1. Control of Gene Expression

2. The Central Dogma From DNA to Proteins DNA RNA Protein Translation Transcription Genotype Phenotype

3. Review of Replication, Transcription and Translation DNA Replication DNA Replication Ch9 Q3 Ch9 Q3 Note primase and Okazaki fragments Note primase and Okazaki fragments Transcription + Translation Transcription + Translation Transcription + Translation Transcription + Translation Protein Synthesis Protein Synthesis Protein Synthesis Protein Synthesis

4. Control of Gene Expression Every somatic cell has the same DNA Every somatic cell has the same DNA Cells are very different because each cell makes certain proteins and not others Cells are very different because each cell makes certain proteins and not others How does a cell know which genes to transcribe and which not to? How does a cell know which genes to transcribe and which not to?

5. Transcription Factors Proteins which control the expression of other genes Proteins which control the expression of other genes Link the genome with the environment Link the genome with the environment Activated by signals from outside the cell (e.g. hormones, sugar, etc.) Activated by signals from outside the cell (e.g. hormones, sugar, etc.) Allow RNA polymerase to bind to the promoter so that transcription can begin Allow RNA polymerase to bind to the promoter so that transcription can begin Gene must also be exposed –DNA must unwind in that area. Gene must also be exposed –DNA must unwind in that area.

7. RNA Processing The average total size of a gene is 27,000 bases but the average size of the coding portion is only 1,340 bases! The average total size of a gene is 27,000 bases but the average size of the coding portion is only 1,340 bases! mRNA transcripts are modified before use as a template for translation: mRNA transcripts are modified before use as a template for translation: Addition of capping nucleotide at the 5’ end Addition of capping nucleotide at the 5’ end Addition of polyA tail to 3’ end Addition of polyA tail to 3’ end Important for moving transcript out of nucleus and for regulating when translation occurs Important for moving transcript out of nucleus and for regulating when translation occurs

8. RNA Processing -Splicing Splicing occurs, removing internal sequences Introns are sequences removed Introns =Intervening sequences Used to be called Junk DNA! Exons are sequences remaining There is alternate splicing of mRNA in different tissues The # of proteins (~200,000) far outnumbers the # of genes (~20,000) An intron in one context may be an exon in another context

9. RNA Processing Figure 10.10

10. Translation: Multiple Copies of a Protein Are Made Simultaneously Figure 10.16

11. Protein Conformation Primary (1  ) structure Primary (1  ) structure Sequence of amino acids Sequence of amino acids Secondary (2  ) structure Secondary (2  ) structure Folding of the protein into  -helices and  -pleated sheets Folding of the protein into  -helices and  -pleated sheets Tertiary (3  ) structure Tertiary (3  ) structure 3D shape 3D shape Quaternary (4  ) structure Quaternary (4  ) structure Complex with other polypeptides (same or different proteins) Complex with other polypeptides (same or different proteins)

13. The Proteasome Misfolded proteins have ubiquitin molecules attached to them Misfolded proteins have ubiquitin molecules attached to them Ubiquitinated proteins are sent to the proteasome to be degraded Ubiquitinated proteins are sent to the proteasome to be degraded

14. Sole difference between normal and disease protein is conformation Sole difference between normal and disease protein is conformation All mammals have PrP but nearby proteins and polysaccharides keep it correctly folded All mammals have PrP but nearby proteins and polysaccharides keep it correctly folded Prions Normal PrP C conformation with many  - helices Infectious PrP Sc conformation with  -sheets

15. Spread of Prion Disease PrP C PrP Sc

16. Spongiform Encephalopathies

17. Gene Expression Can Change Over Time Example: Globin chain switching Example: Globin chain switching Hemoglobin molecules Hemoglobin molecules Transport oxygen molecules in the blood Transport oxygen molecules in the blood Composed of 4 globular proteins Composed of 4 globular proteins

18. Globin Chain Switching Figure 11.2

19. Proteomics Looking at all of the proteins made in a particular cell (or tissue, organ, etc.) Looking at all of the proteins made in a particular cell (or tissue, organ, etc.) i.e. the proteome i.e. the proteome

20. Chromatin Remodeling DNA is wrapped around histones to form nucleosomes DNA is wrapped around histones to form nucleosomes Chromosome packaging Chromosome packaging Chromosome packaging Chromosome packaging Acetylation =acetyl groups are added to histones Acetylation =acetyl groups are added to histones Exposes the primer so RNA polymerase can bind and transcription can begin Exposes the primer so RNA polymerase can bind and transcription can begin Deacetylation =acetyl groups are removed from histones Deacetylation =acetyl groups are removed from histones

21. RNA Interference Occasionally, both DNA strands are transcribed Occasionally, both DNA strands are transcribed Complementary strands bind to one another Complementary strands bind to one another Gene sequence may allow formation of a “hairpin loop” Gene sequence may allow formation of a “hairpin loop” RNA strand binds to itself RNA strand binds to itself Segments of dsRNA attract RNA-induced silencing complexes (RISCs) Segments of dsRNA attract RNA-induced silencing complexes (RISCs) Can be used experimentally (clinically?) Can be used experimentally (clinically?)

22. RNA Interference