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Lecture 3 14.01.14

Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. As opposed to DNA replication, transcription results in an RNA complement that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA complement. Also unlike DNA replication where DNA is synthesized, transcription does not involve an RNA primer to initiate RNA synthesis.

Segment of DNA that undergoes transcription is called TRANSCRIPTION BUBBLE

The sense/coding/non-template strand has the same base sequence as the transcribed mRNA except that the base thymine is replaced by the base uracil. The anti-sense/non-coding/template strand acts as the template for the transcription of mRNA. During transcription, RNA polymerase unwinds a short section of the DNA double helix near the start of the gene. This unwound section is known as the transcription bubble.

RNA Polymerase
RNA polymerase (RNAP or RNApol), also known as DNA-dependent RNA polymerase, is an enzyme that produces primary transcript RNA. RNAP is a nucleotidyl transferase that polymerizes ribonucleotides at the 3' end of an RNA transcript. RNAP can initiate transcription at specific DNA sequences known as promoters. It then produces an RNA chain, which is complementary to the template DNA strand. The RNA polymerase, and the transcription bubble, travels along the non-coding strand in the opposite, 3' to 5', direction, as well as polymerizing a newly synthesized strand in 5' to 3' .

Prokaryotic RNA Polymerase

single type, synthesizes all types of RNArRNA, mRNA, tRNA Large molecule Core enzymes and sigma factors, together also called as HOLOENZYME Core: 2 subunit + & subunit + subunit subunit- helps in assembly of RNAP & subunit- catalytic center of RNAP subunit- stabilizes RNAP Sigma factor recognizes the promoter and recruits RNAP to the promoter and initiate transcription

5 types of RNAP : RNA Polymerase I, II, III, IV, V All are structurally related to each other and to bacterial RNAP.

Promoters of Prokaryotes
promoter is a region of DNA that initiates transcription of a particular gene. Promoters are located near the genes they transcribe, on the same strand and upstream on the DNA (towards the 3' region of the anti-sense strand, also called template strand and non-coding strand). Promoters can be about 1001000 base pairs long. the promoter contains two short sequence elements approximately -10 and -35 nucleotides upstream from the transcription start site.

Promoters of Eukaryotes

Eukaryotic promoters are diverse and are divided in more than 10 classes.





Transcription in Prokaryotes
Sigma factor recognizes the promoter region and facilitates the binding of RNA polymerase.

2. Elongation
RNA Polymerase moves along 3 to 5 on the template strand RNA Polymerase unwinds the DNA strands and adds ribonucleotides complementary to the template in 5 to 3 direction.

Bacteria has to methods for transcription termination - Rho-independent termination and Rho-dependent termination. In Rho independent transcription termination, also called intrinsic termination, RNA transcription stops when the newly synthesized RNA molecule forms a G-C-rich hairpin loop followed by a run of Us.. In the "Rho-dependent" type of termination, a protein factor called "Rho" destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex.

Rho- independent termination Rho-dependent termination


Initiation step involves additional factors called as transcription factors: basal and regulatory.

The gene control region of a typical eukaryotic gene

1. 2. 3.

4. 5. 6.

Coupled transcription and translation. Occurs in the cytoplasm A single RNA polymerase synthesizes all three types of rna: mRNA, tRNA and rRNA. RNAs are released and processed in the cytoplasm. Transcriptional unit has one or more than one gene. (polycistronic) The 23S, 16S and 5S rRNA are formed from single primary transcript.

2. 3.

4. 5. 6.

Coupled transcription and translation not possible. Occurs in the nucleus. The RNA polymerases I, II, and III synthesizes rRNA, mRNA and tRNA respectively. RNAs are released and processed in the nucleus. Transcriptional unit has only one gene (monocistronic). The 28S, 18S, 5.8S and 5S rRNAs are formed from two primary transcripts.


5 end capping

Intron non-coding part of gene Exon coding region