Structure of the Nucleic Acids

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Structure of the Nucleic Acids
J. Paul Simon
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Learning Objectives
Identify the different conformational forms of
DNA. Describe the chemical structure of DNA in
terms of the following Purine and pyrimidine
base composition Deoxyribose sugar
residues Nucleoside and nucleotide N-glycosidic
bond Phosphodiester linkage
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Describe the Watson-Crick structure of B-DNA with
respect to the following Right-handed double
helix Major and minor grooves Anti-parallel
polynucleotide strands Sugar-phosphate
backbone Chargaffs rules Hydrogen bonding
between base pairs Coding of genetic information
Define the following terms in relation to the
organization and packing of DNA within the
nucleus Histones Nucleosomes Nucleosome core
particle Chromatin Heterochromatin Euchromatin
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Describe the central dogma of molecular biology
in terms of information transfer and the
extension of this dogma to include the two
important processes found in RNA viruses.
Describe the stability of DNA in terms of the
following Reversible heat denaturation and
annealing Melting temperature versus GC content
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Deoxyribonucleic acid (DNA ) is the hereditary
molecule in all cellular life forms, as well as
in many viruses.
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Overview
The Central Dogma of Molecular Biology
DNA directs its own replication and its
transcription to RNA which, in turn, directs its
translation to proteins.
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Certain RNA viruses contain an RNA-dependent DNA
polymerase called reverse transcriptase. These
viruses are called retroviruses (HIV, RNA tumor
viruses). This enzyme uses the virial RNA as a
template and synthesizes complementary DNA.
Extension of the Central Dogma
The single-stranded chromosomes of some
bacteriophages of E. coli are replicated by
RNA-dependent RNA polymerases (RNA replicase).
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The fundamental chemical building block of the
nucleic acids is the nucleotide.
Without the phosphate group, this is a nucleoside.
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Nitrogenous bases in DNA and RNA
Parent Compounds
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DNA and RNA are linear polymers of nucleotides
whose phosphates bridge the 3 and 5 positions
of successive sugar residues.
A short nucleic acid is called an
oligonucleotide, or oligo.
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Hydrolysis of RNA under alkaline conditions.
DNA is stable under similar conditions.
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Structural information for DNA
The base composition of DNA varies from one
species to another. DNA isolated from different
tissues of the same species has the same
composition. The base composition of DNA in a
given species does not change with an organisms
age, nutritional state, or changing
environment. In all cellular DNAs, A T and G
C, (A G T C) These quantitative
relationships are known as Chargaffs rules.
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A photograph of the x-ray diffraction pattern
taken by Rosalind Franklin.
This is the photograph that provided key
information for the elucidation of the
Watson-Crick structure.
The central X-shaped pattern of spots is
indicative of a helix, whereas the heavy black
arcs on the top and bottom of the diffraction
pattern correspond to a distance of 3.4 Angstroms
and indicates that the DNA structure largely
repeats every 3.4 Angstroms along the fiber axis.
A 34 Angstrom repeat is also indicated.
Rosalind Franklin
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Major features of the Watson-Crick model for the
structure of DNA
Fibers of DNA consist of two polynucleotide
strands that wind about a common axis with a
right-handed twist to form a double helix. The
two strands are antiparallel (run in opposite
directions), and wrap around each other such that
they cannot be separated without unwinding the
helix. The bases occupy the core of the double
helix while the sugar-phosphate groups are coiled
about the periphery thereby minimizing the
repulsions between the negatively charged
phosphate residues. The planes of the bases are
nearly perpendicular to the axis.
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Each base is hydrogen bonded to a base on the
opposite strand to form a planar base pair. It is
these hydrogen bonded interactions, a phenomena
known as complimentary base pairing, that results
in the specific association of the two chains of
the double helix.
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Common hydrogen bonds in biological systems
Hydrogen bonds form between an electronegative
atom (the hydrogen acceptor, usually oxygen or
nitrogen with an unshared pair of electrons), and
a hydrogen donor (another electronegative atom in
the same or a different molecule. Hydrogen bonds
are highly directional, and are capable of
holding atoms or molecules in specific
geometrical arrangements.
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The Watson-Crick structure can accommodate only
two types of base pairs each adenine residue
must pair with a thymine and vice versa, and each
guanine must pair with a cytosine and vice versa.
The A-T and G-C base pairs are interchangeable in
that they can replace each other in the double
helix without altering the positions of the
sugar-phosphate backbone
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The two deep grooves that wind about the outside
of B-DNA between the sugar-phosphate backbones
are of unequal size. They are called the major
and minor grooves.
Major Groove
Minor Groove
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The Watson-Crick structure can accommodate any
sequence of bases on one polynucleotide strand if
the opposite strand has the complementary base
sequence.
This immediately accounts for Chargaffs rules.
More importantly, it suggests that hereditary
information is encoded in the sequence of bases
on either strand.
James Watson and Francis Crick
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Structural variation in DNA
Structural variation in DNA reflects three things
(1) the different possible conformations of
deoxyribose
(2) rotation about the bonds that constitute the
phosphodiester backbone
(3) free rotation about the N-glycosidic bond
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Conformations of ribose
In solution, the straight chain and ring forms
are in equilibrium. Nucleic acids contain only
the ring form.
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Ring pucker
Furanose rings in nucleotides can exist in four
different puckered conformations. In all cases,
four of the five atoms are in a single plane.
The fifth atom (C-2 or C-3) is on either the
same (endo) or the opposite (exo) side of the
plane relative to the C-5 atom.
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The conformation of a nucleotide in DNA is
affected by rotation about seven different bonds.
Six of the bonds rotate freely. The limited
rotation about bond 4 gives rise to ring pucker.
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For purine bases in nucleotides, only two
conformations with respect to the attached ribose
units are sterically permitted anti or syn.
Pyrimidines generally occur in the anti
conformation.
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The helical structure described by Watson and
Crick, called B-DNA, is only one of several
possible conformations. Other DNA conformations
use the same nucleotides and molecular bonds, but
the three-dimensional structure of the helix is
different.
B-DNA is the most common form of DNA found in
living organisms. Z-DNA has been found in E.
coli and the conversion from the B form to the Z
form may act as a switch in regulating genetic
expression.
Each of these structures has 36 base pairs.
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Comparison of A, B, and Z forms of DNA
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Sequence-dependent structural variations
Palindrome regions of DNA with inverted repeats
of base sequence having two-fold symmetry over
two strands
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When both strands of palindromic DNA are
involved, the structure is called a
cruciform. Some cruciform structures have been
demonstrated in vivo in E. coli. Many DNA-binding
regulatory proteins recognize specific
palindromic sequences.
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Reversible denaturation and annealing of DNA
Disruption of the base stacking and breaking of
the hydrogen bonds between base pairs causes
unwinding of the double helix to form single
strands.
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Heat denaturation of DNA
Melting curves of two DNA species
G C content vs. tm
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Genome Size
One molecule of duplex DNA per chromosome
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Prokaryotes
Eukaryotes
(E. coli, bacillus, archaebacteria)
(Yeast, algae, vertebrates, plants)
DNA localized in a membrane-bound nucleus. The
nuclear envelope separates the nuclear material
from the cytoplasm. This envelope contains
nuclear pores which regulate the passage of
materials between the cytoplasm and the nucleus.
No nucleus DNA is not physically separated from
the cytoplasm by a nuclear membrane.
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DNA packaging
The single DNA molecule of the bacterium E. coli
seen leaking out of a disrupted cell.
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DNA Packaging in Prokaryotes
Supercoiled DNA
In E. coli, the DNA is supercoiled and attached
to an RNA-protein core.
All the genes in E. coli are readily accessible
for transcription.
RNA-protein core
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DNA Packaging in Eukaryotes
Chromatin is a term designating the structure in
which DNA exists within eukaryotic cells. This
structure is determined and stabilized through
the interaction of DNA with DNA-binding proteins.
Histones the major class of DNA-binding proteins
involved in maintaining the compacted structure
of chromatin. Rich in arginine and
lysine. Non-histone chromosomal proteins (enzymes
that act on DNA, factors that regulate
transcription)
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When cells divide, the chromatin is seen as
distinct chromosomes. After cell division, the
chromosomes begin to unravel, and two types of
chromatin become apparent
Heterochromatin dense coiled masses Euchromatin
diffuse, extended microfibrils
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The nucleosome core is an octamer composed of two
molecules of each of the core histones H2A, H2B,
H3, and H4.
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DNA coils around the histone octamer to form the
nucleosome core particle.
Protein is depicted as a gray surface contour.
Bound DNA (in blue)
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