Essentials of Genetics

William S. Klug, Michael R. Cummings, Charlotte A. Spencer

Chapter 17 Recombinant DNA Technology - all with Video Answers

Educators

Chapter Questions

Problem 1

In this chapter, we focused on the analysis of genomes, transcriptomes, and proteomes and considered important applications and findings from these endeavors. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions?
(a) How do we know which contigs are part of the same chromosome?
(b) How do we know if a genomic DNA sequence contains a protein-coding gene?
(c) What evidence supports the concept that humans share substantial sequence similarities and gene functional similarities with model organisms?
(d) How can proteomics identify differences between the number of protein-coding genes predicted for a genome and the number of proteins expressed by a genome?
(e) How has the concept of a reference genome evolved to encompass a broader understanding of genomic variation in humans?
(f) How have microarrays demonstrated that, although all cells of an organism have the same genome, some genes are expressed in almost all cells, whereas other genes show celland tissue-specific expression?

Jennifer Stoner

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02:06

Problem 1

In this chapter we focused on how specific DNA sequences can be copied, identified, characterized, and sequenced. At the same time, we found many opportunities to consider the methods and reasoning underlying these techniques. From the explanations given in the chapter, what answers would you propose to the following fundamental questions?
(a) In a recombinant DNA cloning experiment, how can we determine whether DNA fragments of interest have been incorporated into plasmids and, once host cells are transformed, which cells contain recombinant DNA?
(b) What steps make PCR a chain reaction that can produce millions of copies of a specific DNA molecule in a matter of hours without using host cells?
(c) How has DNA-sequencing technology evolved in response to the emerging needs of genome scientists?
(d) How can gene knockouts, transgenic animals, and geneediting techniques be used to explore gene function?

Jennifer Stoner

Numerade Educator

00:45

Problem 2

Review the Chapter Concepts list on
p. $347 .$ All of these pertain to how genomics, bioinformatics, and proteomics approaches have changed how scientists study genes and proteins. Write a short essay that explains how recombinant DNA techniques were used to identify and study genes compared to how modern genomic techniques have revolutionized the cloning and analysis of genes.

Jennifer Stoner

Numerade Educator

00:45

Problem 2

Review the Chapter Concepts list on
p. $323 .$ All of these refer to recombinant DNA methods and applications. Write a short essay or sketch a diagram that provides an overview of how recombinant DNA techniques help geneticists study genes.

Jennifer Stoner

Numerade Educator

00:52

Problem 3

What roles do restriction enzymes, vectors, and host cells play in recombinant DNA studies? What role does DNA ligase perform in a DNA cloning experiment? How does the action of DNA ligase differ from the function of restriction enzymes?

Sam Limsuwannarot

Numerade Educator

00:36

Problem 3

What is functional genomics? How does it differ from comparative genomics?

Alexander Burbelo

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01:45

Problem 4

The human insulin gene contains a number of sequences that are removed in the processing of the mRNA transcript. Bacterial cells cannot excise these sequences from mRNA transcripts, yet this gene can be cloned into a bacterial cell and produce insulin. Explain how this is possible.

Miwa Wenzel

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01:35

Problem 4

Contrast WGS for gene identification to linkage map-based approaches that you learned about in Chapter 7

Evey Z

Numerade Educator

01:57

Problem 5

Although many cloning applications involve introducing recombinant DNA into bacterial host cells, many other cell types are also used as hosts for recombinant DNA. Why?

Ramesh Singh

Numerade Educator

00:42

Problem 5

What is bioinformatics, and why is this discipline essential for studying genomes? Provide two examples of bioinformatics applications.

Sam Limsuwannarot

Numerade Educator

04:36

Problem 6

Annotation involves identifying genes and gene-regulatory sequences in a genome. List and describe characteristics of a genome that are hallmarks for identifying genes in an unknown sequence. What characteristics would you look for in a bacterial genome? A eukaryotic genome?

Dr. Anas Syed

Numerade Educator

01:41

Problem 6

Using DNA sequencing on a cloned DNA segment, you recover the nucleotide sequence shown below. Does this segment contain a palindromic recognition sequence for a restriction enzyme? If so, what is the double-stranded sequence of the palindrome, and what enzyme would cut at this sequence? (Consult Figure 17.1 for a list of restriction sites.) CAGTATGGATCCCAT

Joanna Quigley

Numerade Educator

01:26

Problem 7

How do high-throughput techniques such as computerautomated, next-generation sequencing, and mass spectrometry facilitate research in genomics and proteomics? Explain.

Josee Pacheco

Numerade Educator

01:39

Problem 7

Restriction sites are palindromic; that is, they read the same in the $5^{\prime}$ to $3^{\prime}$ direction on each strand of DNA. What is the advantage of having restriction sites organized this way?

Deborah Greenspan

Numerade Educator

00:49

Problem 8

List the advantages and disadvantages of using plasmids as cloning vectors. What advantages do BACs and YACs provide over plasmids as cloning vectors?

Sam Limsuwannarot

Numerade Educator

01:31

Problem 8

BLAST searches and related applications are essential for analyzing gene and protein sequences. Define BLAST, describe basic features of this bioinformatics tool, and give an example of information provided by a BLAST search.

Christina Sorrentino

Numerade Educator

03:17

Problem 9

What are the advantages of using a restriction enzyme whose recognition site is relatively rare? When would you use such enzymes?

John Barone

Numerade Educator

08:58

Problem 9

Describe three major goals of the Human Genome Project.

Danielle Ashley

Numerade Educator

01:42

Problem 10

In the context of recombinant DNA technology, of what use is a probe?

Ricajoy Montero

Numerade Educator

00:30

Problem 10

Describe the human genome in terms of genome size, the percentage of the genome that codes for proteins, how much is composed of repetitive sequences, and how many genes it contains. Describe two other features of the human genome.

Sam Limsuwannarot

Numerade Educator

00:31

Problem 11

If you performeda PCR experimentstarting withonly onecopy of double-stranded DNA, approximately how many DNA molecules would be present in the reaction tube after 15 cycles of amplification?

Sam Limsuwannarot

Numerade Educator

02:51

Problem 11

Recall that when the HGP was completed, more than 40 percent of the genes identified had unknown functions. The PANTHER
database provides access to comprehensive and current functional assignments for human genes (and genes from other species). Go to http://www.pantherdb.org/data/. In the frame on the left side of the screen locate the "Quick links" and use the "Whole genome function views" link to a view of a pie chart of current functional classes for human genes. Mouse over the pie chart to answer these questions. What percentage of human genes encode transcription factors? Cytoskeletal proteins? Transmembrane receptor regulatory/adaptor proteins?

James Kiss

Numerade Educator

02:35

Problem 12

What advantages do cDNA libraries provide over genomic DNA libraries? Describe cloning applications where the use of a genomic library is necessary to provide information that a cDNA library cannot.

Kendrick Buford

Numerade Educator

02:27

Problem 12

The Human Genome Project has demonstrated that in humans of all races and nationalities approximately 99.9 percent of the genome sequence is the same, yet different individuals can be identified by DNA fingerprinting techniques. What is one primary variation in the human genome that can be used to distinguish different individuals? Briefly explain your answer.

Ramesh Singh

Numerade Educator

00:45

Problem 13

Through the Human Genome Project (HGP), a relatively accurate human genome sequence was published from combined samples from multiple individuals. It serves as a reference for a haploid genome. How do results from personal genome projects (PGP) differ from those of the HGP?

Sam Limsuwannarot

Numerade Educator

04:28

Problem 13

In a typical PCR reaction, describe what is happening in stages occurring at temperature ranges
(a) $92-95^{\circ} \mathrm{C},$ (b) $45-65^{\circ} \mathrm{C},$ and
(c) $65-75^{\circ} \mathrm{C}$

Dennis Howard

Numerade Educator

00:21

Problem 14

Explain differences between whole-genome sequencing (WGS) and whole-exome sequencing (WES), and describe advantages and disadvantages of each approach for identifying diseasecausing mutations in a genome. Which approach was used for the Human Genome Project?

Sam Limsuwannarot

Numerade Educator

01:15

Problem 14

We usually think of enzymes as being most active at around $37^{\circ} \mathrm{C},$ yet in $\mathrm{PCR}$ the DNA polymerase is subjected to multiple exposures of relatively high temperatures and seems to function appropriately at $65-75^{\circ} \mathrm{C}$. What is special about the DNA polymerase typically used in PCR?

Shireen Shah

Numerade Educator

04:25

Problem 15

Traditional Sanger sequencing has largely been replaced in recent years by next-generation and third-generation sequencing approaches. Describe advantages of these sequencing methods over first-generation Sanger sequencing.

Jenny Wu

Numerade Educator

01:27

Problem 15

Describe the significance of the Genome 10K project.

Shiksha Dutta

Numerade Educator

01:45

Problem 16

It can be said that modern biology is experiencing an "omics" revolution. What does this mean? Explain your answer.

Joanna Quigley

Numerade Educator

01:43

Problem 16

How is fluorescence in situ hybridization (FISH) used to produce a spectral karyotype?

Mir Afzal

Numerade Educator

00:50

Problem 17

Metagenomics studies generate very large amounts of sequence data. Provide examples of genetic insight that can be learned from metagenomics.

Jennifer Stoner

Numerade Educator

02:11

Problem 17

What is the difference between a knockout animal and a transgenic animal?

Bryan Valdivia

Numerade Educator

05:24

Problem 18

What are DNA microarrays? How are they used?

Xiao Zi Huang

Numerade Educator

02:29

Problem 18

One complication of making a transgenic animal is that the transgene might integrate at random into the coding region, or the regulatory region, of an endogenous gene. What might be the consequences of such random integrations? How might this complicate genetic analysis of the transgene?

Aditya Sood

Numerade Educator

01:01

Problem 19

Annotation of the human genome sequence reveals a discrepancy between the number of protein-coding genes and the number of predicted proteins actually expressed by the genome. Proteomic analysis indicates that human cells are capable of synthesizing more than 100,000 different proteins and perhaps three times this number. What is the discrepancy, and how can it be reconciled?

Joanna Quigley

Numerade Educator

01:11

Problem 19

When disrupting a mouse gene by knockout, why is it desirable to breed mice until offspring homozygous $(-/-)$ for the knockout target gene are obtained?

Sana Riaz

Numerade Educator

03:36

Problem 20

In Section 18.8 we briefly discussed The Human Proteome Map (HPM). An interactive Web site for the HPM is available at http:// www.humanproteomemap.org. Visit this site, and then answer the questions in parts (a) and (b) and complete part (c).
(a) How many proteins were identified in this project?
(b) How many fetal tissues were analyzed?
(c) Use the "Query" tab and select the "Gene family" dropdown menu to do a search on the distribution of proteins encoded by a pathway of interest to you. Search in fetal tissues, adult tissues, or both.

Celine Ibrahim

Numerade Educator