1. Paul D. Adams University of Arkansas Mary K. Campbell Shawn O. Farrell http://academic.cengage.com/chemistry/campbell Chapter Eleven Transcription of the Genetic Code: The Biosynthesis of RNA

2. Transcription Overview of Transcription synthesized on a DNA template, catalyzed by DNA- dependent RNA polymerase ATP, GTP, CTP, and UTP are required, as is Mg 2+ no RNA primer is required the RNA chain is synthesized in the 5’ -> 3’ direction; the nucleotide at the 5’ end of the chain retains its triphosphate (ppp) group the DNA base sequence contains signals for initiation and termination of RNA synthesis; the enzyme binds to and moves along the DNA template in the 3’ -> 5’ direction the DNA template is unchanged

3. Transcription in Prokaryotes E. coli RNA Polymerase: molecular weight about ______________________ four different types of subunits: _____________________ _____________ enzymethe _____________ enzyme is  2  ’ _____________the _____________ is  2  ’  ______________ ________________the role of the  subunit is recognition of the ______________; the  subunit is released after ________________ ____________ strand _____________ strandof the two DNA strands, the one that serves as the template for RNA synthesis is called the template strand or ____________ strand; the other is called the coding (or nontemplate) strand or _____________ strand __________the __________ binds to and transcribes only the ___________

4. The Basics of Transcription

5. Promoter Sequence __________________________Simplest of organisms contain a lot of DNA that is __________________________ _____________ __________________________RNA polymerase needs to know which strand is _____________strand, which part to _____________, and where first _____________ of gene to be transcribed is __________________________ - DNA sequence that provide direction for RNA polymerase

6. Promoter Sequence

7. Chain Initiation _____________First phase of transcription is _____________ _____________ __________________________________________begins when RNA polymerase binds to _____________and forms ________________ complex _____________ ____________After this, DNA unwinds at _____________ to form open complex, required for chain ____________

8. Initiation and Elongation in Transcription

9. Chain Elongation _____________After strands separated, transcription _____________ of ~17 bp moves down the DNA sequence to be transcribed _____________ _____________RNA polymerase catalyzes formation of _____________bonds between the incorporated _____________ _____________ _____________ __________ __________Topoisomerases _____________ _____________ in front of & behind __________ bubble __________

10. Chain Elongation (Cont’d)

11. Chain Termination Two types of termination mechanisms: _____________ _____________, _____________ _____________ 1. intrinsic termination- controlled by specific sequences called _____________ _____________, characterized by two _____________ _____________

12. Chain Termination (Cont’d) 2. Other type of termination involves rho (  ) protein  -dependent termination sequences cause hairpin loop to form

13. Transcription Regulation in Prokaryotes In prokaryotes, transcription regulated by:  Alternative  factors ___________ & ____________ exert control over which genes are expressed by producing different  -subunits that direct the RNA _____________ to different genes.

14. Control by Different  Subunits

15. Enhancers Certain genes include sequences upstream of ____________________________________ These genes for ribosomal production have _____ upstream sites, _________ sites Class of DNA sequences that do this are called ______________ Bound by proteins called _________ _________

16. Elements of a Bacterial Promoter

17. Operon :_________ : a group of operator, promoter, and structural genes that codes for proteins the control sites, promoter, and operator genes are physically adjacent to the structural gene in the DNA the regulatory gene can be quite far from the operon operons are usually not transcribed all the time,__________________, an inducible protein coded for by a structural gene, _________ structural gene _________ codes for lactose permease structural gene _________ codes for transacetylase expression of these 3 structural genes is controlled by the regulatory gene ______ that codes for a repressor

18. How Does Repression Work Repressor protein made by lacI gene forms tetramer when it is translated Repressor protein then binds to operator portion of operon Operator and promoter together are the control sites

19. Binding Sites On the lac operon Lac operon is induced when E. coli has _________ as the carbon source Lac protein synthesis repressed by ____________ (catabolite repression) E. coli recognizes presence of glucose by promoter as it has 2 regions: RNA polymerase binding site, _________ _________ _________ (CAP) binding site

20. Binding Sites On lac operon (Cont’d)

21. Catabolite Repression CAP forms complex with _________ Complex binds at CAP site RNA polymerase binds at available binding site, and _____________ occurs

22. Basic Control Mechanisms in Gene Control Control may be _________ or _________, and these may be _________ or _________ controlled

23. Control of the trp operon Trp operon codes for a leader sequence (trpL) & 5 polypeptides The 5 proteins make up 4 different enzymes that catalyze the multistep process that converts chorisimate to tryptophan

24. Alternative 2˚ structures can form in trp operon These structures can form in the leader sequence Pause structure- binding between regions 1 and 2 Terminator loop- binding between regions 3 and 4 Antiterminator structure- Alternative binding between regions 2 and 3

25. Attenuation in the trp operon Pause structure forms when ribosome passes over Trp codons when Trp levels are high Ribosome stalls at the Trp codon when trp levels are low and antiterminator loop forms

26. Transcription in Eukaryotes Three RNA polymerases are known; each transcribes a different set of genes and recognizes a _____________________________________: RNA Polymerase I- found in the _________ and synthesizes precursors of most _________ RNA Polymerase II- found in the _________ and synthesizes _________ precursors RNA Polymerase III- found in the _________ and synthesizes _________, other RNA molecules involved in mRNA _________ and _________ _________

27. RNA Polymerase II Most studied of the polymerases Consists of 12 subunits ______ - RNA Polymerase B

28. How does Pol II Recognize the Correct DNA? 4 elements of the Pol II promoter allow for this phenomenon

29. Initiation of Transcription Any protein regulator of transcription that is not itself a subunit of Pol II is a _________ _________ Initiation begins by forming a _________ _________ Transcription control is based here

30. General Transcription Initiation Factors

31. Transcription Order of Events Less is known about _________ than _________ The phosphorylated Pol II synthesizes RNA and leaves the promoter region behind GTFs are left at the promoter or dissociate from Pol II

32. Elongation and Termination Elongation is controlled by: _________ sites, where RNA Pol will hesitate _________, which proceeds past the normal termination point _________ _________ _________ _________ (P-TEF) and _________ _________ _________ _________ (N-TEF) Termination begins by stopping RNA Pol; the _____________ consensus sequence for termination is ___________

33. Gene Regulation _________ & _________ - regulatory sequences that augment or diminish transcription, respectively DNA _________ brings _________ into contact with transcription _________ and ____________

34. Eukaryotic Gene Regulation _________ _________ are enhancers that respond to certain metabolic factors _________ _________ _________(HSE) _________ _________ _________(GRE) _________ _________ _________(MRE) _________ _________ _________(CRE) Response elements all bind _________(transcription factors) that are produced under certain cell conditions

35. Response Elements

36. Activation of transcription Via CREB and CBP _________________ CREB does not bind to CREB binding protein, and no transcription occurs _________________ of CREB causes binding of CREB to CBP Complex with basal complex (RNA polymerase and GTFs) activates _________________

37. Structural Motifs in DNA-Binding Proteins Most proteins that activate or inhibit RNA Pol II have two _________ _________ : DNA-binding domain transcription-activation domain DNA-Binding domains have domains that are either: _________________________

38. Helix-Turn-Helix Motif Hydrogen bonding between amino acids and DNA

39. Zinc Finger Motif Motif contains 2 cysteines and 2 His --12 amino acids later Zn binds to the repeats

40. Basic Region Leucine Zipper Motif Many transcription factors contain this motif, such as CREB (Biochemical Connections, page 315) Half of the protein composed of basic region of conserved Lys, Arg, and His Half contains series of Leu Leu line up on one side, forming hydrophobic pocket

41. Helical Wheel Structure of Leucine Zipper

42. Transcription Activation Domains _________________________ domains - rich in Asp and Glu. Gal4 has domain of 49 amino acids, 11 are acidic _________________________ domains - Seen in several transcription factors. Sp1 has 2 glutamine- rich domains, one with 39 Glu in 143 amino acids _________________________ domains - Seen in CTF-1 (an activator). It has 84 amino acid domain, of which 19 are Pro

43. Post Transcriptional RNA Modification ____________________________________ are all modified after transcription to give the functional form the initial size of the RNA transcript is greater than the final size because of the leader sequences at the 5’ end and the trailer sequences at the 3’ end the types of processing in prokaryotes can differ greatly from that in eukaryotes, especially for _______________ Modifications ____________________ of leader and trailer sequences addition of _____________ _________ (after transcription) modification of the structure of specific bases (particularly in _______________)

44. Posttranscriptional Modification of tRNA Precursor

45. Modification of tRNA tRNA- the precursor of several tRNAs is can be transcribed as ________ polynucleotide sequence ____________________ ____________________ ____________________ all take place ____________________ & ________________ of ____________________ are the two most usual types of base modification

46. Modification of rRNA Ribosomal RNA processing of rRNA is primarily a matter of ________________________________________ in _______________, 3 rRNAs in one intact ribosome in _______________, ribosomes have 80s, 60s, and 40s subunits base modification in both prokaryotes and eukaryotes is primarily by _____________________

47. Modification of mRNA Includes the capping of the 5’ end with an N-methylated guanine that is bonded to the next residue by a 5’→5’ triphosphate. Also, 2’-O-methylation of terminal ribose(s)

48. mRNA Modification A polyadenylate “tail” that is usually100-200 nucleotides long, is added to the 3’ end before the mRNA leaves the nucleus This tail protects the mRNA from nucleases and phosphatases Eukaryote genes frequently contain intervening base sequences that do not appear in the final mRNA of that gene product exonsExpressed DNA sequences are called exons intronsIntervening DNA sequences that are not expressed are called introns These genes are often referred to as split genesThese genes are often referred to as split genes

49. Organization of Split Genes in Eukaryotes

50. The Splicing Reaction Exons are separated by intervening _______________ When the exons are spliced together, a _______________ forms in the intron

51. Ribozymes The first ribozymes discovered included those that catalyze ______________________________ More recently, ribozymes have been discovered that are involved in _______________ _______________ _______________ ribozymes require an external guanosine example: pre-rRNA of the protozoan Tetrahymena (next screen) _______________ ribozymes display a ______ mechanism similar to mRNA splicing no requirement for an external nucleotide

52. Self-splicing of pre-rRNA