysis. Options D and E are incorrect as they focus on single proteins or genes, whereas proteomics studies the larger-scale protein networks and interactions.

Question 2

Which of the following most correctly describes a shotgun technique for sequencing a genome?

Accepted Answer

Shotgun sequencing involves breaking the genome into smaller fragments, cloning them into vectors of varying sizes, and then sequencing the clones. These sequences are then assembled in the correct order using computer algorithms. This approach allows for efficient sequencing of the entire genome without having to physically map it first.

Question 3

Which procedure is not required when the shotgun approach to sequencing is modified as sequencing by synthesis, in which many small fragments are sequenced simultaneously?

Accepted Answer

In sequencing by synthesis, cloning each fragment into a plasmid is not required. This method relies on the simultaneous sequencing of many small fragments, often using PCR amplification to increase the quantity of DNA, thus bypassing the need for cloning into vectors for propagation in bacteria.

Question 4

If humans have 2,900 Mb, a specific member of the lily family has 120,000 Mb, and a yeast has ~13 Mb, why can't this data allow us to order their evolutionary significance?

Accepted Answer

The size of an organism's genome does not necessarily correlate with its complexity or evolutionary significance, as much of the DNA may be non-coding or "junk" DNA.

Question 5

For mapping studies of genomes, most of which were far along before 2000, the three-stage method was often used. Which of the following is the usual order in which the stages were performed, assuming some overlap of the three?

Accepted Answer

The usual order for the three-stage method in mapping studies of genomes is to first create a linkage map, then a physical map, and finally sequence the fragments. This allows for a systematic approach to understanding the structure and organization of genes and their positions on chromosomes. The other choices listed do not follow this standard order.

Question 6

Why might the cricket genome have 11 times as many base pairs as that of Drosophila melanogaster?

Accepted Answer

The question specifically asks about the number of base pairs in the genome, so A and C are not relevant. It is unlikely that crickets have higher gene density than Drosophila, so B can be eliminated. E is also unlikely as the number of proteins produced by an organism is not directly related to its genome size. Therefore, the most likely explanation is that crickets have more noncoding DNA, which contributes to their larger genome size.

Question 7

What is metagenomics?

Accepted Answer

Metagenomics is the study of genetic material recovered from environmental samples, including the sequencing of DNA from a group of species from the same ecosystem. This approach allows for the analysis of microbial diversity and community structure without the need for isolation and cultivation of individual organisms.

Question 8

How is a physical map of the genome of an organism achieved?

Accepted Answer

A physical map of the genome is achieved using restriction enzyme cutting sites, which help to determine the locations of genes and other significant sequences within the genome.

Question 9

Bioinformatics can be used to scan sequences for probable genes looking for start and stop sites for transcription and for translation, for probable splice sites, and for sequences known to be found in other known genes. Such sequences containing these elements are called

Accepted Answer

The described sequences containing start and stop sites for transcription and translation, splice sites, and sequences known to be found in other genes are most likely expressed sequence tags (ESTs). ESTs are short DNA sequences generated from complementary DNAs (cDNAs) of expressed genes, and they can be used to identify and characterize potential genes in a given sequence. Choice B (cDNA) refers to the reverse transcription of mRNA into cDNA, and it may be used to study gene expression, but it is not directly applicable to the described scenario. Choice C (multigene families) refers to groups of genes with similar sequences and functions, but it is not specifically related to identifying potential genes in a sequence. Choice D (proteomes) refers to the entire set of proteins produced by an organism or system, and it is not directly relevant to identifying genes. Choice E (short tandem repeats) are repetitive DNA sequences that can be used in genetic analysis, but they are not directly relevant to identifying genes based on start and stop sites and splice sites.

Question 10

A microarray known as a GeneChip, with most now-known human protein coding sequences, has been developed to aid in the study of human cancer by first comparing two to three subsets of cancer subtypes. What kind of information might be gleaned from this GeneChip to aid in cancer prevention?

Accepted Answer

The GeneChip can provide information about which kind of cancer a patient is likely to acquire, which can aid in cancer prevention by allowing individuals to take steps to reduce their risk of developing that type of cancer.

Question 11

Why is it unwise to try to relate an organism's complexity with its size or number of cells?

Accepted Answer

The answer of Why is it unwise to try to...

Question 12

What is bioinformatics?

Accepted Answer

Bioinformatics is a field that uses various computational tools and techniques to store, organize, analyze, and retrieve biological data, particularly DNA and protein sequences. One of the key aspects of bioinformatics is the use of very large national and international databases to access and work with sequence information. This allows researchers to compare and analyze different genomes, predict protein structures and functions, and identify potential drug targets.

Question 13

What is gene annotation in bioinformatics?

Accepted Answer

Gene annotation involves identifying elements like transcriptional start and stop sites, RNA splice sites, and ESTs in the genome.

Question 14

Which of the following is a representation of gene density?

Accepted Answer

Gene density is the number of genes per unit of DNA. Choice C represents the number of genes in a given amount of DNA, so it is a representation of gene density.

Answer: E 
 Genome size alone does not necessarily reflect gene density, but it can provide some information about it. In general, larger genomes tend to have lower gene density than smaller genomes. Therefore, Fritillaria having a genome 40 times the size of a human suggests that it likely has a lower gene density than humans.

Question 15

Fragments of DNA have been extracted from the remnants of extinct woolly mammoths, amplified, and sequenced. These can now be used to

Accepted Answer

The fragments of DNA extracted from woolly mammoths can be used to understand the evolutionary relationships among members of related taxa. This is because the DNA contains genetic information that can help in tracing the evolutionary history of related species. By comparing the DNA sequences of different species, scientists can determine how closely related they are and how they have evolved over time. This can help in understanding the evolutionary relationships among woolly mammoths and other wool-producing animals. The other choices are not feasible because introducing mammoth traits into relatives or cloning live woolly mammoths are not currently possible, and studying the relationships among woolly mammoths and other wool-producers does not require DNA sequencing. E is a secondary benefit rather than the main purpose of DNA sequencing woolly mammoths.

Question 16

Barbara McClintock, who achieved fame for discovering that genes could move within genomes, had her meticulous work ignored for nearly four decades, but eventually won the Nobel Prize. Why was her work so distrusted?

Accepted Answer

Geneticists at the time believed that DNA was stable and fixed, and McClintock's discovery challenged this belief. Therefore, her work was initially met with skepticism and distrust.

Question 17

What is the difference between a linkage map and a physical map?

Accepted Answer

A linkage map is based on the frequency of recombination events between genetic markers, whereas a physical map is based on the physical distance between markers in base pairs. This means that the markers on a linkage map will be spaced by recombination frequency, while on a physical map they will be spaced by the number of base pairs between them.

Answer: B
 A physical map is based on the actual sequence of DNA and requires the identification of specific markers or sequences along the DNA molecule. A linkage map, on the other hand, does not require knowledge of the actual DNA sequence, only the frequency of recombination events between markers.

Answer: D
 Distances on a physical map are typically measured in units such as nanometers or base pairs, while distances on a linkage map are typically measured in map units or centimorgans. The physical map is a representation of the actual physical distance between markers, whereas the linkage map represents the genetic distance between markers as determined by recombination frequency.

Question 18

The biggest problem with the shotgun technique is its tendency to underestimate the size of the genome. Which of the following might best account for this?

Accepted Answer

The shotgun technique can miss detecting duplicated sequences, which are common in many genomes. This can lead to an underestimation of genome size.

Question 19

What is the most probable explanation for the continued presence of pseudogenes in a genome such as our own?

Accepted Answer

The answer of What is the most probable explanation for...

Question 20

The comparison between the number of human genes and those of other animal species has led to many conclusions, including

Accepted Answer

While humans have a similar number of genes to many other animal species, we are capable of producing a far greater number of proteins due to alternative splicing and other mechanisms. This means that one gene can result in multiple protein products, leading to a more diverse proteome than would be expected based on gene number alone.

Quiz 21: Genomes and Their Evolution