Download 1. The Building Blocks of DNA

1. The Building Blocks of DNA
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DNA has three types of chemical component:
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Phosphate
a sugar called deoxyribose, and
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four nitrogenous bases:
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Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T).
Two of the bases, adenine and guanine, have a double-ring structure characteristic of a
type of chemical called a purine. The other two bases, cytosine and thymine, have a
single-ring structure of a type called a pyrimidine.
The chemical components of DNA are arranged into groups called
nucleotides, each composed of a phosphate group, a deoxyribose
sugar molecule, and any one of the four bases.
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2. The four nucleotides
Chemical structure of the
four nucleotides (two with
purine bases and two with
pyrimidine bases) that are
the fundamental building
blocks of DNA. The sugar
is called deoxyribose
because it is a variation of
a common sugar, ribose,
which has one more
oxygen atom
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3. The double helix
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DNA is composed of two
side-by-side chains
("strands") of nucleotides
twisted into the shape of
a double helix. The two
nucleotide strands are
held together by weak
associations between the
bases of each strand,
forming a structure like a
spiral staircase
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In three dimensions, the bases form rather flat structures, and these flat bases
partly stack on top of one another in the twisted structure of the double helix. This
stacking of bases adds tremendously to the stability of the molecule by excluding
water molecules from the spaces between the base pairs.
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4. Strand polarity
The arrangement of the components of DNA. A segment of
the double helix has been unwound to show the structures
more clearly. The diagram shows the sugar-phosphate
backbone and the hydrogen bonding of bases in the center of
the molecule.
The sugar-phosphate bonds are called phosphodiester bonds.
The carbons of the sugar groups are numbered 1’ through 5’
(next slide). One part of the phosphodiester bond is between
the phosphate and the 5’ carbon of deoxyribose, and the other
is between the phosphate and the 3’ carbon of deoxyribose.
Thus, each sugar-phosphate backbone is said to have a 5’-to3’ polarity, and understanding this polarity is essential in
understanding DNA properties. In the double-stranded DNA
molecule, the two backbones are in opposite, or antiparallel,
orientation. One strand is oriented 5’3’; the other strand,
though 5’ 3’, runs in the opposite direction, or, looked at
another way, is 3’5’
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5. Base pairing
The bases of DNA interact according to a very
straightforward rule, namely, that there are only two
types of base pairs: A·T and G·C. The bases in
these two base pairs are said to be complementary.
This means that at any "step" of the stair like
double-stranded DNA molecule, the only base-tobase associations that can exist between the two
strands without substantially distorting the doublestranded DNA molecule are A·T and G·C.
Note that because the G·C pair has three
hydrogen bonds, whereas the A·T pair has only
two, one would predict that DNA containing many
G·C pairs would be more stable than DNA
containing many A·T pairs. In fact, this prediction
is confirmed. Heat causes the two strands of the
DNA double helix to separate (a process called
DNA melting or DNA denaturation); it can be
shown that DNAs with higher G+C content require
higher temperatures to melt them
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6. DNA forms giant molecules
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Although hydrogen bonds are individually weak, the two
strands of the DNA molecule are held together in a
relatively stable manner because there are enormous
numbers of these bonds. It is important that the strands be
associated through such weak interactions, since they have
to be separated during DNA replication and during
transcription into RNA
The sugar-phosphate backbone, being connected by
covalent bonds, is also stable; bacterial DNA form a single
giant molecule; in eukaryotes, each chromosome is
composed by a single giant molecule of DNA
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7. How much DNA per genome?
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Almost all cells of all organisms contain at least one copy of the
entire genome of the species (most cell are diploid, i.e. they contains
two copies).
Genome sizes are measured in units of thousands of nucleotide pairs
(called kilobases, kb) or millions of nucleotide pairs (megabases, mb),
or sometimes in picograms (10-12 gr)
In general, the total amount of chromosomal DNA in different animals
and plants does not vary in a consistent manner with the apparent
complexity of the organisms.
Yeasts, fruit flies, chickens, and humans have successively larger
amounts of DNA in their haploid chromosome sets, in keeping with
what we perceive to be the increasing complexity of these organisms.
Yet the vertebrates with the greatest amount of DNA per cell are
amphibians, which are surely less complex than humans in their
structure and behavior.
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8. Genome sizes
Amount of DNA in the genomes of various organisms
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9. Lenght of a DNA molecule
The single chromosome of
Escherichia coli is about 1.3 mm of
DNA. To enable a macromolecule
this large to fit within the bacterium,
histone-like proteins bind to the
DNA, segregating the DNA molecule
into around 50 chromosomal domains
and making it more compact. Then an
enzyme called DNA gyrase
supercoils each domain around itself
forming a compacted, supercoiled
mass of DNA approximately 0.2 µm
in diameter, called nucleoid.
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10. The nucleoid
The nucleoid is one long,
single molecule of double
stranded, helical, supercoiled
DNA. In most bacteria, the
two ends of the doublestranded DNA covalently
bond together to form both a
physical and genetic circle.
The chromosome is generally around 1000
µm long and frequently contains as many as
3500 genes. E. coli, that is 2-3 µm in length
has a chromosome approximately 1400 µm
long.
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11. Eukaryotic Nuclear Genomes
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A human cell contains about 2 meters of DNA, packed into 46
chromosomes, all inside a nucleus only 6 mm in diameter.
Thus, in order to pack the DNA into the nucleus, there must be several
levels of coiling and supercoiling.
Cell wall
Nucleus
Nucleolus
These levels of DNA structure cannot be
resolved by the optical microscope, under
which interphase nuclei stained with
DNA-specific dyes appears composed of
a dense, dark-staining material called
heterochromatin, and is scattered
throughout the nucleus, and a very lightstaining flocculent material which fills the
rest of the nucleus, called euchromatin.
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12. DNA in interphase
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It is thought that most part of each chromosome in an
interphase nucleus (chromatine) has the form of the “30 nm
fiber”
The figure on the left shows
the tangled chromatin fibers
obtained after disrupting a
nucleus. Shearing forces can
be used to further uncoil and
stretch these fibers and the
beaded filaments appear. The
strands between the beads are
segments of double stranded
DNA (right panel).
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13. The 30 nm fibre
Different levels of chromosome
uncoiling. The bottom of the
figure shows the DNA helix
(which is DNA stripped of its
histones). In the normal,
unstripped chromosome, the
double stranded DNA is wrapped
around sets of 8 macromolecules
of histones (proteins) to form a
10 nm filament. These sets of
histones are separated by spacer
regions of 4 nm DNA filament.
They are the 10 nm nucleoprotein
fibrils or "beads on a string" seen
in electron micrographs which are
called nucleosomes. The next
level of coiling produces the 30
nm nucleoprotein fibers .
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14. Compacting factors
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Stuffing the long strands of chromosomal DNA into a
eukaryotic nucleus requires that the DNA be compacted in
length approximately 10,000 to 50,000 -fold. Incredibly,
cells achieve this tight packing of the DNA while still
maintaining the chromosomes in a form that allows
regulatory proteins to gain access to the DNA to turn on (or
off) specific genes or to duplicate the chromosomal DNA
(replication).
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15. The average lenght of coding regions
Organism
Vibrio cholerae (bacterium)
Saccharomyces cerevisiae (yeast)
Drosophila melanogaster (fruit fly)
Cenorhabditis elegans (nematode)
Arabidopsis thaliana (weed)
Homo sapiens
Average length of
gene product (aa)
304
477
492
436
435
497
Estimates of the average length of polypeptide chains
coded by genes of various organisms; these value have to
be multiplied by 3 in order to obtaing the lenght of the
corresponding coding DNA. Tipical values are 1,000 to
1,500 bp.
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16. A “gene” is not only coding sequence
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Definition: A gene is a discrete unit of DNA (or RNA in some viruses)
that encodes a nucleic acid or protein product that contributes to or
influences the phenotype of the cell or the organism.
Genes are the functional units of chromosomal DNA. Each gene not
only encodes the structure of some cellular product, but also bears
control elements (short sequences) that determine when, where, and
how much of that product is synthesized. Most genes encode protein
products; special classes of genes encode for RNA molecules.
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The way genes encode proteins is indirect and involves several steps. The first
step is to copy (transcribe) the information encoded in the DNA of the gene as
a related but single-stranded molecule called messenger RNA. Subsequently the
information in the messenger RNA is translated (decoded) into a string of
amino acids called a polypeptide. The polypeptides, on their own or by
aggregating with other polypeptides and cell constituents, form the functional
proteins of the cell.
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17. Introns and exons
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Trying to pinpoint precisely what genes are is complicated by the fact
that many eukaryotic genes contain mysterious segments of DNA,
called introns, interspersed in the transcribed region of the gene.
Introns do not contain information for functional gene product such as
protein. They are transcribed together with the coding regions
(called exons) but are then excised from the initial transcript.
Since correct sequence in the introns (as well as in the regulatory
region) is necessary in order to generate a properly sized transcript at
the right time and place, introns (along with coding and regulatory
regions) should be considered part of the overall functional unit, in
other words, part of the gene
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18. Schematic gene structure
Generalized gene structure
in prokaryotes and
eukaryotes. The coding
region (dark green) is the
region that contains the
information for the
structure of the gene
product (usually a protein).
The adjacent regulatory
regions (lime green)
contain sequences that are
recognized and bound by
proteins that make the
gene's RNA and by
proteins that influence the
amount of RNA made.
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19. Number of introns-exons per gene
Distribution of the number of exons among genes of
three organisms
Many eukaryotic
genes contain
mysterious segments
of DNA, called
introns, interspersed
in the region of the
gene. Introns do not
contain information
for functional gene
product such as
protein.
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20. Average gene length
Intron/exon statistics for various organisms
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21. Genomes and genes
The number of genes
increases with
genome size, but the
trend is complicated
due to repetitive DNA
and introns.
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22. Most eukaryotic DNA does not include genes
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Between genes there is DNA, mostly of unknown function. The size
and nature of this DNA vary with the genome.
In bacteria and fungi there is little, but in mammals the intergenic
regions can be huge.
Sequences of DNA that exist quite distant from a given gene can
affect the regulation of that gene. They could thus be considered
part of the functional gene unit, even though separated by long
segments of DNA having nothing to do with the gene in question.
In many eukaryotes some of the DNA between genes is repetitive,
consisting of several different types of units repeated throughout the
genome. Some of the repetitive DNA is dispersed; some is found in
contiguous "tandem" arrays. Repetitive DNA is also found in some
introns. The extent of this DNA is different in different species, and
indeed there is variation of repeat number within species.
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23. Comparing gene densities
Schematic diagram of gene topography in four organisms.
Light green = introns; dark green = exons; white = intergenic regions
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24. A small fraction of total eukaryotic DNA is coding
In mammals, only a few percent of the DNA is actualy coding:
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25. Coding sequences are needles in the haystack
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It is apparent that the coding sequences are only a small part
of the genome in most eukaryotes, particularly in human.
Finding these regions is like finding a needle in the
haystack.
In addition, the genes are not uniformly distributed. There
are regions in the genome where the genes are packed
together, and regions where they are sparse, where finding
genes is like finding water in a desert.
Genetica per Scienze Naturali
a.a. 03-04 prof S. Presciuttini