CONCEPT MAP: THE GENERATION OF BIOCHEMICAL ENERGY
26.5 Genomics: Using What We Know
Genomics has a simple and straightforward definition: it is the study of whole sets of genes and their functions. Genomics is inspiring studies that reach into all aspects of plant and animal life. For example, the study of bacterial genomics has been instrumental in linking the three domains of life—Archaea (formerly archeabacteria), Bacteria, and Eukarya—to one another from an evolutionary standpoint. The study of bacterial genomics is not only giving us a better understanding of how bacteria cause disease, it is also helping in the development of new therapies. Plant genomics is enhancing the value and utility of agricultural crops. The genomic study of farm ani- mals is improving their health and availability. Humans will benefit from all of these studies, as well as those that contribute to their own health.
To glimpse where genomics is headed, we have provided descriptions of some of its applications in Table 26.3. These descriptions are not quite definitions; many of these fields are so new that their territory is viewed differently by different individuals. At the opening of this chapter, we noted that we stand at the beginning of a revolution. You may well en- counter some of the endeavors listed in Table 26.3 as the revolution proceeds.
Genetically Modified Plants and Animals
The development of new varieties of plants and animals has been proceeding for cen- turies as the result of natural accidents and occasional success in the hybridization of known varieties. The techniques for mapping, studying, and modifying human genes apply equally as well to the genomes of plants and other animals. The mapping and study of plant and animal genomes can greatly accelerate our ability to generate crop plants and farm animals with desirable characteristics and lacking undesirable ones.
Some genetically modified crops have already been planted in large quantities in the United States. Each year millions of tons of corn are destroyed by a caterpillar (the European corn borer) that does its damage deep inside the corn stalk and out of reach of pesticides. To solve this problem, a bacterial gene (from Bacillus thuringiensis, Bt) has been transplanted into corn. The gene causes the corn to produce a toxin that kills the caterpillars. In 2000, one-quarter of all corn planted in the United States was Bt corn.
Soybeans genetically modified to withstand herbicides are also widely grown. The soy- bean crop remains unharmed when the surrounding weeds are killed by the herbicide.
Genomics The study of whole sets of genes and their functions.
S E C T I O N 2 6 . 5 Genomics: Using What We Know 819
Tests are under way with genetically modified coffee beans that are caffeine-free, potatoes that absorb less fat when they are fried, and “Golden Rice,” a yellow rice that provides the vitamin A desperately needed in poor populations where insufficient vita- min A causes death and blindness.
Fish farming is an expanding industry as natural populations of fish diminish. There are genetically engineered salmon that can grow to 7–10 pounds, a marketable size, in up to one-half the time of their unmodified cousins. Similar genetic modifications are anticipated for other varieties of fish, and there is the prospect of cloning leaner pigs.
Will genetically modified plants and animals intermingle with natural varieties and cause harm to them? Should food labels state whether the food contains genetically modified ingredients? Might unrecognized harmful substances enter the food supply?
These are hotly debated questions and have led to the establishment of the Non-GMO Project, where the GMO stands for genetically modified organism. The goal of this project is to offer consumers a non-GMO choice for organic and natural products that are produced without genetic engineering or recombinant DNA technologies. Many foods found in stores are labeled “Non-GMO.”
Table 26.3 Genomics-Related Fields of Study Biotechnology
A collective term for the application of biological and biochemical research to the development of products that improve the health of humans, other animals, and plants.
Bioinformatics
The use of computers to manage and interpret genomic information and to make predictions about biological systems. Applications of bioinformatics include studies of individual genes and their functions, drug design, and drug development.
Functional genomics
Use of genome sequences to solve biological problems.
Comparative genomics
Comparison of the genome sequences of different organisms to discover regions with similar functions and perhaps similar evolutionary origins.
Proteomics
Study of the complete set of proteins coded for by a genome or synthesized within a given type of cell, including the quest for an understanding of the role of each protein in healthy or diseased conditions. This understanding has potential application in drug design and is being pursued by more than one commercial organization.
Pharmacogenomics
The genetic basis of responses to drug treatment. Goals include the design of more effective drugs and an understanding of why certain drugs work in some patients but not in others.
Pharmacogenetics
The matching of drugs to individuals based on the content of their personal genome in order to avoid administration of drugs that are ineffective or toxic and focus on drugs that are most effective for that individual.
Toxicogenomics
A newly developing application that combines genomics and bioinformatics in studying how toxic agents affect genes and in screening possibly harmful agents.
Genetic engineering
Alteration of the genetic material of a cell or an organism. The goals may be to make the organism produce new substances or perform new functions. Examples are introduction of a gene that causes bacteria to produce a desired protein or allows a crop plant to withstand the effects of a pesticide that repels harmful insects.
Gene therapy
Alteration of an individual’s genetic makeup with the goal of curing or preventing a disease.
Bioethics
The ethical implications of how knowledge of the human genome is used.
▲ ”Golden Rice” has been genetically modified to provide vitamin A.
But genetic modifications can also be used to produce previously unseen beauty.
Consider the blue rose, a f lower that is currently produced by dyeing white roses.
Suntory Limited, in a joint venture with Florigene, has recently been able to successfully implant into roses a gene from petunias that leads to the synthesis of blue pigments;
these roses are currently being grown in test batches in Japan. Even more exciting is the expectation that the introduction of blue pigments into roses will lead to an explosion in the variety of possible rose colors available to the average consumer.
Gene Therapy
Gene therapy, to put it simply, is the use of DNA to treat disease. It is based on the prem- ise that a disease-causing gene within an individual’s cells can be corrected or replaced by inserting a functional, healthy gene into the cells. The most clear-cut expectations for gene therapy lie in treating monogenic diseases, those that result from defects in a single gene.
The focus has been on using non-pathogenic viruses as vectors, the agents that de- liver therapeutic quantities of DNA directly into cell nuclei. The expectation was that this method could result in lifelong elimination of an inherited disease, and many stud- ies have been undertaken. Unfortunately, expectations remain greater than achievements thus far. Investigations into the direct injection of “naked DNA” have begun, with one early report of success in encouraging blood vessel growth in patients with inadequate blood supply to their hearts. The Food and Drug Administration (FDA) has, as of July 2011, not yet approved any human gene therapy product for sale. Current gene therapy is still experimental and has not proven to be widely successful in clinical trials. Although little progress has been made since the first gene therapy clinical trial began in 1990, vigorous research into this area continues as new approaches continue to be examined.
A Personal Genomic Survey
Suppose that prior to diagnosis and treatment for a health problem that a patient’s entire genome could be surveyed. What benefits might result? One possibility is that the choice of drugs could be directed toward those that are most effective for that individual. It is no secret that not everyone reacts in the same manner to a given medication. Perhaps the patient lacks an enzyme needed for a drug’s metabolism. It is known, for example, that codeine is ineffective as a pain killer in people who lack the enzyme that converts codeine into morphine, which is the active analgesic (see Section 15.6). Perhaps the patient has a monogenic defect, a flaw in a single gene that is the direct cause of the disease. Such a patient might, at some time in the future, be a candidate for gene therapy.
In cancer therapy there may be advantages in understanding the genetic differences between normal cells and tumor cells. Such knowledge could assist in chemotherapy, where the goal is use of an agent that kills the tumor cells but does the least possible amount of harm to noncancerous cells.
Another application of having human genomic information may arise from genetic screening of infants. The immediate use of gene therapy might eliminate the threat of a monogenically based disease. Or perhaps a lifestyle adjustment would be in order for an individual with one or more SNPs that predict a susceptibility to heart disease, diabetes, or some other disease that results from combinations of genetic and environ- mental influences. And consider that once done, an individual’s genetic map would be available for the rest of his or her life. Perhaps someday we may even carry a wallet card encoded with our genetic information. With this knowledge, however, also come ethi- cal dilemmas that have made this use of genomics a hotly debated topic.
Snips and Chips
Our understanding of SNPs is already at work in screening implemented by DNA chips. A DNA chip is a solid support bearing large numbers of short, single-stranded bits of DNA of known composition. The DNA is organized on the chip in whatever manner is best for a particular type of screening, for example, to identify the presence or absence of polymor- phisms. A sample to be screened is labeled with a fluorescent tag and applied to the chip.
During an incubation period, sample DNA and chip DNA with complementary nucleic
▲ A DNA chip used for genetic screening.
S U M M A R Y Revisiting the Chapter Goals 821 acid sequences will bond to each other. After excess sample of DNA is washed away, the
fluorescence remaining on the chip is read to discover where the bonding has occurred and thus what DNA variations are present in the sample DNA. A chip can be used, for example, to screen for the polymorphism that wipes out the analgesic effect of codeine.
Or consider a gene with several polymorphisms that codes for an enzyme responsible for metabolizing a cardiovascular agent, antipsychotic, or some other drug. Different indi- viduals may have no effect from a drug, the expected effect, or perhaps have a greater- than-normal response to the drug. Genomic screening can determine whether particular polymorphisms are linked to a patient’s ability to respond to the medication. Once such connections have been established, screening tests for polymorphisms of this enzyme could be a diagnostic test carried out by a DNA chip in a doctor’s office. The results would aid in choosing the right drug and dosage.
DNA-chip screening has already revealed the genetic variations responsible for two types of pediatric leukemia, a distinction that could not be made by examining dis- eased cells under the microscope. Because the two leukemias require quite different therapies, use of the chip to identify the types is a valuable development.
Bioethics
We can mention only briefly an area of major concern that arises from the revolution in genomics. This concern is not chemical, nor is it directly related to curing and pre- venting disease. The existence of this concern is recognized in the ELSI program of the National Human Genome Research Institute. ELSI deals with the Ethical, Legal, and Social Implications of human genetic research. The scope of ELSI is broad and thought-provoking. It deals with many questions such as the following:
• Who should have access to personal genetic information and how will it be used?
• Who should own and control genetic information?
• Should genetic testing be performed when no treatment is available?
• Are disabilities diseases? Do they need to be cured or prevented?
• Preliminary attempts at gene therapy are exorbitantly expensive. Who will have access to these therapies? Who will pay for their use?
• Should we re-engineer the genes we pass on to our children?
If you are interested in the ELSI program, their web page is an excellent resource (http://www.genome.gov/10001618).
PROBLEM 26.9
Classify the following activities according to the fields of study listed in Table 26.3.
(a) Identification of genes that perform identical functions in mice and humans (b) Creation of a variety of wheat that will not be harmed by an herbicide that kills
weeds that threaten wheat crops
(c) Screening of an individual’s genome to choose the most appropriate pain-killing medication for that person
(d) Computer analysis of base-sequence information from groups of people with and without a given disease to discover where the disease-causing polymorphism lies
SUMMARY: REVISITING THE CHAPTER GOALS
1. What is the working draft of the human genome and the circumstances of its creation? The Human Genome Project, an international consortium of not-for-profit institu- tions, along with Celera Genomics, a for-profit company, have both announced completion of working drafts of the human genome. With the exception of large areas of repeti- tive DNA, the DNA base sequences of all chromosomes have
been examined. The Human Genome Project utilized a series of progressively more detailed maps to create a collection of DNA fragments with known location. Celera began by randomly fragmenting all of the DNA without first placing it within the framework of a map. In both groups the fragments were cloned, labeled, ordered, and the individual sequences assembled by computers. The results of the two projects are
KEY WORDS
Clones, p. 807 Centromeres, p. 809 Genomics, p. 818 Mutagen, p. 811
Mutation, p. 811 Polymorphism, p. 811 Recombinant DNA, p. 814
Single-nucleotide polymorphism (SNP), p. 812
Telomeres, p. 809
UNDERSTANDING KEY CONCEPTS
26.10 What steps are necessary in the mapping of the human genome, as outlined by the Human Genome Project?
26.11 Clearly, all humans have variations in their DNA sequences. How is it possible to sequence the human ge- nome if every individual is unique? How was the diversity of the human genome addressed?
26.12 List the 4 types of noncoding DNA. Give the function of each, if it is known.
26.13 What are the similarities and differences between muta- tions and polymorphisms?
26.14 What is recombinant DNA? How can it be used to pro- duce human proteins in bacteria?
26.15 Identify some major potential benefits of the applications of genomics and some major negative outcomes.
ADDITIONAL PROBLEMS
THE HUMAN GENOME MAP
26.16 How did the private corporation Celera Genomics approach the sequencing of the human genome? What was the advantage of this approach?
26.17 How did the competition that developed between the groups developing the human genome map benefit the Human Genome Project?
26.18 Approximately what portion of the human genome is composed of repeat sequences?
26.19 Approximately how many base pairs were identified in the human genome working drafts?
26.20 Among the results of the genome working drafts, (a) were any human genes found to be identical to genes in bacteria generally supportive of each other. There are about three
billion base pairs and 20,000–25,000 genes in the human genome, each gene able to direct the synthesis of more than one protein. The bulk of the genome consists of noncoding, repetitive sequences. About 200 of the human genes are iden- tical to those in bacteria (see Problems 10–11, 16–22).
2. What are the various segments along the length of the DNA in a chromosome? Telomeres, which fall at the ends of chromosomes, are regions of noncoding, repetitive DNA that pro- tect the ends from accidental changes. At each cell division, the telomeres are shortened, with significant shortening associated with senescence and death of the cell. Telomerase, the enzyme that lengthens telomeres, is typically inactivated in adult cells but can become reactivated in cancer cells. Centromeres are the con- stricted regions of chromosomes that form during cell division and also carry noncoding DNA. Exons are the protein-coding regions of DNA and together make up the genes that direct protein syn- thesis. The repetitive noncoding segments of DNA are of either no function or unknown function (see Problems 12, 23–26).
3. What are mutations? A mutation is an error in the base sequence of DNA that is passed along during replication. Mutations arise by random error during replication but may also be caused by ionizing radiation, viruses, or chemical agents (mutagens). Mutations can cause inherited diseases and increase the tendency to acquire others (see Problems 13, 27–30, 36–38, 52, 55, 57).
4. What are polymorphisms and single-nucleotide polymorphisms (SNPs) and how can identifying them be useful? A polymorphism is a variation in DNA that is found
within a population. A SNP is the replacement of one nucleotide by another. The result might be the replacement of one amino acid by another in a protein, no change because the new codon specifies the same amino acid, or the introduction of a stop co- don. Many inherited diseases are known to be caused by SNPs, but they can also be beneficial or “neutral.” Understanding the location and effect of SNPs is expected to lead to new therapies (see Problems 31–35, 54, 56).
5. What is recombinant DNA? Recombinant DNA is produced by joining DNA segments that do not normally occur together.
A gene from one organism is inserted into the DNA of another organism. Recombinant DNA techniques can be used to create large quantities of a particular protein. The gene of interest is inserted into bacterial plasmids (small, extrachromosomal circular DNA). Bacteria carrying these plasmids then serve as factories for the synthesis of large quantities of the encoded protein (see Problems 14, 39–43).
6. What does the future hold for uses of genomic
information? Mapping the human genome holds major promise for applications in health and medicine. Drugs can be precisely chosen based on a patient’s own DNA, thereby avoiding drugs that are ineffective or toxic for that individual. Perhaps one day inherited diseases will be prevented or cured by gene therapy.
By genetic modification of crop plants and farm animals, the productivity, marketability, and health benefits of these products can be enhanced. Progress in each of these areas is bound to be accompanied by controversy and ethical dilemmas (see Problems 15, 45–51, 53).
Additional Problems 823 and (b) what was learned about the number of proteins
produced by a given gene?
26.21 What is the most surprising result found thus far in the human genome studies?
26.22 You may have heard of Dolly, the cloned sheep grown from an embryo created in a laboratory. But in the context of DNA mapping, what are clones and what essential role do they play?
CHROMOSOMES, MUTATIONS, AND POLYMORPHISMS
26.23 What is thought to be the primary purpose of telomeres?
26.24 How is the age of a cell predicted by its telomeric sequences?
26.25 What is the role of the enzyme telomerase? In what kind of cell is it normally most active and most inactive?
26.26 What is the centromere?
26.27 What is a mutagen?
26.28 What is a silent mutation?
26.29 Why is a mutation of a base in a DNA sequence much more serious than a mutation in a transcribed mRNA sequence?
26.30 What are the two general and common ways that muta- tions occur in a DNA sequence?
26.31 What is a SNP?
26.32 How are SNPs linked to traits in individual human beings?
26.33 List some potential biological effects of SNPs.
26.34 What would be a medical advantage of having a catalog of SNPs?
26.35 Does a single base pair substitution in a strand of DNA always result in a new amino acid in the protein coded for by that gene? Why or why not?
26.36 What determines the significance of a change in the iden- tity of an amino acid in a protein?
26.37 Compare the severity of DNA mutations that produce the following changes in mRNA codons:
(a) UCA to UCG (b) UAA to UAU
26.38 Compare the severity of DNA mutations that produce the following changes in mRNA codons:
(a) GCU to GCC (b) ACU to AUU RECOMBINANT DNA
26.39 Why are bacteria excellent hosts for recombinant DNA experiments?
26.40 What is an advantage of using recombinant DNA to make proteins such as insulin, human growth hormone, or blood-clotting factors?
26.41 How can DNA fragments be separated by size?
26.42 In the formation of recombinant DNA, a restriction endonu- clease cuts a bacterial plasmid to give sticky ends. The DNA segments that are to be added to the plasmid are cleaved with the same restriction endonuclease. What are sticky ends and why is it important that the target DNA and the plasmid it will be incorporated into have complementary sticky ends?
26.43 Give the sequence of unpaired bases that would be sticky with the following sequences:
(a) GGTAC (b) ACCCA (c) GTGTC 26.44 Are the following base sequences sticky or not sticky?
Each piece is written 5⬘ to 3⬘.
(a) TTAGC and GCTAA (b) CGTACG and CCTTCG GENOMICS
26.45 What is genomics?
26.46 What is pharmacogenomics and how might it benefit patient care?
26.47 Genetic engineering and gene therapy are similar fields within genomics. What do they have in common and what distinguishes them?
26.48 Provide two examples of genetically engineered crops that are improvements over their predecessors.
26.49 Imagine that you become a parent in an age when a full genetic workup is available for every baby. What advan- tages and disadvantages might there be to having this information?
26.50 What type of technology might be used to diagnose inherited diseases in the doctor’s office of the future?
26.51 Why is the field of bioethics so important in genomics?
GENERAL QUESTIONS AND PROBLEMS 26.52 What is a monogenic disease?
26.53 What is the role of a vector in gene therapy?
26.54 Write the base sequence that would be sticky with the sequence T-A-T-G-A-C-T.
26.55 If the DNA sequence A-T-T-G-G-C-C-T-A on an informa- tional strand mutated and became A-C-T-G-G-C-C-T-A, what effect would the mutation have on the sequence of the protein produced?
26.56 What is a restriction endonuclease?
26.57 In the DNA of what kind of cell must a mutation occur for the genetic change to be passed down to future generations?
CHEMISTRY IN ACTION
26.58 Explain why using either the DNA of a single individual or the DNA of a group of individuals from the same ethnic group would have been a bad choice in mapping the human genome. [One Genome to Represent Us All?, p. 808]
26.59 What is the purpose of the polymerase chain reaction? [Ser- endipity and the Polymerase Chain Reaction, p. 815]
26.60 Briefly describe how the polymerase chain reaction works.
[Serendipity and the Polymerase Chain Reaction, p. 815] 26.61 State the five basic steps of DNA fingerprinting using the
RFLP method. Why do you think the PCR method is of more use in crime scene investigations? [DNA Finger- printing, p. 817]
26.62 What is a VNTR? What is their significance for DNA fin- gerprinting? [DNA Fingerprinting, p. 817]