RNA Structure: Biochemistry Lecture Notes PDF

BIOCHEMISTRY LC 5: RNA STRUCTURE DR. BRENDO JANDOC |01/28/2025 - COURSE OUTLINE I....

BIOCHEMISTRY LC 5: RNA STRUCTURE DR. BRENDO JANDOC |01/28/2025 - COURSE OUTLINE I.​ RNA STRUCTURE A.​ Primary Structure B.​ Secondary Structure C.​ Tertiary Structure II.​ MAJOR CLASSES OF RNA A.​ Messenger RNA (mRNA) B.​ Ribosomal RNA (rRNA) C.​ Transfer RNA (tRNA) III.​ EUKARYOTIC SMALL RNAs Figure 3. DNA Containing Uracil A.​ Small Cytoplasmic RNAs (scRNAs) B.​ Small Nuclear RNAs (snRNAs) ○​ Form - usually exists in single-strand form IV.​ SUMMARY I. RNA STRUCTURE A. PRIMARY STRUCTURE ​ Unbranched polymeric structure. ​ RNA - initially synthesized as single-stranded ​ Composed of mononucleotides joined together by polymer by the process of transcription phosphodiester bonds. ​ Ribonucleotides - linked into a polar molecule by ​ Most RNAs exist as single strands capable of phosphodiester bonds folding into complex structures. ○​ Phosphodiester Bonds- between ​ Three major types of RNA that participate in ​ 3’-hydroxyl on the sugar of 1 ribonucleotide protein synthesis: through a phosphate to ○​ rRNA ​ 5’-hydroxyl on the sugar of another ○​ tRNA ribonucleotide ○​ mRNA ​ Sugar-Phosphate Linkages ​ Differ in Terms of: size, function, structural ○​ form symmetrical backbone modifications ○​ 5’-end of 1 sugar linked through a phosphate to ○​ 3’-end of adjacent sugar ​ Bases ○​ Variable ○​ stick out from the backbone B. SECONDARY STRUCTURE ​ Double-Stranded RNA - is single-stranded but can form regions of double helix by folding back on itself. ○​ Base pairing ​ complementary RNA sequences can be base pairs. Figure 1. Ribonucleic acids (RNA) ​ Differences from DNA ○​ Size - considerably smaller than DNA ○​ Sugar - contain ribose sugar (instead of deoxyribose) Figure 4. Adenine with Uridine Figure 2. DNA Containing Ribose Figure 5. Guanine with Cytosine ○​ Nucleotide- contain uracil (instead of thymine) ○​ A-Form Helix ​ 2’-hydroxyl groups on the ribose sugar sterically hinders the formation of B form >> BATCH TANNAWAG 1E​ 1 BIOCHEM LC 5: RNA STRUCTURE ​ Dr. JANDOC, B. 01/28/2025 double helical regions assume conformations ​ allow for unusual base pairings that resembling A-DNA; enhance RNA structural diversity ​ nature of RNA double helix is similar to DNA; ​ trimming ​ Strands must be antiparallel ​ internal segment removal ○​ DNA-RNA Hybrids ​ splicing ​ show A-form conformations ​ after RNA synthesis ​ Other Structures: varied shapes due to various ​ convert inactive primary transcript functional sections of RNA forming double-stranded regions molecule via specific base pairing. 2. Transfer RNA ○​ 5S Ribosomal RNA (rRNA) ​ Most heavily modified ​ Contains helices, hairpin loops, internal loops, and bulges. II. MAJOR CLASSES OF RNA ​ 3 functionally distinct classes of RNA are produced in prokaryotes. ​ 4 are produced in eukaryotes. A. MESSENGER RNA (mRNA) ​ most heterogeneous type in terms of size (500-6000 nucleotides) ​ base sequence ​ carries genetic information from DNA –> cytosol –> ribosomes –> template for protein synthesis ​ Transcript of DNA ​ mRNA and DNA are exactly the same, when not considering uracil which replaces thymine ​ It is the largest, therefore contains a number of coding regions (exons) Figure 6. Single-stranded loop base-paired stem 3 1. PROKARYOTIC mRNA I.​Basic Features ○​ Transfer RNA (tRNA) ​ Not all portions code for polypeptides ​ Base pairing and extensive stacking ○​ Polycistronic interactions >> compact shape ​ carry information for the production of multiple polypeptides (ia. Cistrons) ​ sequences that code for proteins ○​ Leader Sequence/5’-Untranslated Region (5’-ULR) ​ contain sequences that are never translated into protein ○​ ​Trailer Sequence/3’-Untranslated Region (3’-UTR) ​ contain sequences that are never translated into protein ○​ Intercistronic Regions / Spacers ​ sequences between cistrons Figure 7. Structure of transfer RNA (tRNA) Figure 8. Prokaryotic mRNA II.​Abundance C. TERTIARY STRUCTURE ○​ 5% of total cellular RNA Roles of Some RNAs III.​Stability ​ Structural ○​ Stable for just a few minutes ​ Interact extensively with specific proteins ○​ Lifetime is short ​ Catalytic functions -> form some very complex structures 2. EUKARYOTIC rRNA 1. RNA Modifications I.​Basic Features ​ terminal additions ○​ Monocistronic ​ Base modifications ​ carry information for the production of a ○​ Methylations single polypeptides ​ at numerous positions of the different ​ Has only one coding region bases ​ most common of the modifications BATCH TANNAWAG 1E ​ 2 BIOCHEM LC 5: RNA STRUCTURE ​ Dr. JANDOC, B. 01/28/2025 ​ An RNA molecule that acts like an enzyme. In translation, it helps speed up certain reactions, such as forming peptide bonds between amino acids during protein synthesis. 1. PROKARYOTIC rRNA Figure 9. Eukaryotic mRNA I.​Basic Feature ○​ Precursor Form ○​ 23S rRNA ​ heterogeneous nuclear RNA (hnRNA) ​ 2904 nucleotides ​ most but not all eukaryotic mRNA arise by ​ Component of the large 50S ribosomal extensive post-transcriptional processing of subunit large precursors ○​ 16S rRNA ​ It is the same as DNA ​ 1541 nucleotides ​ Contains all genetic information; sequences of ​ Component of the small 30S ribosomal the DNA subunit ○​ Leader Sequence (5’-ULR) ○​ 5S rRNA ○​ Trailer Sequence (3’-UTR) ​ 120 nucleotides ○​ Polyadenylate (Poly-A) Tail ​ Component of the large 50S ribosomal ​ most but not all eukaryotic mRNA subunit ​ long adenylate residues (200-300) ​ on the 3’-end of the RNA chain ​ Unique in eukaryotes; used to differentiate eukaryotic mRNA and prokaryotic mRNA ○​ Cap ​ on the 5’-end of eukaryotic mRNAs ​ consists of a 7-methylguanylate molecule Figure 11. Prokaryotic rRNAs attached backward through a 5’ to 5’ ​ Svedberg unit “S” triphosphate linkage ○​ Related to molecular weight and shape of the compound ○​ The values are not additive because sedimentation depends on size, shape, and density. Figure 10. Cap II.​Abundance ○​ no more than 5% of the cell RNA ○​ precursor hnRNA ○​ 7% of total cellular RNA ○​ 3% of the cell RNA Figure 12. Prokaryotic Ribosomes III.​Stability ○​ relatively stable II.​Abundance ○​ half-lives of hours to days ○​ Most abundant ○​ 80% of total prokaryotic cellular RNA B. RIBOSOMAL RNA (rRNA) ​ Found in association with different proteins as 2. EUKARYOTIC rRNA components of the ribosomes (site of protein ​ Bigger than those of prokaryotes (larger than synthesis) prokaryotic rRNA because eukaryotic ribosomes ​ Ribosomal RNA (rRNA) combines with various (80S) are bigger and more complex than proteins to form ribosomes, the sites where protein prokaryotic ribosomes (70S). synthesis occurs. ​ 80% of the ribosomal mass (most abundant) I.​Basic Feature a.​Functions ○​ 28S rRNA ○​ Structural ​ 4718 nucleotides ○​ Ribozyme ​ Component of the large 60S ribosomal ​ Catalytic for some of the translation reactions subunit ○​ 18S rRNA BATCH TANNAWAG 1E ​ 3 BIOCHEM LC 5: RNA STRUCTURE ​ Dr. JANDOC, B. 01/28/2025 ​ 1874 nucleotides ​ Component of the small 40S ribosomal subunit ○​ 5.8S rRNA ​ 160 nucleotides ​ Component of the large 60S ribosomal subunit ○​ 5S rRNA ​ Figure 14. Protein synthesis - translation ​ 120 nucleotides ​ Component of the large 60S ribosomal subunit ​ Transcription product of a separate gene Figure 15. Transcription and maturation of RNA II.Abundance ​ 15% of total cellular RNA EUKARYOTIC RNA I.Basic Features ○​ Size - similar to prokaryotes in size and structural features ○​ Heavily modified post-transcriptionally II.Abundance Figure 13. Eukaryotic Ribosomes ​ 15% of total cellular RNA II.​Abundance ○​ 4% of total eukaryotic cellular RNA is 40S precursor rRNA (an unfinished form) ○​ 71% is fully processed rRNAs (ready for ribosome assembly) C. TRANSFER RNA (tRNA) ​ Smallest (4S) ​ 74-95 nucleotide residues ​ 1 specific tRNA type for each of the amino acids ​ Contain unusual bases (ex: pseudouracil) ​ Extensive intrachain base pairing Figure 16. Characteristic transfer RNA (tRNA) secondary structure (cloverleaf). Folded (tertiary) tRNA structure found in cells. ​ Serve as adaptor molecule -> carry specific amino acid (covalently attached to its 3’-end) to the site of protein synthesis -> facilitates incorporation of amino acids into newly synthesized proteins in a template-dependent manner ​ 15% of the total RNA in the cell PROKARYOTIC tRNA I.Basic Features ○​ Size - small (average of 80 nucleotides) ○​ Structure - all tRNAs have common structural features -> function in the ribosome unique structural features necessary for recognition by the enzyme that catalyze amino acid attachment to tRNAs - sequences that pair with appropriate codons in ribosomes are unique for each tRNA ○​ Processing - arise from the processing of Large precursor tRNAs ○​ Modification - heavily modified Figure 17. Structure of transfer RNA (tRNA) post-transcriptionally BATCH TANNAWAG 1E ​ 4 BIOCHEM LC 5: RNA STRUCTURE ​ Dr. JANDOC, B. 01/28/2025 ​ III. EUKARYOTIC SMALL RNAs ​ variety of functions ​ classified into 2 broad types according to where they are located A. Small Cytoplasmic RNAs (scRNAs) ○​ 7S RNA ​ major scRNA ​ 294 nucleotides Figure 18. Comparison of three RNA ​ RNA component of signal recognition ​ particles B. 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 Figure 19. Nucleolus and Synthesis of Ribosomes IV. SUMMARY Figure 20. Summary of RNA Structure Reference(s): ​ Jandoc, B. ( January 2025). RNA Structure [PPT]. ​ Ferrier, D. R. (2014). Biochemistry. Lippincott Williams & Wilkins. BATCH TANNAWAG 1E ​ 5