1 dna + rna dan graur. 2 the hereditary information of all living organisms, with the exception of...

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1 DNA + RNA DNA + RNA Dan Graur Dan Graur

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Page 1: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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DNA + RNADNA + RNA

Dan GraurDan Graur

Page 2: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA) molecules.

Page 3: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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):

Page 4: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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):

Page 5: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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

Page 6: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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The nucleotides are covalently linked in tandem by asymmetrical 5’-3' phosphodiester bonds. The DNA is, thus, polarized.

Page 7: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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’

Page 8: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 9: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

9A purinepurine always pairs with a pyrimidinepyrimidine.

Strongbond

Weakbond

Page 10: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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TheThe antiparaantipara

llelllel structustructure of re of

double-double-strandestranded DNAd DNA

Page 11: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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5’ 3’

downstreamupstream

upstreamdownstream

5’3’

Page 12: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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5’

5’3’

3’

heavy chain

light chain

A preponderance of purines

A preponderance of pyrimidines

Page 13: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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5’

5’3’

3’

CTGGA

Page 14: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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The length of a single-stranded nucleic acid is measured in number of nucleotides.

Page 15: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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).

Page 16: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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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Page 17: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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GenomeGenome

Nongenic or Nongenic or intergenic DNAintergenic DNAGenic DNAGenic DNA

Page 18: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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ReplicationReplicationDNA DNA

Page 19: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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1958: Matthew Meselson & Franklin Stahl

Page 20: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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Page 21: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 22: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 23: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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

Page 24: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 25: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 26: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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

Page 27: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 28: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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(1) Protein-coding genesProtein-coding genes

(2) RNA-specifying genesRNA-specifying genes

Structural or Structural or ProductiveProductive

GenesGenes

Page 29: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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TranscriptionTranscriptionDNA RNA

Page 30: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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

Page 31: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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standard nucleotides

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

Page 32: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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

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

Page 33: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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

TranscriptionTranscription

antisense

sense

Page 34: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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

(transcriptional noise)

Page 35: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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Non-coding RNAs

Page 36: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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RNA processingRNA processingpre-RNA mature-RNA

Page 37: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 38: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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

Page 39: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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Polyadenylation of Polyadenylation of 3' end3' end

Page 40: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

40Postranscriptional modifications

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).

Page 41: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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SplicingSplicing

Page 42: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 43: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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donor

acceptor

Page 44: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 45: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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

Page 46: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

Intron and exon lengths

Page 47: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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The nuclear divide: The nuclear divide:

Page 48: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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Page 49: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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)

Page 50: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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Substitution editing

Page 51: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 52: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 53: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.

Page 54: 1 DNA + RNA Dan Graur. 2 The hereditary information of all living organisms, with the exception of some viruses, is carried by deoxyribonucleic acid (DNA)

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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.