Biology For Dummies

Part II Cell Reproduction and Genetics: Let’s Talk about Sex, Baby

Chapter 9

Engineering the Code: DNA Technology

In This Chapter

Figuring out how DNA technology works

Getting to know the Human Genome Project

Debating the benefits of genetically modified organisms

Gregor Mendel’s pea plant experiments in the 1850s (which we fill you in on in Chapter 7) began a scientific exploration into the mysteries of heredity that continues to this day. After Mendel showed that traits were controlled by hereditary factors that pass from one generation to the next, scientists were determined to figure out the nature of these factors and how they were transmitted. They discovered the presence of DNA in cells, observed the movement of chromosomes during cell division, and conducted experiments demonstrating that DNA is in fact the hereditary material.

Almost 100 years after Mendel, James Watson and Francis Crick figured out that DNA was a double helix and proposed how it might be copied. Scientists deciphered the genetic code and explored how to work with it in the lab. During the last 40 years, scientists have developed an amazing array of tools to read DNA, copy it, cut it, sort it, and put it together in new combinations. The power of this DNA technology is so great that scientists have even determined the sequence of all the chromosomes in human cells as part of the Human Genome Project. A new world of human heredity is now open for exploration as scientists seek to understand the meanings hidden within human DNA — what they find out will likely change the way we see ourselves and our place in the world.

In this chapter, we get you acquainted with all that’s involved in DNA technology and explore the ways scientists have mapped and manipulated the human genome and the genomes of other species.

Understanding Just What’s Involved in DNA Technology

For years the very structure of DNA made studying it rather challenging. After all, DNA is incredibly long and very tiny. Fortunately, the advent of DNA technology, the tools and techniques used for reading and manipulating the DNA code, has made working with DNA much easier. Scientists can even combine DNA from different organisms to artificially create materials such as human proteins or to give crop plants new characteristics. They can also compare different versions of the same gene to see exactly where disease-causing variations occur.

The following sections break down the various aspects of DNA technology so you can see how they all combine to provide a window into the very essence of existence.

Cutting DNA with restriction enzymes

Scientists use restriction enzymes, essentially little molecular scissors, in the lab to cut DNA into smaller pieces so they can analyze and manipulate it more easily. Each restriction enzyme recognizes and can attach to a certain sequence on DNA called a restriction site. The enzymes slide along the DNA, and wherever they find their restriction site, they cut the DNA helix.

Figure 9-1 shows how a restriction enzyme can make a cut in a circular piece of DNA and turn it into a linear piece.

Figure 9-1:Restriction enzymes.

Combining DNA from different sources

After DNA has been chopped into smaller, more workable bits (see the preceding section), scientists can combine pieces of DNA to change the characteristics of a cell. For example, they can put genes into crop plants to make them resistant to pesticides or to increase their nutritional value. This manipulation of a cell’s genetic material in order to change its characteristics is called genetic engineering.

Because the DNA from all cells is essentially the same, scientists can even combine DNA from very different sources. For example, human DNA can be combined with bacterial DNA.

 When a DNA molecule contains DNA from more than one source, it’s called recombinant DNA.

If a recombinant DNA molecule containing bacterial and human genes is put into bacterial cells, the bacteria read the human genes like their own and begin producing human proteins that scientists can use in medicine and scientific research. Table 9-1 lists a few useful proteins that are made through genetic engineering.

Table 9-1 Some Beneficial Genetically Engineered Proteins

Alpha-interferon

Used to shrink tumors and treat hepatitis

Beta-interferon

Used to treat multiple sclerosis

Human insulin

Used to treat people with diabetes as a safer alternative to pig insulin

Tissue plasminogen activator (tPA)

Given to patients who’ve just had a heart attack or stroke to dissolve the blockage that caused the attack

Here’s how scientists go about putting a human gene into a bacterial cell:

1. First, they choose a restriction enzyme that forms sticky ends when it cuts DNA.

Sticky ends are pieces of single-stranded DNA that are complementary to other pieces of single-stranded DNA. Because they’re complementary, the pieces of single-stranded DNA can stick to each other by forming hydrogen bonds (see Chapter 3 for more on bonds and DNA). For example, the sticky ends shown in Figure 9-1 have the sequences 5'AATT3' and 3'TTAA5'. A and T are complementary base pairs, so these ends can form hydrogen bonds and stick to each other.

2. Next, they cut the human DNA and bacterial DNA with the same restriction enzyme.

When you cut bacterial DNA and human DNA with the same restriction enzyme, all the DNA fragments have the same sticky ends.

3. Then they combine human DNA and bacterial DNA.

Because the two types of DNA have the same sticky ends, some of the pieces stick together.

4. Finally, they use the enzyme DNA ligase to seal the sugar-phosphate backbone between the bacterial and human DNA.

DNA ligase forms covalent bonds between the pieces of DNA, sealing together any pieces that are combined.

Using gel electrophoresis to separate molecules

Scientists separate molecules from cells such as DNA and proteins in order to study them. If a scientist wants to study just one protein, for example, she must separate that protein from the other proteins in the cell. When scientists want to separate DNA molecules from cells in order to look for relationships between DNA from two different sources, they use gel electrophoresis, which separates molecules based on their size and electrical charge.

Scientists conduct gel electrophoresis by inserting DNA molecules (see Figure 9-2a) into little pockets called wells within a slab of a gelatin-like substance (see Figure 9-2b). They then place the gel in a box, called an electrophoresis chamber, that’s filled with a salty, electricity-conducting buffer solution.

The DNA molecules, which have a negative charge, are attracted to the gel box’s positive electrode. When the scientists run an electrical current through the gel (see Figure 9-2c), the gel becomes like a racetrack for the DNA molecules, only instead of trying to cross the finish line, the DNA is trying to get to the positively charged end of the box.

When the power is turned off, all the DNA molecules stop where they are in the gel, and the scientists stain them. The stain sticks to the DNA, creating stripes called bands (see Figure 9-2d). Each band represents a collection of DNA molecules that are the same size and stopped in the same place in the gel.

Figure 9-2: Gel electrophoresis.

Copying a gene with PCR

The polymerase chain reaction (PCR) is a process that can turn a single copy of a gene into more than a billion copies in just a few hours. It gives medical researchers the ability to make many copies of a gene whenever they want to genetically engineer something (see the earlier “Combining DNA from different sources” section for more on genetic engineering).

 PCR targets the gene to be copied with primers, single-stranded DNA sequences that are complementary to sequences next to the gene to be copied.

To begin PCR, the DNA sample that contains the gene to be copied is combined with thousands of copies of primers that frame the gene on both sides (see Figure 9-3). DNA polymerase uses the primers to begin DNA replication and copy the gene (refer to Chapter 6 for more on DNA replication). The basic steps of PCR are repeated over and over until you have billions of copies of the DNA sequence between the two primers.

Figure 9-3: The polymerase chain reaction.

 PCR works a little like chain e-mails. If you get a chain e-mail and send it on to two friends, who each send it on to two of their friends, and so on, pretty soon everyone has seen the same e-mail. In PCR, first a DNA molecule is copied, then the copies are copied, and so on, until you have 30 billion copies in just a few hours.

Reading a gene with DNA sequencing

 DNA sequencing, which determines the order of nucleotides in a DNA strand, allows scientists to read the genetic code so they can study the normal versions of genes. It also allows them to make comparisons between normal versions of a gene and disease-causing versions of a gene. After they know the order of nucleotides in both versions, they can identify which changes in the gene cause the disease.

As you can see in Figure 9-4, DNA sequencing uses a special kind of nucleotide, called ddNTP (short for dideoxyribonucleotide triphosphate). Regular DNA nucleotides and ddNTPs are somewhat similar, but the ddNTPs are different enough that they stop DNA replication. When a ddNTP is added to a growing chain of DNA, DNA polymerase can’t add any more nucleotides. DNA sequencing uses this chain interruption to determine the order of nucleotides in a strand of DNA.

Most DNA sequencing done today is cycle sequencing, a process that creates partial copies of a DNA sequence, all of which are stopped at different points. After the partial copies are made, scientists load them into a machine that uses gel electrophoresis to put the copies into order by size. As the partial sequences pass through the machine, a laser reads a fluorescent tag on each ddNTP, noting the DNA sequence.

 Although both cycle sequencing and PCR copy DNA, the two processes are quite different. Cycle sequencing uses both normal DNA nucleotides and ddNTPs and makes only partial copies of DNA that are all slightly different. PCR uses only normal DNA nucleotides and makes exact copies of a DNA sequence.

Mapping the Genes of Humanity

The Human Genome Project (HGP) was a hugely ambitious task to determine the nucleotide sequence of all the DNA in a human cell. To give you an idea just how ambitious this project was, when it was first proposed in 1985, the pace of DNA sequencing was so slow that it would’ve taken 1,000 years to sequence the 24 unique human chromosomes (22 autosomes plus X and Y, as explained in Chapter 6). Fortunately, scientists cooperated and technology improved during the project, allowing the majority of the human genome to be sequenced by 2003. (A genome is the total collection of genes in a species.)

Figure 9-4:DNA sequencing.

 If you’re wondering why the HGP is a big deal, think of it this way. If you were a researcher and you wanted to study a specific human gene, first you’d have to know what chromosome it “lived” on. The map of nucleotide sequences created by the HGP is a huge step forward in providing the “address” of each human gene. Armed with a roadmap of where every gene is located, researchers can turn their attention toward making good use of that information, like seeking out the genes that cause disease.

The HGP and the technological advances that came along with it resulted in many other current and potential benefits to society, including

Drugs designed to best treat an individual person with minimal side effects

Earlier detection of disease

Exploration of microbial genomes for identification of species that can be used to produce new biofuels or clean up pollution

Comparison of DNA from crime scenes to that of suspects in order to help determine likely guilt or innocence

Study of the evolutionary relationships of life on Earth

Designer people?

As scientists delve deeper into the mysteries of the human genome, complex issues about the nature of humanity and the rights of individuals are generating fear and discussion. The questions people are pondering include the following:

If a person’s genome can be read, should insurance companies or employers be allowed to know about increased risks for disease?

Should people be allowed to screen their embryos to prevent diseased children from being born or to select only the ones with desired characteristics?

Should only people with “good” genetic stock be allowed to have children?

These questions may seem far-fetched, but history shows that they aren’t. After the work of Gregor Mendel became known and people understood that genes determine human traits, a group of people founded the eugenics movement. People who joined the eugenics movement believed that certain human characteristics were more desirable than others; they wanted to control human breeding to “better” the human race. These ideas were carried to extremes by the Nazis during World War II, leading to the extermination of whole groups of people who were judged to be undesirable.

Many people are afraid that greater knowledge about the human genome will again be used to harm. The reality is that knowledge brings power, and power can be used for good or evil. Scientists seek knowledge, but they can’t always control how that knowledge is used. What they can do, however, is be part of the conversation as people explore these complex moral issues. In fact, one of the primary goals of the Human Genome Project was to “address the ethical, legal, and social issues that may arise from the project.” That this statement was included in the primary goals of the project is a pretty big deal because scientific proposals are usually just about the science.

Genetically Modifying Organisms

Genetically modified organisms (abbreviated as GMOs and sometimes called genetically engineered organisms or transgenic organisms) contain genes from other species that were introduced using recombinant DNA technology (see the earlier “Combining DNA from different sources” section for more on this type of DNA technology). GMOs are a hot topic these days due to the controversy surrounding genetically modified crop plants and farm animals. The sections that follow take a look at both sides of the “Are GMOs good or bad?” debate.

Why GMOs are beneficial

Genetic modification has its upsides. It not only makes growing crops easier but it can also boost the profitability of those crops. And it may even help improve human health. Here are some specific scenarios that illustrate how GMOs can be beneficial:

If crop plants are given genes to resist herbicides and pesticides, then a farmer can spray the fields with those chemicals, killing only the weeds and pests, not the crop plant. This is much easier and less time-consuming than labor-intensive weeding. It can also increase crop yields and profits for the farmer.

If crop plants or farm animals raised for human consumption are given genes to improve their nutrition, people could be healthier. Improved nutrition in crop plants could be a huge benefit in poor countries where malnutrition stunts the growth and development of children, making them more susceptible to disease. One of the most famous examples of improved nutrition through genetic engineering is the creation of “golden rice” — rice that has been engineered to make increased amounts of a nutrient that’s necessary for vitamin A production. According to the World Health Organization, vitamin A deficiencies cause 250,000 to 500,000 children to go blind each year. The company that produced golden rice is giving the rice to poor countries for free so they can grow it for themselves and make it available to people who need it.

If farm animals raised for human consumption are given genes to increase their yield of meat, eggs, and milk, then more food may be available for the growing human population, and these greater yields may also increase profits for farmers. Currently, many dairy cows are given recombinant bovine growth hormone (rBGH) to increase their milk production. BGH is a normal growth hormone found in cows; rBGH is a slightly altered version that’s produced by genetically engineered bacteria. When rBGH is given to cows, the animals’ milk production increases by 10 to 15 percent.

Why GMOs cause concern

What make GMOs so controversial are the ethical concerns. The list of concerns surrounding genetic modification is long and so serious that some countries in the European Union have banned the sale of foods containing products from GMOs. The concerns expressed include the following:

The use of GMOs in agriculture unfairly benefits big agricultural companies and pushes out smaller farmers. Companies that produce seeds for genetically engineered crops retain patents on their products. The prices on these seeds can be much higher than for traditional crops, giving large agricultural companies an advantage in the marketplace. This issue is particularly worrisome when large agricultural companies from rich nations start competing in the global economy with smaller farmers from poor countries.

The use of GMOs in agriculture encourages unsound environmental practices and discourages best farming practices. Farmers who plant crops engineered for pesticide or herbicide resistance use chemicals rather than manual labor to control weeds and pests. Not only do these pesticides and herbicides affect the health of plants and animals living in the area around farms but they can also get into the drinking water and possibly affect human health. Also, large-scale plantings of just a few species of plants decrease the genetic diversity in food species and put the food supply at risk for large-scale catastrophes should one of the crop species fail.

Animals that are engineered to produce more milk, eggs, or meat may be at greater risk for health problems. Cows treated with rBGH to increase milk production get more infections in their milk ducts and have to be treated with antibiotics more often. Overuse of antibiotics is a human health concern because it reduces the effectiveness of antibiotics on bacteria that cause human infections.

Cross-pollination between genetically engineered plants and wild plants can spread resistant genes into wild plants. Farmers can put up fences, but wind blows all over the place. If a crop plant that contains a gene for herbicide resistance can pollinate a wild plant, then the wild plant could pick up that gene, creating a weed species that can’t be controlled.

Increased levels of bovine hormones in dairy products may have effects on humans who drink the milk. When rBGH is injected into cows to pump up their milk production, the levels of IGF-1 (an insulin-like protein) in their bodies and milk increase. Human bodies also make IGF-1, and increased levels of this hormone have been found in patients with some types of cancer. People are worried that increased IGF-1 in milk from hormone-treated cows may put them at greater risk for cancer, but no clear link has yet been found between IGF-1 in milk and human cancer.

Genetic modification of foods may introduce allergens into foods, and labeling may not be sufficient to protect the consumer. People who have food allergies have to be very careful about which foods they eat. However, if foods contain products from GMOs, it’s possible that the introduced genes produced a product that’s not indicated on the food label.

Fear of “unnatural” practices and new technologies makes people afraid of GMOs and lowers their value in the marketplace. Some people see humans as becoming out of balance with the rest of nature and think we need to slow down and try to leave less of a footprint on the world. For some, this belief includes rejecting technology that alters organisms from their natural state.

DNA fingerprinting

Although the genomes of human beings are extremely similar — 99.9 percent similar, to be exact — people do have some unique sequences that make them, well, unique. In fact, all people have a DNA fingerprint, which is their personal genetic profile. This DNA fingerprint is found in 13 areas of the human genome that tend to be very different from person to person. By looking at all 13 areas, not just 1 or 2 of them, scientists decrease the chances of getting a random match between two samples.

DNA fingerprinting is very helpful in forensics, the science that collects and interprets physical evidence for legal purposes. However, solving crimes isn’t the only use for DNA fingerprinting. Some of its other interesting uses include

Identifying the bodies of victims of disasters or massacres when the bodies themselves are unrecognizable

Testing paternity, maternity, and other familial relationships

Examining foods for evidence of genetically modified organisms (GMOs)

Detecting harmful bacteria in food and water

Making genetic pedigrees of crop plants and different breeds of animals

Revealing the presence of endangered and protected species among materials taken from poachers