1. 3 main types of RNA All are made from a DNA Template mRNA: encode AA sequence of one of more polypeptides from a gene or set of genes tRNA: reads info. In mRNA and transfers appropriate AA to growing peptide chain rRNA: part of ribosome, cellular machines synthesize proteins Transcription 1

2. Synthesis Resembles DNA replication in its chemical mechanism, polarity, use of template Has initiation, elongation, termination phase Does not need a primer, only involves limited segment of DNA molecule 2

3. RNA Polymerase DNA directed RNA polymerase DNA template Nucleotides (ATP, CTP, UTP, GTP) Builds in the 5’ to 3’ direction 3

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5. RNA Polymerase 5

6. Binds to initiation site through sequences called promoter elements that are recognized by  factor 6

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9. Once initiation occurs  factor dissociates 9

10. Recognized by  70 Recognized by  32 10

11. RNA Polymerase has helicase activity Gyrases/topoisomerases are needed to prevent positive supercoiling ahead of the transcription bubble 11

12. An electron micrograph of three contiguous ribosomal genes from oocytes of the salamander Pleurodeles waltl undergoing transcription. 12

13. Transcription is tightly regulated Not all genes are transcribed equally 13

14. Transcription Factor Upstream of RNAP II initiation site, different combinations of specific DNA sequences each is recognized by corresponding site specific DNA binding protein Each combination of DNA sequence and cognate DNA binding protein represent a control module 14

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20. The lac operon 20

21. Eukaryotic transcription Heterochromatin: transcriptionally inactive Euchromatin: may be transcriptionally active Eukaryotic RNAP have almost no affinity for promoters on their own 21

22. Eukaryotic RNA Polymerases RNAP I: synthesis of transcripts called preribosomal RNA – precursor 18s, 5.8s, 28s RNA RNAP II: synthesis of mRNA RNAP III: synthesize tRNA 22

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24. RNA Polymerase II Has 12 subunits Needs transcription factors that stimulate the enzyme to bind to a nearby promoter General TF required at every RNAP II promoter 24

25. Functionally equivalent to  factor 25

26. Gaining access to the DNA template Histones must be modified to access DNA Histone acetyltransferases: decrease + charge Histone deacetylases: increase + charge 26

27. Lysine Acetyllysine 27

28. 5% of cytidine residues are methylated at the 5 position These are most often found at CG sequences Hypermethylation is associated with heterochromatin Gene Silencing 28

29. Recruiting RNA polymerase 29

30. Regulated Transcription 30

31. Regulated Transcription 31

32. RNA Processing Most RNA is processed after synthesis Ribozymes: catalyze post-transcriptional processing Primary Transcript: newly synthesized RNA molecule – occurs in mRNA and tRNA –contains sequence encoding one gene but encoded polypeptide not continuous Noncoding Regions: introns Coding Region: exons 32

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37. Post-transcriptional control 37

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40. RNA Editing Changes the Meaning 40

41. RNA Editing Changes the Meaning C to U A to I 41

42. There are many ways to regulate the meaning of genes after transcription Prevent translation 42

43. There are many ways to regulate the meaning of genes after transcription Degrade the message 43

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46. Target the mRNA 46

47. What about mistakes? Nonsense Mediated Decay 47