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Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis Chapter 1 What Is in a Human Genome? READINGS Chapter Opener What Information Is in a Human Genome? Clinical Connection 1.1 Exome Sequencing Saves a Boy’s Life Bioethics: Choices for the Future Genetic Testing and Privacy CHAPTER OVERVIEW Chapter 1 provides a glimpse of the basic concepts of genetics and genomics, and offers examples of DNA information impacting daily life. In this new era of genomics, individuals have access to their own genetic information, and health care providers are learning how to incorporate DNA data into diagnostic and therapeutic medicine. Bioethics deals with issues of privacy, discrimination, and justice that arise from use and misuse of genetic information. DNA, genes, chromosomes, and genomes are the levels of genetic information, and they impact biology at the cell, tissue, organ, individual, family, and population levels. Genes encode proteins, and the exome is the small part of the genome that does so. Most traits arise from interactions of genes and environmental factors. Genetic information is in health care to identify individuals, in investigating the environment, and in understanding evolution. CHAPTER OUTLINE 1.1 Introducing Genes and Genomes 1. Genetics is a branch of biology concerned with inherited traits and their variation, and how these traits are passed from one generation to the next (heredity). 2. With continuing analysis of human genome sequences, human genetics has grown from a largely academic science to touch many areas of medicine, with practical and societal implications. 3. Genes are the unit of inheritance and are composed of DNA. 4. An organism’s genome is its complete set of genetic information. 5. Genomics is a field of study that reveals how closely related we are to each other and to other species. 6. Bioethics is a field of study concerned with issues of privacy, confidentiality, and discrimination that arise from knowledge of our DNA sequences. Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis 1.2 Levels of Genetics and Genomics The Instructions: DNA, Genes, Chromosomes, and Genomes 1. Genetic investigation of the mechanisms of heredity occurs at multiple levels: from smallest to largest are DNA, gene, chromosome, and genome. 2. A DNA molecule consists of “rails” of alternating sugars and phosphates and “steps” of adenine-thymine (A-T) and guanine-cytosine (G-C) base pairs. Each three contiguous base pairs encode one of 20 types of amino acids, which build proteins. Messenger RNA carries DNA information out of the cell’s headquarters (nucleus) to where it is used to synthesize proteins. 3. A portion of DNA that encodes a protein is a gene. 4. A DNA molecule replicates as the sides of the double helix part and fill in with new bases. 5. Different cell types express different subsets of genes. 6. The exome is the 1.5% of the 20,325 or so genes of the human genome that encodes protein. 7. Mendelian Inheritance in Man (MIM) catalogs disease-related gene variants. 8. Genes can exist in more than one form. Variants (alleles) arise by mutation. 9. Chromosomes consist of genes and associated proteins. 10. The human genome is 22 pairs of autosomes and one pair of sex chromosomes. 11. A karyotype is a photographic chart of an individual’s chromosomes. 12. A Mendelian trait is caused by a single gene. A multifactorial trait is caused by one or more genes and environmental influences. Most genes do not function alone. 13. Genetic determinism is the idea that our genes control everything about us, with little or no outside influences. The Body: Cells, Tissues, and Organs 1. The human body is composed of about 37 trillion cells. All cell types except mature red blood cells contain the entire genome. 2. Differential gene expression creates more than 290 distinctive cell types, which combine to form four basic tissue types that interact to form organs and organ systems. 3. Many organs contain stem cells that “self-renew” as well as produce cells that specialize. These two properties are essential for growth, development, and healing. Relationships: From Individuals to Families 1. Genotype is the allelic makeup of an individual; phenotype is the observable or measureable expression of an individual’s alleles. 2. Dominant alleles are expressed when one copy is present. Recessive alleles require two copies for expression. 3. Pedigree diagrams follow recessive and dominant traits through generations. The Bigger Picture: From Populations to Evolution 1. Population genetics concerns allele frequencies in members of the same species in a specified geographic area. 2. “Gene pool” refers to all of the alleles in a given population. Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis 3. Population genetics has applications in health care, forensics, and evolution. 4. Comparative genomics explores evolutionary relationships among species. 1.3 Applications of Genetics and Genomics Establishing Identity 1. DNA profiling compares DNA sequences among individuals. 2. It is used to establish or rule out identity, clarify relationships or ancestry, and to evaluate crime scenes, probe sites of natural disasters, reunite adopted individuals with birth parents, test food, and study history. Health Care 1. Genetic information is being incorporated into diagnosis and treatment. 2. Many diseases are the result of complex interactions among genes and environmental factors, such as “mossy foot.” 3. Pharmacogenetics predicts responses of individuals to drugs based on genotypes. 4. Single-gene diseases differ from infectious diseases in that recurrence risks are predictable, pre-symptomatic genetic diagnosis may be possible, characteristic frequencies are observed in different populations, and correcting or replacing mutations may be possible. 5. Gene expression commonalities between diseases can reveal new drug targets or suggest drugs that may be repurposed. A diseasome is a diagram that connects diseases that share genes with altered expression. 6. Exome sequencing can lead to diagnoses of conditions that are unrecognized from their symptoms by implicating specific DNA sequences. A Global Perspective on Genomes 1. Metagenomics considers sequences of all DNA in a particular habitat. 2. Variable DNA sequences are used to “bar-code” species to study biodiversity. 3. Social issues that arise from genetic and genomic technologies include access to, misuse of, and abuse of DNA information. 4. Nations are individualizing guidelines to maximize benefit from emerging genetic tests and technologies. IDEAS FOR CLASSROOM DISCUSSION 1. Bioethics is a field of study concerned with issues of privacy, confidentiality, and discrimination that arise from access to DNA sequences and their interpretation. “Bioethics: Choices for the Future” in chapter 1 addresses privacy issues with collecting personal genetic information, in certain situations and scenarios. Cases are also presented in the author’s blog, DNA Science (http://blogs.plos.org /dnascience/). How do students feel about access to their own genetic information? Does a parent have an obligation to inform a child of a possible mutation, and if so, under what circumstances? Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis 2. Students today learn about DNA in grade school. However, coverage of genetics in the media often deals with cases and emotional issues, rather than the science. Have students discuss how information is part of the DNA molecule. How does a DNA polymer differ from a carbohydrate or lipid in terms of information content? How would a drug that replaces a gene be more effective than a drug that replaces a protein? 3. The famous case of Nicholas Volker and his dissolving intestines introduced the world to exome sequencing to diagnose puzzling disorders—the newspaper series chronicling his early childhood won a Pulitzer. Have students present cases of other individuals for whom exome sequencing solved medical mysteries. Ask them to distinguish between the two possible outcomes of family exome sequencing: a de novo case, or an inherited one. (See last section in chapter 4.) 4. Which genes or inherited traits or conditions would students want to know about in their future offspring, and which would they not want to know about? Contrast advantages and dangers of knowing such information. What should be done if parents disagree? 5. Should students be required to have their exomes or genomes sequenced as part of a class exercise? Why or why not? DNA SCIENCE BLOG POSTS (http://blogs.plos.org/dnascience/) Catching Up with 3 Rare Disease Families http://blogs.plos.org/dnascience/2014/06/19/catching-3-rare-disease-families/ Clinical Whole Genome Sequencing: Not Quite Ready for Prime Time? http://blogs.plos.org/dnascience/2014/03/13/clinical-whole-genome-sequencing-quiteready-prime-time/ WEBSITES Genetic Literacy Project http://www.geneticliteracyproject.org/ National Organization for Rare Disorders https://www.rarediseases.org/ Undiagnosed Diseases Program http://www.rarediseases.info.nih.gov/research/pages/27/undiagnosed-diseases-program ANSWERS TO REVIEW QUESTIONS 1. Gene pool, genome, chromosome, gene, DNA Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis 2. a. An autosome does not carry genes that determine sex. A sex chromosome does. b. Genotype is the allele constitution in an individual for a particular gene. Phenotype is the physical expression of an allele combination. c. DNA is a double-stranded nucleic acid that includes deoxyribose and the nitrogenous bases adenine, guanine, cytosine, and thymine. DNA carries the genetic information. RNA is a single-stranded nucleic acid that includes ribose and the nitrogenous bases adenine, guanine, cytosine, and uracil. RNA carries out gene expression. d. A recessive allele determines phenotype in two copies. A dominant allele determines phenotype in one copy. e. A pedigree is a chart of family relationships and traits. A karyotype is a chart of chromosomes. f. A gene is a sequence of DNA that encodes a protein. A genome is all DNA in a set of genetic instructions. Most human cells have two copies of the genome. g. An exome is the protein-encoding part of a genome. A genome is all DNA in a set of genetic instructions. 3. The sequence of DNA nucleotides (A, G, C, T) in a gene comprises a genetic code that is read three nucleotides at a time to direct the building of proteins. 4. Humans may have the same genes but differ genetically in the alleles they carry. 5. Differential gene expression creates the distinctive cell types. 6. The assumption is that changes in DNA sequence accumulate over time. The closer the two species, the more recently they descended from a common ancestor and the more alike their DNA sequences. 7. Answers are in Table 1.2. (a) Risk in people related in certain ways is predictable. (2) Presymptomatic testing may be possible. (3) Different populations may have different disease frequencies. (4) It may be possible to correct or compensate for the underlying genetic abnormality. ANSWERS TO APPLIED QUESTIONS 1. Answers vary depending on student opinion. A reason to have genetic testing is to plan for the future based on probabilities of developing particular diseases. A reason not to have genetic testing is that people die from accidents, injuries, and diseases that are not inherited. 2. Nutrition is an environmental factor that can influence the severity of an inherited disease. Gene variants can increase the risk that an individual develops an environmentally-caused cancer, such as lung cancer. 3. Perhaps a facial image derived from DNA data and displayed in public without the individual’s permission can be treated as illegal use of any identifying photograph. The fact that DNA is involved may introduce a greater level of intrusion into one’s privacy, particularly if it is obtained from garbage, such as discarded gum. Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis ANSWERS TO WEB ACTIVITIES 1. Answers vary depending on website visited and student opinion. FDA has restricted DTC genetic testing to ancestry. 2. Section 4.5 presents another case of diagnosis from exome sequencing, for a little girl, Bea Rienhoff. “One of a Kind” is an article in The New Yorker from July 21, 2014, about a boy with mutation in a gene called NGLY1. 3. Disaster victim identification: http://www.dna-worldwide.com/forensic-dnatesting/disaster-victim-identification/ 4. Parents might want to know what exactly will be done with their children’s DNA at the time of collection and going forward; who will have access to the information; and how the information will be protected. 5. Baylor College of Medicine began one of the first large-scale programs to sequence exomes and genomes of difficult-to-diagnose cases. https://www.bcm.edu/research/medical-genetics-labs/test_detail.cfm?testcode=1500 ANSWERS TO FORENSICS FOCUS 1. A difficult question. The repeats do not encode protein so likely do not affect the phenotype and therefore are likely not subject to natural selection. Therefore the sequences do not determine traits, health, nor do they reveal anything about ancestry because the number of repeats can spontaneously change. See chapter 14 for more detail. 2. Genetic information might be useful in a legal case if a particular genotype can account for a very specific behavior that caused a person to commit a crime. 3. Broaden question beyond TV series—cat and dog hairs used to identify crime scenes. Here’s a good case: http://sandiegolawlibrary.org/straaaaange-cases-catdna-database-convicts-a-killer/ 4. a. Taking part of a dead person’s body is indeed an invasion of privacy. b. Dr. House is much too quick to diagnose. Appropriately used genetic tests would help him differentiate among explanations for symptoms and other laboratory test results. ANSWERS TO CLINICAL CONNECTION 1.1 QUESTIONS 1. The environment affected Nic’s condition because it was food leaking from his digestive tract that caused the repeated infections. 2. Section 4.5 presents another case of diagnosis from exome sequencing, for a little girl, Bea Rienhoff. The author describes the case of Gavin Stevens at Scientific Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis American blogs (http://blogs.scientificamerican.com/guest-blog/2012/07/29/rarediseases-5-recent-reasons-to-cheer/). A review article is in The New England Journal of Medicine (http://www.nejm.org/doi/full/10.1056/NEJMra1312543). 3. Nicholas’s disease had an “atypical presentation.” His symptoms seemed to be gastrointestinal, not immunological. ANSWERS TO BIOETHICS: CHOICES FOR THE FUTURE 1. Answers vary and are personal. Key factors are the severity of the illness, how the disease is inherited (are relatives at risk of disease, or of being a carrier?) and the relationship of the person with the mutation to family members. 2. Perhaps multiple levels of passwords could be used to access DNA data. 3. Risks: stigmatization, restricting some students from participating in certain sports and events. Benefits: prevention of health consequences of sickle cell carriers in lowoxygen environments. 4. Answer depends upon how the DNA information would be used. If linked in a database to records such as passports and driver’s licenses, with appropriate safeguards for privacy, perhaps this could work. 5. Unsolicited findings are discussed in Chapter 22. Individuals having their exomes or genomes sequenced are increasingly being asked to declare the types of information that they do or do not wish to know before the sequencing. ANSWERS TO KEY CONCEPTS QUESTIONS 1.1 1. Genetics is the study of how traits are transmitted. Heredity considers the transmission patterns of inherited traits between generations. 2. A gene is a sequence of DNA that encodes a protein. A genome is a complete set of genetic instructions for an organism. 3. Bioethics combines philosophy, science, and medicine to address controversial issues. Bioethics applied to genetics largely concerns privacy. 1.2 1. Molecules, cells, tissues, organs, organ systems, individuals, families, populations, evolution of species 2. In the sequence of nitrogenous bases (A, C, T and G) 3. A gene consists of hundreds of bases. Alteration of the sequences creates a large number of possible variants. 4. A Mendelian trait is set by inheriting a mutation or mutations in one gene. A multifactorial trait derives from at least one gene plus environmental influences. 5. Cells specialize by expressing subsets of protein-encoding genes in the genome. A bone cell expresses a different subset than a blood cell, for example. 6. Genotype is an allele combination; phenotype is the expression of an allele combination (appearance or health condition). A dominant allele affects the phenotype in one copy. A recessive allele affects the phenotype in two copies. 7. The more recently two species shared an ancestor (are more closely related), the more of their DNA sequence they share. Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis 1.3 1. See how one person is genetically related to another, such as an adopted individual or remains from a crime or natural disaster scene. Identify components of food. Reveal causes of past epidemics. Clarify historical relationships. 2. A gene variant combination can make an individual more susceptible to danger from an environmental factor, such as exposure to a toxin. 3. Answers are in Table 1.2. (a) Risk in people related in certain ways is predictable. (2) Presymptomatic testing may be possible. (3) Different populations may have different disease frequencies. (4) It may be possible to correct or compensate for the underlying genetic abnormality. 4. Identifying gene expression patterns that two diseases share can suggest that a drug used to treat one condition may be helpful in treating the other. If exome sequencing reveals a specific mutation combination responsible for a phenotype, treatments can be developed or repurposed that affect the disease-causing mechanism at the molecular level. 1.4 1. Metagenomics is the study of all of the DNA in a particular geographic or other area. 2. Bacteria cause disease in humans and understanding their DNA sequences can suggest how they infect and how drugs can be used to kill them. ADDITIONAL QUESTIONS 1. Humans contract the infectious disease leishmaniasis from sandflies that transmit the microorganism Leishmania braziliensis. The first sign is a skin lesion, followed by facial disfiguration. The disease is endemic (very common) in Bolivia, where it is seen more in males, younger people, and those who spend the most time in the forest. A genetic susceptibility might also influence who becomes infected, as suggested by highly susceptible strains of mice. What type of evidence in the Bolivian population, which consists of indigenous and immigrant populations, might suggest an inherited component to susceptibility of this infection? Cite a disease mentioned in chapter 1 that is similar to leishmaniasis in terms of whom it affects. 2. Osteoporosis thins bones in millions of people. A much rarer, inherited condition, osteopetrosis, acts oppositely, increasing bone mass. Osteopetrosis does not affect health, and is typically discovered on x-rays. Why might studying how osteopetrosis arises be useful, even though it doesn't cause symptoms? 3. In acute intermittent porphyria, an environmental factor such as abuse of drugs or alcohol, or fasting, triggers potentially fatal attacks on the nervous system. An abnormal enzyme causes the condition. Why is this disorder considered genetic if it only produces symptoms in the presence of a specific environmental trigger? 4. Although seizures are usually not inherited, benign infantile familial convulsions run in families. How can studying this inherited illness provide information that may help people with non-inherited seizures? Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. Full file at http://textbooktestbank.eu/Human-Genetics-Concepts-and-Applications-11th-Edition-SolutionsRicki-Lewis 5. Due to inherited differences in the way the body processes cholesterol, some people can eat a fatty diet yet have healthy blood serum cholesterol, and others develop dangerously high cholesterol levels if they do not eat wisely. Several drugs can lower blood serum cholesterol level. Researchers found that people with a certain variant of a gene encoding a protein that transports cholesterol into liver cells (cholesteryl ester transfer protein, or CETP) are likely to have a cholesterol problem, and are also more likely to benefit from cholesterol-lowering drugs than people with different alleles. What information would be important to have before undergoing a CETP gene test and possibly taking a cholesterol-lowering drug? 6. In Graves disease, the immune system attacks the thyroid gland, which normally produces hormones controlling energy utilization. Siblings of people with Graves disease are 15 times as likely to develop the disorder as people whose siblings are unaffected. Women develop the condition more often than men, and a high percentage of affected individuals smoke. Do you think that Graves disease is caused solely by an abnormal gene, solely by an environmental trigger, or might there be another explanation? ANSWERS TO ADDITIONAL QUESTIONS 1. An inherited susceptibility to leishmaniasis might be involved if blood relatives who are separated geographically become sick more often than people who only have in common where they live. The example of “mossy foot” from Chapter 1 is similar. 2. Studying osteopetrosis can reveal how healthy bone mass is maintained, which might provide insights into osteoporosis, which has an opposite phenotype and is more common. Drugs may be developed that mimic osteopetrosis to treat osteoporosis. 3. The condition is inherited because presence of a particular genetic variant is necessary for symptoms to occur. The susceptibility is inherited, not the disease. 4. Studying this rare inherited condition can reveal basic brain mechanisms that may explain how more common seizures occur. 5. Important information includes: the risk of cardiovascular disease to an individual; side effects of cholesterol-lowering drugs; the role of diet in controlling gene expression; how often a particular genetic variant is associated with increased cholesterol level; success of drug treatment. 6. Graves disease might be caused by an inherited susceptibility triggered by an environmental influence, such as exposure to female sex hormones or cigarette smoke, or the status of the immune system. Copyright © 2016 McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education.