Biochemical Organization & functions of RNA Lecture # 5 Dr. Shumaila Asim

Learning Outcomes Knowledge; Describe the biochemical Organization & Functions of RNA Content Biochemical Organization of RNA Functions of RNA

Chemical structure of RNA The chemical nature of RNA differs from that of DNA RNA is also formed by purines and pyrimidines linked by 3’-5’ phosphodiester bonds Although sharing many features with DNA , RNA possesses several specific differences:

1.In RNA, the sugar moiety to which the phosphates and purine and pyrimidines are attached is ribose instead of deoxyribose of DNA 2. The pyrimidine components of RNA is differ from those of DNA. RNA contains the A, G,C but does not contain T (with a rare exception), instead of T, U is present in RNA 3.RNA exist as a single strand. However, given the proper complementary base sequence with opposite polarity, single strand RNA is capable of folding back on itself like a hairpin thus acquiring double-stranded structure

4. Since the RNA molecule is a single strand complementary to only one of the two strands of a gene, its guanine content does not necessarily eaqual its cytosine content; and its adenine content does not necessarily eaqual its uracil content 5. RNA can be hydrolyzed by alkali to 2’, 3’cyclic diesters of mononucleotides but those molecules can not be formed from alkali-treated DNA because of the absence of a 2’- OH group The alkali lability of RNA is useful both diagnostically and analytically

Covalent & non-covalent bonds in RNA RNA Structure & Function 10/31/05 Covalent & non-covalent bonds in RNA Primary: Covalent bonds Secondary/Tertiary Non-covalent bonds H-bonds (base-pairing) Base stacking D Dobbs ISU - BCB 444/544X

RNA types and their funtions Cytoplasmic RNA molecules that serve as a templates for protein synthesis are designated as messnger RNAs (mRNA). mRNA molecules transfer genetic information from DNA to protein-synthesizing machinary Many other cytoplasmic RNA molecules have structural roles. They contribute to the formation of ribosomes (ribosomal RNA, rRNA) or serve as adapter molecules (transfer RNA, tRNA) for the translation of RNA information into specific sequences of polymerized amino acids

1. Messenger RNA (mRNA) This is the most heterogenous class in size and stability All members of the class function as messengers conveying the information in a gene to the protein-synthesizing machinery Each serves as a template for a specific sequence of amino acids that is polimerized to form a specific protein

mRNAs have some unique chemical characteristics: The 5’ terminal of mRNA is capped by a 7-methylguanosine triphosphate The cap is involved in the recognition of mRNA by translating machinery, and it probably helps stabilize the mRNA by preventing the attack of 5’-exonucleases The protein synthesis begins translating the mRNA into proteins at the 5’or capped terminal

The other end of most mRNAs has attached a polymer of adenylate residues 20-250 nucleotides in lenght so called the poly A tail The funtion of the poly A tail seems that it maintains the stability of the mRNA by preventing the attack of 3’-exonucleases

2. Transfer RNA (tRNA) tRNA molecules vary in lenght from 74 to 95 nucleotides tRNA molecules serve as a adapters for the translation of the information in the sequence of nucleotides of mRNA into specific amino acids There are at least 20 species of tRNA molecules in every cell. At least one, often several corresponding to each of the 20 amino acid are required for protein synthesis

Although each specific tRNA differs from the others in its sequence of nucleotides, the tRNA molecules as a class have many features in common The primary structure of all tRNA molecules allows extensive folding and intrastrand complementarity to generate a secondary structure This structure appears like a cloverleaf

All tRNA molecules contain four main arms The acceptor arm consists of a base-paired stem that terminates in the sequence CCA (5’ to 3’). It is through an ester bond to the 3’ hydroxyl group of the adenosyl moiety that the carboxyl groups of amino acids are attached The anticodon arm at the end of a base-paired stem recognizes the triplet nucleotide or codon of the template mRNA. The D arm is named for the presence of the base dihydrouridine, and the TΨC arm for the sequence T, pseudouridine, and C

The extra arm is the most variable feature of tRNA The extra arm is the most variable feature of tRNA. It accounts for the differences in lenght of the tRNAs; and it provides a basis for classification. Class 1 tRNAs have an extra arm that is 3-5 bp long Class 2 tRNAs have an extra arm that is 13-21 bp long

The secondary structure of tRNA molecules is maintained by the base pairing in these arms and this is a consistent feature : The TΨC and anticodon arms have 5 bp The D arm has 3-4 bp The acceptor arm has 7 bp

3. Ribosomal RNA (rRNA) A ribosome is a cytoplasmic nucleoprotein structure that acts as the machinery for the synthesis of proteins from the mRNA templates On the ribosomes, the mRNA and tRNA molecules interact to translate into a specific protein molecule information transcribed from the gene During the active protein synthesis, many ribosomes are associated with an mRNA molecule in an assembly called the polysome

The mammalian ribosome contains two major nucleoprotein subunits, a larger one with a molecular weight of 2.8x106 (sedimentation velocity is 60S*) and a smaller subunit with a molecular weight of 1.4x106 (40S) The 60S subunit contains a 5S ribosomal RNA, a 5.8S rRNA and a28S rRNA; there are also probably more than 50 specific polypeptides

The 40S subunit is smaller and contains 18S rRNA and approximately 30 polypeptide chains All of the rRNA molecules, except the 5S rRNA are processed from a single 45S precursor RNA molecule in the nucleus 5S rRNA has its own precursor that is independently transcribed The highly methylated rRNA molecules are packaged in the nucleus with the specific ribosomal proteins; but in the cytoplasm, ribosomes remain quite stable and capable of many translaton cycles

Ribosomal RNA molecules are necessary for ribosomal assembly and seem to play key roles in the binding of mRNA to ribosomes and its translation

Small stable RNA (snRNA) A large number of discrete, highly conserved and small stable RNA species are found in the mammalian cells The majority of these molecules exist as ribonucleoproteins and are distributed in the nucleus, cytoplasm or in both They are involved in mRNA processing and gene regulation

Of the several snRNAs, U1,U2,U4,U5 and U6 are involved in intron removaland the processing of primary transcript into mRNA. The U4 and U6 snRNAs are required for poly (A) processing

RNA Structure & Function 10/31/05 RNA functions Storage/transfer of genetic information Structural Catalytic Regulatory D Dobbs ISU - BCB 444/544X

RNA Structure & Function 10/31/05 RNA functions Storage/transfer of genetic information Genomes many viruses have RNA genomes single-stranded (ssRNA) e.g., retroviruses (HIV) double-stranded (dsRNA) Transfer of genetic information mRNA = "coding RNA" - encodes proteins D Dobbs ISU - BCB 444/544X

RNA Structure & Function 10/31/05 RNA functions Structural e.g., rRNA, which is major structural component of ribosomes Catalytic RNA in ribosome has peptidyltransferase activity Enzymatic activity responsible for peptide bond formation between amino acids in growing peptide chain Also, many small RNAs are enzymes "ribozymes” D Dobbs ISU - BCB 444/544X

RNA Structure & Function 10/31/05 RNA functions Regulatory Recently discovered important new roles for RNAs In normal cells: in "defense" - esp. in plants in normal development e.g., siRNAs, miRNA As tools: for gene therapy or to modify gene expression D Dobbs ISU - BCB 444/544X

RNA Structure & Function 10/31/05 RNA types & functions Types of RNAs Primary Function(s) mRNA - messenger translation (protein synthesis) regulatory rRNA - ribosomal translation (protein synthesis) <catalytic> t-RNA - transfer hnRNA - heterogeneous nuclear precursors & intermediates of mature mRNAs & other RNAs scRNA - small cytoplasmic signal recognition particle (SRP) tRNA processing <catalytic> snRNA - small nuclear snoRNA - small nucleolar mRNA processing, poly A addition <catalytic> rRNA processing/maturation/methylation regulatory RNAs (siRNA, miRNA, etc.) regulation of transcription and translation, o D Dobbs ISU - BCB 444/544X