Biology and Biotechnology: Science, Applications, and Issues

This chapter discusses essential functions, common features, chemical basis of cell organization and the two major classes of cells. Biologists examining the microscopic structures of microbes, plants, and animals found that every tissue or organism was made of cells, each enclosed by a membrane separating it from surrounding cells and the external environment. Chemical analysis revealed that even though various cell types looked very different physically, their chemical makeups were remarkably similar. Over time, cells increase in size, and this growth requires building materials and energy. Conveniently, cells get both of these supplies from the same source, the large molecules that make up food: proteins, carbohydrates, fats, and nucleic acids. Just as new animals and plants are generated by the reproduction of animals and plants, new cells are generated by the reproduction of cells. Carrying out activities, building and rebuilding molecules and structures, and maintaining an internal environment that differs from its surroundings all require energy, and cells obtain it from a variety of sources. All cells share certain basic features: they have molecular machinery for duplicating DNA and breaking down and synthesizing molecules, they reproduce by dividing in two, they use the same molecular building blocks, and they are enclosed by a hydrophobic membrane that separates the cell from its surroundings.

Cells contain many small molecules and ions, but their major structural and functional components are formed by four types of large molecules unique to living organisms: lipids, carbohydrates, proteins, nucleic acids (DNA and RNA). This chapter provides an introduction to these molecules, and begins by laying some groundwork for discussing and drawing molecules, including defining some already-in-usage terms. DNA contains the genetic information of organisms. If DNA is thought as a library of instructions, then it’s clear that two different kinds of things have to happen to it during the life of an organism. First, the information encoded by its base sequence has to be translated into the actual ‘’stuff'' of an organism-its form and functions. Second, when a cell divides, the DNA has to be accurately copied so that the new cell can have its own instruction library. An organism’s structure and functions depend on the proteins present in its cells. The large molecules play similar roles in all cells. The similarity of cellular biochemistry is a manifestation of the relatedness of different kinds of cells and organisms-we are made of the same things and, at a cellular level, work in the same ways.

This chapter focuses on how the information in DNA is translated into proteins and how changes in DNA and subsequent changes in proteins can affect their functions. The human genome consists of ~3 billion base pairs of DNA, and over 90% of it does not encode proteins. This noncoding DNA is often in the form of repeated sequences, sometimes in large clusters, which appears to be typical of eukaryotic genomes. Cellular enzymes synthesize a working copy of a gene to carry its genetic code to the ribosomes. This working copy is an RNA molecule called messenger RNA (mRNA), and the process of synthesizing it is called transcription. After transcription and processing are complete, the mRNA moves to the ribosome, the site of protein synthesis. The ribosome and the mRNA fit together so that the mRNA codons can be read correctly. The effect of a mutation on an organism depends on how the mutation affects the expression of genetic information and how the change in gene expression affects the organism within its environment. For example, a sequence change in a region of DNA that wasn’t part of a protein-coding sequence would probably not have any effect on the organism. Antibiotics treat bacterial infections by blocking essential bacterial processes, such as protein synthesis. Bacterial cells are prokaryotic, and their ribosomes are different enough from human ribosomes that antibiotics can interfere with bacterial protein synthesis without harming human protein synthesis.

This chapter focuses on the structure of proteins and how it relates to their functions. When a protein folds, it generally segregates the hydrophobic side chains in the interior of the protein, where they interact with one another away from water molecules in the cytoplasm. Protein structure is held together by hydrogen bonds and disulfide bridges between cysteine residues. Proteins can be denatured by treatments that break these bonds, such as heat or harsh chemicals. If a protein is denatured, it often cannot refold itself even if the denaturing agent is removed. Proteins carry out functions through molecular interactions between specific side chains and their targets. Scientists also learn about new proteins by comparing their amino acid sequences to the sequences of all other known proteins, using national databases and search engines. Researchers are using their knowledge of protein structure and protein function to improve the usefulness of enzymes in industrial and other processes. They do this by manipulating the DNA sequences of genes encoding these proteins, so that the proteins can have altered amino acid sequences and characteristics.

This chapter discusses how food is converted to energy for cells and how cells use that energy to make molecules they need. Metabolic pathways are very often branched because there is more than one possible fate for an intermediate in the pathway. For example, the pathway that cells use to break down fats to get energy converges with the metabolic pathway for breaking down glucose to get energy. In the electron transport pathway, the energy released during the step-by-step breakdown of carbohydrates, lipids, and proteins is harvested from various temporary storage molecules to make adenosine triphosphate (ATP) by attaching a phosphate group to adenosine diphosphate (ADP). ATP thus serves as a sort of energy currency for the cell--it is created during the energy-yielding processes of catabolism and spent in the energy-requiring processes of anabolism. One of the simplest examples of feedback inhibition in metabolism is the pathway for synthesis of the amino acid isoleucine. Comparing the fates of people with enzyme defects at different points in the phenylalanine catabolism pathway resulting in either phenylketonuria (PKU) or alkaptonuria illustrates an important point. Studies of Gaucher’s disease patients have revealed that many different mutations in the gene for the lipid-degrading enzyme can cause the disease.

This chapter discusses how cells sense and respond to their environments, and also talks about various kinds of transport proteins involved in moving substances in and out of cells. The cell membrane determines whether energy is required to transport something and some of the many proteins embedded in the cell membrane are transport proteins. There are different types of transport proteins for different substances and situations. This chapter discusses how transport proteins function to transmit one's nerve impulses and make the heart beat and how disturbances in ion gradients can disrupt these critical body functions. The family members with hereditary heart failure have an altered form of the regulatory protein with a shape that cannot be phosphorylated. Without the phosphate group, the regulatory protein constantly inhibits the pump. Lactose intolerance results from a lack of the enzyme lactase that breaks the complex milk sugar lactose into its simple- sugar components, glucose and galactose. Water-salt imbalance also explains the symptoms of people who have cystic fibrosis, the most common fatal inherited disease of Caucasians. Water follows solutes in the body. Water will move across membranes and through aquaporins, when possible, to maintain osmotic balance in various cell compartments.

This chapter discusses the types of cell signals and cell receptors, examples of direct interaction between the environment and single-celled organisms, how hormones regulate the environment within multicellular organisms regulation of glucose concentration in the blood, regulation of salt and water balance and blood pressure. A key concept for the chapter is that in order for a cell (or, by extension, a multicellular organism) to respond to signals from the environment, all the steps from the signal to the effect must be in place. The chapter discusses some examples of cascades related to some of the ways our bodies regulate salt and water balance. Some basics of signaling and response are illustrated by an example from the bacterium Escherichia coli. The interconnected system of hormones that regulate body’s blood pressure and salt and water balance, and the major hormones involved in blood pressure regulation are explained. Each of these hormones has a receptor through which it exerts its effects. Taking diabetes as an example, one might assume that blood pressure regulation could be impaired by either a failure to make one of the hormones or a failure to respond to it. Kidney failure is treated with dialysis, in which blood is pumped through porous membrane tubes suspended in fluid containing healthy concentrations of salt and glucose.

This chapter discusses the general kinds of genes involved in cancer and shows how two environmental carcinogens work to stimulate its development. DNA replication involves the synthesis of a molecule, and like other cellular synthesis processes, it is carried out by an enzyme. Replication initiation, therefore, is carefully controlled. It begins with the binding of proteins to unique sequences of DNA bases called replication origins. After mitosis is complete, the cell splits in two in a process called cytokinesis. The production of daughter cells that are genetically identical to each other and to the mother cell is the point of cell reproduction. Cell reproduction has to involve the coordinated, regulated processes of growth, DNA replication, chromosome distribution, and cell division. Damaged DNA activates the expression of the p53 gene. The p53 protein activates the G1 checkpoint and halts the division cycle before DNA replication begins. This is important, because otherwise the damaged DNA would be copied and mutations would be transmitted to daughter cells. To become a cancer cell, a normal cell must accumulate mutations in several different genes. These mutations are then transmitted to the cell’s cancerous descendants. The most important message here, though, is that full-fledged cancer requires the accumulation of multiple mutations in genes that normally regulate cell division. Genetic testing is a new tool for managing cancer and its risks.

Much of the understanding of both cell differentiation and development comes from the study of model organisms. Studies of the fruit fly and the nematode, because they are small enough to be housed by the multiple thousands and because they can be easily mutagenized, led to the isolation of developmental mutants and thus to the identification of many genes important in development. Development involves differentiation, the process through which cells become specialized in form and function, and morphogenesis, the combination of cell migration, proliferation, differentiation, and death that produces the final shape of the body. Cells of an early mammalian embryo are said to be totipotent because they can differentiate into all types of adult cells. The various differentiated cells within an organism have the same genetic content, but they express different sets of genes and thus make different specialized protein products. Differential gene expression is usually controlled at the level of transcription. During development, cells signal to one another via proteins or other chemicals. These signals bind to receptors on target cells and elicit changes in the targets. Differentiation begins in a Drosophila embryo because the maternal cells surrounding the egg deposited mRNA and proteins at specific places in the egg.

This chapter explains the basic aspects of heredity, such as the physical basis of heredity, the mechanics of transmission and the basic laws governing genetic inheritance. In sexually reproducing organisms, genes and chromosomes occur in maternal-paternal, or homologous, pairs. Only one member of the pair is transmitted from each parent to its offspring. Meiosis is the cell division process that creates gametes with only one member of each homologous pair. Mendel’s Law of Segregation describes the behavior of homologous chromosomes: in meiosis, they separate prior to gamete formation. Mendel’s Law of Independent Assortment describes the behavior of nonhomologous chromosomes: when homologous chromosomes separate in meiosis, they do so independently of the other chromosomes. Using fruit flies as their experimental organism and relying on findings in cytology,T.H.Morgan and his students proved that genes are located at very specific sites, or loci, on chromosomes. During meiosis, homologous chromosomes exchange genetic material. Chromatids cross over each other, break, and rejoin quite specifically. This is known as recombination, because the genetic material of the two chromosomes has been recombined. The frequency of crossing over allows scientists to determine the relative distance between two genes on a chromosome. When distances among many genes on a chromosome have been determined, scientists are able to create a linkage map that shows the relative positions of genes on a chromosome.

Mendel studied traits that show simple inheritance patterns, now known as Mendelian one-gene traits with distinct, observable phenotypic differences and clear dominance relationships. Very few visible phenotypic traits have this type of genetic basis. The primary misconception is that one gene leads to one trait and that any one trait can be traced to a single gene. However, a gene usually affects many visible phenotypic characteristics, which is known as pleiotropy. On the other hand, a visible phenotypic trait almost always results from the activities of many genes interacting in different ways, such as additive or epistatic interactions. In addition, the same visible phenotypic trait may be traced to mutations in completely different genes, which is known as genetic heterogeneity. The other misconception is related to the power of genes to determine a trait. Many people assume that someone who has a gene for a trait will definitely have that trait and that someone lacking that gene will not have the trait. However, a gene never acts alone; interactions among many genes, as well as environmental factors, create phenotypic traits. As a result, a person with a gene associated with a trait may not exhibit that trait, while someone without that gene may have the phenotype. Many types of environmental factors influence the phenotypic expression of genetic information. Studies of human twins can shed a little light on the relative contributions of genes and environments to human traits, but in general, they tend to overestimate the amount of genetic contribution.

Biological evolution, an inevitable force in nature, is a change in the frequencies of certain alleles in a population over time. It consists essentially of a two-step circular process that is repeated over and over again creating populations of genetically diverse organisms and culling certain individuals, but not others, from that population based on a genetically determined phenotypic trait. Mutations can involve single nucleotides or entire chromosomes. Mutations that affect a large piece of a chromosome can be evolutionarily disadvantageous because they decrease the survival and reproductive success of the bearer of the chromosome mutation or affect the viability of the bearer’s gametes, or both. Transposable genetic elements excise themselves from a location and reinsert elsewhere in the genome, sometimes disrupting gene function. Organisms that reproduce asexually also have methods for increasing genetic variation in their populations: conjugation, transduction, and transformation. Evolution is a change in the genetic makeup of a population of organisms, and the factors that cause the change include mutation, gene flow, genetic drift, nonrandom mating, and natural selection. The rise in antibiotic resistance in bacteria is a frightening, real world example of the evolutionary process. Antibiotic resistance occurs naturally and is inherited. Antibiotic resistance is a serious public health problem that everyone can lessen by using antibiotics for bacterial infections, not viral infections, and, when antibiotics are prescribed, using the complete amount of the drug prescribed.

This chapter describes some ecological interactions and effects at each level, including: the population growth rate and density-dependent regulation of population size, community interactions, such as competition, predation, and symbiosis, and the flow of energy and materials in ecosystems. Photosynthesis provides living organisms with the carbon, hydrogen, and oxygen needed to construct biological molecules, but they also need to synthesize some awfully important nitrogen-containing molecules, such as DNA, ATP, and proteins. Density-dependent regulators of the population growth rate include competition for resources, predation, disease, and habitat degradation, all of which are discussed in the chapter. The most significant factors lowering death rates and contributing to the exponential rate of population growth became operative in the mid- to late 1800s. First of all, the scientific breakthroughs of Louis Pasteur and Robert Koch established the role that bacteria play in causing certain diseases and reinforced the need for improved sanitation and public hygiene. Second, the development of vaccines and antibiotics controlled the spread of many infectious diseases. Agriculture was the first technology that allowed humans to circumvent factors that govern population growth. As human populations congregated around rich agricultural areas, density-dependent factors that decrease population size-disease and parasitism-began to decrease the population growth rate by increasing the death rate.

This chapter highlights at some of the enzymes and other fundamental tools for manipulating DNA and cells that enable us to analyze DNA, including determining its sequence, clone DNA, analyze proteins. It focuses on tools and techniques of biotechnology that are based on natural processes and cellular enzymes. The enzymes used by biotechnologists to manipulate DNA are the same enzymes cells use to cut, paste, and copy DNA. Restriction enzymes cut the phosphodiester backbone of DNA molecules at specific base sequences. DNA ligase seals properly aligned DNA fragments together by forming new phosphodiester bonds. Hybridization between a DNA molecule and a labeled probe is used to indicate the presence of the DNA sequence in the probe. Polymerase chain reaction (PCR) amplifies a defined segment of a DNA molecule through the use of specific primers and a polymerase enzyme. PCR can be used to generate many copies of a fragment for cloning or as a detection method. A specific piece of DNA is cloned by introducing it into a host cell that replicates the DNA as it reproduces, generating many identical copies of the DNA molecule. A complementary DNA (cDNA) library is a special type of DNA library in which the cloned DNA fragments are cDNA copies of mRNA taken from a eukaryotic cell. Cell fusion is used to make cells that produce monoclonal antibodies. The complex, high-technology techniques of X-ray diffraction and nuclear magnetic resonance (NMR) are used to determine the structures of proteins.

This chapter discusses ways in which biological tools are used to accomplish specific goals such as finding genes, analyzing genotypes, generating DNA fingerprints, and genetically engineering both plants and animals. One of the hottest new techniques in biotechnology provides the ability to silence the expression of specific genes. DNA comparisons can be used on a broad scale to assess the degree of relatedness of two species or on a tightly focused individual level to determine whether two DNA-containing samples could have come from the same individual. Mitochondrial DNA analysis is used to determine relatedness through the female line of descent. It can be used in evolutionary studies of fairly recent events to determine the likely ancestry and time of divergence of species or to identify family members of persons living or dead. Genetic markers are easily detected features within a chromosome that are inherited with a specific phenotype or genotype and can be used as a surrogate indicator of the presence of a particular allele. Microarrays, or gene chips, are ordered grids of thousands of nucleotide probes that represent many genes of interest. They are hybridized with sample genomic DNA to reveal genotypes or with sample mRNA to reveal gene expression patterns. Genetic engineering is the directed manipulation of an organism’s genome. Engineering a plant involves techniques of plant tissue culture, in which an entire plant can be regenerated from engineered cells. Engineering animals involves manipulations of eggs or early embryos, since only those cells can develop into whole organisms.

This chapter provides guidance on identifying and evaluating societal issues derived from biotechnology applications, a few tips on how to think about these issues, and an example of how these critical thinking skills can be applied to analyzing complicated issues that arise from biotechnology. It explains critical steps in objectively evaluating societal issues associated with an application of biotechnology. The risks of biotechnology laboratory research, small-scale field testing, and large-scale commercial use and manufacturing differ from each other both qualitatively and quantitatively. Nuclear transfer from embryonic cells is a relatively recent development that bears a resemblance to both embryo splitting and adult cell cloning. The chapter focuses only on the health risks associated with reproductive cloning via nuclear transfer from adult cells. The societal issues raised by advances in biotechnology are often not unique to biotechnology but are the same issues raised by other technologies. However, other issues result solely from the new powers of biotechnology. In charting a course for thoughtful biotechnology development, societies should avoid blaming biotechnology for mistakes of earlier technologies that may or may not apply to biotechnology. Critical analysis of biotechnology applications requires clarity, specificity, and emotional detachment.

This chapter compares emotion-based risk perception to science-based risk assessments, provides an example of the pitfalls of making decisions based on emotions and not facts and discusses the role that government regulatory agencies play in minimizing the potential risks associated with new products, including those developed using biotechnology. The uncertainty of exposure is one of the reasons risks are discussed in terms of probabilities instead of an absolute assessment of the seriousness of the hazard. Bacillus thuringiensis (Bt) corn contains the gene from B. thuringiensis subsp. kurstaki that encodes a protein specifically toxic to lepidopteran insects, including monarch larvae, that ingest any part of the plant expressing the Bt gene. The level of risk defined by the hazard and exposure can be decreased or managed by instituting safeguards that decrease either or both of these factors. In response to media attention and political pressure, government agencies and private companies funded additional research specifically targeted to the effect of Bt corn on monarch butterfly populations. This research provided scientific data to estimate risk mathematically by assessing the hazard (toxic dose) and the probability of exposure of monarch larvae to Bt corn pollen. The data reaffirmed the decision of the regulatory agencies that the benefits of Bt corn outweighed the risks. With regard to agricultural biotechnology products, the regulatory agencies review the product at various stages in development to assess its effects on the environment, agriculture, and human health.

Throughout the 20th century, advances in imaging technology provided diagnostic tools that made invisible symptoms visible and helped physicians catch some diseases earlier. For example, new visualization techniques could reveal cancers before clinical symptoms appeared and sometimes before they had spread to other organs. Early intervention lessens the harmful impacts of the disease and may even provide an opportunity to cure the disease rather than simply manage it. Early detection and treatment of infectious diseases have important public health implications, as well. Biotechnology-based improvements in diagnosing human immunodeficiency virus (HIV) infections provide a striking example of the public health benefits of early detection. Although the relationship between genes and health is receiving more public attention now than ever before, using genetics as a diagnostic component of health care is not new. The link between genes and a certain disorder becomes increasingly vague and ambiguous when either many genes contribute to the disorder (multigenic disorder) or genes and environmental factors interact and lead to the disorder (multifactorial disorder). Gene therapy would use genes, or related molecules, such as RNA, to treat diseases. Rather than giving daily injections of missing or malfunctioning proteins, medical researchers dream of supplying patients with accurate instruction manuals-nondefective genes. The most familiar form of cell transplant therapy is the 20+-year practice of transplanting bone marrow cells into cancer patients. Medical scientists are excited about the prospect of using the body’s natural healing processes not simply to treat debilitating diseases but perhaps to cure them.

This chapter provides relevant scientific and historical information relating to genetic testing and human embryonic stem (hES) cell therapies and describes some of the societal issues surrounding them. The risks of invasive diagnostic tests that require physicians to remove tissue samples are obvious, as are those based on X rays and injected dyes, radioactive molecules, or other imaging agents. Greater availability of gene-based diagnostic tests, made possible by the Human Genome Project (HGP), carries with it the same problems shared by all diagnostic tests. Genetic information differs from clinical measures because sometimes genes shed light on future health problems. The results of genetic tests might allow physicians to predict the possible appearance of cardiovascular or lung disease in the absence of any clinical symptoms. Using factual information and specific language in discussions of complex technical issues is always important; both become even more essential if the topic elicits strong emotional feelings about moral issues. Human embryonic cells have the potential to treat a variety of serious diseases, but some people find the derivation of embryonic cell lines to be ethically troubling. Government policies influence the direction of scientific research through funding, laws, and policies that encourage some types of research and restrict others. By directing the course of scientific inquiry, governments determine which medical advances occur.

The human body synthesizes 12 amino acids from scratch and depends on dietary sources for essential amino acids. Insufficient protein is the most pervasive macronutrient deficiency, but often the problem is not the total amount of protein consumed, but one or two amino acids. Researchers in India successfully increased the amino acid content of the potato by providing it with a gene from amaranth, a high-protein grain used in South American and Asian cultures for centuries. Micronutrients are food components, such as vitamins and minerals, needed in small amounts because they play key roles in specific cellular processes, such as oxygen transport (iron), hormone function (iodine), enzyme catalysis (zinc), or vision (vitamin A). Researchers from around the world are using recombinant DNA technology and plant breeding to increase the amounts of micronutrients in staple grains. Plant genetic diversity, created naturally through sexual reproduction, is a valuable natural resource that humans have exploited for centuries. Individual plants had traits people valued. They saved the seeds of those plants, grew them into parent plants for the next generation, selected the best of their offspring, and discarded the rest. The techniques for generating genetic diversity differ, but plant breeding, mutagenesis, and genetic engineering share the same objective: creating a crop variety with a new trait.

This chapter discusses plant agriculture with respect to ecology and evolution, and provides an opportunity to know more about ecological interactions and evolutionary adaptations using row crop agriculture as the hook. It attempts to lessen the information gap that exists between farmers and citizens in the industrialized world. The chapter provides information on the: evolution of crop plants from wild relatives, conflicts between plant adaptations for increased fitness and human requirements for food crops, developments in agriculture that have allowed crop productivity to keep pace with the exponential growth of the human population, and ecological problems caused by agricultural activities. Farmers use preplant herbicides to rid their fields of weeds without fear of harming their crops because the herbicides become inactivated very soon after application. By allowing no-till or minimum-till agriculture, the preplant herbicides prevent soil erosion caused by plowing and conserve soil moisture, lessening the need for irrigation. Flowers and fruits are tactics for meeting a plant’s primary objective: reproduction. To encourage cross-pollination in order to create genetic diversity, many plants have evolved mechanisms to prevent or minimize self-fertilization. Many flowering plants depend on animals for pollination and seed dispersal and reward them for their services. Basing agriculture on annual plants necessitates annual habitat disturbance. This leads to soil erosion, agriculture's most significant negative impact on both the environment and the long-term sustainability of agricultural ecosystems.

This chapter describes the goal of sustainable agriculture which includes the management practices that decrease the sustainability of modern agriculture, how an understanding of basic plant biology could lead to better agricultural products, the ways that the current group of transgenic crops encourages or discourages sustainable practices and the potential environmental impacts of transgenic crops. Biotechnology contributes to sustainable agriculture if it helps farmers maintain the quality and quantity of the biotic and abiotic resources they depend upon or decreases agriculture’s consumption of nonrenewable resources. All plants have at least some genetic infrastructure for tolerating water shortages, but only some plants survive droughts. Those that survive are more responsive to external changes in water levels. Perhaps their genetic regulatory mechanisms become activated by smaller changes in water availability, or maybe they have gene duplications for the drought resistance genes. Plant pathogens can be deterred by microbes that kill or outcompete them. Other insects and microbes can control weed populations. In addition, a form of biocontrol can be provided by the crop plant if it produces molecules for defending itself against herbivory and infections. The increased understanding of plant biology provided by biotechnology research applications may lead to products that promote sustainable agricultural practices, such as drought-resistant crops, crops that require less fertilizer, and biological methods of pest control.

The microbial metabolic pathway being exploited in food fermentation, then and now, is the glucose breakdown pathway. Yeasts break down the glucose in wheat flour to carbon dioxide, which causes bread to rise. If the starting material is fruit sugar, the product of glucose breakdown in yeast is wine. As with plant and animal agriculture, even though humans have always used microbial processes, the new biotechnologies, especially the bioprocess technologies and recombinant DNA technology, greatly expand the ways in which microbial processes contribute to human society. Life in unusual habitats makes for unique biocatalysts, and the great majority of that biochemical potential remains untapped. In the absence of bioprocess technologies that allow companies to manufacture a sufficient amount of product at an affordable price, the impact of recombinant DNA technology would be limited primarily to the research laboratory. The cost of converting cornstarch into sugar is one barrier to increasing the use of bioethanol. Genetically engineered microbes that decrease the cost of this step have been developed, but even so, in the absence of the government subsidies that are now provided for bioethanol, the cost of ethanol derived from cornstarch cannot compete with that of petroleum. The vast majority of bioremediation applications use naturally occurring microorganisms either to identify and filter manufacturing waste before it is introduced into the environment or to clean up existing pollution problems. Microbial catabolic pathways make it possible to use biomass as a raw material for generating biofuels and feedstock chemicals.