1. Transcription occurs throughout the cell cycle EXCEPT during mitosis - strand + strand 5’ 3’

2. Each of the 30+ unique tRNAs is a substrate for a different aminoacyl- tRNA synthetase enzyme that attaches the appropriate amino acid — in this case tyrosine — to the appropriate tRNA, using ATP energy. All tRNAs bind their amino acid at a 3’ –OH group on ribose. Aminoacyl bond

3. How it’s all regulated Ch 15

4. For Thursday, 10/31 If we don’t complete Ch 15, we’ll complete it on Tuesday, 11/5 All of Ch 15 will be on Exam 2 (Nov 7) If we need to use Tuesday’s class to complete Ch 15, we’ll end class as soon as we finish Ch 15. Feel free to wear your costume to class.

5. The original conceptual model for regulation of genetic expression is the bacterial lac operon. Even though operons are not found in eukaryotes, the picture remains valid — a group of genes is turned “on” or “off” depending on the availability of the promoter for binding RNA polymerase. With the lac operon, the promoter is actively inhibited — repressed — by the product of another gene, the lacI gene, that is always transcribed. The repressor is removed by an environmentally regulated INDUCER, allolactose (an isomer of lactose) Notice that gene regulation and changing environment are intrinsically linked! Since the genes are shut down under common environmental conditions, so the genes are under NEGATIVE REGULATION. Direction of transcription is often identified by an arrow

6. The environmental cues for E. coli that affect lac operon function are their common energy sources, glucose and lactose. Often both are present, but bacteria (like humans) can more efficiently use glucose than lactose. POSITIVE REGULATION also occurs, where even in the presence of lactose, the operon is largely non-functional because the lac promoter is a weak promoter and requires a transcription factor for RNA Pol II to bind efficiently. In low [glucose], cAMP levels are elevated. cAMP binds to CAP protein, a transcription factor, to change its conformation so that it acts as a transcription factor. When [glucose] is high, cAMP is low and CAP doesn’t bind. RNA Pol binds inefficiently, and the bacteria doesn’t waste energy on transcription.

7. In eukaryotes, with their vastly more complex genomes, regulation is proportionately more complex too. At the level of nucleosome structure, histones may be acetylated or non- acetylated. In general, as the diagram shows, unacetylated histones wrap DNA into more condensed regions that are unavailable to RNA polymerase. These regions are called heterochromatin. By acetylating certain amino acids on histones, the nucleosomes disperse into true chromatin — euchromatin — that unwraps regions of DNA for transcription. Like the loss of acetyl groups, methylation (—CH 3 ) also promotes the formation of heterochromatin. DNA bases within genes are often methylated, which also correlates with decreased transcription.

8. Viewing epigenetics http://learn.genetics.utah.edu/content/epigeneti cs/intro/ http://learn.genetics.utah.edu/content/epigeneti cs/intro/ What is an epigenome, and how does it differ from a genome? http://learn.genetics.utah.edu/content/epigeneti cs/brain/ http://learn.genetics.utah.edu/content/epigeneti cs/brain/ What is the implied influence of the environment on genetic regulation? Does epigenetic regulation differ from regulation of the lac operon?

9. Epigenetic tags can frequently be different in males and females. These different epigenetic markers are usually stay in place for the life of an organism but are reset during meiosis for the formation of sperm and eggs. The result is that some genes are uniquely silenced in males and some in females, starting with the sperm and eggs that fuse during fertilization. In 2012, a large number of imprinted genes were first uncovered in the brain of mammals. Imprinting is found only in mammals and flowering plants — at least 1% of human genes are imprinted. Abnormal imprinting, or the lack of imprinting, is associated with severe disorders and cancer. Prader- Willi syndrome is linked to an imprinted region of chromosome 15 – learning disability, compulsive eating, short stature. Stems from missing imprinted paternal gene, or two copies of imprinted maternal gene. Famous example is also the differences between a hinny and a mule. Mules are from male donkey and female horse. Smaller, less strong hinny is from male horse and female donkey!

10. Beckwith-Wiedemann Syndrome. The Igf2 gene codes for a hormone — insulin-like growth factor 2 — that stimulates embryonic/fetal growth. Maternal Igf2 genes are normally silent from imprinting. If not, the 2 copies of the gene (maternal and paternal) result in BWS, overgrowth, about 95% larger than their peers along with an increased cancer risk. Loss of the father’s imprinted gene results in dwarf offspring. BWS is consistent with the “genetic conflict” hypothesis that states that paternal imprinting favors larger offspring, at the expense of maternal resources, to foster inheritance of paternal genes. Maternal imprinting fosters smaller offspring with less drain on maternal resources during development. Imprinted genes found in the brain may influence differences in male- female behaviors.

11. Eukaryotic control mechanisms are subtle and complex. They can include genomic regions hundreds or thousands of bases upstream of the promoter. These regions, called ENHANCERS, require a unique combination of transcription factors to form a transcription complex with RNA polymerase to start transcription. Different cell types (and different organisms) will typically have different combinations of factors, allowing some cells to transcribe a gene while other cells (or other organisms) do not transcribe the same gene. Which cells have which factors is the challenging subject of developmental biology, coming up in Chapter 16

12. Alternative splicing is another way genes are regulated. The book (p 304) shows alternative splicing of troponin, a muscle protein, in different muscle tissues. Here’s an example from fruit flies. SXL is a master gene for sex determination in fruit flies. The gene is active only in females. The protein the gene codes for, SXL, is a splicing inhibitor in females. SXL prevents one of spliceosome proteins, U2AF, from binding to the right intron sequence, thereby causing exon 2 to splice with exon 4. In male flies, without SXL, the spliceosome recognizes the sequence and splices exon 2 with exon 3. That launches a cascade leading to differential male and female development. Exon 2 splices to Exon 3 Exon 2 splices to Exon 4