Nobel Prize in Chemistry 2009: Mapping the Ribosome's Atomic Structure

This note covers the Nobel Prize in Chemistry 2009: who won it, how the three laureates used X-ray crystallography to map the ribosome atom by atom, why the ribosome matters for making proteins and designing antibiotics, how the discovery unfolded over several decades, and quick facts for exams.

What was the Nobel Prize in Chemistry 2009 awarded for?

The Royal Swedish Academy of Sciences awarded the Nobel Prize in Chemistry 2009 jointly to three scientists "for studies of the structure and function of the ribosome". This is the official citation, and the prize itself is formally called the Nobel Prize in Chemistry.

In plain words, the three laureates worked out what a ribosome looks like, right down to the position of each atom, and how it actually works inside a living cell.

A ribosome is a tiny machine found in every cell of every living thing, from bacteria to humans. It reads genetic instructions and builds proteins, the molecules that carry out almost every job in the body.

Until this work, scientists knew ribosomes existed and roughly what they did, but nobody could see their detailed atomic shape or explain exactly how they avoided making mistakes.

The Academy's press release described the achievement simply: the Nobel Prize in Chemistry for 2009 "awards studies of one of life's core processes: the ribosome's translation of DNA information into life." The three laureates used the same basic technique, X-ray crystallography, but worked largely independently and on different parts of the ribosome, before converging on complete atomic maps around the year 2000.

Who are the laureates?

All three laureates shared the prize equally, each receiving one third, worth a total of 10,000,000 Swedish kronor split between them.

Venkatraman Ramakrishnan

Venkatraman Ramakrishnan was born in 1952 in Chidambaram, Tamil Nadu, India. At the time of the award he worked at the MRC Laboratory of Molecular Biology in Cambridge, United Kingdom, as Senior Scientist and Group Leader in the Structural Studies Division.

He held one third of the prize. Ramakrishnan solved the atomic structure of the ribosome's small subunit (30S) and showed how this part of the machine reads the genetic code accurately, using what the Academy's popular information page described as a kind of molecular ruler that checks the pairing between messenger RNA and transfer RNA twice before accepting an amino acid.

Thomas A. Steitz

Thomas A. Steitz was born on 23 August 1940 in Milwaukee, Wisconsin, USA, and died on 23 August 2018 in Branford, Connecticut, USA.

At the time of the award he was Sterling Professor of Molecular Biophysics and Biochemistry at Yale University, New Haven, and an investigator of the Howard Hughes Medical Institute. He held one third of the prize.

Steitz solved the structure of the ribosome's large subunit (50S), first publishing a low-resolution structure in 1998 and a detailed atomic-level structure in 2000, and his later work clarified how the large subunit forms the chemical bond that links amino acids together.

Ada E. Yonath

Ada E. Yonath was born on 22 June 1939 in Jerusalem, in what was then the British Mandate of Palestine and is now Israel; she died on 31 August 2026.

At the time of the award she was Martin S. and Helen Kimmel Professor of Structural Biology and Director of the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly at the Weizmann Institute of Science, Rehovot, Israel.

She held one third of the prize. Yonath began trying to crystallise ribosomes in the late 1970s, when most scientists thought it was impossible, and in 1980 produced the first crystals of the ribosome's large subunit grown in three dimensions, work that the scientific background called a significant step forward for the whole field.

What problem were the laureates trying to solve?

By the mid-twentieth century, biologists had worked out that DNA carries hereditary information and that James Watson and Francis Crick had modelled its double-helix structure in 1953.

They also knew that information in DNA is copied into messenger RNA (mRNA) and that small particles called ribosomes, found in the cytoplasm of cells, somehow turn that information into proteins.

In 1958 these protein-making particles were named ribosomes, and scientists soon found they are built from both proteins and ribosomal RNA.

By the 1960s scientists had deciphered the genetic code itself: the ribosome reads mRNA in groups of three letters called codons, and a separate molecule called transfer RNA (tRNA) matches each codon to the correct amino acid.

Yet, as the popular information page quotes James Watson writing in 1964, "Unfortunately, we cannot accurately describe at the chemical level how a molecule functions unless we know first its structure." Nobody knew exactly how the ribosome's hundreds of thousands of atoms were arranged, so nobody could explain, at the atomic level, how it worked, how it avoided errors, or how certain antibiotics managed to jam it.

This gap set the challenge that the three 2009 laureates spent decades trying to close: to generate a true atomic-resolution picture of the ribosome using X-ray crystallography, a technique that had already earned earlier Nobel Prizes for mapping DNA (1962) and the machinery that copies DNA into RNA (2006).

How does X-ray crystallography reveal a ribosome's structure?

X-ray crystallography works by firing X-rays at a crystal and studying how the rays scatter.

The Academy's popular information page explains that when the rays hit the atoms in a crystal they are scattered, and on the far side of the crystal scientists record the pattern this scattering makes, once with photographic film and today with CCD detectors similar to those in digital cameras.

1. Grow a crystal of the ribosome or one of its subunits, in which the particles are packed in a precise, repeating pattern.
2. Aim a beam of X-rays, generated in a synchrotron that speeds electrons up until they move almost as fast as light, at the crystal.
3. Record the pattern of scattered spots that lands on a detector on the far side of the crystal.
4. Work out the "phase angle" for each spot, often by comparing crystals with and without heavy atoms such as mercury attached, to solve what crystallographers call the phase problem.
5. Combine the spot pattern and the phase information using software to calculate the position of every atom and build a three-dimensional model.

This was far harder for ribosomes than for small proteins. The scientific background notes that a ribosome is not a small, neat particle but has a mass of roughly 2.5 million daltons and, unlike many viruses, lacks a symmetrical shape that would make crystallisation easier.

Yonath chose to crystallise ribosomes from bacteria that live in extreme conditions, such as the hot-spring organism Geobacillus stearothermophilus and the Dead Sea organism Haloarcula marismortui, reasoning that their ribosomes must be unusually stable and so would form better crystals.

She also pioneered freezing crystals in liquid nitrogen to reduce radiation damage.

Sketch a crystal of ribosome particles, an X-ray beam striking it from one side, the rays scattering outward, and a detector on the other side covered in dots; label the dot pattern as the clue that computers use to calculate where every atom sits.

The phase problem for the large subunit was finally solved by Steitz, who used electron-microscopy images of the ribosome, generated by Joachim Frank, to work out how the subunits were oriented inside the crystal, combining this with the heavy-atom data.

His first published structure in 1998 had a resolution of 9 Ångström, too coarse to see individual atoms but sharp enough to detect the long RNA molecules inside, a result the Academy called a decisive breakthrough.

What does the ribosome actually do, and how do antibiotics attack it?

The popular information page explains that the human body has tens of thousands of different kinds of proteins, each built from chains of twenty kinds of amino acids linked like "pearls on a string" by a very stable bond.

Examples the page gives include haemoglobin, which carries oxygen; insulin, which controls blood sugar; antibodies that capture viruses; and keratin, which builds hair and nails.

Ribosomes make every one of these, and the Academy stresses that the ribosome rarely makes mistakes, with errors occurring only about once per 100,000 amino acids added, because the small subunit checks the codon-anticodon pairing more than once before letting an amino acid join the growing chain.

Because every living cell, including every disease-causing bacterium, needs working ribosomes, the ribosome is an ideal target for drugs.

The press release notes that many of today's antibiotics already cure disease by blocking bacterial ribosome function, since bacteria cannot survive without it.

All three laureates produced three-dimensional models showing exactly how different antibiotics bind to the ribosome: some block the tunnel through which the growing protein chain leaves the ribosome, some stop the peptide bond from forming, and others disrupt the reading of the genetic code itself.

The Academy's presentation speech said this knowledge is used "in the on-going medical struggle against the ever emerging drug resistance among bacterial pathogens."

Draw an oval ribosome made of two lobes (the small and large subunits), colour the RNA strands orange and the proteins blue and green as in the Academy's figure, and mark a small red shape wedged into the small subunit to represent a bound antibiotic blocking its function.

How did the discovery unfold?

The Academy framed this prize as the third in a series showing how Darwin's nineteenth-century theory of evolution actually works at the level of atoms, following the 1962 prize for the DNA structure and the 2006 prize to Roger D. Kornberg for showing how information is copied into messenger RNA.

Why does it matter?

The press release stated plainly that "they are also a major target for new antibiotics", because ribosomes are essential to every living cell and blocking a bacterium's ribosome can stop an infection without harming the patient's own ribosomes in the same way.

The popular information page adds that several companies were already using the laureates' ribosome structures to design new antibiotics, some of which had reached clinical testing aimed at treating multi-resistant bacteria such as MRSA.

Beyond medicine, the work gave biologists their first true atomic picture of one of life's most fundamental machines, confirming decades of biochemical guesswork about how genetic information becomes physical protein.

The Academy's presentation speech called the story of how proteins are built on the ribosome "a tale of the existential basis of our civilisation", underlining how central this single molecular machine is to every function of the human body, from sight and hearing to thought and movement.

Open questions remained even after 2000: scientific work continued on exactly how the ribosome handles the "stop" signals that end protein-building and on enigmatic helper proteins that assist translation, areas the scientific background described as still being clarified through further crystal structures in the years after the prize-winning breakthroughs.

How does this connect to what you study?

This prize links directly to the basic biology idea of the central dogma: DNA makes RNA, and RNA makes protein. The scientific background describes this chain as information flowing from the DNA gene, through transcription into messenger RNA, and then through translation into a protein's amino acid sequence.

If you have studied how genes are expressed, the ribosome is the machine that carries out the final step, translation, turning a messenger RNA sequence into a chain of amino acids using the genetic code of three-letter codons. Each codon on the mRNA is matched by an anticodon on a transfer RNA molecule, which brings in the correct amino acid to be added to the growing protein chain.

Understanding why ribosomes rarely make mistakes, roughly one error in every 100,000 amino acids added, and why blocking them with antibiotics can kill harmful bacteria without harming human cells, builds directly on these foundational ideas about cells and molecules.

The idea that proteins such as haemoglobin and insulin are built as chains of amino acids, "like pearls on a string" joined by stable peptide bonds, also connects to basic chemistry lessons on bonding and to biology lessons on enzymes, hormones and the immune system, since antibodies are proteins too.

Finally, this prize shows how a single technique, X-ray crystallography, has been used across different Nobel Prizes, first to reveal the structure of DNA in 1962, then the machinery that copies DNA into RNA in 2006, and finally the ribosome itself in 2009, illustrating how one method of studying crystals can answer very different biological questions over several decades.

Quick facts for exams

The Nobel Prize in Chemistry 2009 was awarded jointly to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath "for studies of the structure and function of the ribosome".

The announcement was made on 7 October 2009 by the Royal Swedish Academy of Sciences. Each laureate received one third of the prize, worth a total of 10,000,000 Swedish kronor.

Ramakrishnan was born in Chidambaram, Tamil Nadu, India, and worked at the MRC Laboratory of Molecular Biology in the United Kingdom.

Steitz was born in Milwaukee, USA, and worked at Yale University and the Howard Hughes Medical Institute in the United States. Yonath was born in Jerusalem and worked at the Weizmann Institute of Science in Israel.

Together they used X-ray crystallography to map the ribosome at atomic resolution, work completed around the year 2000, with major applications in understanding antibiotics.

Note: Source. The prize facts in this note are from the Nobel Prize's official site, nobelprize.org.

Glossary

• Ribosome — a particle in every cell, made of RNA and protein, that builds proteins by reading messenger RNA
• DNA — deoxyribonucleic acid, the double-stranded molecule that stores an organism's hereditary information
• Messenger RNA (mRNA) — a molecule copied from DNA that carries the genetic instructions to the ribosome
• Transfer RNA (tRNA) — a molecule that matches a codon on mRNA to the correct amino acid during protein building
• Codon — a group of three letters on mRNA that specifies one amino acid or a start or stop signal
• Amino acid — one of twenty building-block molecules that are linked together to form a protein
• Peptide bond — the stable chemical bond that joins one amino acid to the next in a protein chain
• X-ray crystallography — a technique that uses the scattering pattern of X-rays off a crystal to work out the position of its atoms
• Phase problem — the mathematical difficulty of working out the angle information needed to turn an X-ray scattering pattern into a structure
• Small subunit (30S) — the part of the bacterial ribosome that reads the codons on mRNA
• Large subunit (50S) — the part of the bacterial ribosome that forms the peptide bond between amino acids
• Antibiotic — a drug that kills or stops bacteria, often by blocking the function of their ribosomes
• Central dogma — the principle that genetic information flows from DNA to RNA to protein

Common errors and misconceptions

• Misconception: The three laureates worked together as one team. Correct: They worked largely independently in different laboratories, Yonath in Israel, Steitz in the USA and Ramakrishnan in the UK, and converged on atomic-resolution structures around the same time in 2000.
• Misconception: The ribosome is made only of protein. Correct: A ribosome is built from both ribosomal RNA and proteins, and much of its chemistry is carried out by the RNA itself.
• Misconception: This prize is about discovering DNA. Correct: DNA's structure was solved earlier, in 1953, and rewarded with a separate Nobel Prize in 1962; the 2009 prize is about the ribosome that reads RNA copies of DNA to build proteins.
• Misconception: Ribosomes never make mistakes. Correct: The Academy states the ribosome is highly accurate but still errs roughly once in every 100,000 amino acids added.
• Misconception: Antibiotics work by destroying DNA. Correct: Many antibiotics described in this prize work by binding to and blocking the ribosome, not by directly attacking DNA.
• Misconception: X-ray crystallography photographs atoms directly. Correct: It records a pattern of scattered X-ray spots, which scientists then use mathematics to convert into a three-dimensional atomic model.

Exam-style questions with model answers

Q1. For what citation was the Nobel Prize in Chemistry 2009 awarded? [2 marks]

1. It was awarded "for studies of the structure and function of the ribosome", the particle in cells that builds proteins from genetic information.

Q2. Name the three laureates of the Nobel Prize in Chemistry 2009 and their affiliations at the time of the award. [2 marks]

1. Venkatraman Ramakrishnan worked at the MRC Laboratory of Molecular Biology in the UK; Thomas A. Steitz worked at Yale University and the Howard Hughes Medical Institute in the USA; Ada E. Yonath worked at the Weizmann Institute of Science in Israel.

Q3. Explain how X-ray crystallography is used to find the structure of a ribosome. [4 marks]

1. Scientists first grow a crystal in which many copies of the ribosome or its subunit are packed in a precise, repeating pattern.
2. X-rays, often produced in a synchrotron, are fired at the crystal.
3. The rays scatter off the crystal's atoms and land as a pattern of spots on a detector.
4. Solving the "phase angle" for each spot, for example by comparing crystals with and without attached heavy atoms, lets scientists calculate where every atom sits and build a three-dimensional model of the whole ribosome.

Q4. Why is the ribosome an important target for antibiotics? [3 marks]

1. Every living cell, including bacteria, depends on its ribosomes to make proteins, and the press release notes that bacteria cannot survive without functional ribosomes.
2. Many antibiotics work by blocking bacterial ribosome function, which stops the bacteria from making proteins and so stops the infection.
3. The laureates' atomic structures show exactly how different antibiotics bind to the ribosome, which scientists use to design new drugs against resistant bacteria.

Q5. Describe the contribution of each of the three 2009 Chemistry laureates to solving the ribosome's structure. [6 marks]

1. Ada Yonath began trying to crystallise ribosomes in the late 1970s, when most scientists thought it impossible, and in 1980 produced the first three-dimensional crystals of the large subunit, using bacteria from extreme environments such as hot springs and the Dead Sea to obtain stable, well-ordered crystals.
2. Thomas Steitz solved the phase problem for the large subunit, publishing a low-resolution structure in 1998 and a full atomic-resolution structure in 2000, and his later work explained how the large subunit catalyses the peptide bond that joins amino acids together.
3. Venkatraman Ramakrishnan solved the atomic structure of the small subunit around the same time in 2000 and showed how a molecular-ruler mechanism in this subunit checks codon-anticodon pairing twice, explaining why the ribosome makes very few errors.
4. Together, their structures gave the first complete atomic picture of how the ribosome reads genetic information and builds proteins, and how various antibiotics interfere with this process.

Q6. What is the "phase problem" in X-ray crystallography, and who solved it for the ribosome's large subunit? [3 marks]

1. The phase problem is the difficulty of working out the phase angle for each spot in an X-ray scattering pattern, information that is needed along with the spot pattern itself to calculate the positions of atoms in a crystal.
2. Thomas Steitz solved this problem for the ribosome's large subunit, combining electron-microscopy images from Joachim Frank with data from crystals containing heavy atoms, and published the first resulting structure in 1998.

Q7. State two proteins mentioned by the Nobel committee as examples of what ribosomes build. [2 marks]

1. The Academy's popular information page gives haemoglobin, which carries oxygen in the blood, and insulin, which controls blood sugar levels, as examples of proteins built by ribosomes.

Q8. How does the small subunit of the ribosome help to keep protein-building accurate? [4 marks]

1. The small subunit reads codons on the messenger RNA and matches them against the anticodon carried by each transfer RNA.
2. Nucleotides in the small subunit act like a molecular ruler, measuring the distance between the codon and anticodon.
3. If the distance or pairing is not correct, the transfer RNA falls off the ribosome rather than being used.
4. Because this ruler mechanism is effectively applied more than once, the Academy states that errors occur only about once per 100,000 amino acids added.

Key takeaways

• The Nobel Prize in Chemistry 2009 honoured three scientists for mapping the ribosome's atomic structure and explaining how it functions.
• The official citation was "for studies of the structure and function of the ribosome".
• Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath each received one third of the prize.
• All three used X-ray crystallography, firing X-rays at ribosome crystals and analysing the scattered pattern.
• Ada Yonath pioneered ribosome crystallography from the late 1970s and made the first large-subunit crystals in 1980.
• Thomas Steitz solved the phase problem and published the large subunit's atomic structure by 2000.
• Venkatraman Ramakrishnan's structures of the small subunit explained how the ribosome reads codons with high accuracy.
• Ribosomes are essential in every living cell and are the target of about half of all antibacterial drugs, according to the scientific background.
• The laureates' structures showed exactly how different antibiotics bind to and block the ribosome, aiding new drug design.

Test yourself

What did the ribosome structures reveal about how proteins are made?

They showed, atom by atom, how the ribosome reads messenger RNA codons and links amino acids together to build proteins.

Where was Venkatraman Ramakrishnan based when he won the prize?

Venkatraman Ramakrishnan worked at the MRC Laboratory of Molecular Biology in Cambridge, United Kingdom, at the time of the award.

In which year did Ada Yonath make the first three-dimensional crystals of a ribosome subunit?

Ada Yonath produced the first three-dimensional crystals of the ribosome's large subunit in 1980.

What technique did all three laureates use to study the ribosome?

All three used X-ray crystallography, analysing how X-rays scatter off ribosome crystals to locate every atom.

Why are ribosomes a useful target for antibiotics?

Every living cell, including bacteria, depends on ribosomes to make proteins, so blocking a bacterium's ribosome can stop the infection.

What did Thomas Steitz's 1998 structure show, and at what resolution?

Steitz's 1998 structure of the large subunit, at 9 Ångström resolution, revealed its long RNA molecules and solved the phase problem.

How does the small subunit help the ribosome avoid errors?

Its molecular-ruler mechanism checks the codon-anticodon pairing more than once before an amino acid is accepted into the growing protein chain.

What was the total prize amount for the 2009 Chemistry Nobel, and how was it shared?

The prize was 10,000,000 Swedish kronor, shared equally between Ramakrishnan, Steitz and Yonath, one third each.