Sunday, December 23, 2012

RNA Metabolism : Basics



RNA METABOLISM

RNA is the only macromolecule having role in storage and transmission of information and in catalysis (ribozyme).

Fig. Classes of Eukaryotic RNA (Source: Harper's Illustrated Biochemistry, 28th Edition)

DNA-Dependent RNA synthesis

Synthesis by RNA Polymerase (RNAP)  that adds NTPs to 3’-OH end using one strand of DNA as template, similar to DNA Polymerase (DNAP). RNA formed is similar to coding strand.

Elongated from 5’ to 3’ end with reading from 3’ to 5’ end on DNA.


Ribonucleotides are used in RNA synthesis rather than deoxyribonucleotides in DNA, primers are not involved in RNA synthesis. U replaces T in RNA. Only portions of genome are vigorously transcribed into RNA whereas the entire genome must be copied, once and only once during DNA replication and There is no highly effective proofreading function during RNA transcription.

Mechanism:

Fig. Mechanism of RNAP (Source: Lehninger's Biochemistry, 4th Edition)
Binding of RNAP to promoter site in DNA initiates synthesis without the need of primer.

Growing end of RNA forms hybrid RNA-DNA doublex 8 bp long, which peels off shortly.

Fig. Transcription bubble (Source: Lehninger's Biochemistry, 4th Edition)   
During rewinding and unwinding positive and negative (loose or unwound DNA) supercoils are maintained by topoisomerase.

Uracil is used in place of T which base pairs with A.

RNAP has no 3’ to 5’ proofreading mechanism so error rate is one error per every 10­4105
nucleotides addition.

Requirement for Transcription:

  1. DNA template i.e. one strand of DNA duplex.
  2. RNA polymerase


In prokaryotes has 6 subunits.

α2β’βω + σ is the holoenzyme, where former is the core subunit and later binds transiently to core and it directs core subunit to attach to nucleotide of promoter region.

Different types of sigma are Specific for specific promoter. In Eukaryotes the RNAP is multiple subunits.
(Source: Lehninger's Biochemistry 4th edn.)

  1. RNAP –I = Insensitive to alpha aminitin, synthesis of rRNA
  2. RNAP –II = highly sensitive to alpha aminitin, Synthesis of mRNA (hnRNA) and snRNA, miRNA
  3. RANP – III = moderately sensitive to alpha aminitin, synthesis of tRNA, 5S rRNA.


Only RNAP-II and III are sensitive to inhibition by alpha aminitin former at low concentration and later at high concentration. 




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