Molecular Biology and Genetics - Explorations: An Open Invitation to Biological Anthropology (2nd Edition) PDF

Home Read Sign in Search in book … Want to create or adapt books like this? Learn more about how Pressbooks supports open publishing practices. CONTENTS E...

Home Read Sign in Search in book … Want to create or adapt books like this? Learn more about how Pressbooks supports open publishing practices. CONTENTS EXPLORATIONS: AN OPEN INVITATION TO BIOLOGICAL ANTHROPOLOGY, 2ND EDITION 3. Molecular Biology and Genetics Hayley Mann, M.A., Binghamton University This chapter is a revision from “Chapter 3: Molecular Biology and Genetics” by Hayley Mann, Xazmin Lowman, and Malaina Gaddis. In Explorations: An Open Invitation to Biological Anthropology, first edition, edited by Beth Shook, Katie Nelson, Kelsie Aguilera, and Lara Braff, which is licensed under CC BY-NC 4.0. Learning Objectives Previous: A History of Evolutionary Thought Next: Forces of Evolution Explain and identify the purpose of both DNA replication and the cell cycle. Identify key differences between mitosis and meiosis. Outline the process of protein synthesis, including transcription and translation. Use principles of Mendelian inheritance to predict genotypes and phenotypes of future generations. Explain complexities surrounding patterns of genetic inheritance and polygenic traits. Discuss challenges to and bioethical concerns of genetic testing. I [Hayley Mann] started my Bachelor’s degree in 2003, which was the same year the Human Genome Project released its first draft sequence. I initially declared a genetics major because I thought it sounded cool. However, upon taking an actual class, I discovered that genetics was challenging. In addition to my genetics major, I signed up for biological anthropology classes and soon learned that anthropology could bring all those molecular lessons to life. For instance, we are composed of cells, proteins, nucleic acids, carbohydrates, and lipids. Anthropologists often include these molecules in their studies to identify how humans vary; if there are meaningful differences, they propose theories to explain them. Anthropologists study biomolecules in both living and ancient individuals. Ancient biomolecules can also be found on artifacts such as stone tools and cooking vessels. Over the years, scientific techniques for studying organic molecules have improved, which has unlocked new insights into the deep human past. This chapter provides the basics for understanding human variation and how the evolutionary process works. A few advanced genetics topics are also presented because biotechnology is now commonplace in health and society. Understanding the science behind this remarkable field means you will be able to participate in bioethical and anthropological discussions as well as make more informed decisions regarding genetic testing. Cells and Molecules Molecules of Life All organisms are composed of four basic types of molecules that are essential for cell structure and function: proteins, lipids, carbohydrates, and nucleic acids (Figure 3.1). Proteins are crucial for cell shape and nearly all cellular tasks, including receiving signals from outside the cell and mobilizing intra-cellular responses. Lipids are a class of organic compounds that include fats, oils, and hormones. As discussed later in the chapter, lipids are also responsible for the characteristic phospholipid bilayer structure of the cell membrane. Carbohydrates are sugar molecules and serve as energy to cells in the form of glucose. Lastly, nucleic acids, including deoxyribonucleic acid (DNA), carry genetic information about a living organism. Molecule Definition Example Composed of one or more long chains of amino acids (i.e., basic units of protein) Proteins come in different categories including structural (e.g., collagen, keratin, Often folded into complex lactase, hemoglobin, cell membrane Proteins 3D shapes that relate to proteins), defense proteins (e.g, antibodies), function enzymes (e.g., lactase), hormones (e.g., Proteins interact with other insulin), and motor proteins (e.g., actin) types of proteins and molecules Fats, such as triglycerides, store energy for your body Insoluble in water due to hydrophilic (water-loving) Steroid hormones (e.g., estrogen and Lipids head and a hydrophobic testosterone) act as chemical messengers to (water-repelling) tail communicate between cells and tissues, as well as biochemical pathways inside of the cell Large group of organic molecules that are Starches and sugars, including blood Carbohydrates composed of carbon and glucose, provide cells with energy hydrogen atoms Carries the genetic DNA Nucleic Acids information of an organism RNA Figure 3.1: Information about the four biomolecules. Credit: Biomolecules Table original to Explorations: An Open Invitation to Biological Anthropology (2nd ed.) by Hayley Mann is under a CC BY-NC 4.0 License. Cells In 1665, Robert Hooke observed slices of plant cork using a microscope. Hooke noted that the microscopic plant structures he saw resembled cella, meaning “a small room” in Latin. Approximately two centuries later, biologists recognized the cell as being the most fundamental unit of life and that all life is composed of cells. Cellular organisms can be characterized as two main cell types: prokaryotes and eukaryotes (Figure 3.2). Prokaryotes include bacteria and archaea, and they are composed of a single cell. Additionally, their DNA and organelles are not surrounded by individual membranes. Thus, no compartments separate their DNA from the rest of the cell (see Figure 3.2). It is well known that some bacteria can cause illness in humans. For instance, Escherichia coli (E. coli) and Salmonella contamination can result in food poisoning symptoms. Pneumonia and strep throat are caused by Streptococcal bacteria. Neisseria gonorrhoeae is a sexually transmitted Figure 3.2: Prokaryotic cell and eukaryotic cell. Credit: Prokaryote bacterial disease. Although bacteria are vs. eukaryote original to Explorations: An Open Invitation to commonly associated with illness, not all Biological Anthropology (2nd ed.) by Mary Nelson is under a CC bacteria are harmful. For example, BY-NC 4.0 License. [Image Description] researchers are studying the relationship between the microbiome and human health. The bacteria that are part of the healthy human microbiome perform beneficial roles, such as digesting food, boosting the immune system, and even making vitamins (e.g., B12 and K). Eukaryotes can be single-celled or multi-celled in their body composition. In contrast to prokaryotes, eukaryotes possess membranes that surround their DNA and organelles. An example of a single-celled eukaryote is the microscopic algae found in ponds (phytoplankton), which can produce oxygen from the sun. Yeasts are also single-celled, and fungi can be single- or multicellular. Plants and animals are all multicellular. Although plant and animal cells have a surprising number of similarities, there are some key differences (Figure 3.3). For example, plant cells possess a thick outer cell membrane made of a fibrous carbohydrate called cellulose. Animal and plant cells also have different tissues. A tissue is an aggregation of cells that are morphologically similar and perform the same task. For most plants, the outermost layer of cells forms a waxy cuticle that helps to protect the cells and to prevent water loss. Humans have skin, which is the outermost cell layer that is predominantly composed of a tough protein called keratin. Overall, humans have a diversity of tissue types (e.g., cartilage, brain, and heart). Figure 3.3: Plant cell compared to an animal cell. Credit: Simple plant and animal cell by Tomáš Kebert & umimeto.org has been modified (labels added) and is under a CC BY-NC-SA 4.0 License. [Image Description]. Animal Cell Organelles An animal cell is surrounded by a double membrane called the phospholipid bilayer (Figure 3.4). A closer look reveals that this protective barrier is made of lipids and proteins that provide structure and function for cellular activities, such as regulating the passage of molecules and ions (e.g., H2O and sodium) into and out of the cell. Cytoplasm is the jelly-like matrix inside of the cell membrane. Part of the cytoplasm comprises organelles, which perform different specialized tasks for the cell (Figure 3.5). An example of an organelle is the nucleus, where the cell’s DNA is located. Figure 3.4: A phospholipid bilayer with membrane-bound carbohydrates and proteins. Credit: Cell Membrane (Anatomy & Physiology, Figure 3.4) by OpenStax is under a CC BY 4.0 License. [Image Description]. Figure 3.5: An animal cell with membrane-enclosed organelles. Credit: Organelle by NIH National Human Genome Research Institute is in the public domain. [Image Description]. Another organelle is the mitochondrion. Mitochondria are often referred to as “powerhouse centers” because they produce energy for the cell in the form of adenosine triphosphate (ATP). Depending on the species and tissue type, multicellular eukaryotes can have hundreds to thousands of mitochondria in each of their cells. Scientists have determined that mitochondria were once symbiotic prokaryotic organisms (i.e., helpful bacteria) that transformed into cellular organelles over time. This evolutionary explanation helps explain why mitochondria also have their own DNA, called mitochondrial DNA (mtDNA). All organelles have important physiological functions and disease can occur when organelles do not perform their role optimally. Figure 3.6 lists other organelles found in the cell and their specialized cellular roles. Cell structure Description Assist with the organization of mitotic spindles, which extend and contract for the Centrioles purpose of cellular movement during mitosis and meiosis. Gelatinous fluid located inside of cell Cytoplasm membrane that contains organelles. Continuous membrane with the nucleus that Endoplasmic helps transport, synthesize, modify, and fold reticulum (ER) proteins. Rough ER has embedded ribosomes, whereas smooth ER lacks ribosomes. Layers of flattened sacs that receive and Golgi body transmit messages from the ER to secrete and transport proteins within the cell. Located in the cytoplasm; contains enzymes Lysosome to degrade cellular components. Involved with cellular movement including Microtubule intracellular transport and cell division. Responsible for cellular respiration, where Mitochondrion energy is produced by converting nutrients into ATP. Resides inside of the nucleus and is the site of Nucleolus ribosomal RNA (rRNA) transcription, processing, and assembly. Pores in the nuclear envelope that are Nucleopore selectively permeable. Contains the cell’s DNA and is surrounded by Nucleus the nuclear envelope. Located in the cytoplasm and also the membrane of the rough endoplasmic Ribosome reticulum. Messenger RNA (mRNA) binds to ribosomes and proteins are synthesized. Figure 3.6: This table depicts the names of organelles and their cellular functions. Credit: Cell Structure table (Figure 3.11) original to Explorations: An Open Invitation to Biological Anthropology by Hayley Mann, Xazmin Lowman, and Malaina Gaddis is under a CC BY-NC 4.0 License. Introduction to Genetics Genetics is the study of heredity. Biological parents pass down their genetic traits to their offspring. Although children resemble their parents, genetic traits often vary in appearance or molecular function. For example, two parents with normal color vision can sometimes produce a son with red-green colorblindness. Patterns of genetic inheritance will be discussed in a later section. Molecular geneticists study the biological mechanisms responsible for creating variation between individuals, such as DNA mutations (see Chapter 4), cell division, and genetic regulation. Molecular anthropologists use genetic data to test anthropological questions. Some of these anthropologists utilize ancient DNA (aDNA), which is DNA that is extracted from anything once living, including human, animal, and plant remains. Over time, DNA becomes degraded (i.e., less intact), but specialized laboratory techniques can make copies of short degraded aDNA segments, which can then be reassembled to provide more complete DNA information. A recent example of an aDNA study is provided in Special Topic: Native American Immunity and European Diseases, and aDNA is also explored in Appendix D. DNA Structure The discovery, in 1953, of the molecular structure of deoxyribonucleic acid (DNA) was one of the greatest scientific achievements of all time. Using X-ray crystallography, Rosalind Franklin (Figure 3.7) provided the image that clearly showed the double helix shape of DNA. However, due to a great deal of controversy, Franklin’s colleague and outside associates received greater publicity for the discovery. In 1962, James Watson, Francis Crick, and Maurice Wilkins received a Nobel Prize for developing a biochemical model of DNA. Unfortunately, Rosalind Franklin had passed away in 1958 from ovarian cancer. In current times, Franklin’s important contribution and her reputation as a skilled scientist are widely acknowledged. The double helix shape of DNA can be described as a twisted ladder (Figure 3.8). More specifically, DNA is a double-stranded molecule with its two strands oriented in opposite directions (i.e., antiparallel). Each strand is composed of nucleotides with a sugar phosphate backbone. There are four different types of DNA nucleotides: adenine (A), thymine (T), cytosine (C), and guanine (G). The two DNA strands are held together by nucleotide base pairs, which have chemical bonding rules. The complementary base- pairing rules are as follows: A and T bond with each other, while C and G form a bond. The chemical bonds between A-T and C-G are formed by “weak” hydrogen atom interactions, which means the two strands can be Figure 3.7: Chemist and X-ray crystallographer Rosalind easily separated. A DNA sequence is the order of nucleotide bases (A, T, G, Franklin. Credit: Rosalind C) along only one DNA strand. If one DNA strand has the sequence Franklin from the personal CATGCT, then the other strand will have a complementary sequence collection of Jenifer Glynn by GTACGA. This is an example of a short DNA sequence. In reality, there are MRC Laboratory of Molecular approximately three billion DNA base pairs in human cells. Biology is under a CC BY-SA 4.0 License. DNA Is Highly Organized within the Nucleus If you removed the DNA from a single human cell and stretched it out completely, it would measure approximately two meters (about 6.5 feet). Therefore, DNA molecules must be compactly organized in the nucleus. To achieve this, the double helix configuration of DNA undergoes coiling. An analogy would be twisting a string until coils are formed and then continuing to twist so that secondary coils are formed, and so on. To assist with coiling, DNA is first wrapped around proteins called histones. This creates a complex called chromatin, which resembles “beads on a string” (Figure 3.9). Next, chromatin is further coiled into a chromosome. Another important feature of Figure 3.8: Structural components that form DNA is that chromosomes can be altered from tightly coiled double-stranded nucleic acid (DNA). Credit: (chromatin) to loosely coiled (euchromatin). Most of the Difference DNA RNA-EN by Sponk (translation by Sponk, cropped by Katie Nelson) is under a time, chromosomes in the nucleus remain in a euchromatin CC BY-NC-SA 4.0 License. state so that DNA sequences are accessible for regulatory processes to occur. Figure 3.9: The hierarchical organization of chromosomes. Credit: Histone (2019) by NIH National Human Genome Research Institute is in the public domain. [Image Description]. Human body cells typically have 23 pairs of chromosomes, for a total of 46 chromosomes in each cell’s nucleus. An interesting fact is that the number of chromosomes an organism possesses varies by species, and this figure is not dependent upon the size or complexity of the organism. For instance, chimpanzees have a total of 48 chromosomes, while hermit crabs have 254. Chromosomes also have a distinct physical structure, including centromeres (the “center”) and telomeres (the ends) (Figure 3.10). Because of the centromeric region, chromosomes are described as having two different “arms,” where Figure 3.10: The regions of a chromosome. Credit: Chromosome one arm is long and the other is shorter. Centromeres play an (Figure 3.16) original to important role during cell division, which will be discussed in the next Explorations: An Open Invitation to section. Telomeres are located at the ends of chromosomes; they help Biological Anthropology by Katie protect the chromosomes from degradation after every round of cell Nelson is under a CC BY-NC 4.0 division. License. Special Topic: Native American Immunity and European Diseases— A Study of Ancient DNA Beginning in the early fifteenth century, Native Americans progressively suffered from high mortality rates as the result of colonization from foreign powers. European-borne diseases such as measles, tuberculosis, influenza, and smallpox are largely responsible for the population collapse of indigenous peoples in the Americas. Many Europeans who immigrated to the Americas had lived in large sedentary populations, which also included coexisting with domestic Figure 3.11a: Tsimshian Native Americans of the animals and pests. Although a few prehistoric Native Pacific Northwest Coast. Credit: A group of American populations can be characterized as large Tsimshian people having a tea party in a tent, agricultural societies (especially in Mesoamerica), their overall Lax Kw’alaams (formerly Port Simpson), B.C., c. culture, community lifestyle, and subsistence practices were 1890 by unknown photographer is in the Public markedly different from that of Europeans. Therefore, Domain. This image is available from the Library and Archives Canada, item number because they did not share the same urban living 3368729. environments as Europeans, it is believed that Native Americans were susceptible to many European diseases. In 2016, a Nature article published by John Lindo and colleagues was the first to investigate whether pre-contact Native Americans possessed a genetic susceptibility to European diseases. Their study included Tsimshians, a First Nation community from British Columbia (Figure 3.11a-b). DNA from both present-day and ancient individuals (who lived between 500 and 6,000 years ago) was analyzed. The research team discovered that a change occurred in the HLA-DQA1 gene, which is a member of the major histocompatibility complex (MHC) immune system molecules. MHC molecules are responsible for detecting and triggering an immune response against pathogens. Lindo and colleagues (2016) concluded that HLA- DQA1 gene helped Native Americans adapt to their local environmental ecology. However, when European- borne epidemics occurred in the Northwest during the 1800s, a certain HLA-DQA1 DNA sequence variant Figure 3.11b: Tsimshian territory in present-day British Columbia. Credit: (allele) associated with ancient Tsimshian Territory map (Figure 3.12b) original to Explorations: An Open Tsimshian immunity was no longer Invitation to Biological Anthropology by Elyssa Ebding at GeoPlace, adaptive. As the result of past selective California State University, Chico is under a CC BY-NC 4.0 License. pressures from European diseases, present-day Tsimshians have different HLA-DQA1 allele frequencies. The precise role that HLA-DQA1 plays in immune adaptation requires further investigation. But overall, this study serves as an example of how studying ancient DNA from the remains of deceased individuals can help provide insight into living human populations and historical events. DNA Replication and Cell Division For life to continue and flourish, cells must be able to divide. Tissue growth and cellular damage repair are also necessary to maintain an organism throughout its life. All these rely on the dynamic processes of DNA replication and the cell cycle. The mechanisms highlighted in this section are tightly regulated and represent only part of the life cycle of a cell. DNA Replication DNA replication is the process by which new DNA is copied from an original DNA template. It is one phase of the highly coordinated cell cycle, and it requires a variety of enzymes with special functions. The creation of a complementary DNA strand from a template strand is described as semi-conservative replication. The result of semi-conservative replication is two separate double-stranded DNA molecules, each of which is composed of an original “parent” template strand and a newly synthesized “daughter” DNA strand. DNA replication progresses in three steps referred to as initiation, elongation, and termination. During initiation, enzymes are recruited to specific sites along the DNA sequence (Figure 3.12). For example, an initiator enzyme, called helicase, “unwinds” DNA by breaking the hydrogen bonds between the two parent strands. The unraveling of the helix into two separated strands exposes the strands and creates a fork, which is the active site of DNA replication. Figure 3.12: DNA replication and the different enzymes associated with it. Credit: 0323 DNA Replication by OpenStax is under a CC BY 4.0 License. [Image Description]. Elongation is the assembly of new DNA daughter strands from the exposed original parent strands. The two parent strands can further be classified as leading strand or lagging strand and are distinguished by the direction of replication. Enzymes called DNA polymerases read parent template strands in a specific direction. Complementary nucleotides are added, and the newly formed daughter strands will grow. On the leading parent strand, a DNA polymerase will create one continuous strand. The lagging parent strand is created in several disconnected sections and other enzymes fill in the missing nucleotide gaps between these sections. Finally, termination refers to the end of DNA replication activity. It is signaled by a stop sequence in the DNA that is recognized by machinery at the replication fork. The end result of DNA replication is that the number of chromosomes are doubled so that the cell can divide into two. DNA Mutations DNA replication should result in the creation of two identical DNA nucleotide sequences. However, although DNA polymerases are quite precise during DNA replication, copying mistakes are estimated to occur every 107 DNA nucleotides. Variation from the original DNA sequence is known as a mutation. The different types of mutations will be discussed in greater detail in Chapter 4. Briefly, mutations can result in single nucleotide changes, as well as the insertion or deletion of nucleotides and repeated sequences. Depending on where they occur in the genome, mutations can be deleterious (harmful). For example, mutations may occur in regions that control cell cycle regulation, which can result in cancer (see Special Topic: The Cell Cycle and Immortality of Cancer Cells). Many other types of mutations, however, are not harmful to an organism. Regardless of their effect, the cell attempts to reduce the frequency of mutations that occur during DNA replication. To accomplish this, there are polymerases with proofreading capacities that can identify and correct mismatched nucleotides. These safeguards reduce the frequency of DNA mutations so that they only occur every 109 nucleotides. Mitotic Cell Division There are two types of cells in the body: germ cells (sperm and egg) and somatic cells. The body and its various tissues comprises somatic cells. Organisms that contain two sets of chromosomes in their somatic cells are called diploid organisms. Humans have 46 chromosomes and they are diploid because they inherit one set of chromosomes (n = 23) from each parent. As a result, they have 23 matching pairs of chromosomes, which are known as homologous chromosomes. As seen in Figure 3.13, homologous chromosome pairs vary in size and are generally numbered from largest (chromosome 1) to smallest (chromosome 22) with the exception of the 23rd pair, which is made up of the sex chromosomes (X and Y). Typically, the female sex is XX and the male sex is XY. Individuals inherit an X chromosome from their chromosomal mother and an X or Y from their chromosomal father. To grow and repair tissues, somatic cells must divide. As discussed previously, for cell division to occur, a cell must first replicate its genetic material. During DNA replication, each chromosome produces double the amount of genetic information. The duplicated arms of chromosomes are known as sister chromatids, and they are attached at the centromeric region. To Figure 3.13: The 23 human chromosome pairs. Credit: Genome elaborate, the number of chromosomes (2019) by NIH National Human Genome Research Institute is in stays the same (n = 46); however, the the public domain. amount of genetic material is doubled in the cell as the result of replication. Mitosis is the process of somatic cell division that gives rise to two diploid daughter cells. Figure 3.14 includes a brief overview of mitosis. Once DNA and other organelles in the cell have finished replication, mitotic spindle fibers physically align each chromosome at the center of the cell. Next, the spindle fibers divide the sister chromatids and move each one to opposite sides of the cell. At this phase, there are 46 chromosomes on each side of a human cell. The cell can now divide into two fully separated daughter cells. Figure 3.14: The steps of mitotic cell division and meiotic cell division. Credit: Mitosis and meiosis original to Explorations: An Open Invitation to Biological Anthropology (2nd ed.) by Katie Nelson is a collective work under a CC BY-NC 4.0 License. [Includes Mitosis (Figure 3.20) and Meiosis (Figure 3.21) by Mary Nelson; CC BY-NC 4.0 License.] Meiotic Cell Division Gametogenesis is the production of gametes (sperm and egg cells); it involves two rounds of cell division called meiosis. Similar to mitosis, the parent cell in meiosis is diploid. However, meiosis has a few key differences, including the number of daughter cells produced (four cells, which require two rounds of cell division to produce) and the number of chromosomes each daughter cell has (see Figure 3.14). During the first round of division (known as meiosis I), each chromosome (n = 46) replicates its DNA so that sister chromatids are formed. Next, with the help of spindle fibers, homologous chromosomes align near the center of the cell and sister chromatids physically swap genetic material. In other words, the sister chromatids of matching chromosomes cross over with each other at matching DNA nucleotide positions. The occurrence of homologous chromosomes crossing over, swapping DNA, and then rejoining segments is called genetic recombination. The “genetic shuffling” that occurs in gametes increases organismal genetic diversity by creating new combinations of genes on chromosomes that are different from the parent cell. Genetic mutations can also arise during recombination. For example, there may be an unequal swapping of genetic material that occurs between the two sister chromatids, which can result in deletions or duplications of DNA nucleotides. Once genetic recombination is complete, homologous chromosomes are separated and two daughter cells are formed. The daughter cells after the first round of meiosis are haploid, meaning they only have one set of chromosomes (n = 23). During the second round of cell division (known as meiosis II), sister chromatids are separated and two additional haploid daughter cells are formed. Therefore, the four resulting daughter cells have one set of chromosomes (n = 23), and they also have a genetic composition that is not identical to the parent cells nor to each other. Although both sperm and egg gamete production undergo meiosis, they differ in the final number of viable daughter cells. In the case of spermatogenesis, four mature sperm cells are produced. Although four egg cells are also produced in oogenesis, only one of these egg cells will result in an ovum (mature egg). During fertilization, an egg cell and sperm cell fuse, which creates a diploid cell that develops into an embryo. The ovum also provides the cellular organelles necessary for embryonic cell division. This includes mitochondria, which is why humans, and most other multicellular eukaryotes, have the same mtDNA sequence as their mothers. Chromosomal Disorders: Aneuploidies During mitosis or meiosis, entire deletions or duplications of chromosomes can occur due to error. For example, homologous chromosomes may fail to separate properly, so one daughter cell may end up with an extra chromosome while the other daughter cell has one less. Cells with an unexpected (or abnormal) number of chromosomes are known as aneuploid. Adult or embryonic cells can be tested for chromosome number (karyotyping). Aneuploid cells are typically detrimental to a dividing cell or developing embryo, which can lead to a loss of pregnancy. However, the occurrence of individuals being born with three copies of the 21st chromosome is relatively common; this genetic condition is known as Down Syndrome. Moreover, individuals can also be born with aneuploid sex chromosome conditions such as XXY, XXX, and XO (referring to only one X chromosome). Special Topic: The Cell Cycle and Immortality of Cancer Cells DNA replication is part of a series of preparatory phases that a cell undergoes prior to cell division, collectively known as interphase (Figure 3.15). During interphase, the cell not only doubles its chromosomes through DNA replication, but it also increases its metabolic capacity to provide energy for growth and division. Transition into each phase of the cell cycle is tightly controlled by proteins that serve as checkpoints. If a cell fails to pass a checkpoint, then DNA replication and/or cell division will not continue. Some of the reasons why a cell may fail at a checkpoint is DNA damage, lack of nutrients to continue the process, or insufficient size. In turn, a cell may undergo apoptosis, which is a mechanism for cell death. Figure 3.15: The phases and checkpoints of the cell cycle. Credit: Cell cycle (Biology 2e, Figure 10.5) by OpenStax is under a CC BY 4.0 License. [Image Description]. Unchecked cellular growth is a distinguishing hallmark of cancer. In other words, as cancer cells grow and proliferate, they acquire the capacity to avoid death and replicate indefinitely. This uncontrolled and continuous cell division is also known as “immortality.” As previously mentioned, most cells lose the ability to divide due to shortening of telomeres on the ends of chromosomes over time. One way in which cancer cells retain replicative immortality is that the length of their telomeres is continuously protected. Chemotherapy, often used to treat cancer, targets the cell cycle (especially cell division) to halt the propagation of genetically abnormal cells. Another therapeutic approach that continues to be investigated is targeting telomere activity to stop the division of cancer cells. Researchers have exploited the immortality of cancer cells for molecular research. The oldest immortal cell line is HeLa cells (Figure 3.16), which were harvested from Henrietta Lacks, an African American woman diagnosed with cervical cancer in 1955. At that time, extracted cells frequently died during experiments, but surprisingly HeLa cells continued to replicate. Propagation of Lacks’s cell line has significantly contributed to medical research, including contributing to ongoing cancer research and helping to test the polio vaccine in the 1950s. However, Lacks had not given her consent for her tumor Figure 3.16: A microscopic slide of HeLa cancer biopsy to be used in cell culture research. Moreover, her family cells. Credit: HeLa-III by National Institutes of was unaware of the extraction and remarkable application of Health (NIH) is in the public domain. her cells for two decades. The history of HeLa cell origin was first revealed in 1976. The controversy voiced by the Lacks family was included in an extensive account of HeLa cells published in Rebecca Skloot’s 2010 book, The Immortal Life of Henrietta Lacks. A film based on the book was also released in 2017 (Wolfe 2017). Protein Synthesis At the beginning of the chapter, we defined proteins as strings of amino acids that fold into complex 3-D shapes. There are 20 standard amino acids that can be strung together in different combinations in humans, and the result is that proteins can perform an impressive amount of different functions. For instance, muscle fibers are proteins that help facilitate movement. A special class of proteins (immunoglobulins) help protect the organism by detecting disease-causing pathogens in the body. Protein hormones, such as insulin, help regulate physiological activity. Blood hemoglobin is a protein that transports oxygen throughout the body. Enzymes are also proteins, and they are catalysts for biochemical reactions that occur in the cell (e.g., metabolism). Larger-scale protein structures can be visibly seen as physical features of an organism (e.g., hair and nails). Transcription and Translation Nucleotides in our DNA provide the coding instructions on how to make proteins. Making proteins, also known as protein synthesis, can be broken down into two main steps referred to as transcription and translation. The purpose of transcription, the first step, is to make an ribonucleic acid (RNA) copy of our genetic code. Although there are many different types of RNA molecules that have a variety of functions within the cell, we will mainly focus on messenger RNA (mRNA). Transcription concludes with the processing (splicing) of the mRNA. The second step, translation, uses mRNA as the instructions for chaining together amino acids into a new protein molecule (Figure 3.17). Unlike double- Figure 3.17: The major steps of protein stranded DNA, RNA synthesis. Credit: Protein synthesis molecules are single- original to Explorations: An Open stranded nucleotide Invitation to Biological Anthropology (2nd ed.) by Mary Nelson is under a sequences (Figure CC BY-NC 4.0 License. [Image 3.18). Additionally, Description]. while DNA contains the nucleotide thymine (T), RNA does not—instead its fourth nucleotide is uracil (U). Uracil is complementary to (or can pair with) adenine (A), while cytosine (C) and guanine (G) continue to be complementary to each other. For transcription to proceed, a gene must first be turned “on” by the cell. A gene is a segment of DNA that codes for RNA, and genes can vary in length from a few hundred to as many as two million base pairs in length. The double- stranded DNA is then separated, and one side of the DNA is Figure 3.18: Structural components that form used as a coding template that is read by RNA polymerase. ribonucleic acid (RNA). Credit: Difference DNA RNA-EN by Sponk (translation by Sponk, Next, complementary free-floating RNA nucleotides are cropped by Katie Nelson) is under a CC BY-NC- linked together (Figure 3.19) to form a single-stranded SA 4.0 License. [Image Description]. mRNA. For example, if a DNA template is TACGGATGC, then the newly constructed mRNA sequence will be AUGCCUACG. Genes contain segments called introns and exons. Exons are considered “coding” while introns are considered “noncoding”—meaning the information they contain will not be needed to construct proteins. When a gene is first transcribed into pre-mRNA, introns and exons are both included (Figure 3.20). However, once transcription is finished, introns are removed in a process called splicing. During splicing, a protein/RNA complex attaches itself to the pre-mRNA. Next, introns are removed and the remaining exons are connected, thus creating a shorter mature mRNA that serves as a template for building proteins. Figure 3.19: RNA polymerase catalyzing DNA transcription. Credit: Transcription (2019) by NIH National Human Genome Research Institute has been modified (cropped and labels changed by Katie Nelson) and is under a CC BY-NC 4.0 License. [Image Description]. Figure 3.20: RNA processing is the modification of RNA, including the removal of introns, called splicing, between transcription and translation. Credit: Protein synthesis (Figure 3.23) original to Explorations: An Open Invitation to Biological Anthropology by Mary Nelson is under a CC BY-NC 4.0 License. [Image Description]. As described above, the result of transcription is a single-stranded mRNA copy of a gene. Translation is the process by which amino acids are chained together to form a new protein. During translation, the mature mRNA is transported outside of the nucleus, where it is bound to a ribosome (Figure 3.21). The nucleotides in the mRNA are read in triplets, which are called codons. Each mRNA codon corresponds to an amino acid, which is carried to the ribosome by a transfer RNA (tRNA). Thus, tRNAs is the link between the mRNA molecule and the growing amino acid chain. Figure 3.21: Translation of mRNA into a polypeptide chain composed of the twenty different types of amino acids. Credit: Amino Acids by NIH National Human Genome Research Institute is in the public domain. [Image Description]. Continuing with our mRNA sequence example from above, the mRNA sequence AUG-CCU-ACG codes for three amino acids. Using a codon table (Figure 3.22), AUG is a codon for methionine (Met), CCU is proline (Pro), and ACG is threonine (Thr). Therefore, the protein sequence is Met-Pro-Thr. Methionine is the most common “start codon” (AUG) for the initiation of protein translation in eukaryotes. As the ribosome moves along the mRNA, the growing amino acid chain exits the ribosome and folds into a protein. When the ribosome reaches a “stop” codon (UAA, UAG, or UGA), the ribosome stops adding any new amino acids, detaches from the mRNA, and the protein is released. Depending upon the amino acid sequence, a linear protein may undergo additional “folding.” The final three-dimensional protein shape is integral to completing a specific structural or functional task. Dig Deeper: Protein Synthesis To see protein synthesis in animation, please check out the From DNA to Protein video on YourGenome.org. Figure 3.22: This table can be used to identify which mRNA codons (sequence of three nucleotides) correspond with each of the 20 different amino acids. For each mRNA codon, you work in the 5’ to 3’ direction (inside the circle to outside). For example, if the mRNA codon is CAU, you look at the inner circle for the “C,” the middle circle for “A,” and outside circle for “U,” indicating that the CAU codon corresponds with the amino acid “histidine” (abbreviated “His” or “H”). The table also indicates that the “start codon” (AUG) correlates with Methionine, and the three “stop” codons are UAA, UAG, and UGA. An accessible full text RNA codon to amino acid table is available. Credit: Aminoacids table by Mouagip has been designated to the public domain (CC0). Special Topic: Genetic Regulation of the Lactase (LCT) Gene The LCT gene codes for a protein called lactase, an enzyme produced in the small intestine. It is responsible for breaking down the sugar “lactose,” which is found in milk. Lactose intolerance occurs when not enough lactase enzyme is produced and, in turn, digestive symptoms occur. To avoid this discomfort, individuals may take lactase supplements, drink lactose-free milk, or avoid milk products altogether. The LCT gene is a good example of how cells regulate protein synthesis. The promoter region of the LCT gene helps regulate whether it is transcribed or not transcribed (i.e., turned “on” or “off,” respectively). Lactase production is initiated when a regulatory protein known as a transcription factor binds to a site on the LCT promoter. RNA polymerases are then recruited; they read DNA and string together nucleotides to make RNA molecules. An LCT pre-mRNA is synthesized (made) in the nucleus, and further chemical modifications flank the ends of the mRNA to ensure the molecule will not be degraded in the cell. Next, a spliceosome complex removes the introns from the LCT pre-mRNA and connects the exons to form a mature mRNA. Translation of the LCT mRNA occurs and the growing protein then folds into the lactase enzyme, which can break down lactose. Most animals lose their ability to digest milk as they mature due to the decreasing transcriptional “silence” of the LCT gene over time. However, some humans have the ability to digest lactose into adulthood (also known as “lactase persistence”). This means they have a genetic mutation that leads to continuous transcriptional activity of LCT. Lactase persistence mutations are common in populations with a long history of pastoral farming, such as northern European and North African populations. It is believed that lactase persistence evolved because the ability to digest milk was nutritionally beneficial. More information about lactase persistence will be covered in Chapter 14. Mendelian Genetics Gregor Johann Mendel (1822–1884) is often described as the “Father of Genetics.” Mendel was a monk who conducted pea plant breeding experiments in a monastery located in the present-day Czech Republic (Figure 3.23). After several years of experiments, Mendel presented his work to a local scientific community in 1865 and published his findings the following year. Although his meticulous effort was notable, the importance of his work was not recognized for another 35 years. One reason for this delay in recognition is that his findings did not agree with the predominant scientific viewpoints on inheritance at the time. For example, it was believed that parental physical traits “blended” together and offspring inherited an intermediate form of that trait. In contrast, Figure 3.23: Statue of Mendel located at the Mendel showed that certain pea plant physical traits (e.g., flower color) were Mendel Museum, located passed down separately to the next generation in a statistically predictable at Masaryk University in manner. Mendel also observed that some parental traits disappeared in Brno, Czech Republic. offspring but then reappeared in later generations. He explained this occurrence Credit: Mendel´s statue by introducing the concept of “dominant” and “recessive” traits. Mendel by Coeli has been designated to the public established a few fundamental laws of inheritance, and this section reviews domain (CC0). some of these concepts. Moreover, the study of traits and diseases that are controlled by a single gene is commonly referred to as Mendelian genetics. Figure 3.24: Various phenotypic characteristics of pea plants resulting from different genotypes. Credit: Mendels peas by Mariana Ruiz LadyofHats has been designated to the public domain (CC0 1.0). The physical appearance of a trait is called an organism’s phenotype. Figure 3.24 shows pea plant (Pisum sativum) phenotypes that were studied by Mendel, and in each of these cases the physical traits are controlled by a single gene. In the case of Mendelian genetics, a phenotype is determined by an organism’s genotype. A genotype consists of two gene copies, wherein one copy was inherited from each parent. Gene copies are also known as alleles (Figure 3.25), which means they are found in the same gene location on homologous chromosomes. Alleles have a nonidentical DNA sequence, which means their phenotypic effect can be different. In other words, although alleles code for the same trait, different phenotypes can be produced depending on which two alleles (i.e., genotypes) an organism possesses. For example, Mendel’s pea plants all have flowers, but their flower color can be purple or white. Flower color is therefore dependent upon which two color alleles are present in a genotype. Figure 3.25: Homozygous refers to having the same alleles (e.g. two capital Bs or two lowercase bs). Heterozygous refers to having two different alleles (e.g. one capital B and one lowercase b). Credit: Homozygous by NIH National Human Genome Research Institute is in the public domain. A Punnett square is a diagram that can help visualize Mendelian inheritance patterns. For instance, when parents of known genotypes mate, a Punnett square can help predict the ratio of Mendelian genotypes and phenotypes that their offspring would possess. When discussing genotype, biologists use upper and lower case letters to denote the different allele copies. Figure 3.26 is a Punnett square that includes two heterozygous parents for flower color (Bb). A heterozygous genotype means there are two different alleles for the same gene. Therefore, a pea plant that is heterozygous for flower color has one purple allele and one white allele. When an organism is homozygous for a specific trait, it means their genotype consists of two copies of the same allele. Using the Punnett square example, the two heterozygous pea plant parents can produce offspring with two different homozygous genotypes (BB or bb) or offspring that are heterozygous (Bb). A pea plant with purple flowers could be heterozygous (Bb) or homozygous (BB). This is because the purple color allele (B) is dominant to the white color allele (b), and therefore it only needs one copy of that allele to phenotypically express purple flowers. Because the white flower allele is recessive, a pea plant must be homozygous for the recessive allele in order to have a white color phenotype (bb). As seen by the Punnett square example (Figure 3.26), three of four offspring will have purple flowers and the other one will have white flowers. Figure 3.26: Punnett square depicting the possible genetic The Law of Segregation was introduced by Mendel to explain why we can combinations of offspring predict the ratio of genotypes and phenotypes in offspring. As discussed from two heterozygous previously, a parent will have two alleles for a certain gene (with each copy parents. Credit: Punnett square mendel flowers by on a different homologous chromosome). The Law of Segregation states Madeleine Price Ball that the two copies will be segregated from each other and will each be (Madprime) is under a CC BY- distributed to their own gamete. We now know that the process where SA 3.0 License. [Image that occurs is meiosis. Description]. Offspring are the products of two gametes combining, which means the offspring inherits one allele from each gamete for most genes. When multiple offspring are produced (like with pea plant breeding), the predicted phenotype ratios are more clearly observed. The pea plants Mendel studied provide a simplistic model to understand single-gene genetics. While many traits anthropologists are interested in have a more complicated inheritance (e.g., are informed by many genes), there are a few known Mendelian traits in humans. Additionally, some human diseases also follow a Mendelian pattern of inheritance (Figure 3.27). Because humans do not have as many offspring as other organisms, we may not recognize Mendelian patterns as easily. However, understanding these principles and being able to calculate the probability that an offspring will have a Mendelian phenotype is still important. Mendelian disorder Gene Alpha Thalassemia HBA1 Cystic Fibrosis CFTR Fragile X Syndrome FMR1 Glucose-6-Phosphate Dehydrogenase G6PD Deficiency Hemophilia A F8 Huntington disease HTT Mitochondrial DNA Depletion Syndrome TYMP Oculocutaneous Albinism: Type 1 TYR Polycystic Kidney Disease PKHD1 Sickle-cell anemia HBB Spinal Muscular Atrophy: SMN1 Linked SMN1 Tay-Sachs Disease HEXA Wilson Disease ATP7B Figure 3.27: Examples of human diseases with their gene names that follow a Mendelian pattern of inheritance. Example of Mendelian Inheritance: The ABO Blood Group System In 1901, Karl Landsteiner at the University of Vienna published his discovery of ABO blood groups. While conducting blood immunology experiments in which he combined the blood of individuals who possess different blood cell types, he observed an agglutination (clotting) reaction. The presence of agglutination implies there is an incompatible immunological reaction; no agglutination will occur in individuals with the same blood type. This work was clearly important because it resulted in a higher survival rate of patients who received blood transfusions. Blood transfusions from someone with a different type of blood causes agglutinations, and the resulting coagulated blood can not easily pass through blood vessels, resulting in death. Landsteiner received the Nobel Prize (1930) for his discovery and explaination of the ABO blood group system. Blood cell surface antigens are proteins that coat the surface of red blood cells, and antibodies are specifically “against” or “anti” to the antigens from other blood types. Thus, antibodies are responsible for causing agglutination between incompatible blood types. Understanding the interaction of antigens and antibodies helps to determine ABO compatibility amongst blood donors and recipients. To better comprehend blood phenotypes and ABO compatibility, blood cell antigens and plasma antibodies are presented in Figure 3.28. Individuals that are blood type A have A antigens on the red blood cell surface, and anti-B antibodies, which will bind to B antigens should they come in contact. Alternatively, individuals with blood type B have B antigens and anti-A antibodies. Individuals with blood type AB have both A and B antigens but do not produce antibodies for the ABO system. This does not mean type AB does not have any antibodies present, just that specifically anti-A and anti-B antibodies are not produced. Individuals who are blood type O have nonspecific antigens and produce both anti-A and anti- B antibodies. Figure 3.28: The different ABO and Rhesus blood types with their associated antibodies and antigens. Credit: Different Blood Types by Michael540170 has been modified (antibodies images swapped) and is under a CC BY-NC-SA 4.0 License. [Image Description]. Figure 3.29 shows a table of the ABO allele system, which has a Mendelian pattern of inheritance. Both the A and B alleles function as dominant alleles, so the A allele always codes for the A antigen, and the B allele codes for the B antigen. The O allele differs from A and B, because it codes for a nonfunctional antigen protein, which means there is no antigen present on the cell surface of O blood cells. To have blood type O, two copies of the O allele must be inherited, one from each parent, thus the O allele is considered recessive. Therefore, someone who is a heterozygous AO genotype is phenotypically blood type A, and a genotype of BO is blood type B. The ABO blood system also provides an example of codominance, which is when both alleles are observed in the phenotype. This is true for blood