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THE STRUCTURE OF RNA

 • RNA has a much greater structural and functional versatility (çok yönlü olmak/bir çok fonksiyona ship olmak) compared with DNA.

• RNA chains fold into unique three-dimensional structures which act similarly to globular proteins

• RNA is involved in a wide range of essential cellular processes from DNA replication to protein synthesis.

• Two main class of RNAs

1. coding (mRNA)

2. non-coding (others)

Small nuclear RNA snRNA Splicing and other functions Eukaryotes and archaea

Small nucleolar RNA snoRNA Nucleotide modification of  RNAs Eukaryotes and archaea

MicroRNA miRNA Gene regulation, post  transcriptional modifications.  Usually, gene silencing Most eukaryotes

siRNA/RNAi It interferes with the expression of specific genes.

gRNA A guide RNA is a piece of RNA that functions as a guide for RNA or DNA-targeting enzymes.

circRNA Circular RNA is a type of single-stranded circular RNA. Circular RNA has been linked to some diseases such as cancer.

Secondary Structure of RNA can be predicted with good accuracy by; computer analysis sequence analysis X-ray crystallography.

Some Of the Common Secondary Structures of RNA Architecture.

Bulges, Base-paired helices or “stems,” , Single-stranded hairpin, Internal loops, Junctions

Base-paired RNA adopts an A-type double helix.

RNA Helices Often Contain Noncanonical Base Pairs more than 20 different types of noncanonical base pairs, involving two or more hydrogen bonds, that have been encountered (happened/discovered) in RNA structures.

The Most Common Noncanonical Base Pairs In RNA

• GU wobble

• Sheared GA pair

• Reverse Hoogsteen pair

• GA imino pair. (imino group C=NH)

Noncanonical base pairs and base triples are important mediators of RNA self-assembly and of RNA–protein and RNA–ligand interactions. For example, noncanonical base pairs widen the major Groove and make it more accessible to ligands.

Modified Bases

In general, tRNAs contain more than 50 modified bases.

Secondary And Tertiary Structure Of tRNA

tRNA Loops Functions

• Certain structural elements, of course, are unique to the function of tRNA.

• Each of the three tRNA loops that form the “cloverleaf ” secondary structure seems to serve a specific purpose.

1-


every tRNA so far examined has the sequence ACC on the 3′ end to which the amino acid is attached.

2-      the T loop is involved in recognition by the ribosomes,

3-      the D loop (or dihydrouridine loop) is associated with recognition by the aminoacyl tRNA synthetases, and the anticodon loop base pairs with the codon in mRNA.

4-      the anticodon loop in all tRNA is bounded by uracil on the 5′ side and a modified purine on the 3′ side.

This purine is always modified, but the modification varies widely.



Common Tertiary Structure Motifs In RNA

a-hydrogen bonding                                                              b-base stacking

Secondary structural domains of RNA interact to form the tertiary structure.

1.       Pseudoknot

• Example: plant RNA virus, human telomerase RNA.

• Mutations in the pseudoknot region are involved in the human genetic disease, dyskeratosis congenita.

2.       A-Minor Motif,

• The A-minor motif is one of the most abundant long-range interactions in large RNA molecules.

• This motif is found extensively in ribosomal RNAs.

• In this folding pattern, single-stranded adenosines make tertiary contacts with the minor grooves of RNA double helices by hydrogen bonding.

3.       Tetraloops, the stability of a stem-loop structure is often enhanced by the special properties of the loop.

4.       Ribose Zippers, Helix–helix interactions are often formed by “ribose zippers.”

5.      Kink-Turns Kink-turns are asymmetric internal loops embedded in RNA double helices commonly found in the large ribosomal RNA of the extreme halophilic (salt-tolerant) archaean Haloarcula marismortui.

RNA is involved in a wide range of cellular processes along the pathway of

• Gene expression

• DNA replication

• RNA processing

• mRNA turnover

• Protein synthesis

• Protein targeting

RNA MOLECULES CAN CATALYZE CHEMICAL REACTIONS IN LIVING CELLS.

Functional Results Of RNA-Nucleic Acids And RNA-Protein Interactions

1. RNA can serve as a “scaffold.”  Proteins recognize the primary nucleotide sequence of RNA and/or secondary and tertiary structural motifs.

2. RNA–protein interactions can influence the catalytic activity of proteins.

3. RNA can be catalytic.

4. Small RNAs can directly control gene expression including differential RNA folding and riboswitches and RNA interference and microRNAs.

5. RNA can be the hereditary material.

THE DISCOVERY OF SELF-SPLICING RNA WAS COMPLETELY UNEXPECTED.


Ribozymes Catalyze a Variety of Chemical Reactions

•RNA molecules with catalytic activity are called RNA enzymes or “RIBOZYMES. ”

•Naturally occurring ribozymes are often autocatalytic, which leads to their own modification.

•The 23S rRNA in the ribosome catalyzes peptide bond formation without being modified in the process.

Naturally Occurring Ribozymes Are Classified into Two Different Groups,

Large Ribozymes

•Group I and group II ribozymes are self-splicing introns.

• Large ribozymes are the RNA components of the spliceosome

Small Ribozymes

• Hammerhead motif: so, called for its three helices in a T shape, is the most frequently found catalytic motif in plant pathogenic RNAs, such as viroids.

• Hairpin motif: The hairpin ribozyme has only been found in some virusoids.

• Hepatitis delta virus (HDV) RNA: is a viroid like satellite virus of the human hepatitis B virus (HBV) that when present causes an exceptionally strong type of hepatitis in infected patients. • Hepatit delta virüsü (HDV) RNA'sı: insan hepatit B virüsünün (HBV) viroid benzeri bir uydu virüsüdür ve mevcut olduğunda enfekte hastalarda son derece güçlü bir hepatit tipine neden olur.

• Varkud satellite (VS) RNA: The VS ribozyme is part of a larger RNA that is transcribed from a plasmid found in the mitochondria of some strains of Neurospora crassa, a filamentous fungus. • Varkud uydu (VS) RNA'sı: VS ribozimi, filamentli bir mantar olan Neurospora crassa'nın bazı suşlarının mitokondrisinde bulunan bir plazmitten kopyalanan daha büyük bir RNA'nın parçasıdır.

• glmS riboswitch ribozyme: The glmS riboswitch ribozyme is involved in regulating bacterial gene expression.• glmS riboswitch ribozimi: glmS riboswitch ribozimi bakteriyel gen ekspresyonunun düzenlenmesinde rol oynar.

• In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA.

• The glms gene is transcribed into mRNA.




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