1. 1 SURVEY OF BIOCHEMISTRY Transcription and Translation

2. 2 PRS Which of the following is not an example of a DNA-binding motif in proteins? 1.Beta Sheet 2.Helix-turn-Helix 3.Zinc Finger 4.Leu Zipper

3. 3 PRS Which amino acid contains a hydroxyl in its side chain? 1.Threonine 2.Methionine 3.Aspartic Acid 4.Phenylalanine

4. 4 Transcription Transcription is the process by which RNA is produced from a DNA template.  Initiation  Elongation  Termination Steps involved in transcription

5. 5 Transcription DNA has to separate at the position where transcription occurs. Fig. 26-3

6. 6 Transcription 5’-…GATCCGTAGGTC…-3’ 3’-…CTAGGCATCCAG…-5’ 5’-…GATCCGTAGGTC…-3’ Sense Strand Antisense Strand (template) 5’----GAUCCGUAGGUC…3’ 3’-…CTAGGCATCCAG…-5’ Newly synthesized RNA has the same general sequence as the sense strand; U in RNA, T in DNA

7. 7 Transcription Initiates at Promoter Sequences What is a gene? Example of E.coli Lactose Operon Organization Fig. 26-4 P: Promoter O: Operator I: Inhibitor

8. 8 Structural genes follow promoter sequences In E. coli, the lactose operon consists of 3 structural genes:  Beta-Galactosidase (Z)  Galactoside Permease (Y)  Thiogalactoside Transacetylase (A)

9. 9 E. coli Promoter Sequences Usually single purine Notice how sequence is numbered!

10. 10 Prokaryotic RNA Polymerases Core enzyme Holoenzyme The sigma factor binds specifically to the promoter. Core enzyme affinity to DNA ~5x10 -12 M. = sigma factor

11. 11 Elongation: RNA Chain Growth 3’-OH group acts as a nucleophile, attacking the alpha phosphate group, with subsequent release of inorganic pyrophosphate.

12. 12 DNA Supercoiling Positive supercoiling Negative supercoiling 1.RNA polymerase is processive 2.Once an RNAP has moved from the promoter, another can bind 3.Transcription is fast: constitutive enzymes vs. inducible enzymes

13. 13 Termination of Transcription Because the newly synthesized RNA is single-stranded, hairpin structures can easily form from the termination sequence.

14. 14 Hairpin Structure in RNA Poly-U tail G-C rich bp region What happens when a known terminator sequence is missing?

15. 15 Termination: Rho Factor Helicase: RNA-RNA and RNA-DNA complex unwinding.

16. 16 Transcription in Eukaryotes RNA Polymerase I –Precursors to rRNA RNA Polymerase II –Precursors to mRNA RNA Polymerase III –Precursors to 5S rRNA, tRNA –Precursors to other small RNA’s

17. 17 Eukaryotic Transcription Factors Transcription factors are req’d to initiate transcription, and facilitate elongation in eukaryotes. Eukaryotic Termination: Not well understood

18. 18 Portion of the Genetic Code Wobble

19. 19 Reading Frames

20. 20 Translation: Protein Synthesis Messenger RNA –Template Transfer RNA –Carries amino acids Ribosomal RNA –Aids protein synthesis

21. 21 tRNA Structures 2D 3D

22. 22 tRNA’s have modified bases Be able to name, draw, recognize structures from Figure 27-4.

23. 23 Aminoacyl tRNA Synthetases Aminoacyl tRNA synthetases add aa’s to tRNA. Step 1.

24. 24 Aminoacyl tRNA Synthetases Step 2. + tRNA

25. 25 Ribosome

26. 26 Sites in the Ribosome A Aminoacyl P Peptidyl E Exit A PE

27. 27 Chain Initiation in Translation Start Codon: AUGMethionine

28. 28 Shine-Dalgarno Sequence upstream downstream

29. 29 Initiation

30. 30

31. 31 Translation: Polypeptide Synthesis Peptidyl Transferase Activity

32. 32 Elongation

33. 33 Administrative Updates Exam 1 on Thursday, 4-5 pm –20 questions –Short answers and Multiple Choice –Closed-book –Calculators allowed –No cell phones, blackberries, etc. Office Hours: M, T, R 2-4 pm