ANATOMY AND PHYSIOLOGY
GENETICS AND CELLULAR FUNCTIONS

LEARN THROUGH YOUR COURSE AND FORTIFY ALL YOUR WEAKNESS WITH MEDICAL KNOWLEDGE

The Nucleic Acids 130
• Organization of the Chromatin 130
• DNA Structure and Function 130
• RNA Structure and Function 133
Protein Synthesis and Secretion 134
• Preview 134
• The Genetic Code 134
• Transcription 136
• Translation 136
• Chaperones and Protein Structure 137

• Posttranslational Modification 138
• Packaging and Secretion 139

DNA Replication and the Cell Cycle 139
• DNA Replication 139
• Errors and Mutations 142
• The Cell Cycle 142
• Mitosis 143
• Timing of Cell Division 145

Chromosomes and Heredity 145
• The Karyotype 146
• Genes and Alleles 147
• Multiple Alleles, Codominance, and

Incomplete Dominance 148
• Polygenic Inheritance and Pleiotropy 148
• Sex Linkage 149
• Penetrance and Environmental Effects 149
• Dominant and Recessive Alleles at the
Population Level 149
Chapter Review 152

INSIGHTS
4.1 Medical History: Miescher and the
Discovery of DNA 130
4.2 Medical History: Discovery of the
Double Helix 132
4.3 Clinical Application: Can We Replace Brain Cells? 143

4.4 Clinical Application: Cancer 151


Some of the basic ideas of heredity have been known since antiquity, but a scientific understanding of how traits are passed from parent to offspring began with the Austrian monk Gregor Mendel (1822–84) and his famous experiments on garden peas. In the early twentieth century, the importance of Mendel’s work was realized and chromosomes were first seen with the microscope. Cytogenetics now uses techniques of cytology and microscopy to study chromosomes and their relationship to hereditary traits. Molecular genetics uses the techniques of biochemistry to study the structure and function of DNA. In this chapter, we bring together some of the findings of molecular genetics, cytogenetics, and mendelian heredity to explore what the genes are, how they regulate cellular function, and how they are passed on when cells divide and people reproduce. A few basic concepts of heredity are introduced as a foundation for understanding concepts ranging from color blindness to blood types in the chapters that follow.

The Nucleic Acids
Objectives
When you have completed this section, you should be able to • describe how DNA is organized in the nucleus; and
• compare the structures and functions of DNA and RNA.
With improvements in the microscope, nineteenth-century cytologists saw that the nucleus divides in preparation for cell division, and they came to regard the nucleus as the most likely center of heredity. This led to a search for the biochemical keys to heredity in the nucleus, and thus to the discovery of deoxyribonucleic acid (DNA) (insight 4.1). DNA directly or indirectly regulates all cellular form and function.

Insight 4.1 Medical History
Miescher and the Discovery of DNA
Swiss biochemist Johann Friedrich Miescher (1844–95) was one of the first scientists intent on identifying the hereditary material in nuclei. In order to isolate nuclei with minimal contamination, Miescher chose to work with cells that have large nuclei and very little cytoplasm. At first he chose white blood cells extracted from the pus in used bandages from a hospital; later, he used the sperm of salmon—probably more agreeable to work with than used bandages! Miescher isolated an acidic substance rich in phosphorus, which he named nuclein. His student, Richard Altmann, later called it nucleic acid—a term we now use for both DNA and RNA. Miescher correctly guessed that “nuclein” (DNA) was the hereditary matter of the cell, but he was unable to provide strong evidence for this conjecture, and his work was harshly criticized. He died of tuberculosis at the age of 51.

Organization of the Chromatin
A human cell usually has 46 molecules of DNA with an average length of 44 mm (total slightly over 2 m). Each molecule is 2 nm in diameter. To put this in perspective, if a DNA molecule were the thickness of a telephone pole (20 cm, or 8 in.), it would reach about 4,400 km (2,700 mi) into space—far higher than the orbits of satellites and space shuttles. Imagine trying to make a pole 20 cm thick and 4,400 km long without breaking it! The problem for a cell is even greater. It has 46 DNA molecules packed together in a single nucleus, and it has to make an exact copy of every one of them and distribute these equally to its two daughter cells when the cell divides. Keeping the DNA organized and intact is a tremendous feat. Molecular biology and high-resolution electron microscopy have provided some insight into how this task is accomplished. Chromatin looks like a granular thread (fig. 4.1a). The granules, called nucleosomes, consist of a cluster of eight proteins called histones, with the DNA molecule wound around the cluster. Histones serve as spools that protect and organize the DNA. Other nuclear proteins called nonhistones seem to provide structural support for the chromatin and regulate gene activity. Winding DNA around the nucleosomes makes the chromatin shorter and more compact, but chromatin also has higher orders of structure. The “granular thread,” about 10 nm wide, further twists into a coil about 30 nm wide. When a cell prepares to undergo division, the chromatin further supercoils into a fiber about 200 nm wide (fig. 4.1b). Thus, the 2 m of DNA in each cell becomes shortened and compacted in an orderly way that prevents tangling and breakage without interfering with genetic function.

DNA Structure and Function
Nucleic acids are polymers of nucleotides (NEW-clee-ohtides). A nucleotide consists of a sugar, a phosphate group, and a single- or double-ringed nitrogenous (ny-TRODJ-ehnus) base. Three bases—cytosine (C), thymine (T), and uracil (U)—have a single carbon-nitrogen ring and are classified as pyrimidines (py-RIM-ih-deens). The other two bases—adenine (A) and guanine (G)—have double rings and are classified as purines (fig. 4.2). The bases of DNA are C, T, A, and G, whereas the bases of RNA are C, U, A, and G. The structure of DNA resembles a ladder (fig. 4.3a). Each sidepiece is a backbone composed of phosphate groups alternating with the sugar deoxyribose. The steplike connections between the backbones are pairs of nitrogenous bases. Imagine this as a soft rubber ladder that you can twist, so that the two backbones become entwined to resemble a spiral staircase. This is analogous to the shape of the DNA molecule, described as a double helix. The nitrogenous bases face the inside of the helix and hold the two backbones together with hydrogen bonds. Across from a purine on one backbone, there is a pyrimidine on the other. A given purine cannot arbitrarily bind to just any pyrimidine. Adenine and thymine form two hydrogen bonds with each other, and guanine and cytosine form three, as shown in figure 4.3b. Therefore, wherever there is an A on one backbone, there is a T across from it, and every C is paired with a G. A–T and C–G are called the base pairs. The fact that one strand governs the base sequence of the other is called the law of complementary base pairing. It enables us to predict the base sequence of one strand if we know the sequence of the complementary strand. The pairing of each small, single-ringed pyrimidine with a large, double-ringed purine gives the DNA molecule its uniform 2-nm width. Think About It
What would be the base sequence of the DNA strand across from ATTGACTCG? If a DNA molecule were known to be 20% adenine, predict its percentage of cytosine and explain your answer.

Medical History
Discovery of the Double Helix
The components of DNA were known by 1900—the sugar, phosphate, and bases—but the technology did not exist then to determine how they were put together. The credit for that discovery went mainly to James Watson and Francis Crick in 1953 (fig. 4.4). The events surrounding their discovery of the double helix represent one of the most dramatic stories of modern science—the subject of many books and a movie. When Watson and Crick came to share a laboratory at Cambridge University in 1951, both had barely begun their careers. Watson, age 23, had just completed his Ph.D. in the United States, and Crick, 11 years older, was a doctoral candidate. Yet the two were about to become the most famous molecular biologists of the twentieth century, and the discovery that won them such acclaim came without a single laboratory experiment of their own. Others were fervently at work on DNA, including Rosalind Franklin and Maurice Wilkins at King’s College in London. Using a technique called X-ray diffraction, Franklin had determined that DNA had a repetitious helical structure with sugar and phosphate on the outside of the helix. Without her permission, Wilkins showed one of Franklin’s best X-ray photographs to Watson. Watson said, “The instant I saw the picture my mouth fell open and my pulse began to race.” It provided a flash of insight that allowed the Watson and Crick team to beat Franklin to the goal. They were quickly able to piece together a scale model from cardboard and sheet metal that fully accounted for the known geometry of DNA. They rushed a paper into print in 1953 describing the double helix, barely mentioning the importance of Franklin’s two years of painstaking X-ray diffraction work in unlocking the mystery of life’s most important molecule. For this discovery, Watson, Crick, and Wilkins shared the Nobel Prize in 1962. Nobel Prizes are awarded only to the living, and in the final irony of her career, Rosalind Franklin had died in 1958, at the age of 37, of a cancer possibly induced by the X rays that were her window on DNA architecture.The essential function of DNA is to serve as a code for the structure of polypeptides synthesized by a cell. A gene is a DNA nucleotide sequence that codes for one polypeptide. The next section of this chapter explains in detail how the genes direct polypeptide synthesis. All the genes of one person are called the genome (JEE-nome); geneticists estimate that a human has about 35,000 genes. These account for only 3% of our DNA; the other 97% does not code for anything. Some of the noncoding DNA serves important organizing roles in the chromatin, and some of it is useless “junk DNA” that has accumulated over the course of human evolution. The latest triumph of molecular genetics is the human genome project, an enormous multinational effort that led to the mapping of the base sequence of the entire human genome. Its completion (in all but some fine details) in June 2000 was hailed as a scientific achievement comparable to putting the first man on the moon.

RNA Structure and Function
DNA directs the synthesis of proteins by means of its smaller cousins, the ribonucleic acids (RNAs). There are three types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Their individual roles are described shortly. For now we consider what they have in common and how they differ from DNA (table 4.1). The most significant difference is that RNA is much smaller, ranging from about 70 to 90 bases in tRNA to slightly over 10,000 bases in the largest mRNA. DNA, by contrast, may be over a billion base pairs long. Also, while DNA is a double helix, RNA consists of only one nucleotide chain, not held together by complementary base pairs except in certain regions of tRNA where the molecule folds back on itself. The sugar in RNA is ribose instead of deoxyribose, and one of the pyrimidines of DNA, thymine, is replaced by uracil (U) in RNA (see fig. 4.2). The essential function of RNA is to interpret the code in DNA and direct the synthesis of proteins. RNA works mainly in the cytoplasm, while DNA remains safely behind in the nucleus, “giving orders” from there. This process is described in the next section of this chapter.

Protein Synthesis and Secretion

Objectives
When you have completed this section, you should be able to
• define genetic code and describe how DNA codes for protein structure;
• describe the process of assembling amino acids to form a protein;
• explain what happens to a protein after its amino acid sequence has been synthesized;
• explain how DNA indirectly regulates the synthesis of nonprotein molecules.
Everything a cell does ultimately results from the action of its proteins; DNA directs the synthesis of those proteins. Cells, of course, synthesize many other substances as well—glycogen, fat, phospholipids, steroids, pigments, and so on. There are no genes for these cell products, but their synthesis depends on enzymes that are coded for by the genes. For example, even though a cell of the testis has no genes for testosterone, testosterone synthesis is indirectly under genetic control (fig. 4.5). Since testosterone strongly influences such behaviors as aggression and sexual drive (in both sexes), we can see that genes also make a significant contribution to behavior. In this section, we examine how protein synthesis results from the instructions given in the genes.
Preview
Before studying the details of protein synthesis, it will be helpful to consider the big picture. In brief, DNA contains a genetic code that specifies which proteins a cell can make. All the body’s cells except the sex cells contain identical genes, but different genes are activated in different cells; for example, the genes for digestive enzymes are active in stomach cells but not in muscle cells. When a gene is activated, a molecule of messenger RNA (mRNA), a sort of mirror-image copy of the gene, is made. Most mRNA migrates from the nucleus to the cytoplasm, where its code is “read” by a ribosome. Ribosomes are composed of ribosomal RNA (rRNA) and enzymes. Transfer RNA (tRNA) delivers amino acids to the ribosome, and the ribosome chooses from among these to assemble amino acids in the order directed by the mRNA. In summary, you can think of the process of protein synthesis as DNA→mRNA→protein, with each arrow reading as “codes for the production of.” The step from DNA to mRNA is called transcription, and the step from mRNA to protein is called translation. Transcription occurs in the nucleus, where the DNA is, and most translation occurs in the cytoplasm. Recent research has shown, however, that 10% to 15% of proteins are synthesized in the nucleus, with both steps occurring there. The Genetic Code
The body makes more than 2 million different proteins, all from the same 20 amino acids and all encoded by genes made of just 4 nucleotides (A, T, C, G)—a striking illustration of how a great variety of complex structures can be made from a small variety of simpler components. The genetic code is a system that enables these 4 nucleotides to code for the amino acid sequences of all proteins. It is not unusual for simple codes to represent complex information. Computers store and transmit complex information, including pictures and sounds, in a binary code with only the symbols 1 and 0. It is not surprising, then, that a mere 20 amino acids can be represented by a code of 4 nucleotides; all that is required is to combine these symbols in varied ways. It requires more than 2 nucleotides to code for each amino acid, because A, U, C, and G can combine in only 16 ways (AA, AU, AC, AG, UA, UU, etc.). The minimum code to symbolize 20 amino acids is 3 nucleotides per amino acid, and indeed this is the case in DNA. A sequence of 3 DNA nucleotides that stands for 1 amino acid is called a base triplet. The “mirror image”sequence in mRNA is called a codon. The genetic code is expressed in terms of codons. Table 4.2 shows a few representative triplets and codons along with the amino acids they represent. You can see from this listing that two or more codons can represent the same amino acid. The reason for this is easy to explain mathematically. Four symbols (N) taken three at a time (x) can be combined in Nx different ways; that is, there are 43  64 possible codons available to represent the 20 amino acids. Only 61 of these code for amino acids. The other 3—UAG, UGA, and UAA—are called stop codons; they signal “end of message,” like the period at the end of a sentence. A stop codon enables the cell’s protein-synthesizing machinery to sense that it has reached the end of the gene for a particular protein. The codon AUG plays two roles—it serves as a code for methionine and as a start codon. This dual function is explained shortly

Transcription
Most protein synthesis occurs in the cytoplasm, but DNA is too large to leave the nucleus. It is necessary, therefore, to make a small RNA copy that can migrate through a nuclear pore into the cytoplasm. Just as we might transcribe (copy) a document, transcription in genetics means the process of copying genetic instructions from DNA to RNA. It is triggered by chemical messengers from the cytoplasm that enter the nucleus and bind to the chromatin at the site of the relevant gene. An enzyme called RNA polymerase (po-LIM-ur-ase) then binds to the DNA at this point and begins making RNA. Certain base sequences (often TATATA or TATAAA) inform the polymerase where to begin. RNA polymerase opens up the DNA helix about 17 base pairs at a time. It transcribes the bases from one strand of the DNA and makes a corresponding RNA. Where it finds a C on the DNA, it adds a G to the RNA; where it finds an A, it adds a U; and so forth. The enzyme then rewinds the DNA helix behind it. Another RNA polymerase may follow closely behind the first one; thus, a gene may be transcribed by several polymerase molecules at once, and numerous copies of the same RNA are made. At the end of the gene is a base sequence that serves as a terminator, which signals the polymerase to release the RNA and separate from the DNA. The RNA produced by transcription is an “immature” form called pre-mRNA. This molecule contains “sense” portions called exons that will be translated into a peptide and “nonsense” portions called introns that must be removed before translation. Enzymes remove the introns and splice the exons together into a functional mRNA molecule.

Translation
Just as we might translate a work from Spanish into English, genetic translation converts the language of nucleotides into the language of amino acids (fig. 4.6). This job is done by ribosomes, which are found mainly in the cytosol and on the rough ER and nuclear envelope. A ribosome consists of two granular subunits, large and small, each made of several rRNA and enzyme molecules. The mRNA molecule begins with a leader sequence of bases that are not translated to protein but serve as a binding site for the ribosome. The small ribosomal subunit binds to it, the large subunit joins the complex, and the ribosome begins pulling the mRNA through it like a ribbon, reading bases as it goes. When it reaches the start codon, AUG, it begins making protein. Since AUG codes for methionine, all proteins begin with methionine when first synthesized, although this may be removed later. Translation requires the participation of 61 types of transfer RNA (tRNA), one for each codon (except stop codons). Transfer RNA is a small RNA molecule that turns back and coils on itself to form a cloverleaf shape, which is then twisted into an angular L-shape (fig. 4.7). One end of the L includes three nucleotides called an anticodon, and the other end has a binding site specific for one amino acid. Each tRNA picks up an amino acid from a pool of free amino acids in the cytosol. One ATP molecule is used to bind the amino acid to this site and provide the energy that is used later to join that amino acid to the growing protein. Thus, protein synthesis consumes one ATP for each peptide bond formed. When the small ribosomal subunit reads a codon such as CGC, it must find an activated tRNA with the corresponding anticodon; in this case, GCG. This particular tRNA would have the amino acid alanine at its other end. The ribosome binds and holds this tRNA and then reads the next codon—say GGU. Here, it would bind a tRNA with anticodon CCA, which carries glycine. The large ribosomal subunit contains an enzyme that forms peptide bonds, and now that alanine and glycine are side by side, it links them together. The first tRNA is no longer needed, so it is released from the ribosome. The second tRNA is used, temporarily, to anchor the growing peptide to the ribosome. Now, the ribosome reads the third codon—say GUA. It finds the tRNA with the anticodon CAU, which carries the amino acid valine. The large subunit adds valine to the growing chain, now three amino acids long. By repetition of this process, the entire protein is assembled. Eventually, the ribosome reaches a stop codon and is finished translating this mRNA. The polypeptide is turned loose, and the ribosome dissociates into its two subunits. One ribosome can assemble a protein of 400 amino acids in about 20 seconds, but it does not work at the task alone. After the mRNA leader sequence passes through one ribosome, a neighboring ribosome takes it up and begins translating the mRNA before the first ribosome has finished. One mRNA often holds 10 or 20 ribosomes together in a cluster called a polyribosome (fig. 4.8). Not only is each mRNA translated by all these ribosomes at once, but a cell may have 300,000 identical mRNA molecules undergoing simultaneous translation. Thus, a cell may produce over 150,000 protein molecules per second—a remarkably productive protein factory! As much as 25% of the dry weight of liver cells, which are highly active in protein synthesis, is composed of ribosomes. Many proteins, when first synthesized, begin with a chain of amino acids called the signal peptide. Like a molecular address label, the signal peptide determines the protein’s destination—for example, whether it will be sent to the rough endoplasmic reticulum, a peroxisome, or a mitochondrion. (Proteins used in the cytosol lack signal peptides.) Some diseases result from errors in the signal peptide, causing a protein to be sent to the wrong address, such as going to a mitochondrion when it should have gone to a peroxisome, or causing it to be secreted from a cell when it should have been stored in a lysosome. Gunter Blöbel of Rockefeller University received the 1999 Nobel Prize for Physiology or Medicine for discovering signal peptides in the 1970s. Figure 4.9 summarizes transcription and translation and shows how a nucleotide sequence translates to a hypothetical peptide of 6 amino acids. A protein 500 amino acids long would have to be represented, at a minimum, by a sequence of 1,503 nucleotides (3 for each amino acid, plus a stop codon). The average gene is probably around 1,200 nucleotides long; a few may be 10 times this long.

Chaperones and Protein Structure
The amino acid sequence of a protein (primary structure) is only the beginning; the end of translation is not the end of protein synthesis. The protein now coils or folds into its secondary and tertiary structures and, in some cases, associates with other polypeptide chains (quaternary structure) or conjugates with a nonprotein moiety, such as a vitamin or carbohydrate. It is essential that these processes not begin prematurely as the amino acid sequence is being assembled, since the correct final shape may depend on amino acids that have not been added yet. Therefore, as new proteins are assembled by ribosomes, they are sometimes picked up by older proteins called chaperones. A chaperone prevents a new protein from folding prematurely and assists in its proper folding once the amino acid sequence has been completed. It may also escort a newly synthesized protein to the correct destination in a cell, such as the plasma membrane, and help to prevent improper associations between different proteins. As in the colloquial sense of the word, a chaperone is an older protein that escorts and regulates the behavior of the “youngsters.” Some chaperones are also called stress proteins or heat-shock proteins because they are produced in response to heat or other stress on a cell and help damaged proteins fold back into their correct functional shapes.

Posttranslational Modification
If a protein is going to be used in the cytosol (for example, the enzymes of glycolysis), it is likely to be made by free ribosomes in the cytosol. If it is going to be packaged into a lysosome or secreted from the cell, however, its signal peptide causes the entire polyribosome to migrate to the rough ER and dock on its surface. Assembly of the amino acid chain is then completed on the rough ER and the protein is sent to the Golgi complex for final modification. Thus, we turn to the functions of these organelles in the modification, packaging, and secretion of a protein. When a protein is produced on the rough ER, its signal peptide threads itself through a pore in the ER membrane and drags the rest of the protein into the cisterna. Enzymes in the cisterna then remove the signal peptide and modify the new protein in a variety of ways—removing some amino acids segments, folding the protein and stabilizing it with disulfide bridges, adding carbohydrate moieties, and so forth. Such changes are called posttranslational modification. Insulin, for example, is first synthesized as a polypeptide of 86 amino acids. In posttranslational modification, the chain folds back on itself, three disulfide bridges are formed, and 35 amino acids are removed. The final insulin molecule is therefore made of two chains of 21 and 30 amino acids held together by disulfide bridges (see fig. 17.15). When the rough ER is finished with a protein, it pinches off clathrin-coated transport vesicles. Like the address on a letter, clathrin may direct the vesicle to its destination, the Golgi complex. The Golgi complex removes the clathrin, fuses with the vesicle, and takes the protein into its cisterna. Here, it may further modify the protein, for example by adding carbohydrate to it. Such modifications begin in the cisterna closest to the rough ER. Each cisterna forms transport vesicles that carry the protein to the next cisterna, where different enzymes may further modify the new protein.

Packaging and Secretion
When the protein is processed by the last Golgi cisterna, farthest from the rough ER, that cisterna pinches off membranebounded Golgi vesicles containing the finished product. Some Golgi vesicles become secretory vesicles, which migrate to the plasma membrane and release the product by exocytosis. This is how a cell of the salivary gland, for example, secretes mucus and digestive enzymes. The destinations of these and some other newly synthesized proteins are summarized in table 4.3.

DNA Replication and the Cell Cycle

Objectives
When you have completed this section, you should be able to
• describe how DNA is replicated;
• discuss the consequences of replication errors;
• describe the life history of a cell, including the events of mitosis; and
• explain how the timing of cell division is regulated.
Before a cell divides, it must duplicate its DNA so it can give a complete copy of the genome to each daughter cell. Since DNA controls all cellular function, this replication process must be very exact. We now examine how it is accomplished and consider the consequences of mistakes.

DNA Replication
The law of complementary base pairing shows that we can predict the base sequence of one DNA strand if we know the sequence of the other. More importantly, it enables a cell to reproduce one strand based on information in the other. This immediately occurred to Watson and Crick when they discovered the structure of DNA. Watson was hesitant to make such a grandiose claim in their first publication, but Crick implored, “Well, we’ve got to say something! Otherwise people will think these two unknown chaps are so dumb they don’t even realize the implications of their own work!” Thus, the last sentence of their first paper modestly stated, “It has not escaped our notice that the specific pairing we have postulated . . . immediately suggests a possible copying mechanism for the genetic material.” Five weeks later they published a second paper pressing this point more vigorously. The basic idea of DNA replication is evident from its base pairing, but the way in which DNA is organized in the chromatin introduces some complications that were not apparent when Watson and Crick first wrote. The fundamental steps of the replication process are as follows:

1. The double helix unwinds from the histones.
2. Like a zipper, an enzyme called DNA helicase
opens up a short segment of the helix, exposing its nitrogenous bases. The point where one strand of DNA is “unzipped” and separates from its complementary strand is called a replication fork
. 3. An enzyme called DNA polymerase moves along the opened strands, reads the exposed bases, and like a matchmaker, arranges “marriages” with complementary free nucleotides in the nucleoplasm. If the polymerase finds the sequence TCG, for example, it assembles AGC across from it. One polymerase molecule moves away from the replication fork replicating one strand of the opened DNA, and another polymerase molecule moves in the opposite direction, replicating the other strand. Thus, from the old DNA molecule, two new ones are made. Each new DNA consists of one new helix synthesized from free nucleotides and one helix conserved from the parent DNA . The process is therefore called semiconservative replication.
4. While DNA is synthesized in the nucleus, new histones are synthesized in the cytoplasm. Millions of histones are transported into the nucleus within a few minutes after DNA replication, and each new DNA helix wraps around them to make new nucleosomes.

Despite the complexity of this process, each DNA polymerase works at an impressive rate of about 100 base pairs per second. Even at this rate, however, it would take weeks for one polymerase molecule to replicate even one chromosome. But in reality, thousands of polymerase molecules work simultaneously on each DNA molecule and all 46 chromosomes are replicated in a mere 6 to 8 hours.

Errors and Mutations
DNA polymerase is fast and accurate, but it makes mistakes. For example, it might read A and place a C across from it where it should have placed a T. In Escherichia coli, a bacterial species in which DNA replication has been most thoroughly studied, about three errors occur for every 100,000 bases copied. At this rate of error, every generation of cells would have about 1,000 faulty proteins, coded for by DNA that had been miscopied. To help prevent such catastrophic damage to the organism, the DNA is continuously scanned for errors. After DNA polymerase has replicated a strand, a smaller polymerase comes along, “proofreads” it, and makes corrections where needed—for example, removing C and replacing it with T. This improves the accuracy of replication to one error per billion bases—only one faulty protein for every 10 cell divisions (in E. coli). Changes in DNA structure, called mutations,1 can result from replication errors or environmental factors. Uncorrected mutations can be passed on to the descendants of that cell, but some of them have no adverse effect. One reason is that a new base sequence sometimes codes for the same thing as the old one. For example, ACC and ACG both code for threonine (see table 4.2), so a mutation from C to G in the third place would not change protein structure. Another reason is that a change in protein structure is not always critical to its function. For example, humans and horses differ in 25 of the 146 amino acids that make up their hemoglobin, yet the hemoglobin is fully functional in both species. Some mutations, however, may kill a cell, turn it cancerous, or cause genetic defects in future generations. When a mutation changes the sixth amino acid of hemoglobin from glutamic acid to valine, for example, the result is a crippling disorder called sickle-cell disease. Clearly some amino acid substitutions are more critical than others, and this affects the severity of a mutation.
The Cell Cycle
Most cells periodically divide into two daughter cells, so a cell has a life cycle extending from one division to the next. This cell cycle (fig. 4.12) is divided into four main phases: G1, S, G2, and M. G1 is the first gap phase, an interval between cell division and DNA replication. During this time, a cell synthesizes proteins, grows, and carries out its preordained tasks for the body. Almost all of the discussion in this book relates to what cells do in the G1 phase. Cells in G1 also begin to replicate their centrioles in preparation for the next cell division and accumulate the materials needed to replicate their DNA in the next phase. In cultured cells called fibroblasts, which divide every 18 to 24 hours, G1 lasts 8 to 10 hours. S is the synthesis phase, in which a cell carries out DNA replication. This produces two identical sets of DNA molecules, which are then available, like the centrioles, to be divided up between daughter cells at the next cell division. This phase takes 6 to 8 hours in cultured fibroblasts. G2, the second gap phase, is a relatively brief interval (4 to 6 hours) between DNA replication and cell division. In G2, a cell finishes replicating its centrioles and synthesizes enzymes that control cell division. M is the mitotic phase, in which a cell replicates its nucleus and then pinches in two to form two new daughter cells. In cultured fibroblasts, the M phase takes 1 to 2 hours. The details of this phase are considered in the next section. Phases G1, S, and G2 are collectively called interphase—the time between M phases. The length of the cell cycle varies greatly from one cell type to another. Stomach and skin cells divide rapidly, bone and cartilage cells slowly, and skeletal muscle cells and nerve cells not at all (see insight 4.3). Some cells leave the cell cycle for a “rest” and cease to divide for days, years, or the rest of one’s life. Such cells are said to be in the G0 (G-zero) phase. The balance between cells that are actively cycling and those standing by in G0 is an important factor in determining the number of cells in the body. An inability to stop cycling and enter G0 is characteristic of cancer cells

Insight 4.3 Clinical Application
Can We Replace Brain Cells?
Until recently, neurons (nerve cells) of the brain were thought to be irreplaceable; when they died, we thought, they were gone forever. We believed, indeed, that there was good reason for this. Motor skills and memories are encoded in intricate neural circuits, and the growth of new neurons might disrupt those circuits. Now we are not so sure. A chemical called BrDU (bromodeoxyuridine) can be used to trace the birth of new cells, because it becomes incorporated into their DNA. BrDU is too toxic to use ordinarily in human research. However, in cancer patients, BrDU is sometimes used to monitor the growth of tumors. Peter Eriksson, at Göteborg University in Sweden, obtained permission from the families of cancer victims to examine the brain tissue of BrDU-treated patients who had died. In the hippocampus, a region of the brain concerned with memory, he and collaborator Fred Gage found as many as 200 new neurons per cubic millimeter of tissue, and estimated that up to 1,000 new neurons may be born per day even in people in their 50s to 70s. These new neurons apparently arise not by mitosis of mature neurons (which are believed to be incapable of mitosis), but from a reserve pool of embryonic stem cells. It remains unknown whether new neurons are produced late in life in other regions of the brain.

Mitosis
Mitosis (my-TOE-sis), in the sense used here, is the process by which a cell divides into two daughter cells with identical copies of its DNA. (Some define it as division of the nucleus only and do not include the subsequent cell division.) Mitosis has four main functions:

1. formation of a multicellular embryo from a fertilized egg;
2. tissue growth
3. replacement of old and dead cells; and
4. repair of injured tissues.
Egg and sperm cells are produced by a combination of mitosis and another form of cell division, meiosis, described in chapter 27. Otherwise, all cells of the body are produced entirely by mitosis. Four phases of mitosis are recognizable—prophase, metaphase, anaphase, and telophase (fig. 4.13). In prophase,2 at the outset of mitosis, the chromosomes supercoil into short, dense rods (fig. 4.14) which are easier to distribute to daughter cells than the long, delicate chromatin. A chromosome at this stage consists of two genetically identical bodies called sister chromatids, joined together at a pinched spot called the centromere. At prophase, there are 46 chromosomes, two chromatids per chromosome, and one molecule of DNA in each chromatid. The nuclear envelope disintegrates during prophase and releases the chromosomes into the cytosol. The centrioles begin to sprout elongated microtubules, which push the centrioles apart as they grow. Eventually, a pair of centrioles lies at each pole of the cell. In metaphase,3 the chromosomes line up at random along the midline of the cell. Microtubules grow toward them from each centriole and some attach to the centromeres. This forms a football-shaped array called the mitotic spindle. Shorter microtubules also radiate from each centriole pair to form a star-shaped array called an aster.4 These microtubules anchor the centrioles to the nearby plasma membrane. In anaphase,5 each centromere divides in two and chromatids separate from each other. Each chromatid is now a chromosome in its own right. These two daughter chromosomes migrate to opposite poles of the cell, with their centromeres leading the way and their arms trailing behind. There is some evidence that the spindle fiber acts a little like a railroad track, and a protein complex in the centromere called the kinetochore6 (kih-NEE-toe-core) acts as a molecular motor that propels the chromosome along the track. One of the kinetochore proteins is dynein, the same motor molecule that causes movement of cilia and flagella (see chapter 3). Since sister chromatids are genetically identical, and since each daughter cell receives one chromatid from each metaphase chromosome, you can see why the daughter cells of mitosis are genetically identical. In telophase,7 the chromosomes cluster on each side of the cell. The rough ER produces a new nuclear envelope around each cluster, and the chromosomes begin to uncoil and return to the thinly dispersed chromatin form. The mitotic spindle breaks up and vanishes. Each new nucleus forms nucleoli, indicating it has already begun making RNA and preparing for protein synthesis. Telophase is the end of nuclear division but overlaps with cytokinesis8 (SY-toe-kih-NEE-sis), division of the cytoplasm. Cytokinesis is achieved by the motor protein myosin pulling on microfilaments of actin in the membrane skeleton. This creates a crease called the cleavage furrow around the equator of the cell, and the cell eventually pinches in two. Interphase has now begun for these new cells.

Timing of Cell Division
One of the most important questions in biology is what signals cells when to divide and when to stop. The activation and inhibition of cell division are subjects of intense research for obvious reasons such as management of cancer and tissue repair. Cells divide when (1) they grow large enough to have enough cytoplasm to distribute to their two daughter cells; (2) they have replicated their DNA, so they can give each daughter cell a duplicate set of genes; (3) they receive an adequate supply of nutrients; (4) they are stimulated by growth factors, chemical signals secreted by blood platelets, kidney cells, and other sources; or (5) neighboring cells die, opening up space in a tissue to be occupied by new cells. Cells stop dividing when nutrients or growth factors are withdrawn or when they snugly contact neighboring cells. The cessation of cell division in response to contact with other cells is called contact inhibition.

Chromosomes and Heredity
Objectives
When you have completed this section, you should be able to
• describe the paired arrangement of chromosomes in the human karyotype;
• define allele and discuss how alleles affect the traits of an individual; and
• discuss the interaction of heredity and environment in producing individual traits.
Heredity is the transmission of genetic characteristics from parent to offspring. Several traits and diseases discussed in the forthcoming chapters are hereditary: baldness, blood types, color blindness, and hemophilia, for example. Thus it is appropriate at this point to lay the groundwork for these discussions by introducing a few basic principles of normal heredity. Hereditary defects are described in chapter 29 along with nonhereditary birth defects.

The Karyotype
A karyotype (fig. 4.15) is a chart of the chromosomes isolated from a cell at metaphase, arranged in order by size and structure. It reveals that most human cells, with the exception of germ cells (described shortly), contain 23 pairs of similar-looking chromosomes (except for X and Y chromosomes). The two chromosomes in each pair are called homologous9 (ho-MOLL-uh-gus) chromosomes. One is inherited from the mother and one from the father. Two chromosomes, designated X and Y, are called sex chromosomes and the other 22 pairs are called autosomes (AW-toe-somes). A female normally has a homologous pair of X chromosomes, whereas a male has one X chromosome and a much smaller Y chromosome The paired state of the homologous chromosomes results from the fact that a sperm cell bearing 23 chromosomes fertilizes an egg, which also has 23. Sperm and egg cells, and the cells on their way to becoming sperm and eggs, are called germ cells. All other cells of the body are called somatic cells. Somatic cells are described as diploid10 because their chromosomes are in homologous pairs, whereas germ cells beyond a certain stage of development are haploid,11 meaning they contain half as many chromosomes as the somatic cells. In meiosis (see chapter 27), homologous chromosomes become segregated from each other into separate daughter cells leading to the haploid sex cells. At fertilization, one set of paternal (sperm) chromosomes unites with one set of maternal (egg) chromosomes, restoring the diploid number to the fertilized egg and the somatic cells that arise from it. Although the two chromosomes of a homologous pair appear to be identical, they come from different parents and therefore are not genetically identical.

Genes and Alleles
Each chromosome carries many genes. The location of a particular gene on a chromosome is called its locus. Homologous chromosomes have the same gene at the same locus, although they may carry different forms of that gene, called alleles12 (ah-LEELS), which produce alternative forms of a particular trait. Frequently, one allele is dominant and the other one recessive. If at least one chromosome carries the dominant allele, the corresponding trait is usually detectable in the individual. A dominant allele masks the effect of any recessive allele that may be present. Recessive alleles are therefore expressed only when present on both of the homologous chromosomes— that is, when the individual has no dominant allele at that locus. Typically, but not always, dominant alleles code for a normal, functional protein and recessive alleles for a nonfunctional variant of the protein. The shape of the outer ear presents an example of dominant and recessive genetic effects. When the ears are developing in a fetus, a “death signal” is often activated in cells that attach the earlobe to the side of the head. These cells die, causing the earlobe to separate from the head. A person will then have “detached earlobes.” This occurs in people who have either one or two copies of a dominant allele which we will denote D. If both homologous chromosomes have the recessive version of this gene, d, the cell suicide program is not activated, and the earlobes remain attached (fig. 4.16a). (It is customary to represent a dominant allele with a capital letter and a recessive allele with its lowercase equivalent.) Individuals with two identical alleles, such as DD or dd, are said to be homozygous13 (HO-mo-ZY-gus) for that trait. If the homologous chromosomes have different alleles for that gene (Dd), the individual is heterozygous14 (HET-eroh-ZY-gus). The alleles that an individual possesses for a particular trait constitute the genotype (JEE-no-type). A detectable trait such as attached or detached earlobes, resulting either from the genotype or from environmental influences, is called the phenotype15 (FEE-no-type). We say that an allele is expressed if it shows in the phenotype of an individual. Earlobe allele d is expressed only when it is present in a homozygous state (dd); allele D is expressed whether it is homozygous (DD) or heterozygous (Dd). The only way most recessive alleles can be expressed is for an individual to inherit them from both parents. Recessive traits can “skip” one or more generations. A diagram called a Punnett square (fig. 4.16b) shows how two heterozygous parents with detached earlobes can produce a child with attached lobes. Across the top are the two genetically possible types of eggs the mother could produce, and on the left side are the possible types of sperm from the father. The four cells of the square show the genotypes and phenotypes that would result from each possible combination of sperm and egg. You can see that three of the possible combinations would produce a child with detached lobes (genotypes DD and Dd), but one combination (dd) would produce a child with attached lobes. Therefore, the attached-lobe trait skipped the parental generation in this case but could be expressed in their child. This phenomenon becomes more significant when parents are heterozygous carriers of hereditary diseases such as cystic fibrosis—individuals who carry a recessive allele and may pass it on, but do not phenotypically express it in themselves. For some hereditary diseases, tests are available to detect carriers and allow couples to weigh their risk of having children with genetic disorders. Genetic counselors perform genetic testing or refer clients for tests, advise couples on the probability of transmitting genetic diseases, and assist people in coping with genetic disease

.

Multiple Alleles, Codominance, and Incomplete Dominance

.

Some genes exist in more than two allelic forms—that is, there are multiple alleles within the collective genetic makeup, or gene pool, of the population as a whole. For example, there are over 100 alleles responsible for cystic fibrosis, and there are 3 alleles for ABO blood types. Two of the ABO blood type alleles are dominant and symbolized with a capital I (for immunoglobulin) and a superscript: I A and I B . There is one recessive allele, symbolized with a lowercase i. Which two alleles one inherits determines the blood type, as follows
.
. Genotype Phenotype IAIA Type A
. IAi Type A
. IBIB Type B
. IBi Type B
. IAIB Type AB
. ii Type O
.
Some alleles are equally dominant, or codominant. When both of them are present, both are phenotypically expressed. For example, a person who inherits allele I A from one parent and I B from the other has blood type AB. These alleles code for enzymes that produce the surface glycoproteins of red blood cells. Type AB means that both A and B glycoproteins are present, and type O means that neither of them is present. Other alleles exhibit incomplete dominance. When two different alleles are present, the phenotype is intermediate between the traits that each allele would produce alone. Familial hypercholesterolemia, the disease discussed in insight 3.3 (p. 113), is a good example. Individuals with two abnormal alleles die of heart attacks in childhood, those with only one abnormal allele typically die as young adults, and those with two normal alleles have normal life expectancies. Thus, the heterozygous individuals suffer an effect between the two extremes.

Polygenic Inheritance and
Polygenic (multiple-gene) inheritance (fig. 4.17a) is a phenomenon in which genes at two or more loci, or even on different chromosomes, contribute to a single phenotypic trait. Human eye and skin colors are normal polygenic traits, for example. They result from the combined expression of all the genes for each trait. Several diseases are also thought to stem from polygenic inheritance, including some forms of alcoholism, mental illness, cancer, and heart disease. Pleiotropy (ply-OT-roe-pee) (fig. 4.17b) is a phenomenon in which one gene produces multiple phenotypic effects. Sickle-cell disease, for example, is caused by a recessive allele that changes one amino acid in hemoglobin. It causes red blood cells (RBCs) to assume an abnormally elongated, pointed shape when oxygen levels are low, and it makes them sticky and fragile. As RBCs rupture, a person becomes anemic and the spleen becomes enlarged. Because of the deficiency of RBCs, the blood carries insufficient oxygen to the tissues, resulting in multiple, far-reaching effects on different parts of the body (see chapter 18).

Sex Linkage
Sex-linked traits are carried on the X or Y chromosome and therefore tend to be inherited by one sex more than the other. Men are more likely than women to have redgreen color blindness or hemophilia, for example, because the allele for each is recessive and located on the X chromosome (X-linked). Women have two X chromosomes. If a woman inherits the recessive hemophilia allele (h) on one of her X chromosomes, there is still a good chance that her other X chromosome will carry a dominant allele (H). H codes for normal blood-clotting proteins, so her blood clots normally. Men, on the other hand, have only one X chromosome and normally express any recessive allele found there (fig. 4.18). Ironically, even though this hemophilia is far more common among men than women, a man can inherit it only from his mother. Why? Because only his mother contributes an X chromosome to him. If he inherits h on his mother’s X chromosome, he will have hemophilia. He has no “second chance” to inherit a normal allele on a second X chromosome. A woman, however, gets an X chromosome from both parents. Even if one parent transmits the recessive allele to her, the chances are high that she will inherit a normal allele from her other parent. She would have to have the extraordinarily bad luck to inherit it from both parents in order for her to have a trait such as hemophilia or red-green color blindness. The X chromosome is thought to carry about 260 genes, most of which have nothing to do with determining an individual’s sex. There are so few functional genes on the Y chromosome—concerned mainly with development of the testes—that virtually all sex-linked traits are associated with the X chromosome.

Penetrance and Environmental Effects
People do not inevitably exhibit the phenotypes that would be predicted from their genotypes. For example, there is a dominant allele that causes polydactyly,16 the presence of extra fingers or toes. We might predict that since it is dominant, anyone who inherited the allele would exhibit this trait. Most do, but others known to have the allele have the normal number of digits. Penetrance is the percentage of a population with a given genotype that actually exhibits the predicted phenotype. If 80% of people with the polydactyly allele actually exhibit extra digits, the allele has 80% penetrance. Another reason the connection between genotype and phenotype is not inevitable is that environmental factors play an important role in the expression of all genes. At the very least, all gene expression depends on nutrition (fig. 4.19). Children born with the hereditary disease phenylketonuria (FEN-il-KEE-toe-NEW-ree-uh) (PKU), for example, become retarded if they eat a normal diet. However, if PKU is detected early, a child can be placed on a diet low in phenylalanine (an amino acid) and achieve normal mental development. No gene can produce a phenotypic effect without nutritional and other environmental input, and no nutrients can produce a body or specific phenotype without genetic instructions that tell cells what to do with them. Just as you need both a recipe and ingredients to make a cake, it takes both heredity and environment to make a phenotype.

Dominant and Recessive Alleles at the Population Level
It is a common misconception that dominant alleles must be more common in the gene pool than recessive alleles. The truth is that dominance and recessiveness have little to do with how common an allele is. For example, type O is the most common ABO blood type in North America, but it is caused by the recessive allele i. Blood type AB, caused by the two dominant ABO alleles, is the rarest. Polydactyly, caused by a dominant allele, also is rare in the population

ncer Proper tissue development depends on a balance between cell division and cell death. When cells multiply faster than they die, they sometimes produce abnormal growths called tumors, or neoplasms.17 The study of tumors is called oncology.18 Benign19 (beh-NINE) tumors are surrounded by a connective tissue capsule, grow slowly, and do not spread to other organs. They are still potentially lethal—even slowgrowing tumors can kill by compressing brain tissue, nerves, blood vessels, or airways. The term cancer refers to malignant20 (muh-LIG-nent) tumors, which are unencapsulated, fast-growing, and spread easily to other organs by way of the blood or lymph. The word cancer21 dates to Hippocrates, who compared the distended veins in some breast tumors to the outstretched legs of a crab. Malignant cells exhibit no contact inhibition or respect for tissue boundaries; they readily grow into other tissues and replace healthy cells. About 90% of cancer deaths result from this spreading, called metastasis22 (meh-TASS-tuh-sis), rather than from the primary (original) tumor. Cancer is classified according to the cells or tissues in which the tumor originates: Name Origin Carcinoma Epithelial cells Melanoma Pigment-producing skin cells (melanocytes) Sarcoma Bone, other connective tissue, or muscle Leukemia Blood-forming tissues Lymphoma Lymph nodes Causes of Cancer The World Health Organization estimates that 60% to 70% of cancer is caused by environmental agents called carcinogens23 (car-SIN-ohjens). These fall into three categories: 1. Chemicals such as cigarette tar, nitrites and other food preservatives, and numerous industrial chemicals. 2. Radiation such as  rays,  particles, particles, and ultraviolet radiation. 3. Viruses such as type 2 herpes simplex (implicated in some cases of uterine cancer) and hepatitis C (implicated in some liver cancer). Carcinogens are mutagens24 (MEW-tuh-jens)—they trigger gene mutations. We have several defenses against mutagens: (1) scavenger cells may remove them before they cause genetic damage; (2) peroxisomes neutralize nitrites, free radicals, and other carcinogenic oxidizing agents; and (3) nuclear enzymes detect and repair damaged DNA. If these mechanisms fail, or if they are overworked by heavy exposure to mutagens, a cell may die of genetic damage, it may be recognized and destroyed by the immune system before it can multiply, or it may multiply and produce a tumor. Even then, tumors may be destroyed by a substance called tumor necrosis factor (TNF), secreted by macrophages and certain white blood cells. Growth Factors and Cancer Genes Cancer researchers have linked many forms of cancer to abnormal growth factors or growth factor receptors. Most cells cannot divide unless a growth factor binds to a receptor on their surface. When a growth factor binds to its receptor, the receptor activates cell-division enzymes in the cell. This stimulates a cell to leave the G0 phase, undergo mitosis, and develop (differentiate) into various kinds of mature, functional cells. Two types of genes have been identified as responsible for malignant tumors—oncogenes and tumor suppressor genes. Oncogenes are mutated, “misbehaving” forms of normal genes called protooncogenes. Healthy proto-oncogenes code for growth-factors or growth-factor receptors, whereas mutated oncogenes cause malfunctions in the growth-factor mechanism. An oncogene called sis, for example, causes excessive secretion of growth factors that stimulate blood vessels to grow into a tumor and supply it with the rich blood supply that it requires. An oncogene known as ras, responsible for about one-quarter of human cancers, codes for abnormal growth-factor receptors. These receptors act like a switch stuck in the on position, sending constant cell division signals even when there is no growth factor bound to them. Many cases of breast and ovarian cancer are caused by an oncogene called erbB2. Tumor suppressor (TS) genes inhibit the development of cancer. They may act by opposing the action of oncogenes, promoting DNA repair, or controlling the normal histological organization of tissues, which is notably lacking in malignancies. A TS gene called p16 acts by inhibiting one of the enzymes that drives the cell cycle. Thus, if oncogenes are like the “accelerator” of the cell cycle, then TS genes are like the “brake.” Like other genes, TS genes occur in homologous pairs, and even one normal TS gene in a pair is sometimes sufficient to suppress cancer. Damage to both members of a pair, however, removes normal controls over cell division and tends to trigger cancer. The first TS gene discovered was the Rb gene, which causes retinoblastoma, an eye cancer of infants. Retinoblastoma occurs only if both copies of the Rb gene are damaged. In the case of a TS gene called p53, however, damage to just one copy is enough to trigger cancer. Gene p53 is a large gene vulnerable to many cancer-causing mutations; it is involved in leukemia and in colon, lung, breast, liver, brain, and esophageal tumors. Cancer often occurs only when several mutations have accumulated at different gene sites. Colon cancer, for example, requires damage to at least three TS genes on chromosomes 5, 17, and 18 and activation of an oncogene on chromosome 12. It takes time for so many mutations to accumulate, and this is one reason why colon cancer afflicts elderly people more than the young. In addition, the longer we live, the more carcinogens we are exposed to, the less efficient our DNA and tissue repair mechanisms become, and the less effective our immune system is at recognizing and destroying malignant cells.

The Lethal Effects of Cancer
Cancer is almost always fatal if it is not treated. Malignant tumors can kill in several ways: • Cancer displaces normal tissue, so the function of the affected organ deteriorates. Lung cancer, for example, can destroy so much tissue that oxygenation of the blood becomes inadequate to support life. You might think that an increased number of cells in an organ such as the liver would enable it to function better. In malignant tumors, however, the cells are in an immature state and unable to carry out the functions of mature cells of the same organ. Also, a tumor often consists of cells that have metastasized from elsewhere and are not typical of the host organ anyway. A colon cancer whose malignant cells have metastasized to the liver, for example, replaces liver tissue but cannot perform any of the liver’s essential functions.
• Tumors can invade blood vessels, causing fatal hemorrhages.
• Tumors can block vital passageways. The growth of a tumor can put pressure on a bronchus of the lung, obstructing air flow and causing pulmonary collapse, or it can compress a major blood vessel, reducing the delivery of blood to a vital organ or its return to the heart.
• Tumors have a high metabolic rate and compete with healthy tissues for nutrition. Other organs of the body may even break down their own proteins to nourish the tumor. This leads to general weakness, fatigue, emaciation, and susceptibility to infections. Some forms of cancer cause cachexia (ka-KEX-ee-ah), an extreme wasting away of muscular and adipose tissue that cannot be corrected with nutritional therapy.

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