RNA Structure and Function

• RNA is an unbranched polymeric structure comprising mononucleotides linked by phosphodiester bonds.
• Most RNAs exist as single strands capable of folding into complex structures.
• The three major types of RNA involved in protein synthesis are rRNA, tRNA, and mRNA.
• These types differ in size, function, and structural modifications.

Primary Structure

• RNA is initially synthesized as a single-stranded polymer through transcription.
• Ribonucleotides are linked into a polar molecule by phosphodiester bonds.
• Phosphodiester bonds form between the 3'-hydroxyl on the sugar of one ribonucleotide and the 5'-hydroxyl on the sugar of another.
• Sugar-phosphate linkages create a symmetrical backbone, with the 5'-end of one sugar linked through a phosphate to the 3'-end of an adjacent sugar.
• Bases are variable and stick out from the backbone.

Differences from DNA

• RNA molecules are smaller.
• RNA contains ribose sugar instead of deoxyribose.
• RNA contains uracil instead of thymine.
• RNA form exists usually in a single strand form

Secondary Structure

• Double-stranded RNA is single-stranded but can form double helix regions by folding back on itself.
• Complementary RNA sequences can form base pairs.
• Double helical regions assume A-DNA-like conformations with antiparallel strands.
• DNA-RNA hybrids also show A-form conformations.
• Varied shapes arise from different RNA sections forming double-stranded regions via specific base pairing.
• 5S ribosomal RNA (rRNA) contains helices, hairpin loops, internal loops, and bulges.
• Transfer RNA (tRNA) is a compact shape due to base pairing and extensive stacking interactions.

Tertiary Structure

• Some RNAs have structural and catalytic functions, interacting extensively with specific proteins to form complex structures.
• RNA modifications include terminal additions, base modifications, and methylations at various base positions.
• Heavily modified

Major Classes of RNA

• In prokaryotes, three functionally distinct classes of RNA are produced, while eukaryotes produce four.

Messenger RNA (mRNA)

• Messenger RNA (mRNA) is the most heterogeneous in terms of size (500-6000 nucleotides) and base sequence.
• mRNA carries genetic information from DNA to the cytosol to ribosomes and acts as a template for protein synthesis.
• mRNA is a transcript of DNA, similar except that uracil replaces thymine.
• It is the largest and contains a number of coding regions (exons).

Prokaryotic mRNA

• Not all portions code for polypeptides
• Polycistronic mRNA carries information for the production of multiple polypeptides (ia. Cistrons), which are sequences that code for proteins.
• Prokaryotic mRNA contains a leader sequence/5'-untranslated region (5'-ULR) and a trailer sequence/3'-untranslated region (3'-UTR) with sequences that are never translated into protein, and intercistronic regions/spacers, which are sequences between cistrons.

Eukaryotic mRNA

• Eukaryotic mRNA is monocistronic, carrying information for the production of a single polypeptide and has only one coding region.
• Eukaryotic mRNA arises from extensive post-transcriptional processing of large precursors, known as heterogeneous nuclear RNA (hnRNA)
• It contains all genetic information; sequences of the DNA
• Unique to eukaryotes, it is used to differentiate eukaryotic mRNA and prokaryotic mRNA
• It has a Cap on the 5'-end
• The cap consists of a 7-methylguanylate molecule attached backward through a 5' to 5' triphosphate linkage.
• Most, but not all, eukaryotic mRNAs have a polyadenylate (poly-A) tail, a long string of adenylate residues (200-300) on the 3'-end of the RNA chain.

Ribosomal RNA (rRNA)

• Ribosomal RNA (rRNA) associates with different proteins as components of the ribosomes, the site of protein synthesis.
• It constitutes 80% of the ribosomal mass and is the most abundant.
• It functions as a structural component and as a ribozyme, catalyzing some translation reactions.
• An RNA molecule acts like an enzyme, helping speed up certain reactions.
• In translation, it helps speed up certain reactions, such as forming peptide bonds between amino acids during protein synthesis

Prokaryotic rRNA

• Prokaryotic rRNA includes 23S rRNA (2904 nucleotides, component of the large 50S ribosomal subunit), 16S rRNA (1541 nucleotides, component of the small 30S ribosomal subunit), and 5S rRNA (120 nucleotides, component of the large 50S ribosomal subunit).
• Related to molecular weight and shape of the compound
• The values are not additive because sedimentation depends on size, shape, and density.
• Most abundant, 80% of total prokaryotic cellular RNA

Eukaryotic rRNA

• Eukaryotic rRNAs are larger and more complex than prokaryotic rRNAs
• Includes 28S rRNA (4718 nucleotides, component of the large 60S ribosomal subunit), 18S rRNA (1874 nucleotides, component of the small 40S ribosomal subunit), 5.8S rRNA (160 nucleotides, component of the large 60S ribosomal subunit), and 5S rRNA (120 nucleotides, component of the large 60S ribosomal subunit, transcription product of a separate gene).
• 71% is fully processed rRNAs (ready for ribosome assembly)

Transfer RNA (tRNA)

• Is the smallest (4S), with 74-95 nucleotide residues.
• There is one specific tRNA for each of the amino acids.
• tRNA contains unusual bases like pseudouracil and extensive intrachain base pairing.
• It serves as an adaptor molecule, carrying a specific amino acid (covalently attached to its 3'-end) to the site of protein synthesis, facilitating the incorporation of amino acids into newly synthesized proteins in a template-dependent manner.

Prokaryotic tRNA

• The size is small (average of 80 nucleotides)
• All tRNAs have common structural features that function in the ribosome, with unique structural features necessary for recognition by the enzyme that catalyzes amino acid attachment to tRNAs.
• The processing arises from the processing of Large precursor tRNAs.
• It has a size- similar to prokaryotes in size and structural features and is heavily modified post-transcriptionally
• The abundance is 15% of total cellular RNA

Eukaryotic Small RNAs

• A variety of functions Classified into 2 broad types according to where they are located

Small Cytoplasmic RNAs (scRNAs)

• Contain a 7S RNA
• Major ScRNA
• 294 nucleotides
• RNA component of signal recognition particles

Small Nuclear RNAs (snRNAs)

• Associated with proteins in small nuclear ribonucleoprotein particles (snRNPs pronounced "snurps")
• SnRNPs function in the splicing reactions needed to process hnRNA to mRNA.