YILDIRIM BEYAZIT UNIVERSITY FACULTY OF MEDICINE THE DEPARTMENT OF MEDICAL BIOLOGY

1. Genetic Information Flow: Transcription of Class I, II, III Genes YILDIRIM BEYAZIT UNIVERSITY FACULTY OF MEDICINE THE DEPARTMENT OF MEDICAL BIOLOGY ASST. PROF. DR. ENDER ŞİMŞEK

2. Transcription • Initiation, elongation, termination • Catalyzed by RNA polymerase

3. Transcription • “Transcription bubble”: DNA transiently separated into single strands • Only one strand is used as a template • Unwinding point & rewinding point

4. OVERVIEW OF TRANSCRIPTION • The first stage in the expression of genetic information is transcription.

5. OVERVIEW OF TRANSCRIPTION • The first stage in the expression of genetic information is transcription. • For any particular gene, only one strand of the DNA molecule(the template strand) is copied by RNA polymerase.

6. OVERVIEW OF TRANSCRIPTION • RNA polymerase moves along the template strand in the 3' to 5' direction as it synthesizes the RNA product in the 5' to 3' direction using NTPs (ATP, GTP, CTP, UTP) as substrates.

7. OVERVIEW OF TRANSCRIPTION • RNA polymerase moves along the template strand in the 3' to 5' direction as it synthesizes the RNA product in the 5' to 3' direction using NTPs (ATP, GTP, CTP, UTP) as substrates. • The coding (non-template) strand is not used during transcription. It is identical in sequence to the RNA molecule, except that RNA contains uracil instead of the thymine found in DNA.

8. TRANSCRIPTION: RNA polymerase locates genes in DNA by searching for promoter regions. The promoter is the binding site for transcription factors and RNA polymerase. Bindingestablishes where transcription begins and in which direction transcription proceeds.

9. Prokaryotic (E.coli) Promoters: “Pribnow Box’‘

10. In a gene, a numbering system is used to identify the location of important bases. The first base transcribed as RNA is defined as the + 1 base of that gene region.

11. In a gene, a numbering system is used to identify the location of important bases. The first base transcribed as RNA is defined as the + 1 base of that gene region. To the left (5', or upstream) of this starting point for transcription, bases are -1, -2, -3, etc. to the right (3', or downstream) of this point, bases are +2, +3, etc.

12. -35 and -10 Consensus Sequences of E.coli promoters:

13. Prokaryotic RNA Polymerase • There is a single prokaryotic RNA polymerase that synthesizes all types of RNA in the cell.

14. Prokaryotic RNA Polymerase • There is a single prokaryotic RNA polymerase that synthesizes all types of RNA in the cell. • The core polymerase responsible for making the RNA molecule has the subunit structure (ααββ`).

15. The transcription Steps of Core & Sigma: DNA binding Promoter search Closed promoter complex formation Open promoter complex formation

16. INITIATION:

17. A protein factor calledsigma (σ) is required for the initiation of transcription at a promoter.

19. The first ribonucleotideof RNA molecules in both prokaryotes and eukaryotesis a purine (A or G).

20. ELONGATION:

21. Sigma (σ) factor is released immediately after the initiation of transcription.

22. ELONGATION

23. TERMINATION:

24. The following events occur during the expression of a prokaryotic gene: • With the help of sigma factor, RNA polymerase recognizes and binds to the promoterregion. • The bacterial promoter contains two "consensus" sequences, called the Pribnow box (or TATA box) and the -35 sequence. The promoter identifies the start site for transcription and orients the enzyme on the template strand.

25. The following events occur during the expression of a prokaryotic gene: 2. Transcription begins at the + 1 base pair. Sigma factor is released as soon as transcription is initiated.

26. The following events occur during the expression of a prokaryotic gene: 3. The core polymerase continues moving along the template strand in the 3' to 5' direction, synthesizing the mRNA in the 5' to 3' direction.

27. The following events occur during the expression of a prokaryotic gene: 4. RNA polymerase eventually reaches a transcription termination signal, at which point it will stop transcription and release the completed mRNA molecule.

28. There are two kinds of transcription terminators commonly found in prokaryotic genes: • Rho-independent termination occurs when the newly formed RNA folds back on itself to form a GC-rich hairpin loop closely followed by 6-8 U residues. These two structural features of the newly synthesized RNA promote dissociation of the RNA from the DNA template.

32. There are two kinds of transcription terminators commonly found in prokaryotic genes: • Rho-dependent termination requires participation of rho factor. The rho protein binds to the newly formed RNA and moves toward the RNA polymerase that has paused at a termination site. Rho then displaces RNA polymerase from the 3' end of the RNA.

35. Rho protein

36. The following events occur during the expression of a prokaryotic gene: 5. Transcription and translation can occur simultaneously in bacteria. Because there is no processing of prokaryotic mRNA (generally no introns), ribosomes can begin translating the message even before transcription is complete.

37. The following events occur during the expression of a prokaryotic gene: 6. The ribosome translates the message in the 5' to 3' direction, synthesizing the protein from amino terminus to carboxyl terminus.

38. A Prokaryotic Transcription Unit • Prokaryotic Polycistronic Message Codes for Several Different Proteins In these cases, related genes grouped together in the DNA are transcribed as one unit. (The mRNA in this case contains information from several genes and codes for several different proteins.)

39. The Eukaryotic RNA polymerases

40. There are three eukaryotic RNA polymerases, distinguished by the particular types of RNA, they produce: • RNA polymerase I (Class I gene) is located in the nucleolus and synthesizes 28S, 18S, and 5.8S rRNAs.

41. There are three eukaryotic RNA polymerases, distinguished by the particular types of RNA, they produce: • RNA polymerase I (Class I gene) is located in the nucleolus and synthesizes 28S, 18S, and 5.8S rRNAs. • RNA polymerase II (Class II gene) is located in the nucleoplasm and synthesizes hnRNA/mRNA and some snRNA.

42. There are three eukaryotic RNA polymerases, distinguished by the particular types of RNA, they produce: • RNA polymerase I (Class I gene) is located in the nucleolus and synthesizes 28S, 18S, and 5.8S rRNAs. • RNA polymerase II (Class II gene) is located in the nucleoplasm and synthesizes hnRNA/mRNA and some snRNA. • RNA polymerase III (Class III gene) is located in the nucleoplasm and synthesizes tRNA, some snRNA, and 5S rRNA.

43. Comparison of Prokaryotic and EukaryoticRNAPolymerases * * *

44. A Eukaryotic Transcription Unit

45. INITIATION: • The core of RNA pol II enzyme can not recognize the promoter itself, it requires general transcription factors (GTFs).

46. INITIATION: • The core of RNA pol II enzyme can not recognize the promoter itself, it requires general transcription factors (GTFs). • These proteins, however, do not take part in the RNA synthesis but their binding to the promoter forms an attraction for RNA polymerase. • GTFs: TFIIA, TFIIB, etc.

47. Eukaryotic promoter is located in the 5’ end of the transcription starting point.

48. Eukaryotic promoter is located in the 5’ end of the transcription starting point. • TATA box of the promoter from the start of transcription (+1) is ahead of about 25-30 nucleotides upstream and has the transcription start point.

49. Eukaryotic promoter is located in the 5’ end of the transcription starting point. • TATA box of the promoter from the start of transcription (+1) is ahead of about 25-30 nucleotides upstream and has the transcription start point. • The region is called as TATA box is located in the region -30 and Transcription Binding Proteins (TBPs) bind to this region.

50. The TATA box is firstly recognized by transcription factor TFIID, after that TFIIB binds there.