Concept


The genetic code had to be a "language" — using the DNA alphabet of A, T, C, and G — that produced enough DNA "words" to specify each of the 20 known amino acids. Simple math showed that only 16 words are possible from a two-letter combination, but a three-letter code produces 64 words. Operating on the principle that the simplest solution is often correct, researchers assumed a three-letter code called a codon. Research teams at University of British Colombia and the National Institutes of Health laboriously synthesized different RNA molecules, each a long strand composed of a single repeated codon. Then, each type of synthetic RNA was added to a cell-free translation system containing ribosomes, transfer RNAs, and amino acids. As predicted, each type of synthetic RNA produced a polypeptide chain composed of repeated units of a single amino acid. Several codons are "stop" signals and many amino acids are specified by several different codons, accounting for all 64 three-letter combinations.

Animation


I'm Marshall Nirenberg. Har Khorana's group and mine "cracked" the genetic code. We figured out how the nucleotide language of mRNA is "translated" into the amino acid language of proteins. Genetic data from Crick and others showed that three nucleotides form a "codon" — an mRNA word that specifies one amino acid. This made sense, because a codon made from only one or two nucleotides would not produce enough combinations (words) to code for all 20 of the known amino acids. However, a three-nucleotide codon produces 64 combinations. This would produce a redundant, or degenerate, code where several different codons specify the same amino acid. The parsimony principle — that the simplest solution is often right — ruled out a four-nucleotide codon. In 1961, Johann Matthaei, a visiting post-doc, and I started experiments to test the triplet codon hypothesis. We used a cell-free extract of E. coli because we believed that this extract should contain all the components needed to translate mRNA into proteins. The extract was treated with DNase to destroy any remaining E. coli DNA — so there was no template from which messenger RNA could be made. Using a method perfected by Marianne Grunberg-Manago and Severo Ochoa, we made synthetic mRNA composed entirely of uracil. We added this poly-U RNA to the extract. Radiolabeled amino acids were also added. When we examined the products produced in this cell-free system, we found polypeptides composed entirely of the amino acid phenylalanine (PHE). From this result, we concluded that a sequence of three uracils — UUU — must code for phenylalanine. We had determined one of the 64 triplet codons! Matthaei and I tried other polynucleotide chains. Poly-C made a proline (PRO) chain; poly-A made a lysine (LYS) chain. Interestingly, no protein was made with the poly-G chain. Other researchers and I quickly recognized the power of this approach. Using RNA templates containing different nucleotide combinations, we assigned amino acids to about 50 triplet codons. This is a genetic code table. To find a specific codon, look down the left hand side for the first letter of the codon. For the second letter, look across the table. For the last letter, look down the right hand side of the table. For example, the codon C G A: The codon C G A codes for the amino acid arginine (ARG). Hi, I'm Phil Leder. I helped Marshall Nirenberg with the rest of the genetic code. Some of the codons were hard to decipher, because we couldn't establish their order biochemically. For example, a triplet with two Gs and one C could be in the order CGG or GCG or GGC. Marshall and I used the activation of tRNA to solve this problem. tRNA is the molecule that carries amino acids to the ribosomes for protein synthesis. In 1962, Robert Holley solved the structure of tRNA. Although tRNA is single stranded, stretches of complementary nucleotides hydrogen bond to form short double-stranded regions, which bend the tRNA into a characteristic cloverleaf shape. Holley showed that all tRNAs have a similar cloverleaf structure. At a position on one of the "leaves," a sequence of three nucleotides forms an anti-codon, which base pairs with a specific mRNA codon. Thus, there is a different tRNA molecule corresponding to each mRNA codon. Using their cell-free translation system, Zamecnik and his group showed that tRNA becomes activated when the amino acid binds to the tRNA's stem. This step requires chemical energy in the form of ATP. I first made short RNA chains composed of three or six nucleotides. When added to a cell-free extract, an activated tRNA will read these trinucleotide or hexanucleotide sequences. I then devised a way to separate the bound tRNA and identify the amino acid. After that, all I had to do was make specific trinucleotide and hexanucleotide chains to confirm the genetic code. We also found that translation starts with a specific codon AUG — the only unique codon — and there are stop codons that end translation. So, in addition to words, the genetic code also has punctuation points. So, to put this all together: Within the nucleus, the DNA code is transcribed into a complementary mRNA molecule. The mRNA enters the cytoplasm, where it associates with a ribosome. The mRNA code is then translated into a polypeptide chain. The codon AUG signals the start of translation. An activated tRNA ferries the first amino acid — methionine — to the ribosome. The tRNA anti-codon binds to the AUG codon on the mRNA. The whole complex shifts, and the next codon is read by another tRNA. As the two amino acids are held in position, a peptide bond is formed between them. The second tRNA accepts the growing protein chain, and the methionine tRNA is released. The process is repeated until a stop codon is encountered. When the stop codon, in this case UAA, is reached, translation is finished. Stop codons do not have matching tRNAs. The ribosome disassembles to be reused for translating another mRNA and one complete peptide chain is released.

Gallery


1966 Cold Spring Harbor Symposium on protein synthesis. (L-R) Marshall Nirenberg, B. P. Doctor, C. T. Caskey.
Marshall Nirenberg at the White House explaining the genetic code to President Lyndon Johnson.
Marshall Nirenberg in his office at the NIH, 1960.
Marshall Nirenberg at the NIH, 1999. He is holding one of the original charts with 'code-cracking' data.
1966 Cold Spring Harbor Symposium on protein synthesis. (L-R) Har Gobind Khorana, Francis Crick, Marianne Grunberg-Manago.
1966 Cold Spring Harbor Symposium on protein synthesis. (L-R) John Cairns, Phil Leder and Robert Thach.
1966 Cold Spring Harbor Symposium on protein synthesis. Phil Leder in the midst of a discussion.
Har Khorana in his laboratory at the University of Wisconsin, mid-1960's.

Audio/Video


Audio Glossary

Gene, Codon, Genetic code (ATGC), Messenger RNA (mRNA), Amino acids, Ribosome

Video Interviews

Marshall Nirenberg

Marshall Nirenberg is a member of the National Heart, Lung, and Blood Institute of the National Institutes of Health.

Clip 1 (1:01)
Explaining the experiment to determine the RNA able to direct the synthesis of proteins.

Clip 2 (1:00)
Discovering that polyU directs the synthesis of polyPhenylalanine.

Clip 3 (0:33)
Working out the base compositions for the codons in the genetic code.

Clip 4 (1:29)
Using charged tRNAs to prove triplet nature of the genetic code, and to determine the base sequences of codons.

Clip 5 (1:04)
Working out the 64 codon combinations: the joy of doing science at this time.

Clip 6 (1:28)
Doing the experiments to determine whether the genetic code is universal, and their subsequent philosophical impact.

Clip 7 (0:33)
Finding out he won the Nobel prize.

Biography


 

Marshall Nirenberg, Har Gobind Khorana, and Robert Holley shared the 1968 Nobel Prize for Physiology and Medicine. Nirenberg and Khorana cracked the genetic code. Holley sequenced and deduced the structure of the first tRNA molecule.

MARSHALL WARREN NIRENBERG (1927-)

Marshall Nirenberg was born in New York City. When he was 12, he and his family moved to Orlando, Florida. His early interest in bird-watching led him to the science of biology. Nirenberg was able to explore the diverse ecology of Florida's wetlands. He also benefited from the instruction provided by professionals - museum curators, biochemists - who were at nearby World War II training camps.

In 1948, Nirenberg graduated from the University of Florida with a Bachelor of Science degree. He stayed at the University of Florida to complete a Master's degree in Zoology on the ecology and taxonomy of caddis flies.

Nirenberg then went to the University of Michigan and in 1957 finished his Ph.D. He had become more interested in the question of life itself and wanted to know the essence. His Ph.D. work on sugar transport in tumor cells reflected his interest in the chemistry of life.

After his Ph.D., Nirenberg went to the National Institutes of Health (NIH) for a 2-year postdoctoral fellowship at the American Cancer Society. In 1960, he accepted the position of research biochemist in the Section of Metabolic Enzymes at the NIH. Nirenberg had already begun working on the problem of how to decipher the RNA code.

In 1961, Nirenberg and J. H. Matthaei published their landmark paper in Proceedings of the National Academy of Science. They showed that a synthetic messenger RNA made of only uracils can direct protein synthesis. The polyU mRNA resulted in a poly-phenylalanine protein ? they had the first piece of the genetic code.

In subsequent years, Nirenberg and his group deciphered the entire genetic code by matching amino acids to synthetic triplet nucleotides. They found that there is redundancy in that some amino acids are encoded by more than one codon and some codons are "punctuation marks" in the mRNA message. Nirenberg and his group also showed that with few exceptions, the genetic code was universal to all life on earth. Nirenberg shared the 1968 Nobel Prize in Physiology or Medicine with Har Gobind Khorana and Robert Holley. Khorana also worked on cracking the genetic code; Holley was the first to sequence a tRNA and determine its structure.

Nirenberg's research now focuses on the development of the nervous system of Drosophila melanogaster. He runs a lab in the National Heart, Lung, and Blood Institute of the NIH. He is still passionate about research ? the joy of discovery and the wonder of Nature's plan.

HAR GOBIND KHORANA (1922-)

Har Khorana was born in Raipur, West Pakistan. His father was a clerk in the British Indian government. Although the family was not well-to-do, Khorana's father made sure that his children had an education.

Khorana went to Punjab University in Lahore and graduated with a Master of Science. In 1945, a fellowship from the government of India gave him the opportunity to study abroad. He went to the University of Liverpool where he obtained his doctorate.

Khorana spent the next few years doing post-doctorate work, first at the Eidgenössische Technische Hochschule in Zurich, then at Cambridge University with G. W. Kenner and Lord Alexander R. Todd. It was at Cambridge that Khorana developed an interest in proteins and nucleic acids.

In 1952, Khorana was offered a job at the University of British Columbia where he was able to work fairly independently on various research projects involving phosphate esters and nucleic acids. The work on the chemical synthesis of ribotrinucleotides for protein synthesis was initiated at this time.

In 1960, Khorana accepted a position in the Institute for Enzyme Research at the University of Wisconsin. He continued working on nucleotide synthesis and cracking the genetic code. For this work Khorana shared the 1968 Nobel Prize in Physiology or Medicine with Robert Holley and Marshall Nirenberg.

Since 1970, Khorana has been the Alfred P. Sloan Professor of Biology and Chemistry at the Massachusetts Institute of Technology.

Factoid

Links


 

Links

The American Scientist

Appearing in the January 1998 issue, the article The Invention of the Genetic Code reviews the main lines of thought leading up to the genetic code theory.

The Protein Machine

This program from the European Bioinformatics Institute (EBI) is a translation program that starts with a DNA sequence. You can input your own sequence or choose one from the databanks. The program also tests different reading frames and color-codes the protein product.

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.

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

  • Nobel Lectures in Molecular Biology 1933-1975, 1977, Elsevier North-Holland, Inc., 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


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.
Codon - Three bases in a DNA or RNA sequence which specify a single amino acid.
Genetic code (ATGC) -
Messenger RNA (mRNA) -
Amino acids - A group of 20 different kinds of small molecules that link together in long chains to form proteins. Often referred to as the "building blocks" of proteins.
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.
RNA is an intermediary between DNA and protein.
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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