Structural features of rna

structure of mrna and description of heterogenous nuclear rna,rrna and trna and fuctions of rna

1. STRUCTURAL FEATURES OF mRNA,rRNA,tRNA D.INDRAJA

2. mRNA Also called as messenger RNA Accounts for about 5% of the total RNA in the cell . It is a single-stranded RNA molecule that is complementary to one of the DNA strands of a gene Discovery In 1961, French scientists François Jacob   and Jacques  Monod  hypothesized the existence of an intermediary between DNA and its protein products, which they called messenger RNA .

3. Central dogma of molecular biology The mRNA carries the message from the DNA, which controls all of the cellular activities in a cell. If a cell requires a certain protein to be synthesized, the gene for this product is “turned on” and the mRNA is synthesized through the process of transcription  . The mRNA then interacts with  ribosomes  and other cellular machinery to direct the synthesis of the protein it encodes during the process of translation

4. Molecules of mRNA are composed of relatively short, single strands of molecules made up of adenine, cytosine, guanine and uracil bases held together by a sugar phosphate backbone. Like in  DNA , mRNA genetic information is in the sequence of  nucleotides , which are arranged into  codons  consisting of three  base pairs  each. Each codon codes for a specific amino acid, except the  stop codons , which terminate protein synthesis . mRNA in cytoplasm exist as ribonucleoproteins (covered by proteins called informosomes ) that protect mRNA from digestion by nucleases .

5. Types of m rna Based on the types of cell they are of two types Eukaryotic mRNA Prokaryotic mRNA Eukaryotic mRNA In eukaryotes, mRNA is transcribed on chromosomes in the nucleus, and after processing, is shuttled through nuclear pores and into the cytoplasm Inside each nucleus, a multi subunit protein called RNA polymerase II (RNAP II) reads DNA and simultaneously fabricates a “message” or transcript Pre-mRNA is synthesized from a  DNA  template in the  cell nucleus  by  transcription . Pre-mRNA comprises the bulk of  heterogeneous nuclear RNA  ( hnRNA ). The hnRNA is the collective term for the unprocessed  mRNA  molecules in the  nucleus . It contains unique sequences and has about 10 times as many sequences as the mature mRNA

6. The hnRNA that is associated with proteins form the heterogenous nuclear ribonucleoprotein ( hnRNP ).  In mammalian nuclei , hnRNA is the immediate product of gene transcription The nuclear product is heterogeneous in size(Variable) and is very large. Molecular weight may be more than 10 7 , while the molecular weight of m RNA is less than 2x 10 6 75 % of hnRNA is degraded in the nucleus, only 25% is processed to mature m RNA  Once pre-mRNA has been completely  processed , it is termed " mature messenger RNA ", or simply " messenger RNA " which is called messenger RNA (mRNA), in a process called transcription Molecules of mRNA are composed of relatively short and long lived Eukaryotic mRNA is monocistronic which means it contains single open reading frame (ORF) for translating only one polypeptide chain

7. In eukaryotes, the 5’ end of mRNA is capped with a guanosine triphosphate nucleotide, which helps in mRNA recognition during translation or protein synthesis. Similarly, the 3’ end of an mRNA has a poly-A tail or multiple adenylate residues added to it, which prevents enzymatic degradation of mRNA. Both the 5’ and 3’ end of an mRNA imparts stability to the mRNA.

8. Cap is followed by non coding (UTR) untranslated region and then foyllowed by a start codon and followed by a coding regions called exons and non coding regions exons and followed by a stop codons and untranslated region when transcription is about to end it adds a poly A nucleotides at 3 I end of RNA with the help of an enzyme poly A polymerase The existence of an mRNA molecule begins with transcription, and ultimately ends in degradation. During its life, an mRNA molecule may also be processed, edited, and transported prior to translation. Eukaryotic mRNA molecules often require extensive processing and transport

9. The extensive processing of eukaryotic pre-mRNA that leads to the mature mRNA is the  RNA splicing , a mechanism by which  introns  or  outrons  (non-coding regions) are removed and  exons  (coding regions) are joined together The RNA that we get after transcription is called heterogenous RNA ( hn RNA) it should be processed to become fully matured RNA

10. Prokaryotic mRNA In prokaryotes mRNA is produced by the process of transcription with the help of an enzyme called RNA polymerase Prokaryotes lack organelles and a well defined nuclear envelope, and therefore mRNA translation can be coupled with mRNA  transcription  in the  cytoplasm Prokaryotic mRNA is constantly degraded by ribonucleases , enzymes that cut RNA. For example, the half-life of mRNA in  E. Coli  is approximately two minutes. Bacterial mRNAs are short-lived to allow for flexibility in adjusting to rapidly changing environmental conditions.

11. In  prokaryotes  (organisms that lack a distinct nucleus), mRNAs contain an exact transcribed copy of the original DNA sequence with a terminal 5′-triphosphate group and a 3′-hydroxyl residue 5′ region has a (UTR) untranslated region and followed by a coding region which has a start codon and stop codon and again followed by a UTR region 5′ end of a prokaryotic mRNA it has a shine dalgarno sequence which is rich in purine nucleotides and helps in binding of mRNA to 30s subunit of ribosome by establishing H bonds wit pyramidine nucleotide sequence present on the 3′ end of single mRNA (16s) of smaller subunit

12. mRNA in prokaryotes is polycistronic it means it carries several  open reading frames  (ORFs), each of which is translated into a polypeptide

13. rRNA It accounts for 80% of the total RNA in the cell The rRNA is the component of the ribosome and are located within the in the cytoplasm of a cell, where ribosomes are found. In all living cells, the ribosomal RNA plays a fundamental role in the synthesis and translation of mRNA into proteins Molecules of rRNA are synthesized in a specialized region of the cell  nucleus  called the  nucleolus , which appears as a dense area within the nucleus and contains the  genes  that encode rRNA . Discovery Ribosomal RNA was discovered during  cell  fractionation experiments investigating the role of RNA viruses in causing cancer.

14. Ribosomes  consist of two major components: the small ribosomal subunits, which read the RNA, and the large subunits, which join amino acids to form a polypeptide chain. Each subunit comprises one or more ribosomal RNA ( rRNA ) molecules and a variety of ribosomal proteins (r-protein ). These subunits generally are named according to their rate of sedimentation, measured in Svedberg units Ribosomal proteins are synthesized in the cytoplasm and transported to the nucleus for subassembly in the nucleolus. The subunits are then returned to the cytoplasm for final assembly .

15. rRNAs combine with proteins in the cytoplasm to form ribosomes , which act as the site of protein synthesis and has the enzymes needed for the process . Types of rRNA Ribosomal RNA organizes into two ribosomal subunits: the large ribosomal subunit ( LSU ) and small ribosomal subunit ( SSU ). Between these subunits, the rRNA types used to form the subunit differ . In the ribosomes of prokaryotes such as  bacteria , the SSU contains a single small rRNA molecule (~1500 nucleotides) while the LSU contains one single small rRNA and a single large rRNA molecule (~3000 nucleotides).These are combined with ribosomal  proteins  to form ribosomal subunits .

16. In the ribosomes of eukaryotes such as  humans , the SSU contains a single small rRNA (~1800 nucleotides) while the LSU contains two small rRNAs and one molecule of large rRNA (~5000 nucleotides). Eukaryotic rRNA combine with ribosomal  proteins  which interact to form larger and more polymorphic ribosomal units in comparison to prokaryotes. 16S rRNA In bacteria the gene that has proved to be the most informative for investigating evolutionary relatedness is  16S rRNA it is present in all bacteria, and a related form occurs in all cells, including those of eukaryotes. Analysis of the  16S rRNA  sequences from many organisms has revealed that some portions of the molecule undergo rapid genetic changes, thereby distinguishing between different species within the same genus . 

17.   Phylogenic  information derived from the 16s rRNA is currently used as the main method of delineation between similar prokaryotic species by calculating  nucleotide  similarity The 3' end of the 16S ribosomal RNA (in a ribosome) recognizes a sequence on the 5' end of  mRNA  called the  Shine- Dalgarno sequence . Whichis used for the correct positioning of mRNA and ribosome during the process of translation The rRNA of the ribosome also has an enzymatic activity ( peptidyl transferase ) and catalyzes the formation of the peptide bonds between two aligned amino acids during protein synthesis(and thus is an enzyme ribozyme )

18. structure The  primary structure  of rRNA sequences can vary across organisms,  base-pairing  within these sequences commonly forms  stem-loop  configurations. The length and position of these rRNA stem-loops allow them to create three-dimensional rRNA structures that are similar across  species . Because of these configurations, rRNA can form tight and specific interactions with ribosomal proteins to form ribosomal subunits. These ribosomal proteins contain basic  residues and aromatic residues allowing them to form chemical interactions with their associated RNA regions, such as  stacking interactions . Ribosomal proteins can also cross-link to the sugar-phosphate backbone of rRNA with binding sites that consist of basic residues . Assembly Ribosomal RNA's integration and assembly into  ribosomes  begins with their folding, modification, processing and assembly with  ribosomal proteins  to form the two ribosomal subunits, the LSU and the SSU. In  Prokaryotes , rRNA incorporation occurs in the cytoplasm due to the lack of membrane-bound organelles

19. In  Eukaryotes , however, this process primarily takes place in the  nucleolus  and is initiated by the synthesis of pre-RNA.  The pre-RNA then undergoes modifications such as  methylation  or pseudouridinylation before ribosome assembly factors and ribosomal proteins assemble with the pre-RNA to form pre-ribosomal particles. Upon going under more maturation steps and subsequent exit from the nucleolus into the cytoplasm, these particles combine to form the ribosomes Fully assembled subunit with proteins and rRNA General structure of rRNA

20. tRNA 10 – 15% of total cellular RNA is t-RNA.  t-RNA (transfer RNA) is also named as S-RNA (soluble or supernatant RNA) and adaptor RNA.  t-RNAs are small molecules with about 74 – 95 ribonucleotides , Sedimentation constant – 3.8S, Molecular weight – nearly 25,000 – 30,000 Dalton, t-RNAs are made up of a single stranded polynucleotide chain. Transfer RNAs or tRNAs are molecules that act as temporary carriers of  amino acids , bringing the appropriate amino acids to the  ribosome  based on the messenger RNA ( mRNA )  nucleotide  sequence. In this way, they act as the intermediaries between nucleotide and amino acid sequences

21. tRNAs are ribonucleic acids and therefore capable of forming hydrogen bonds with mRNA. Additionally, they can also form ester linkages with amino acids Unique feature of tRNA In addition to usual N-bases (A,U,G,C) tRNA contains number of unusual bases. These unusual bases are important as they protect t-RNA molecules from dehydration by Rnase , when tRNAs are floating freely in cytoplasm. Hydrogen bonds Ester bond

22. Bases that have been modified, especially by  methylation  (e.g.  tRNA (guanine-N7-)- methyltransferase ), occur in several positions throughout the tRNA . The first anticodon base, or wobble-position, is sometimes modified to   inosine    from adenine   queuosine    guanine uridine-5-oxyacetic acid  uracil 5-methylaminomethyl-2-thiouridine  derived from uracil   lysidine    cytosine Activation of tRNA / charging of tRNA / aminoacylation of tRNA Done with the help of enzymes called aminoacyl tRNA synthetases It catalyses the esterification of specific aminoacid This enzyme catalyzes the union of amino acid to the tRNA

23. Structure of tRNA   Primary structure - linear sequence of nucleotides Secondary structure -Clover leaf model Tertiary structure - 3-D structure of tRNA , L shape, Helix stacking

24. Primary structure Linear sequence of nucleotides is 60-90 in nt long but most commonly 76 Many modified bases, sometimes accounting for 20% of the total bases in any one tRNA molecules All of them are created post transcriptionally . Secondary structure Robert Holley proposed clover leaf model for the first time in 1968. It is a two dimensional description of the t-RNA.

25. The acceptor stem is a 7- to 9-base pair ( bp ) stem made by the base pairing of the 5'-terminal nucleotide with the 3'-terminal nucleotide (which contains the CCA 3'-terminal group used to attach the amino acid). In general, such 3'-terminal tRNA -like structures are referred to as ' genomic tags The amino acid loaded onto the tRNA by  aminoacyl tRNA synthetases , to form  aminoacyl-tRNA , is covalently bonded to the 3'-hydroxyl group on the CCA tail. This sequence is important for the recognition of tRNA by enzymes and critical in translation.In prokaryotes, the CCA sequence is transcribed in some tRNA sequences. In most prokaryotic tRNAs and eukaryotic tRNAs , the CCA sequence is added during processing and therefore does not appear in the tRNA gene

26. The  D arm  is a 4- to 6-bp stem ending in a loop that often contains  dihydrouridine . The anticodon arm is a 5-bp stem whose loop contains the  anticodon .The tRNA 5'-to-3' primary structure contains the anticodon but in reverse order, since 3'-to-5' directionality is required to read the mRNA from 5'-to-3'. The  T arm  is a 4- to 5- bp stem containing the sequence TΨC where Ψ is  pseudouridine , a modified  uridine

27. Variable arm it has between 3 and 21 nucleotides, depending on which amino acid the tRNA encodes. Between anticodon loop and TΨU loop This tRNA's variable arm is very short so it looks quite different from the other arms of the molecule. May present or absent, it depends on species. The length of the variable arm is important in the recognition of the aminoacyl tRNA synthetase for the tRNA . Variable arm helps is stability of tRNA tRNAs are called class 1 if they lack it, and class 2 if they have it.

28. Teritiary structure It is 3D model and L shaped Discovered in amino acid of phenylalanine in yeast The acceptor stem and T-arm forming an extended helix and the anticodon loop and D-arm similarly making another extended helix. These two helices align perpendicularly to each other in a way that brings the D-arm and T-arm into close proximity while the anticodon loop and the acceptor arm are positioned on opposite ends of the molecule . In this image, the 3’ CCA region is in yellow, the acceptor arm is in purple, the variable loop in orange, the D-arm is in red, the T-arm in green and the anticodon loop is in blue.

29. Stability of L-structure Tertiary structure of t-RNA is produced by hydrogen bonding Between N-bases Between N-bases and ribose- phosphate backbone Between ribose-phosphate backbone

30. Structure and Function of RNA mRNA rRNA tRNA STRUCTURE Short, unstable, single-stranded RNA corresponding to a gene encoded within DNA Longer, stable RNA molecules composing 60% of ribosome’s mass Short (70-90 nucleotides), stable RNA with extensive intramolecular base pairing; contains an amino acid binding site and an mRNA binding site FUNCTION Serves as intermediary between DNA and protein; used by ribosome to direct synthesis of protein it encodes Ensures the proper alignment of mRNA, tRNA , and ribosome during protein synthesis; catalyzes peptide bond formation between amino acids Carries the correct amino acid to the site of protein synthesis in the ribosome