European and Asian philosophers
Alchemists
Phlogistonists
Modern chemists
The Aristotelian tradition and medieval alchemy
eventually gave rise to modern chemistry
• Carbohydrates (sugar)
• Lipids (membranes)
• Nucleic acids (DNA, RNA, Gene)
• Polypeptides (proteins, enzymes, lectins etc.)
The Macromolecules of Life
Bragg, Kendrew, and Perutz and the
structure of proteins
Proceedings of Royal Society, A 205, 321-357, 1950
Bragg, Kendrew, and Perutz, in
Cambridge, based on X-ray diffraction
published a paper describing a number
of helical structures of polypeptide
chains obtained in their search for an
alpha-keratin structure --”
“From my point of view, all of these structures
were wrong, because they did not involve
planarity around the nitrogen atom. I thought
that it was likely, however, that in the course of
time they would learn enough chemistry to see
what peptide group had a planar structure, and
would discover the alpha helix, so Professor
Corey and I decided to publish a short
description of the alpha helix and the gamma
helix.”
Pauling showed the proposed
structures to be wrong
Pauling on Bragg, Kendrew, and Perutz protein structure, Protein Science, 2,
1060-1063, 1993.
Resonance forms
Perutz’s reaction to Pauling’s publication
“I was thunderstruck by Pauling and Corey’s paper. In contrast to
Kendrew’s and my helices, theirs was free of strain; all the amide groups
were planar, and every carboxyl group formed a perfect hydrogen bond
with an amino group four residues further along the chain. The structure
looked dead right. How could I have missed it? Why had I not kept the
amide groups planar? Why had I stuck blindly to Astbury’s 5.1 angstrom
repeat? On the other hand, how could Pauling and Corey’s helix be right,
however nice it looked, if it had the wrong repeat? My mind was in a
turmoil. I cycled home to lunch and ate it oblivious of my children’s chatter
and unresponsive to my wife’s inquiries as to what the matter was with me
today.”
“Brilliant Blunders: From Darwin to Einstein”
Pauling and Corey papers
Series in PNAS
1. Pauling, L., Corey, R.B. and Branson H. R. The Structure of Proteins: Two HydrogenBonded
Helical Configurations of the Polypeptide Chain. PNAS, 37, 205-211, (1951).
2. Pauling, L. & Corey, R. B. Atomic Coordinates and Structure Factors for Two Helical
Configurations of Polypeptide Chains. PNAS, 37, 235-240, (1951).
3. Pauling, L. & Corey, R. B. The Structure of Synthetic Polypeptides. PNAS, 37, 241-250,
(1951).
4. Pauling, L. & Corey, R. B. The Pleated Sheet, A New Layer Configuration of
Polypeptide Chains. PNAS, 37, 251-256, (1951).
5. Pauling, L. & Corey, R. B. The Structure of Feather Rachis Keratin. PNAS, 37, 256-261,
(1951).
6. Pauling, L. & Corey, R. B. The Structure of Hair, Muscle, and Related Proteins. PNAS,
37, 261-271, (1951).
7. Pauling, L. & Corey, R. B. The Structure of Fibrous Proteins of the Collagen-Gelatin
Group. PNAS, 37, 272-281, (1951).
8. Pauling, L. & Corey, R. B. The Polypeptide-Chain Configuration in Hemoglobin and
Other Globular Proteins. PNAS, 37, 282-285, (1951).
Pauling and a-helix of proteins
• Pioneered model building well before the days of computers
• Understood structural features – bond lengths, hydrogen bond,
resonance
Why did Pauling and Corey succeed
where others failed?
• Understanding the importance of hydrogen bonds
• Taking into account the planar peptide bond
• Better knowledge of covalent bond lengths and
angles (chemical intuition)
• They were NOT crystallographers, and did not
consider only models with integer number of
residues per turn!
During the 1930s Linus Pauling was among the pioneers who used quantum
mechanics to understand and describe chemical bonding. Linus Pauling worked
in a broad range of areas within chemistry. In 1951 he published the structure
of the alpha helix, which is an important basic component of many
proteins.
Nobel Prize in Chemistry 1954
Nobel Peace Prize 1962
The Nobel Prize in Chemistry was
awarded "for his research into the
nature of the chemical bond and its
application to the elucidation of
the structure of complex
substances."
Linus C. Pauling
Hierarchy of Protein Structure
Linear chain made of 20 possible
amino acids
Alpha-helices, beta-sheets, turns
Motifs, domains
Oligomers, complexes
Hierarchy of Protein Structure
The Nobel Prize in Chemistry 1962 was awarded jointly to
Max Ferdinand Perutz and John Cowdery Kendrew "for their
studies of the structures of globular proteins."
Max Ferdinand Perutz
John Cowdery Kendrew
HemoglobinMyoglobin
Pioneered the use of X-ray crystallography to solve the structure of macromolecules
Architects of Structural Biology: Bragg, Perutz, Kendrew and Hodgkin, J. M. Thomas,
Oxford Uni. Press, 2020
In the long run X-ray structure
determination works better
The Nobel Prize in Chemistry 2009
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."
Ribosome is the machinery that
synthesizes proteins.
Protein folding – research continues
• Late 1980’s - Wolynes et al. present the “Energy Landscape”
or “Folding Funnel” model for protein folding
• 2006 – There is still no precise understanding how proteins
fold fast (µsec time scale), reliably and accurately to their
native structure
Energy
Entropy
Native
(folded) state
Colin MacLeodOswald Avery Maclyn McCarty
Avery, O.T., MacLeod, C.M., and McCarty, M. Studies on the chemical nature of the
substance inducing transformation of pneumococcal types. Induction of transformation by
a desoxyribosenucleic acid fraction isolated from pneumococcus type III.
J. Exp. Med. 79, 137–158, 1944
“If the results of the present study on the chemical nature of the
transforming principle are confirmed, then nucleic acids must be
regarded as possessing biological specificity the chemical basis of
which is as yet undetermined.”
DNA is the polymer that transfers the genetic information
E. Chargaff Columbia Uni
J. Donahue Caltech, Uni. Southern California
L. Pauling Caltech
Lawrence Bragg Cambridge
John Randal King’s College
J. Watson Cambridge
F. Crick Cambridge
P. Pauling Cambridge
Casts involved in the structure determination of DNA
R. Franklin King’s College
M. Wilkins King’s College
Watson, J. D., & Crick, F. H. C.. Nature 171, 737–738, 1953
Wilkins , M. H. F., Stokes, A. R. & Wilson, H. R. Nature 171, 738–740, 1953
Franklin, R. & Gosling, R. G. Nature 171, 740–741; 1953
The Nobel Prize in Physiology or Medicine 1962 was awarded jointly to
Francis H. C. Crick, James D. Watson and Maurice H. F. Wilkins
"for their discoveries concerning the molecular structure of nucleic acids
and its significance for information transfer in living material."
Watson, Crick and Wilkins
Based on the rules of
Chargaff and the
information from the
work of Rosalind
Franklin, James
Watson and Francis
Crick, determined
the structure of DNA
by making models.
Watson and Crick
James Watson was an American,
born in 1928, was only 24 when the
discovery was made. He went to
University of Chicago at the age of
15.
Francis Crick was born in 1916. He
went to London University and
trained as a physicist. After the war
he changed the direction of his
research to molecular biology.
Crick and Watson wanted to work on
DNA's structure, but they didn't have the
high-quality DNA samples necessary for Xray
diffraction. They approached it building
a physical model of how its atoms fit
together. This is the approach pioneered by
L. Pauling and R. M. Corey for their
protein structure solution.
Watson and Crick’s Method of Choice:
The Model Building Approach Pioneered by Linus Pauling
Building a model with space filling CPK model set is
similar to building toys with LEGO blocks
Corey, Linus Pauling, and Walter Koltun
DNA is made up of three parts
Four DNA bases
Four kinds of nitrogenous bases:
Purine bases
Pyrimidine bases
24
Chargaff's Rule -> A+G=C+T=50%
Percentage of Various Nucleotides in Genome
Organisms A T G C
Humans 30.9 29.4 19.9 19.5
Wheat 27.3 27.1 22.7 22.8
Sarcina
lutea
13.4 12.4 37.1 37.1
T 7 26.3 26 23.8 23.9
Based on the observations above, two rules can be deduced
1. A + G = C + T
2. The percentages of the nucleotide vary for different species
Chargaff’s experiments and conclusions
Base-pairing Paradigm
Chargaff’s Base-Pair Rule
Chargaff determined that in any sample of
DNA:
– The # of adenines (A) = the # of
thymines (T)
– The # of cytosines (C) = the # of
guanines (G)
Thus in DNA, the bases A and T pair
together, and C and G pair together.
Chargaff’s Contribution: Base pairing
“I told them all I knew. If they had heard before about the pairing rules, they
concealed it. But as they did not seem to know much about anything, I was
not unduly surprised. I mentioned our early attempts to explain the
complementarity relationships by the assumption that, in the nucleic acid
chain, adenylic was always next to thymidylic acid and cytidylic next to
guanylic acid...I believe that the double-stranded model of DNA came about
as a consequence of our conversation.”
Chargaff, 1978
''The base composition was an essential clue for finding the structure of DNA,
there's no doubt about that. 'We could have come up with the answer, but no
one would have believed it.’’ Watson
The correct structure of bases revealed by
Jerry Donohue, Pauling’s student
Before he told them the correct structure, they were using the enol form
copied from a book that was wrong.
“We have, we believe, discovered the structure of the
nucleic acids. I think that it will be about a month before we
send off a manuscript describing the structure, but I have
practically no doubt about the correctness of the structure
that we have discovered ... The structure is really a beautiful
one."
Linus Pauling to Alexander Todd and
The President of Guggenheim Foundation
Dec 19, 1952
Briliant Blunders, M. Livio, Simon & Schuster, 2013
Linus Pauling
L. Pauling and R. M. Cory, "A proposed structure for the nucleic acids."
Proc. Natl. Acad. Sci. 39, 84-97, February 1953.
Pauling’s triple helix for DNA
The Great Man’s Blunder
Peter Pauling
• Peter Pauling, before publication, revealed to
Watson and Crick that the Pauling-Corey model
was a triple helix. This moment was a major
turning point for Watson and Crick, who only
then realized that they still had a chance to
discover the structure before Linus Pauling.
• They did not reveal to Linus Pauling that the
structure is wrong based on X-ray diffraction
pattern of Rosalind Franklin. They were
delighted to find a major flaw in his concept,
but, instead of warning him, they basked in his
humiliation when the mistake was publicly
discovered.
Linus Pauling’s Role in DNA double helix
X-ray Diffraction Experiments Played a Crucial Role
Sir Lawrence Bragg, NL 1915
at the age of 25
X-ray differaction: developed by Bragg (father and son)
Each Spot Represents a Unique Set of Bragg Planes
h=2, k=1, l=3
h=10, k=3, l=8
q1 q2 q3
detector
λ = 2 d sinθ
Points in k-space
(Fourier Space)
Trained as a chemist, Franklin created an X-ray photograph that provided
evidence of the double-helix structure of DNA molecules. In 1953, Watson, who
had been investigating the structure of DNA as well, was shown the image and
immediately knew its significance.
Rosalind Franklin
Rosalind Franklin
• Born in London, England July 25,1920
• Graduated from Newnham College 1941
• Earned a doctorate in physical chemistry from Cambridge
University 1945 (coal chemistry)
• From 1947-1950 Franklin learned the technique of X-ray
diffraction in Paris.
• Franklin decided to move back to London in 1951 to work in
a laboratory at King’s College.
• However, she had a very difficult time when she was there as
women didn’t have the same rights as men, such as not being
allowed in certain parts of the university including faculty
lunchroom.
Life in London
During 1951-1953 Rosalind’s worked primarily on the DNA
project. Took the famous photograph entitled photo 51
Her research partner, Maurice Wilkins, treated her like an
assistant, rather than being head of her own project.
Rosalind Franklin used x-ray crystallography to determine
that DNA was double stranded, a helix, phosphates were on
the outside and three distances, 2.0 nm, 0.34 nm, and 3.4 nm
showed up in a pattern over and over again in the diffraction
pattern.
She presented her work to colleagues at King’s College.
James Watson attended the lecture, took notes and informed
Francis Crick.
I am afraid the average vote of opinion here [at King's
College], most reluctantly and with many regrets, is
against your proposal to continue to work on nucleic acids
in Cambridge. An argument here is put forward to show
that your ideas are derived directly from statements made
in a colloquium and this seems to me as convincing as
your own argument that your approach is quite out of the
blue.
Maurice Wilkins wrote to Crick on December 11, 1951
(Letter discovered in 2010)
Briliant Blunders, M. Livio, Simon & Schuster, 2013
Stop it
Rosalind Franklin used x-ray crystallography to determine that
DNA was double stranded, a helix, phosphates were on the
outside and three distances, 2.0 nm, 0.34 nm, and 3.4 nm showed
up in a pattern over and over again in the diffraction pattern.
Rosalind FranklinMaurice Wilkins The famous photo 51
Work of Rosalind Franklin
What did Franklin discover and what
happened to it?
Wilkins (her research partner) showed
Franklin’s picture of DNA (which is known
as Photo 51) to their colleagues Watson and
Crick, in secret, without Franklin knowing!
After a few years of tough fights with
Wilkins she was transferred to Birbeck’s
College with the condition she should not
work on DNA. She worked on the structure
of viruses. Her colleague Aaron Klug
continued her work that led to Nobel Prize.
Died in London, England April 16, 1958, of
ovarian cancer (38 yrs).
“I think you will be interested to know that our dark
lady leaves us next week…I am now reasonably clear
of other commitments and have started up a general
offensive on Nature’s secret strongholds…At least the
decks are clear, and we can put all hands to the
pumps!”
It won’t be long now.
Regards to all
Yours ever
M
Wilkins had a tough time dealing with
Rosalind Franklin, celebrated her departure
A model for the structure of DNA was proposed by Watson and Crick in
1953. Their model was based on a number of pieces of information that
were available at the time about the composition of DNA and the x-ray
diffraction properties of DNA fibers. Most importantly, x-ray diffraction
studies of DNA fibers performed by Rosalind Franklin and Maurice Wilkins
showed that DNA molecules are helical and exhibit two periodicities
repeating along the length of the fiber--a primary repeat of 3.4 Å and a
secondary repeat of 34 Å.
Erwin Chargaff and colleagues had shown through DNA compositional
analysis that the number of T residues always equals the number of A
residues (A = T), and the number of G residues always equals the number of
C residues (G = C).
Watson-Crick Model for the Structure of
Double-helical DNA
Then a paper was published by Bragg, Kendrew, and Perutz, in Cambridge, describing a
number of helical structures of polypeptide chains obtained in their search for an alphakeratin
structure. From my point of view, all of these structures were wrong, because they
did not involve planarity around the nitrogen atom. I thought that it was likely, however,
that in the course of time they would learn enough chemistry to see what peptide group
had a planar structure, and would discover the alpha helix, so Professor Corey and I
decided to publish a short description of the alpha helix and the gamma helix.
Pauling on Bragg, Kendrew, and Perutz protein structure (Protein Science, 2, 1060-1063,
1993, reminescence).
(Bragg, L., Kendrew, J. C., and Perutz, M. F., Proc. Roy. Soc., A203, 321 (1950).
Watson and Crick on Pauling’s DNA structure (Nature 171, 737, 1953)
(Pauling, J,., and Corey, R. B. Proc. U.S. Nat. Acad. Sci., 39, 84 (1953).
A structure for nucleic acid has already been proposed by Pauling and Corey. Their
model consists of three intertwined chains, with the phosphates near the fiber axis, and
the bases on the outside. In our opinion, this structure is unsatisfactory for two reasons --.
Linus Pauling paid the price
• Chargaff felt there had been an injustice done when he did not receive the
Nobel Prize in 1962 along with Watson, Crick and Wilkins.
• Wilkins’ contribution to the structure of DNA was to show James Watson the
work of Rosalind Franklin without her permission.
• Franklin did not share the Nobel Prize as she passed away from ovarian cancer
in 1958 and posthumous nominations are forbidden.
Chargaff Snubbed, Franklin ignored
Chargaff is quoted as saying, “I told them all I knew. If they had
heard before about the pairing rules, they concealed it. But as they
did not seem to know much about anything, I was not unduly
surprised..”
''The base composition was an essential clue for finding the
structure of DNA, there's no doubt about that,'' Dr. Watson
said in an interview. ''We could have come up with the
answer, but no one would have believed it.''
44
Sides of the Ladder
45
Hydrogen Bonding and Nitrogenous Bases
46
Hydrogen Bonding and Nitrogenous Bases
47
Hydrogen Bonding and Nitrogenous Bases
Many people were involved, very few got the credit