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RNA- Structure, Types and Functions


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RNA- A polymer of ribonucleotides, is a single stranded structure. There are three major types of RNA- m RNA,t RNA and r RNA. Besides that there are small nuclear,micro RNAs, small interfering and heterogeneous RNAs. Each of them has a specific structure and performs a specific function.

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RNA- Structure, Types and Functions

  1. 1. Biochemistry for Medics Biochemistry For Medics 1
  2. 2. RNA (Ribonucleic acid )RNA is apolymer ofribonucleotideslinked togetherby 3’-5’phosphodiesterlinkage Biochemistry For Medics 2
  3. 3. RNA V/S DNA Biochemistry For Medics 3
  4. 4. Differences between RNA and DNA S.No. RNA DNA 1) Single stranded mainly except Double stranded (Except for when self complementary certain viral DNA s which are sequences are there it forms a single stranded) double stranded structure (Hair pin structure) 2) Ribose is the main sugar The sugar moiety is deoxy ribose 3) Pyrimidine components differ. Thymine is always there but Thymine is never found(Except uracil is never found tRNA) 4) Being single stranded structure- It does follow Chargaffs rule. It does not follow Chargaff’s rule The total purine content in a double stranded DNA is always equal to pyrimidine content. Biochemistry For Medics 4
  5. 5. Differences between RNA and DNA S.No. RNA DNA 5) RNA can be easily destroyed by DNA resists alkali action due to alkalies to cyclic diesters of the absence of OH group at 2’ mono nucleotides. position 6) RNA is a relatively a labile DNA is a stable molecule. The molecule, undergoes easy and spontaneous degradation is spontaneous degradation very 2 slow. The genetic information can be stored for years together without any change. 7) Mainly cytoplasmic, but also Mainly found in nucleus, extra present in nucleus (primary nuclear DNA is found in transcript and small nuclear mitochondria, and plasmids RNA) etc 8) The base content varies from Millions of base pairs are there 100- 5000. The size is variable. depending upon the organism Biochemistry For Medics 5
  6. 6. Differences between RNA and DNA S.No. RNA DNA 9) There are various types of RNA – DNA is always of one type and mRNA, r RNA, t RNA, Sn RNA, Si performs the function of RNA, mi RNA and hn RNA. These storage and transfer of genetic RNAs perform different and information. specific functions. 10) No variable physiological forms There are variable forms of of RNA are found. The different DNA (A to E and Z) types of RNA do not change their forms 11) RNA is synthesized from DNA, it DNA can form DNA by can not form DNA(except by the replication, it can also form action of reverse transcriptase). RNA by transcription. It can not duplicate (except in certain viruses where it is a genomic material ) 12) Many copies of RNA are present Single copy of DNA is present per cell per cell. Biochemistry For Medics 6
  7. 7. Types of RNAIn all prokaryotic and eukaryoticorganisms, three main classes of RNAmolecules exist-1) Messenger RNA(m RNA)2) Transfer RNA (t RNA)3) Ribosomal RNA (r RNA)The other are –o small nuclear RNA (SnRNA),o micro RNA(mi RNA) ando small interfering RNA(Si RNA) ando heterogeneous nuclear RNA (hnRNA). Biochemistry For Medics 7
  8. 8. Messenger RNA (m-RNA)Comprises only 5% of the RNA in the cellMost heterogeneous in size and base sequenceAll members of the class function asmessengers carrying the information in a gene tothe protein synthesizing machinery Biochemistry For Medics 8
  9. 9. Structural Characteristics ofm-RNA The 5’ terminal end is capped by 7- methyl guanosine triphosphate cap. The cap is involved in the recognition of mRNA by the translating machinery It stabilizes m RNA by protecting it from 5’ exonuclease Biochemistry For Medics 9
  10. 10. Structural Characteristics ofm-RNA(contd.) The 3’end of most m-RNAs have a polymer ofAdenylate residues( 20-250) The tail prevents the attack by 3’ exonucleasesHistones and interferons do not contain poly Atails On both 5’ and 3’ end there are non codingsequences which are not translated (NCS)The intervening region between non codingsequences present between 5’ and 3’ end iscalled coding region. This region encodes for thesynthesis of a protein. Biochemistry For Medics 10
  11. 11. Structural Characteristics ofm-RNA5’ cap and 3’ tail impart stability to m RNA by protecting fromspecific exo nucleases. Biochemistry For Medics 11
  12. 12. Structural Characteristics ofm-RNA(Contd.)The m- RNA molecules are formed with the help ofDNA template during the process of transcription.The sequence of nucleotides in m RNA iscomplementary to the sequence of nucleotides ontemplate DNA.The sequence carried on m -RNA is read in the formof codons.A codon is made up of 3 nucleotidesThe m-RNA is formed after processing ofheterogeneous nuclear RNA Biochemistry For Medics 12
  13. 13. Heterogeneous nuclear RNA(hnRNA) In mammalian nuclei , hnRNA is theimmediate product of gene transcription The nuclear product is heterogeneous in size(Variable) and is very large.Molecular weight may be more than 107, whilethe molecular weight of m RNA is less than 2x 106 75 % of hnRNA is degraded in the nucleus,only 25% is processed to maturem RNA Biochemistry For Medics 13
  14. 14. Heterogeneous nuclear RNA(hnRNA)Mature m –RNA is formed from primary transcript by capping, tailing, splicing and base modification. Biochemistry For Medics 14
  15. 15. Transfer RNA (t- RNA)Transfer RNA are the smallest of three major species ofRNA moleculesThey have 74-95 nucleotide residues They are synthesized by the nuclear processing of aprecursor moleculeThey transfer the amino acids from cytoplasm to theprotein synthesizing machinery, hence the name t RNA.They are easily soluble , hence called “Soluble RNA or sRNAThey are also called Adapter molecules, since they act asadapters for the translation of the sequence of nucleotidesof the m RNA in to specific amino acidsThere are at least 20 species of t RNA one correspondingto each of the 20 amino acids required for proteinsynthesis. Biochemistry For Medics 15
  16. 16. Structural characteristics of t- RNA 1) Primary structure- The nucleotide sequence of all the t RNA molecules allows extensive intrastand complimentarity that generates a secondary structure. 2) Secondary structure- Each single t- RNA shows extensive internal base pairing and acquires a clover leaf like structure. The structure is stabilized by hydrogen bonding between the bases and is a consistent feature. Biochemistry For Medics 16
  17. 17. Structural characteristics of t-RNASecondary structure (Clover leaf structure)All t-RNA contain 5 main arms or loopswhich are as follows-a) Acceptor armb) Anticodon armc) D HU armd) TΨ C arme) Extra arm Biochemistry For Medics 17
  18. 18. Secondary structure of t- RNAa)Acceptor arm The acceptor arm is at 3’ end It has 7 base pairs The end sequence is unpaired Cytosine, Cytosine-Adenine at the 3’ end The 3’ OH group terminal of Adenine binds with carboxyl group of amino acids The t RNA bound with amino acid is called Amino acyl t RNA CCA attachment is done post transcriptionally Biochemistry For Medics 18
  19. 19. Secondary structure of t- RNAThe carboxyl group of amino acid is attached to 3’OH group of Adeninenucleotide of the acceptor arm. The anticodon arm base pairs with the codonpresent on the m- RNA Biochemistry For Medics 19
  20. 20. Secondary structure of t-RNA(contd.)b) Anticodon arm Lies at the opposite end of acceptor arm5 base pairs longRecognizes the triplet codon present in the mRNABase sequence of anticodon arm iscomplementary to the base sequence of m RNAcodon. Due to complimentarity it can bind specificallywith m RNA by hydrogen bonds. Biochemistry For Medics 20
  21. 21. Secondary structure of t-RNA(contd.)c) DHU arm It has 3-4 base pairsServes as the recognition site for the enzyme (aminoacyl t RNA synthetase) that adds the amino acid to theacceptor arm.d) TΨC armThis arm is opposite to DHU armSince it contains pseudo uridine that is why it is sonamed It is involved in the binding of t RNA to the ribosomes Biochemistry For Medics 21
  22. 22. Secondary structure of t-RNA(contd.)e) Extra arm or Variable arm About 75 % of t RNA molecules possessa short extra armIf about 3-5 base pairs are present thet-RNA is said to be belonging to class 1.Majority t -RNA belong to class 1. The t –RNA belonging to class 2 havelong extra arm, 13-21 base pairs in length. Biochemistry For Medics 22
  23. 23. Tertiary structure of t- RNA The L shaped tertiarystructure is formed byfurther folding of the cloverleaf due to hydrogen bondsbetween T and D arms. The base paired doublehelical stems get arranged into two double helicalcolumns, continuous andperpendicular to oneanother. Biochemistry For Medics 23
  24. 24. Ribosomal RNA (rRNA)The mammalian ribosome contains two majornucleoprotein subunits—a larger one with a molecularweight of 2.8 x 106 (60S) and a smaller subunit with amolecular weight of 1.4 x 106 (40S).The 60S subunit contains a 5S ribosomal RNA (rRNA), a5.8S rRNA, and a 28S rRNA; there are also probably morethan 50 specific polypeptides.The 40S subunit is smaller and contains a single 18SrRNA and approximately 30 distinct polypeptide chains.All of the ribosomal RNA molecules except the 5S rRNAare processed from a single 45S precursor RNA moleculein the nucleolus .5S rRNA is independently transcribed. Biochemistry For Medics 24
  25. 25. Ribosomal RNA (rRNA) Biochemistry For Medics 25
  26. 26. Ribosomal RNA (rRNA)The functions of the ribosomal RNAmolecules in the ribosomal particle are notfully understood, but they are necessary forribosomal assembly and seem to play keyroles in the binding of mRNA to ribosomesand its translationRecent studies suggest that an rRNAcomponent performs the peptidyl transferaseactivity and thus is an enzyme (a ribozyme). Biochemistry For Medics 26
  27. 27. Small RNAMost of these molecules arecomplexed with proteins to formribonucleoproteins and are distributed inthe nucleus, in the cytoplasm, or in both.They range in size from 20 to 300nucleotides and are present in 100,000–1,000,000 copies per cell. Biochemistry For Medics 27
  28. 28. Small Nuclear RNAs (snRNAs)snRNAs, a subset of the small RNAs, aresignificantly involved in mRNA processing andgene regulationOf the several snRNAs, U1, U2, U4, U5, andU6 are involved in intron removal and theprocessing of hnRNA into mRNAThe U7 snRNA is involved in production ofthe correct 3 ends of histone mRNA—whichlacks a poly(A) tail. Biochemistry For Medics 28
  29. 29. Small Nuclear RNAs (snRNAs).Sn RNA s are involved in the process of splicing (intron removal) of primarytranscript to form mature m RNA. The Sn RNA s form complexes with proteinsto form Ribonucleoprotein particles called snRNPs Biochemistry For Medics 29
  30. 30. Micro RNAs, miRNAs, and Small Interfering RNAs, siRNAsThese two classes of RNAs represent asubset of small RNAs; both play importantroles in gene regulation.miRNAs and siRNAs cause inhibition ofgene expression by decreasing specificprotein production albeit apparently viadistinct mechanisms Biochemistry For Medics 30
  31. 31. Micro RNAs (miRNAs)miRNAs are typically 21–25 nucleotides inlength and are generated by nucleolyticprocessing of the products of distinctgenes/transcription unitsThe small processed mature miRNAstypically hybridize, via the formation ofimperfect RNA-RNA duplexes within the 3-untranslated regions of specific targetmRNAs, leading via unknown mechanisms totranslation arrest. Biochemistry For Medics 31
  32. 32. Micro RNAs (miRNAs)microRNAs, short non-coding RNAs present in all living organisms, havebeen shown to regulate the expression of at least half of all humangenes. These single-stranded RNAs exert their regulatory action bybinding messenger RNAs and preventing their translation intoproteins. Biochemistry For Medics 32
  33. 33. Small Interfering RNAs (siRNAs) siRNAs are derived by the specific nucleolytic cleavageof larger, double-stranded RNAs to again form small 21–25 nucleotide-long products.These short siRNAs usually form perfect RNA-RNAhybrids with their distinct targets potentially anywherewithin the length of the mRNA where the complementarysequence exists. Formation of such RNA-RNA duplexes between siRNAand mRNA results in reduced specific protein productionbecause the siRNA-mRNA complexes are degraded bydedicated nucleolytic machinery; some or all of this mRNA degradation occurs in specificorganelles termed P bodies. Biochemistry For Medics 33
  34. 34. Small Interfering RNAs (siRNAs)Small interfering RNA (siRNA) are 20-25 nucleotide-long double-stranded RNAmolecules that have a variety of roles in the cell. They are involved in the RNAinterference (RNAi) pathway, where it interferes with the expression of aspecific gene by hybridizing to its corresponding RNA sequence in thetarget mRNA. This then activates the degrading mRNA. Once the targetmRNA is degraded, the mRNA cannot be translated into protein. Biochemistry For Medics 34
  35. 35. Significance of mi RNAs and siRNAsBoth miRNAs and siRNAs representexciting new potential targets fortherapeutic drug development in humans.In addition, siRNAs are frequently used todecrease or "knock-down" specific proteinlevels in experimental procedures in thelaboratory, an extremely useful andpowerful alternative to gene-knockouttechnology. Biochemistry For Medics 35
  36. 36. SummaryRNA exists in several different single-strandedstructures, most of which are directly or indirectlyinvolved in protein synthesis or its regulation.The linear array of nucleotides in RNA consists of A, G,C, and U, and the sugar moiety is ribose.The major forms of RNA include messenger RNA(mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA),and small nuclear RNAs (snRNAs; miRNAs). Certain RNA molecules act as catalysts (ribozymes).miRNAs and siRNAs represent exciting new potentialtargets for therapeutic drug development in humans. Biochemistry For Medics 36