RNA

From Proteopedia

Fragment of an RNA strand, with nucleobases U and A, the sugar ribose and the phosphate diester linkages labeled

RNA (ribonucleic acid) is a biological macromolecule that stores and processes genetic information, catalyzes chemical reactions and regulates biological processes. Just like the other nucleic acid (DNA), it is a linear polymer (a "strand") of nucleotide building blocks. These building blocks themselves are made up of a sugar linked to a (nitrogenous) base and a phosphate. RNA utilizes a different set of bases than DNA, and it sugar (ribose) contains one additional hydroxyl group compared to that of DNA (deoxyribose). Different than DNA, which mostly occurs in pairs of complementary strands in its biological context, RNA mostly lacks a complementary strand, leading to a larger variety of 3D structures and biological functions.

1 RNA structure and function
- 1.1 Chemistry
- 1.2 Transcription and Translation
2 See Also
3 External Resources
4 References

RNA structure and function

This tour of different biological processes showcases the role of RNA. In many of these roles, RNA interacts with DNA and proteins to support life. Early on in the evolution of life, according to the "RNA world" hypothesis, DNA and proteins did not yet exist and RNA had DNA-like roles (genetic storage) and protein-like roles (metabolism, biosynthesis, etc), some of which it retains to the present day.

Genetic information

RNA plays key roles in gene expression. The classic three types of RNA are mRNA (messenger RNA), tRNA (transfer RNA) and rRNA (ribosomal RNA), all of which have a crucial role in gene expression. Beyond these roles, RNA also serves to store genetic information, to regulate gene expression and to modulate the sequences of protein through alternate splicing.

Transcription

RNA is synthesized by RNA polymerases using DNA (or sometimes RNA) as a template. During synthesis, the template and the newly synthesized RNA form a base-paired, anti-parallel structure. Shown here is the () ^[1]

Post-transcriptional modification

Introns are segments of RNA that have catalytic activity. These elements can splice RNA (remove the intron) and sometimes act as retrotransposons (i.e. they can insert themselves into pieces of RNA, which then - via reverse transcription - changes the sequence of DNA). The shown here in complex with a small piece of its substrate (the exon) catalyzes phophodiester transesterification using bound magnesium ions.^[2]

Translation

Ribosomes synthesize proteins with sequences determined by mRNA. The ribosome is a complex of rRNA and protein. Shown here is a small part of the ribosome illustrating protein-RNA interactions: (). When synthesizing proteins, ribosomes follow the genetic code to translate an RNA sequence (grouped into codons of 3 nucleotides) into a protein sequence. are the adapter molecules that embody the genetic code. Each tRNA is covalently bound to a specific amino acid at one end and display an anti-codon on the other end (for more details, see transfer RNA)

Storage of genetic information

All known organisms store genetic information on DNA. Some viruses, however, use RNA instead. Depending on how they use RNA to store genetic information, they are classified as double-stranded RNA viruses and plus or minus single-stranded RNA viruses . For example, human immunodeficiency virus carries genetic information in the form of single stranded RNA. In the figure, the RNA is located in the dark rectangular blob inside the circular virus particles. The single-stranded RNA folds onto itself, as illustrated for the part of the RNA called .

Catalysis

In addition to the examples of catalytic RNA already mentioned in the previous section (ribosome, introns), other ribozymes exist.

Hammerhead RNA

()

RNAse P

RNAse P modifies folded tRNA.

Regulation

Only a small fraction of the human genome codes for proteins, tRNA or rRNA. The remainder has been called "junk DNA" in the past, but some of it codes for RNA that plays a role in gene regulation.

Riboswitches

Riboswitches work by binding to segments of RNA, thereby changing the structure of it (for example, by competing with an interaction supporting one structure, they allow it to fold into a different structure. The structure of the riboswitches is sometimes dependent on binding to small molecules, like the .

RNA silencing

()

Chemistry

Base: flat, aromatic, hydrogen-bonding capability, base modifications, base pairing, base stacking
Sugar phosphate backbone: torsion angles, sugar pucker, phosphate-phosphate distance

Transcription and Translation

The expression of genes into proteins and is a process involving two stages called transcription and translation. In the transcription stage a strand of DNA molecule serves as a template for the synthesis of an RNA molecule called messenger RNA. In the case of RNAs that code for polypetides, this messenger RNA is then translated into proteins on ribosomes.

Post-transcriptionally, specific nucleotides in RNA are often further modified. This is most frequent in [tRNA|transfer ribonucleic acid (tRNAs)]], the adapter molecules of Translation, and ribosomal ribonucleic acids (rRNAs) of the ribosome.

External Resources

HD-RNAS: Hierarchical Database of RNA Structures is a systematic hierarchical organization classifying all RNAs available in the Protein Data Bank. This helps make it easier to navigate the availble structural data given the large numbers of redundant files and ambiguous synthetic sequences.
Liley Database

References

↑ Steitz TA. The structural changes of T7 RNA polymerase from transcription initiation to elongation. Curr Opin Struct Biol. 2009 Dec;19(6):683-90. doi: 10.1016/j.sbi.2009.09.001., Epub 2009 Oct 5. PMID:19811903 doi:http://dx.doi.org/10.1016/j.sbi.2009.09.001
↑ Toor N, Rajashankar K, Keating KS, Pyle AM. Structural basis for exon recognition by a group II intron. Nat Struct Mol Biol. 2008 Nov;15(11):1221-2. Epub 2008 Oct 26. PMID:18953333 doi:10.1038/nsmb.1509

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RNA