DNA RNA

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DNA RNA

• Dan Graur

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The hereditary information of all living
organisms, with the exception of some viruses, is
carried by deoxyribonucleic acid (DNA) molecules.
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sugar (deoxyribose)
phosphate
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DNA is made of four nucleotides
2 purines
2 pyrimidines
A
C
G
T
one ring
two rings
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The nucleotides are covalently linked in tandem
by asymmetrical 5-3' phosphodiester bonds. The
DNA is, thus, polarized.
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Thus, the sequence 5-GCAAT-3 is different
from the sequence 3-GCAAT-5
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Deoxyribonucleic acid (DNA) consists of two
complementary strands twisted around each other
to form a right-handed double helix. The two
chains are joined throughout their lengths by
hydrogen bonds between pairs of nucleotides.
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Weak bond
Strong bond
A purine always pairs with a pyrimidine.
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The antiparallel structure of double-stranded DNA
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downstream
upstream
5
3
5
3
upstream
downstream
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heavy chain (Watson)
A preponderance of purines
3
5
light chain (Crick)
5
3
A preponderance of pyrimidines
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3
5
5
3
CTGGA
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The length of a single-stranded nucleic acid is
measured in number of nucleotides.
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The length a double-stranded sequence is measured
in base pairs (bp), thousands of base pairs
(kilobases, Kb), millions of base pairs
(megabases, Mb), or billions of base pairs
(gigabases, Gb).
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The entire complement of genetic material carried
by an individual is called the genome. Eukaryotic
cells may have up to three subcellular genomes
nuclear1, mitochondrial2, chloroplastid3.
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1
2
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Genome
Non-genic DNA
Genic DNA
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What is a Gene?
A gene is a sequence of DNA that is essential
for a specific function. (1) Protein-coding
genes, which are transcribed into RNA and
subsequently translated into proteins (2)
RNA-specifying genes, which are only transcribed
into RNA (3) Untranscribed genes.
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What is a Gene?
(1) Protein-coding genes (2) RNA-specifying
genes
Productive genes
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Replication
DNA ? DNA
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1958 Matthew Meselson Franklin Stahl
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The origin of replication is at the replication
bubble, a local region where the two strands of
the DNA helix have been separated from each
other. Replication proceeds in both directions as
two replication forks.
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Bacteria have one origin of replication. A
bacterial genome can replicate in 40 minutes. In
eukaryotes, many replication origins exist. They
are spaced at intervals of up to 300,000 bp from
one another. Replication in eukaryotic cells may
take several hours.
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DNA replication occurs only in the 5'-to-3'
direction.
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The leading strand is replicated continuously.
The lagging strand is replicated as Okazaki
fragments.
Okazaki fragments Bacteria 1,000 - 2,000
nucleotides Vertebrates 100 - 200 nucleotides
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Transcription
DNA ? RNA
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RNA differs from DNA by having ribose instead of
deoxyribose
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RNA differs from DNA by using uracil instead of
thymine
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DNA is mostly double-stranded. RNA is mostly
single-stranded.
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Transcription
antisense
The 5 to 3 DNA is transcribed into 3 to 5 RNA
sense
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RNA

• Coding RNA mRNA
• Non-coding RNA

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HOTAIR HOx Antisense Intergenic Rna
Rinn et al. (2007) discovered a long noncoding
RNA, encoded in the HOXC cluster, HOTAIR, that
unexpectedly regulates the HOXD cluster on a
different chromosome than the HOXC. HOTAIR is a
2158 nucleotide-long, spliced and polyadenylated
transcript.
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RNA processing
pre-RNA? mature-RNA
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Examples of RNA processing 1. Capping of 5'
end. 2. Polyadenylation of 3' end. 3.
Postranscriptional modifications. 4. Splicing. 5.
RNA editing.
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Capping is the addition of a 7-methylated
guanine to the 5 end via a 5 to 5 bond.
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Polyadenylation of 3' end
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I Inosine (needed for wobble). ? Pseudouridine
(only in Eukarya and Archaea). D
Dihydrouridine. T Thymine (unusual for
RNA). Y Wybutosine (found just after the
anticodon).
Postranscriptional modifications
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Splicing
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Protein-coding genes The number of introns
varies greatly from gene to gene. The
distribution of intron sizes in vertebrate genes
is very broad. The distribution of exon sizes is
much narrower with a peak at around 150 bp. The
vast majority of protein-coding genes in
vertebrates consist mostly of introns.
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acceptor
donor
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The human factor-IX gene Total length of
exons 1,386 bp Total length of introns
29,954 bp 5' untranslated region 30
bp 3' untranslated region 1,389 bp Only
about 4 of the pre-mRNA sequence actually encode
the protein. Note the uneven distribution of
exons.
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Homo sapiens
Rattus rattus
Arabidopsis thaliana
Mean size 144 bp
Mean size 123 bp
Mean size 165 bp
exons
Mean size 2364 bp
Mean size 733 bp
Mean size 171 bp
introns
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The nuclear divide
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RNA editing

• Mononucleotide insertion (C, G, U)
• Mononucleotide deletion (U)
• Dinucleotide insertion (GC, GU, CU, AU, AA)
• Substitutions (U?A, U?G, U?C, A?G, C?U, C?A, G?A)
• Modifications to a nonstandard nucleotide (A?I)

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Substitution editing
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Insertion/deletion editing
When RNA editing is extensive, so that the
resulting RNA bears little resemblance to the DNA
sequence, the DNA template is called a cryptogene.
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Pseudogenes A pseudogene is a DNA segment that
is similar to a gene, but which contains defects
that render it non-functional. Pseudogenes are
marked by the prefix ? followed by the name of
the gene to which they are similar, e.g.,
??-globin. In computerized databanks, the
suffix P is used, e.g., CA5P for the ?-carbonic
anhydrase pseudogene 5.
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Most pseudogenes are not transcribed. A
significant minority of pseudogenes is
transcribed but not translated. A handful of
pseudogenes is translated. Pseudogenes are
ubiquitous at all genomic locations and in all
organisms, although some organisms and some
locations tend to harbor more pseudogenes than
others. There are several categories of
pseudogenes distinguished by the molecular
evolutionary processes which created them.