1. RNA and RNA world
WHICH CAME FIRST, THE chicken or the egg? The biological silences have a variation: which came first, DNA or protein? You see, among the many tasks performed by proteins is assembling DNA molecules. But DNA contains the in formation needed to make proteins. So which came first?

2. Transcription

3. Transcription-the synthesis of RNA using DNA as a template.
Four stages: Initiation, Elongation, Termination, Post-transcriptional modification

4. Similarities and Differences from Replication
Similarities Differences
5' →3' direction •RNA polymerase instead
many proteins involved of DNA polymerase
initiation, elongation, • no proofreading termination • posttranscriptional
transcription bubble modification
starts and stops at • 1 strand copied not 2 specific places • not all copied
Nt not dNt

5. Terminology of Transcription
(3') ACG GAA TAA TTA TGT TTA TCA CAA TTT AGA (5') + (plus) strand
template strand
(5') TGC CTT ATT AAT ACA AAT AGT GTT AAA TCT (3') -(minus) strand
non-template strand
coding strand
(5') UGC CUU AUU AAU ACA AAU AGU GUU AAA UCU (3') RNA
transcript
Upstream 5’ end vs. Downstream 3’ end

6. The function of RNA polymerase is to copy one strand of
duplex DNA into RNA.

7. Transcription in prokaryotes

9. Transcription Unit

10. Optimal Promoter
T82 T84 G78 A65 C54 A45
T80 A95 T45 A60 A50 T96

11. The –35 sequence is used for initial recognition, and the –10 sequence is used for the melting reaction that converts a closed complex to an open complex.

13. During transcription, the bubble is maintained within bacterial RNA
polymerase, which unwinds and rewinds DNA, maintains the conditions
of the partner and template DNA strands, and synthesizes RNA.

14. Bacterial RNA Polymerases
How does RNA polymerase work?
A single type of RNA polymerase is responsible for almost all synthesis of mRNA, rRNA and tRNA in a eubacterium.
About 7,000 RNA polymerase molecules are present in an E. coli cell. Probably 2,000~5,000 enzymes are synthesizing RNA at any one time, the number depending on the growth conditions.

15. A map of the E. coli s70 factor identifies conserved regions
How many sigma factors exist
in E. coli ?
A map of the E. coli s70 factor
identifies conserved regions

17. How does transcription initiate? Four stages of Transcription

18. Termination
Rho (ρ)-dependent vs. ρ-independent

19. How does transcription terminate? Intrinsic terminators

20. A Rho-dependent terminator has a sequence rich in C and poor in G preceding the actual site(s) of termination.

21. ρ-Dependent Termination
A hairpin forms
if protein called ρis present, polymerase detaches
Dissociation is somehow coupled to ATP hydrolysis

22. Rho factor pursues RNA polymerase along the RNA and can cause termination when it catches the enzyme pausing at a
rho-dependent terminator.

23. Transcription in Eukaryotes
RNA polymerase I transcribes rRNA
RNA polymerase II transcribes mRNA
RNA polymerase III transcribes tRNA and other small RNAs.

24. Animal RNA Polymerases
Animal DNA-dependent RNA Polymerases
Class α-amantin sensitivity Major Products
I Insensitive rRNA
II Low Conc. (1-10 nM) hnRNA
III High conc tRNA, 5S RNA
and small RNAs
All have in common 2 large subunits and a number of smaller subunits, as well as being zinc metalloenzymes.

26. What is the promoter difference between prokaryote and eukaryote genes?

27. Enhancer
Enhancers Work Upstream, Downstream or in the Middle of a Gene
They also work forwards or backwards
Possible ways of working
Different transcription factors
Order of binding (differing concentrations) Affinity of transcription factors

28. Elements combination in type II Promoters
TATA box is a septamer (TATAAAA ) at -25 and is involved in positioning the enzyme for correct initiation.
Initiator has a general form Py2ANT/APy2 and has the simplest possible form recognizable by RNA polymerase II.
GC box is at -90 contains the sequence GGGCGG and is recognized by the factor SP1.
CAAT box (CCAATCT) is at –75 and is recognized by a large group of transcription factors and plays a strong role in determining the efficiency of the promoter.
Enhancer; Dehancer; Silencer;
Upstream Activating Sequences (UAS)

29. How to determine promoter elements
Change promoter sequence
Promoter elements are defined by
mutations and footprinting

31. Have you ever wondered how your genome works
Have you ever wondered how your genome works? Well, thanks to scientists like Roger Kornberg, awarded the 2006 Nobel prize for Chemistry, who has painstakingly studied the micromechanics of transcription, we’re getting a much clearer picture of what happens inside the nucleus, and how the billions of metres of DNA in your body are converted into RNA by an enzyme called RNA polymerase II.
- from the announcement of 2006 Nobel prize for chemistry

32. More than 10 Subunits to form RNA polymerase II

33. How does RNA polymerase II initiate transcription?
TBP: TATA-binding protein
TAFs: TBP-associated factors
TFIID protects a region extending farther upstream
TFIIA activates TBP by relieving the repression that is caused by the TAFs
TFIIB binds adjacent to TBP and TATA box
TFIIF consists of two subunits. The larger subunit has an ATP-dependent DNA helicase activity and the small one contacts the core polymerase.
TFIIE and TFIIH are required for promoter clearance to allow RNA polymerase to commence movement away from the promoter.
TFIID

34. Most of the TFII factors are released before RNA polymerase II leaves the promoter.
TFIIH has several activities, including an ATPase, a helicase, and a kinase activity that can phosphorylate the CTD tail of RNA polymerase II; it is also involved in repair of damage to DNA.
Phosphorylation of the CTD by the kinase activity of TFIIH may be needed to release RNA polymerase to start transcription.

35. TBP is a universal factor

36. DNA-binding and activating functions in a transcription factor may comprise independent domains of the protein.

37. What are Transcription units for RNA polymerase I ?

38. How many promoters in type III gene ?
Two types promoters
upstream promoter and internal promoter
upstream promoter: U6 snRNA
Internal promoter: 5S RNA and tRNA

39. How does initiate in type III gene with polymerase III ?
5S RNA
tRNA

41. Termination of Eukaryotic transcription
Type II genes: Transcription stops after AATAAA-Polyadenylation signal.
Type I genes:3-4 consecutive Ts
Type III genes: Stop after synthesis of serial Us.