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

Cellular Functions

• Primary structure

• Secondary structure

The Structure of RNA

Classes of RNA

• Ribosomal RNA – rRNA

• Messenger RNA – mRNA

• Transfer RNA – tRNA

• 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

RNA polymerase enzyme reads template and synthesizes complementary RNA sequence

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.

Usually only one strand will serve as template in a region of DNA, however, throughout the DNA molecule each strand can be used as template

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 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

What binds to the −10 consensus sequence found in most bacterial promoters?

a. The holoenzyme (core enzyme + sigma factor)

b. The sigma factor alone

c. The core enzyme alone

d. mRNA

Concept Check 2

What binds to the −10 consensus sequence found in most bacterial promoters?

a. The holoenzyme (core enzyme + sigma factor)

b. The sigma factor alone

c. The core enzyme alone

d. 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

Much the same as in prokaryotes

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

What is the difference between the core promoter and the regulatory promoter?

a. Only the core promoter has consensus sequences.

b. The regulatory promoter is farther upstream from the gene.

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

d. Both b and c above

Concept Check 3

What is the difference between the core promoter and the regulatory promoter?

a. Only the core promoter has consensus sequences.

b. The regulatory promoter is farther upstream from the gene.

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

d. 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.