Islamic University Faculty of Medicine

Transcription

1 Islamic University Faculty of Medicine

2 2 RNA is a modular structure built from a combination of secondary and tertiary structural motifs. RNA chains fold into unique 3 D structures, which act similarly to globular proteins. RNA is involved in a wide range of cellular processes from DNA replication to protein synthesis.

3 3 1. Ribosomal RNA (rrna) an essential component of the ribosome. 2. Messenger RNA (mrna) a copy of the genomic DNA sequence that encodes a gene product and binds to ribosomes in the cytoplasm. 3. Transfer RNAs (trnas) deliver appropriate amino acid to the ribosome via interaction of trna anticodon with mrna codon.

4 4 4. Small nuclear RNA (snrna) has a role in pre mrna splicing, a process which prepares the mrna for translation 5. Small nucleolar RNA (snorna) has a role in rrna processing. 6. MicroRNA (mirna) involved in post transcriptional gene regulation Each binds to complementary sequence in a target RNA degradation of mrna or blocking translation gene silencing.

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6 6 RNA can form complementary base pairs with other RNA molecules and with singlestranded DNA. RNA can interact with proteins: Most RNA in a eukaryotic cell is associated with protein as part of ribonucleoprotein (RNP) particles. Most, if not all, RNA based catalytic reactions are thought to take place in conjunction with proteins.

7 7 1. RNA can serve as a scaffold upon which proteins can be assembled. Proteins recognize the RNA primary sequence and/or secondary and tertiary structural motifs. e.g. signal recognition particle 2. RNA protein interactions can influence the catalytic activity of proteins. e.g. telomerase The protein functions as the enzyme e.g. ribonuclease (RNase) P and the ribosome the RNA is catalytic, not the protein.

8 8 3. RNA can be catalytic e.g. RNA molecules termed ribozymes can catalyze a number of the chemical reactions in living cells 4. Small RNAs can directly control gene expression RNA interference and micrornas. 5. RNA can be the hereditary material Many viruses have RNA genomes self replicating or replicate through a DNA intermediate

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10 10 RNA is a chain like molecule composed of subunits called nucleotides joined by phosphodiester bonds. The common bases in RNA are adenine (A), guanine (G), cytosine (C), and uracil (U).

11 11 The folding of an RNA chain into a variety of structural motifs.

12 12 2' OH group hinders formation of a B type helix. Shallow, broad minor groove includes the ribose 2' OH. RNA is often recognized by RNA binding proteins in the minor groove.

13 13 >20 different types of noncanonical (non Watson Crick) base pairs. Widen the major groove and make it more accessible to ligands or proteins. The most common of these are the: GU wobble GA sheared AU reverse Hoogsteen GA imino

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15 15 Typically involve one standard base pair. The third base interacts in a variety of unconventional ways.

16 16 Important mediators of: RNA self assembly. RNA protein interactions. RNA ligand interactions.

17 17 The average trna is about 76 nt long. All of the different trnas of a cell fold into the same general shape General principles Modified bases. trna loops each have a separate function. Coaxial stacking of stems. All trnas fold into the same general shape. Cloverleaf secondary structure L shaped tertiary structure

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19 19 More than 50 modified bases in trna. Simple methylation to complete restructuring of the purine ring. Inosine (I) was the first modified nucleoside to be identified in trna. Pseudouridine ( ) was the first identified in any RNA. Extensive base modification also occurs in other RNAs e.g. during maturation of ribosomal RNA.

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21 21 Every trna has the sequence ACC on the 3 end to which the amino acid is attached T loop: recognition by the ribosome. D loop: recognition by the aminoacyl trna synthetases Anticodon loop: base pairs with the mrna codon.

22 22 Base paired stems often are involved in longrange interactions with other stems.

23 23 One of the most important findings in molecular biology in the last 30 years The discovery that RNA molecules can catalyze chemical reactions in living cells. 1982: catalytic RNA discovered in a Tetrahymena ribosomal RNA intron. 1983: RNA component of E. coli RNase P shown to be catalytic.

24 24 Thomas Cech and co workers were studying transcription of ribosomal RNA (rrna) genes in Tetrahymena thermophila. an intervening sequence (IVS) or intron is spliced out in the final 26S rrna product. Thomas Cech and colleagues developed an in vitro assay to study intron splicing. In the presence of GTP and Mg2+ alone, the protein free RNA underwent splicing. Conclusion: the RNA was splicing itself.

25 : Sidney Altman and coworkers showed that bacterial RNase P is an RNA enzyme. Eukaryotic RNase P acts as a catalytic ribonucleoprotein (RNP)

26 26 Classic definition of an enzyme: A substance that increases the rate, or velocity, of a chemical reaction without itself being changed in the overall process. Because many naturally occurring RNA enzymes are self splicing, the term ribozyme was coined.

27 27 Form substrate binding sites. Lower the activation energy. Allow reaction to proceed much faster. Many are metalloenzymes. e.g. binding of Mg2+ in active site Two different groups of Naturally occurring ribozymes based on difference in size and reaction mechanism: Large ribozymes Small ribozymes

28 28 Vary in size from a few hundred to 3000 nucleotides. RNA components of RNase P group I and group II intron family RNA components of the spliceosome ribosomal RNA.

29 29 Cleave RNA to generate 3 OH termini.

30 30 Vary in size from 40 to 154 nucleotides. Hammerhead motif hairpin motif hepatitis delta virus (HDV) RNA Varkud satellite (VS) RNA the glms riboswitch ribozyme. Most are involved in self replication. Potential tools to combat viral disease.

31 31 Cleave RNA to generate a 2 3 cyclic phosphate and a product with a 5 OH terminus.

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33 33 RNA serves as the genome for a number of infectious agents: eukaryotic RNA viruses, retroviruses, viroids, and other subviral pathogens. Mutation rate 1000 fold higher than DNA based genomes. Lack of proofreading activity by RNA polymerases. high mutation rates are advantageous to the virus alters its proteins rapidly can evade recognition by host defense systems.

34 34 Infect many different hosts, including plants and animals. Many significant human or veterinary pathogens. Single stranded or double stranded RNA genome. Enveloped or nonenveloped capsids. Replicate without forming DNA intermediates. distinguishes them from the retroviruses, which also have an RNA genome.

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36 36 1. Plus strand (coding strand) viruses make protein directly because their genomic RNA also serves as the mrna for about a dozen genes e.g. picornaviruses polio and common cold in humans, and foot and mouth disease in livestock 2. Minus strand (non coding strand) viruses must first make the complementary plus strand before using the RNA in protein synthesis. Examples: rabies, mumps, measles, influenza, severe acute respiratory syndrome (SARS), and the more exotic Ebola and Marburg filoviruses, which have caused epidemics of fatal hemorrhagic fever in Africa. 3. Double stranded RNA e.g. rotavirus, agent of infant diarrhea

37 37 Pandemics arise when a virus to which most people have no immunity, usually an avian strain, acquires the ability to transmit from animal to person.and then from person to person.

38 38 The genes for two outer coat proteins, hemagglutinin and neuraminidase are constantly mutating. Possibility for exchange of genes with a common human flu strain. Reassortment produces new viruses with a variety of segment combinations.

39 39 Also called RNA tumor viruses many members play a role in cancer Single stranded RNA genome. Replicate through a DNA intermediate. Upon infecting an animal cell: converts the ssrna into a dsdna copy. The DNA is then inserted into the host cell DNA remains permanently inserted in the host genome. Many well known animal pathogens. One prominent human pathogen: Human immunodeficiency virus 1 (HIV 1) Important vectors for gene therapy.

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41 41 Viroids are plant pathogens. e.g. avocado sunblotch viroid and coconut cadang cadang viroid The viroid genome is a single, very small (250 to 400 nt), circular molecule of RNA. The viroid RNA is the infectious agent; it does not encode any protein. Viroids replicate using host encoded RNA polymerase.

42 42 Satellite RNAs Single stranded RNA genome. Found in plants and animals. e.g. hepatitis delta virus, a small singlestranded RNA satellite of hepatitis B virus Some larger RNAs may encode a protein. Require a helper virus to replicate.

43 43 Virusoids Circular, single stranded RNA genome. Plant pathogens that do not encode any protein. e.g. velvet tobacco mottle, subterranean clover mottle Require a helper virus for replication and capsid formation.