pchem lecture 15 - stockton university...2015 nobel prize in chemistry images from nobelprize.org...

Wednesday, October 7

Last Time:– Combined first and second laws– Maxwell relations– Equilibrium – thermal equilibrium

Reminders:•Take-home version of Exam 1 distributed

Handouts:

Readings:•Chang & Thoman: 5.1–3

Today:– Mechanical equilibrium– Equilibrium in more interesting systems– Gibbs Free Energy– Example: surface work

”for mechanistic studies of DNA repair”2015 Nobel Prize in Chemistry

Images from nobelprize.org

Tomas LindahlFrancis Crick Institute,

Hertfordshire, United Kingdom,

Clare Hall Laboratory, Hertfordshire, United Kingdom

Paul ModrichHoward Hughes Medical Institute,

Durham, NC, USA, Duke

University School of Medicine, Durham, NC, USA

Aziz SancarUniversity of North Carolina,

Chapel Hill, NC, USA

2(8) THE NOBEL PRIZE IN CHEMISTRY 2015 � THE ROYAL SWEDISH ACADEMY OF SCIENCES � HTTP://KVA.SE

Chromosome

New DNA strand

New DNA strand

DNA-helix

A A AC C C

CA AGGG TTT AA CCCC

T TT TGG G G G

Adenine Cytosine

Thymine Guanine

CA

GT

AC

CA A

A

A

G

G

T T

T

T

TA

C

CA A

A

A

G

G

T T

T

T

TC

C

C

AA

A

A

G

G

G

T T

T

T

TC

C

C

AA

A

A

G

G

G

T T

AC

AG

TT

AC

AG

TT

T

T

CA AG TCA AG T

T

When the cell divides, all the chromosomes are copied. The DNA replication machinery unwinds the DNA helix and forms two new DNA strands, using the old strands as templates. Again, adenin pairs with thymine, and guanine with cytosine.

The structure of DNA

A chromosome contains double-stranded DNA, made from nucleotides with four different bases. Adenine always pairs with thymine, and guanine with cytosine. Together they form “base pairs.” The cell’s 46 chromosomes comprise approxima-tely 6 billion base pairs.

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Biochemistry preferable to life as a doctorAziz Sancar’s fascination with life’s molecules developed while he was studying for a medical degree in Istanbul. After graduating, he worked for a few years as phycisian in the Turkish countryside, but in 1973 he decided to study biochemistry. His interest was piqued by one phenomenon in particular: when bacteria are exposed to deadly doses of UV radiation, they can suddenly recover if they are illuminated with visible blue light. Sancar was curious about this almost magical effect; how did it function chemically?

Claud Rupert, an American, had studied this phenomenon and Aziz Sancar joined his laboratory at the University of Texas in Dallas, USA. In 1976, using that time’s blunt tools for molecular biology, he succeeded in cloning the gene for the enzyme that repairs UV-damaged DNA, photolyase, and also in getting bacteria to over-produce the enzyme. This work became a doctoral dissertation, but people were hardly impressed; three applications for postdoc positions resulted in as many rejections. His studies of photolyase had to be shelved. In order to continue working on DNA repair, Aziz Sancar took up a position as laboratory technician at the Yale University School of Medicine, a leading institution in the field. Here he started the work that would eventually result in the Nobel Prize in Chemistry.

Aziz Sancar - investigating how cells repair UV damageBy then it was clear that bacteria have two systems for repairing UV damage: in addition to light-dependent photolyase, a second system that functions in the dark had been discovered. Aziz Sancar’s new colleagues at Yale had studied this dark system since the mid-1960s, using three UV-sensitive strains of bacteria that carried three different genetic mutations: uvrA, uvrB and uvrC.

As in his previous studies of photolyase, Sancar began investigating the molecular machinery of the dark system. Within a few years he had managed to identify, isolate and characterise the enzymes coded by the genes uvrA, uvrB and uvrC. In ground-breaking in vitro experiments he showed that these enzymes can identify a UV-damage, then making two incisions in the DNA strand, one on each side of the damaged part. A fragment of 12-13 nucleotides, including the injury, is then removed.

Base excision repairC

A AG

T T

C

A AG

T T C

A

G

AG

T T

G

C

A AG

T T

C

A AG

T T

U

G

1 2

3 4 5

C

G

U

G

C

Base excision repairs DNA when a base of a nucleotide is damaged, for example cytosine.

Cytosine can easily lose an amino group, forming a base called uracil.

An enzyme, glycosylase, discovers the defect and excises the base of uracil.

Another couple of enzymes remove the rest of the nucleotide from the DNA strand.

Uracil cannot form a base pair with guanine.

DNA polymerase fills in the gap and the DNA strand is sealed by DNA ligase.

Tomas Lindahl


Chromosome

New DNA strand

New DNA strand

DNA-helix

A A AC C C

CA AGGG TTT AA CCCC

T TT TGG G G G

Adenine Cytosine

Thymine Guanine

CA

GT

AC

CA A

A

A

G

G

T T

T

T

TA

C

CA A

A

A

G

G

T T

T

T

TC

C

C

AA

A

A

G

G

G

T T

T

T

TC

C

C

AA

A

A

G

G

G

T T

AC

AG

TT

AC

AG

TT

T

T

CA AG TCA AG T

T

When the cell divides, all the chromosomes are copied. The DNA replication machinery unwinds the DNA helix and forms two new DNA strands, using the old strands as templates. Again, adenin pairs with thymine, and guanine with cytosine.

The structure of DNA

A chromosome contains double-stranded DNA, made from nucleotides with four different bases. Adenine always pairs with thymine, and guanine with cytosine. Together they form “base pairs.” The cell’s 46 chromosomes comprise approxima-tely 6 billion base pairs.

+ +



7(8)THE NOBEL PRIZE IN CHEMISTRY 2015 � THE ROYAL SWEDISH ACADEMY OF SCIENCES � HTTP://KVA.SE

the disease xeroderma pigmentosum; individuals who suffer from this disease are extremely sensitive to UV radia-tion and develop skin cancer after exposure to the sun. Defects in DNA mismatch repair increase the risk of developing hereditary colon cancer, for instance.

In fact, in many forms of cancer, one or more of these repair systems have been entirely or partially switched off. This makes the cancer cells’ DNA unstable, which is one reason why cancer cells often mutate and become resistant to chemotherapy. At the same time, these sick cells are even more dependent on the repair systems that are still functioning; without these, their DNA will become too damaged and the cells will die. Researchers are attempting to utilise this weakness in the development of new cancer drugs. Inhibiting a remaining repair system allows them to slow down or completely stop the growth of the cancer. One example of a pharmaceutical that inhibits a repair system in cancer cells is olaparib.

In conclusion, the basic research carried out by the 2015 Nobel Laureates in Chemistry has not only deep-ened our knowledge of how we function, but could also lead to the development of lifesaving treatments. Or, in the words of Paul Modrich: “That is why curiosity-based research is so important. You never know where it is going to lead… A little luck helps, too.”

Original strandwith methyl groups

DNA polymerase fills in the gap and DNA ligase seals the DNA strand.

The mismatch is removed.

Two enzymes, MutS and MutL, detect the mismatch in DNA.

The faulty copy is cut. The enzyme MutH recognises methyl groups on DNA. Only the original strand, which acted as a template during the copying process, will have methyl groups attached to it.

Mismatch repairWhen DNA is copied during cell division, mismatching nucleotides are sometimes incorporated into the new strand. Out of a thousand such mistakes, mismatch repair fixes all but one.

Faulty base-pairing

MutS

MutL

MutH4 5

1

MutSMutL MutS

MutL

MutH32 MutH

copy

MutS

MutL

Paul Modrich

5(8)THE NOBEL PRIZE IN CHEMISTRY 2015 � THE ROYAL SWEDISH ACADEMY OF SCIENCES � HTTP://KVA.SE

Similar mechanisms for UV damage repair in humans and bacteriaAziz Sancar’s ability to generate knowledge about the molecular details of the process changed the entire research field. He published his findings in 1983. His achievements led to an offer of an associate professorship in biochemistry at the University of North Carolina at Chapel Hill. There, and with the same precision, he mapped the next stages of nucleotide excision repair. In parallel with other research-ers, including Tomas Lindahl, Sancar investigated nucleotide excision repair in humans. The molecular machinery that excises UV damage from human DNA is more complex than its bacterial counterpart but, in chemical terms, nucleotide excision repair functions similarly in all organisms.

So, what happened to Sancar’s initial interest in photolyase? Well, he eventually returned to this enzyme, uncovering the mechanism responsible for reviving the bacteria. In addition, he helped to demonstrate that a human equivalent to photolyase helps us set the circadian clock.

Time to turn to the work of Paul Modrich. He also began with a vague idea about a repair mechanism, which he then chiselled out in elegant molecular detail.

It pays off to learn about “DNA stuff”Paul Modrich grew up in a small town in northern New Mexico, USA. The diversity of the expansive landscape spurred his interest in nature, but one day his father, a biology teacher, said: “You should learn about this DNA stuff.” This was in 1963, the year after James Watson and Francis Crick had been awarded the Nobel Prize for discovering the structure of DNA.

A few years later, that “DNA stuff” really became central to Paul Modrich’s life. Early in his research career, as doctoral student at Stanford, during his postdoc at Harvard, and as an assistant professor at Duke University, he examined a series of enzymes that affect DNA: DNA ligase, DNA polymerase and the

1

UV radiation

3 4

2

Nucleotide excision repairNucleotide excision repairs DNA-injuries caused by UV radiation or carcinogenic substances like those found in cigarette smoke.

UV radiation can make two thymines bind to each other incorrectly.

The enzyme exinuclease finds the damage and cuts the DNA strand. Twelve nucleotides are removed.

DNA polymerase fills in the resulting gap.

DNA ligase seals the DNA strand. Now the injury has been dealt with.

A

TT

A

A

T

A

A

T

A

T

A

T

T

TGA TT AT

A

T T

A

A A

Aziz Sancar

2015 Nobel Prize in Physics


TakaakiKajitaUniversity of Tokyo,

Kashiwa, Japan

“for the discovery of neutrino oscillations, which shows that neutrinos have mass”

Arthur B. McDonaldQueen's University, Kingston, Canada

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The chameleons of space

They solved the neutrino puzzle and opened a new realm in particle physics. Takaaki Kajita and Arthur B. McDonald were key scientists of two large research groups, Super-Kamiokande andSudbury Neutrino Observatory, which discovered the neutrinos mid-flight metamorphosis.

The hunt was on – deep inside the Earth in gigantic facilities where thousands of artificial eyes waited for the right moment to uncover the secrets of neutrinos. In 1998, Takaaki Kajita presented the discovery that neutrinos seem to undergo metamorphosis; they switch identities on their way to the Super-Kamiokande detec-tor in Japan. The neutrinos captured there are created in reactions between cosmic rays and the Earth’s atmosphere.

Meanwhile, on the other side of the globe, scientists at the Sudbury Neutrino Observatory in Canada, SNO, were studying neutrinos coming from the Sun. In 2001, the research group led by Arthur B. McDonald proved that these neutrinos, too, switch identities.

Together, the two experiments have discovered a new phenomenon – neutrino oscillations. A far-reaching conclusion of the experiments is that the neutrino, for a long time considered to be massless, must have a mass. This is of ground-breaking importance for particle physics and for our understanding of the universe.

Reluctant heroesWe live in a world of neutrinos. Thousands of billions of neutrinos are flowing through your body every second. You cannot see them and you do not feel them. Neutrinos rush through space almost at the speed of light and hardly ever interact with matter. Where do they come from?

Some were created already in the Big Bang, others are constantly being created in various processes in space and on Earth – from exploding supernovas, the death of massive stars, to reactions in nuclear power plants and naturally occurring radioactive decays. Even inside our bodies an average of 5,000 neutrinos per second is released when an isotope of potassium decays. The majority of those that reach the Earth originate in nuclear reactions inside the Sun. Second only to particles of light, photons, the neutrinos are the most numerous particles in the entire universe.

For a long time, however, their existence was not even certain. Quite the opposite; when the particle’s existence was proposed by the Austrian Wolfgang Pauli (Nobel Prize Laureate in 1945) it was mainly in a desperate attempt to explain conservation of energy in beta decay, a type of radioactive decay in atomic nuclei. In December 1930, Pauli wrote a letter to his physicist colleagues whom he addressed as Dear Radioactive Ladies and Gentlemen. In this letter he suggested that some of the energy is carried away by an electrically neutral, weakly interacting and very light particle. Pauli, himself, hardly believed in the existence of this particle. He supposedly stated: “I have done a terrible thing, I have postulated a particle that cannot be detected”.

Torn between identities – tau-, electron- or myon-neutrino?

2015 Nobel Prize in Physics


“for the discovery of neutrino oscillations, which shows that neutrinos have mass”

3(6)THE NOBEL PRIZE IN PHYSICS 2015 � THE ROYAL SWEDISH ACADEMY OF SCIENCES � HTTP://KVA.SE

faster than light in vacuum. In the water, the light is slowed down to 75 per cent of its maximum speed, and can be “overtaken” by the charged particles. The shape and intensity of the Cherenkov light reveals what type of neutrino it is caused by, and from where it comes.

A solution to the enigmaDuring its first two years of operation, Super-Kamiokande sifted out about 5,000 neutrino signals. This was a lot more than in previous experiments, but still fewer than what was expected when scientists esti-mated the amount of neutrinos created by the cosmic radiation. Cosmic radiation particles come from all directions in space and when they collide at full speed with molecules in the Earth’s atmosphere, neutrino showers are produced.

Super-Kamiokande caught muon-neutrinos coming straight from the atmosphere above, as well as those hitting the detector from below after having traversed the entire globe. There ought to be equal numbers of neutrinos coming from the two directions; the Earth does not constitute any considerable obstacle to them. But the muon-neutrinos that came straight down to Super-Kamiokande were more numerous than those first passing through the globe.

This indicated that muon-neutrinos that travelled longer had time to undergo an identity change, which was not the case for the muon-neutrinos that came straight from above and only had travelled a few dozen kilometres. As the number of electron-neutrinos arriving from different directions were in agreement with expectations, the muon-neutrinos must have switched into the third type – tau-neutrinos. However, their passage could not be observed in the detector.

Muon-neutrinos give signals inthe water tank.

COSMIC RADIATION ATMOSPHERE

SUPER-KAMIOKANDE

Light detectors measuring Cherenkov radiation

1 000 m

Muon-neutrinos arriving directly from the atmosphere

Muon-neutrinos that have travelled through the Earth

CHERENKOV RADIATION

PROTECTING ROCK

40 m

SUPER-KAMIOKANDE

NEUTRINOS FROM COSMIC RADIATION

KAMIOKA, JAPAN

MUON-NEUTRINO

Super-Kamiokande detects atmospheric neutrinos. When a neutrino collides with a water molecule in the tank, a rapid, electrically charged particle is created. This generates Cherenkov radiation that is measured by the light sensors. The shape and intensity of the Cherenkov radiation reveals the type of neutrino that caused it and from where it came. The muon-neutrinos that arrived at Super-Kamiokande from above were more numerous than those that travelled through the entire globe. This indicated that the muon-neutrinos that travelled longer had time to change into another identity on their way.

4(6) THE NOBEL PRIZE IN PHYSICS 2015 � THE ROYAL SWEDISH ACADEMY OF SCIENCES � HTTP://KVA.SE

A decisive piece of the puzzle fell in place when Sudbury Neutrino Observatory, SNO, performed their measure-ments of neutrinos arriving from the Sun, where the nuclear processes only give rise to electron-neutrinos. Two kilometres below the Earth’s surface the rushing electron-neutrinos were monitored by 9,500 light detectors in a tank filled with 1,000 tonnes of heavy water. It is different from ordinary water in that each hydrogen atom in the water molecules has an extra neutron in its nucleus, creating the hydrogen isotope deuterium.

The deuterium nucleus offers additional possibilities for the neutrinos to collide in the detector. For some reactions only the amount of electron-neutrinos could be determined, while others allowed scientists to measure the amount of all three types of neutrinos together, without distinguishing them from each other.

Since only electron-neutrinos were supposed to arrive from the Sun, both ways of measuring the number of neutrinos should yield the same result. Hence, if the detected electron-neutrinos were fewer in number than all three neutrino types together, this would indicate that something had happened to the electron-neutrinos during their 150 million kilometre long journey from the Sun.

Out of the over 60 billion neutrinos per square centimetre that every second reach the Earth on their way from the Sun, the Sudbury Neutrino Observatory captured only three per day during its first two years of operation. This corresponded to a third of the expected number of electron-neutrinos that should have been caught in the detector. Two thirds had disappeared. The sum however, if counting all three types together, corresponded to the expected number of neutrinos. The conclusion was that the electron-neutrinos must have changed identities on the way.

SUDBURY NEUTRINO OBSERVATORY (SNO)

SNO

ONTARIO, CANADA

Electron-neutrinos are produced in the solar core.

2 100 m

18 m

CHERENKOV RADIATION

NEUTRINOS FROMTHE SUN

PROTECTING ROCK

HEAVYWATER

Both electron neutrinos alone and all three types of neutrinos together give sig-nals in the heavy water tank.

Sudbury Neutrino Observatory detects neutrinos from the Sun, where only electron-neutrinos are produced. The reactions between neutrinos and the heavy water in the tank yielded the possibility to measure both electron-neutrinos and all three types of neutrinos combined. It was discovered that the electron-neutrinos were fewer than expected, while the total number of all three types of neutrinos combined still corresponded to expectations. The conclusion was that some of the electron-neutrinos had changed into another identity.

pchem lecture 15 - stockton university...2015 nobel prize in chemistry images from nobelprize.org...

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