Chapter 1: How Genes Work: The New Genetics - National Institute of General Medical Sciences
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Chapter 1: How Genes Work
People have known for many years that living things inherit traits from        their parents. That common-sense observation led to agriculture, the purposeful        breeding and cultivation of animals and plants for desirable characteristics.        Firming up the details took quite some time, though. Researchers did not        understand exactly how traits were passed to the next generation until the        middle of the 20th century.
Now it is clear that genes are what carry our traits through generations and that genes are made of deoxyribonucleic acid (DNA) .        But genes themselves don't do the actual work. Rather, they serve as instruction        books for making functional molecules such as ribonucleic        acid (RNA) and proteins ,        which perform the chemical reactions in our bodies.
Proteins do many other things, too. They provide the body's main building        materials, forming the cell's architecture and structural components. But        one thing proteins can't do is make copies of themselves. When a cell needs        more proteins, it uses the manufacturing instructions coded in DNA.
The DNA code of a gene—the sequence of its individual DNA building        blocks, labeled A (adenine), T (thymine), C (cytosine) and G (guanine) and        collectively called nucleotides — spells out the exact order of a protein's building blocks, amino        acids .
Occasionally, there is a kind of typographical error in a gene's DNA sequence.        This mistake— which can be a change, gap or duplication—is called        a mutation .
A mutation can cause a gene to encode a protein that works incorrectly        or that doesn't work at all. Sometimes, the error means that no protein        is made.
But not all DNA changes are harmful. Some mutations        have no effect, and others produce new versions of proteins that may give        a survival advantage to the organisms that have them. Over time, mutations        supply the raw material from which new life forms evolve (see Chapter        3, "Life's Genetic Tree" ).
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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.
COLD SPRING HARBOR LABORATORY ARCHIVES
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.
OREGON STATE UNIVERSITY LIBRARIES SPECIAL COLLECTIONS
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 about genetics .        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.
 
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.
CYTOGENETICS LABORATORY, BRIGHAM AND WOMEN'S HOSPITAL
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 called DNA        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.
STEVEN BLOCK
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.
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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.
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All Together Now
Until recently, researchers looked at genes, and the proteins they encode,        one at a time. Now, they can look at how large numbers of genes and proteins        act, as well as how they interact. This gives them a much better picture        of what goes on in a living organism.
Already, scientists can identify all of the genes that are transcribed        in a cell—or in an organ, like the heart. And although researchers        can't tell you, right now, what's going on in every cell of your body while        you read a book or walk down the street, they can do this sort of "whole-body" scan for simpler, single-celled organisms like yeast.
Using a technique called genome-wide location analysis, Richard Young of        the Massachusetts Institute of Technology unraveled a "regulatory code" of living yeast cells, which have more than 6,000 genes in their genome.        Young's technique enabled him to determine the exact places where RNA polymerase's        helper proteins sit on DNA and tell RNA polymerase to begin transcribing        a gene.
Since he did the experiment with the yeast exposed to a variety of different        conditions,Young was able to figure out how transcription patterns differ        when the yeast cell is under stress (say, in a dry environment) or thriving        in a sugary-rich nutrient solution. Done one gene at a time, using methods        considered state-of-the-art just a few years ago, this kind of analysis        would have taken hundreds of years.
After demonstrating that his technique worked in yeast, Young then took        his research a step forward. He used a variation of the yeast method to        scan the entire human genome in small samples of cells taken from the pancreases        and livers of people with type 2 diabetes. He used the results to identify        genes that aren't transcribed correctly in people with the disease.
This information provides researchers with an important tool for understanding        how diabetes and other diseases are influenced by defective genes. By building        models to predict how genes respond in diverse situations, researchers may        be able to learn how to stop or jump-start genes on demand, change the course        of a disease or prevent it from ever happening.
Genetics and You: Nursery Genetics
While most genetic research uses lab organisms, test tubes and petri            dishes, the results have real consequences for people. Your first encounter            with genetic analysis probably happened shortly after you were born,            when a doctor or nurse took a drop of blood from the heel of your tiny            foot.
Lab tests performed with that single drop of blood can diagnose certain            rare genetic disorders as well as metabolic problems like phenylketonuria            (PKU).
Screening newborns in this way began in the 1960s in Massachusetts            with testing for PKU, a disease affecting 1 in 14,000 people. PKU is            caused by an enzyme that doesn't work properly due to a genetic mutation.            Those born with this disorder cannot metabolize the amino acid phenylalanine,            which is present in many foods. Left untreated, PKU can lead to mental            retardation and neurological damage, but a special diet can prevent            these outcomes. Testing for this condition has made a huge difference            in many lives.
Newborn screening is governed by individual states. This means that            the state in which a baby is born determines the genetic conditions            for which he or she will be screened. Currently, states test for between            28 and 54 conditions. All states test for PKU.
Although expanded screening for genetic diseases in newborns is advocated            by some, others question the value of screening for conditions that            are currently untreatable. Another issue is that some children with            mild versions of certain genetic diseases may be treated needlessly.
In 2006, the Advisory Committee on Heritable Disorders in Newborns            and Children, which assists the Secretary of the U.S. Department of            Health and Human Services, recommended a standard, national set of newborn            tests for 29 conditions, ranging from relatively common hearing problems            to very rare metabolic diseases.
Found in Translation
A ribosome consists of large and small protein subunits          with transfer RNAs nestled in the middle.
RIBOSOME STRUCTURE COURTESY OF JAMIE CATE, MARAT YUSUPOV, GULNARA YUSUPOVA,          THOMAS EARNEST AND HARRY NOLLER. GRAPHIC COURTESY OF ALBION BAUCOM, UNIVERSITY          OF CALIFORNIA, SANTA CRUZ.
After a gene has been read by RNA polymerase and the RNA is spliced, what        happens next in the journey from gene to protein? The next step is reading        the RNA information and fitting the building blocks of a protein together.        This is called translation ,        and its principal actors are the ribosome and amino acids.
Ribosomes are among the biggest and most intricate structures in the cell.        The ribosomes of bacteria contain not only huge amounts of RNA, but also        more than 50 different proteins. Human ribosomes have even more RNA and        between 70 and 80 different proteins!
Harry Noller of the University of California, Santa Cruz, has found that        a ribosome performs several key jobs when it translates the genetic code        of mRNA. As the messenger RNA threads through the ribosome protein machine,        the ribosome reads the mRNA sequence and helps recognize and recruit the        correct amino acid-carrying transfer RNA to match the mRNA code. The ribosome        also links each additional amino acid into a growing protein chain ( see        drawing ).
For many years, researchers believed that even though RNAs formed a part        of the ribosome, the protein portion of the ribosome did all of the work.        Noller thought, instead, that maybe RNA, not proteins, performed the ribosome's        job. His idea was not popular at first, because at that time it was thought        that RNA could not perform such complex functions.
Some first-aid ointments contain the antibiotic          neomycin, which treats infections by attacking ribosomes in bacteria.
Some time later, however, the consensus changed. Sidney Altman of Yale        University in New Haven, Connecticut, and Thomas Cech, who was then at the        University of Colorado in Boulder, each discovered that RNA can perform        work as complex as that done by protein enzymes. Their "RNA-as-an-enzyme" discovery turned the research world on its head and earned Cech and Altman        the 1989 Nobel Prize in chemistry.
Noller and other researchers have continued the painstaking work of understanding        ribosomes. In 1999, he showed how different parts of a bacterial ribosome        interact with one another and how the ribosome interacts with molecules        involved in protein synthesis. These studies provided near proof that the        fundamental mechanism of translation is performed by RNA, not by the proteins        of the ribosome.
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RNA Surprises
But which ribosomal RNAs are doing the work? Most scientists assumed that        RNA nucleotides buried deep within the ribosome complex—the ones that        have the same sequence in every species from bacteria to people—were the important ones for piecing the growing protein together.
However, recent research by Rachel Green, who worked with Noller before        moving to Johns Hopkins University in Baltimore, Maryland, showed that this        is not the case. Green discovered that those RNA nucleotides are not needed        for assembling a protein. Instead, she found, the nucleotides do something        else entirely: They help the growing protein slip off the ribosome once        it's finished.
Noller, Green and hundreds of other scientists work with the ribosomes        of bacteria. Why should you care about how bacteria create proteins from        their genes?
One reason is that this knowledge is important for learning how to disrupt        the actions of disease-causing microorganisms. For example, antibiotics        like erythromycin and neomycin work by attacking the ribosomes of bacteria,        which are different enough from human ribosomes that our cells are not affected        by these drugs.
As researchers gain new information about bacterial translation, the knowledge        may lead to more antibiotics for people.
New antibiotics are urgently needed because many bacteria have developed        resistance to the current arsenal. This resistance is sometimes the result        of changes in the bacteria's ribosomal RNA. It can be difficult to find        those small, but critical, changes that may lead to resistance, so it is        important to find completely new ways to block bacterial translation.
Green is working on that problem too. Her strategy is to make random mutations        to the genes in a bacterium that affect its ribosomes. But what if the mutation        disables the ribosome so much that it can't make proteins? Then the bacterium        won't grow, and Green wouldn't find it.
Using clever molecular tricks, Green figured out a way to rescue some of        the bacteria with defective ribosomes so they could grow. While some of        the rescued bacteria have changes in their ribosomal RNA that make them        resistant to certain antibiotics (and thus would not make good antibiotic        targets) other RNA changes that don't affect resistance may point to promising        ideas for new antibiotics.
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An Interesting Development
In the human body, one of the most important jobs for proteins is to control        how embryos develop. Scientists discovered a hugely important set of proteins        involved in development by studying mutations that cause bizarre malformations        in fruit flies.
The most famous such abnormality is a fruit fly with a leg, rather than        the usual antenna, growing out of its head (see photo). According to Thomas        C. Kaufman of Indiana University in Bloomington, the leg is perfectly normal—it's        just growing in the wrong place.
Normal fruit fly head.
Fruit fly head showing the effects of the Antennapedia          gene. This fly has legs where its antennae should be.
FLYBASE; R. TURNER
In this type of mutation and many others, something goes wrong with the        genetic program that directs some of the cells in an embryo to follow developmental        pathways, which are a series of chemical reactions that occur in a specific        order. In the antenna-into-leg problem, it is as if the cells growing from        the fly's head, which normally would become an antenna, mistakenly believe that they are in the fly's thorax, and therefore ought to grow into a leg.        And so they do.
Thinking about this odd situation taught scientists an important lesson—that        the proteins made by some genes can act as switches. Switch genes are master        controllers that provide each body part with a kind of identification card.        If a protein that normally instructs cells to become an antenna is disrupted,        cells can receive new instructions to become a leg instead.
Scientists determined that several different genes, each with a common        sequence, provide these anatomical identification card instructions. Kaufman        isolated and described one of these genes, which became known as Antennapedia,        a word that means "antenna feet."
Kaufman then began looking a lot more closely at the molecular structure        of the Antennapedia gene. In the early 1980s, he and other researchers        made a discovery that has been fundamental to understanding evolution as        well as developmental biology.
The scientists found a short sequence of DNA, now called the homeobox ,        that is present not only in
Antennapedia
but in the several        genes next to it and in genes in many other organisms. When geneticists        find very similar DNA sequences in the genes of different organisms, it's        a good clue that these genes do something so important and useful that evolution        uses the same sequence over and over and permits very few changes in its        structure as new species evolve.
Researchers quickly discovered nearly identical versions of homeobox DNA        in almost every non-bacterial cell they examined—from yeast to plants,        frogs, worms, beetles, chickens, mice and people.
Hundreds of homeobox-containing genes have been identified, and the proteins        they make turn out to be involved in the early stages of development of        many species. For example, researchers have found that abnormalities in        the homeobox genes can lead to extra fingers or toes in humans.