Asbestos Hazard Emergency Response Act

Problems which led to this act.

• Asbestos was turning up in schools all over the country.

• This posed a serious health risks to our nation’s greatest resource, the children.

• There was a lack of guidance from the EPA concerning asbestos disposal and regulation of it at the time.

Cont…..

• Asbestos is quite costly to remove, and with the educational system in our country being severely under-funded many corners are cut, and many stones are left unturned.

• It kills people.

What is asbestos?

• Asbestos is a naturally occurring mineral fiber found in metamorphic rocks.

• It has great fire, heat, and chemical resistant properties.

• With its relative low cost and good physical strength, asbestos was commonly used textile, friction, cement, paper, and insulation, along with many other products.

• Many of these products can be found in almost any building built in America.

Potential Health Risks

• Asbestosis—a long-term, chronic and debilitating lung disease caused by long- term, uncontrolled exposures to asbestos.

• Mesothelioma—a rare cancer of the chest and abdominal lining.

• Also, cancers of the lung, esophagus, stomach and colon have been attributed to asbestos.

Just the facts…

• Asbestos containing building materials (ACBMs) only pose a health risk when damaged, releasing their deadly fibers into the breathable zone.

• The fed. Gov. estimates that more than 40,000 school building and 700,000 public schools contain ACBMs.

• Also, millions of American’s homes contain these deadly materials.

The Purpose of this Act

• To provide a well-drawn map for weeding out potential asbestos infected schools.

• To establish Federal regulations which require the inspection of asbestos containing materials.

• And if such asbestos exists, to implement steps of removing the ACBMs, provided that it is done in a safe and healthful manner.

• Require the Administrator to study the effects of asbestos and to find the extent of danger that it poses to the American public.

Who’s in charge?

• The Administrator of the Environmental Protection Agency.

• It is the Administrator’s responsibility to insure the safety of our nation’s children.

• To assist in the motivation of our schools a civil penalty of 5,000 will be assessed.

Regulations • Sec .203. “15 USC 2643” EPA Regulations • (c) Circumstances Requiring Response actions.

– (1) The administrator shall promulgate regulations which define the appropriate response action in a school building under the authority of a local educational agency in at least the following circumstances:

(A) Damage – Circumstances in which friable ….. (B) Significant Damage – ….ACM or its covering… (C) Potential Damage — …(i) friable ACM is in an

area regularly used by building occupants….

To Sum it Up…

• Asbestos is a poison that has been known to be deadly since the 30’s. It’s a sad fact that we are still finding such a deadly chemical in many aspects of our lives; where we work, where we live, and most importantly where are kids go to better themselves. This Act has and will continue to provide the nation’s most precious resource, the children, a safe and healthful learning environment.

EXPLORATIONS: AN OPEN INVITATION TO BIOLOGICAL ANTHROPOLOGY

Editors: Beth Shook, Katie Nelson, Kelsie Aguilera and Lara Braff

American Anthropological Association Arlington, VA

2019

CC BY-NC 4.0 International, except where otherwise noted

ISBN – 978-1-931303-63-7

www.explorations.americananthro.org

Chapter 3: Molecular Biology and Genetics:

Hayley Mann, M.A., Binghamton University

Xazmin Lowman, Ph.D., University of California, Irvine

Malaina Gaddis, Ph.D.

Learning Objectives

• Define terms useful to molecular biology and genetics.

• 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.

Since the release of the first human genome sequence, the field of genetics has grown into genomics. Researchers now address these complex questions on a large scale. To process “big data,” some scientists have moved to working on a

computer full time doing computational biology. As you learned in Chapter 1, molecular anthropologists use genetics

to compare ancient and modern populations as well as study nonhuman primates. Molecular anthropologists must also

stay current with advancing technology you will learn about the results of some of this genomic research as it has been

applied to fossils in Chapters 11 and 12). If you wish to be part of this dynamic field, then take advantage of available

campus laboratory classes and internships and also never stop reading scientific papers.

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.

58 | Molecular Biology and Genetics

CELLS AND MOLECULES

Molecules of Life

Figure 3.1 Phospholipid molecules forming a bilayer with their hydrophobic tails and hydrophilic heads.

Organisms are composed of four basic types of molecules

that are essential for cell structure and function: proteins, lipids, carbohydrates, and nucleic acids. Proteins are strings of amino acids that are often folded into complex

3-D shapes. The structure of lipids can be described as having a hydrophilic water-loving) head and a

hydrophobic water-repelling) tail Figure 3.1). When

lipids are chained together, they form more-complex

molecules called fats and triglycerides. Carbohydrates are composed of carbon and hydrogen atoms that can be

broken down to supply energy for an organism. Lastly,

nucleic acids carry genetic information about a living organism.

Probably the most familiar nucleic acid is

deoxyribonucleic acid (DNA). DNA comprises a sugar phosphate backbone and nucleotides Figure 3.2). More details on the physical structure of DNA and what

information DNA nucleotides provide will be discussed

later.) Anthropologists can analyze sequences of DNA

nucleotides and determine how different organisms are

related to each other, since they all have their own unique

DNA genetic code. In the case of humans, forensic scientists can identify individuals by analyzing 20

different short DNA sequences known as “CODIS Core Loci.” Another nucleic acid is called ribonucleic acid (RNA). One type of RNA molecule is responsible for chaining amino acids together in order to build proteins

Figure 3.3 and Figure 3.4). How RNA synthesizes amino

acids into proteins will be reviewed further on in the

chapter.

Figure 3.2 Structural components that form double-stranded nucleic acid (DNA) or single-stranded nucleic acid (RNA).

Molecular Biology and Genetics | 59

Figure 3.3 Chemical elements that characterize an amino acid. C: carbon; N: Nitrogen; O: Oxygen; H: Hydrogen.

Figure 3.4 Amino acids (20 different types) strung together form a polypeptide chain.

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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 3.5 A representation of the single-celled body of E. coli bacteria.

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

Figure 3.5). 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 bacterial sexually transmitted disease. Although bacteria are commonly associated with illness, not all bacteria are harmful. For example, 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 food digestion, boosting the immune system, and even making vitamins e.g., B12 and K).

Molecular Biology and Genetics | 61

Archaea, the other type of prokaryotic organism, were

once believed to be closely related to bacteria. However,

it was determined through genetic analysis that archaea

have their own distinct evolutionary lineage so biologists

reclassified them into their own taxonomic domain.

Archaea were discovered living in extreme environments

and are therefore known as “extremophiles.” For example,

archaea can be found in high temperatures, such as Old

Faithful Geyser in Yellowstone National Park.

Eukaryotes can be single-celled or multicelled 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. For example,

plant cells possess a thick outer cell membrane made of a fibrous carbohydrate called cellulose Figure 3.6). 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. However, humans have skin, the outermost cell layer of which is mostly composed of a tough protein

called keratin. Overall, humans have a diversity of tissue types e.g., cartilage, brain, and heart).

Figure 3.6 A microscopic view of plant cell membranes.

Animal Cell Organelles

Figure 3.7 A phospholipid bilayer with membrane-bound carbohydrates and proteins.

62 | Molecular Biology and Genetics

An animal cell is surrounded by a double membrane called the phospholipid bilayer Figure 3.7). A closer look reveals that this protective barrier is made of lipids and proteins that provide structure and function for cellular activities. For

example, lipids and proteins embedded in the cell’s membrane work together to regulate 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 3.8). An example of

an organelle is the nucleus, where the cell’s DNA is located Figure 3.9). The double membrane that encloses the nucleus is known as the nuclear envelope; its purpose is to regulate molecules into and out of the nucleus and serve as a barrier to protect DNA integrity.

Figure 3.8 An animal cell with membrane-enclosed organelles.

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Figure 3.9 A membrane-enclosed nucleus of an animal cell.

Another important organelle is the mitochondrion Figure 3.10). 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 played an important role in the evolution of the eukaryotic cell.

Mitochondria were once symbiotic prokaryotic organisms i.e., helpful bacteria) that transformed into cellular organelles over time. Because mitochondria used to be separate organisms, this explains why mitochondria also have their own

DNA, called mitochondrial DNA (mtDNA). All organelles have important physiological functions, and when they cannot perform their role optimally, it can result in disease. For example, there are mitochondrial diseases for which cells have

abnormally less mitochondria. In humans, this leads to various neurological symptoms and disorders. Figure 3.11 lists

other organelles found in the cell and their specialized cellular roles.

Figure 3.10 Microscopic view of an animal mitochondrion organelle.

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Cell structure Description

Cytoplasm Fluid substance located inside of cell membrane that contains organelles

Nucleopore Pores in the nuclear envelope that are selectively permeable

Nucleus Contains the cell’s DNA and is surrounded by the nuclear envelope

Nucleolus Resides inside of the nucleus and is the site of ribosomal RNA rRNA) transcription, processing, and assembly

Mitochondrion Responsible for cellular respiration, where energy is produced by converting nutrients into ATP

Ribosome Located in the cytoplasm and also the membrane of the rough endoplasmic reticulum. Messenger RNA mRNA) binds to ribosomes and proteins are synthesized

Endoplasmic reticulum ER)

Continuous membrane with the nucleus that helps transport, synthesize, modify, and fold proteins. Rough ER has embedded ribosomes, whereas smooth ER lacks ribosomes

Golgi body Layers of flattened sacs that receive and transmit messages from the ER to secrete and transport proteins within the cell

Lysosome Located in the cytoplasm and contains enzymes to degrade cellular components

Microtubule Involved with cellular movement including intracellular transport and cell division

Centrioles Assist with the organization of mitotic spindles which extend and contract for the purpose of cellular movement during mitosis and meiosis

Figure 3.11 Names of organelles and their cellular functions.

INTRODUCTION TO GENETICS

Genetics is the study of heredity. Parents pass down their genetic traits to their offspring. Although children resemble

their parents, 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. Although their interests are diverse,

areas of molecular anthropology research include the following: human origins, dispersals, evolution, adaptation,

demography, health, disease, behavior, and animal domestication. In addition to conducting research in a laboratory,

Molecular Biology and Genetics | 65

molecular anthropologists also work in the field with different communities of people. Some anthropologists also study

DNA from individuals who have been deceased for decades—even hundreds or thousands of years. The study of ancient DNA (aDNA) has led to the development of specialized laboratory techniques. Over time, the DNA in skeletons of ancient individuals becomes degraded i.e., less intact), which is why careful methodological considerations must be taken. A

recent example of an aDNA study is provided in Special Topic: Native American Immunity and European Diseases, and

another will be presented in Chapter 10.

SPECIAL TOPIC: FOCUS ON NATIVE AMERICAN IMMUNITY AND EUROPEAN DISEASES—A STUDY OF ANCIENT DNA

Figure 3.12a Tsimshian Native Americans of the Pacific Northwest Coast.

Beginning in the early 15th 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 New World had lived in large sedentary populations,

which also included coexisting with domestic animals and pests. Although a few prehistoric Native American

populations can be characterized as large agricultural societies especially in Mesoamerica), their overall

culture, community lifestyle, and subsistence practices were markedly different from that of Europeans.

Therefore, because they did not share the same urban living environments as Europeans, it is believed that

Native Americans were susceptible to old-world diseases.

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Figure 3.12b Tsimshian territory in present-day British Columbia.

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 3.12). The 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 genetic region HLADQ-1, which is a

member of the major histocompatibility complex

MHC) immune system molecules. These molecules

are responsible for detecting and triggering an

immune response against pathogens. Lindo and

colleagues 2016) concluded that HLADQ-1 helped

Native Americans adapt to their local environmental

ecology. However, when European-borne epidemics

occurred in the Northwest during the 1800s, a

certain HLADQ-1 DNA sequence associated with

ancient Tsimshian immunity was no longer adaptive.

As the result of past selective pressures from

European diseases, present-day Tsimshians have a different frequency of HLADQ-1 sequences. The precise

role that HLADQ-1 plays in immune adaptation still 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 Carries Hereditary Information

Surprisingly, the study of inheritance preceded the discovery of DNA. For a period of time, it was believed that proteins

carried the hereditary information passed from parents to offspring. Then, in 1944, Oswald Avery, Colin MacLeod, and

Maclyn McCarty discovered an association between extracted nucleic acids and the success of their bacterial genetic

experiments. Specifically, they demonstrated that DNA was the molecule responsible for the genetic transformation

of their pneumonia bacterial strains. Although this was revolutionary work at the time, the field of molecular biology

did not fully embrace their findings it has also been suggested that they were overlooked for a Nobel Prize). It was

eventually accepted by the scientific community that DNA is the hereditary material of an organism, especially after the

chemical structure of DNA was revealed.

Molecular Biology and Genetics | 67

DNA Structure

The 1953 discovery of the molecular structure of DNA was one of

the greatest scientific achievements of all time. Using X-ray

crystallography, Rosalind Franklin Figure 3.13) 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

refer back to Figure 3.2). 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

easily separated. A DNA sequence is the order of nucleotide bases A, T, G, C) along only one DNA strand. If one DNA

strand has the sequence CATGCT, then the other strand will have a complementary sequence GTACGA. This is an

example of a short DNA sequence. In reality, there are approximately three billion DNA base pairs in human cells.

Figure 3.13 Chemist and X-ray crystallographer Rosalind Franklin.

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 3.14). Next, chromatin is further coiled into a chromosome. Another important feature of DNA is that chromosomes can be altered from tightly coiled chromatin) to loosely coiled euchromatin). Most of the time, chromosomes in the nucleus remain in a euchromatin state so that DNA sequences are accessible for regulatory processes to occur.

68 | Molecular Biology and Genetics

Figure 3.14 The hierarchical organization of chromosomes.

Human body cells typically have 23 pairs of chromosomes, for a total of 46 chromosomes in each cell’s nucleus Figure

3.15). An interesting fact is that the number of chromosomes an organism possesses varies, 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 “centers”) and telomeres the ends) Figure 3.16). Because of centromeres, chromosomes are described as having two different “arms,” where one arm is long and the other is shorter. Centromeres play an important role during cell division, which

will be discussed in the next section. Telomeres are located at the ends of chromosomes and they help protect the

chromosomes from degradation after every round of cell division. However, our telomeres become shorter as we age,

and if chromosome telomeres become too short, then the cell will stop dividing. Therefore, the link between the

regulation of telomere length and cellular aging is of great interest to researchers.

Molecular Biology and Genetics | 69

Figure 3.15 The 23 human chromosome pairs. DNA

Figure 3.16 The regions of a chromosome.

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 requires a variety of enzymes with special functions. Specifically, enzymes carry

out the structural and high-energy reactions associated with replicating a double helical molecule. 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. Initiation denotes the start of DNA replication by recruiting enzymes to specific sites along the DNA sequence. For example, the double helix

of DNA presents structural challenges for replication, so 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 creates a

fork, which is the active site of replication machinery Figure 3.17). Once both strands are separated, the parent template

strands are exposed, meaning they can be read and replicated.

70 | Molecular Biology and Genetics

Figure 3.17 The different enzymes associated with DNA replication.

Elongation describes the assembly of new DNA daughter strands from parent strands. The two parent strands can

further be classified as leading strand or lagging strand and are distinguished by the continuous or discontinuous direction of replication, respectively. A short fragment of RNA nucleotides acts as a primer, which binds to the parent DNA strand that will be copied. The leading strand receives one primer and the lagging strand receives several.

Elongation proceeds with help from enzymes called DNA polymerases, which read parent template strands in a specific direction. Complementary nucleotides are added, and the newly formed daughter strand will grow. The direction in

which replication proceeds depends on whether it is the leading or lagging strand. On the leading parent strand, a DNA

polymerase will create one continuous strand. Because the lagging parent strand requires several primers, disjointed

strands called Okazaki fragments) will be generated. Other enzymes will fill in the missing nucleotide gaps between the disconnected lagging strand Okazaki fragments.

Finally, termination refers to the end of DNA replication activity. It is signaled by a stop sequence in the DNA, which 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 molecules with identical DNA nucleotide sequences. 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, 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 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.

Molecular Biology and Genetics | 71

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.

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 3.18). 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 3.18 The phases and checkpoints of the cell cycle.

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 discussed, 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

is often used to treat cancer by targeting cell division, which halts the propagation of genetically abnormal

72 | Molecular Biology and Genetics

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 3.19), which was 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 ongoing cancer

research and helping to test the polio vaccine in the 1950s.

Unfortunately, Lacks had not given her consent for her tumor

biopsy to be used in cell culture research. Moreover, her family

was unaware of the extraction and remarkable application of

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.

Figure 3.19 A microscopic slide of HeLa cancer cells.

Mitotic Cell Division

The body and its various tissues are comprised of 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. These homologous pairs vary in size and are generally numbered from largest chromosome 1) to smallest chromosome 22), as seen in Figure 3.15, 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 mother and an X or Y from their father.

In order to grow and repair tissues, somatic cells must divide. As discussed previously, a cell must first replicate its

genetic material for cell division to occur. 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 elaborate, the number of chromosomes stays the same n = 46); however, the 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 3.20 shows a brief overview of mitosis. Once DNA and other organelles in the cell have finished replication, mitotic spindle fibers

microtubules) assist with chromosomal movement by attaching to the centromeric region of each chromosome.

Specifically, the 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 the cell. The cell can now divide into two fully separated daughter cells.

Molecular Biology and Genetics | 73

Figure 3.20 Steps of mitotic cell division.

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 Figure 3.21). 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.

Figure 3.21 Meiotic cell division.

74 | Molecular Biology and Genetics

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

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, human males and females can be born with aneuploid sex

chromosome conditions such as XXY, XXX, and XO referring to only one X chromosome).

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 orders 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

Coding nucleotides in our DNA provide 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. Protein synthesis relies on many molecules in the cell including different types of regulatory proteins and RNAs for each step in the process.

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).

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 purpose of transcription is to make an RNA copy of that genetic code Figure

3.22). Unlike double-stranded DNA, RNA molecules are single-stranded nucleotide sequences refer back to Figure

3.2). Additionally, 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

Molecular Biology and Genetics | 75

complementary to each other. For transcription to proceed, a gene must first be turned “on” by the cell see Special

Topic: Genetic Regulation of the Lactase LCT) Gene for a more detailed discussion of gene regulation). The double- stranded DNA is then separated, and one side of the DNA strand is used as a template where complementary RNA

nucleotides are strung together. For example, if a DNA template is TACGGATGC, then the newly constructed mRNA

sequence will be AUGCCUACG. Sometimes the end product needed by the cell is that transcribed RNA, but for protein

synthesis constructing the RNA specifically pre-messenger RNA, or pre-mRNA) is just the first step.

Figure 3.22 RNA polymerase catalyzing DNA transcription.

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 3.23). 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 and removes introns and then connects the remaining exons, thus creating a shorter mature mRNA.

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Figure 3.23 RNA processing is the modification of RNA, including the removal of introns, called splicing, between transcription and translation.

The process by which mRNA is “read” and amino acids chained together to form new proteins is called translation.

During translation, mature mRNA is transported outside of the nucleus where it is bound to a ribosome Figure 3.24). The nucleotides in the mRNA are read as triplets, which are called codons. Each codon corresponds to an amino acid, and this is the basis for building a protein. Continuing with our example from above, the mRNA sequence AUG-CCU-

ACG codes for three amino acids. Using a codon table Figure 3.25), 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 Figure 3.26). When the ribosome reaches a “stop”

codon UAA, UAG, or UGA), the ribosome stops adding new amino acids, detaches from the mRNA, and the protein is

released. Folded proteins can then be used to complete a structural or functional task.

Figure 3.24 Translation of mRNA into an amino acid.

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Figure 3.25 This table can be used to identify which mRNA codons (sequence of three nucleotides) correspond with each of the 20 different amino acids. For example, if the codon is CAU, the first position is “C” and you would look in that corresponding row, the second position is “A” and you would look in that column. “U’ is the third position—narrowing the row and indicating that the CAU codon corresponds with the amino acid “histidine” (abbreviated “His”). The table also indicates the most common “start codon” (AUG) that correlates with Methionine, and the three “stop” codons (UAA, UAG, or UGA).

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Figure 3.26 Indicates levels of protein organization from the simple amino acid chain that is then folded and organized into more complex protein structures.

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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” 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 Figure 3.22). 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, RNA processing occurs. A spliceosome complex removes the introns and connects exons to form

the mature mRNA. Once the LCT mRNA is transported outside of the nucleus, it is bound to a ribosome,

which is a multi-protein complex that includes ribosomal RNA (rRNA). The ribosome of eukaryotes has two main subunits: the smaller bottom subunit that binds to the mRNA and the larger top subunit that contains

transfer RNA (tRNA) binding sites see Figure 3.24). Each tRNA has a nucleotide anticodon that recognizes an mRNA codon. When a tRNA binds to an mRNA codon in the ribosome, the tRNA transfers the corresponding

amino acid. rRNA ensures the newly added amino acid is linked in the correct order. 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.

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MENDELIAN GENETICS AND OTHER PATTERNS OF INHERITANCE

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 3.27). 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, Mendel showed that certain pea plant physical traits e.g.,

flower color) were passed down separately to the next generation in a

statistically predictable manner. Mendel also observed that some

parental traits disappeared in offspring but then reappeared in later generations. He explained this occurrence by

introducing the concept of “dominant” and “recessive” traits. Mendel established a few fundamental laws of inheritance,

and this section reviews 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 3.27 Statue of Mendel located at the Mendel Museum located at Masaryk University in Brno, Czech Republic.

Mendelian Genetics

Figure 3.28 Various phenotypic characteristics of pea plants resulting from different genotypes.

The physical appearance of a trait is called an organism’s phenotype. Figure 3.28 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 3.29), which means they are found in the same gene location on homologous chromosomes. Alleles have a nonidentical DNA

Molecular Biology and Genetics | 81

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 3.29 Homologous chromosome pairs showing the different homozygous and heterozygous combinations that can exist from two different alleles (B and b).

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. Figure 3.30 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 Figure 3.30),

the two heterozygous pea plant parents can produce offspring with two different homozygous genotypes BB or bb) or

offspring that are heterozygous Bb).

Figure 3.30 Punnett square depicting the possible genetic combinations of offspring from two heterozygous parents.

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 3.30), three of four offspring will have purple flowers and

the other one will have white flowers.

The Law of Segregation was introduced by Mendel to explain why we can predict the ratio of genotypes and phenotypes in offspring. As discussed

previously, a parent will have two alleles for a certain gene with each copy

on a different homologous chromosome). The Law of Segregation states

that the two copies will be segregated from each other and will each be

distributed to their own gamete. We now know that the process where that

occurs is meiosis.

Offspring are the products of two gametes combining, which means the offspring inherits one allele from each gamete

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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 3.31). 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 Mendelian disorder Gene

Alpha Thalassemia HBA1 Maple Syrup Urine Disease: Type 1A BCKDHA

Androgen Insensitivity Syndrome AR Mitochondrial DNA Depletion Syndrome TYMP

Bloom Syndrome BLM MTHFR Deficiency MTHFR

Canavan Disease ASPA Oculocutaneous Albinism: Type 1 TYR

Cartilage-Hair Hypoplasia RMRP Oculocutaneous Albinism: Type 3 TYRP1

Cystic Fibrosis CFTR Persistent Mullerian Duct Syndrome: Type I AMH

Familial Chloride Diarrhea SLC26A3 Polycystic Kidney Disease PKHD1

Fragile X Syndrome FMR1 Sickle-cell anemia HBB

Glucose-6-Phosphate Dehydrogenase Deficiency G6PD Spermatogenic failure USP9Y

Hemophilia A F8 Spinal Muscular Atrophy: SMN1 Linked SMN1

Huntington disease HTT Tay-Sachs Disease HEXA

Hurler Syndrome IDUA Wilson Disease ATP7B

Figure 3.31 Human diseases 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. This was a result

of conducting blood immunology experiments in which he combined the blood of individuals who possess different

blood cell types and observed an agglutination clotting) reaction. The presence of agglutination implies there is an

incompatible immunological reaction, whereas 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.

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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. Accordingly, Landsteiner received the Nobel Prize

1930) for explaining 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. In order to better understand blood phenotypes and ABO

compatibility, blood cell antigens and plasma antibodies are presented in Figure 3.32. Individuals that are blood type A

have A antigens on the red blood cell surface, and anti-B antibodies, which will bind with 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, just that anti-A or anti-B antibodies are not produced. Individuals who are blood type O have

nonspecific antigens but produce both anti-A and anti-B antibodies.

Figure 3.32 The different ABO blood types with their associated antibodies and antigens.

Figure 3.33 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

Figure 3.33 The different combinations of ABO blood alleles (A, B, and O) to form ABO blood genotypes.

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also provides an example of codominance, which is when the effect of both alleles is observed in the phenotype. This is true for blood type AB: when an individual inherits both the A and B alleles, then both A and B antigens will be present

on the cell surface.

Also found on the surface of red blood cells is the rhesus group antigen, known as “Rh factor.” In reality, there are

several antigens on red blood cells independent from the ABO blood system, however, the Rh factor is the second most

important antigen to consider when determining blood donor and recipient compatibility. Rh antigens must also be

considered when a pregnant mother and her baby have incompatible Rh factors. In such cases, a doctor can administer

necessary treatment steps to prevent pregnancy complications and hemolytic disease, which is when the mother’s

antibodies break down the newborn’s red blood cells.

An individual can possess the Rh antigen be Rh positive) or lack the Rh antigen be Rh negative). The Rh factor is

controlled by a single gene and is inherited independently of the ABO alleles. Therefore, all blood types can either be

positive O+, A+, B+, AB+) or negative O-, A-, B-, AB-).

Individuals with O+ red blood cells can donate blood to A+, B+, AB+, and O+ blood type recipients. Because O- individuals

do not have AB or Rh antigens, they are compatible with all blood cell types and are referred to as “universal donors.”

Individuals that are AB+ are considered to be “universal recipients” because they do not possess antibodies against other

blood types.

Mendelian Patterns of Inheritance and Pedigrees

A pedigree can be used to investigate a family’s medical history by determining if a health issue is inheritable and will

possibly require medical intervention. A pedigree can also help determine if it is a Mendelian recessive or dominant

genetic condition. Figure 3.34 is a pedigree example of a family with Huntington’s disease, which has a Mendelian

dominant pattern of inheritance. In a standard pedigree, males are represented by a square and females are represented

by a circle. When an individual is affected with a certain condition, the square or circle is filled in as a solid color.

With a dominant condition, at least one of the parents will have the disease and an offspring will have a 50% chance of

inheriting the affected chromosome. Therefore, dominant genetic conditions tend to be present in every generation. In

the case of Huntington’s, some individuals may not be diagnosed until later in adulthood, so parents may unknowingly

pass this dominantly inherited disease to their children.

Figure 3.34 A three-generation pedigree depicting an example of dominant Mendelian inheritance like Huntington’s.

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Because the probability of inheriting a disease-causing recessive allele is more rare, recessive medical conditions can

skip generations. Figure 3.35 is an example of a family that carries a recessive cystic fibrosis mutation. A parent that

is heterozygous for the cystic fibrosis allele has a 50% chance of passing down their affected chromosome to the next

generation. If a child has a recessive disease, then it means both of their parents are carriers heterozygous) for that condition. In most cases, carriers for recessive conditions show no serious medical symptoms. Individuals whose family

have a known medical history for certain conditions sometimes seek family planning services see the Genetic Testing

section).

Figure 3.35 A three-generation pedigree depicting an example of recessive Mendelian inheritance like cystic fibrosis.

Pedigrees can also help distinguish if a health issue has an autosomal or X-linked pattern of inheritance. As previously discussed, there are 23 pairs of chromosomes and 22 of these pairs are known as autosomes. The provided pedigree examples Figure 3.34–35) are autosomally linked genetic diseases. This means the genes that cause the disease are

located on one of the chromosomes numbered 1 to 22. Disease causing genes can also be X-linked, which means they

are located on the X chromosome.

Figure 3.36 depicts a family in which the mother is a carrier for the X-linked recessive disease Duchenne Muscular

Dystrophy DMD). The mother is a carrier for DMD, so daughters and sons will have a 50% chance of inheriting the

pathogenic DMD allele. Because females have two X chromosomes, females will not have the disease although in rare cases, female carriers may show some symptoms of the disease). On the other hand, males who inherit a copy of an

X-linked pathogenic DMD allele will typically be affected with the condition. Males are more susceptible to X-linked conditions because they only have one X chromosome. Therefore, when evaluating a pedigree, if a higher proportion of

males are affected with the disease, this could suggest the disease is X-linked recessive. Finally, Y-linked traits are very

rare because compared to other chromosomes, the Y chromosome is smaller and only has a few active transcribed)

genes.

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Figure 3.36 A three-generation pedigree depicting an example of X-linked Mendelian inheritance like Duchenne Muscular Dystrophy (DMD).

Complexity Surrounding Mendelian Inheritance

Figure 3.37 Snap dragons with different genotypes resulting in different flower color phenotypes.

Pea plant trait genetics are relatively simple compared to

what we know about genetic inheritance today. The vast

majority of genetically controlled traits are not strictly

dominant or recessive, so the relationship among alleles and

predicting phenotype is often more complicated. For

example, a heterozygous genotype that exhibits an

intermediate phenotype of both alleles is known as

incomplete dominance. In snapdragon flowers, the red

flower color R) is dominant and white is recessive r).

Therefore, the homozygous dominant RR is red and

homozygous recessive rr is white. However, because the R

allele is not completely dominant, the heterozygote Rr is a

blend of red and white, which results in a pink flower Figure

3.37).

An example of incomplete dominance in humans is the enzyme β-hexosaminidase A Hex A), which is encoded by the gene HEXA. Patients with two dysfunctional HEXA alleles are unable to metabolize a specific lipid-sugar molecule GM2 ganglioside); because of this, the molecule builds up and causes damage to nerve cells in the brain and spinal cord. This

condition is known as Tay-Sachs disease, and it usually appears in infants who are three to six months old. Most children

with Tay-Sachs do not live past early childhood. Individuals who are heterozygous for the functional type HEXA allele and one dysfunctional allele have reduced Hex A activity. However, the amount of enzyme activity is still sufficient, so

carriers do not exhibit any neurological phenotypes and appear healthy.

Some genes and alleles can also have higher penetrance than others. Penetrance can be defined as the proportion of individuals who have a certain allele and also express an expected phenotype. If a genotype always produces an expected

phenotype, then those alleles are said to be fully penetrant. However, in the case of incomplete or reduced) penetrance,

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an expected phenotype may not occur even if an individual possesses the alleles that are known to control a trait or

cause a disease.

A well-studied example of genetic penetrance is the cancer-related genes BRCA1 and BRCA2. Mutations in these genes

can affect crucial processes such as DNA repair, which can lead to breast and ovarian cancers. Although BRCA1 and

BRCA2 mutations have an autosomal dominant pattern of inheritance, it does not mean an individual will develop cancer if they inherit a pathogenic allele. Several lifestyle and environmental factors can also influence the risk for developing

cancer. Regardless, if a family has a history of certain types of cancers, then it is often recommended that genetic testing

be performed for individuals who are at risk. Moreover, publically available genetic testing companies are now offering

health reports that include BRCA1/2 allele testing see the Genetic Testing section).

POLYGENIC TRAITS

While Mendelian traits tend to be influenced by a single gene, the vast majority of human phenotypes are polygenic traits. The term polygenic means “many genes.” Therefore, a polygenic trait is influenced by many genes that work together to produce the phenotype. Human phenotypes such as hair color, eye color, height, and weight are examples of

polygenic traits. Complex diseases e.g., cardiovascular diseases, Alzheimer’s, and Schizophrenia) also have a polygenic basis.

Human hair color is an example of a polygenic trait. Hair color is largely determined by the type and quantity of a

pigment called melanin, which is produced by a specialized cell type within the skin called melanocytes. The quantity

and ratio of melanin pigments determine black, brown, blond, and red hair colors. MC1R is a well-studied gene that encodes a protein expressed on the surface of melanocytes that is involved in the production of eumelanin pigment.

Typically, people with two functional copies of MC1R have brown hair. People with reduced functioning MC1R allele

copies tend to produce pheomelanin, which results in blond or red hair. However, MC1R alleles have variable penetrance,

and studies are continually identifying new genes e.g., TYR, TYRP1, SLC24A5, and KITLG) that also influence hair color.

Individuals with two non-functioning copies of the gene TYR have a condition called oculocuteaneous albinism—their melanocytes are unable to produce melanin so these individuals have white hair, light eyes, and pale skin.

In comparison to Mendelian disease, complex diseases tend to be more prevalent in humans. Complex diseases can

also run in families, but they often do not have a clear pattern of inheritance. Geneticists may not know all of the

genes involved with a given complex disease. In addition to different gene combinations, complex diseases are also

influenced by environment and lifestyle factors. Moreover, how much each of these determinants contribute to a disease

phenotype can be difficult to decipher. Therefore, predicting medical risk is often a significant challenge. For instance,

cardiovascular diseases CVDs) continue to be one of the leading causes of death around the world. Development of

CVDs has been linked to malnutrition during fetal development, high fat and sedentary lifestyles, smoking/drug usage,

adverse socioeconomic conditions, and various genes. Human environments are diverse, and public health research

including the field of Human Biology can help identify risk factors and behaviors associated with chronic diseases.

Large-scale genetic studies can also help elucidate some of these complex relationships.

GENOMICS AND EPIGENETICS

The genome is all of the genetic material for an organism. In the case of humans, this includes 46 chromosomes and mtDNA. The human genome contains approximately three billion base pairs of DNA and has regions that are both

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noncoding and coding. Scientists now estimate that the human genome contains 20,000–25,000 protein-coding genes,

with each chromosome containing a few hundred to a few thousand genes. As our knowledge of heredity increases,

researchers have begun to realize the importance of epigenetics, or changes in gene expression that do not result in a change of the underlying DNA sequence. Epigenetics research is also crucial for unraveling gene regulation, which

involves complex interactions between DNA, RNA, proteins, and the environment.

Genomics

The vast majority of the human genome is noncoding, meaning there are no instructions to make a protein or RNA

product in these regions. Historically, noncoding DNA was referred to as “junk DNA” because these vast segments of

the genome were thought to be irrelevant and non-functional. However, continual improvement of DNA sequencing technology along with world-wide scientific collaborations and consortia have contributed to our increased

understanding of how the genome functions. Through these technological advances and collaborations, we have since

discovered that many of these noncoding DNA regions are involved in dynamic genetic regulatory processes.

Genomics is a diverse field of molecular biology that focuses on genomic evolution, structure and function; gene

mapping; and genotyping determining the alleles present). Evolutionary genomics determined that humans and chimpanzees share a significant portion of shared DNA sequence about 98.8%). Given the phenotypic differences

between humans and chimpanzees, having a DNA sequence difference of 1.2% seems surprising. However, a lot of

genomics research is also focused on understanding how noncoding genomic regions influence how individual genes

are turned “on” and “off” i.e., regulated). Therefore, although DNA sequences are identical, regulatory differences in

noncoding genetic regions e.g., promoters) are believed to be largely responsible for the physical differences between

humans and chimpanzees.

Further understanding of genomic regulatory elements can lead to new therapies and personalized treatments for a

broad range of diseases. For example, targeting the regulatory region of a pathogenic gene to “turn off” its expression

can prevent its otherwise harmful effects. Such molecular targeting approaches can be personalized based on an

individual’s genetic makeup. Genome-wide association studies GWAS) seek to determine genes that are linked to

complex traits and diseases and typically require significant computational efforts. This is because millions of DNA

sequences must be analyzed and GWAS sometimes include thousands of participants. During the beginning of the

genomics field, most of the large-scale genomics studies only included North American, European, and East Asian

participants and patients. Researchers are now focusing on increasing ethnic diversity in genomic studies and

databases. In turn, accuracy of individual disease risk across all human populations will be improved and more rare-

disease-causing alleles will be identified.

Epigenetics

All cells within your body have the same copy of DNA. For example, a brain neuron has the same DNA blueprint as does

a skin cell on your arm. Although these cells have the same genetic information, they are considered specialized. The

reason all cells within the body have the same DNA but different morphologies and functions is that different subsets

of genes are turned “on” and “off” within the different cell types. A more precise explanation is that there is differential

expression of genes among different cell types. In the case of neuronal cells, a unique subset of genes are active that

allow them to grow axons to send and receive messages. This subset of genes will be inactive in non-neuronal cell types

such as skin cells. Epigenetics is a branch of genetics that studies how these genes are regulated through mechanisms

Molecular Biology and Genetics | 89

that do not change the underlying DNA sequence. Special Topics: Epigenetics and X Chromosome Inactivation details a

well-known example of epigenetic regulation.

The prefix epi means “on, above, or near,” and epigenetic mechanisms such as DNA methylation and histone modifications occur on, above, or near DNA. The addition of a methyl group —CH₃) to DNA is known as DNA methylation Figure 3.38). DNA methylation and other modifications made to the histones around which DNA are wrapped are

thought to make chromatin more compact. This DNA is inaccessible to transcription factors and RNA polymerases,

thus preventing genes from being turned on i.e., transcribed). Other histone modifications have the opposite effect by

loosening chromatin, which makes genes accessible to transcription factors.

It is important to note that environmental factors can alter DNA methylation and histone modifications and also that

these changes can be passed from generation to generation. For example, someone’s epigenetic profile can be altered during a stressful time e.g., natural disasters, famine, etc.), and those regulatory changes can be inherited by the

next generation. Moreover, our epigenetic expression profile changes as we age. For example, certain places in our

genome become “hyper” or “hypo” methylated over time. Identical twins also have epigenetic profiles that become

more different as they age. Researchers are only beginning to understand what all of these genome-wide epigenetic

changes mean. Scientists have also discovered that changes in epigenetic modifications can alter gene expression in

ways that contribute to diseases. It is also important to note that, unlike DNA mutations which permanently change the

nucleotide sequence), epigenetic changes can be easily reversed. A lot of research now focuses on how drugs can alter

or modulate changes in DNA methylation and histone modifications to treat diseases such as cancer.

Figure 3.38 Different types of epigenetic histone tail modifications that can tighten (top) and loosen (bottom) the chromatin of DNA.

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SPECIAL TOPIC: EPIGENETICS AND X CHROMOSOME INACTIVATION

Mary Lyon was a British geneticist that presented a hypothesis for X

chromosome inactivation called the Lyon hypothesis) based on her

Figure 3.39 A multicolored coat pattern as the result of X chromosome inactivation during development.

work and other studies of the day. Females inherit two X chromosomes,

one from each parent. Males have one functional X chromosome;

however, this does not mean females have more active genes than

males. During the genetic embryonic development of many female

mammals, one of the X chromosomes is inactivated at random, so

females have one functional X chromosome. The process of X

chromosome inactivation in females occurs through epigenetic

mechanisms, such as DNA methylation and histone modifications.

Recent studies have analyzed the role of a long noncoding RNA called

X-inactive specific transcript XIST), which is largely responsible for the

random silencing of one of the X chromosomes. The presence of two X

chromosomes is the signal for XIST RNA to be expressed so that one X

chromosome can be inactivated. However, some cells may have an

active paternal X chromosome while other cells may have an active maternal X chromosome. This

phenomenon is easily seen in calico and tortoiseshell cats Figure 3.39). In cats, the gene that controls coat

color is found on the X chromosome. During early embryo development, random inactivation of X

chromosomes gives rise to populations of cells that express black or orange, which results in the unique coat

patterning. Therefore, calico cats are typically always female.

GENETIC TESTING

In order to assist with public health efforts, newborn screening for genetic diseases have been available in the United

States for over 50 years. One of the first available genetic tests was to confirm a phenylketonuria PKU) diagnosis in infants, which is easily treatable with a dietary change. Currently, each state decides what genes are included on

newborn screening panels and some states even have programs to help with infant medical follow-ups.

There are now hundreds of laboratories that provide testing for a few thousand different genes that can inform

medical decisions for infants and adults. What has made this industry possible are the advancements in technology and

decreased cost to patients. Moreover, genetic testing has been made available publicly to anyone without the assistance

of medical professionals.

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Polymerase Chain Reaction (PCR) and Sanger Sequencing

One of the most important inventions in the genetics field was polymerase chain reaction (PCR). In order for researchers to visualize and therefore analyze DNA, the concentration must meet certain thresholds. In 1985, Kary Mullis

developed PCR, which can amplify millions of copies of DNA from a very small amount of template DNA Figure 3.40). For

example, a trace amount of DNA at a crime scene can be amplified and tested for a DNA match. Also, aDNA is typically

degraded, so a few remaining molecules of DNA can be amplified to reconstruct ancient genomes. The PCR assay uses

similar biochemical reactions to our own cells during DNA replication.

Figure 3.40 Gel electrophoresis used to visualize DNA after PCR amplification.

In Sanger sequencing, PCR sequences can be analyzed at the nucleotide level with the help of fluorescent labeling. Several different types of alleles and genetic changes can be detected in DNA by using this analysis. Figure 3.41 shows

someone who is heterozygous for a single nucleotide allele. These methods continue to be used extensively alongside

larger-scale genome technologies.

Figure 3.41 Sanger sequencing results showing a heterozygous DNA nucleotide.

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Genetic Biotechnology and Clinical Testing

Figure 3.42 Microarray chip with fluorescent labeled probes that hybridize with DNA to detect homozygous and heterozygous nucleotides throughout the genome.

Genetic innovations are transforming the healthcare industry. However, the

different types of technology and the results of these tests often include a

learning curve for patients, the public, and medical practitioners.

Microarray technology, when DNA samples are genotyped or “screened”) for specific alleles, has been available for quite some time Figure 3.42).

Presently, microarray chips can include hundreds of alleles that are known

to be associated with various diseases. The microarray chip only binds with

a DNA sample if it is “positive” for that particular allele and a fluorescent

signal is emitted, which can be further analyzed.

If a patient is suspected of having a rare genetic condition that cannot be

easily diagnosed or the diagnosis is entirely unknown, whole genome

sequencing may be recommended by a doctor. Next-generation sequencing (NGS) is a newer technology that can screen the entire genome by analyzing millions of sequences within a single machine run Figure 3.43).

However, sequencing the entire genome yields a significant amount of data

and information. Therefore, clinical NGS genetic testing typically only

includes a small subset of the genome known to have pathogenic disease-causing mutations.

Figure 3.43 Next-generation sequencing machines.

There is a diversity of clinical genetics tests available to assist patients with making medically informed decisions

about family planning and health, including assistance with in vitro fertilization IVF) procedures and embryo genetic screening. To ensure accuracy, it is highly important that all clinical laboratories are continually regulated. The Clinical

Laboratory Improvement Amendments CLIA) are United States federal standards that all human laboratory testing

clinics must follow. A major benefit provided by some clinical genetic testing companies is access to genetic counselors,

who have specialized education and training in medical genetics and counseling. Both partners are usually tested to see

if there is a risk for passing on a disease to a child. Counselors use their skillset to aid patients and doctors with risk

assessment for genetic diseases and interpretation of genetic testing results. Genetic counselors also guide and support

patients when making impactful medical decisions.

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Direct-to-Consumer (DTC) Genetic Testing

Figure 3.44 A positive result for a genetic allele associated with an increased risk for celiac disease.

Genetic testing that is performed without the guidance of medical professionals is called direct-to-consumer DTC)

genetic testing. Companies that sell affordable genome sequencing products to the public continue to increase in

number and popularity. These companies have marketing campaigns typically based on the notion of “personal

empowerment,” which can be achieved by “knowing more about your DNA.” For example, if you are identified as having

a slightly increased risk for developing celiac disease Figure 3.44), then you may be motivated to modify your dietary

consumption by removing gluten from your diet. Another scenari