Primary structure Secondary structure

1. 13.1 RNA Consisting of a Single Strand of Ribonucleotides Participates in a Variety of Cellular Functions

2. The Structure of RNA • Primary structure • Secondary structure

5. Classes of RNA • Ribosomal RNA – rRNA • Messenger RNA – mRNA • Transfer RNA – tRNA • Small nuclear RNAs – snRNAs • Small nuclear ribonucleoproteins – snRNPs • Small nuclear RNAs – snoRNAs

6. Classes of RNA • Small cytoplasmic RNAs – scRNAs • MicroRNAs – miRNAs • Small interfering RNAs – siRNAs • Piwi-interacting RNAs – PiRNAs

8. 13.2 Transcription Is the Synthesis of an RNA Molecule from a DNA Template RNA polymerase enzyme reads template and synthesizes complementary RNA sequence

9. 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.

11. 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

13. 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

15. Initiation • The substrate for transcription: • Ribonucleoside triphosphates – rNTPs added to the 3′ end of the RNA molecule • rGTP, rCTP, rATP, and rUTP

16. 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

18. Initiation • The substrate for transcription: • Ribonucleoside triphosphates – rNTPs added to the 3′ end of the RNA molecule • The transcription apparatus: • Eukaryotic RNA polymerases

20. 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

22. Concept Check 2 What binds to the −10 consensus sequence found in most bacterial promoters? • The holoenzyme (core enzyme + sigma factor) • The sigma factor alone • The core enzyme alone • mRNA

23. Concept Check 2 What binds to the −10 consensus sequence found in most bacterial promoters? • The holoenzyme (core enzyme + sigma factor) • The sigma factor alone • The core enzyme alone • mRNA

24. Initiation • Initial RNA synthesis: No primer is required. • The location of the consensus sequence determines the position of the start site.

25. Elongation • RNA elongation is carried out by the action of RNA polymerase.

26. 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

29. 13.4 The Process of Eukaryotic Transcription Is Similar to Bacterial Transcription but Has Some Important Differences

30. 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

31. 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

33. 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

34. Initiation • RNA polymerase II + transcription factors • TATA binding protein

36. Elongation Much the same as in prokaryotes

38. 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.

40. Concept Check 3 What is the difference between the core promoter and the regulatory promoter? • 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

41. Concept Check 3 What is the difference between the core promoter and the regulatory promoter? • 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

42. 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.