Transcript Nerve activates contraction

A structure for Deoxyribose Nucleic Acid
2 April 1953
MOLECULAR STRUCTURE OF NUCLEIC ACIDS
We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.
A structure for nucleic acid has already been proposed by Pauling and Corey (1). They kindly made their manuscript available to us in advance of publication. Their model consists of three
intertwined chains, with the phosphates near the fibre axis, and the bases on the outside. In our opinion, this structure is unsatisfactory for two reasons: (1) We believe that the material which
gives the X-ray diagrams is the salt, not the free acid. Without the acidic hydrogen atoms it is not clear what forces would hold the structure together, especially as the negatively charged
phosphates near the axis will repel each other. (2) Some of the van der Waals distances appear to be too small.
Another three-chain structure has also been suggested by Fraser (in the press). In his model the phosphates are on the outside and the bases on the inside, linked together by hydrogen bonds.
This structure as described is rather ill-defined, and for this reason we shall not comment on it.
We wish to put forward a radically different structure for the salt of deoxyribose nucleic acid. This structure has two helical chains each coiled round the same axis (see diagram). We have
made the usual chemical assumptions, namely, that each chain consists of phosphate diester groups joining ß-D-deoxyribofuranose residues with 3',5' linkages. The two chains (but not their
bases) are related by a dyad perpendicular to the fibre axis. Both chains follow right- handed helices, but owing to the dyad the sequences of the atoms in the two chains run in opposite
directions. Each chain loosely resembles Furberg's2 model No. 1; that is, the bases are on the inside of the helix and the phosphates on the outside. The configuration of the sugar and the
atoms near it is close to Furberg's 'standard configuration', the sugar being roughly perpendicular to the attached base. There is a residue on each every 3.4 A. in the z-direction. We have
assumed an angle of 36° between adjacent residues in the same chain, so that the structure repeats after 10 residues on each chain, that is, after 34 A. The distance of a phosphorus atom from
the fibre axis is 10 A. As the phosphates are on the outside, cations have easy access to them.
The structure is an open one, and its water content is rather high. At lower water contents we would expect the bases to tilt so that the structure could become more compact.
The novel feature of the structure is the manner in which the two chains are held together by the purine and pyrimidine bases. The planes of the bases are perpendicular to the fibre axis. The
are joined together in pairs, a single base from the other chain, so that the two lie side by side with identical z-co-ordinates. One of the pair must be a purine and the other a pyrimidine for
bonding to occur. The hydrogen bonds are made as follows : purine position 1 to pyrimidine position 1 ; purine position 6 to pyrimidine position 6.
If it is assumed that the bases only occur in the structure in the most plausible tautomeric forms (that is, with the keto rather than the enol configurations) it is found that only specific pairs of
bases can bond together. These pairs are : adenine (purine) with thymine (pyrimidine), and guanine (purine) with cytosine (pyrimidine).
In other words, if an adenine forms one member of a pair, on either chain, then on these assumptions the other member must be thymine ; similarly for guanine and cytosine. The sequence of
bases on a single chain does not appear to be restricted in any way. However, if only specific pairs of bases can be formed, it follows that if the sequence of bases on one chain is given, then
the sequence on the other chain is automatically determined.
It has been found experimentally (3,4) that the ratio of the amounts of adenine to thymine, and the ration of guanine to cytosine, are always bery close to unity for deoxyribose nucleic acid.
It is probably impossible to build this structure with a ribose sugar in place of the deoxyribose, as the extra oxygen atom would make too close a van der Waals contact. The previously
published X-ray data (5,6) on deoxyribose nucleic acid are insufficient for a rigorous test of our structure. So far as we can tell, it is roughly compatible with the experimental data, but it must
be regarded as unproved until it has been checked against more exact results. Some of these are given in the following communications. We were not aware of the details of the results
presented there when we devised our structure, which rests mainly though not entirely on published experimental data and stereochemical arguments.
It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.
Full details of the structure, including the conditions assumed in building it, together with a set of co-ordinates for the atoms, will be published elsewhere.
We are much indebted to Dr. Jerry Donohue for constant advice and criticism, especially on interatomic distances. We have also been stimulated by a knowledge of the general nature of the
unpublished experimental results and ideas of Dr. M. H. F. Wilkins, Dr. R. E. Franklin and their co-workers at King's College, London. One of us (J. D. W.) has been aided by a fellowship
from the National Foundation for Infantile Paralysis.
J. D. WATSON F. H. C. CRICK
Medical Research Council Unit for the Study of Molecular Structure of Biological Systems, Cavendish Laboratory, Cambridge. April 2.
1. Pauling, L., and Corey, R. B., Nature, 171, 346 (1953); Proc. U.S. Nat. Acad. Sci., 39, 84 (1953).
2. Furberg, S., Acta Chem. Scand., 6, 634 (1952).
3. Chargaff, E., for references see Zamenhof, S., Brawerman, G., and Chargaff, E., Biochim. et Biophys. Acta, 9, 402 (1952).
4. Wyatt, G. R., J. Gen. Physiol., 36, 201 (1952).
5. Astbury, W. T., Symp. Soc. Exp. Biol. 1, Nucleic Acid, 66 (Camb. Univ. Press, 1947).
Rosalind Franklin
We wish to suggest a structure for the salt of deoxyribose nucleic acid
(D.N.A.). This structure has novel features which are of considerable
biological interest."
-- James Watson and Francis Crick, in a brief letter to the journal Nature,
April 2, 1953
The search for genetic
material lead to DNA
Genetic Material –DNA or Protein?????
• Frederick Griffith (1928)
•Transformation- a change in genotype
and phenotype due to the assimilation
of a foreign substance (now known to
be DNA) by a cell.
• Oswald Avery – discovers DNA as
the transforming substance (1944)
• Hershey and Chase – 1952
• Bacteriophage – virus that infects
bacteria
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Known so far:
• DNA is polymer made of Nucleotides
• Nucleotides have sugar-phosphateand a nitrogen base
• Nitrogen bases can be Adenine,
Guanine, Cytosine, or Thymine
• Not known - how the monomers
connect to make a molecule that can
carry genetic material
Relative Proportions (%) of Bases in DNA
Organism
Human
Chicken
Grasshopper
Sea Urchin
Wheat
Yeast
E. Coli
A
T
G
30.9 29.41 9.91
28.8 29.2 20.5
29.3 29.3 20.5
32.8 32.1 17.7
27.3 27.1 22.7
31.3 32.9 18.7
24.7 23.6 26.0
C
9.8
21.5
20.7
17.3
22.8
17.1
25.7
Chargaff’s Rule (1947)
DNA composition varies in
different species
• Nucleotide:
• Sugar
In any one species, all 4 (deoxyribose)
bases are not equal in number
• Phosphate
• Nitrogenous
 # of A = # of T (A=T)
base (Adenine,
Guanine,
 # of G = # of C (G = C) Cytosine, or
Thymine)
• DNA – a double
helix
Hydrogen Bonding
• Between purine
and pyrimidine
• Purines are
Adenine and
Guanine
• Pyrimidines are
Thymine and
Cytosine
• A and T
• G and C
Sugar
Phosphate
Backbone
• The phosphate group
of one nucleotide is
attached to the sugar of
the next nucleotide in
line.
• The result is a
“backbone” of
alternating phosphates
and sugars, from which
the bases project.
Fig. 16.3
Sugar Phosphate
Backbone
• The 2 strands are
antiparallel (5’ to
3’ in one strand
and 3’ to 5’ in the
other)
• 5’ end has a P
• 3’ end has a -OH
Sugar Phosphate Backbone
Double Helix
 10 bases per turn
of helix
 Major and minor
grooves – sites of
protein interaction
 Base
complementarity =
easy replication
When does this occur???
DNA Replication
Template strands
• Semiconservative
replication:
- when a double
helix replicates,
each of the
daughter
molecules will
have one old
strand and one
newly made
strand.
• Meselson and Stahl (1958)
A large team of enzymes and
other proteins carries out DNA
replication
• It takes E. coli less than an hour to copy each of
the 5 million base pairs in its single
chromosome and divide to form two identical
daughter cells.
• A human cell can copy its 6 billion base pairs
and divide into daughter cells in only a few
hours.
• This process is remarkably accurate, with only
one error per billion nucleotides.
• More than a dozen enzymes and other proteins
participate in DNA replication.
• The replication of a DNA molecule
begins at special sites, origins of
replication.
ORI SITE = special
DNA sequence
recognized by proteins
 1 ORI Site in
bacteria (circular
chromosome)
Many ORI Sites in
eukaryotes (replication
bubbles and forks)
1) Helicase unwinds DNA.
•A new DNA strand can only
elongate in the 5’->3’ direction.
•5’ end has a
P
•3’ end has a
-OH
2) Leading and Lagging strands
are synthesized by 2 different
mechanisms
Leading strand – is
synthesized
continuously in 5’-> 3’
direction towards the
replication fork
 Lagging strand uses
Okazaki fragments –
short segments copied
away from the fork
3)DNA polymerase adds
nucleotides to 3’ end of growing
strand
• DNA polymerases catalyze the
elongation of new DNA at a
replication fork using nucleoside
triphosphates
So has DNA
Polymerase!!
• DNA polymerases cannot initiate synthesis
of a polynucleotide because they can only
add nucleotides to the end of an existing
chain that is base-paired with the template
strand.
4) Solution – use Primase to make
a short ‘Primer’
• To start a new
chain requires a
primer, a short
segment of RNA.
– The RNA primer
is about 10
nucleotides long
in eukaryotes.
• Another DNA
polymerase later
replaces the primer
ribonucleotides with
deoxyribonucleotides
complimentary to the
template.
• Leading strand requires the
formation of only a single primer
as the replication fork continues to
separate.
• The lagging strand requires
formation of a new primer as the
replication fork progresses.
5) DNA
Ligase
• DNA ligase joins
the fragments
together.
Oops, it’s a wrong base!!!
• One error per 10,000 base pairs.
• DNA polymerase proofreads each new
nucleotide
• If there is an incorrect pairing, the
enzyme removes the wrong nucleotide
and then resumes synthesis.
• The final error rate is only one per
billion nucleotides.
X Rays
• Can cause DNA
mutations
Cosmic Rays
• Can cause DNA
mutations
UV Rays
• Can cause DNA
mutations
–produces thymine dimers between
adjacent thymine nucleotides.
– Each cell continually monitors and
repairs its genetic material, with over
130 repair enzymes identified in
humans.
• In nucleotide
excision
repair, a nuclease
cuts
out a segment of a
damaged strand.
– The gap is filled in
by DNA polymerase
and ligase.
• In mismatch repair, special
enzymes fix incorrectly paired
nucleotides.
The ends of DNA molecules are
replicated by a special mechanism
– Repeated rounds of replication produce
shorter and shorter DNA molecules.
This animation is WRONG!
Fig. 16.18
• The ends of eukaryotic chromosomal DNA
molecules, the telomeres, have special
nucleotide sequences.
– In human telomeres, this sequence is typically
TTAGGG, repeated between 100 and 1,000 times.
• Telomeres protect genes from being eroded
through multiple rounds of DNA replication.
• Telomerase is not present in most cells
of multicellular organisms.
• Therefore, the DNA of dividing somatic
cells and cultured cells does tend to
become shorter.
• Thus, telomere length may be a limiting
factor in the life span of certain tissues
and the organism.
• Telomerase is present in germ-line cells,
ensuring that zygotes have long
telomeres.
• Active telomerase is also found in
cancerous somatic cells.
– This overcomes the progressive shortening
that would eventually lead to self-destruction
of the cancer.