1. AP Biology Eukaryotic Genome Control Mechanisms for Gene expression

2. Chromatin vs. Chromosomes appearance within the cell.

3. Histone Proteins and Supercoiling DNA double helix Histone tails His- tones Linker DNA (“string”) Nucleosome (“bead”) 10 nm 2 nm Histone H1 Nucleosomes (10-nm fiber)

4. Supercoiling of Chromatin

5.  Histones-proteins DNA wraps around  Nucleosome-unit of DNA wrapped around histones  Supercoiling-Chromatin  chromosomes  Heterochromatin-remains condensed  Euchromatin-loose during interphase  Cellular differentiation-making cells different; accomplished by turning genes “on” or “off”  differential gene expression

6. Euchromatin vs. Heterochromatin (The dark spots are the hetero)

7. During Transcription  DNA Methylation-heavy coat-prevents- source of genomic imprinting  Histone acetylation-breaks bond btwn DNA and proteins;allows RNA polymerase to attach  piwi-associated RNAs(piRNAs) induce formation of heterochromatin  Building transcription initiation complex  Enhancers& activators-control rate  Repressor or silencer sit on TATA box

8. DNA Control stages in Protein Synthesis Signal NUCLEUS DNA RNA Chromatin Gene available for transcription Gene Exon Intro Transcription Primary transcript RNA processing Cap Tail mRNA in nucleus Transport to cytoplasm CYTOPLASM mRNA in cytoplasm Translation Degradation of mRNA Polypeptide Cleavage Chemical modification Transport to cellular destination Degradation of protein Active protein Degraded protein

9. Methylation

10. . Histone tails Amino acids available for chemical modification DNA double helix Histone tails protrude outward from a nucleosome Acetylation of histone tails promotes loose chromatin structure that permits transcription Unacetylated histones Acetylated histones

11. “Build the factory”

12. Enhancers Distal control element Activators Enhancer DNA DNA-bending protein TATA box Promoter Gene General transcription factors Group of mediator proteins RNA polymerase II RNA polymerase II RNA synthesis Transcription Initiation complex

13. Notice the different nucleotide control sequences (red vs, pink) Control elements EnhancerPromoter Albumin gene Crystallin gene Available activators Available activators Albumin gene not expressed Albumin gene expressed Liver cell Lens cell Crystallin gene not expressed Crystallin gene expressed Liver cell nucleus Lens cell nucleus

14. miRNA &siRNA Dicer Hydrogen bond Protein complex miRNA Target mRNA Degradation of mRNA OR Blockage of translation

15.  Coordinated control of genes families- multiple copies of same gene, all transcribed at one  MicroRNA (miRNA) and small interfering RNA (siRNA)-little pieces that attach to mRNA to control transcription  Post transcription Regulation  Alternative RNA Splicing using snRPS  Cytoplasmic degradation

17. Control of exons

18. Translation control mechanisms  Build Translation Initiation Complex  Faulty cap  Tail too short

19. How many As on the tail?

20. “Build the factory”

21. Post Translation control  Chaperonin or SRP  Phosphorylation-turns on or off  Proteosomes-control how long protein lasts-mainly work on intracellularly produced proteins ex. Cyclins, remove transcription factors, recycle amino acids  (Lysosomes work on extracellularly produced proteins)

22. Chaperonin Protein will stay in the cell

23. RER Protein will leave the cell

24. Proteosomes Protein to be degraded Ubiquitinated protein Proteasome Protein entering a proteasome Protein fragments (peptides) Proteasome and ubiquitin to be recycled Ubiquitin

25. Nuclear membrane’s role?

26. What is Dark Matter?  A five-year project called ENCODE, for "Encyclopedia of DNA Elements," found that about 80 percent of the human genome is biologically active, influencing how nearby genes are expressed and in which types of cells. It's not junk DNA, which was previously thought — instead, these non-coding regions of DNA could have major bearing on diseases and genetic mutations, researchers say.

27. Epigenetic  Inheritance of traits not directly involving nucleotide sequence  Modifications of chromatin can be reversed  Methylation  ID twins: one normal; one schizophrenic