What does the word Promoter mean?

1. What does the word Promoter mean? It is the place at which RNA Pol II binds. But the word is incorrectly used to describe Enhancers plus Promoter.

2. Initiation by RNA Polymerase II

5. TFIID recognition site is TATAA How often is this site found in the genome? 1/45 Once every 1000 nucleotides 109 nucleotides or 106 times

8. Transient transfection More Cells But on a per cell Basis expression levels of -gal is about the same

9. Stable transfection

10. The 7-Methyl Guanosine(7-MG) Cap

11. The 3’ Poly(A) Tail AATAAA

12. Interrupted Genes in Eukaryotes: Exons and Introns Most eukaryotic genes contain noncoding sequences called introns that interrupt the coding sequences, or exons. The introns are excised from the RNA transcripts prior to their transport to the cytoplasm.

13. Removal of Intron Sequences by RNA Splicing The noncoding introns are excised from gene transcripts by several different mechanisms.

14. Excision of Intron Sequences

15. Splicing • Removal of introns must be very precise. • Conserved sequences for removal of the introns of nuclear mRNA genes are minimal. • Dinucleotide sequences at the 5’ and 3’ ends of introns. • An A residue about 30 nucleotides upstream from the 3’ splice site is needed for lariat formation.

16. Types of Intron Excision • The introns of tRNA precursors are excised by precise endonucleolytic cleavage and ligation reactions catalyzed by special splicing endonuclease and ligase activities. • The introns of nuclear pre-mRNA (hnRNA) transcripts are spliced out in two-step reactions carried out by spliceosomes.

17. The Spliceosome • Five snRNAs: U1, U2, U4, U5, and U6 • Some snRNAs associate with proteins to form snRNAs (small nuclear ribonucleoproteins)

19. What are Logo plots?

20. Logo for a) Splice acceptor b) Splice Donor c) Initiator Met

21. AG/GT CAG/NT exon 1 intron 1 exon 2

22. Chapter 12Translation and the Genetic Code

23. Protein Structure Proteins are complex macromolecules composed of 20 (?) different amino acids.

24. Amino Acids • Proteins are made of polypeptides. • A polypeptide is a long chain of amino acids. • Amino acids have a free amino group, a free carboxyl group, and a side group (R).

26. Peptide Bonds • Amino acids are joined by peptide bonds. • The carboxyl group of one amino acid is covalently attached to the amino group of the next amino acid.

27. Protein Synthesis: Translation The genetic information in mRNA molecules is translated into the amino acid sequences of polypeptides according to the specifications of the genetic code.

28. The Macromolecules of Translation • Polypeptides and rRNA molecules Euk: 28S, 18S, 5.8S, 5S • Amino-acid Activating Enzymes • tRNA Molecules • Soluble proteins involved in polypeptide chain initiation, elongation, and termination

29. Why does one need the ribosome to translate mRNA?

30. Ribosomes What does “S” mean? Why do sizes get bigger?

31. The Nucleolus • In eukaryotes, the nucleolus is the site of rRNA synthesis and ribosome assembly

32. Synthesis and Processing of the 30S rRNA Precursor in E. coli ProKaryote numbers

33. Synthesis and Processing of the 45S rRNA Precursor in Mammals

34. rRNA Genes • rRNA Genes in E. coli • Seven rRNA genes distributed among three sites on the chromosome • rRNA Genes in Eukaryotes • rRNA genes are present in hundreds to thousands of copies • The 5.8S-18S-28S rRNA genes are present in tandem arrays in the nucleolar organizer regions of the chromosomes. • The 5S rRNA genes are distributed over several chromosomes.

35. Transfer RNAs (tRNAs) • tRNAs are adapters between amino acids and the codons in mRNA molecules. • The anticodon of the tRNA base pairs with the codon of mRNA. • The amino acid is covalently attached to the 3’ end of the tRNA. • tRNAs often contain modified nucleosides.

36. What is Inosine?

38. Inosine

39. tRNA Structure

40. Specificity of tRNAs • tRNA molecules must have the correct anticodon sequence. • tRNA molecules must be recognized by the correct aminoacyl-tRNA synthetase. • tRNA molecules must bind to the appropriate sites on the ribosomes.

41. Codon Specificity Resides in the tRNA, Not the Attached Amino Acid.

42. tRNA Binding Sites on the Ribosome (Ribosme moves like an enzyme)

43. Stages of Translation • Polypeptide Chain Initiation • Chain Elongation • Chain Termination

44. Translation Initiation in E. coli • 30S subunit of the ribosome • Initiator tRNA (tRNAMet) • mRNA • Initiation Factors IF-1, IF-2, and IF-3 • One molecule of GTP • 50S subunit of the ribosome

47. The Shine-Dalgarno Sequence

48. Translation Initiation in Eukaryotes • The amino group of the methionine on the initiator tRNA is not formylated. • The initiation complex forms at the 5’ terminus of the mRNA, not at the Shine-Dalgarno/AUG translation start site. • The initiation complex scans the mRNA for an AUG initiation codon. Translation usually begins at the first AUG. • Kozak’s Rules describe the optimal sequence for efficient translation initiation in eukaryotes.

50. Polypeptide Chain Elongation • An aminoacyl-tRNA binds to the A site of the ribosome. • The growing polypeptide chain is transferred from the tRNA in the P site to the tRNA in the A site by the formation of a new peptide bond. • The ribosome translocates along the mRNA to position the next codon in the A site. At the same time, • The nascent polypeptide-tRNA is translocated from the A site to the P site. • The uncharged tRNA is translocated from the P site to the E site.