Download Watson - Crick model explains

The Chemical Nature of the
Gene
Base Structure and Topology
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
The structure of DNA
• Base composition – pyrimidines (cytosine [C], thymine [T])
– purines (adenine [A], guanine [G])
– backbone of alternating sugar & phosphate
groups
– joined by 3'-5'-phosphodiester bond
– Nucleotide (& polymer) is polarized - 5'
phosphate & 3'-OH
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
The structure of DNA
• Some terminology
– nucleoside (deoxyribose, nitrogenous base)
– nucleotide (add phosphates)
– RNA nucleotides are often employed in energy
metabolism like ATP, GTP
• X-ray diffraction revealed dimensions
– 3.4 Å between nucleotides in stack
– large structural repeat every 34 Å (3.4 nm)
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
The structure of DNA
• Erwin Chargaff (Columbia, 1950)
– Found relative base amounts varied
– not always 1:1:1:1, but always constant within
species
– Purines equaled pyrimidines: [A] = [T]; [G] = [C]
– A:G ratio of Btub = 0.4; human DNA - 1.56
– Chargaff gave DNA molecule specificity &
individuality
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Watson - Crick Model
• Composed of 2 nucleotide chains
• 2 chains spiral as right-handed helices
– clockwise path moving away from observer
• 2 chains of double helix antiparallel
• sugar-phosphate-sugar-phosphate—outside
• bases project toward center
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Figure 10.10a & b
Watson - Crick Model
• Planes of bases stack on top of each other
– Hydrophobic interactions & van der Waal forces
add stability
• Chains held together by H bonds
• radius 10 Å (1 nm); DNA width 20 Å (2 nm)
• Pyrimidine pairs with purine
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Watson - Crick Model
• A with T; G with C (matches Chargaff's
Rules)
– Nitrogen atoms on cytosine C4 & adenine C6
are mostly in amino (NH2) not imino (NH) form
– Oxygens on guanine C6 & thymine C4 mostly in
keto (C=O), not enol (C—OH) form
– These structural restrictions on base
configurations are responsible for pairing
restrictions
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Figure 10.10a & b
Watson - Crick Model
• 2 grooves of different width
– Wider major groove; more narrow minor groove
– DNA binding proteins have domains that fit into
grooves
• 10 residues (3.4 nm) per turn
• complementarity (one strand complement to
the other)
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Utility of DNA Duplex
• Primary functions of genetic material
– Storage of genetic information - determines
heritable characteristics; amino acid sequence of
all proteins in organism must be contained within
the DNA structure
– Self-duplication and inheritance – DNA must
contain the information for its own replication
– Expression of genetic message - genes usually
encode proteins; DNA must direct protein
synthesis
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Figure 10.11
Utility of DNA Duplex
• Watson - Crick model explains:
– Information resides in DNA base sequence; change
DNA sequence —> change protein coded for
– Chains can separate as H bonds break & serve as
template for synthesis of new strand —> at the end,
of replication get 2 strands identical to each other &
the original DNA molecule
• According to the proposal, each new DNA double
helix would contain one strand from original DNA
molecule & one newly synthesized strand
• A semiconservative mode of replication
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
DNA supercoiling
• Jerome Vinograd et al. (Caltech, 1963)
– found that 2 closed DNA circles of identical
molecular mass could show very different
sedimentation rates
– Fast sedimenting DNA had more compact shape
because molecule was twisted (supercoiled)
upon itself (rubber band, phone cord)
– Occupies less volume; moves more rapidly in
response to centrifugal force or electrical field
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
DNA supercoiling
• Relaxed: 10 base pairs per turn
– Fuse two ends of strands to form circle without
twisting: relaxed
– DNA is underwound = negatively supercoiled
– Circular DNA in nature is usually negatively
supercoiled
– Positively supercoiled DNA is overwound
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
DNA supercoiling
• Supercoiling also occurs in eukaryotic DNA
– Linear DNA around protein cores
(nucleosomes) also supercoils
– Negative supercoiling allows compaction
– Long DNA’s fit into microscopic cell nucleus
– Underwinding helps to separate the 2 strands of
the helix
– Aids both replication & transcription
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Figure 10.13
Topoisomerases
• Type I topoisomerases –
– create transient break in one strand, & then
– allows a controlled rotation, which relaxes the
molecule
– Prevents supercoiling “build-up” during
replication, transcription
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Topoisomerases
• Type II topoisomerases –
– create transient break in both duplex strands,
then
– pass double stranded DNA segment through
break
– reseal severed strands to freeze structure
– can also tie DNA molecule into knots, untie
knots,
– interlink independent circles (catenation) or
separate
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E
Figure 10.14a-c
Topoisomerases
• Topoisomerase II is required to unlink DNA
molecules before duplicated chromosomes
can be separated during mitosis
• Human topoisomerase II is target for a
number of drugs (etoposide, doxorubicin)
used to kill rapidly dividing cancer cells;
drugs bind to enzyme & keep cleaved DNA
strands from resealing
Copyright, ©, 2002, John Wiley & Sons, Inc.,
Karp/CELL & MOLECULAR BIOLOGY 3E