lecture 3.2

LECTURE 3.2LECTURE 3.2

LECTURE OUTLINELECTURE OUTLINE

The ZigguratsThe ZigguratsCarbonCarbonRosalind FranklinRosalind Franklin

CATAL HUYUKCATAL HUYUK

THE ZIGGURAT AT URTHE ZIGGURAT AT UR

THE ZIGGURAT AT URTHE ZIGGURAT AT UR

OCTANE AND DECANEOCTANE AND DECANE

A DIGRESSION ON THE CRYSTAL A DIGRESSION ON THE CRYSTAL STRUCTURE OF GRAPHITE, AND STRUCTURE OF GRAPHITE, AND THE STRUCTURE OF CHARCOALTHE STRUCTURE OF CHARCOAL

In graphite, each carbon atom strongly In graphite, each carbon atom strongly bonds to three other carbon atoms, to bonds to three other carbon atoms, to create six-membered ringscreate six-membered rings

THE CRYSTAL STRUCTURE THE CRYSTAL STRUCTURE OF GRAPHITEOF GRAPHITE

The six-membered rings The six-membered rings form parallel sheetsform parallel sheets

THE CRYSTAL STRUCTURE THE CRYSTAL STRUCTURE OF GRAPHITEOF GRAPHITE

The three-dimensional The three-dimensional structure of graphite structure of graphite consists of parallel sheets consists of parallel sheets of carbon atomsof carbon atoms

Within the sheets, the Within the sheets, the carbon atoms are strongly carbon atoms are strongly bonded to each other.bonded to each other.

Between the sheets, the Between the sheets, the bonding is weak.bonding is weak.

The sheets of carbon The sheets of carbon easily slide over each easily slide over each other…..graphite is a other…..graphite is a good lubricant!good lubricant!

THE STRUCTURE OF THE STRUCTURE OF DIAMONDDIAMOND

THE STRUCTURE OF THE STRUCTURE OF CHARCOALCHARCOAL

The carbon atoms are The carbon atoms are found in a mixture of found in a mixture of 5-, 6-, and 7-5-, 6-, and 7-membered ringsmembered rings

The sheet of carbon The sheet of carbon atoms is no longer flat atoms is no longer flat or planar: it is or planar: it is convoluted!convoluted!

THE STRUCTURE OF THE STRUCTURE OF CHARCOALCHARCOAL

The structure of The structure of charcoal as a charcoal as a mixture of 5-, and mixture of 5-, and 6- membered 6- membered ringsrings

THE “BUCKYBALL”THE “BUCKYBALL”

When “mistakes” are made at regular intervals, some When “mistakes” are made at regular intervals, some beautiful structures may result!beautiful structures may result!

A regular distribution of 5-, and 6- membered rings A regular distribution of 5-, and 6- membered rings results in a soccer ball: also called a triacontahedron: aka results in a soccer ball: also called a triacontahedron: aka a “buckyball”/”fullerene”a “buckyball”/”fullerene”

The beast is a CThe beast is a C6060 “molecule”, with carbon atoms at the “molecule”, with carbon atoms at the vertices of the pentagons and hexagons.vertices of the pentagons and hexagons.

THE DODECAHEDRONTHE DODECAHEDRON

Build a material with only pentagons?Build a material with only pentagons? The “dodecahedron” results: it is one of the five The “dodecahedron” results: it is one of the five

“Platonic Solids”… all faces are regular “Platonic Solids”… all faces are regular polygons, and are identical; all vertices are polygons, and are identical; all vertices are identicalidentical

ROSALIND FRANKLIN: THE ROSALIND FRANKLIN: THE DARK LADY OF DNADARK LADY OF DNA

X-Ray X-Ray CrystallographyCrystallography

~1942-1950. The ~1942-1950. The structure of coals and structure of coals and carbons.carbons.

1951-1953. The 1951-1953. The structure of DNAstructure of DNA

1951-1958. The 1951-1958. The structure of virusesstructure of viruses

ROSALIND FRANKLIN: THE ROSALIND FRANKLIN: THE DARK LADY OF DNADARK LADY OF DNA

““Our dark lady is leaving us next Our dark lady is leaving us next week”week”

Letter from Maurice Wilkins to Francis Letter from Maurice Wilkins to Francis Crick, 7th March, 1953Crick, 7th March, 1953

““THE DOUBLE HELIX”THE DOUBLE HELIX”

A best-selling account of A best-selling account of the “race” to solve the the “race” to solve the structure of DNAstructure of DNA

A less than flattering A less than flattering account of Rosalind account of Rosalind Franklin’s contribution to Franklin’s contribution to the “race”.the “race”.

Also shows the author in Also shows the author in a less than flattering a less than flattering light!!light!!

““THE DARK LADY OF DNA” THE DARK LADY OF DNA”

A “balanced view” of A “balanced view” of Rosalind Franklin’s Rosalind Franklin’s contribution to the contribution to the “race”!“race”!

Rosalind Franklin was a Rosalind Franklin was a superb experimentalist.superb experimentalist.

Did death cheat her of Did death cheat her of the “Nobel Prize”?the “Nobel Prize”?

ROSALIND FRANKLIN (1920-ROSALIND FRANKLIN (1920-1958)1958)

1938. “Goes up” to Newnham College, 1938. “Goes up” to Newnham College, University of CambridgeUniversity of Cambridge

1941. Obtains bachelor’s degree in Chemistry1941. Obtains bachelor’s degree in Chemistry 1942-1946 Works for the British Coal Utilization 1942-1946 Works for the British Coal Utilization

Research Association, in LondonResearch Association, in London 1945. Obtains a Ph.D in Physical Chemistry 1945. Obtains a Ph.D in Physical Chemistry

from Cambridgefrom Cambridge 1947-1951. Works at the “Laboratorie Central 1947-1951. Works at the “Laboratorie Central

des Services Chemique de L’Etat” in Parisdes Services Chemique de L’Etat” in Paris

ROSALIND FRANKLIN (1920-ROSALIND FRANKLIN (1920-1958)1958)

1951-1953 King’s College, University of 1951-1953 King’s College, University of LondonLondon

1953-1958 Birkbeck College, University of 1953-1958 Birkbeck College, University of LondonLondon

PUNTING ON THE RIVER CAMPUNTING ON THE RIVER CAM

Although the Although the photograph was taken photograph was taken in 1983, the scene in 1983, the scene could well represent could well represent the 1940s when the 1940s when Rosalind was in Rosalind was in CambridgeCambridge

THE EAGLE IN CAMBRIDGETHE EAGLE IN CAMBRIDGE

The “Eagle” is the most The “Eagle” is the most famous pub in Cambridgefamous pub in Cambridge

Crick and Watson used to Crick and Watson used to lunch there most dayslunch there most days

The ceiling of the bar still The ceiling of the bar still displays the signatures of displays the signatures of hundreds of American hundreds of American airmen and women who airmen and women who visited the pub from the visited the pub from the neighboring air-force neighboring air-force bases, during World War bases, during World War IIII

““GRAPHITIZING CARBON”, GRAPHITIZING CARBON”, ACCORDING TO FRANKLINACCORDING TO FRANKLIN

Classic papers in “Proc. Classic papers in “Proc. Roy. Soc. Lond.Roy. Soc. Lond.

Rosalind Franklin’s Rosalind Franklin’s schematic drawing of a schematic drawing of a “graphitizing” carbon.“graphitizing” carbon.

The “structure consists The “structure consists of microcrystals of of microcrystals of graphite-like material, all graphite-like material, all of which are of a similar of which are of a similar orientation.orientation.

This material will easily This material will easily “crystallize”“crystallize”

““NON-GRAPHITIZING NON-GRAPHITIZING CARBON”, ACCORDING TO CARBON”, ACCORDING TO

FRANKLINFRANKLIN

Rosalind Franklin’s Rosalind Franklin’s schematic drawing of a schematic drawing of a “non-graphitizing” carbon.“non-graphitizing” carbon.

The “structure consists of The “structure consists of microcrystals of graphite-microcrystals of graphite-like material, but in many, like material, but in many, very different orientationsvery different orientations

This material will be very This material will be very difficult to crystallize.difficult to crystallize.

X-RAY DIFFRACTIOON X-RAY DIFFRACTIOON PATTERN OF THE B-FORM OF PATTERN OF THE B-FORM OF

DNADNA The most famous x-The most famous x-

ray diffraction pattern ray diffraction pattern of all time! From the of all time! From the pattern, Franklin, pattern, Franklin, Watson and Crick Watson and Crick were able to were able to determine:determine: DNA is crystallineDNA is crystalline The crystal structure of DNAThe crystal structure of DNA The presence of two The presence of two

interpenetrating helices: one interpenetrating helices: one “up” and one “down”“up” and one “down”

The “pitch” of the helicesThe “pitch” of the helices

THE DOUBLE HELIX OF CRICK THE DOUBLE HELIX OF CRICK AND WATSONAND WATSON

A schematic drawing of A schematic drawing of “The Double Helix” (from “The Double Helix” (from Watson’s book)Watson’s book)

Note that DNA is a Note that DNA is a polymer: each helix is a polymer: each helix is a macromolecule, and the macromolecule, and the two macromolecules are two macromolecules are linked by “hydrogen linked by “hydrogen bonds”…… see later! bonds”…… see later!

THE DNA OF CRICK AND THE DNA OF CRICK AND WATSON: REPLICATIONWATSON: REPLICATION

““It has not escaped our It has not escaped our notice that the specific notice that the specific pairing we have postulated pairing we have postulated immediately suggests a immediately suggests a possible copying mechanism possible copying mechanism for the genetic material”for the genetic material”

Quoted from Crick and Quoted from Crick and Watson’s paper in Nature, Watson’s paper in Nature, April 1953.April 1953.

Image is from Watson’s Image is from Watson’s book.book.

THE TOBACCO MOSAIC VIRUS THE TOBACCO MOSAIC VIRUS ACCORDING TO FRANKLINACCORDING TO FRANKLIN

A drawing of the structure of A drawing of the structure of the Tobacco Mosaic Virus the Tobacco Mosaic Virus (TMV). (TMV).

For the last five years of her For the last five years of her life, Rosalind Franklin worked life, Rosalind Franklin worked on the structures of complex on the structures of complex organic macromolecules, at organic macromolecules, at Birkbeck College in LondonBirkbeck College in London