Concept


DNA is found mostly in the cell nucleus, but another type of nucleic acid, RNA, is common in the cytoplasm. Watson and Crick proposed that RNA must copy the DNA message in the nucleus and carry it out to the cytoplasm, where proteins are synthesized. Crick also predicted the existence of an "adaptor" chain. This proposed flow of genetic information from DNA to RNA to protein became known as the "Central Dogma." As it turned out several types of RNA are involved in the utilization of genetic information. In the nucleus, the DNA code is "transcribed," or copied, into a messenger RNA (mRNA) molecule. In the cytoplasm, the mRNA code is "translated" into amino acids. Translation is orchestrated at the ribosome — itself partly composed of RNA — with transfer RNA playing the role of adaptor.

Animation


Hello, I'm Francis Crick. The story of DNA does not end with Watson and me solving its three-dimensional structure. Because DNA is the hereditary molecule of the cell, we reasoned that the sequence of nucleotides in the molecule must function as a code, able to direct the synthesis of proteins. One puzzle we had to figure out was how DNA, which is found mainly in the cell's nucleus, can direct the synthesis of proteins that are made exclusively in the cell's cytoplasm. I proposed the "Central Dogma" where information flows from DNA to protein via a carrier molecule. A candidate for this information carrier was ribonucleic acid — RNA. RNA is a nucleic acid found mostly in the cell's cytoplasm. Like DNA, RNA has a sugar-phosphate backbone. However, RNA uses the sugar ribose instead of deoxyribose. DNA and RNA uses the same nitrogenous bases except that DNA uses the nucleotide base thymine, whereas RNA uses uracil. Uracil can hydrogen bond with adenine just like thymine. DNA, as you know, is usually a double-stranded molecule. RNA, however, is usually single-stranded. After proposing the Central Dogma — where information flows from DNA to RNA to protein — I realized there was another problem. How did the amino acids interact with the carrier RNA? There must be adaptor molecules; in fact there must be 20 different adaptors, one for each amino acid. Hi, I'm Paul Zamecnik and I was interested in protein synthesis. In the 50's, I didn't know about Crick's Central Dogma or his adaptor hypothesis, and I approached the problem from a biochemical point of view. I made an extract using rat liver cells; it was basically a water-based solution that contained all the parts from a culture of cells. In 1953, I showed that this extract had everything needed to make proteins in a test tube. Remember that a protein is a polypeptide chain of amino acids linked to one another by peptide bonds. To follow protein construction, I added radiolabeled amino acids to the cell-free extract. After incubating the reaction at body temperature, I then centrifuged the tube. I expected that the newly-made polypeptides, being heavier, would pellet at the bottom of the tube. Unincorporated amino acids, being lighter, would remained in the supernatant. Sure enough, the radiolabel was present in the pellet, showing that new polypeptides had been synthesized. Mingled with the labeled polypeptides in the pellet, I identified a large cellular structure, later named the ribosome. It seemed clear the ribosome is the cytoplasmic organelle where protein assembly occurs. Ribosomes are constructed of both RNA and proteins. While the RNA part of the ribosome (rRNA) is involved in protein synthesis, its role was unclear. However, Mahlon Hoagland and I identified another RNA molecule associated with the unincorporated amino acids in the supernatant. I started working in Zamecnik's lab in '53 and worked on identifying this "new" RNA. We called it soluble RNA because it was found in the soluble fraction of our cell-free system. Soluble RNA is small and extremely stable. Because it never sedimented with the proteins, we reasoned that it binds only temporarily with amino acids. Through some very careful measurements, we found that there are 20 different RNA molecules — and each associates with just one of the 20 amino acids. On a visit to our lab, Jim Watson recognized that soluble RNA met the requirements of Crick's adaptor hypothesis. Each of the 20 soluble RNAs could pair to its partner amino acid and ferry the amino acid to the ribosome for protein synthesis. Soluble RNA was later renamed transfer RNA (tRNA) to better reflect this role. But, still, there was no answer to the problem of how the genetic code instructed cytoplasmic tRNAs and amino acids to make proteins. While some thought rRNA was the "template" on which proteins were built, it was becoming clear that rRNA did not have the right properties. So, now the hunt was on for the "information" molecule. Hello, I'm Sydney Brenner. With my colleagues, François Jacob, and Matthew Meselson, I showed that rRNA was not the template for building proteins. There was a third type of RNA — an unstable intermediate — that carries the DNA message to the ribosome. We did this by using phage-infected bacteria. We started by growing bacteria in "heavy" isotopes of carbon and nitrogen to radiolabel all of the bacterial RNA and proteins. We then infected this bacterial culture with phage... …and immediately transferred the infected bacteria to media that lacked the heavy isotopes but contained radioactive 32P. We stopped phage growth before the bacteria were lysed and extracted RNA and ribosomes from the bacteria. We spun the bacterial extract in a density gradient in a centrifuge. This separated the various components and I was able to analyze the distribution of heavy and light isotopes in the bacterial ribosomes, and the incorporation of 32P in newly-made phage RNA. First, let's look at the ribosomes. One ribosome is made up of two subunits. In a density gradient, ribosomes can separate into two bands. The heavier band consists of whole ribosomes; the lighter band consists of dissociated subunits. I reasoned that if the rRNA in the ribosomes were the template for building new phage proteins, then new ribosomes with phage rRNA would have to be made after phage infection. As I suspected, this was not the case. All the ribosomes were made with heavy isotopes. Then I looked at where 32P had been incorporated in the production of new phage RNA. I found that 32P associated with the whole ribosome band and there was also 32P at the bottom of the tube. This turned out to be a new type of RNA. It was associated with the ribosomes so it must have a role in protein synthesis. However, it must be a large molecule since some of it was found in the sediment at the bottom of the tube. This was the information carrier envisioned by Crick in his Central Dogma, and I named it messenger RNA (mRNA).

Gallery


1949 Cold Spring Harbor Symposium. The man busy taking notes is Paul Zamecnik. Also in picture J. S. Fruton (L), K. Linderstrom-Lang (R).
Paul Zamecnik in his office at Massachusetts General Hospital, 1999.
1966 Cold Spring Harbor Symposium. Mahlon Hoagland (R) in discussion with Ernest Borek (L).
Mahlon Hoagland at his home in Vermont, 1999.
Sydney Brenner at a 1980 Cold Spring Harbor meeting.
Letter from Sydney Brenner to Matt Meselson. Brenner congratulates Meselson on the success of their experiment and proposes other possible experiments.
(Page 1 of 2) Letter from Sydney Brenner to Matt Meselson trying to arrange a visit to Meselson's lab. Meselson forwarded the letter to George 'Beets' Beadle, department chair, to request financial assistance for Brenner.
(Page 2 of 2) Letter from Sydney Brenner to Matt Meselson trying to arrange a visit to Meselson's lab. Meselson forwarded the letter to George 'Beets' Beadle, department chair, to request financial assistance for Brenner.
François Jacob's letter to Matt Meselson about his planned trip to Meselson's lab.
(Page 1 of 2) Sydney Brenner's letter to Matt Meselson where he lays out the experiment for mRNA isolation.
(page 2 of 2) Sydney Brenner's letter to Matt Meselson where he lays out the experiment for mRNA isolation.

Audio/Video


Audio Glossary

Allele, Gene, Genetic map, Genome, Protein, Ribonucleic acid (RNA), Ribosome

Video Interviews

Paul Zamecnik

Dr. Zamecnik is Professor Emeritus at Harvard University, and is a member of the Board of Directors of Hybridon, Inc., a biotechnology company he helped found.

Clip 1 (1:06)
Describing an early experience that led to interest in studying protein synthesis.

Clip 2 (0:31)
The background and motivation for developing a cell-free protein synthesis system, and how the focus soon changed to finding out "what the machinery was like."

Clip 3 (1:29)
Describing the cell fractionation experiments to isolate the components needed for protein synthesis.

Clip 4 (1:24)
The role of "pseudo-serendipity" in making discoveries: finding the missing RNA components in the protein synthesis system.

Clip 5 (0:28)
Finding tRNA and identifying its role in protein synthesis.

Biography


 

Paul Zamecnik developed a cell-free extract that he and Mahlon Hoagland used to study protein synthesis. They identified tRNA as the adaptor predicted by Francis Crick in his Central Dogma. Sydney Brenner showed that mRNA was the unstable intermediate that carried the message from DNA to the ribosomes.

PAUL CHARLES ZAMECNIK (1913- )

Paul Zamecnik was born in Cleveland, Ohio. He went to Dartmouth College and graduated from Dartmouth Medical School in 1934. Although he trained to be a medical doctor, Zamecnik was always interested in science. He eventually decided to go into research because there was so much to discover. His interest in protein synthesis started with a question. In 1938, as an intern, Zamecnik was doing an autopsy on an obese woman. He wondered why there was fat when there should have been protein and muscle ? no one knew the answer.

In 1939, Zamecnik approached Max Bergmann, a protein chemist at the Rockefeller Institute. He was hoping to get a job in Bergmann's lab so he could work on the problem of protein synthesis. Bergmann turned him down because Zamecnik was an M.D, not a Ph.D.

Zamecnik did get a fellowship to work with Kaj Linderstrøm-Lang at the Carlsberg Laboratory in Denmark. Linderstrøm-Lang was a leader in the field of protein chemistry and Zamecnik obtained enough training and experience that Bergmann gave him a job when he came back to the States.

Zamecnik didn't stay at the Rockefeller for long. He was offered a job at the Huntington Laboratory at the Massachusetts General Hospital in Boston. Here, he worked with Fritz Lipmann (1953 Nobel laureate) and used radioactive isotopes to prove that proteins were built from amino acids in a process requiring chemical energy ? ATP. Zamecnik then became interested in how protein sequences were specified and to understand that he tried to isolate and identify all the components necessary for protein synthesis.

In 1952, Zamecnik was partially successful in that he made a cell-free extract from rat liver with which he was able to synthesize proteins from amino acids. In 1953, using this system, Zamecnik and Mahlon Hoagland showed that amino acids had to be energized, "activated," by ATP before they were incorporated into a peptide chain. Then in 1956, Hoagland followed up on an observation Zamecnik made earlier. Zamecnik noticed that low molecular weight RNA in the cell-free extract could be associated with radiolabeled amino acids. This led to the identification of tRNA ? the adaptors Francis Crick predicted in his Central Dogma.

In 1956, Zamecnik was appointed head of the Huntington Laboratory. In 1960, his lab developed a cell-free extract from the bacteria E. coli. He shared the preparation method with other scientists. Marshall Nirenberg and Johann Matthaei used the cell-free extract from E. coli to crack the genetic code.

Zamecnik continued to work on tRNA purification and sequencing. Then in 1978, he made another interesting observation. He found that oligonucleotides were able to enter cells. This led to a new area of research and possible therapy. Anti-sense RNA could be used to block the translation of viral messenger RNA. Since 1993, Zamecnik has been on the Board of Directors of a biotech company called Hybridon Inc. that develops therapeutic drugs based on the idea of anti-sense blockers.

Zamecnik still runs a lab at Massachusetts General Hospital and is a Professor Emeritus at Harvard University. He doesn't have any immediate plans for retirement; there are still many things to discover.

MAHLON HOAGLAND (1921- )

Mahlon Hoagland was born in Boston. His father was a research scientist with an interest in neurobiology. His dedication and passion for his work both drew and repelled the younger Hoagland, who learned first-hand what it was like to be a scientist. Hoagland knew fairly early on that he wanted a profession but wasn't sure that he wanted to be a scientist.

Hoagland decided he would be a medical doctor so as not to be in direct competition with his father. He went to college, first Williams College and then transferred to Harvard after a year. World War II had just started and with the need for medical doctors, Hoagland entered medical school even before graduating from college. He found he had the aptitude for being a surgeon ? he was manually adept and anatomy was one of his favorite classes. Unfortunately, three months before graduation, Hoagland was diagnosed with tuberculosis. He was sent to the Trudeau Sanatorium at Saranac Lake ? the same one where Phoebus Levene stayed ? for the classic bed rest cure. Treatment of tuberculosis with antibiotics wasn't available until near the end of his stay and by that time, Hoagland was deemed healthy enough.

In 1947, Hoagland returned to Harvard Medical School to finish his interrupted year. He still wanted to become a surgeon and applied to work as a surgical intern after graduation in 1948. It was soon obvious that he needed a less taxing career; after only weeks, Hoagland reactivated his tuberculosis. Disappointed, Hoagland applied for a postdoctoral position with Dr. Joseph Aub, the director of the Huntington Laboratories at Massachusetts General Hospital.

At Huntington, Hoagland learned to be a scientist. He worked on the effects of beryllium on enzymatic activity and in the process became more interested in biochemistry and the protein synthesis work going on in Paul Zamecnik's lab. Hoagland arranged sabbaticals to learn more about biochemistry with the goal of working in Zamecnik's lab on his return.

In 1953, Hoagland started work in Zamecnik's lab on the problem of amino acid activation. Using Zamecnik's cell-free system, Hoagland worked out the mechanics and published his results in 1955. He then began working on a project that Zamecnik had put on hold. This led to the discovery of tRNA, the adaptor (predicted by Francis Crick) that shuttles amino acids to messenger RNA. The results were published in 1957 and served to connect two fields of science research, biochemistry and molecular biology.

Hoagland spent 1958 at Cambridge University and worked with Francis Crick to try and use tRNA to solve the genetic code. He returned to the U.S. as associate professor of microbiology at Harvard Medical School. In his seven years at Harvard, Hoagland found great satisfaction in teaching and was distressed at the lack of "teachers" among the scientists who were only interested in research. He left Harvard to accept a position at Dartmouth Medical School where he improved the biochemistry curriculum.

In 1970, Hoagland accepted the directorship of the Worcester Foundation, the institute founded by his father. Hoagland was able to attract new researchers and established and strengthened research programs in cell biology, endocrinology, neurobiology, and reproductive biology at Worcester. In 1980, he was successful in recruiting Paul Zamecnik.

Although Hoagland is now retired, he still has a strong interest in education and teaching. Over the years, he has written a number of "non-scholarly" books on the subject of genes and molecular biology. The Way Life Works is being re-edited to be used as a textbook in high school biology classes. Hoagland lives in Vermont with his wife and as a hobby creates art by carving and sculpting wood.

SYDNEY BRENNER (1913- )

Sydney Brenner was born in Germiston, South Africa. At the age of 15, Brenner won a scholarship to the University of the Witwatersrand in South Africa. At the time, the South African university system was underdeveloped and Brenner did a lot of independent research and self-teaching on the subject of molecular biology. When he graduated from Witwatersrand, there was no graduate research program. Brenner applied to and went to Oxford and started graduate work on bacteriophage.

In 1953, Brenner was one of a group invited to Cambridge University to view Watson and Crick's DNA structure. This became the first of many meetings and collaborations Brenner had with Watson, and even more so with Crick.

In 1954, Brenner received his doctorate degree and returned to lecture at the University of the Witwatersrand. By now he was working on the problem of the genetic code and the role of RNA in information transfer. In 1956, Brenner sent a paper to members of the RNA tie club On the Impossibility of All Overlapping Triplet Codes - an elegant proof that used statistics and amino acid protein sequences to show that three nucleotides code for one amino acid. That same year, Francis Crick, who was also interested in the problem of information transfer, helped Brenner get a research position at the Medical Research Council in Cambridge.

In 1957, Brenner, Seymour Benzer, Francis Crick, and Leslie Barnett published a paper in Nature on the fine mapping of mutations in phage. By correlating the genetic mutations with changes in the amino acid sequence, they were able to prove colinearity between the genetic message and the protein product. Brenner then moved onto the problem of how the information was transferred between DNA and protein. In 1960, Brenner, François Jacob, and Matthew Meselson designed and worked on another series of experiments establishing the existence and function of messenger RNA.

In the late 60's, Brenner became interested in the problem of development, especially that of the nervous system. In 1968, having decided against Drosophila melanogaster as too complex, Brenner chose Caenorhabditis elegans as a model organism for study. C. elegans is now a research field onto itself, and in 1998, was the first multi-cellular organism to have its complete genome sequenced.

In the 90's, Brenner chose yet another organism, Fugu rubripes, the Japanese puffer fish. Although it has about as many genes as humans, the puffer fish does not have as much "junk" DNA. Brenner is in charge of the Fugu fish genome sequencing project at the Medical Research Council.

In 1998, with a donation from tobacco giant Phillip Morris, Brenner established and is the director of the Molecular Science Institution (MSI) in Berkeley, California. A non-profit organization, part of the role of the MSI is to process the flood of information from the various genome sequencing projects.

Brenner splits his time between Berkeley and Cambridge. He likes travelling and good wine and writes an opinion column called Loose Ends for the journal Current Biology.

Brenner shared the 2002 Nobel Prize in Physiology or Medicine with colleagues John Sulston and Robert Horvitz. All three made major contributions in the field of developmental biology using the model organism Caenorhabditis elegans.

Factoid

Links


 

Links

RNA Folding

From Dr. Michael Zuker's lab at Rensselaer Polytechnic Institute's School of Science. Input an RNA sequence and the computer program will predict the RNA secondary structures.

The RNA World

This is a database of RNA structure from the Institute of Molecular Biology in Germany. There are thumbnail pictures of proposed structures as well as links to references and other information about the RNA sequences. With the right plug-ins, Rasmol/Chime, you get 3-D views of the proposed structures. Use the PDB (protein data bank) entry.

Bibliography

  • Alberts, Bruce et al., 1983, Molecular Biology of the Cell, Garland Publishing Inc., New York.

  • Borek, Ernest, 1965, The Code of Life, Columbia University Press, New York.

  • Dunn, L.C., 1991, A Short History of Genetics: The Development of Some of the Main Lines of Thought: 1864-1939, Iowa State University Press, Ames.

  • Griffiths, Anthony, et al., 1996, An Introduction to Genetic Analysis, W. H. Freeman and Company, New York.

  • Hoagland, Mahlon, and Dodson, Bert, 1998, The Way Life Works, Random House Inc., New York.

  • Hoagland, Mahlon, 1990, Towards the Habit of Truth: A Life in Science, W. W. Norton & Company, New York.

  • Judson, Horace Freeland, 1979, The Eighth Day of Creation: Makers of the Revolution in Biology, Simon and Schuster, New York.

  • Lagerkvist, Ulf, 1998, DNA Pioneers and Their Legacy, Yale University Press, New Haven.

  • Lundardini, Rosemary, 1993, DNA Drama, Dartmouth Medicine, 18, No. 1, Dartmouth College, Hanover, New Hampshire.

  • Micklos, David A., and Freyer, Greg A., 1990, DNA Science: A First Course in Recombinant DNA Technology, Cold Spring Harbor Laboratory Press, New York.

  • Rosenfield, Israel, Ziff, Edward, and Van Loon, Borin, 1983, DNA for Beginners, Writers and Readers Publishing, Inc.

  • Taylor, J. Herbert, 1965, Selected Papers on Molecular Genetics, Academic Press, New York.

  • Watson, James D., Gilman, Michael, Witkowski, Jan, Zoller, Mark, 1982, Recombinant DNA, 2nd edition, W. H. Freeman and Company, New York.

  • Woese, Carl R., 1967, The Genetic Code: The Molecular Basis for Genetic Expression, Harper & Row, New York.

Glossary


Allele - One of the variant forms of a gene at a particular locus, or location, on a chromosome. Different alleles produce variation in inherited characteristics such as hair color or blood type. In an individual, one form of the allele (the dominant one) may be expressed more than another form (the recessive one).
Gene - The functional and physical unit of heredity passed from parent to offpsring. Genes are pieces of DNA, and most genes contain the information for making a specific protein.
Genetic map - (Also known as a linkage map) a chromosome map of a species that shows the position of its known genes and/or markers relative to each other, rather than as specific physical points on each chromosome.
Genome - All the DNA contained in an organism or a cell, which includes both the chromosomes within the nucleus and the DNA in mitochondria.
Protein - A large complex molecule made up of one or more chains of amino acids. Proteins perform a wide variety of activities in the cell.
Ribonucleic acid (RNA) -
Ribosome - Cellular organelle that is the site of protein synthesis

Children resemble their parents.
Genes come in pairs.
Genes don't blend.
Some genes are dominant.
Genetic inheritance follows rules.
Genes are real things.
All cells arise from pre-existing cells.
Sex cells have one set of chromosomes; body cells have two.
Specialized chromosomes determine gender.
Chromosomes carry genes.
Genes get shuffled when chromosomes exchange pieces.
Evolution begins with the inheritance of gene variation.
Mendelian laws apply to human beings.
Mendelian genetics cannot fully explain human health and behavior.
DNA and proteins are the molecules of the cell nucleus.
One gene makes one protein.
A gene is made of DNA.
Bacteria and viruses have DNA too.
The DNA molecule is shaped like a twisted ladder.
A half DNA ladder is a template for copying the whole.
DNA words are three letters long.
A gene is a discrete sequence of DNA nucleotides.
The RNA message is sometimes edited.
Some viruses store genetic information in RNA.
RNA was the first genetic molecule.
Mutations are changes in genetic information.
Some types of mutations are automatically repaired.
A chromosome is a package for DNA.
Higher cells incorporate an ancient chromosome.
Some DNA does not encode protein.
Some DNA can jump.
Genes can be turned on and off.
Genes can be moved between species.
DNA responds to signals from outside the cell.
Different genes are active in different kinds of cells.
Master genes control basic body plans.
Development balances cell growth and death.
A genome is an entire set of genes.
Living things share common genes.
DNA is only the starting point for understanding human biology.
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