Question 1

Use the following information to answer the questions below.
You have isolated a gene sequence from the mustard plant Arabidopsis and have BLAST searched the NCBI database.Your sequence hit several EST sequences that were identified as transcription factors.These sequences were found in E.coli,Chlamydomonas (a green algae),yeast,mice,and humans and only had a few base pair differences.
-What can be said about this sequence?

Accepted Answer

The fact that the gene sequence is present in multiple species and only has a few base pair differences suggests that it is highly conserved.

Question 2

Which of the following techniques would be most appropriate to test the hypothesis that humans and chimps differ in the expression of a large set of shared genes?

Accepted Answer

DNA microarray analysis would be the most appropriate choice for testing the hypothesis that humans and chimps differ in the expression of a large set of shared genes. This technique can simultaneously measure the expression of thousands of genes and compare the gene expression profiles between species. PCR and DNA sequencing are better suited for studying individual genes or small sets of genes rather than large sets. Protein-protein interaction assays are used to study protein-protein interactions, not gene expression. Bioinformatics can be used to analyze and interpret the data obtained from DNA microarray analysis.

Question 3

Homeotic genes

Accepted Answer

Homeotic genes are responsible for controlling the development of specific anatomical structures by encoding transcription factors that regulate the expression of other genes. They are found in a wide range of organisms, including humans, and are not limited to arthropods. While many homeotic genes do contain a homeobox domain, this is not a defining characteristic. Finally, while homeotic genes can play a role in patterning during plant development, they are best known for their role in animal development.

Question 4

Use the following figure to answer the next few questions.
  
This figure shows a diagram of blocks of genes on human chromosome 16 and the locations of blocks of similar genes on four chromosomes of the mouse.
-Why is sequencing of eukaryotic genomes more difficult than sequencing genomes of bacteria or archaea?

Accepted Answer

Eukaryotic genomes are typically much larger and contain a larger proportion of repetitive DNA sequences than bacterial or archaeal genomes. This makes sequencing and assembly more complex and time-consuming.

Question 5

Use the following information to answer the questions below.
You have isolated a gene sequence from the mustard plant Arabidopsis and have BLAST searched the NCBI database.Your sequence hit several EST sequences that were identified as transcription factors.These sequences were found in E.coli,Chlamydomonas (a green algae),yeast,mice,and humans and only had a few base pair differences.
-What can be surmised about your transcription factor?

Accepted Answer

The answer of Use the following information to answer the...

Question 6

Using modern techniques of sequencing by synthesis and the shotgun approach,how are sequences assembled into chromosomes?

Accepted Answer

Sequences obtained using sequencing by synthesis and shotgun approach are short fragments. They are analyzed using bioinformatic tools that look for sequence overlaps to assemble them into longer contiguous sequences called contigs. These contigs are further assembled into chromosomes using computer programs that use genetic maps for scaffolding. Once the contigs are ordered based on their relative positions on the genetic map, the gaps between them are filled by resequencing targeted areas, and the entire sequence is polished to increase its accuracy.

Question 7

Use the following information to answer the questions below.
You have isolated a gene sequence from the mustard plant Arabidopsis and have BLAST searched the NCBI database.Your sequence hit several EST sequences that were identified as transcription factors.These sequences were found in E.coli,Chlamydomonas (a green algae),yeast,mice,and humans and only had a few base pair differences.
-When you compared your sequence to the database,what were you practising?

Accepted Answer

The BLAST search of the NCBI database is a common bioinformatics tool used to compare nucleotide or protein sequences to known sequences in the database. Therefore, comparing the gene sequence to the database is an example of bioinformatics.

Question 8

What is an early step in shotgun sequencing?

Accepted Answer

The first step in shotgun sequencing is to break the genomic DNA into random fragments. This is usually done using physical or chemical methods, such as sonication or restriction enzymes. Only option A mentions this step. The other options describe later steps in the process.

Question 9

Use the following figure to answer the next few questions.
  
This figure shows a diagram of blocks of genes on human chromosome 16 and the locations of blocks of similar genes on four chromosomes of the mouse.
-The movement of these blocks suggests that

Accepted Answer

The blocks of genes have moved between chromosomes in different species, suggesting chromosomal translocations.

Question 10

What does it mean if genomic DNA matches the sequence of a cDNA?

Accepted Answer

cDNA is synthesized from mRNA, which typically only includes coding regions of the gene without introns. If the genomic DNA matches the sequence of the cDNA, it indicates that the coding sequence is present in the genomic DNA, and therefore likely codes for a protein.

Question 11

After finding a new medicinal plant,a pharmaceutical company decides to determine if the plant has genes similar to those of other known medicinal plants by annotating the genome of the new plant.Why does the company do this?

Accepted Answer

Annotating the genome would identify genes and their functions, which would allow for a better understanding of the plant's potential medicinal properties. This information could be used to develop drugs or treatments based on the plant's unique genetics. Examining mRNA transcripts and protein production may also be important, but the primary objective of genome annotation is to identify genes and their functions. The location of mRNA or introns may not be as relevant for this particular goal.

Question 12

Use the following figure to answer the next few questions.
  
This figure shows a diagram of blocks of genes on human chromosome 16 and the locations of blocks of similar genes on four chromosomes of the mouse.
-In humans,hemoglobin in the embryo has a higher affinity for oxygen than in adults.What is this due to?

Accepted Answer

The question is focused on the difference in hemoglobin affinity for oxygen during development in humans. This suggests that the answer involves a difference in the genes or gene expression during development. Choice A is the most directly related to this concept, as it suggests that nonidentical genes produce different versions of globins during development, which would explain the difference in hemoglobin affinity. The other choices are not directly related to this concept or are incorrect (such as pseudogenes interfering with gene expression in adults).

Question 13

Bioinformatics includes all of the following except

Accepted Answer

Using molecular biology to combine DNA from two different sources in a test tube does not fall under the scope of bioinformatics. It is a technique commonly used in genetic engineering and biotechnology. The other choices are all related to bioinformatics, which involves the application of computational and statistical methods to analyze and interpret biological data.

Question 14

Use the following figure to answer the next few questions.
  
This figure shows a diagram of blocks of genes on human chromosome 16 and the locations of blocks of similar genes on four chromosomes of the mouse.
-Several of the different globin genes are expressed in humans,but at different times in development.What mechanism could allow for this?

Accepted Answer

Differential gene regulation over time allows for different genes to be expressed at different developmental stages, including the different globin genes.

Question 15

Use the following figure to answer the next few questions.
  
This figure shows a diagram of blocks of genes on human chromosome 16 and the locations of blocks of similar genes on four chromosomes of the mouse.
-How might identical and obviously duplicated gene sequences have gotten from one chromosome to another?

Accepted Answer

Chromosomal translocation is the movement of a segment of one chromosome to another nonhomologous chromosome. This could result in the transfer of gene sequences from one chromosome to another.

Question 16

A DNA microarray is a tool that owes its existence to earlier genomics investigations.What essential contribution of genomics makes microarrays possible?

Accepted Answer

Knowledge of which DNA sequences to synthesize for the array is essential for designing and producing the microarray. Without the prior knowledge of DNA sequences, microarrays would not be possible.

Question 17

What can proteomics reveal that genomics cannot?

Accepted Answer

Proteomics can reveal the set of proteins present within a cell or tissue type, which genomics cannot because genomics only deals with the sequence information of DNA. While genomics can predict the amino acid sequence of a protein, proteomics can confirm the presence, abundance, and modifications of proteins in a sample. Proteomics can provide information on post-translational modifications, protein-protein interactions, and the activity of proteins, which can be crucial for understanding cellular processes and disease mechanisms.

Question 18

Based on the systems approach employed by the ENCODE project,what percentage of the genome is estimated to contain functional elements (including functional RNAs and regulatory sequences)?

Accepted Answer

The ENCODE project estimated that at least 80% of the genome contains functional elements, including functional RNAs and regulatory sequences, based on a systems approach. This is a much higher percentage than previously thought when considering only genes that code for proteins.

Question 19

Two eukaryotic proteins have one domain in common but are otherwise very different.Which of the following processes is most likely to have contributed to this similarity?

Accepted Answer

Exon shuffling is the process by which individual exons from genes are mixed and matched to create new combinations of genes. This can result in the formation of new proteins that have domains in common with other proteins, even if the rest of the protein is very different. Therefore, exon shuffling is the most likely process that contributed to the similarity of the two eukaryotic proteins.

Question 20

One of the characteristics of retrotransposons is that

Accepted Answer

Retrotransposons are a type of transposable element that uses a reverse transcriptase enzyme to make a DNA copy of their RNA transcript, which is then integrated into a new site in the genome. This process is similar to the replication strategy used by retroviruses. Thus, retrotransposons encode the enzyme reverse transcriptase, which synthesizes DNA using an RNA template.

Quiz 21: Genomes and Their Evolution