Beautiful DNA

Up until the 1950s, scientists knew a good deal about heredity, but they didn't have a clue what DNA looked like. In order to learn more about DNA and its structure, some scientists experimented with using X rays as a form of molecular photography.

In 1953, Watson and Crick created their historic model of the shape of DNA: the double helix.
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Rosalind Franklin, a physical chemist working with Maurice Wilkins at King's College in London, was among the first to use this method to analyze genetic material. Her experiments produced what were referred to at the time as "the most beautiful X-ray photographs of any substance ever taken."

Other scientists, including zoologist James Watson and physicist Francis Crick, both working at Cambridge University in the United Kingdom, were trying to determine the shape of DNA too. Ultimately, this line of research revealed one of the most profound scientific discoveries of the 20th century: that DNA exists as a double helix.

The 1962 Nobel Prize in physiology or medicine was awarded to Watson, Crick and Wilkins for this work. Although Franklin did not earn a share of the prize due to her untimely death at age 38, she is widely recognized as having played a significant role in the discovery.

Rosalind Franklin's original X-ray diffraction photo revealed the physical structure of DNA.
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The spiral staircase-shaped double helix has attained global status as the symbol for DNA. But what is so beautiful about the discovery of the twisting ladder structure isn't just its good looks. Rather, the structure of DNA taught researchers a fundamental lesson aboutgenetics. It taught them that the two connected strands—winding together like parallel handrails—were complementary to each other, and this unlocked the secret of how genetic information is stored, transferred and copied.

In genetics, complementary means that if you know the sequence of nucleotide building blocks on one strand, you know the sequence of nucleotide building blocks on the other strand: A always matches up with T and C always links to G (see drawing).

Long strings of nucleotides form genes, and groups of genes are packaged tightly into structures called chromosomes. Every cell in your body except for eggs, sperm and red blood cells contains a full set of chromosomes in its nucleus.

If the chromosomes in one of your cells were uncoiled and placed end to end, the DNA would be about 6 feet long. If all the DNA in your body were connected in this way, it would stretch approximately 67 billion miles! That's nearly 150,000 round trips to the Moon.

DNA Structure

The long, stringy DNA that makes up genes is spooled within chromosomes inside the nucleus of a cell. (Note that a gene would actually be a much longer stretch of DNA than what is shown here.)

DNA consists of two long, twisted chains made up of nucleotides. Each nucleotide contains one base, one phosphate molecule and the sugar molecule deoxyribose. The bases in DNA nucleotides are adenine, thymine, cytosine and guanine.

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Copycat

Humans have 23 pairs of chromosomes. Male DNA (pictured here) contains an X and a Y chromosome, whereas female DNA contains two X chromosomes.
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It's astounding to think that your body consists of trillions of cells. But what's most amazing is that it all starts with one cell. How does this massive expansion take place?

As an embryo progresses through development, its cells must reproduce. But before a cell divides into two new, nearly identical cells, it must copy its DNA so there will be a complete set of genes to pass on to each of the new cells.

To make a copy of itself, the twisted, compacted double helix of DNA has to unwind and separate its two strands. Each strand becomes a pattern, or template, for making a new strand, so the two new DNA molecules have one new strand and one old strand.

The copy is courtesy of a cellular protein machine calledDNA polymerase, which reads the template DNA strand and stitches together the complementary new strand. The process, called replication, is astonishingly fast and accurate, although occasional mistakes, such as deletions or duplications, occur. Fortunately, a cellular spell-checker catches and corrects nearly all of these errors.

When DNA polymerase makes an error while copying a gene's DNA sequence, the mistake is called a mutation. In this example, the nucleotide G has been changed to an A.

During DNA replication, each strand of the original molecule acts as a template for the synthesis of a new, complementary DNA strand.

Mistakes that are not corrected can lead to diseases such as cancer and certain genetic disorders. Some of these include Fanconi anemia, early aging diseases and other conditions in which people are extremely sensitive to sunlight and some chemicals.

DNA copying is not the only time when DNA damage can happen. Prolonged, unprotected sun exposure can cause DNA changes that lead to skin cancer, and toxins in cigarette smoke can cause lung cancer.

It may seem ironic, then, that many drugs used to treat cancer work by attacking DNA. That's because these chemotherapy drugs disrupt the DNA copying process, which goes on much faster in rapidly dividing cancer cells than in other cells of the body. The trouble is that most of these drugs do affect normal cells that grow and divide frequently, such as cells of the immune system and hair cells.

Understanding DNA replication better could be a key to limiting a drug's action to cancer cells only.

Let's Call It Even

After copying its DNA, a cell's next challenge is getting just the right amount of genetic material into each of its two offspring.

Most of your cells are called diploid ("di" means two, and "ploid" refers to sets of chromosomes) because they have two sets of chromosomes (23 pairs). Eggs and sperm are different; these are known as haploid cells. Each haploid cell has only one set of 23 chromosomes so that at fertilization the math will work out: A haploid egg cell will combine with a haploid sperm cell to form a diploid cell with the right number of chromosomes: 46.

Chromosomes are numbered 1 to 22, according to size, with 1 being the largest chromosome. The 23rd pair, known as the sex chromosomes, are called X and Y. In humans, abnormalities of chromosome number usually occur during meiosis, the time when a cell reduces its chromosomes from diploid to haploid in creating eggs or sperm.

What happens if an egg or a sperm cell gets the wrong number of chromosomes, and how often does this happen?

Trisomy, the hallmark of Down syndrome, results when a baby is born with three copies of chromosome 21 instead of the usual two.

Molecular biologist Angelika Amon of the Massachusetts Institute of Technology in Cambridge says that mistakes in dividing DNA between daughter cells during meiosis are the leading cause of human birth defects and miscarriages. Current estimates are that 10 percent of all embryos have an incorrect chromosome number. Most of these don't go to full term and are miscarried.

In women, the likelihood that chromosomes won't be apportioned properly increases with age. One of every 18 babies born to women over 45 has three copies of chromosome 13, 18 or 21 instead of the normal two, and this improper balancing can cause trouble. For example, three copies of chromosome 21 lead to Down syndrome.

To make her work easier, Amon—like many other basic scientists—studies yeast cells, which separate their chromosomes almost exactly the same way human cells do, except that yeast do it much faster. A yeast cell copies its DNA and produces daughter cells in about 1 1/2 hours, compared to a whole day for human cells.

The yeast cells she uses are the same kind bakeries use to make bread and breweries use to make beer!

Amon has made major progress in understanding the details of meiosis. Her research shows how, in healthy cells, gluelike protein complexes called cohesins release pairs of chromosomes at exactly the right time. This allows the chromosomes to separate properly.

These findings have important implications for understanding and treating infertility, birth defects and cancer.

Meiosis

Getting the Message

So, we've described DNA—its basic properties and how our bodies make more of it. But how does DNA serve as the language of life? How do you get a protein from a gene?

There are two major steps in making a protein. The first is transcription, where the information coded in DNA is copied into RNA. The RNA nucleotides are complementary to those on the DNA: a C on the RNA strand matches a G on the DNA strand.

1. RNA polymerase transcribes DNA to make messenger RNA (mRNA). 2. The mRNA sequence (dark red strand) is complementary to the DNA sequence (blue strand). 3. On ribosomes, transfer RNA (tRNA) helps convert mRNA into protein. 4. Amino acids link up to make a protein.

The only difference is that RNA pairs a nucleotide called uracil (U), instead of a T, with an A on the DNA.

A protein machine called RNA polymerase reads the DNA and makes the RNA copy. This copy is called messenger RNA, or mRNA, because it delivers the gene's message to the protein-producing machinery.

At this point you may be wondering why all of the cells in the human body aren't exactly alike, since they all contain the same DNA.What makes a liver cell different from a brain cell? How do the cells in the heart make the organ contract, but those in skin allow us to sweat?

Cells can look and act differently, and do entirely different jobs, because each cell "turns on," or expresses, only the genes appropriate for what it needs to do.

RNA polymerase (green) and one end of a DNA strand (blue) are attached to clear beads pinned down in two optical traps. As RNA polymerase moves along the DNA, it creates an RNA copy of a gene, shown here as a pink strand.
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That's because RNA polymerase does not work alone, but rather functions with the aid of many helper proteins. While the core part of RNA polymerase is the same in all cells, the helpers vary in different cell types throughout the body.

You'd think that for a process so essential to life, researchers would know a lot about how transcription works. While it's true that the basics are clear—biologists have been studying gene transcribing by RNA polymerases since these proteins were first discovered in 1960— some of the details are actually still murky.

The biggest obstacle to learning more has been a lack of tools. Until recently, researchers were unable to get a picture at the atomic level of the giant RNA polymerase protein assemblies inside cells to understand how the many pieces of this amazing, living machine do what they do, and do it so well.

But our understanding is improving fast, thanks to spectacular technological advances. We have new X-ray pictures that are far more sophisticated than those that revealed the structure of DNA. Roger Kornberg of Stanford University in California used such methods to determine the structure of RNA polymerase. This work earned him the 2006 Nobel Prize in chemistry. In addition, very powerful microscopes and other tools that allow us to watch one molecule at a time provide a new look at RNA polymerase while it's at work reading DNA and producing RNA.

For example, Steven Block, also of Stanford, has used a physics technique called optical trapping to track RNA polymerase as it inches along DNA. Block and his team performed this work by designing a specialized microscope sensitive enough to watch the real-time motion of a single polymerase traveling down a gene on one chromosome.

The researchers discovered that molecules of RNA polymerase behave like battery-powered spiders as they crawl along the DNA ladder, adding nucleotides one at a time to the growing RNA strand. The enzyme works much like a motor, Block believes, powered by energy released during the chemical synthesis of RNA.

Nature's Cut-and-Paste Job

Genes are often interrupted by stretches of DNA (introns, blue) that do not contain instructions for making a protein. The DNA segments that do contain protein-making instructions are known as exons (green).

Several types of RNA play key roles in making a protein. The gene transcript (the mRNA) transfers information from DNA in the nucleus to the ribosomes that make protein. Ribosomal RNA forms about 60 percent of the ribosomes. Lastly, transfer RNA carries amino acids to the ribosomes. As you can see, all three types of cellular RNAs come together to produce new proteins.

But the journey from gene to protein isn't quite as simple as we've just made it out to be. After transcription, several things need to happen to mRNA before a protein can be made. For example, the genetic material of humans and other eukaryotes (organisms that have a nucleus) includes a lot of DNA that doesn't encode proteins. Some of this DNA is stuck right in the middle of genes.

To distinguish the two types of DNA, scientists call the coding sequences of genes exons and the pieces in between introns (for intervening sequences).

If RNA polymerase were to transcribe DNA from the start of an intron-containing gene to the end, the RNA would be complementary to the introns as well as the exons.

To get an mRNA molecule that yields a working protein, the cell needs to trim out the intron sections and then stitch only the exon pieces together (see drawing). This process is called RNA splicing.

Arranging exons in different patterns, called alternative splicing, enables cells to make different proteins from a single gene.

Splicing has to be extremely accurate. An error in the splicing process, even one that results in the deletion of just one nucleotide in an exon or the addition of just one nucleotide in an intron, will throw the whole sequence out of alignment. The result is usually an abnormal protein—or no protein at all. One form of Alzheimer's disease, for example, is caused by this kind of splicing error.

Molecular biologist Christine Guthrie of the University of California, San Francisco, wants to understand more fully the mechanism for removing intron RNA and find out how it stays so accurate.

She uses yeast cells for these experiments. Just like human DNA, yeast DNA has introns, but they are fewer and simpler in structure and are therefore easier to study. Guthrie can identify which genes are required for splicing by finding abnormal yeast cells that mangle splicing.

So why do introns exist, if they're just going to be chopped out? Without introns, cells wouldn't need to go through the splicing process and keep monitoring it to be sure it's working right.

As it turns out, splicing also makes it possible for cells to create more proteins.

Think about all the exons in a gene. If a cell stitches together exons 1, 2 and 4, leaving out exon 3, the mRNA will specify the production of a particular protein. But instead, if the cell stitches together exons 1, 2 and 3, this time leaving out exon 4, then the mRNA will be translated into a different protein (see drawing).

By cutting and pasting the exons in different patterns, which scientists call alternative splicing, a cell can create different proteins from a single gene. Alternative splicing is one of the reasons why human cells, which have about 20,000 genes, can make hundreds of thousands of different proteins.