BSC 219

10/11/12

Transcription

13.1 RNA Consisting of a Single Strand of Ribonucleotides Participates in a Variety of Cellular Functions

Primary structure

Secondary structure

Classes of RNA

Ribosomal RNA – rRNA-part of ribosome

Messenger RNA – mRNA-template of protein to be synthesized

Transfer RNA – tRNA-transports amino acids to ribosome for translation

Small nuclear RNAs – snRNAs

Small nuclear ribonucleoproteins – snRNPs

Small nuclear RNAs – snoRNAs

Classes of RNA

Small cytoplasmic RNAs – scRNAs

MicroRNAs – miRNAs

Small interfering RNAs – siRNAs

Piwi-interacting RNAs – PiRNAs

13.2 Transcription Is the Synthesis of an RNA Molecule from a DNA Template

The Template

The transcribed strand: template strand

Transcription will produce an RNA molecule that resembles the opposite strand or the nontemplate strand

RNA polymerase moves along template strand in 3’-5’ direction and produces new RNA in 5’-3’ much as in DNA replication.

The Template

The transcription unit

Promoter-initiates transcription

RNA coding sequence-contains sequence that will be reflected in RNA molecule

Terminator-halts transcription and releases RNA molecule

Initiation

The substrate for transcription:

Ribonucleoside triphosphates – rNTPs added to the 3′ end of the RNA molecule

rGTP, rCTP, rATP, and rUTP

Initiation

The transcription apparatus:

Bacterial RNA polymerase: five subunits made up of the core enzyme:

Two copies of α

Single copy of β

Single copy of β′

A stabilize enzyme: ω

The sigma s factor: binding to the promoter when transcription starts

Initiation

The substrate for transcription:

Ribonucleoside triphosphates – rNTPs added to the 3′ end of the RNA molecule

The transcription apparatus:

Eukaryotic RNA polymerases

Initiation

Bacterial promoters:

Consensus sequences: sequences that possess considerable similarity

−10 consensus: 10 bp upstream of the start site

Pribnow box:

5′ TATAAT 3′

3′ ATATTA 5′

−35 consensus sequence: TTGACA

Concept Check 2

The holoenzyme (core enzyme + sigma factor)

The sigma factor alone

The core enzyme alone

mRNA

Concept Check 2

The holoenzyme (core enzyme + sigma factor)

The sigma factor alone

The core enzyme alone

mRNA

Initiation

Initial RNA synthesis: No primer is required.

The location of the consensus sequence determines the position of the start site.

Elongation

RNA elongation is carried out by the action of RNA polymerase.

Termination

Rho-independent termination: hairpin structure formed by inverted repeats, followed by a string of uracils

Rho-dependent termination: a hairpin slows down polymerase allowing a trailing protein called rho to catch up and dislodge the polymerase from the template

13.4 The Process of Eukaryotic Transcription Is Similar to Bacterial Transcription but Has Some Important Differences

Transcription and Nucleosome Structure – Chromatin modification before transcription

Promoters:

Basal transcription apparatus

Transcriptional activator proteins

RNA polymerase II – mRNA synthesis

Core promoter TATA box TATAAAA, −25 to −30 bp, binded by transcription factors

Transcription and Nucleosome Structure – Chromatin modification before transcription

Promoters:

Regulatory promoter

A variety of different consensus sequences may be found in the regulatory promoters.

Main difference between prokaryotes and eukaryotes is in assembly of complex structures at promoter in eukaryotes

Transcription and Nucleosome Structure – Chromatin modification before transcription

Enhancers: distant regions of DNA that increase transcription levels

Bound by initiation complex proteins and loop around to interact with promoter region

Polymerase I and polymerase III promoters

Distinct from those of polymerase II

May sometimes be downstream of transcription start site

Initiation

RNA polymerase II + transcription factors

TATA binding protein

Elongation

Termination

RNA polymerase I-terminated by protein that binds DNA downstream of termination sequence

RNA polymerase II-terminated by complex mechanism involving RNA cleavage and Rat1 protein

RNA polymerase III-terminates after long poly-U transcript.

Concept Check 3

Only the core promoter has consensus sequences.

The regulatory promoter is farther upstream from the gene.

Transcription factors bind to the core promoter; transcriptional activator proteins bind to the regulatory promoters.

Both b and c above

Concept Check 3

Only the core promoter has consensus sequences.

The regulatory promoter is farther upstream from the gene.

Transcription factors bind to the core promoter; transcriptional activator proteins bind to the regulatory promoters.

Both b and c above

13.5 Transcription in Archaea Is More Similar to Transcription in Eukaryotes than to Transcription in Eubacteria

This suggests a closer relationship between archaea and eukaryotes.