1. Chapter 15, Part I

2. Topic Outline Translation Prokaryotic Gene Regulation Eukaryotic Gene Regulation Mutations Cancer

3. Gene: the definition What’s a gene? –Think of it as simply a sequence of DNA that gives rise to a piece of RNA. Genes that encode for mRNA (which code for proteins) are called “protein coding genes” Genes that encode for tRNA and rRNA are called “noncoding” genes. There are also genes that encode pieces of RNA that bind to mRNA… inhibiting them from being translated. This is called RNA inhibition, or simply RNAi. This is a new world of research, and one of the largest areas of new work today.

4. Prokaryotic Genome Circular small Genes are arranged in “Operons” –Single promoter region. –“structural” genes –“regulatory” genes (activators or inhibitors) Co-activators, co-inhibitors A single origin of replication DNA doesn’t contain histones, so gene regulation is much simpler.

5. Prokaryotic Gene Regulation Simpler organisms: simpler system. Easier to study. “Operon”: A region of the prokaryotic genome that encodes for several polypeptides all involved in a single metabolic pathway ACD E1 E2 E3 B

6. ACD E1 E2 E3 B E1 E2E3 PromoterOperator

7. Concepts Repressible –Example: trp operon. –Encodes enzymes to synthesize the amino acid tryptophan. Usually this operon is “on”. However, if there is a lot of tryptophan, the operon will turn “off”. Generally associated with anabolic pathways (building stuff that isn’t there) Inducible –Example: lac operon –Encodes enyzmes that break down lactose into usable molecules (like glucose) –Usually off (the cell prefers glucose, not lactose). When there is little glucose, the cell turns this on so it can use an alternative energy supply. Generally associated with catabolic pathways (breaking stuff down)

8. Prokaryotic Gene Regulation E1, E2, E3, are all encoded along a single stretch of DNA, and all controlled by a single promoter region. Movie: the lac operon E1 E2E3 PromoterOperator

9. Additional Control To “fine tune” gene expression, all genes are controlled in more than one way (it’s not as simple as a repressor protein binding to an operator). Example: in addition to the [lactose] (which causes the repressor to fall off, remember), the [glucose] also helps control gene expression.

10. Additional Control High glucose –Low cAMP Low glucose –High cAMP –Binds to “CAP” (catabolite activating protein) –CAP/cAMP binds to CAP binding site next to the promoter. –Causes DNA to bend, favoring attachement of RNA polymerase High lactose –Repressor falls off, activating the lac operon Low lactose –Repressor stays attached to operator, preventing transcription

11. Eukaryotic Genome Characteristics HIGHLY complex. No Operons. No circular DNA; only linear chromosomes. Introns and Exons. Many layers of regulation – not just transcriptional control. Contain many repetitive sequences. –Many of these are mobile, and are called “transposons”

12. Genes A sequence of DNA that leads to an RNA product. –Coding genes (also called structureal genes) encode information to build polypeptide chains. They contain introns and exons. –Noncoding genes do NOT contain information to build proteins. Instead, there transcription product is the final gene product. These genes include tRNA and rRNA genes. Genes are regulated. –They aren’t always on or off; they are controlled. Therefore, there are regions of DNA that are not genes, that control genes. –These are called “regulatory elements”.

13. Gene Regulation The most basic regulatory element is the promoter. Transcription Factors bind to promoters, and recruit RNA polymerase. When this happens, the gene is active, or “on”. Things that turn on genes are called activators. Things that turn off genes are called repressors. Genes that are always on, but can be turned off, are called “repressible”. Genes that are always off, but can be turned on, are called “inducible”.

14. Eukaryotic Gene Regulation What makes two cells different? The genes that are on and off. What kinds of basic mechanisms do cells utilize to turn genes on and off?

15. Chromatin Structure “open” DNA = euchromatin. Genes can be turned on. “closed” DNA = heterochromatin. Genes are off.

17. What determines whether DNA is “open” or “closed”? –The interaction between histones and DNA. Histones have tails that are + charged. They interact with DNA, which is - charged. This causes them to coil up DNA, keeping it “off” (transcription factors can’t bind to promoters) Enzymes transfer acetyl groups to histones. This causes the charge to be neutralized, and for histones to dissociate (fall off) the DNA. Now, transcription factors can bind and activate promoters.

18. Eukaryotic Chromatin DNA itself can have its charge neutralized. Cytosine (in CG base pairs) can be methylated, which causes this region of DNA to become uncharged. The DNA acts like oil in water, and crumples up. Shutting off genes.