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the formation of the transcription initiation complex and the disconnection of the mRNA strand from DNA. 652 Chapter 16 | Gene Regulation The Promoter and the Transcription Machinery Genes are organized to make the control of gene expression easier. The promoter region is immediately upstream of the coding sequence. This region can be short (only a few nucleotides in length) or quite long (hundreds of nucleotides long). The longer the promoter, the more available space for proteins to bind. This also adds more control to the transcription process. The length of the promoter is gene-specific and can differ dramatically between genes. Consequently, the level of control of gene expression can also differ quite dramatically between genes. The purpose of the promoter is to bind transcription factors that control the initiation of transcription. Within the promoter region, just upstream of the transcriptional start site, resides the TATA box. This box is simply a repeat of thymine and adenine dinucleotides (literally, TATA repeats). RNA polymerase binds to the transcription initiation complex, allowing transcription to occur. To initiate transcription, a transcription factor (TFIID) is the first to bind to the TATA box. Binding of TFIID recruits other transcription factors, including TFIIB, TFIIE, TFIIF, and TFIIH to the TATA box. Once this complex is assembled, RNA polymerase can bind to its upstream sequence. When bound along with the transcription factors, RNA polymerase is phosphorylated. This releases part of the protein from the DNA to activate the transcription initiation complex and places RNA polymerase in the correct orientation to begin transcription; DNA-bending protein brings the enhancer, which can be quite a distance from the gene, in contact with transcription factors and mediator proteins (Figure 16.10). Figure 16.10 An enhancer is a DNA sequence that promotes transcription. Each enhancer is made up of short DNA sequences called distal control elements. Activators bound to the distal control elements interact with mediator proteins and transcription factors. Two different genes may have the same promoter but different distal control elements, enabling differential gene expression. In addition to the general transcription factors, other transcription factors can bind to the promoter to regulate gene transcription. These transcription factors bind to the promoters of a specific set of genes. They are not general transcription factors that bind to every promoter complex, but are recruited to a specific sequence on the promoter of a specific gene. There are hundreds of transcription factors in a cell that |
each bind specifically to a particular DNA sequence motif. When transcription factors bind to the promoter just upstream of the encoded gene, it is referred to as a cis-acting element, because it is on the same chromosome just next to the gene. The region that a particular transcription factor binds to is called the transcription factor binding site. Transcription factors respond to environmental stimuli that cause the proteins to find their binding sites and initiate transcription of the gene that is needed. Enhancers and Transcription In some eukaryotic genes, there are regions that help increase or enhance transcription. These regions, called enhancers, This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 653 are not necessarily close to the genes they enhance. They can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or may be thousands of nucleotides away. Enhancer regions are binding sequences, or sites, for transcription factors. When a DNA-bending protein binds, the shape of the DNA changes (Figure 16.10). This shape change allows for the interaction of the activators bound to the enhancers with the transcription factors bound to the promoter region and the RNA polymerase. Whereas DNA is generally depicted as a straight line in two dimensions, it is actually a three-dimensional object. Therefore, a nucleotide sequence thousands of nucleotides away can fold over and interact with a specific promoter. Turning Genes Off: Transcriptional Repressors Like prokaryotic cells, eukaryotic cells also have mechanisms to prevent transcription. Transcriptional repressors can bind to promoter or enhancer regions and block transcription. Like the transcriptional activators, repressors respond to external stimuli to prevent the binding of activating transcription factors. Think About It How can cells in a multicellular eukaryotic organism be of different types given that they all share the same genome? 16.5 | Eukaryotic Post-transcriptional Gene Regulation In this section, you will explore the following question: • How is gene expression controlled through post-transcriptional modifications of RNA molecules? Connection for AP® Courses Post-transcriptional regulation can occur at any stage after transcription. One important post-transcriptional mechanism is RNA splicing. After RNA is transcribed, it is often modified to create a mature RNA that is ready to be translated. As we studied in previous chapters, |
processing messenger RNA involves the removal of introns that do not code for protein. Spliceosomes remove the introns and ligate the exons together, often in different sequences than their original order on the newly transcribed (immature) messenger RNA. A GTP cap is added to the 5’-end and a poly-A tail is added to the 3’-end. This mature messenger RNA then leaves the nucleus and enters the cytoplasm. Once in the cytoplasm, the length of time the messenger RNA resides there before being degraded—a characteristic lifespan or “shelf-life” of the molecule called RNA stability—can be altered to control the amount of protein that is synthesized. RNA stability is controlled by several factors, including microRNAs (miRNA or RNAi, RNA interference); miRNAs always decrease stability and promote decay of messenger RNA. Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP® Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A learning objective merges required content with one or more of the seven science practices. Big Idea 3 Enduring Understanding 3.A Essential Knowledge Living systems store, retrieve, transmit and respond to information essential to life processes. Heritable information provides for continuity of life. 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. 654 Science Practice Learning Objective Essential Knowledge Science Practice Learning Objective Chapter 16 | Gene Regulation 6.5 The student can evaluate alternative scientific explanations. 3.1 The student is able to construct scientific explanations that use the structures and mechanisms of DNA and RNA to support the claim that DNA and, in some cases, RNA are the primary source of heritable information. 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. 3.6 The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression. RNA is transcribed, but must be processed into a mature form before translation can begin. This processing after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification. As with |
the epigenetic and transcriptional stages of processing, this post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, then no protein will be synthesized. RNA Splicing, the First Stage of Post-transcriptional Control In eukaryotic cells, the RNA transcript often contains regions, called introns, that are removed prior to translation. The regions of RNA that code for protein are called exons (Figure 16.11). After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing. Figure 16.11 Pre-mRNA can be alternatively spliced to create different proteins. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 655 Alternative RNA Splicing In the 1970s, genes were first observed that exhibited alternative RNA splicing. Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns, and sometimes exons, are removed from the transcript (Figure 16.12). This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of different splicing alternatives controlled by the cell as a way to control the production of different protein products in different cells or at different stages of development. Alternative splicing is now understood to be a common mechanism of gene regulation in eukaryotes; according to one estimate, 70 percent of genes in humans are expressed as multiple proteins through alternative splicing. Figure 16.12 There are five basic modes of alternative splicing. Does alternative gene splicing increase or decrease the flexibility of gene expression? Explain your answer. a. Flexibility increases because mRNA can be altered after transcription is completed. b. Flexibility increases because genes can be divided and recombined into new genes. c. Flexibility decreases because the mRNA molecule becomes smaller. d. Flexibility decreases because DNA is degraded during alternative splicing. 656 Chapter 16 | Gene Regulation Visualize how mRNA splicing happens by watching the process in action in this video (http://openstaxcollege.org/l/ mRNA_splicing). Several human diseases are caused by an error in mRNA splicing. Explain why this occurs. a. Once an mRNA is spliced |
, the original mRNA cannot be created again. b. Spliced RNA cannot produce proper proteins. c. Splicing does not occur at all. d. Splicing occurs in the wrong location on mRNA. Think About It What is an evolutionary advantage of alternative gene splicing of introns during post-transcriptional modification of mRNA? Control of RNA Stability Before the mRNA leaves the nucleus, it is given two protective "caps" that prevent the end of the strand from degrading during its journey. The 5' cap, which is placed on the 5' end of the mRNA, is usually composed of a methylated guanosine triphosphate molecule (GTP). The poly-A tail, which is attached to the 3' end, is usually composed of a series of adenine nucleotides. Once the RNA is transported to the cytoplasm, the length of time that the RNA resides there can be controlled. Each RNA molecule has a defined lifespan and decays at a specific rate. This rate of decay can influence how much protein is in the cell. If the decay rate is increased, the RNA will not exist in the cytoplasm as long, shortening the time for translation to occur. Conversely, if the rate of decay is decreased, the RNA molecule will reside in the cytoplasm longer and more protein can be translated. This rate of decay is referred to as the RNA stability. If the RNA is stable, it will be detected for longer periods of time in the cytoplasm. Binding of proteins to the RNA can influence its stability. Proteins, called RNA-binding proteins, or RBPs, can bind to the regions of the RNA just upstream or downstream of the protein-coding region. These regions in the RNA that are not translated into protein are called the untranslated regions, or UTRs. They are not introns (those have been removed in the nucleus). Rather, these are regions that regulate mRNA localization, stability, and protein translation. The region just before the protein-coding region is called the 5' UTR, whereas the region after the coding region is called the 3' UTR (Figure 16.13). The binding of RBPs to these regions can increase or decrease the stability of an RNA molecule, depending on the specific RBP that binds. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 657 |
Figure 16.13 The protein-coding region of mRNA is flanked by 5' and 3' untranslated regions (UTRs). The presence of RNA-binding proteins at the 5' or 3' UTR influences the stability of the RNA molecule. RNA Stability and microRNAs In addition to RBPs that bind to and control (increase or decrease) RNA stability, other elements called microRNAs can bind to the RNA molecule. These microRNAs, or miRNAs, are short RNA molecules that are only 21–24 nucleotides in length. The miRNAs are made in the nucleus as longer pre-miRNAs. These pre-miRNAs are chopped into mature miRNAs by a protein called dicer. Like transcription factors and RBPs, mature miRNAs recognize a specific sequence and bind to the RNA; however, miRNAs also associate with a ribonucleoprotein complex called the RNA-induced silencing complex (RISC). RISC binds along with the miRNA to degrade the target mRNA. Together, miRNAs and the RISC complex rapidly destroy the RNA molecule. 16.6 | Eukaryotic Translational and Post-translational Gene Regulation In this section, you will explore the following question: • What are different ways in which translational and post-translational control of gene expression take place? Connection for AP® Courses Changing the status of the RNA or the protein itself can affect the amount of protein produced, the function of the protein, or how long the protein resides in the cell. Modifications such as phosphorylation and environmental stimuli can affect the stability and function of the protein. Information presented and the examples highlighted in the section support concepts outlined in Big Idea 4 of the AP® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. Big Idea 4 Enduring Understanding 4.A Biological systems interact, and these systems and their interactions possess complex properties. Interactions within biological systems lead to complex properties. Essential Knowledge 4.A.3 Interactions between external stimuli and regulated gene expression result in specialization of cells, tissues and organs. Science Practice Learning Objective 1.3 The student can refine representations and models of natural or man-made phenomena and systems in the domain. 4 |
.7 The student is able to refine representations to illustrate how interactions between external stimuli and gene expression result in specialization of cells, tissues, and organs. After the RNA has been transported to the cytoplasm, it is translated into protein. Control of this process is largely dependent on the RNA molecule. As previously discussed, the stability of the RNA will have a large impact on its translation into a protein. As the stability changes, the amount of time that it is available for translation also changes. 658 Chapter 16 | Gene Regulation The Initiation Complex and Translation Rate Like transcription, translation is controlled by proteins that bind and initiate the process. In translation, the complex that assembles to start the process is referred to as the initiation complex. The first protein to bind to the RNA to initiate translation is the eukaryotic initiation factor-2 (eIF-2). The eIF-2 protein is active when it binds to the high-energy molecule guanosine triphosphate (GTP). GTP provides the energy to start the reaction by giving up a phosphate and becoming guanosine diphosphate (GDP). The eIF-2 protein bound to GTP binds to the small 40S ribosomal subunit. When bound, the methionine initiator tRNA associates with the eIF-2/40S ribosome complex, bringing along with it the mRNA to be translated. At this point, when the initiator complex is assembled, the GTP is converted into GDP and energy is released. The phosphate and the eIF-2 protein are released from the complex and the large 60S ribosomal subunit binds to translate the RNA. The binding of eIF-2 to the RNA is controlled by phosphorylation. If eIF-2 is phosphorylated, it undergoes a conformational change and cannot bind to GTP. Therefore, the initiation complex cannot form properly and translation is impeded (Figure 16.14). When eIF-2 remains unphosphorylated, it binds the RNA and actively translates the protein. Figure 16.14 Gene expression can be controlled by factors that bind the translation initiation complex. An increase in phosphorylation levels of eIF-2 has been observed in patients with neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s. What impact do you think this might have on protein synthesis? a. b. c. d. It will increase the rate of translation. |
It will not affect the translation process. It will block the translation of certain proteins. It will produce multiple fragments of polypeptides. Chemical Modifications, Protein Activity, and Longevity Proteins can be chemically modified with the addition of groups including methyl, phosphate, acetyl, and ubiquitin groups. The addition or removal of these groups from proteins regulates their activity or the length of time they exist in the cell. Sometimes these modifications can regulate where a protein is found in the cell—for example, in the nucleus, the cytoplasm, or attached to the plasma membrane. Chemical modifications occur in response to external stimuli such as stress, the lack of nutrients, heat, or ultraviolet light exposure. These changes can alter epigenetic accessibility, transcription, mRNA stability, or translation—all resulting in changes in expression of various genes. This is an efficient way for the cell to rapidly change the levels of specific proteins in response to the environment. Because proteins are involved in every stage of gene regulation, the phosphorylation of a protein (depending on the protein that is modified) can alter accessibility to the chromosome, can alter translation (by altering transcription factor binding or function), can change nuclear shuttling (by influencing modifications to the nuclear pore complex), can alter RNA stability (by binding or not binding to the RNA to regulate its stability), can modify translation (increase or decrease), or can change post-translational modifications (add or remove phosphates or other chemical modifications). This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 659 The addition of an ubiquitin group to a protein marks that protein for degradation. Ubiquitin acts like a flag indicating that the protein lifespan is complete. These proteins are moved to the proteasome, an organelle that functions to remove proteins, to be degraded (Figure 16.15). One way to control gene expression, therefore, is to alter the longevity of the protein. Figure 16.15 Proteins with ubiquitin tags are marked for degradation within the proteasome. Think About It How can environmental stimuli such as ultraviolet light exposure or nutrient deficiency modify gene expression? 16.7 | Cancer and Gene Regulation In this section, you will explore the following questions: • How can changes in gene expression cause cancer? • How can changes to gene expression at different levels disrupt the cell cycle? Connection for AP® Courses Cancer is a disease |
of altered gene expression that can occur at every level of control, including at the levels of DNA methylation, histone acetylation, and activation of transcription factors. By understanding how each stage of gene regulation works in normal cells, we can understand what goes wrong in diseased states. For example, changes in the activity of the tumor suppressor gene p53 can result in cancer. Phosphorylation and other protein modifications have also been implicated in cancer. Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP® Biology Curriculum Framework. The learning objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. Big Idea 3 Enduring Understanding 3.B Living systems store, retrieve, transmit and respond to information essential to life processes. Expression of genetic information involves cellular and molecular mechanisms. 660 Chapter 16 | Gene Regulation Essential Knowledge 3.B.2 A variety of intercellular and intracellular signal transmissions mediate gene expression. Science Practice 6.2 The student can construct explanations of phenomena based on evidence produced through scientific practices. Learning Objective Essential Knowledge 3.22 The student is able to explain how signal pathways mediate gene expression, including how this process can affect protein production. 3.B.2 A variety of intercellular and intracellular signal transmissions mediate gene expression. Science Practice 1.4 The student can use representations and models to analyze situations or solve problems qualitatively and quantitatively. Learning Objective 3.23 The student can use representations to describe mechanisms of the regulation of gene expression. Cancer is not a single disease but includes many different diseases. In cancer cells, mutations modify cell-cycle control and cells don’t stop growing as they normally would. Mutations can also alter the growth rate or the progression of the cell through the cell cycle. One example of a gene modification that alters the growth rate is increased phosphorylation of cyclin B, a protein that controls the progression of a cell through the cell cycle and serves as a cell-cycle checkpoint protein. For cells to move through each phase of the cell cycle, the cell must pass through checkpoints. This ensures that the cell has properly completed the step and has not encountered any mutation that will alter its function. Many proteins, including cyclin B, control these checkpoints. The phosphorylation of |
cyclin B, a post-translational event, alters its function. As a result, cells can progress through the cell cycle unimpeded, even if mutations exist in the cell and its growth should be terminated. This post-translational change of cyclin B prevents it from controlling the cell cycle and contributes to the development of cancer. Cancer: Disease of Altered Gene Expression Cancer can be described as a disease of altered gene expression. There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell. A gene that is not normally expressed in that cell can be switched on and expressed at high levels. This can be the result of gene mutation or changes in gene regulation (epigenetic, transcription, post-transcription, translation, or post-translation). Changes in epigenetic regulation, transcription, RNA stability, protein translation, and post-translational control can be detected in cancer. While these changes don’t occur simultaneously in one cancer, changes at each of these levels can be detected when observing cancer at different sites in different individuals. Therefore, changes in histone acetylation (epigenetic modification that leads to gene silencing), activation of transcription factors by phosphorylation, increased RNA stability, increased translational control, and protein modification can all be detected at some point in various cancer cells. Scientists are working to understand the common changes that give rise to certain types of cancer or how a modification might be exploited to destroy a tumor cell. Tumor Suppressor Genes, Oncogenes, and Cancer In normal cells, some genes function to prevent excess, inappropriate cell growth. These are tumor suppressor genes, which are active in normal cells to prevent uncontrolled cell growth. There are many tumor suppressor genes in cells. The most studied tumor suppressor gene is p53, which is mutated in over 50 percent of all cancer types. The p53 protein itself functions as a transcription factor. It can bind to sites in the promoters of genes to initiate transcription. Therefore, the mutation of p53 in cancer will dramatically alter the transcriptional activity of its target genes. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 661 Watch this animation (http://openstaxcollege.org/l/p53_cancer) to learn more about the use of p53 in fighting cancer. Treatment of |
cancer is often called a “fight against biology.” Explain why the use of p53 supports this statement. a. because normal cells are often negatively affected by cancer treatments, including p53 b. because cancer cells are always affected by current cancer treatments, including p53 c. because normal cells are often negatively affected by cancer treatments, with the exception of p53 d. because cancer cells often aren’t affected by cancer treatments, with the exception of p53 Proto-oncogenes are positive cell-cycle regulators. When mutated, proto-oncogenes can become oncogenes and cause cancer. Overexpression of the oncogene can lead to uncontrolled cell growth. This is because oncogenes can alter transcriptional activity, stability, or protein translation of another gene that directly or indirectly controls cell growth. An example of an oncogene involved in cancer is a protein called myc. Myc is a transcription factor that is aberrantly activated in Burkett’s Lymphoma, a cancer of the lymph system. Overexpression of myc transforms normal B cells into cancerous cells that continue to grow uncontrollably. High B-cell numbers can result in tumors that can interfere with normal bodily function. Patients with Burkett’s lymphoma can develop tumors on their jaw or in their mouth that interfere with the ability to eat. Cancer and Epigenetic Alterations Silencing genes through epigenetic mechanisms is also very common in cancer cells. There are characteristic modifications to histone proteins and DNA that are associated with silenced genes. In cancer cells, the DNA in the promoter region of silenced genes is methylated on cytosine DNA residues in CpG islands. Histone proteins that surround that region lack the acetylation modification that is present when the genes are expressed in normal cells. This combination of DNA methylation and histone deacetylation (epigenetic modifications that lead to gene silencing) is commonly found in cancer. When these modifications occur, the gene present in that chromosomal region is silenced. Increasingly, scientists understand how epigenetic changes are altered in cancer. Because these changes are temporary and can be reversed—for example, by preventing the action of the histone deacetylase protein that removes acetyl groups, or by DNA methyl transferase enzymes that add methyl groups to cytosines in DNA—it is possible to design new drugs and new therapies to take advantage of the reversible nature of these processes. Indeed, |
many researchers are testing how a silenced gene can be switched back on in a cancer cell to help re-establish normal growth patterns. Genes involved in the development of many other illnesses, ranging from allergies to inflammation to autism, are thought to be regulated by epigenetic mechanisms. As our knowledge of how genes are controlled deepens, new ways to treat diseases like cancer will emerge. Cancer and Transcriptional Control Alterations in cells that give rise to cancer can affect the transcriptional control of gene expression. Mutations that activate transcription factors, such as increased phosphorylation, can increase the binding of a transcription factor to its binding site in a promoter. This could lead to increased transcriptional activation of that gene that results in modified cell growth. Alternatively, a mutation in the DNA of a promoter or enhancer region can increase the binding ability of a transcription factor. This could also lead to the increased transcription and aberrant gene expression that is seen in cancer cells. Researchers have been investigating how to control the transcriptional activation of gene expression in cancer. Identifying how a transcription factor binds, or a pathway that activates where a gene can be turned off, has led to new drugs and new ways to treat cancer. In breast cancer, for example, many proteins are overexpressed. This can lead to increased phosphorylation of key transcription factors that increase transcription. One such example is the overexpression of the epidermal growth factor receptor (EGFR) in a subset of breast cancers. The EGFR pathway activates many protein kinases that, in turn, activate many transcription factors that control genes involved in cell growth. New drugs that prevent the 662 Chapter 16 | Gene Regulation activation of EGFR have been developed and are used to treat these cancers. Cancer and Post-transcriptional Control Changes in the post-transcriptional control of a gene can also result in cancer. Recently, several groups of researchers have shown that specific cancers have altered expression of miRNAs. Because miRNAs bind to the 3' UTR of RNA molecules to degrade them, overexpression of these miRNAs could be detrimental to normal cellular activity. Too many miRNAs could dramatically decrease the RNA population leading to a decrease in protein expression. Several studies have demonstrated a change in the miRNA population in specific cancer types. It appears that the subset of miRNAs expressed in breast cancer cells is quite different from the subset expressed in lung cancer cells or even from normal breast cells. This suggests that alterations in miRNA activity can contribute to the |
growth of breast cancer cells. These types of studies also suggest that if some miRNAs are specifically expressed only in cancer cells, they could be potential drug targets. It would, therefore, be conceivable that new drugs that turn off miRNA expression in cancer could be an effective method to treat cancer. Cancer and Translational/Post-translational Control There are many examples of how translational or post-translational modifications of proteins arise in cancer. Modifications are found in cancer cells from the increased translation of a protein to changes in protein phosphorylation to alternative splice variants of a protein. An example of how the expression of an alternative form of a protein can have dramatically different outcomes is seen in colon cancer cells. The c-Flip protein, a protein involved in mediating the cell death pathway, comes in two forms: long (c-FLIPL) and short (c-FLIPS). Both forms appear to be involved in initiating controlled cell death mechanisms in normal cells. However, in colon cancer cells, expression of the long form results in increased cell growth in<|endoftext|>stead of cell death. Clearly, the expression of the wrong protein dramatically alters cell function and contributes to the development of cancer. New Drugs to Combat Cancer: Targeted Therapies Scientists are using what is known about the regulation of gene expression in disease states, including cancer, to develop new ways to treat and prevent disease development. Many scientists are designing drugs on the basis of the gene expression patterns within individual tumors. This idea, that therapy and medicines can be tailored to an individual, has given rise to the field of personalized medicine. With an increased understanding of gene regulation and gene function, medicines can be designed to specifically target diseased cells without harming healthy cells. Some new medicines, called targeted therapies, have exploited the overexpression of a specific protein or the mutation of a gene to develop a new medication to treat disease. One such example is the use of anti-EGF receptor medications to treat the subset of breast cancer tumors that have very high levels of the EGF protein. Undoubtedly, more targeted therapies will be developed as scientists learn more about how gene expression changes can cause cancer. Clinical Trial Coordinator A clinical trial coordinator is the person managing the proceedings of the clinical trial. This job includes coordinating patient schedules and appointments, maintaining detailed notes, building the database to track patients (especially for long-term follow-up studies), ensuring proper documentation has been acquired and accepted, and working with the nurses and |
doctors to facilitate the trial and publication of the results. A clinical trial coordinator may have a science background, like a nursing degree, or other certification. People who have worked in science labs or in clinical offices are also qualified to become a clinical trial coordinator. These jobs are generally in hospitals; however, some clinics and doctor’s offices also conduct clinical trials and may hire a coordinator. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 663 Think About It New drugs are being developed that decrease DNA methylation and prevent the removal of acetyl groups from histone proteins. Explain how these drugs could affect gene expression to help kill tumor cells. How can understanding the gene expression in a cancer cell tell you something about that specific form of cancer? 664 Chapter 16 | Gene Regulation KEY TERMS 3' UTR 3' untranslated region; region just downstream of the protein-coding region in an RNA molecule that is not translated 5' cap a methylated guanosine triphosphate (GTP) molecule that is attached to the 5' end of a messenger RNA to protect the end from degradation 5' UTR 5' untranslated region; region just upstream of the protein-coding region in an RNA molecule that is not translated activator protein that binds to prokaryotic operators to increase transcription catabolite activator protein (CAP) protein that complexes with cAMP to bind to the promoter sequences of operons that control sugar processing when glucose is not available cis-acting element transcription factor binding sites within the promoter that regulate the transcription of a gene adjacent to it dicer enzyme that chops the pre-miRNA into the mature form of the miRNA DNA methylation epigenetic modification that leads to gene silencing; commonly found in cancer cells enhancer segment of DNA that is upstream, downstream, perhaps thousands of nucleotides away, or on another chromosome that influence the transcription of a specific gene epigenetic heritable changes that do not involve changes in the DNA sequence eukaryotic initiation factor-2 (eIF-2) protein that binds first to an mRNA to initiate translation gene expression processes that control the turning on or turning off of a gene guanine diphosphate (GDP) molecule that is left after the energy is used to start translation guanine triphosphate (GTP) energy-providing molecule that binds to eIF-2 and is |
needed for translation histone acetylation epigenetic modification that leads to gene silencing; commonly found in cancer cells. inducible operon operon that can be activated or repressed depending on cellular needs and the surrounding environment initiation complex protein complex containing eIF2-2 that starts translation lac operon operon in prokaryotic cells that encodes genes required for processing and intake of lactose large 60S ribosomal subunit second, larger ribosomal subunit that binds to the RNA to translate it into protein microRNA (miRNA) degrade them small RNA molecules (approximately 21 nucleotides in length) that bind to RNA molecules to myc oncogene that causes cancer in many cancer cells negative regulator protein that prevents transcription operator region of DNA outside of the promoter region that binds activators or repressors that control gene expression in prokaryotic cells operon collection of genes involved in a pathway that are transcribed together as a single mRNA in prokaryotic cells poly-A tail a series of adenine nucleotides that are attached to the 3' end of an mRNA to protect the end from degradation positive regulator protein that increases transcription post-transcriptional control of gene expression after the RNA molecule has been created but before it is translated into This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 665 protein post-translational control of gene expression after a protein has been created proteasome organelle that degrades proteins repressor protein that binds to the operator of prokaryotic genes to prevent transcription RISC protein complex that binds along with the miRNA to the RNA to degrade it RNA stability how long an RNA molecule will remain intact in the cytoplasm RNA-binding protein (RBP) protein that binds to the 3' or 5' UTR to increase or decrease the RNA stability small 40S ribosomal subunit ribosomal subunit that binds to the RNA to translate it into protein trans-acting element transcription factor binding site found outside the promoter or on another chromosome that influences the transcription of a particular gene transcription factor protein that binds to the DNA at the promoter or enhancer region and that influences transcription of a gene transcription factor binding site sequence of DNA to which a transcription factor binds transcriptional start site site at which transcription begins trp operon series of genes necessary to synthesize tryptophan in prokaryotic cells trypt |
ophan amino acid that can be synthesized by prokaryotic cells when necessary untranslated region segment of the RNA molecule that are not translated into protein. These regions lie before (upstream or 5') and after (downstream or 3') the protein-coding region CHAPTER SUMMARY 16.1 Regulation of Gene Expression While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is mostly regulated at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and posttranslational levels. 16.2 Prokaryotic Gene Regulation The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. There are three ways to control the transcription of an operon: repressive control, activator control, and inducible control. Repressive control, typified by the trp operon, uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase and the activation of transcription. Therefore, if tryptophan is not needed, the repressor is bound to the operator and transcription remains off. Activator control, typified by the action of CAP, increases the binding ability of RNA polymerase to the promoter when CAP is bound. In this case, low levels of glucose result in the binding of cAMP to CAP. CAP then binds the promoter, which allows RNA polymerase to bind to the promoter better. In the last example—the lac operon—two conditions must be met to initiate transcription. Glucose must not be present, and lactose must be available for the lac operon to be transcribed. If glucose is absent, CAP binds to the operator. If lactose |
is present, the repressor protein does not bind to its operator. Only when both conditions are met will RNA polymerase bind to the promoter to induce transcription. 666 Chapter 16 | Gene Regulation 16.3 Eukaryotic Epigenetic Gene Regulation In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription. 16.4 Eukaryotic Transcriptional Gene Regulation To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors to cis-acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription. 16.5 Eukaryotic Post-transcriptional Gene Regulation Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. The RNA stability can be increased, leading to longer residency time in the cytopl |
asm, or decreased, leading to shortened time and less protein synthesis. RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5' UTR or the 3' UTR of the RNA to increase or decrease RNA stability. Depending on the RBP, the stability can be increased or decreased significantly; however, miRNAs always decrease stability and promote decay. 16.6 Eukaryotic Translational and Post-translational Gene Regulation Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein. 16.7 Cancer and Gene Regulation Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer. REVIEW QUESTIONS 1. Control of gene expression in eukaryotic cells occurs at which level(s)? 2. a. only the transcriptional level b. epigenetic and transcriptional levels c. epigenetic and transcriptional and translational levels d. epigenetic and transcriptional, translational, and post-translational levels This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 667 a. b. In the presence of lactose, the lac operon will not be transcribed. In the absence of lactose, the lac operon will be transcribed. c. The cAMP-CAP complex will not increase RNA synthesis. d. The RNA polymerase will not bind the promoter. 5. What would |
happen if the operator sequence of the trp operon contained a mutation that prevented the repressor protein from binding to the operator? a. b. c. d. In the absence of tryptophan, the genes trpA-E will not be transcribed. In the absence of tryptophan, only genes trpE and trpD will be transcribed. In the presence of tryptophan, the genes trpA-E will be transcribed. In the presence of tryptophan, the trpE gene will not be transcribed. 6. What are epigenetic modifications? a. b. c. the addition of reversible changes to histone proteins and DNA the removal of nucleosomes from the DNA the addition of more nucleosomes to the DNA d. mutation of the DNA sequence 7. Which of the following statements about epigenetic regulation is false? a. Histone protein charge becomes more positive when acetyl groups are added. b. DNA molecules are modified within CpG islands. c. Methylation of DNA and histones causes nucleosomes to pack tightly together. d. Histone acetylation results in the loose packing of nucleosomes. 8. Which of the following is true of epigenetic changes? a. They only allow gene expression. b. They allow movement of histones. c. They change the DNA sequence. d. They are always heritable. 9. The binding of what is required for transcription start? a. a protein b. DNA polymerase c. RNA polymerase d. a transcription factor 10. What would be the outcome of a mutation that prevented DNA binding proteins from being produced? What do figures X and Y in the graphic illustrate? a. Transcription and translation in a eukaryotic cell (figure X) and a prokaryotic cell (figure Y). b. Transcription and translation in a prokaryotic cell (figure X) and a eukaryotic cell (figure Y). c. Transcription in a eukaryotic cell (figure X) and translation in a prokaryotic cell (figure Y). d. Transcription in a prokaryotic cell (figure X) and translation in a eukaryotic cell (figure Y) 3. If glucose is absent but lactose is present, the lac operon will be: a. activated b. repressed c. partially activated d. mutated 4. What would happen if the operator sequence of |
the lac operon contained a mutation that prevented the repressor protein from binding the operator? 668 Chapter 16 | Gene Regulation a. decreased transcription because transcription factors would not bind to transcription binding sites b. decreased transcription because enhancers would not be able to bind to transcription factors c. d. increased transcription because repressors would not be able to bind to promoter regions increased transcription because RNA polymerase would be able to increase binding to promoter regions 11. What will result from the binding of a transcription factor to an enhancer region? a. decreased transcription of an adjacent gene b. increased transcription of a distant gene c. alteration of the translation of an adjacent gene d. initiation of the recruitment of RNA polymerase 12. Which of the following are involved in posttranscriptional control? a. control of RNA splicing b. ubiquitination c. proteolytic cleavage d. phosphorylation 13. Gene A is thought to be associated with color blindness. The protein corresponding to gene A is isolated. Analysis of the protein recovered shows there are actually two different proteins that differ in molecular weight that correspond to gene A. What is one reason why there may be two proteins corresponding to the gene? a. One protein had a 5’ cap and a poly-A tail in its mRNA, and the other protein did not. b. One protein had a 5’ UTR and a 3’ UTR in its RNA, and the other protein did not. c. The gene was alternatively spliced. d. The gene produced mRNA molecules with differing stability. 14. Binding of an RNA binding protein will change the stability of the RNA molecule in what way? a. increase b. decrease c. neither increase nor decrease d. either increase or decrease 15. A mutation in the 5’UTR that prevents any proteins from binding to the region will: a. increase or decrease the stability of the RNA molecule b. prevent translation of the RNA molecule c. prevent splicing of the RNA molecule d. increase or decrease the length of the poly-A tail 16. Post-translational modifications of proteins can affect which of the following? a. mRNA splicing b. 5’capping c. 3’polyadenylation d. chemical modifications 17. A mutation is found in eIF-2 that impairs the initiation of translation. The mutation could affect all but one of the following functions of eIF-2. Which one would not be affected? a. The mutation prevents eIF |
-2 from binding to RNA. b. The mutation prevents eIF-2 from being phosphorylated. c. The mutation prevents eIF-2 from binding to GTP. d. The mutation prevents eIF-2 from binding to the 40S ribosomal subunit. 18. The addition of a ubiquitin group to a protein does what? a. increases the stability of the protein b. decreases translation of the protein c. increases translation of the protein d. marks the protein for degradation 19. What are cancer-causing genes called? a. b. transformation genes tumor suppressor genes c. oncogenes d. protooncogenes 20. Targeted therapies are used in patients with a certain gene expression pattern. A targeted therapy that prevents the activation of the estrogen receptor in breast cancer would be beneficial to what type of patient? a. patients who express the EGFR receptor in normal cells b. patients with a mutation that inactivates the estrogen receptor c. patients with over-expression of ER alpha in their tumor cells d. patients with over-expression of VEGF, which helps in tumor angiogenesis 21. In a new cancer treatment, a cold virus is genetically This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 669 modified so that it binds to, enters, and is replicated in cells, causing them to burst. The modified cold virus cannot replicate when wildtype p53 protein is present in the cell. How does this treatment treat cancer without harming healthy cells? a. The modified virus only infects and enters cancer cells. b. The modified virus replicates in normal and cancer cells. c. The modified virus only infects and enters normal cells. d. The modified virus replicates only in cancer cells. 22. A drug designed to switch silenced genes back on in cancer cells would result in what? CRITICAL THINKING QUESTIONS 24. Which best distinguishes prokaryotic and eukaryotic cells? a. Prokaryotes possess a nucleus whereas eukaryotes do not, but eukaryotes show greater compartmentalization that allows for greater regulation of gene expression. b. Eukaryotic cells contain a nucleus whereas prokaryotes do not, and eukaryotes show greater compartmentalization that allows for greater regulation of gene expression. c. Prokaryotic cells are less complex and |
perform highly-regulated gene expression whereas eukaryotes perform less-regulated gene expression. d. Eukaryotic cells are more complex and perform less-regulated gene expression whereas prokaryotic cells perform highly-regulated gene expression. 25. Which statement is correct regarding the distinction between prokaryotic and eukaryotic gene expression? a. prevent methylation of DNA and deacetylation of histones b. prevent methylation of DNA and acetylation of histones c. prevent deacetylation of DNA and methylation of histones d. prevent acetylation of DNA and demethylation of histones 23. What are positive cell-cycle regulators that can cause cancer when mutated called? a. b. transformation genes tumor suppressor genes c. oncogenes d. mutated genes a. Prokaryotes regulate gene expression at the level of transcription whereas eukaryotes regulate at multiple levels including epigenetic, transcriptional and translational. b. Prokaryotes regulate gene expression at the level of translation whereas eukaryotes regulate at the level of transcription to manipulate protein levels. c. Prokaryotes regulate gene expression with the help of repressors and activators whereas eukaryotes regulate expression by degrading mRNA transcripts, thereby controlling protein levels. d. Prokaryotes control protein levels using epigenetic modifications whereas eukaryotes control protein levels by regulating the rate of transcription and translation. 26. All the cells of one organisms share the genome. However, during development, some cells develop into skin cells while others develop into muscle cells. How can the same genetic instructions result in two different cell types in the same organism? Thoroughly explain your answer. 27. Which of the following statements describes prokaryotic transcription of the lac operon? a. When lactose and glucose are present in the medium, transcription of the lac operon is induced. b. When lactose is present but glucose is absent, the lac operon is repressed. c. Lactose acts as an inducer of the lac operon when glucose is absent. d. Lactose acts as an inducer of the lac operon when glucose is present. 670 Chapter 16 | Gene Regulation 28. The lac operon consists of regulatory regions such as the promoter as well as the structural genes lacZ, lacY, and lacA, which code for proteins involved in lactose metabolism. What would be the outcome of a mutation in one of the structural genes of |
the lac operon? a. Mutation in structural genes will stop transcription. b. Mutated lacY will produce an abnormal β galactosidase protein. c. Mutated lacA will produce a protein that will transfer an acetyl group to β galactosidase. d. Transcription will continue but lactose will not be metabolized properly. 29. In some diseases, alteration to epigenetic modifications turns off genes that are normally expressed. Hypothetically, how could you reverse this process to turn these genes back on? 30. Flowering Locus C (FLC) is a gene that is responsible for flowering in certain plants. FLC is expressed in new seedlings, which prevents flowering. Upon exposure to cold temperatures, FLC expression decreases and the plant flowers. FLC is regulated through epigenetic modifications. What type of epigenetic modifications are present in new seedlings and after cold exposure? a. b. c. d. In new seedlings, histone acetylations are present; upon cold exposure, methylation occurs. In new seedlings, histone deacetylations are present; upon cold exposure, methylation occurs. In new seedlings, histone methylations are present; upon cold exposure, acetylation occurs. In new seedlings, histone methylations are present; upon cold exposure, deacetylation occurs. 31. A mutation within the promoter region can alter gene transcription. Describe how this can happen. a. Mutated promoters decrease the rate of transcription by altering the binding site for the transcription factor. b. Mutated promoters increase the rate of transcription by altering the binding site for the transcription factor. c. Mutated promoters alter the binding site for transcription factors to increase or decrease the rate of transcription. d. Mutated promoters alter the binding site for transcription factors and thereby cease transcription of the adjacent gene. 32. What could happen if a cell had too much of an activating transcription factor present? This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 a. The transcription rate would increase, altering cell function. b. The transcription rate would decrease, inhibiting cell functions. c. The transcription rate decreases due to clogging of the transcription factors. d. The transcription rate increases due to clogging of the transcription factors. 33. The wnt transcription pathway is responsible for key changes during animal development. Based on the transcription pathway shown below. In this diagram |
, arrows indicate the transformation of one substance into another. Square lines, or the lines with no arrowheads, indicate inhibition of the product below the line. Based on this, how would increased wnt gene expression affect the expression of Bar-1? Figure 16.16 34. Describe how RBPs can prevent miRNAs from degrading an RNA molecule. Chapter 16 | Gene Regulation 671 38. New drugs are being developed that decrease DNA methylation and prevent the removal of acetyl groups from histone proteins. Explain how these drugs could affect gene expression to help kill tumor cells. a. These drugs maintain the demethylated and the acetylated forms of the DNA to keep transcription of necessary genes “on”. b. The demethylated and the acetylated forms of the DNA are reversed when the silenced gene is expressed. c. The drug methylates and acetylates the silenced genes to turn them back “on”. d. Drugs maintain DNA methylation and acetylation to silence unimportant genes in cancer cells. 39. How can understanding the gene expression pattern in a cancer cell tell you something about that specific form of cancer? a. Understanding gene expression patterns in cancer cells will identify the faulty genes, which is helpful in providing the relevant drug treatment. b. Understanding gene expression will help diagnose tumor cells for antigen therapy. c. Gene profiling would identify the target genes of the cancer-causing pathogens. d. Breast cancer patients who do not express EGFR can respond to anti-EGFR therapy. 40. Explain what personalized medicine is and how it can be used to treat cancer. a. Personalized medicines would vary based on the type of mutations and the gene’s expression pattern. b. The medicines are given based on the type of tumor found in the body of an individual. c. The personalized medicines are provided based only on the symptoms of the patient. d. The medicines tend to vary depending on the severity and the stage of the cancer. a. RBPs can bind first to the RNA, thus preventing the binding of miRNA, which degrades RNA. b. RBPs bind the miRNA, thereby protecting the mRNA from degradation. c. RBPs methylate miRNA to inhibit its function and thus stop mRNA degradation. d. RBPs direct miRNA degradation with the help of a DICER protein complex. 35. How can external stimuli alter post-transcriptional control of gene expression? a. UV rays can alter methylation and acet |
ylation of proteins. b. RNA binding proteins are modified through phosphorylation. c. External stimuli can cause deacetylation and demethylation of the transcript. d. UV rays can cause dimerization of the RNA binding proteins. 36. Protein modifications can alter gene expression in many ways. Describe how phosphorylation of proteins can alter gene expression. a. Phosphorylation of proteins can alter translation, RNA shuttling, RNA stability or post transcriptional modification. b. Phosphorylation of proteins can alter DNA replication, cell division, pathogen recognition and RNA stability. c. Phosphorylated proteins affect only translation and can cause cancer by altering the p53 function. d. Phosphorylated proteins affect only RNA shuttling, RNA stability, and post-translational modifications. 37. Changes in epigenetic modifications alter the accessibility and transcription of DNA. Describe how environmental stimuli, such as ultraviolet light exposure, could modify gene expression. a. UV rays could cause methylation and deacetylation of the genes that could alter the accessibility and transcription of DNA. b. The UV rays could cause phosphorylation and acetylation of the DNA and histones which could alter the transcriptional capabilities of the DNA. c. UV rays could cause methylation and phosphorylation of the DNA bases which could become dimerized rendering no accessibility of DNA. d. The UV rays can cause methylation and acetylation of histones making the DNA more tightly packed and leading to inaccessibility. 672 Chapter 16 | Gene Regulation TEST PREP FOR AP® COURSES 41. Which of the following is found in both prokaryotes and eukaryotes? a. 3’ poly-A tails b. 5’ caps c. promoters d. introns 42. The enzyme ployadenylate polymerase catalyzes the addition of adenosine monophosphate to the 3’ ends of mRNAs to form a poly-A tail. If the enzyme were blocked so that it could not function, the result would be: a. increased mRNA stability in eukaryotes, and decreased mRNA stability in prokaryotes b. decreased mRNA stability in eukaryotes, and no effect in prokaryotes c. no effect in eukaryotes, and increased mRNA stability in prokaryotes d. no effect in eukaryotes, and decreased mRNA stability in prokaryotes 43. Desc |
ribe two ways in which gene regulation differs and two ways in which it is similar in prokaryotes and eukaryotes. a. Prokaryotes show co-transcriptional translation whereas eukaryotes perform transcription prior to translation; in both cell types, regulation occurs through the binding of transcription factors, activators, and repressors. b. Prokaryotes perform transcription prior to translation whereas eukaryotes show cotranscriptional translation (the processes occur in the same organelle). c. Prokaryotes show co-transcriptional translation that is regulated prior to translation whereas eukaryotes perform transcription prior to translation that is regulated only at the level of transcription. In both domains, transcription factors, activators, and repressors provide regulation. d. Prokaryotes show co-transcriptional translation that occurs in the nucleus whereas eukaryotes show transcription prior to translation. In both cell types, regulation occurs using transcription factors, activators, and repressors. 44. Lactose digestion in E. coli begins with its hydrolysis by the enzyme β -galactosidase. The gene encoding β -galactosidase, lacZ, is part of a coordinately regulated operon containing other genes required for lactose utilization. Which of the following figures correctly depicts the interactions at the lac operon when lactose is not being utilized? This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 a. b. c. d. 45. What would be the result of a mutation in the repressor protein that prevented it from binding lactose? a. The repressor will bind to lactose when it is removed from the operator. b. The repressor will bind the operator in the presence of lactose. c. The repressor will not bind the operator in the presence of lactose. d. The repressor will not bind the operator in the absence of lactose. 46. What type of modification might be observed in the GR gene in all newborn rats? a. The DNA will have many methyl molecules. b. The DNA will have many acetyl molecules. c. The DNA will have few methyl groups. d. The histones will have many acetyl groups. 47. What type of modification will be observed in the GR gene in the highly nurtured rats? a. The DNA will have many methyl molecules. b. The |
DNA will have many acetyl molecules. c. The DNA will have few methyl groups. d. The histones will have few acetyl groups. 48. Chapter 16 | Gene Regulation 673 gene? 50. a. deletion 1 b. deletion 2 c. deletion 3 d. deletion 4 The diagram provided shows different regions (1-5) of a pre-mRNA molecule, a mature-mRNA molecule, and the protein corresponding to the mRNA. A mutation in which region is most likely to be damaging to the cell? The level of transcription of a gene is tested by creating deletions in the gene as shown in the illustration. These modified genes are tested for their level of transcription: (++) normal transcription levels; (+) low transcription levels; (+++) high transcription levels. Which deletion is in an enhancer involved in regulating the gene? a. deletion 1 b. deletion 2 c. deletion 3 d. deletion 4 49. a. 1 b. 2 c. 3 d. 5 51. What do regions 1 and 5 correspond to? a. exons b. introns c. promoters d. untranslated regions 52. Which deletion is in a repressor involved in regulating the 674 Chapter 16 | Gene Regulation What are regions 1 through 5 in the diagram? a. 1, 3, and 5 are exons; 2 and 4 are introns. b. 2 and 4 are exons; 1,3, and 5 are introns. c. 1 and 5 are exons; 2, 3, and 4 are introns. d. 2, 3, and 4 are exons; 1 and 5 are introns. 53. A mutation results in the formation of the mutated maturemRNA as indicated in the diagram. Describe what type of mutation occurred and what the likely outcome of the mutation is. a. Mutation in the GU-AG sites of introns produced a non-functional protein. b. A transversion mutation in the introns led to alternative splicing, producing a functional protein. c. A transversion mutation in the GU-AG site mutated this mRNA, producing a non-functional protein. d. Transition mutations in the introns could produce a functional protein. 54. The diagram illustrates the role of p53 in response to UV exposure. What would be the result of a mutation in the p53 gene that inactivates it? a. Skin will peel in response to UV exposure. b. Apoptosis will occur in response to UV exposure. |
c. No DNA damage will occur in response to UV exposure. d. No peeling of skin will occur in response to UV exposure. 55. Which of the following will not occur in response to UV exposure if a p53 mutation inactivates the p53 protein? 1. Damage to DNA 2. p53 activation 3. p21 activation 4. Apoptosis This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 16 | Gene Regulation 675 a. 1, 2, and 3 b. 3 and 4 c. 3 d. 2, 3, and 4 56. What happens when tryptophan is present? a. The repressor binds to the operator, and RNA synthesis is blocked. b. RNA polymerase binds to the operator, and RNA synthesis is blocked. c. Tryptophan binds to the repressor, and RNA synthesis proceeds. d. Tryptophan binds to RNA polymerase, and RNA synthesis proceeds. 57. What happens in the absence of tryptophan? a. RNA polymerase binds to the repressor b. c. the repressor binds to the promoter the repressor dissociates from the operator d. RNA polymerase dissociates from the promoter 58. Anabaena is a simple multicellular photosynthetic cyanobacterium. In the absence of fixed nitrogen, certain newly developing cells along a filament express genes that code for nitrogen-fixing enzymes and become nonphotosynthetic heterocysts. The specialization is advantageous because some nitrogen-fixing enzymes function best in the absence of oxygen. Heterocysts do not carry out photosynthesis but instead provides adjacent cells with fixed nitrogen and receives fixed carbon and reduced energy carriers in return. As shown in the diagram above, when there is low fixed nitrogen in the environment, an increase in the concentration of free calcium ions and 2-oxyglutarate stimulates the expression of genes that produce two transcription factors (NtcA and HetR) that promote the expression of genes responsible for heterocyst development. HetR also causes production of a signal, PatS, that prevents adjacent cells from developing as heterocysts. Based on your understanding of the ways in which signal transmission mediates cell function, which of the following predictions is most consistent with the information given above? Chapter 16 | Gene Regulation 676 59. a. In an environment with low fixed nitrogen, treating the Anabaena cells with |
a calciumbinding compound should prevent heterocyst differentiation. b. A strain that overexpresses the patS gene should develop many more heterocysts in a low nitrogen environment. c. d. In an environment with abundant fixed nitrogen, free calcium levels should be high in all cells, preventing heterocysts from developing. In environments with abundant fixed nitrogen, loss of the hetR gene should induce heterocyst development. Which of the following statements about Anabaena is false? a. Decreasing the concentration of free calcium ions will prevent heterocyst development. b. In the presence of fixed nitrogen, NtcA will not be expressed. c. Low fixed nitrogen levels result in increased PatS levels. d. A mutation in NtcA that makes it nonfunctional will also allow adjacent cells to develop as heterocysts. SCIENCE PRACTICE CHALLENGE QUESTIONS 60. The operon model describes expression in prokaryotes. Describe this model and the essential difference in the way in which expression is regulated in eukaryotes. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 677 17 | BIOTECHNOLOGY AND GENOMICS Figure 17.1 In genomics, the DNA of different organisms is compared, enabling scientists to create maps with which to navigate the DNA of different organisms. (credit "map": modification of photo by NASA) Chapter Outline 17.1: Biotechnology 17.2: Mapping Genomes 17.3: Whole-Genome Sequencing 17.4: Applying Genomics 17.5: Genomics and Proteomics Introduction Some of the greatest accomplishments of biotechnology are in the fields of medicine and medical research. For example, intestinal failure due to missing or abnormal intestinal tissue is a frequent problem in premature babies. Intestinal problems are also common for people who have had parts of their small intestines removed for reasons, such as Crohn’s Disease, cancer, and blockages. Complications from intestinal failure may include liver disease, bacterial overgrowth, dehydration, and malnutrition. Scientists have recently developed a way to engineer human intestines from human cells using mice. Using a mixture of healthy mouse and human intestinal cells and placing it on scaffolding in the abdominal cavity of immunocompromised mice, functional human intestinal cells grow within four weeks. This could be the breakthrough needed to help |
patients suffering from intestinal failure. More details about this exciting research can be found here (http://openstaxcollege.org/l/ 32grwinmouse). 678 Chapter 17 | Biotechnology and Genomics 17.1 | Biotechnology In this section, you will explore the following questions: • What are examples of basic techniques used to manipulate genetic material (DNA and RNA)? • What is the difference between molecular and reproductive cloning? • What are examples of uses of biotechnology in medicine and agriculture? Connection for AP® Courses Did you eat cereal for breakfast or tomatoes in your dinner salad? Do you know someone who has received gene therapy to treat a disease such as cancer? Should your school, health insurance provider, or employer have access to your genetic profile? Understanding how DNA works has allowed scientists to recombine DNA molecules, clone organisms, and produce mice that glow in the dark. We likely have eaten genetically modified foods and are familiar with how DNA analysis is used to solve crimes. Manipulation of DNA by humans has resulted in bacteria that can protect plants from insect pests and restore ecosystems. Biotechnologies also have been used to produce insulin, hormones, antibiotics, and medicine that dissolve blood clots. Comparative genomics yields new insights into relationships among species, and DNA sequences reveal our personal genetic make-up. However, manipulation of DNA comes with social and ethical responsibilities, raising questions about its appropriate uses. Nucleic acids can be isolated from cells for analysis by lysing cell membranes and enzymatically destroying all other macromolecules. Fragmented or whole chromosomes can be separated on the basis of size (base pair length) by gel electrophoresis. Short sequences of DNA or RNA can be amplified using the polymerase chain reaction (PCR). Recombinant DNA technology can combine DNA from different sources using bacterial plasmids or viruses as vectors to carry foreign genes into host cells, resulting in genetically modified organisms (GMOs). Transgenic bacteria, agricultural plants such as corn and rice, and farm animals produce protein products such as hormones and vaccines that benefit humans. (It is important to remind ourselves that recombinant technology is possible because the genetic code is universal, and the processes of transcription and translation are fundamentally the same in all organisms.) Cloning produces genetically identical copies of DNA, cells, or even entire organisms (reproductive cloning). Genetic testing identifies disease-causing genes, and gene therapy can be used to treat or cure an inheritable disease. However, questions emerge |
from these technologies including the safety of GMOs and privacy issues. Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. Big Idea 3 Enduring Understanding 3.A Essential Knowledge Science Practice Learning Objective Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. Heritable information provides for continuity of life. 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. 3.5 The student can justify the claim that humans can manipulate heritable information by identifying an example of a commonly used technology. Living systems store, retrieve, transmit and respond to information essential to life processes. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 679 Enduring Understanding 3.C Essential Knowledge Science Practice Learning Objective The processing of genetic information is imperfect and is a source of genetic variation. 3.C.1 Changes in genotype can result in changes in phenotype. 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. 3.24 The student is able to predict how a change in genotype, when expressed as a phenotype, provides a variation that can be subject to natural selection. The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards: [APLO 3.13][APLO 3.23][APLO 3.28][APLO 3.24][APLO 1.11][APLO 3.5][APLO 4.2][APLO 4.8] Biotechnology is the use of biological agents for technological advancement. Biotechnology was used for breeding livestock and crops long before the scientific basis of these techniques was understood. Since the discovery of the structure of DNA in 1953, the field of biotechnology has grown rapidly through both academic research and private companies. The primary applications of this technology |
are in medicine (production of vaccines and antibiotics) and agriculture (genetic modification of crops, such as to increase yields). Biotechnology also has many industrial applications, such as fermentation, the treatment of oil spills, and the production of biofuels. Basic Techniques to Manipulate Genetic Material (DNA and RNA) To understand the basic techniques used to work with nucleic acids, remember that nucleic acids are macromolecules made of nucleotides (a sugar, a phosphate, and a nitrogenous base) linked by phosphodiester bonds. The phosphate groups on these molecules each have a net negative charge. An entire set of DNA molecules in the nucleus is called the genome. DNA has two complementary strands linked by hydrogen bonds between the paired bases. The two strands can be separated by exposure to high temperatures (DNA denaturation) and can be reannealed by cooling. The DNA can be replicated by the DNA polymerase enzyme. Unlike DNA, which is located in the nucleus of eukaryotic cells, RNA molecules leave the nucleus. The most common type of RNA that is analyzed is the messenger RNA (mRNA) because it represents the proteincoding genes that are actively expressed. However, RNA molecules present some other challenges to analysis, as they are often less stable than DNA. DNA and RNA Extraction To study or manipulate nucleic acids, the DNA or RNA must first be isolated or extracted from the cells. Various techniques are used to extract different types of DNA (Figure 17.2). Most nucleic acid extraction techniques involve steps to break open the cell and use enzymatic reactions to destroy all macromolecules that are not desired (such as degradation of unwanted molecules and separation from the DNA sample). Cells are broken using a lysis buffer (a solution which is mostly a detergent); lysis means “to split.” These enzymes break apart lipid molecules in the cell membranes and nuclear membranes. Macromolecules are inactivated using enzymes such as proteases that break down proteins, and ribonucleases (RNAses) that break down RNA. The DNA is then precipitated using alcohol. Human genomic DNA is usually visible as a gelatinous, white mass. The DNA samples can be stored frozen at –80°C for several years. 680 Chapter 17 | Biotechnology and Genomics Figure 17.2 This diagram shows the basic method used for extraction of DNA. RNA analysis is performed to study gene expression patterns in cells. RNA is naturally very unstable because RNAses are commonly present |
in nature and very difficult to inactivate. Similar to DNA, RNA extraction involves the use of various buffers and enzymes to inactivate macromolecules and preserve the RNA. Gel Electrophoresis Because nucleic acids are negatively charged ions at neutral or basic pH in an aqueous environment, they can be mobilized by an electric field. Gel electrophoresis is a technique used to separate molecules on the basis of size, using this charge. The nucleic acids can be separated as whole chromosomes or fragments. The nucleic acids are loaded into a slot near the negative electrode of a semisolid, porous gel matrix and pulled toward the positive electrode at the opposite end of the gel. Smaller molecules move through the pores in the gel faster than larger molecules; this difference in the rate of migration separates the fragments on the basis of size. There are molecular weight standard samples that can be run alongside the molecules to provide a size comparison. Nucleic acids in a gel matrix can be observed using various fluorescent or colored dyes. Distinct nucleic acid fragments appear as bands at specific distances from the top of the gel (the negative electrode end) on the basis of their size (Figure 17.3). A mixture of genomic DNA fragments of varying sizes appear as a long smear, whereas uncut genomic DNA is usually too large to run through the gel and forms a single large band at the top of the gel. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 681 Figure 17.3 Shown are DNA fragments from seven samples run on a gel, stained with a fluorescent dye, and viewed under UV light. (credit: James Jacob, Tompkins Cortland Community College) Amplification of Nucleic Acid Fragments by Polymerase Chain Reaction Although genomic DNA is visible to the naked eye when it is extracted in bulk, DNA analysis often requires focusing on one or more specific regions of the genome. Polymerase chain reaction (PCR) is a technique used to amplify specific regions of DNA for further analysis (Figure 17.4). PCR is used for many purposes in laboratories, such as the cloning of gene fragments to analyze genetic diseases, identification of contaminant foreign DNA in a sample, and the amplification of DNA for sequencing. More practical applications include the detection of genetic diseases. 682 Chapter 17 | Biotechnology and Genomics Figure 17.4 Polymerase chain reaction, or |
PCR, is used to amplify a specific sequence of DNA. Primers—short pieces of DNA complementary to each end of the target sequence—are combined with genomic DNA, Taq polymerase, and deoxynucleotides. Taq polymerase is a DNA polymerase isolated from the thermostable bacterium Thermus aquaticus that is able to withstand the high temperatures used in PCR. Thermus aquaticus grows in the Lower Geyser Basin of Yellowstone National Park. Reverse transcriptase PCR (RT-PCR) is similar to PCR, but cDNA is made from an RNA template before PCR begins. DNA fragments can also be amplified from an RNA template in a process called reverse transcriptase PCR (RT-PCR). The first step is to recreate the original DNA template strand (called cDNA) by applying DNA nucleotides to the mRNA. This process is called reverse transcription. This requires the presence of an enzyme called reverse transcriptase. After the cDNA is made, regular PCR can be used to amplify it. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 683 Deepen your understanding of (http://openstaxcollege.org/l/PCR). the polymerase chain reaction by clicking through this interactive exercise Explain an advantage the polymerase chain reaction (PCR) has for DNA research. a. The process of PCR can isolate a particular piece of DNA for copying, which allows scientists to copy millions of strands of DNA in a short amount of time. b. The process of PCR can purify a particular piece of DNA, and very small amounts of DNA can be used for purification. c. The process of PCR separates and analyzes DNA and its fragments, which requires very little DNA. d. The process of PCR anneals DNA molecules to complementary DNA strands, which maintains the same amount of DNA. Hybridization, Southern Blotting, and Northern Blotting Nucleic acid samples, such as fragmented genomic DNA and RNA extracts, can be probed for the presence of certain sequences. Short DNA fragments called probes are designed and labeled with radioactive or fluorescent dyes to aid detection. Gel electrophoresis separates the nucleic acid fragments according to their size. The fragments in the gel are then transferred onto a nylon membrane in a procedure called blotting (Figure 17.5). The nucleic acid fragments that are bound to the |
surface of the membrane can then be probed with specific radioactively or fluorescently labeled probe sequences. When DNA is transferred to a nylon membrane, the technique is called Southern blotting, and when RNA is transferred to a nylon membrane, it is called northern blotting. Southern blots are used to detect the presence of certain DNA sequences in a given genome, and northern blots are used to detect gene expression. Figure 17.5 Southern blotting is used to find a particular sequence in a sample of DNA. DNA fragments are separated on a gel, transferred to a nylon membrane, and incubated with a DNA probe complementary to the sequence of interest. Northern blotting is similar to Southern blotting, but RNA is run on the gel instead of DNA. In western blotting, proteins are run on a gel and detected using antibodies. 684 Chapter 17 | Biotechnology and Genomics Molecular Cloning In general, the word “cloning” means the creation of a perfect replica; however, in biology, the re-creation of a whole organism is referred to as “reproductive cloning.” Long before attempts were made to clone an entire organism, researchers learned how to reproduce desired regions or fragments of the genome, a process that is referred to as molecular cloning. Cloning small fragments of the genome allows for the manipulation and study of specific genes (and their protein products), or noncoding regions in isolation. A plasmid (also called a vector) is a small circular DNA molecule that replicates independently of the chromosomal DNA. In cloning, the plasmid molecules can be used to provide a "folder" in which to insert a desired DNA fragment. Plasmids are usually introduced into a bacterial host for proliferation. In the bacterial context, the fragment of DNA from the human genome (or the genome of another organism that is being studied) is referred to as foreign DNA, or a transgene, to differentiate it from the DNA of the bacterium, which is called the host DNA. Plasmids occur naturally in bacterial populations (such as Escherichia coli) and have genes that can contribute favorable traits to the organism, such as antibiotic resistance (the ability to be unaffected by antibiotics). Plasmids have been repurposed and engineered as vectors for molecular cloning and the large-scale production of important reagents, such as insulin and human growth hormone. An important feature of plasmid vectors is the ease with which a foreign DNA fragment can be introduced via the multiple cloning site |
(MCS). The MCS is a short DNA sequence containing multiple sites that can be cut with different commonly available restriction endonucleases. Restriction endonucleases recognize specific DNA sequences and cut them in a predictable manner; they are naturally produced by bacteria as a defense mechanism against foreign DNA. Many restriction endonucleases make staggered cuts in the two strands of DNA, such that the cut ends have a 2- or 4-base single-stranded overhang. Because these overhangs are capable of annealing with complementary overhangs, these are called “sticky ends.” Addition of an enzyme called DNA ligase permanently joins the DNA fragments via phosphodiester bonds. In this way, any DNA fragment generated by restriction endonuclease cleavage can be spliced between the two ends of a plasmid DNA that has been cut with the same restriction endonuclease (Figure 17.6). Recombinant DNA Molecules Plasmids with foreign DNA inserted into them are called recombinant DNA molecules because they are created artificially and do not occur in nature. They are also called chimeric molecules because the origin of different parts of the molecules can be traced back to different species of biological organisms or even to chemical synthesis. Proteins that are expressed from recombinant DNA molecules are called recombinant proteins. Not all recombinant plasmids are capable of expressing genes. The recombinant DNA may need to be moved into a different vector (or host) that is better designed for gene expression. Plasmids may also be engineered to express proteins only when stimulated by certain environmental factors, so that scientists can control the expression of the recombinant proteins. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 685 Figure 17.6 This diagram shows the steps involved in molecular cloning. 686 Chapter 17 | Biotechnology and Genomics You are working in a molecular biology lab and, unbeknownst to you, your lab partner left the foreign genomic DNA you are planning to clone on the lab bench overnight instead of storing it in the freezer. As a result, it was degraded by nucleases, but still used in the experiment. The plasmid, on the other hand, is fine. What results would you expect from your molecular cloning experiment? a. There will be no colonies on the bacterial plate. b. There will be blue colonies only. |
c. There will be blue and white colonies. d. The will be white colonies only. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 687 View an animation of recombination in cloning (http://openstaxcollege.org/l/recombination) from the DNA Learning Center. What are the functions of the restriction enzymes and DNA ligase in recombination? a. Restriction enzymes restrict the recombination process. DNA ligase ligates the products of recombination with each other. b. DNA ligase splices DNA at a specific point, so the new piece of DNA can be inserted. Restriction enzymes stitch together the new gene to the existing piece of DNA. c. Restriction enzymes splice DNA at a specific point, so the new piece of DNA can be inserted. DNA ligase stitches together the new foreign gene to the existing piece of DNA. d. Restriction enzymes splice the existing piece of DNA only to accommodate the new piece of DNA. DNA ligase ligates the new DNA with the existing DNA. Activity Cloning can be used to quickly replicate crop plants that have advantageous genes, such as greater disease resistance or greater fruit production. However, cloning also produces crop plants that have little genetic variation. In a group, discuss the advantages and disadvantages of using clones as human food sources in an era where the Earth is undergoing a period of climate change. How well will cloned populations of crop plants be able to adapt to climate change, compared to non-clone crop plants? Then, defend your group’s position against those of other groups in a classroom debate. Think About It How would a scientist introduce a gene for herbicide resistance into a plant, such as corn? Cellular Cloning Unicellular organisms, such as bacteria and yeast, naturally produce clones of themselves when they replicate asexually by binary fission; this is known as cellular cloning. The nuclear DNA duplicates by the process of mitosis, which creates an exact replica of the genetic material. Reproductive Cloning Reproductive cloning is a method used to make a clone or an identical copy of an entire multicellular organism. Most multicellular organisms undergo reproduction by sexual means, which involves genetic hybridization of two individuals (parents), making it impossible for generation of an identical copy or a clone of either parent. Recent advances in biotechnology have made it possible to artificially induce asexual |
reproduction of mammals in the laboratory. Parthenogenesis, or “virgin birth,” occurs when an embryo grows and develops without the fertilization of the egg occurring; this is a form of asexual reproduction. An example of parthenogenesis occurs in species in which the female lays an egg and if the egg is fertilized, it is a diploid egg and the individual develops into a female; if the egg is not fertilized, it 688 Chapter 17 | Biotechnology and Genomics remains a haploid egg and develops into a male. The unfertilized egg is called a parthenogenic, or virgin, egg. Some insects and reptiles lay parthenogenic eggs that can develop into adults. Sexual reproduction requires two cells; when the haploid egg and sperm cells fuse, a diploid zygote results. The zygote nucleus contains the genetic information to produce a new individual. However, early embryonic development requires the cytoplasmic material contained in the egg cell. This idea forms the basis for reproductive cloning. Therefore, if the haploid nucleus of an egg cell is replaced with a diploid nucleus from the cell of any individual of the same species (called a donor), it will become a zygote that is genetically identical to the donor. Somatic cell nuclear transfer is the technique of transferring a diploid nucleus into an enucleated egg. It can be used for either therapeutic cloning or reproductive cloning. The first cloned animal was Dolly, a sheep who was born in 1996. The success rate of reproductive cloning at the time was very low. Dolly lived for seven years and died of respiratory complications (Figure 17.7). There is speculation that because the cell DNA belongs to an older individual, the age of the DNA may affect the life expectancy of a cloned individual. Since Dolly, several animals such as horses, bulls, and goats have been successfully cloned, although these individuals often exhibit facial, limb, and cardiac abnormalities. There have been attempts at producing cloned human embryos as sources of embryonic stem cells, sometimes referred to as cloning for therapeutic purposes. Therapeutic cloning produces stem cells to attempt to remedy detrimental diseases or defects (unlike reproductive cloning, which aims to reproduce an organism). Still, therapeutic cloning efforts have met with resistance because of bioethical considerations. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology |
and Genomics 689 Figure 17.7 Dolly the sheep was the first mammal to be cloned. To create Dolly, the nucleus was removed from a donor egg cell. The nucleus from a second sheep was then introduced into the cell, which was allowed to divide to the blastocyst stage before being implanted in a surrogate mother. (credit: modification of work by "Squidonius"/Wikimedia Commons) 690 Chapter 17 | Biotechnology and Genomics Do you think Dolly was a Finn-Dorset or a Scottish Blackface sheep? a. Blackface because this follows cytoplasmic inheritance. b. Dolly was a Finn-Dorset sheep; the nucleus in the process was taken from a Finn-Dorset mother. c. Dorset sheep because this follows cytoplasmic inheritance. d. Dolly the sheep was a Scottish blackface due to epigenetic inheritance. Genetic Engineering Genetic engineering is the alteration of an organism’s genotype using recombinant DNA technology to modify an organism’s DNA to achieve desirable traits. The addition of foreign DNA in the form of recombinant DNA vectors generated by molecular cloning is the most common method of genetic engineering. The organism that receives the recombinant DNA is called a genetically modified organism (GMO). If the foreign DNA that is introduced comes from a different species, the host organism is called transgenic. Bacteria, plants, and animals have been genetically modified since the early 1970s for academic, medical, agricultural, and industrial purposes. In the US, GMOs such as herbicide-resistant soybeans and borer-resistant corn are part of many common processed foods. Gene Targeting Although classical methods of studying the function of genes began with a given phenotype and determined the genetic basis of that phenotype, modern techniques allow researchers to start at the DNA sequence level and ask: "What does this gene or DNA element do?" This technique, called reverse genetics, has resulted in reversing the classic genetic This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 691 methodology. This method would be similar to damaging a body part to determine its function. An insect that loses a wing cannot fly, which means that the function of the wing is flight. The classical genetic method would compare insects that cannot fly with insects that can fly, and observe that the non-flying insects have lost wings. Similarly, mutating or deleting |
genes provides researchers with clues about gene function. The methods used to disable gene function are collectively called gene targeting. Gene targeting is the use of recombinant DNA vectors to alter the expression of a particular gene, either by introducing mutations in a gene, or by eliminating the expression of a certain gene by deleting a part or all of the gene sequence from the genome of an organism. Biotechnology in Medicine and Agriculture It is easy to see how biotechnology can be used for medicinal purposes. Knowledge of the genetic makeup of our species, the genetic basis of heritable diseases, and the invention of technology to manipulate and fix mutant genes provides methods to treat the disease. Biotechnology in agriculture can enhance resistance to disease, pest, and environmental stress, and improve both crop yield and quality. Genetic Diagnosis and Gene Therapy The process of testing for suspected genetic defects before administering treatment is called genetic diagnosis by genetic testing. Depending on the inheritance patterns of a disease-causing gene, family members are advised to undergo genetic testing. For example, women diagnosed with breast cancer are usually advised to have a biopsy so that the medical team can determine the genetic basis of cancer development. Treatment plans are based on the findings of genetic tests that determine the type of cancer. If the cancer is caused by inherited gene mutations, other female relatives are also advised to undergo genetic testing and periodic screening for breast cancer. Genetic testing is also offered for fetuses (or embryos with in vitro fertilization) to determine the presence or absence of disease-causing genes in families with specific debilitating diseases. Gene therapy is a genetic engineering technique used to cure disease. In its simplest form, it involves the introduction of a good gene at a random location in the genome to aid the cure of a disease that is caused by a mutated gene. The good gene is usually introduced into diseased cells as part of a vector transmitted by a virus that can infect the host cell and deliver the foreign DNA (Figure 17.8). More advanced forms of gene therapy try to correct the mutation at the original site in the genome, such as is the case with treatment of severe combined immunodeficiency (SCID). Figure 17.8 Gene therapy using an adenovirus vector can be used to cure certain genetic diseases in which a person has a defective gene. (credit: NIH) Production of Vaccines, Antibiotics, and Hormones Traditional vaccination strategies use weakened or inactive forms of microorganisms to mount the initial immune response. 692 Chapter 17 | Biotechnology and Genomics Modern techniques use |
the genes of microorganisms cloned into vectors to mass produce the desired antigen. The antigen is then introduced into the body to stimulate the primary immune response and trigger immune memory. Genes cloned from the influenza virus have been used to combat the constantly changing strains of this virus. Antibiotics are a biotechnological product. They are naturally produced by microorganisms, such as fungi, to attain an advantage over bacterial populations. Antibiotics are produced on a large scale by cultivating and manipulating fungal cells. Recombinant DNA technology was used to produce large-scale quantities of human insulin in E. coli as early as 1978. Previously, it was only possible to treat diabetes with pig insulin, which caused allergic reactions in humans because of differences in the gene product. In addition, human growth hormone (HGH) is used to treat growth disorders in children. The HGH gene was cloned from a cDNA library and inserted into E. coli cells by cloning it into a bacterial vector. Transgenic Animals Although several recombinant proteins used in medicine are successfully produced in bacteria, some proteins require a eukaryotic animal host for proper processing. For this reason, the desired genes are cloned and expressed in animals, such as sheep, goats, chickens, and mice. Animals that have been modified to express recombinant DNA are called transgenic animals. Several human proteins are expressed in the milk of transgenic sheep and goats, and some are expressed in the eggs of chickens. Mice have been used extensively for expressing and studying the effects of recombinant genes and mutations. Transgenic Plants Manipulating the DNA of plants (i.e., creating GMOs) has helped to create desirable traits, such as disease resistance, herbicide and pesticide resistance, better nutritional value, and better shelf-life (Figure 17.9). Plants are the most important source of food for the human population. Farmers developed ways to select for plant varieties with desirable traits long before modern-day biotechnology practices were established. Figure 17.9 Corn, a major agricultural crop used to create products for a variety of industries, is often modified through plant biotechnology. (credit: Keith Weller, USDA) Plants that have received recombinant DNA from other species are called transgenic plants. Because they are not natural, transgenic plants and other GMOs are closely monitored by government agencies to ensure that they are fit for human consumption and do not endanger other plant and animal life. Because foreign genes can spread to other species in the environment, extensive testing is required to |
ensure ecological stability. Staples like corn, potatoes, and tomatoes were the first crop plants to be genetically engineered. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 693 Transformation of Plants Using Agrobacterium tumefaciens Gene transfer occurs naturally between species in microbial populations. Many viruses that cause human diseases act by incorporating their DNA into the human genome. In plants, tumors caused by the bacterium Agrobacterium tumefaciens occur by transfer of DNA from the bacterium to the plant. Although the tumors do not kill the plants, they make the plants stunted and more susceptible to harsh environmental conditions. Many plants, such as walnuts, grapes, nut trees, and beets, are affected by A. tumefaciens. The artificial introduction of DNA into plant cells is more challenging than in animal cells because of the thick plant cell wall. Researchers used the natural transfer of DNA from Agrobacterium to a plant host to introduce DNA fragments of their choice into plant hosts. In nature, the disease-causing A. tumefaciens have a set of plasmids, called the Ti plasmids (tumorinducing plasmids), that contain genes for the production of tumors in plants. DNA from the Ti plasmid integrates into the infected plant cell’s genome. Researchers manipulate the Ti plasmids to remove the tumor-causing genes and insert the desired DNA fragment for transfer into the plant genome. The Ti plasmids carry antibiotic resistance genes to aid selection and can be propagated in E. coli cells as well. The Organic Insecticide Bacillus thuringiensis Bacillus thuringiensis (Bt) is a bacterium that produces protein crystals during sporulation that are toxic to many insect species that affect plants. Bt toxin has to be ingested by insects for the toxin to be activated. Insects that have eaten Bt toxin stop feeding on the plants within a few hours. After the toxin is activated in the intestines of the insects, death occurs within a couple of days. Modern biotechnology has allowed plants to encode their own crystal Bt toxin that acts against insects. The crystal toxin genes have been cloned from Bt and introduced into plants. Bt toxin has been found to be safe for the environment, non-toxic to humans and other mammals, and is approved for use by organic |
farmers as a natural insecticide. Flavr Savr Tomato The first GM crop was in 1994. It was a tomato that resisted rotting and maintained flavor for longer periods of time. Antisense RNA technology was used to slow down the process of softening and rotting caused by fungal infections, which led to increased shelf life of the GM tomatoes. Additional genetic modification improved the flavor of this tomato. This GM tomato did not successfully stay in the market because of problems maintaining and shipping the crop. 17.2 | Mapping Genomes In this section, you will explore the following questions: • What is genomics? • What is a genetic map? • What is an example of a genomic mapping method? Connection for AP® Courses Genome mapping is similar to solving a big, complicated puzzle with pieces of information collected from laboratories all over the world. Genetic maps provide an outline for the location of genes within a chromosome. Distances between genes and genetic markers are estimated on the basis of recombination (crossing over) frequencies during meiosis. The Human Genome Project helped researchers identify thousands of human genes and their protein products. Noncoding regions of DNA may be involved in regulating gene expression, and other sequences once considered “junk” may play an important role in genome evolution. Few differences exist between human DNA sequences and those of many other organisms. Information presented and the examples highlighted in the section support concepts outlined in Big Idea 3 of the AP® Biology Curriculum Framework. The Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A Learning Objective merges required content with one or more of the seven Science Practices. Big Idea 3 Living systems store, retrieve, transmit and respond to information essential to life processes. 694 Chapter 17 | Biotechnology and Genomics Enduring Understanding 3.A Essential Knowledge Heritable information provides for continuity of life. 3.A.1 DNA, and in some cases RNA, is the primary source of heritable information. Science Practice 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Learning Objective Essential Knowledge 3.5 The student can justify the claim that humans can manipulate heritable information by identifying examples of commonly used technologies. 3.A.2 In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or meiosis. Science Practice |
7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective Essential Knowledge 3.10 The student is able to represent the connection between meiosis and increased genetic diversity necessary for evolution. 3.A.3 The chromosomal basis of inheritance provides an understanding of the pattern of passage (transmission) of genes from parent to offspring. Science Practice 1.1 The student can create representations and models of natural or man-made phenomena and systems in the domain. Learning Objective 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. Genome mapping is the process of finding the locations of genes on each chromosome. The maps created by genome mapping are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture (similar to a map of interstate highways) and use genetic markers (similar to landmarks). A genetic marker is a gene or sequence on a chromosome that co-segregates (shows genetic linkage) with a specific trait. Early geneticists called this linkage analysis. Physical maps present the intimate details of smaller regions of the chromosomes (similar to a detailed road map). A physical map is a representation of the physical distance, in nucleotides, between genes or genetic markers. Both genetic linkage maps and physical maps are required to build a complete picture of the genome. Having a complete map of the genome makes it easier for researchers to study individual genes. Human genome maps help researchers in their efforts to identify human disease-causing genes related to illnesses like cancer, heart disease, and cystic fibrosis. Genome mapping can be used in a variety of other applications, such as using live microbes to clean up pollutants or even prevent pollution. Research involving plant genome mapping may lead to producing higher crop yields or developing plants that better adapt to climate change. Genetic Maps The study of genetic maps begins with linkage analysis, a procedure that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. The term linkage was used before the discovery of DNA. Early geneticists relied on the observation of phenotypic changes to understand the genotype of an organism. Shortly after Gregor Mendel (the father of modern |
genetics) proposed that traits were determined by what are now known as genes, other researchers observed that different traits were often inherited together, and thereby deduced that the genes were physically linked by being located on the same chromosome. The mapping of genes relative to each other based on linkage analysis led to the development of the first genetic maps. Observations that certain traits were always linked and certain others were not linked came from studying the offspring of crosses between parents with different traits. For example, in experiments performed on the garden pea, it was discovered that the color of the flower and shape of the plant’s pollen were linked traits, and therefore the genes encoding these traits were in close proximity on the same chromosome. The exchange of DNA between homologous pairs of chromosomes is called genetic recombination, which occurs by the crossing over of DNA between homologous strands of DNA, such as nonsister chromatids. Linkage analysis involves studying the recombination frequency between any two genes. The greater the distance between two genes, the higher the chance that a recombination event will occur between them, and the higher the recombination frequency between them. Two possibilities for recombination between two nonsister chromatids during This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 695 meiosis are shown in Figure 17.10. If the recombination frequency between two genes is less than 50 percent, they are said to be linked. Figure 17.10 Crossover may occur at different locations on the chromosome. Recombination between genes A and B is more frequent than recombination between genes B and C because genes A and B are farther apart; a crossover is therefore more likely to occur between them. The generation of genetic maps requires markers, just as a road map requires landmarks (such as rivers and mountains). Early genetic maps were based on the use of known genes as markers. More sophisticated markers, including those based on non-coding DNA, are now used to compare the genomes of individuals in a population. Although individuals of a given species are genetically similar, they are not identical; every individual has a unique set of traits. These minor differences in the genome between individuals in a population are useful for the purposes of genetic mapping. In general, a good genetic marker is a region on the chromosome that shows variability or polymorphism (multiple forms) in the population. Some genetic markers used in generating genetic maps are restriction fragment length |
polymorphisms (RFLP), variable number of tandem repeats (VNTRs), microsatellite polymorphisms, and the single nucleotide polymorphisms (SNPs). RFLPs (sometimes pronounced “rif-lips”) are detected when the DNA of an individual is cut with a restriction endonuclease that recognizes specific sequences in the DNA to generate a series of DNA fragments, which are then analyzed by gel electrophoresis. The DNA of every individual will give rise to a unique pattern of bands when cut with a particular set of restriction endonucleases; this is sometimes referred to as an individual’s DNA “fingerprint.” Certain regions of the chromosome that are subject to polymorphism will lead to the generation of the unique banding pattern. VNTRs are repeated sets of nucleotides present in the non-coding regions of DNA. Non-coding, or “junk,” DNA has no known biological function; however, research shows that much of this DNA is actually transcribed. While its function is uncertain, it is certainly active, and it may be involved in the regulation of coding genes. The number of repeats may vary in individual organisms of a population. Microsatellite polymorphisms are similar to VNTRs, but the repeat unit is very small. SNPs are variations in a single nucleotide. Because genetic maps rely completely on the natural process of recombination, mapping is affected by natural increases or decreases in the level of recombination in any given area of the genome. Some parts of the genome are recombination hotspots, whereas others do not show a propensity for recombination. For this reason, it is important to look at mapping information developed by multiple methods. Physical Maps A physical map provides detail of the actual physical distance between genetic markers, as well as the number of nucleotides. There are three methods used to create a physical map: cytogenetic mapping, radiation hybrid mapping, and sequence mapping. Cytogenetic mapping uses information obtained by microscopic analysis of stained sections of the chromosome (Figure 17.11). It is possible to determine the approximate distance between genetic markers using cytogenetic mapping, but not the exact distance (number of base pairs). Radiation hybrid mapping uses radiation, such as x-rays, to break the DNA into fragments. The amount of radiation can be adjusted to create smaller or larger fragments. This technique 696 Chapter 17 | Biotechnology and Genomics overcomes the limitation |
of genetic mapping and is not affected by increased or decreased recombination frequency. Sequence mapping resulted from DNA sequencing technology that allowed for the creation of detailed physical maps with distances measured in terms of the number of base pairs. The creation of genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome) has sped up the process of physical mapping. A genetic site used to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location. An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs. An EST is a short STS that is identified with cDNA libraries, while SSLPs are obtained from known genetic markers and provide a link between genetic maps and physical maps. Figure 17.11 A cytogenetic map shows the appearance of a chromosome after it is stained and examined under a microscope. (credit: National Human Genome Research Institute) Integration of Genetic and Physical Maps Genetic maps provide the outline and physical maps provide the details. It is easy to understand why both types of genome mapping techniques are important to show the big picture. Information obtained from each technique is used in combination to study the genome. Genomic mapping is being used with different model organisms that are used for research. Genome mapping is still an ongoing process, and as more advanced techniques are developed, more advances are expected. Genome mapping is similar to completing a complicated puzzle using every piece of available data. Mapping information generated in laboratories all over the world is entered into central databases, such as GenBank at the National Center for Biotechnology Information (NCBI). Efforts are being made to make the information more easily accessible to researchers and the general public. Just as we use global positioning systems instead of paper maps to navigate through roadways, NCBI has created a genome viewer tool to simplify the data-mining process. How to Use a Genome Map Viewer This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 697 Problem statement: Do the human, macaque, and mouse genomes contain common DNA sequences? Develop a hypothesis. To test the hypothesis, click this link (http://openstaxcollege.org/l/32mapview). In Search box on the left panel, type any gene name or phenotyp |
ic characteristic, such as iris pigmentation (eye color). Select the species you want to study, and then press Enter. The genome map viewer will indicate which chromosome encodes the gene in your search. Click each hit in the genome viewer for more detailed information. This type of search is the most basic use of the genome viewer; it can also be used to compare sequences between species, as well as many other complicated tasks. Is the hypothesis correct? Why or why not? Online Mendelian Inheritance in Man (OMIM) is a searchable online catalog of human genes and genetic disorders. This website shows genome mapping information, and also details the history and research of each trait and disorder. Click this link (http://openstaxcollege.org/l/OMIM) to search for traits (such as handedness) and genetic disorders (such as diabetes). How can this database help to support and guide research for rare genetic conditions, like progeria? a. The database provides information related to the prevention of a genetic disease. b. The database provides all the information about genes for genetic diseases, their inheritance and their expression. It also provides suggestions for some treatments. c. The database provides information about the symptoms of the disease. d. The database provides information only about the early reported cases. Think About It Why is so much effort being poured into genome mapping applications? How could a genetic map of the human genome help find a treatment for genetically based cancers? 17.3 | Whole-Genome Sequencing In this section, you will explore the following questions: • What are three types of gene sequencing? • What is whole-genome sequencing? 698 Chapter 17 | Biotechnology and Genomics Connection for AP® Courses Information presented in section is not in scope for AP®. However, you can study information in the section as optional or illustrative material. Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by some diseases, and they are using whole-genome sequencing to get to the bottom of the problem. Whole-genome sequencing is a process that determines the DNA sequence of an entire genome. Whole-genome sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease. Several laboratories now provide services to sequence, analyze, and interpret entire genomes. Whole-exome sequencing is a lower-cost alternative to whole genome sequencing. In exome sequencing, only the coding, exon-producing |
regions of the DNA are sequenced. In 2010, whole-exome sequencing was used to save a young boy whose intestines had multiple mysterious abscesses. The child had several colon operations with no relief. Finally, whole-exome sequencing was performed, which revealed a defect in a pathway that controls apoptosis (programmed cell death). A bonemarrow transplant was used to overcome this genetic disorder, leading to a cure for the boy. He was the first person to be successfully treated based on a diagnosis made by whole-exome sequencing. The Science Practice Challenge Questions contain additional test questions related to the material in this section that will help you prepare for the AP exam. These questions address the following standards: [APLO 2.23][APLO 3.5][APLO 3.20][APLO 3.21] Strategies Used in Sequencing Projects The basic sequencing technique used in all modern day sequencing projects is the chain termination method (also known as the dideoxy method), which was developed by Fred Sanger in the 1970s. The chain termination method involves DNA replication of a single-stranded template with the use of a primer and a regular deoxynucleotide (dNTP), which is a monomer, or a single unit, of DNA. The primer and dNTP are mixed with a small proportion of fluorescently labeled dideoxynucleotides (ddNTPs). The ddNTPs are monomers that are missing a hydroxyl group (–OH) at the site at which another nucleotide usually attaches to form a chain (Figure 17.12). Each ddNTP is labeled with a different color of fluorophore. Every time a ddNTP is incorporated in the growing complementary strand, it terminates the process of DNA replication, which results in multiple short strands of replicated DNA that are each terminated at a different point during replication. When the reaction mixture is processed by gel electrophoresis after being separated into single strands, the multiple newly replicated DNA strands form a ladder because of the differing sizes. Because the ddNTPs are fluorescently labeled, each band on the gel reflects the size of the DNA strand and the ddNTP that terminated the reaction. The different colors of the fluorophore-labeled ddNTPs help identify the ddNTP incorporated at that position. Reading the gel on the basis of the color of each band on the ladder produces the sequence of the template strand (Figure 17.13). Figure 17 |
.12 A dideoxynucleotide is similar in structure to a deoxynucleotide, but is missing the 3' hydroxyl group (indicated by the box). When a dideoxynucleotide is incorporated into a DNA strand, DNA synthesis stops. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 699 Figure 17.13 Frederick Sanger's dideoxy chain termination method is illustrated. Using dideoxynucleotides, the DNA fragment can be terminated at different points. The DNA is separated on the basis of size, and these bands, based on the size of the fragments, can be read. Early Strategies: Shotgun Sequencing and Pair-Wise End Sequencing In shotgun sequencing method, several copies of a DNA fragment are cut randomly into many smaller pieces (somewhat like what happens to a round shot cartridge when fired from a shotgun). All of the segments are then sequenced using the chain-sequencing method. Then, with the help of a computer, the fragments are analyzed to see where their sequences overlap. By matching up overlapping sequences at the end of each fragment, the entire DNA sequence can be reformed. A larger sequence that is assembled from overlapping shorter sequences is called a contig. As an analogy, consider that someone has four copies of a landscape photograph that you have never seen before and know nothing about how it should appear. The person then rips up each photograph with their hands, so that different size pieces are present from each copy. The person then mixes all of the pieces together and asks you to reconstruct the photograph. In one of the smaller pieces you see a mountain. In a larger piece, you see that the same mountain is behind a lake. A third fragment shows only the lake, but it reveals that there is a cabin on the shore of the lake. Therefore, from looking at the overlapping information in these three fragments, you know that the picture contains a mountain behind a lake that has a cabin on its shore. This is the principle behind reconstructing entire DNA sequences using shotgun sequencing. Originally, shotgun sequencing only analyzed one end of each fragment for overlaps. This was sufficient for sequencing small genomes. However, the desire to sequence larger genomes, such as that of a human, led to the development of doublebarrel shotgun sequencing, more formally known as pairwise-end sequencing. In pairwise-end sequencing, |
both ends of each fragment are analyzed for overlap. Pairwise-end sequencing is, therefore, more cumbersome than shotgun sequencing, but it is easier to reconstruct the sequence because there is more available information. Next-generation Sequencing Since 2005, automated sequencing techniques used by laboratories are under the umbrella of next-generation sequencing, which is a group of automated techniques used for rapid DNA sequencing. These automated low-cost sequencers can generate sequences of hundreds of thousands or millions of short fragments (25 to 500 base pairs) in the span of one day. These sequencers use sophisticated software to get through the cumbersome process of putting all the fragments in order. 700 Chapter 17 | Biotechnology and Genomics Comparing Sequences A sequence alignment is an arrangement of proteins, DNA, or RNA; it is used to identify regions of similarity between cell types or species, which may indicate conservation of function or structures. Sequence alignments may be used to construct phylogenetic trees. The following website uses a software program called BLAST (basic local alignment search tool) (http://openstaxcollege.org/l/32blast). Under “Basic Blast,” click “Nucleotide Blast.” Input the following sequence into the large "query sequence" box: ATTGCTTCGATTGCA. Below the box, locate the "Species" field and type "human" or "Homo sapiens". Then click “BLAST” to compare the inputted sequence against known sequences of the human genome. The result is that this sequence occurs in over a hundred places in the human genome. Scroll down below the graphic with the horizontal bars and you will see short description of each of the matching hits. Pick one of the hits near the top of the list and click on "Graphics". This will bring you to a page that shows where the sequence is found within the entire human genome. You can move the slider that looks like a green flag back and forth to view the sequences immediately around the selected gene. You can then return to your selected sequence by clicking the "ATG" button. Cytochrome c oxidase is a highly conserved protein found in bacteria and in the mitochondria of eukaryotes. Based on your knowledge of evolutionary relationships, which of the following statements would you expect to be true of the cytochrome c oxidase protein sequence? a. The bacterial protein will be more similar to the human protein than the yeast protein. b. The yeast protein will be more similar to |
the human protein than the bacterial protein. c. The bacterial protein will be more similar to the yeast protein than the human protein. d. The bacterial and yeast protein will share a similar sequence, but the human protein will be unrelated. Use of Whole-Genome Sequences of Model Organisms The first genome to be completely sequenced was of a bacterial virus, the bacteriophage fx174 (5368 base pairs); this was accomplished by Fred Sanger using shotgun sequencing. Several other organelle and viral genomes were later sequenced. The first organism whose genome was sequenced was the bacterium Haemophilus influenzae; this was accomplished by Craig Venter in the 1980s. Approximately 74 different laboratories collaborated on the sequencing of the genome of the yeast Saccharomyces cerevisiae, which began in 1989 and was completed in 1996, because it was 60 times bigger than any other genome that had been sequenced. By 1997, the genome sequences of two important model organisms were available: the bacterium Escherichia coli K12 and the yeast Saccharomyces cerevisiae. Genomes of other model organisms, such as the mouse Mus musculus, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis. elegans, and humans Homo sapiens are now known. A lot of basic research is performed in model organisms because the information can be applied to genetically similar organisms. A model organism is a species that is studied as a model to understand the biological processes in other species represented by the model organism. Having entire genomes sequenced helps with the research efforts in these model organisms. The process of attaching biological information to gene sequences is called genome annotation. Annotation of gene sequences helps with basic experiments in molecular biology, such as designing PCR primers and RNA targets. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 701 Click through each step of genome sequencing at this site (http://openstaxcollege.org/l/DNA_sequence). How is deep sequencing an improvement on Sanger sequencing? a. Deep sequencing allows for much faster sequencing of short strands of DNA as compared to Sanger sequencing which, reads only short sequences of DNA at a slow rate. Also, there is a high risk of chain termination and problems with separation during Sanger sequencing. b. Sequence coverage is higher in Sanger sequencing as compared |
to deep sequencing. c. Sanger sequencing is suitable when there is only one nucleotide different between chains whereas deep sequencing is suitable when there is one or more than one nucleotide different between chains. d. Sanger sequencing reads and sequences a genome multiple times whereas deep sequencing accurately sequences the whole genome in a single time. Uses of Genome Sequences DNA microarrays are methods used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences. Almost one million genotypic abnormalities can be discovered using microarrays, whereas whole-genome sequencing can provide information about all six billion base pairs in the human genome. Although the study of medical applications of genome sequencing is interesting, this discipline tends to dwell on abnormal gene function. Knowledge of the entire genome will allow future onset diseases and other genetic disorders to be discovered early, which will allow for more informed decisions to be made about lifestyle, medication, and having children. Genomics is still in its infancy, although someday it may become routine to use whole-genome sequencing to screen every newborn to detect genetic abnormalities. In addition to disease and medicine, genomics can contribute to the development of novel enzymes that convert biomass to biofuel, which results in higher crop and fuel production, and lower cost to the consumer. This knowledge should allow better methods of control over the microbes that are used in the production of biofuels. Genomics could also improve the methods used to monitor the impact of pollutants on ecosystems and help clean up environmental contaminants. Genomics has allowed for the development of agrochemicals and pharmaceuticals that could benefit medical science and agriculture. It sounds great to have all the knowledge we can get from whole-genome sequencing; however, humans have a responsibility to use this knowledge wisely. Otherwise, it could be easy to misuse the power of such knowledge, leading to discrimination based on a person's genetics, human genetic engineering, and other ethical concerns. This information could also lead to legal issues regarding health and privacy. 17.4 | Applying Genomics In this section, you will explore the following questions: • What is pharmacogenomics? • What is an example of a polygenic human disease? Connection for AP® Courses Information presented in section is not in scope for AP®. However, you can study information in the section as optional or illustrative material. 702 Chapter 17 | Biotechnology and Genomics The introduction of DNA sequencing and whole genome sequencing projects, particularly the |
Human Genome project, has expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known application of genomics is to understand and find cures for diseases. Predicting Disease Risk at the Individual Level Predicting the risk of disease involves screening currently healthy individuals by genome analysis at the individual level. Intervention with lifestyle changes and drugs can be recommended before disease onset. However, this approach is most applicable when the problem resides within a single gene defect. Such defects only account for approximately 5 percent of diseases in developed countries. Most of the common diseases, such as heart disease, are multi-factored or polygenic, which is a phenotypic characteristic that involves two or more genes, and also involve environmental factors such as diet. In April 2010, scientists at Stanford University published the genome analysis of a healthy individual (Stephen Quake, a scientist at Stanford University, who had his genome sequenced); the analysis predicted his propensity to acquire various diseases. A risk assessment was performed to analyze Quake’s percentage of risk for 55 different medical conditions. A rare genetic mutation was found, which showed him to be at risk for sudden heart attack. He was also predicted to have a 23 percent risk of developing prostate cancer and a 1.4 percent risk of developing Alzheimer’s. The scientists used databases and several publications to analyze the genomic data. Even though genomic sequencing is becoming more affordable and analytical tools are becoming more reliable, ethical issues surrounding genomic analysis at a population level remain to be addressed. Figure 17.14 PCA3 is a gene that is expressed in prostate epithelial cells and overexpressed in cancerous cells. A high concentration of PCA3 in urine is indicative of prostate cancer. The PCA3 test is considered to be a better indicator of cancer than the more well know PSA test, which measures the level of PSA (prostate-specific antigen) in the blood. In 2011, the United States Preventative Services Task Force recommended against using the PSA test to screen healthy men for prostate cancer. Their recommendation is based on evidence that screening does not reduce the risk of death from prostate cancer. Prostate cancer often develops very slowly and does not cause problems, while the cancer treatment can have severe side effects. The PCA3 test is considered to be more accurate, but screening may still result in men who would not have been harmed by the cancer itself suffering side effects from |
treatment. What do you think? Should all healthy men be screened for prostate cancer using the PCA3 or PSA test? Should people in general be screened to find out if they have a genetic risk for cancer or other diseases? a. b. c. In general, all men should be screened as it is necessary to take the risk. In general, all men should be given treatment irrespective of the presence or absence of cancer symptoms. In general, only men suspecting cancer should be screened. d. There is no requirement of any screening, as cancer shows no problems. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 703 Pharmacogenomics and Toxicogenomics Pharmacogenomics, also called toxicogenomics, involves evaluating the effectiveness and safety of drugs on the basis of information from an individual's genomic sequence. Genomic responses to drugs can be studied using experimental animals (such as laboratory rats or mice) or live cells in the laboratory before embarking on studies with humans. Studying changes in gene expression could provide information about the transcription profile in the presence of the drug, which can be used as an early indicator of the potential for toxic effects. For example, genes involved in cellular growth and controlled cell death, when disturbed, could lead to the growth of cancerous cells. Genome-wide studies can also help to find new genes involved in drug toxicity. Personal genome sequence information can be used to prescribe medications that will be most effective and least toxic on the basis of the individual patient’s genotype. The gene signatures may not be completely accurate, but can be tested further before pathologic symptoms arise. Microbial Genomics: Metagenomics Traditionally, microbiology has been taught with the view that microorganisms are best studied under pure culture conditions, which involves isolating a single type of cell and culturing it in the laboratory. Because microorganisms can go through several generations in a matter of hours, their gene expression profiles adapt to the new laboratory environment very quickly. In addition, the vast majority of bacterial species resist being cultured in isolation. Most microorganisms do not live as isolated entities, but in microbial communities known as biofilms. For all of these reasons, pure culture is not always the best way to study microorganisms. Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify |
new species more rapidly and to analyze the effect of pollutants on the environment (Figure 17.15). Figure 17.15 Metagenomics involves isolating DNA from multiple species within an environmental niche. Microbial Genomics: Creation of New Biofuels Knowledge of the genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria. The primary sources of fuel today are coal, oil, wood, and other plant products, such as ethanol. Although plants are renewable resources, there is still a need to find more alternative renewable sources of energy to meet our population’s energy demands. The microbial world is one of the largest resources for genes that encode new enzymes and produce new organic compounds, and it remains largely untapped. Microorganisms are used to create products, such as enzymes that are used in research, antibiotics, and other anti-microbial mechanisms. Microbial genomics is helping to develop diagnostic tools, improved vaccines, new disease treatments, and advanced environmental cleanup techniques. Mitochondrial Genomics Mitochondria are intracellular organelles that contain their own DNA. Mitochondrial DNA mutates at a rapid rate and is often used to study evolutionary relationships. Another feature that makes studying the mitochondrial genome interesting is that the mitochondrial DNA in most multicellular organisms is passed on from the mother during the process of fertilization. 704 Chapter 17 | Biotechnology and Genomics For this reason, mitochondrial genomics is often used to trace genealogy. Information and clues obtained from DNA samples found at crime scenes have been used as evidence in court cases, and genetic markers have been used in forensic analysis. Genomic analysis has also become useful in this field. In 2001, the first use of genomics in forensics was published. It was a collaborative attempt between academic research institutions and the FBI to solve the mysterious cases of anthrax communicated via the US Postal Service. Using microbial genomics, researchers determined that a specific strain of anthrax was used in all the mailings. Genomics in Agriculture Genomics can reduce the trials and failures involved in scientific research to a certain extent, which could improve the quality and quantity of crop yields in agriculture. Linking traits to genes or gene signatures helps to improve crop breeding to generate hybrids with the most desirable qualities. Scientists use genomic data to identify desirable traits, and then transfer those traits to a different organism. Scientists are discovering how genomics can improve the quality and quantity of agricultural production. For example, scientists could use desirable traits to create |
a useful product or enhance an existing product, such as making a drought-sensitive crop more tolerant of the dry season. 17.5 | Genomics and Proteomics In this section, you will explore the following questions: • What is a proteome? • What is a protein signature and what is its relevance to cancer screening? Connection for AP® Courses Information presented in section is not in scope for AP®. However, you can study information in the section as optional or illustrative material. Proteins are the final products of genes, which help perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins that act as catalysts to affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins. In the diseased state, protein function can be impaired because of changes at the genetic level or because of direct impact on a specific protein. A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins. The study of the function of proteomes is called proteomics. Proteomics complements genomics and is useful when scientists want to test their hypotheses that were based on genes. Even though all cells of a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternately spliced (cut and pasted to create novel combinations and novel proteins) and many proteins are modified after translation by processes such as proteolytic cleavage, phosphorylation, glycosylation, and ubiquitination. There are also protein-protein interactions, which complicate the study of proteomes. Although the genome provides a blueprint, the final architecture depends on several factors that can change the progression of events that generate the proteome. Metabolomics is related to genomics and proteomics. Metabolomics involves the study of small molecule metabolites found in an organism. The metabolome is the complete |
set of metabolites that are related to the genetic makeup of an organism. Metabolomics offers an opportunity to compare genetic makeup and physical characteristics, as well as genetic makeup and environmental factors. The goal of metabolome research is to identify, quantify, and catalogue all of the metabolites that are found in the tissues and fluids of living organisms. Basic Techniques in Protein Analysis The ultimate goal of proteomics is to identify or compare the proteins expressed from a given genome under specific conditions, study the interactions between the proteins, and use the information to predict cell behavior or develop drug targets. Just as the genome is analyzed using the basic technique of DNA sequencing, proteomics requires techniques This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 705 for protein analysis. The basic technique for protein analysis, analogous to DNA sequencing, is mass spectrometry. Mass spectrometry is used to identify and determine the characteristics of a molecule. Advances in spectrometry have allowed researchers to analyze very small samples of protein. X-ray crystallography, for example, enables scientists to determine the three-dimensional structure of a protein crystal at atomic resolution. Another protein imaging technique, nuclear magnetic resonance (NMR), uses the magnetic properties of atoms to determine the three-dimensional structure of proteins in aqueous solution. Protein microarrays have also been used to study interactions between proteins. Large-scale adaptations of the basic two-hybrid screen (Figure 17.16) have provided the basis for protein microarrays. Computer software is used to analyze the vast amount of data generated for proteomic analysis. Genomic- and proteomic-scale analyses are part of systems biology. Systems biology is the study of whole biological systems (genomes and proteomes) based on interactions within the system. The European Bioinformatics Institute and the Human Proteome Organization (HUPO) are developing and establishing effective tools to sort through the enormous pile of systems biology data. Because proteins are the direct products of genes and reflect activity at the genomic level, it is natural to use proteomes to compare the protein profiles of different cells to identify proteins and genes involved in disease processes. Most pharmaceutical drug trials target proteins. Information obtained from proteomics is being used to identify novel drugs and understand their mechanisms of action. Figure 17.16 Two-hybrid screening is used to determine whether two proteins interact. In this method, a transcription factor is split into |
a DNA-binding domain (BD) and an activator domain (AD). The binding domain is able to bind the promoter in the absence of the activator domain, but it does not turn on transcription. A protein called the bait is attached to the BD, and a protein called the prey is attached to the AD. Transcription occurs only if the prey “catches” the bait. The challenge of techniques used for proteomic analyses is the difficulty in detecting small quantities of proteins. Although mass spectrometry is good for detecting small amounts of proteins, variations in protein expression in diseased states can be difficult to discern. Proteins are naturally unstable molecules, which makes proteomic analysis much more difficult than genomic analysis. Cancer Proteomics Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the disease. The most prominent disease being studied with proteomic approaches is cancer. Proteomic approaches are being used to improve screening and early detection of cancer; this is achieved by identifying proteins whose expression is affected by the disease process. An individual protein is called a biomarker, whereas a set of proteins with altered expression levels is called a protein signature. For a biomarker or protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in body fluids, such as sweat, blood, or urine, such that largescale screenings can be performed in a non-invasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results. A false negative is an incorrect test result that should have been positive. In other words, many cases of cancer go undetected, which makes biomarkers unreliable. Some examples of 706 Chapter 17 | Biotechnology and Genomics protein biomarkers used in cancer detection are CA-125 for ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers to detect cancer cells. Proteomics is also being used to develop individualized treatment plans, which involves the prediction of whether or not an individual will respond to specific drugs and the side effects that the individual may experience. Proteomics is also being used to predict the possibility of disease recurrence. The National Cancer Institute has developed programs to improve the detection and treatment of cancer. The Clinical Proteomic Technologies for Cancer and the Early Detection Research Network are efforts to identify protein signatures specific to different types of cancers. The Biomedical Proteomics Program is designed to |
present in the genome of the organism of interest 708 Chapter 17 | Biotechnology and Genomics linkage analysis procedure that analyzes the recombination of genes to determine if they are linked lysis buffer solution used to break the cell membrane and release cell contents metabolome complete set of metabolites which are related to the genetic makeup of an organism metabolomics study of small molecule metabolites found in an organism metagenomics study of the collective genomes of multiple species that grow and interact in an environmental niche microsatellite polymorphism variation between individuals in the sequence and number of repeats of microsatellite DNA model organism species that is studied and used as a model to understand the biological processes in other species represented by the model organism molecular cloning cloning of DNA fragments multiple cloning site (MCS) site that can be recognized by multiple restriction endonucleases next-generation sequencing group of automated techniques used for rapid DNA sequencing northern blotting transfer of RNA from a gel to a nylon membrane pharmacogenomics study of drug interactions with the genome or proteome; also called toxicogenomics physical map representation of the physical distance between genes or genetic markers polygenic phenotypic characteristic caused by two or more genes polymerase chain reaction (PCR) technique used to amplify DNA probe small DNA fragment used to determine if the complementary sequence is present in a DNA sample protease enzyme that breaks down proteins protein signature set of uniquely expressed proteins in the diseased state proteome entire set of proteins produced by a cell type proteomics study of the function of proteomes pure culture growth of a single type of cell in the laboratory radiation hybrid mapping information obtained by fragmenting the chromosome with x-rays recombinant DNA combination of DNA fragments generated by molecular cloning that does not exist in nature; also known as a chimeric molecule recombinant protein protein product of a gene derived by molecular cloning reproductive cloning cloning of entire organisms restriction endonuclease enzyme that can recognize and cleave specific DNA sequences restriction fragment length polymorphism (RFLP) variation between individuals in the length of DNA fragments generated by restriction endonucleases reverse genetics gene product method of determining the function of a gene by starting with the gene itself instead of starting with the reverse transcriptase PCR (RT-PCR) PCR technique that involves converting RNA to DNA by reverse transcriptase ribonuclease enzyme that breaks down RNA This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 709 sequence mapping mapping information obtained after |
DNA sequencing shotgun sequencing method used to sequence multiple DNA fragments to generate the sequence of a large piece of DNA single nucleotide polymorphism (SNP) variation between individuals in a single nucleotide Southern blotting transfer of DNA from a gel to a nylon membrane systems biology study of whole biological systems (genomes and proteomes) based on interactions within the system Ti plasmid plasmid system derived from Agrobacterium tumifaciens that has been used by scientists to introduce foreign DNA into plant cells transgenic organism that receives DNA from a different species variable number of tandem repeats (VNTRs) variation in the number of tandem repeats between individuals in the population whole-genome sequencing process that determines the DNA sequence of an entire genome CHAPTER SUMMARY 17.1 Biotechnology Nucleic acids can be isolated from cells for the purposes of further analysis by breaking open the cells and enzymatically destroying all other major macromolecules. Fragmented or whole chromosomes can be separated on the basis of size by gel electrophoresis. Short stretches of DNA or RNA can be amplified by PCR. Southern and northern blotting can be used to detect the presence of specific short sequences in a DNA or RNA sample. The term “cloning” may refer to cloning small DNA fragments (molecular cloning), cloning cell populations (cellular cloning), or cloning entire organisms (reproductive cloning). Genetic testing is performed to identify disease-causing genes, and gene therapy is used to cure an inheritable disease. Transgenic organisms possess DNA from a different species, usually generated by molecular cloning techniques. Vaccines, antibiotics, and hormones are examples of products obtained by recombinant DNA technology. Transgenic plants are usually created to improve characteristics of crop plants. 17.2 Mapping Genomes Genome mapping is similar to solving a big, complicated puzzle with pieces of information coming from laboratories all over the world. Genetic maps provide an outline for the location of genes within a genome, and they estimate the distance between genes and genetic markers on the basis of recombination frequencies during meiosis. Physical maps provide detailed information about the physical distance between the genes. The most detailed information is available through sequence mapping. Information from all mapping and sequencing sources is combined to study an entire genome. 17.3 Whole-Genome Sequencing Whole-genome sequencing is the latest available resource to treat genetic diseases. Some doctors are using whole-genome sequencing to save lives. Genomics has many industrial applications including biofuel development, agriculture |
, pharmaceuticals, and pollution control. The basic principle of all modern-day sequencing strategies involves the chain termination method of sequencing. Although the human genome sequences provide key insights to medical professionals, researchers use whole-genome sequences of model organisms to better understand the genome of the species. Automation and the decreased cost of whole-genome sequencing may lead to personalized medicine in the future. 17.4 Applying Genomics Imagination is the only barrier to the applicability of genomics. Genomics is being applied to most fields of biology; it is being used for personalized medicine, prediction of disease risks at an individual level, the study of drug interactions before the conduct of clinical trials, and the study of microorganisms in the environment as opposed to the laboratory. It is also being applied to developments such as the generation of new biofuels, genealogical assessment using mitochondria, 710 Chapter 17 | Biotechnology and Genomics advances in forensic science, and improvements in agriculture. 17.5 Genomics and Proteomics Proteomics is the study of the entire set of proteins expressed by a given type of cell under certain environmental conditions. In a multicellular organism, different cell types will have different proteomes, and these will vary with changes in the environment. Unlike a genome, a proteome is dynamic and in constant flux, which makes it both more complicated and more useful than the knowledge of genomes alone. Proteomics approaches rely on protein analysis; these techniques are constantly being upgraded. Proteomics has been used to study different types of cancer. Different biomarkers and protein signatures are being used to analyze each type of cancer. The future goal is to have a personalized treatment plan for each individual. REVIEW QUESTIONS 1. How are GMOs created? a. has a better shelf life a. introducing recombinant DNA into an organism by any means b. is not a variety of vine-ripened tomato in the supermarket b. in vitro fertilization methods c. was not created to have better flavor c. mutagenesis d. undergoes soft rot d. plant breeding techniques 7. What is the first step in isolating DNA? 2. Which technique used to manipulate genetic material results in a significant increase in DNA or RNA fragments? a. gel electrophoresis b. nucleic acid extraction c. nuclear hybridization a. generating genomic DNA fragments with restriction endonucleases b. introducing recombinant DNA into an organism by any means c. overexpressing proteins in E. coli d. |
lysing the cells in the sample d. polymerase chain reaction (PCR) 8. What is genomics? 3. What is the role of the plasmid in molecular cloning? a. They are used to create clones. b. They are used as vectors to insert genes into bacteria. c. They are a functional part of binary fission. d. They contain the circular chromosome of prokaryotic organisms. 4. What is meant by a recombinant DNA molecule? a. chimeric molecules b. bacteria transformed into another species c. molecules that have been through the PCR process d. the result of crossing over during cell reproduction 5. Bt toxin is considered to be what? a. a gene for modifying insect DNA b. an organic insecticide produced by bacteria c. useful for humans to fight against insects d. a recombinant protein 6. What is one trait of the Flavr Savr Tomato? a. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. b. Genomics is the process of finding the locations of genes on each chromosome. c. Genomics is an illustration that lists genes and their location on a chromosome. d. Genomics is a genetic marker, a gene or sequence on a chromosome that co-segregates (shows genetic linkage) with a specific trait. 9. What is required in addition to a genetic linkage map to build a complete picture of the genome? a. a genetic marker b. a physical map c. linkage analysis of chromosomes d. plasmids 10. Genetic recombination occurs by which process? This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 711 a. crossing over b. chromosome segregation c. d. independent assortment sister chromatids 11. Individual genetic maps in a given species are ________. a. genetically similar b. genetically identical c. genetically dissimilar d. not useful in species analysis 12. Information obtained by microscopic analysis of stained chromosomes is used in what procedure? a. cytogenetic mapping b. radiation hybrid mapping c. RFLP mapping d. sequence mapping 13. Which of the following is true about linkage analysis? a. b. c. It is used to create a physical map. It is based on the natural recombination process. It involves the breaking and re |
-joining of DNA artificially. d. It requires radiation hybrid mapping. 14. The chain termination method of sequencing uses what? a. labeled ddNTPs b. only dideoxynucleotides c. only deoxynucleotides d. labeled dNTPs 15. What sequencing technique is used to identify regions of similarity between cell types or species? a. dideoxy chain termination b. proteins, DNA, or RNA sequence alignment c. shotgun sequencing d. whole-exome sequencing 16. Whole-genome sequencing can be used for advances in what field? a. bioinformatics b. iron industry c. multimedia d. the medical field 17. Sequencing an individual person’s genome ______. a. is currently impossible b. helps in predicting faulty genes in diseases c. will not lead to legal issues regarding discrimination and privacy d. will not help make informed choices about medical treatment 18. Genomics can be used in agriculture to do what? a. gener<|endoftext|>ate new hybrid strains b. c. d. improve disease resistance improve yield improve yield and resistance and generate hybrids 19. What are the uses of metagenomics? a. b. identification of biofuels testing for multiple drug susceptibility in a population c. use in increasing agricultural yields d. identifying new species more rapidly and analyzing the effect of pollutants on the environment 20. Genomics can be used on a personal level to do what? a. determine the risks of genetic diseases for an individual’s children b. increase transplant rejection c. predict protein profile of a person d. produce antibodies for an antigen 21. What is the percentage of single gene defects causing disease in developed countries? a. b. c. d. 0.05 0.1 0.2 0.4 22. The rapid identification of new species and the analysis of the effect of pollutants on the environment is a function of what? a. metagenomics b. linkage analysis c. genomics d. shotgun sequencing 23. The risks of genetic diseases for an individual’s children can be determined through ______. 712 Chapter 17 | Biotechnology and Genomics a. metagenomics b. linkage analysis c. genomics d. shotgun sequencing 24. What is a biomarker? a. the color coding of different genes b. a protein uniquely produced in a diseased state c. a molecule in the genome or proteome d. a marker that is genetically inherited 25. What is a metabolome |
? a. a provisional listing of the genome of a species b. a unique metabolite used to identify an individual c. a method used for protein analysis d. the complete set of metabolites related to the genetic makeup of an organism 26. How would you describe a set of proteins with altered expression levels? a. a group of biomarkers b. a protein signature c. d. the result of a defect in mRNA transcription the results of crossing over during cell replication CRITICAL THINKING QUESTIONS 30. Describe the process of Southern blotting. a. Southern Blotting is used to find DNA sequences. Fragments are separated on gel, incubated with probes to check for the sequence of interest, and transferred to a nylon membrane. b. Southern blotting is used to find DNA sequences. Fragments are separated on gel, transferred to a nylon membrane, and incubated with probes to check for the sequence of interest. c. When RNA is used, the process is called Northern blotting. d. Southern blotting is used to find RNA sequences. Fragments are separated on gel, incubated with probes to check for the sequence of interest, and transferred to a nylon membrane. 31. A researcher wants to study cancer cells from a patient with breast cancer. Is cloning the cancer cells an option? 27. What is a protein signature? a. a protein expressed on the cell surface b. a unique set of proteins present in a diseased state c. the path followed by a protein after it is synthesized in the nucleus d. the path followed by a protein in the cytoplasm 28. What describes a protein that is uniquely produced in a diseased state? a. a genomic protein b. a genetic defect c. a chimeric molecule d. a biomarker 29. The metabolites that results from the anabolic and catabolic reactions of an organisms is called what? a. genetic metabolic profile b. metabolic signature c. metabolome d. metagenomics a. The cancer cells should be cloned along with a biomarker for better detection and study. b. The cells should be screened first in order to assure their carcinogenic nature. c. The cancer cells, being clones of each other already, should directly be grown in a culture media and then studied. d. The cancer cells should be extracted using the specific antibodies. 32. Discuss the uses of genome mapping. a. Genome mapping is useful in identifying human disease-causing genes, developing microbes to clean up pollutants, and increasing |
crop yield. b. Genome mapping is directly required to produce recombinants, in FISH detection, and detecting the methylated parts of genetic material. c. Genome mapping is useful for knowing the pedigree of diseases in humans and tracing the movement of transposons in plants. d. Genome mapping identifies human disease- causing genes only. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 713 33. If you had a chance to get your genome sequenced, what are some questions you might be able to have answered about yourself? a. One can determine the drugs that can rectify a disease, symptoms of the disease and its severity. b. One can determine the ancestry and genetic origin of diseases and their susceptibility to drugs. c. One can predict the symptoms of a disease, the vectors to be used in gene therapy and the causal organism of the disease. d. One can determine the pedigree of a disease, produce recombinants and detect the presence of extracellular genes using FISH. 34. Describe an example of a genomic mapping method a. The radiation mapping method is an example which uses radiation to break the DNA and is affected by changes in recombination frequency. b. Cytogenetic mapping obtains information from microscopic analysis of stained chromosomes. It can estimate the approximate distance between markers. c. In restriction mapping, the DNA fragments are cut by using the restriction enzymes and then stained fragments are viewed on gel. d. Cytogenetic mapping obtains information from microscopic analysis of stained chromosomes. It can estimate the exact base pair distance between markers. 35. Describe three methods of gene sequencing. a. Chain termination method - automated sequencers are used to generate sequences of short fragments; Shotgun sequencing method incorporation of ddNTP during DNA replication; Next-generation sequencing - cutting DNA into random fragments, sequencing using chain termination, and assembling overlapping sequences b. Chain termination method - incorporation of ddNTP during DNA replication; Shotgun sequencing method - cutting DNA into random fragments, sequencing using chain termination, and assembling overlapping sequences; Nextgeneration sequencing - automated sequencers are used to generate sequences of short fragments c. Chain termination method - incorporation of ddNTP during DNA replication; Shotgun sequencing method - automated sequencers are used to generate sequences of short fragments; Next-generation sequencing - cutting DNA into random fragments, sequencing using chain termination, and assembling overlapping sequences d. Chain |
termination method - automated sequencers are used to generate sequences of short fragments; Shotgun sequencing method cutting DNA into random fragments, sequencing using chain termination, and assembling overlapping sequences; Next-generation sequencing - incorporation of ddNTP during DNA replication 36. What is the greatest challenge facing genome sequencing? a. b. c. d. the lack of resources and use of chemicals for the sequencing of the DNA fragments the ethical issues such as discrimination based on person’s genetics the use of chemicals during the sequencing methods that could incorporate mutations the scientific issues, like conserving the human genome sequences 37. How is shotgun sequencing performed? 714 Chapter 17 | Biotechnology and Genomics a. The DNA is cut into fragments, sequencing is done using the chain termination method, fragments are analyzed to see the overlapping sequences, and the entire fragment is reformed. b. The DNA is cut into fragments, overlapping sequences are analyzed using a computer, sequencing is done using the chain termination method, and the DNA fragment is reformed. c. The DNA is cut into fragments, stained with fluorescent dye, sequenced using the chain termination method, fragments are analyzed to see the overlapping sequences, and the entire DNA fragment is reformed. d. The DNA is cut into fragments, sequencing is done using the chain termination method, the DNA is stained with fluorescent dye, and a computer is used to analyze and reform the entire DNA fragment. 38. Coumadin is a drug frequently given to prevent excessive blood clotting in stroke or heart attack patients, which could lead to another stroke or heart attack. Administration of the drug also can result in an overdose in some patients, depending on the liver function of a patient. How could pharmacogenomics be used to assist these patients? a. Pharmacogenomics will be able to provide a counter-acting drug to decrease the effect of Coumadin. b. Pharmacogenomics will test every patient for their sensitivity to the drug. c. Pharmacogenomics will not be able to provide any help to patients highly sensitive to the drug. d. Pharmacogenomics will provide an overdose to each patient to test for the symptoms of the drug. 39. Why is so much effort being poured into genome mapping applications? a. Genome mapping is necessary to know the base pair difference between the markers. b. The mapping would help scientists understand the role of proteins in specific organelles. c. The mapping technique identifies the role of transposons. d. Genome mapping helps identify faulty alleles, which could cause diseases. 40. |
What is the reason for studying mitochondrial genomics that is most directly important for humans? a. Mitochondria evolved from bacteria; therefore, their genome is important to study. b. Mitochondria undergo rapid mutation and it is essential that this pattern be studied. c. Mitochondria contain DNA, and it is passed on from mother to offspring, which renders it helpful in tracing genealogy. d. Mitochondria are the only ATP-producing organelles of the cell, thus their genome is important. 41. How can proteomics complement genomics? a. The genes are responsible to produce proteins and this implies that proteomics complements genomics. b. Genomics is responsible to decide the structure of the proteins, and, thereby, the result of proteomic studies. c. The genome is constant but the proteome is dynamic as different tissues possess the same genes but express different genes, thereby complementing genomics. d. The study of genes is incomplete without the study of their respective proteins and thus they complement each other. 42. How could a proteomic map of the human genome help find a cure for cancer? a. A genetic map could help in identifying genes that could counteract the cause of cancer. b. Metabolomics can be used to study the genes producing metabolites during cancer. c. Proteomics detects biomarkers whose expression is affected by the disease process. d. The mapping helps in analyzing the inheritance of cancer-causing genes. 43. What contributions have been made through the use of microbial genomics? a. Microbial genomics has provided various tools to study the psychological behaviors of organisms. b. Microbial genomics has been useful in producing antibiotics, enzymes, improved vaccines, disease treatments and advanced cleanup techniques. c. Microbial genomics has contributed resistance in other bacteria by horizontal and lateral gene transfer mechanisms. d. Microbial genomics has contributed to fighting global warming. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 715 TEST PREP FOR AP® COURSES 44. In separating DNA for genomic analysis, it is important to consider RNA contaminating the sample during the cell lysis step of a DNA extraction. Which is likely to cause what to occur? a. DNA separates into the supernatant. b. DNA is destroyed by the protease. c. DNA is unaffected by the RNA. d. DNA combines with the |
RNA. 45. There are many techniques for investigating human genomic disorders. Western blotting looks for protein, Eastern blotting looks for post-translational changes, Northern blotting looks at mRNA, and Southern blotting looks at DNA. If you were to look at sickle cell anemia, a disorder affecting hemoglobin produced in red blood cells, which technique would be the most useful in detecting polymorphism in a sample? a. Northern blotting b. Southern blotting c. Western blotting d. Eastern blotting 46. A population of insects were formally distinguished by a mix of colors on their thorax and legs. This population now appears to be split into 2 sub-groups, purple and orange-legged. Researchers hypothesize that the purplelegged group may be increasingly resistant to the Bt (Bacillus thuringiensis) toxin. Which idea supports this observation? a. transgenesis b. natural selection c. hybridization d. recombination 47. Describe the process of molecular cloning. a. The foreign DNA and plasmid are cut with the same restriction enzyme and DNA is inserted within the lacZ gene, whose product metabolizes lactose. The foreign DNA and vector are allowed to anneal. The vector is transferred to a bacterial host that is ampicillin sensitive and those with a disrupted lacZ gene show inability to metabolize X-gal. b. The foreign DNA and plasmid are denatured using high heat, and DNA is inserted within the lacZ gene, whose product metabolizes glucose. The foreign DNA and vector are allowed to anneal. The vector is transferred to a bacterial host that is ampicillin sensitive and disrupted lacZ gene will metabolize X-gal c. The foreign DNA and plasmid are cut with the same restriction enzyme and DNA is inserted randomly in the plasmid. The foreign DNA and vector are allowed to anneal. The vector is transferred to a bacterial host that is ampicillin sensitive and the disrupted lacZ gene shows inability to synthesize X-gal. d. The foreign DNA and plasmid are cut with the same restriction enzyme and DNA is inserted within the lacZ gene, whose product metabolizes lactose. The foreign DNA and vector are allowed to anneal. The vector is transformed into a viral host that is ampicillin sensitive and the disrupted lacZ gene show inability to synthesize X-gal. 48. There are three methods of creating maps to evaluate genomes: cytogenetic ( |
staining chromosomes); radiation hybrid maps (fragments with x-rays); and sequence maps (comparing DNA sequences). Which of the following accurately describes the three methods? 716 Chapter 17 | Biotechnology and Genomics 49. How many cells with different genetic variations are possible after a single round of meiosis? a. b. c. two three four d. eight a. Cytogenetic mapping - stained sections of chromosomes are analyzed using microscope, the distance between genetic markers can be found; Radiation hybrid mapping - breaks DNA using radiation and is affected by recombination frequency; Sequence mapping - DNA sequencing technology used to create physical maps. b. Cytogenetic mapping - stained sections of chromosomes are analyzed using microscope, the approximate distance between genetic markers can be found; Radiation hybrid mapping - breaks DNA using radiation and is unaffected by recombination frequency; Sequence mapping - DNA sequencing technology used to create physical maps. c. Cytogenetic mapping - stained sections of chromosomes are analyzed using microscope, the distance in base pairs between genetic markers can be found; Radiation hybrid mapping - breaks DNA using radiation and is unaffected by recombination frequency; Sequence mapping - DNA sequencing technology used to create physical maps. d. Cytogenetic mapping - stained sections of chromosomes are analyzed using a telescope, the distance between genetic markers can be found; Radiation hybrid mapping - breaks DNA using radiation and is affected by recombination frequency; Sequence mapping - DNA sequencing technology used to create physical maps. SCIENCE PRACTICE CHALLENGE QUESTIONS 50. Prokaryotes have an adaptive strategy to identify and respond to viral infections. This strategy uses segments of the cyclic DNA called CRISPRs and genes encoding CRISPR-associated (cas) proteins. When a virus enters the cell, a strand of viral DNA is excised by a cas protein and inserted into the bacterial DNA in a CRISPR region. When the same viral DNA is encountered subsequently, this foreign DNA is targeted by cas proteins that carry RNA markers transcribed from the inserted segment. The cas proteins cleave the viral DNA. The bacteria “remember” the infectious agent, providing a form of immunity. Figure 17.17 A. Use the diagram above to identify the components of a transcript-based response of bacteria to the presence of This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 17 | Biotechnology and Genomics 717 viral DNA by placing the corresponding number next to |
each feature of the diagram: ___ viral DNA ___ degraded viral DNA ___ cell membrane ___ cellular DNA ___ cas protein ___ stored viral DNA template ___ excised viral DNA ___ cas protein-RNA complex ___ cas protein-RNA-viral DNA complex The CRISPR system was discovered in cultures of yogurt in 2002. Subsequently, researchers developed a technology based on the manipulation of this system. The code for the prokaryotic CRISPR/cas system is highly conserved and is found in the human genome. DNA sequences are known to encode proteins responsible for many heritable diseases. CRISPR/cas is a technology that allows DNA to be cleaved at the boundaries of a nucleotide sequence, making the protein dysfunctional. The break in the strand is then recognized and replaced with the code for the functional protein. If the editing is done with zygoteforming cells, the change is inherited. Not only the patient, but all progeny of the patient, are cured. This technology is the first to easily make genomic modifications of a germ line. In the words of a prominent molecular biologist, this technology, which was recognized as the Breakthrough of 2015 in the journal Science, “democratizes genetic engineering.” Just as PCR became a standard, widely used tool, any molecular biology lab is now able to apply this technology. B. Pose three questions—whose pursuit would require an understanding of genetics—regarding the ethical and social issues that accompany the use of this medical technology. C. Explain the value of genetic variation within a population. Predict a possible effect that this technology could have, if unregulated, on human genetic variation. 51. Gel electrophoresis of polymers and polymer fragments is an important element in many investigations. Samples of a solution are pipetted into the wells of a gel. The gel is placed in a solution that maintains a constant pH, and an electric field is applied over the length of the gel. Separated components are transferred to a substrate where they can be visualized and identified by comparison with samples of standards. Application of this method to DNA is called a Southern blot, named for the inventor of the technology. The method’s application to RNA is called a northern blot, another demonstration that biologist have fun (there are also western, eastern, and far-eastern blots, but these techniques are not named for their inventors). A. Consider the three amino acids shown below and explain how, when pipetted into a gel and subjected to an electric |
field, the amino acids move; how the amino acids are separated as they move; and which amino acid moves furthest. Figure 17.18 B. A biologist wants to determine whether a new protocol is successful in constructing and amplifying a molecular clone of a segment of DNA introduced as a plasmid. After the procedure is complete, the bacterial cells containing the plasmid with the inserted segment are lysed, and a gel is run into which samples of the lysate and the sequences to be cloned have been pipetted. Use the data displayed in the developed gel shown below to evaluate the question of whether the protocol was successful. Figure 17.19 718 Chapter 17 | Biotechnology and Genomics C. Design a plan to answer the question of whether the new DNA has been incorporated into the DNA of the host organism. 52. Genetic engineering can be applied to heritable information to produce what is referred to as a “knockdown organism.” Biotechnology also can be applied to produce nonheritable changes in a “knockdown gene.” Post-transcriptional strategies target the mRNA product of a gene. One such strategy uses the conserved genes that encode RNA interference (RNAi) proteins for the regulation of levels of mRNA transcription. Some viral RNA is double stranded (dsRNA). A cell responds to the presence of double-stranded RNA by the attachment of the enzyme DICER, which cuts dsRNA into short fragments. One strand of the fragment is transferred to the RNA-induced silencing complex (RISC), which searches for an mRNA with a sequence matching that of the fragment strand. When detected, this mRNA is degraded. A. Common in cancer cells is a mutation of the gene that encodes the protein p53, whose role is to detect and repair errors in DNA; if repairs cannot be made, p53 initiates apoptosis. Create a visual representation to explain how the DICER-RISC system within the cell can be used to suppress the translation of a mutated form of the gene encoding p53, potentially destroying a tumor. B. Whole-genome sequences provide a library of potentially expressed proteins, but they do not provide information on the functions of each protein. In an approach called reverse genetics, investigations attempt to determine the function of the gene, often by silencing the gene using RNAi technology. Assume that you have the ability to synthesize dsRNA from a DNA segment taken from an organism whose whole genome |
has been determined. Design a plan for collecting data that could be used to assign a function to the protein encoded by this sequence. (Hint: Don’t worry about the number of experiments that might need to be conducted to implement your plan. An automated technique called high-throughput screening robotically supports thousands of simultaneous experiments.) This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 719 18 | EVOLUTION AND ORIGIN OF SPECIES Figure 18.1 All organisms are products of evolution adapted to their environment. (a) Saguaro (Carnegiea gigantea) can soak up 750 liters of water in a single rain storm, enabling these cacti to survive the dry conditions of the Sonora desert in Mexico and the Southwestern United States. (b) The Andean semiaquatic lizard (Potamites montanicola) discovered in Peru in 2010 lives between 1,570 to 2,100 meters in elevation, and, unlike most lizards, is nocturnal and swims. Scientists still do no know how these ectotherms, which rely on external sources of body heat, are able to move in the cold (10 to 15°C) temperatures of the Andean night. (credit a: modification of work by Gentry George, U.S. Fish and Wildlife Service; credit b: modification of work by Germán Chávez and Diego Vásquez, ZooKeys) Chapter Outline 18.1: Understanding Evolution 18.2: Formation of New Species 18.3: Reconnection and Rates of Speciation Introduction The field of biology is a diverse one that includes the study of organisms from the small and simple to the large and complex. From biological molecules to biomes, the one theme that remains consistent is evolution. All species of living organisms are descended from a common ancestor. Although it may seem that living things today stay much the same, this is not the case. Evolution is actually an ongoing process. Additionally, new species are discovered regularly. For example, scientists have used a method called fluorescent in situ hybridization, which uses fluorescent probes to locate specific genes on chromosomes, to discover a green sea slug that can perform photosynthesis just like a plant. The slug obtains genes related to photosynthesis from the algae it eats through a process called horizontal gene transfer. In this process, genes can be transferred directly from one cell |
to another. The algal genes code for products that repair and maintain chloroplasts eaten by the slug. You can read more about it at this website (http://openstaxcollege.org/l/32slug). [1] 1. Biol. Bull. 227: 300–312. (December 2014) 720 Chapter 18 | Evolution and Origin of Species 18.1 | Understanding Evolution In this section, you will explore the following questions: • How was the present-day theory of evolution developed? • What is adaptation, and how does adaptation relate to natural selection? • What are the differences between convergent and divergent evolution, and what are examples of each that support evolution by natural selection? • What are examples of homologous and vestigial structures, and what evidence do these structures provide to support patterns of evolution? • What are common misconceptions about the theory of evolution? Connection for AP® Courses Millions of species, from bacteria to blueberries to baboons, currently call Earth their home, but these organisms evolved from different species. Furthermore, scientists estimate that several million more species will become extinct before they have been classified and studied. But why don’t polar bears naturally inhabit deserts or rain forests, except, perhaps, in movies? Why do humans possess traits, such as opposable thumbs, that are unique to primates but not other mammals? How did observations of finches by Charles Darwin visiting the Galapagos Islands in the 1800s provide the foundation for our modern understanding of evolution? The theory of evolution as proposed by Darwin is the unifying theory of biology. The tenet that all life has evolved and diversified from a common ancestor is the foundation from which we approach all questions in biology. As we learned in our exploration of the structure and function of DNA, variations in individuals within a population occur through mutation, allowing more desirable traits to be passed to the next generation. Due to competition for resources and other environmental pressures, individuals possessing more favorable adaptive characteristics are more likely to survive and reproduce, passing those characteristics to the next generation with increased frequency. When environments change, what was once an unfavorable trait may become a favorable one. Organisms may evolve in response to their changing environment by the accumulation of favorable traits in succeeding generations. Thus, evolution by natural selection explains both the unity and diversity of life. Convergent evolution occurs when similar traits with the same function evolve in multiple species exposed to similar selection pressure, such as the wings of bats and insects. In divergent evolution, two species |
evolve in different directions from a common point, such as the forelimbs of humans, dogs, birds, and whales. Although Darwin’s theory was revolutionary for its time because it contrasted with long-held ideas (for example, Lamarck proposed the inheritance of acquired characteristics), evidence drawn from many scientific disciplines, including the fossil record, the existence of homologous and vestigial structures, mathematics, and DNA analysis supports evolution through natural selection. It is also important to understand that evolution continues to occur; for example, bacteria that evolve resistance to antibiotics or plants that become resistant to pesticides provide evidence for continuing change. Information presented and the examples highlighted in this section support concepts outlined in Big Idea 1 of the AP® Biology Curriculum Framework. The AP® Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A learning objective merges required content with one or more of the seven science practices. Big Idea 1 The process of evolution drives the diversity and unity of life. Enduring Understanding 1.A Essential Knowledge Change in the genetic makeup of a population over time is evolution. 1.A.1 Natural selection is a major mechanism of evolution. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 721 Science Practice 5.3 The student can evaluate the evidence provided by data sets in relation to a particular scientific question. Learning Objective Essential Knowledge 1.9 The student is able to evaluate evidence provided by data from many scientific disciplines that support biological evolution. 1.A.2 Natural selection acts on phenotypic variations in populations. Science Practice 1.2 The student can describe representations and models of natural or man-made phenomena and systems in the domain. Learning Objective Essential Knowledge 1.5 The student is able to connect evolutionary changes in a population over time to a change in the environment. 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 2.2 The student can apply mathematical routines to quantities that describe natural phenomena. Learning Objective Essential Knowledge 1.2 The student is able to evaluate evidence provided by data to qualitatively and quantitatively investigate the role of natural selection in evolution. 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 5.3 The student can evaluate the |
evidence provided by data sets in relation to a particular scientific question. Learning Objective Essential Knowledge 1.12 The student is able to connect scientific evidence from many scientific disciplines to support the modern concept of evolution. 1.A.4 Biological evolution is supported by scientific evidence from many disciplines, including mathematics. Science Practice 5.2 The student can refine observations and measurements based on data analysis. Learning Objective 1.10 The student is able to refine evidence based on data from many scientific disciplines that support biological evolution. Enduring Understanding 1.C Essential Knowledge Life continues to evolve within a changing environment. 1.C.3 Populations of organisms continue to evolve. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective Essential Knowledge 1.26 The student is able to evaluate given data sets that illustrate evolution as an ongoing processes. 1.C.3 Populations of organisms continue to evolve. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective Essential Knowledge 1.25 The student is able to describe a model that represents evolution within a population. 1.C.3 Populations of organisms continue to evolve. Science Practice 7.1 The student can connect phenomena and models across spatial and temporal scales. Learning Objective 1.4 The student is able to evaluate data-based evidence that describes evolutionary changes in the genetic makeup of a population over time. 722 Chapter 18 | Evolution and Origin of Species The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards: [APLO 1.10][APLO 1.12][APLO 1.13][APLO 1.31][APLO 1.32][APLO 1.27][APLO 1.28][APLO 1.30][APLO 1.14][APLO 1.29][APLO 1.26][APLO 4.8] The Origin of Life Humans have adopted many theories regarding the origin of life over the course of our time on Earth. Early civilizations believed that life was created by supernatural forces. Organisms were “hand-made” to be perfectly adapted to their environment and, therefore, did not change over time. Some early thinkers, such as the Greek philosopher Aristotle, believed that organisms belonged to a ladder of increasing complexity. Based on this understanding, scientists such as Carolus Linnaeus attempted to organize all living things into classification schemes that demonstrated an increasing complexity of life. |
Over time, however, scientists came to understand that life was constantly evolving on Earth. Georges Cuvier found that fossilized remains or organisms changed as he dug into deeper rock layers (strata), indicating that the organisms present in the area had changed over time. This observation led Jean-Baptiste de Lamarck to hypothesize that organisms adapted to their environment by changing over time. As organisms used different parts of their body, those parts improved, and these changes were passed down to their offspring. Ultimately, these theories were disproven by scientists, but their development contributed to the theory of evolution that was finally formulated by Charles Darwin. Charles Darwin and Natural Selection In the mid-nineteenth century, the actual mechanism for evolution was independently conceived of and described by two naturalists: Charles Darwin and Alfred Russel Wallace. Importantly, each naturalist spent time exploring the natural world on expeditions to the tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle, including stops in South America, Australia, and the southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys to the Malay Archipelago, included stops at several island chains, the last being the Galápagos Islands west of Ecuador. On these islands, Darwin observed species of organisms on different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos Islands comprised several species with a unique beak shape (Figure 18.2). The species on the islands had a graded series of beak sizes and shapes with very small differences between the most similar. He observed that these finches closely resembled another finch species on the mainland of South America. Darwin imagined that the island species might be species modified from one of the original mainland species. Upon further study, he realized that the varied beaks of each finch helped the birds acquire a specific type of food. For example, seed-eating finches had stronger, thicker beaks for breaking seeds, and insect-eating finches had spear-like beaks for stabbing their prey. Figure 18.2 Darwin observed that beak shape varies among finch species. He postulated that the beak of an ancestral species had adapted over time to equip the finches to acquire different food sources. Wallace |
and Darwin both observed similar patterns in other organisms and they independently developed the same explanation for how and why such changes could take place. Darwin called this mechanism natural selection. Natural This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 723 selection, also known as “survival of the fittest,” is the more prolific reproduction of individuals with favorable traits that survive environmental change because of those traits; this leads to evolutionary change. For example, a population of giant tortoises found in the Galapagos Archipelago was observed by Darwin to have longer necks than those that lived on other islands with dry lowlands. These tortoises were “selected” because they could reach more leaves and access more food than those with short necks. In times of drought when fewer leaves would be available, those that could reach more leaves had a better chance to eat and survive than those that couldn’t reach the food source. Consequently, long-necked tortoises would be more likely to be reproductively successful and pass the long-necked trait to their offspring. Over time, only long-necked tortoises would be present in the population. Natural selection, Darwin argued, was an inevitable outcome of three principles that operated in nature. First, most characteristics of organisms are inherited, or passed from parent to offspring. Although no one, including Darwin and Wallace, knew how this happened at the time, it was a common understanding. Second, more offspring are produced than are able to survive, so resources for survival and reproduction are limited. The capacity for reproduction in all organisms outstrips the availability of resources to support their numbers. Thus, there is competition for those resources in each generation. Both Darwin and Wallace’s understanding of this principle came from reading an essay by the economist Thomas Malthus who discussed this principle in relation to human populations. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Darwin and Wallace reasoned that offspring with inherited characteristics which allow them to best compete for limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations over generations in a process that Darwin called descent with modification. Ultimately, natural selection leads to greater adaptation of the population to its local environment; it |
is the only mechanism known for adaptive evolution. Papers by Darwin and Wallace (Figure 18.3) presenting the idea of natural selection were read together in 1858 before the Linnean Society in London. The following year Darwin’s book, On the Origin of Species, was published. His book outlined in considerable detail his arguments for evolution by natural selection. Figure 18.3 Both (a) Charles Darwin and (b) Alfred Wallace wrote scientific papers on natural selection that were presented together before the Linnean Society in 1858. Demonstrations of evolution by natural selection are time consuming and difficult to obtain. One of the best examples has been demonstrated in the very birds that helped to inspire Darwin’s theory: the Galápagos finches. Peter and Rosemary Grant and their colleagues have studied Galápagos finch populations every year since 1976 and have provided important demonstrations of natural selection. The Grants found changes from one generation to the next in the distribution of beak shapes with the medium ground finch on the Galápagos island of Daphne Major. The birds have inherited variation in the bill shape with some birds having wide deep bills and others having thinner bills. During a period in which rainfall was higher than normal because of an El Niño, the large hard seeds that large-billed birds ate were reduced in number; however, there was an abundance of the small soft seeds which the small-billed birds ate. Therefore, survival and reproduction were much better in the following years for the small-billed birds. In the years following this El Niño, the Grants measured beak sizes in the population and found that the average bill size was smaller. Since bill size is an inherited trait, parents with smaller bills had more offspring and the size of bills had evolved to be smaller. As conditions improved in 1987 and larger 724 Chapter 18 | Evolution and Origin of Species seeds became more available, the trend toward smaller average bill size ceased. Field Biologist Many people hike, explore caves, scuba dive, or climb mountains for recreation. People often participate in these activities hoping to see wildlife. Experiencing the outdoors can be incredibly enjoyable and invigorating. What if your job was to be outside in the wilderness? Field biologists by definition work outdoors in the “field.” The term field in this case refers to any location outdoors, even under water. A field biologist typically focuses research on a certain species, group of organisms, or a single habitat (Figure 18.4). |
Figure 18.4 A field biologist tranquilizes a polar bear for study. (credit: Karen Rhode) One objective of many field biologists includes discovering new species that have never been recorded. Not only do such findings expand our understanding of the natural world, but they also lead to important innovations in fields such as medicine and agriculture. Plant and microbial species, in particular, can reveal new medicinal and nutritive knowledge. Other organisms can play key roles in ecosystems or be considered rare and in need of protection. When discovered, these important species can be used as evidence for environmental regulations and laws. Processes and Patterns of Evolution Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these differences must have some genetic basis; otherwise, the selection will not lead to change in the next generation. This is critical because variation among individuals can be caused by non-genetic reasons such as an individual being taller because of better nutrition rather than different genes. Genetic diversity in a population comes from two main mechanisms: mutation and sexual reproduction. Mutation, a change in DNA, is the ultimate source of new alleles, or new genetic variation in any population. The genetic changes caused by mutation can have one of three outcomes on the phenotype. A mutation can affect the phenotype of the organism in a way that gives it reduced fitness—lower likelihood of survival or fewer offspring. Alternatively, a mutation may produce a phenotype with a beneficial effect on fitness. And, many mutations will also have no effect on the fitness of the phenotype; these are called neutral mutations. Mutations may also have a whole range of effect sizes on the fitness of the organism that expresses them in their phenotype, from a small effect to a great effect. Sexual reproduction also leads to genetic diversity: when two parents reproduce, unique combinations of alleles assemble to produce the unique genotypes and thus phenotypes in each of the offspring. A heritable trait that helps the survival and reproduction of an organism in its present environment is called an adaptation. Scientists describe groups of organisms becoming adapted to their environment when a change in the range of genetic variation occurs over time that increases or maintains the “fit” of the population to its environment. The webbed feet This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 725 of platypuses are an adaptation for swimming. The snow leopards’ thick fur is |
an adaptation for living in the cold. The cheetahs’ fast speed is an adaptation for catching prey. These adaptations can occur through the rearrangements of entire genomes or can be caused by the mutation of a single gene. For example, dogs have 78 chromosomes while cats have 38. A large number of the characteristics that distinguish dogs from cats arose from chromosomal rearrangements that have occurred since both groups diverged from their last common ancestor. On the other hand, certain mice are white and other mice are black. The difference in fur color occurs through the mutation of a single gene. Thus, as a result of a single mutation, a mouse population can become more adapted to survive in snowy environments versus a dark, forest floor. Whether or not a trait is favorable depends on the environmental conditions at the time. The same traits are not always selected because environmental conditions can change. For example, consider a species of plant that grew in a moist climate and did not need to conserve water. Large leaves were selected because they allowed the plant to obtain more energy from the sun. Large leaves require more water to maintain than small leaves, and the moist environment provided favorable conditions to support large leaves. After thousands of years, the climate changed, and the area no longer had excess water. The direction of natural selection shifted so that plants with small leaves were selected because those populations were able to conserve water to survive the new environmental conditions. The evolution of species has resulted in enormous variation in form and function. Sometimes, evolution gives rise to groups of organisms that become tremendously different from each other. When two species evolve in diverse directions from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs of flowering plants which share the same basic anatomies; however, they can look very different as a result of selection in different physical environments and adaptation to different kinds of pollinators (Figure 18.5). Figure 18.5 Flowering plants evolved from a common ancestor. Notice that the (a) dense blazing star (Liatrus spicata) and the (b) purple coneflower (Echinacea purpurea) vary in appearance, yet both share a similar basic morphology. (credit a: modification of work by Drew Avery; credit b: modification of work by Cory Zanker) In other cases, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats and insects, and they both have structures we refer to as |
wings, which are adaptations to flight. However, the wings of bats and insects have evolved from very different original structures. This phenomenon is called convergent evolution, where similar traits evolve independently in species that do not share a common ancestry. The two species came to the same function, flying, but did so separately from each other. These physical changes occur over enormous spans of time and help explain how evolution occurs. Natural selection acts on individual organisms, which in turn can shape an entire species. Although natural selection may work in a single generation on an individual, it can take thousands or even millions of years for the genotype of an entire species to evolve. It is over these large time spans that life on earth has changed and continues to change. Evidence of Evolution The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, to identifying patterns in nature that were consistent with evolution, and since Darwin, our understanding has become clearer and broader. Fossils Fossils provide solid evidence that organisms from the past are not the same as those found today, and fossils show a progression of evolution. Scientists determine the age of fossils and categorize them from all over the world to determine 726 Chapter 18 | Evolution and Origin of Species when the organisms lived relative to each other. The resulting fossil record tells the story of the past and shows the evolution of form over millions of years (Figure 18.6). For example, scientists have recovered highly detailed records showing the evolution of humans and horses. Figure 18.6 In this (a) display, fossil hominids are arranged from oldest (bottom) to newest (top). As hominids evolved, the shape of the skull changed. An artist’s rendition of (b) extinct species of the genus Equus reveals that these ancient species resembled the modern horse (Equus ferus) but varied in size. Anatomy and Embryology Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the bones in the appendages of a human, dog, bird, and whale all share the same overall construction (Figure 18.7) resulting from their origin in the appendages of a common ancestor. Over time, evolution led to changes in the shapes and sizes of these bones in different species, but they have maintained the same overall layout. Scientists call these synonymous parts homologous structures |
. Figure 18.7 The similar construction of these appendages indicates that these organisms share a common ancestor. Some structures exist in organisms that have no apparent function at all, and appear to be residual parts from a past common ancestor. These unused structures without function are called vestigial structures. Examples of vestigial structures include wings on flightless birds, leaves on some cacti, and hind leg bones in whales. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 727 this interactive site (http://openstaxcollege.org/l/bone_structures) Visit homologous and which are analogous, and see examples of evolutionary adaptations to illustrate these concepts. to guess which bones structures are What is the basic difference between things that are homologous and things that are analogous? a. Things that are analogous look similar and things that are homologous do not. b. Things that are analogous have the same function and things that are homologous have different functions. c. Things that are analogous are not a result of evolution, whereas things that are homologous are. d. Things that are analogous result from convergence and things that are homologous result from common ancestry Another evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of unrelated animals, such as the arctic fox and ptarmigan, living in the arctic region have been selected for seasonal white phenotypes during winter to blend with the snow and ice (Figure 18.8ab). These similarities occur not because of common ancestry, but because of similar selection pressures—the benefits of not being seen by predators. Figure 18.8 The white winter coat of the (a) arctic fox and the (b) ptarmigan’s plumage are adaptations to their environments. (credit a: modification of work by Keith Morehouse) Embryology, the study of the development of the anatomy of an organism to its adult form, also provides evidence of relatedness between now widely divergent groups of organisms. Mutational tweaking in the embryo can have such magnified consequences in the adult that embryo formation tends to be conserved. As a result, structures that are absent in some groups often appear in their embryonic forms and disappear by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans, exhibit gill slits and |
tails at some point in their early development. These disappear in the adults of terrestrial groups but are maintained in adult forms of aquatic groups such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during their development that is lost by the time of birth. Biogeography The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the 728 Chapter 18 | Evolution and Origin of Species supercontinent Pangaea (about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the planet, such as the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the southern continents that formed from the supercontinent Gondwana. The presence of members of the plant family Proteaceae in Australia, southern Africa, and South America, for example, is best explained by their presence prior to the southern supercontinent Gondwana breaking up. The great diversification of marsupials in Australia and the absence of other mammals reflect Australia’s long isolation. Australia has an abundance of endemic species—species found nowhere else—which is typical of islands whose isolation by expanses of water prevents species from migrating. Over time, these species diverge evolutionarily into new species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the Galápagos, and many species on the Hawaiian Islands are all unique to their one point of origin, yet they display distant relationships to ancestral species on mainlands. Molecular Biology Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor for all of life is reflected in the universality of DNA as the genetic material and in the near universality of the genetic code and the machinery of DNA replication and expression. Fundamental divisions in life between the three domains are reflected in major structural differences in otherwise conservative structures such as the components of ribosomes and the structures of membranes. In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences—exactly the pattern that would be expected from descent and diversification from a common ancestor. DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new functions for proteins commonly occurs after gene duplication events that allow the free |
modification of one copy by mutation, selection, or drift (changes in a population’s gene pool resulting from chance), while the second copy continues to produce a functional protein. Direct Observations Scientists have also observed evolution occurring in both the laboratory and in the wild. A common example of this is the spread of antibiotic resistant genes in a population of bacteria. When bacteria are exposed to antibiotics, alleles that help the organism survive increase in frequency Figure 18.9. This is because individuals that cannot resist the antibacterial die off, leaving only individuals with the resistance gene to reproduce. Figure 18.9 Adaptations for homeostasis One major reason that organisms adapt is to maintain homeostasis, one of the main characteristics of life. All organisms have likely descended from a single common ancestor, which is why so many organisms share anatomical, morphological, and molecular features. However, each organism has adapted these similar features to suit their environment and adapt to This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 729 environmental changes over time. For example, all organisms use DNA polymerase to replicate their genomes. However, whereas organisms with small genomes can get away with just a single polymerase molecule working at one point in the genome at time, organisms with larger genomes replicate many points of the genome simultaneously. Other organisms that live in extremely hot environments, such as deep-sea thermal vents, have specialized polymerase molecules that can withstand the heat that would quickly denature the polymerases in land-based animals. Although the basis for each of these different DNA polymerase molecules is the same, each one has been adapted to function in the organism’s environmental niche. Misconceptions of Evolution Although the theory of evolution generated some controversy when it was first proposed, it was almost universally accepted by biologists, particularly younger biologists, within 20 years after publication of On the Origin of Species. Nevertheless, the theory of evolution is a difficult concept and misconceptions about how it works abound. This site (http://openstaxcollege.org/l/misconceptions) addresses some of the main misconceptions associated with the theory of evolution. Select one misconception about evolution and explain what you might say to someone to dispel it. a. Misconception: Evolution is not a well-founded theory. Correction: Although evolution cannot be observed occurring today, there is strong evidence in the fossil record and in shared DNA sequences to support the theory b |
. Misconception: Humans are not currently evolving. Correction: The environmental pressures humans face are different than the ones they faced several thousands of years ago, but they are still there, and they are still producing (slowly!) evolutionary change. c. Misconception: Evolution produces individuals that are perfectly fit to their environment. Correction: Evolution produces random changes in the genetic code that sometimes lead to adaptations d. Misconception: Evolution is a random process. Correction: evolution is a force that makes animals adapt to perfectly fit the environment they are living in Evolution Is Just a Theory Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with the way scientists use the word. In science, a “theory” is understood to be a body of thoroughly tested and verified explanations for a set of observations of the natural world. Scientists have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes understood facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a theory in science has survived significant efforts to discredit it by scientists. In contrast, a “theory” in common vernacular is a word meaning a guess or suggested explanation; this meaning is more akin to the scientific concept of “hypothesis.” When critics of evolution say evolution is “just a theory,” they are implying that there is little evidence supporting it and that it is still in the process of being rigorously tested. This is a mischaracterization. Individuals Evolve Evolution is the change in genetic composition of a population over time, specifically over generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime, obviously, but this is called development and involves changes programmed by the set of genes the individual acquired at birth in coordination with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size change in medium-ground finches in the Galápagos, this does not mean that individual bills on the finches are 730 Chapter 18 | Evolution and Origin of Species changing. If one measures the average bill size among all individuals in the population at one time and then measures the average bill size in the population several years later, |
this average value will be different as a result of evolution. Although some individuals may survive from the first time to the second, they will still have the same bill size; however, there will be many new individuals that contribute to the shift in average bill size. Evolution Explains the Origin of Life It is a common misunderstanding that evolution includes an explanation of life’s origins. Conversely, some of the theory’s critics believe that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution explains how populations change over time and how life diversifies the origin of species. It does not shed light on the beginnings of life including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on Earth are a particularly difficult problem because it occurred a very long time ago, and presumably it just occurred once. Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can be repeated because the intermediate stages would immediately become food for existing living things. However, once a mechanism of inheritance was in place in the form of a molecule like DNA either within a cell or pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in frequency at the expense of inefficient reproducers. So while evolution does not explain the origin of life, it may have something to say about some of the processes operating once pre-living entities acquired certain properties. Organisms Evolve on Purpose Statements such as “organisms evolve in response to a change in an environment” are quite common, but such statements can lead to two types of misunderstandings. First, the statement must not be understood to mean that individual organisms evolve. The statement is shorthand for “a population evolves in response to a changing environment.” However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and therefore producing proportionately more offspring than other phenotypes. This results in change in the population if the characteristics are genetically determined. It is also important to understand that the variation that natural selection works on is already in a population and does not arise in response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select a population of bacteria that are resistant to antibiotics. The resistance, which is caused by |
a gene, did not arise by mutation because of the application of the antibiotic. The gene for resistance was already present in the gene pool of the bacteria, likely at a low frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects individuals that are resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for antibiotic resistance do not arise as a result of antibiotic. In a larger sense, evolution is not goal directed. Species do not become “better” over time; they simply track their changing environment with adaptations that maximize their reproduction in a particular environment at a particular time. Evolution has no goal of making faster, bigger, more complex, or even smarter species, despite the commonness of this kind of language in popular discourse. What characteristics evolve in a species are a function of the variation present and the environment, both of which are constantly changing in a non-directional way. What trait is fit in one environment at one time may well be fatal at some point in the future. This holds equally well for a species of insect as it does the human species. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 731 Activity Using information from a book or online resource such as Jonathan Weiner’s The Beak of the Finch, explain how contemporary evidence drawn from multiple scientific disciplines supports the observations of Charles Darwin regarding evolution by natural selection. Then, in small groups or as a whole class discussion or debate, present an argument to dispel misconceptions about evolution and how it works. Lab Investigation AP® Biology Investigative Labs: Inquiry-Based, Investigation 8: Biotechnology: Bacterial Transformation. You will explore how genetic engineering techniques can be used to manipulate heritable information by inserting plasmids into bacterial cells. Think About It What selection pressures may affect the survival and reproduction of a group of pea seeds scattered by a person along the ground? 18.2 | Formation of New Species In this section, you will explore the following questions: • What defines a species, and how can different species be distinguished from each other? • How does genetic variation lead to speciation? • What is the role of pre-zygotic and post-zygotic reproductive barriers in speciation? • What is the difference between allopatric speciation and sympatric speciation? • How does adaptive radiation explain the diversification? Connection for |
AP® Courses Speciation explains the diversity of organisms that inhabit the Earth. Although all life shares various genetic similarities, only certain organisms combine genetic information by sexual reproduction and produce viable and fertile offspring that, in turn, can successfully reproduce. Scientists call such organisms members of a biological species. As we will study in later, changes in allele frequencies within a population over generations result in microevolution. However, macroevolution leads to the evolution of new species when populations diverge from a common ancestor and, for one reason or another, become reproductively isolated from the original population. Speciation occurs along two main pathways: geographic separation (allopatric speciation) and through mechanisms that occur within a shared habitat (sympatric speciation). In both cases, populations become reproductively isolated. When populations become geographically isolated, the free-flow of alleles is prevented. Over time—and because of different selective pressures—the populations diverge and become genetically independent species. Prezygotic barriers block reproduction prior to formation of a zygote, whereas postzygotic barriers block reproduction after fertilization occurs. Obviously, if two populations are separated by a vast ocean, they will not come in contact with each other to reproduce. However, if speciation has occurred, even when brought back together, they will retain their species identity. There are many examples of this in nature, including Darwin’s finches, northern and Mexican spotted owls, and Hawaiian honeycreeper. Adaptive radiation occurs when a single ancestral species gives rise to many new species. This may occur, for example, when new habitats become available. It can also be seen historically in the rise of mammals following the extinction of dinosaurs. Other examples of prezygotic isolating mechanisms include mating seasons and unique courtship behaviors. Sometimes mating occurs between two different species, resulting in a hybrid such as the mule, which is a cross between a horse and a donkey. However, most hybrids are inviable or sterile. 732 Chapter 18 | Evolution and Origin of Species Sympatric speciation does not require a geographic barrier and explains how many different species can inhabit the same area. One form of sympatric speciation begins with a serious chromosomal error during cell division. As you recall from our exploration of meiosis, sometimes errors occur in the separation of chromosomes or chromatids, resulting in gametes with extra chromosomes (polyploidy). This type of speciation is more common in plants |
than in animals, though some examples in animals exist. For example, two groups of cichlid fish in Africa’s Lake Victoria, which have distinct morphologies and diets, may be in the early stage of sympatric speciation without polyploidy, as genetic differences arise between the two groups. Information presented and the examples highlighted in this section support concepts outlined in Big Idea 1 and Big Idea 3 of the AP® Biology Curriculum Framework. The AP® Learning Objectives listed in the Curriculum Framework provide a transparent foundation for the AP® Biology course, an inquiry-based laboratory experience, instructional activities, and AP® exam questions. A learning objective merges required content with one or more of the seven science practices. Big Idea 1 The process of evolution drives the diversity and unity of life. Enduring Understanding 1.C Essential Knowledge Science Practice Learning Objective Essential Knowledge Science Practice Learning Objective Life continues to evolve within a changing environment. 1.C.1 Speciation and extinction have occurred throughout the Earth’s history. 5.1 The student can analyze data to identify patterns or relationships. 1.20 The student is able to analyze data related to questions of speciation and extinction throughout the Earth’s history. 1.C.1 Speciation and extinction have occurred throughout the Earth’s 4.2 The student can design a plan for collecting data to answer a particular scientific question. 1.21 The student is able to design a plan for collecting data to investigate the scientific claim that speciation and extinction have occurred throughout the Earth’s history. Essential Knowledge 1.C.2 Speciation may occur when two populations become reproductively isolated from each other. Science Practice Learning Objective 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. 1.22 The student is able to use data from a real or simulated population(s), based on graphs or models of types of selection, to predict what will happen to the population in the future. Essential Knowledge 1.C.2 Speciation may occur when two populations become reproductively isolated from each other. Science Practice Learning Objective 4.1 The student can justify the selection of the kind of data needed to answer a particular scientific question. 1.23 The student is able to justify the selection of data that address questions related to reproductive isolation and speciation. Essential Knowledge 1.C.2 Speciation may occur when two populations become reproductively isolated from each other. Science Practice Learning Objective |
Big Idea 3 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. 1.24 The student is able to describe speciation in an isolated population and connect it to change in gene frequency, change in environment, natural selection, and/or genetic drift. Living systems store, retrieve, transmit and respond to information essential to life processes. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 733 Enduring Understanding 3.C Essential Knowledge Science Practice Learning Objective Essential Knowledge Science Practice Learning Objective The processing of genetic information is imperfect and is a source of genetic variation. 3.C.1 Changes in genotype can result in changes in phenotype. 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. 3.24 The student is able to predict how a change in genotype, when expressed as a phenotype, provides a variation that can be subject to natural selection. 3.C.1 Changes in genotype can result in changes in phenotype. 7.2 The student can connect concepts in and across domain(s) to generalize or extrapolate in and/or across enduring understandings and/or big ideas. 3.26 The student is able to explain the connection between genetic variations in organisms and phenotypic variations in populations. The Science Practice Challenge Questions contain additional test questions for this section that will help you prepare for the AP exam. These questions address the following standards: [APLO 2.27][APLO 1.8][APLO 1.23] Species and the Ability to Reproduce A species is a group of individual organisms that interbreed and produce fertile, viable offspring. According to this definition, one species is distinguished from another when, in nature, it is not possible for matings between individuals from each species to produce fertile offspring. Members of the same species share both external and internal characteristics, which develop from their DNA. The closer relationship two organisms share, the more DNA they have in common, just like people and their families. People’s DNA is likely to be more like their father or mother’s DNA than their cousin or grandparent’s DNA. Organisms of the same species have the highest level of DNA alignment and therefore share characteristics and behaviors that lead to successful reproduction. Species’ appearance can be misleading in suggesting an ability or inability to mate. For example |
, even though domestic dogs (Canis lupus familiaris) display phenotypic differences, such as size, build, and coat, most dogs can interbreed and produce viable puppies that can mature and sexually reproduce (Figure 18.10). Figure 18.10 The (a) poodle and (b) cocker spaniel can reproduce to produce a breed known as (c) the cockapoo. (credit a: modification of work by Sally Eller, Tom Reese; credit b: modification of work by Jeremy McWilliams; credit c: modification of work by Kathleen Conklin) In other cases, individuals may appear similar although they are not members of the same species. For example, even though bald eagles (Haliaeetus leucocephalus) and African fish eagles (Haliaeetus vocifer) are both birds and eagles, each belongs to a separate species group (Figure 18.11). If humans were to artificially intervene and fertilize the egg of a bald eagle with the sperm of an African fish eagle and a chick did hatch, that offspring, called a hybrid (a cross between two species), would probably be infertile—unable to successfully reproduce after it reached maturity. Different species may have different genes 734 Chapter 18 | Evolution and Origin of Species that are active in development; therefore, it may not be possible to develop a viable offspring with two different sets of directions. Thus, even though hybridization may take place, the two species still remain separate. Figure 18.11 The (a) African fish eagle is similar in appearance to the (b) bald eagle, but the two birds are members of different species. (credit a: modification of work by Nigel Wedge; credit b: modification of work by U.S. Fish and Wildlife Service) Populations of species share a gene pool: a collection of all the variants of genes in the species. Again, the basis to any changes in a group or population of organisms must be genetic for this is the only way to share and pass on traits. When variations occur within a species, they can only be passed to the next generation along two main pathways: asexual reproduction or sexual reproduction. The change will be passed on asexually simply if the reproducing cell possesses the changed trait. For the changed trait to be passed on by sexual reproduction, a gamete, such as a sperm or egg cell, must possess the changed trait. In other words, sexually-reproducing organisms can experience |
several genetic changes in their body cells, but if these changes do not occur in a sperm or egg cell, the changed trait will never reach the next generation. Only heritable traits can evolve. Therefore, reproduction plays a paramount role for genetic change to take root in a population or species. In short, organisms must be able to reproduce with each other to pass new traits to offspring. Until recently, these three species of short-tailed pythons, Python curtus, Python brongersmai (middle), and Python breitensteini were considered one species. However, due to the different locations in which they are found, they have become three distinct species. Figure 18.12 Until recently, these three species of short-tailed pythons, Python curtus, Python brongersmai (middle), and Python breitensteini were considered one species. However, due to the different locations in which they are found, they have become three distinct species. What is this an example of? a. divergent evolution b. sympatric speciation c. allopatric speciation d. variation This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 735 Speciation The biological definition of species, which works for sexually reproducing organisms, is a group of actually or potentially interbreeding individuals. There are exceptions to this rule. Many species are similar enough that hybrid offspring are possible and may often occur in nature, but for the majority of species this rule generally holds. In fact, the presence in nature of hybrids between similar species suggests that they may have descended from a single interbreeding species, and the speciation process may not yet be complete. Given the extraordinary diversity of life on the planet there must be mechanisms for speciation: the formation of two species from one original species. Darwin envisioned this process as a branching event and diagrammed the process in the only illustration found in On the Origin of Species (Figure 18.13a). Compare this illustration to the diagram of elephant evolution (Figure 18.13b), which shows that as one species changes over time, it branches to form more than one new species, repeatedly, as long as the population survives or until the organism becomes extinct. Figure 18.13 The only illustration in Darwin's On the Origin of Species is (a) a diagram showing speciation events leading to biological diversity. The diagram shows similarities to phylogen |
etic charts that are drawn today to illustrate the relationships of species. (b) Modern elephants evolved from the Palaeomastodon, a species that lived in Egypt 35–50 million years ago. For speciation to occur, two new populations must be formed from one original population and they must evolve in such a way that it becomes impossible for individuals from the two new populations to interbreed. Biologists have proposed mechanisms by which this could occur that fall into two broad categories. Allopatric speciation (allo- = "other"; -patric = "homeland") involves geographic separation of populations from a parent species and subsequent evolution. Sympatric speciation (sym- = "same"; -patric = "homeland") involves speciation occurring within a parent species remaining in one location. Biologists think of speciation events as the splitting of one ancestral species into two descendant species. There is no reason why there might not be more than two species formed at one time except that it is less likely and multiple events can be conceptualized as single splits occurring close in time. Allopatric Speciation A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across the range of the species, is relatively free because individuals can move and then mate with individuals in their new location. Thus, the frequency of an allele at one end of a distribution will be similar to the frequency of the allele at the other end. When populations become geographically discontinuous, that free-flow of alleles is prevented. When that separation lasts for a period of time, the two populations are able to evolve along different trajectories. Thus, their allele frequencies at numerous genetic loci gradually become more and more different as new alleles independently arise by mutation in each population. Typically, environmental conditions, such as climate, resources, predators, and competitors for the two populations will differ causing natural selection to favor divergent adaptations in each group. Isolation of populations leading to allopatric speciation can occur in a variety of ways: a river forming a new branch, erosion forming a new valley, a group of organisms traveling to a new location without the ability to return, or seeds floating over the ocean to an island. The nature of the geographic separation necessary to isolate populations depends entirely on the biology of the organism and its potential for dispersal. If two flying insect populations took up residence in separate nearby valleys, chances are, individuals from each population would fly back and forth continuing gene |
flow. However, if 736 Chapter 18 | Evolution and Origin of Species two rodent populations became divided by the formation of a new lake, continued gene flow would be unlikely; therefore, speciation would be more likely. Biologists group allopatric processes into two categories: dispersal and vicariance. Dispersal is when a few members of a species move to a new geographical area, and vicariance is when a natural situation arises to physically divide organisms. Scientists have documented numerous cases of allopatric speciation taking place. For example, along the west coast of the United States, two separate sub-species of spotted owls exist. The northern spotted owl has genetic and phenotypic differences from its close relative: the Mexican spotted owl, which lives in the south (Figure 18.14). Figure 18.14 The northern spotted owl and the Mexican spotted owl inhabit geographically separate locations with different climates and ecosystems. The owl is an example of allopatric speciation. (credit "northern spotted owl": modification of work by John and Karen Hollingsworth; credit "Mexican spotted owl": modification of work by Bill Radke) Additionally, scientists have found that the farther the distance between two groups that once were the same species, the more likely it is that speciation will occur. This seems logical because as the distance increases, the various environmental factors would likely have less in common than locations in close proximity. Consider the two owls: in the north, the climate is cooler than in the south; the types of organisms in each ecosystem differ, as do their behaviors and habits; also, the hunting habits and prey choices of the southern owls vary from the northern owls. These variances can lead to evolved differences in the owls, and speciation likely will occur. Adaptive Radiation In some cases, a population of one species disperses throughout an area, and each population finds a distinct niche or isolated habitat. Over time, the varied demands of their new lifestyles lead to multiple speciation events originating from a single species. This is called adaptive radiation because many adaptations evolve from a single point of origin; thus, causing the species to radiate into several new ones. Island archipelagos like the Hawaiian Islands provide an ideal context for adaptive radiation events because water surrounds each island which leads to geographical isolation for many organisms. The Hawaiian honeycreeper illustrates one example of adaptive radiation. From a single species, called the founder species, numerous species have evolved, including the six shown in |
Figure 18.15. This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 737 Figure 18.15 The honeycreeper birds illustrate adaptive radiation. From one original species of bird, multiple others evolved, each with its own distinctive characteristics. Notice the differences in the species’ beaks in Figure 18.15. Evolution in response to natural selection based on specific food sources in each new habitat led to evolution of a different beak suited to the specific food source. The seed-eating bird has a thicker, stronger beak which is suited to break hard nuts. The nectar-eating birds have long beaks to dip into flowers to reach the nectar. The insect-eating birds have beaks like swords, appropriate for stabbing and impaling insects. Darwin’s finches are another example of adaptive radiation in an archipelago. 738 Chapter 18 | Evolution and Origin of Species Click through this interactive site (http://openstaxcollege.org/l/bird_evolution) to see how island birds evolved in evolutionary increments from 5 million years ago to today. Name three examples of adaptive radiation, and provide a brief statement about each one. a. Domestic dogs – There are over 300 distinct dog breeds. Cows – There are over 800 cow breeds recognized worldwide. Domestic cats – Cats have changed drastically in just a few thousand years. b. Whales and fish – Although it has been roughly 400 million years since fish and mammals diverged, whales and fish are morphologically similar. Birds and butterflies – Although the common ancestor between vertebrates and insects lived even longer ago than the common ancestor between whales and fish, birds and butterflies both developed flight. Rabbits and kangaroos – Although it has been over 150 million years since their divergence, rabbits and kangaroos both developed powerful jumping legs. c. Hawaiian silverswords-There are about 30 species evolved from one parent species. Madagascar lemursTheir common ancestor likely arrived to Madagascar over 60 million years ago. Hawaiian fruit fly-There are 500 species of fruit fly from one parent species. d. Beetles – There are about 350,000 species of beetles that we know of. Birds – There are almost 10,000 species of birds in existence. Frogs – There are almost 5,000 species of frogs worldwide. Sympatric Speciation Can divergence occur if no physical barriers are in place to separate |
individuals who continue to live and reproduce in the same habitat? The answer is yes. The process of speciation within the same space is called sympatric speciation; the prefix “sym” means same, so “sympatric” means “same homeland” in contrast to “allopatric” meaning “other homeland.” A number of mechanisms for sympatric speciation have been proposed and studied. One form of sympatric speciation can begin with a serious chromosomal error during cell division. In a normal cell division event chromosomes replicate, pair up, and then separate so that each new cell has the same number of chromosomes. However, sometimes the pairs separate and the end cell product has too many or too few individual chromosomes in a condition called aneuploidy (Figure 18.16). This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 739 Figure 18.16 Aneuploidy results when the gametes have too many or too few chromosomes due to nondisjunction during meiosis. In the example shown here, the resulting offspring will have 2n+1 or 2n-1 chromosomes In your own words, define aneuploidy. a. Aneuploidy is a mutation that causes the genome of a cell to break down. b. neuploidy is the condition of having too many or too few chromosomes as a result of an error during cell division c. Aneuploidy is the condition of having an extra copy of every chromosome in the genome. d. Aneuploidy is a prezygotic barrier in which the gametes of two distinct species will not fertilize each other. Polyploidy is a condition in which a cell or organism has an extra set, or sets, of chromosomes. Scientists have identified two main types of polyploidy that can lead to reproductive isolation of an individual in the polyploidy state. Reproductive isolation is the inability to interbreed. In some cases, a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called autopolyploidy (Figure 18.17). The prefix “auto-” means “self,” so the term means multiple chromosomes from one’s own species |
. Polyploidy results from an error in meiosis in which all of the chromosomes move into one cell instead of separating. Figure 18.17 Autopolyploidy results when mitosis is not followed by cytokinesis. For example, if a plant species with 2n = 6 produces autopolyploid gametes that are also diploid (2n = 6, when they should be n = 3), the gametes now have twice as many chromosomes as they should have. These new gametes will be incompatible with the normal gametes produced by this plant species. However, they could either self-pollinate or reproduce with other autopolyploid plants with gametes having the same diploid number. In this way, sympatric speciation can occur quickly by 740 Chapter 18 | Evolution and Origin of Species forming offspring with 4n called a tetraploid. These individuals would immediately be able to reproduce only with those of this new kind and not those of the ancestral species. The other form of polyploidy occurs when individuals of two different species reproduce to form a viable offspring called an allopolyploid. The prefix “allo-” means “other” (recall from allopatric): therefore, an allopolyploid occurs when gametes from two different species combine. Figure 18.18 illustrates one possible way an allopolyploid can form. Notice how it takes two generations, or two reproductive acts, before the viable fertile hybrid results. Figure 18.18 Alloploidy results when two species mate to produce viable offspring. In the example shown, a normal gamete from one species fuses with a polyploidy gamete from another. Two matings are necessary to produce viable offspring. The cultivated forms of wheat, cotton, and tobacco plants are all allopolyploids. Although polyploidy occurs occasionally in animals, it takes place most commonly in plants. (Animals with any of the types of chromosomal aberrations described here are unlikely to survive and produce normal offspring.) Scientists have discovered more than half of all plant species studied relate back to a species evolved through polyploidy. With such a high rate of polyploidy in plants, some scientists hypothesize that this mechanism takes place more as an adaptation than as an error. Activity Create a visual representation such as a diagram with annotation to explain how island chains provide ideal conditions for allopatric speciation and adaptive radiation |
to occur. Then design a plan for collecting data to support the claim that speciation has occurred. Think About It • Two species of fish had recently undergone sympatric speciation. The males of each species had a different coloring through which the females could identify and choose a partner from her own species. After some time, pollution made the lake so cloudy that it was hard for females to distinguish colors. What might take place in this situation? • In a lake where most fish of a single species exhibit colorful stripes, a few individual animals have muted colors. The local fisherman receives a large order to catch the most colorful fish for a local aquarium store. The fisherman casts wide nets across the lake to catch a large number of the fish. He then keeps the colorful fish for the aquarium and throws back the dull colored fish. How will this single event change the make-up of the fish population? Reproductive Isolation Given enough time, the genetic and phenotypic divergence between populations will affect characters that influence reproduction: if individuals of the two populations were to be brought together, mating would be less likely, but if mating This OpenStax book is available for free at http://cnx.org/content/col12078/1.6 Chapter 18 | Evolution and Origin of Species 741 occurred, offspring would be non-viable or infertile. Many types of diverging characters may affect the reproductive isolation (the inability to interbreed) of the two populations. Reproductive isolation can take place in a variety of ways. Scientists organize them into two groups: prezygotic barriers and postzygotic barriers. Recall that a zygote is a fertilized egg: the first cell of the development of an organism that reproduces sexually. Therefore, a prezygotic barrier is a mechanism that blocks reproduction from taking place; this includes barriers that prevent fertilization when organisms attempt reproduction. A postzygotic barrier occurs after zygote formation; this includes organisms that don’t survive the embryonic stage and those that are born sterile. Some types of prezygotic barriers prevent reproduction entirely. Many organisms only reproduce at certain times of the year, often just annually. Differences in breeding schedules, called temporal isolation, can act as a form of reproductive isolation. For example, two species of frogs inhabit the same area, but one reproduces from January to March, whereas the other reproduces from March to May (Figure 18.19). Figure 18.19 These two related frog |
species exhibit temporal reproductive isolation. (a) Rana aurora breeds earlier in the year than (b) Rana boylii. (credit a: modification of work by Mark R. Jennings, USFWS; credit b: modification of work by Alessandro Catenazzi) In some cases, populations of a species move or are moved to a new habitat and take up residence in a place that no longer overlaps with the other populations of the same species. This situation is called habitat isolation. Reproduction with the parent species ceases, and a new group exists that is now reproductively and genetically independent. For example, a cricket population that was divided after a flood could no longer interact with each other. Over time, the forces of natural selection, mutation, and genetic drift will likely result in the divergence of the two groups (Figure 18.20). Figure 18.20 Speciation can occur when two populations occupy different habitats. The habitats need not be far apart. The cricket (a) Gryllus pennsylvanicus prefers sandy soil, and the cricket (b) Gryllus firmus prefers loamy soil. The two species can live in close proximity, but because of their different soil preferences, they became genetically isolated. Behavioral isolation occurs when the presence or absence of a specific behavior prevents reproduction from taking place. For example, male fireflies use specific light patterns to attract females. Various species of fireflies display their lights differently. If a male of one species tried to attract the female of another, she would not recognize the light pattern and would not mate with the male. Other prezygotic barriers work when differences in their gamete cells (eggs and sperm) prevent fertilization from taking place; this is called a gametic barrier. Similarly, in some cases closely related organisms try to mate, but their reproductive structures simply do not fit together. For example, damselfly males and females of different species have differently shaped reproductive organs. If one species tries to mate with another, their body parts simply do not fit together. (Figure 18.21). 742 Chapter 18 | Evolution and Origin of Species Figure 18.21 The shape of the male reproductive organ varies among male damselfly species, and is only compatible with the female of the same species. Reproductive organ incompatibility keeps each species reproductively isolated. In plants, certain structures aimed to attract one type of pollinator simultaneously prevent a different pollinator from accessing the pollen. The tunnel through which an animal must access nectar |
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