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DNA + RNADNA + RNA

Dan GraurDan 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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DNA is made of DNA is made of fourfour nucleotides nucleotides

adenine (A)adenine (A) cytosine (C)cytosine (C)guanine (G)guanine (G) thymine (T)thymine (T)

2 purines (R):2 purines (R): 2 pyrimidines (Y):2 pyrimidines (Y):

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sugar (deoxyribose) phosphate

DNA is made of DNA is made of fourfour nucleotides nucleotides

adenine (A)adenine (A) cytosine (C)cytosine (C)guanine (G)guanine (G) thymine (T)thymine (T)

2 purines (R):2 purines (R): 2 pyrimidines (Y):2 pyrimidines (Y):

5two ringstwo rings one ringone ring

DNA is made of DNA is made of fourfour nucleotides nucleotides

2 purines (R):2 purines (R): 2 pyrimidines (Y):2 pyrimidines (Y):

AA CCGG TT

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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 sequenceThus, the sequence

5’-GCAAT-5’-GCAAT-3’3’

is different from the is different from the sequencesequence

3’-GCAAT-3’-GCAAT-5’5’

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Deoxyribonucleic acid (DNA) Deoxyribonucleic acid (DNA) consists of two complementary consists of two complementary strands twisted around each other strands twisted around each other to form a to form a ririgght-handed double ht-handed double helixhelix. .

The two chains are joined The two chains are joined throughout their lengths by throughout their lengths by hydrohydroggen bondsen bonds between pairs of between pairs of nucleotides. nucleotides.

9A purinepurine always pairs with a pyrimidinepyrimidine.

Strongbond

Weakbond

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TheThe antiparaantipara

llelllel structustructure of re of

double-double-strandestranded DNAd DNA

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5’ 3’

downstreamupstream

upstreamdownstream

5’3’

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5’

5’3’

3’

heavy chain

light chain

A preponderance of purines

A preponderance of pyrimidines

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5’

5’3’

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 usually have more than one genome: nuclear1, mitochondrial2, & plastid3.Some eukaryotes have a single genome; some have4 or more genomes .

1122

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GenomeGenome

Nongenic or Nongenic or intergenic DNAintergenic DNAGenic DNAGenic DNA

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ReplicationReplicationDNA 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.

23DNA replication occurs only in the 5'-DNA replication occurs only in the 5'-to-3' direction. to-3' direction.

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Okazaki fragments Bacteria = 1,000 - 2,000 nucleotidesVertebrates = 100 - 200 nucleotides

The leading strand is replicated continuously. The lagging strand is replicated as Okazaki fragmentsOkazaki fragments.

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When Wilhelm Johannsen coined the word “gene” in 1909, the term meant “a unit of heredity.” Its material basis was unimportant for its usefulness as a concept.

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“Where the meaning of most four-letter words is all too clear, that of gene is not. The more expert scientists become in molecular genetics, the less easy it is to be sure about what, if anything, a gene actually is.”

Helen Pearson

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“A gene is a sequence of DNA that is essential for a specific function.”

(1) Protein-codinProtein-codingg ggenesenes, which are transcribed into RNA and subsequently translated into proteins(2) RNA-specifRNA-specifyyiningg ggenesenes, which are only transcribed into RNA(3) Untranscribed Untranscribed ggenesenes.

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(1) Protein-coding genesProtein-coding genes

(2) RNA-specifying genesRNA-specifying genes

Structural or Structural or ProductiveProductive

GenesGenes

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TranscriptionTranscriptionDNA RNA

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RNARNA differs differs from from DNADNA by by having having riboseribose instead of instead of deoxyribosedeoxyribose……

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standard nucleotides

RNARNA differs differs from from DNADNA by using by using uraciluracil instead of instead of thyminethymine… …

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DNADNA is is mostly mostly double-double-strandedstranded. .

RNARNA is is mostly mostly single-single-strandedstranded..

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The 5’ to 3’ DNA is transcribed into 3’ to 5’ RNA

TranscriptionTranscription

antisense

sense

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RNA1. Coding RNA = mRNA2. Non-coding RNA3. Non-functional RNA

(transcriptional noise)

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Non-coding RNAs

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RNA processingRNA processingpre-RNA mature-RNA

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Examples of RNA Examples of RNA processing:processing:

1. Capping of 5' end. 1. Capping of 5' end. 2. Polyadenylation of 3' 2. Polyadenylation of 3' end.end.3. Postranscriptional 3. Postranscriptional modifications.modifications.4. Splicing.4. Splicing.5. RNA editing.5. RNA editing.

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CappingCapping is the addition of a 7’-methylated guanine to the 5’ end via a 5’ to 5’ bond.

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Polyadenylation of Polyadenylation of 3' end3' end

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I: Inosine (needed for wobble).

Ψ: Pseudouridine (only in Eukarya and Archaea).

D: Dihydrouridine.

T: Thymine (unusual for RNA).

Y: Wybutosine (found just after the anticodon).

I: Inosine (needed for wobble).

Ψ: Pseudouridine (only in Eukarya and Archaea).

D: Dihydrouridine.

T: Thymine (unusual for RNA).

Y: Wybutosine (found just after the anticodon).

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SplicingSplicing

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Protein-coding genesProtein-coding genesThe 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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donor

acceptor

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The human factor-IX geneThe human factor-IX gene

Total length of exons = 1,386 bp Total length of introns = 29,954 bp 5' untranslated region = 30 bp3' untranslated region = 1,389 bp

Only about 4%4% of the pre-mRNA sequence actually encode the protein.

Note the uneven distribution of exons.

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Mean size = 144 bp

Mean size = 123 bp

Mean size = 165 bp

Homo sapiens Rattus rattus Arabidopsis thaliana

Mean size = 2364 bp

Mean size = 733 bp

Mean size = 171 bp

exons

introns

Intron and exon lengths

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The nuclear divide: The nuclear divide:

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RNA editing

SubstitutionInsertion/deletion•Mononucleotide insertion (C, G, U)•Mononucleotide deletion (U)•Dinucleotide insertion (GC, GU, CU, AU, AA)•Substitutions (UA, UG, UC, AG, CU, CA, GA)•Modifications to a nonstandard nucleotide (AI)

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Substitution editing

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Insertion/deletion editingWhen RNA editing is extensive, so that the resulting RNA bears little resemblance to the DNA sequence, the DNA template is called a cryptogenecryptogene.

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Pseudogenes = Dead Gene:Pseudogenes = Dead Gene:

A pseudogene is a DNA segment A pseudogene is a DNA segment that is similar to a gene, but that is similar to a gene, but which contains defects that which contains defects that render it non-functional. render it non-functional.

Pseudogenes are marked by the Pseudogenes are marked by the prefix prefix followed by the name of followed by the name of the gene to which they are similar, the gene to which they are similar, e.g., e.g., -globin.-globin.

In computerized databanks, the In computerized databanks, the suffix P is used, e.g., CA5P for suffix P is used, e.g., CA5P for the the -carbonic anhydrase pseudogene -carbonic anhydrase pseudogene 5.5.

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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.

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There are three main categories of pseudogenes distinguished by the molecular evolutionary processes which created them:

1. Unitary2. Unprocessed3. Processed

Each of these can be duplicated or unduplicated.

There are also mosaic pseudogenes.