1. Agenda 3/22 Stickleback switches video
Stickleback switches model and activity
Homework: Gene expression essay (due 3/23)
Turn in: Video notes
Warm up: How does DNA organization differ in eukaryotes and prokaryotes?

2. How is eukaryotic gene expression different than prokaryotic gene expression?
How do our cells become different and specialized?

3. Agenda 3/23 Eukaryotic control lecture Lactase click and learn
Homework: Development Video and Notes *, Finish Essay
Turn in: Nothing ...unless essay is finished

4. Control of Eukaryotic
Gene Expression

5. Eukaryotic Gene Regulation
Prokaryotic regulation is different from eukaryotic regulation.
Eukaryotic cells have many more genes (23,700 in human cells) in their genomes than prokaryotic cells (average 3000).
Physically there are more obstacles as eukaryotic chromatin is wrapped around histone proteins.
There are more non-histone proteins that are used in eukaryotic gene expression than in prokaryotic gene expression.
Current estimates from the Human Genome Project show that there are about 23,700 protein-coding genes in the human genome; BUT they are responsible for producing about 160,000 different proteins. This is possible due to alternative splicing during RNA Processing. Each protein coding gene has an average of 7 different products. 5 5

6. Eukaryotic Gene Regulation in Multicellular Organisms
Almost all the cells in an organism are genetically identical or totipotent.
Differences between cell types result from differential gene expression -- the expression of different genes by cells with the same genome.
Errors in gene expression can lead to diseases including cancer.
Gene expression is regulated at many stages.
“Totipotent” = a cell with a full set of genes; i.e. has the total potential to become any type of cell.
White blood cells (lymphocytes) are cells that are not totipotent and are different from one another in the genes that produce antibodies.

7. Organization of DNA http://www.youtube.com/watch?v=gbSIBhFwQ4s
Organization of the genome in eukaryotic cells has an impact on gene regulation. The genome is organized with the help of proteins. The DNA is double stranded and forms a helix. That helix then is wound around 8 histone proteins g (2 copies of 4 different histone proteins) forming beads called nucleosomes. There is a fifth histone protein (H1) that binds to the DNA outside the nucleosome. There are five different histone proteins, H2A, H2B, H3, and H4. The histones remain attached to the DNA except when DNA is replicating. Even when the DNA is being transcribed, the histones remain attached. Histones have the ability to change position and shape to allow RNA polymerases to transcribe the DNA gene.
Double stranded DNA is wrapped around histone proteins like beads on a string.
With the help with H1 histone protein, the nucleosomes coil to form chromatin fibers of 30 nm in diameter.
At the next level are looped domains that are connected to a nonhistone protein scaffold.
The chromatin folds further for a maximum compacted chromosome.
During interphase, (G1, S, G2), the DNA uncoils to the looped domain level. Certain looped domains are restricted to certain areas of the nucleus.
Approximately 97% of the DNA found in a human cell is not used for protein-coding genes. Each specialized cell activates a variety of genes.

8. Three Levels of Control
1. Pre-transcriptional
Methylation
Acetylation
Transcription factors
2. Post-transcriptional
Alternative splicing
3. Post-translational
ubiquitination

9. Epigenetics
Epigenetics refers to processes that influence gene expression or function without changing the underlying DNA sequence.
Acetylation
Methylation

10. Acetylation
Acetylation of lysine found on the histone decreases the affinity of histones for DNA and other histones, thereby making DNA more accessible for transcription.

11. Methylation
A methyl group can be added to the nitrogenous bases of cytosine that are followed by guanine
Different cells have different methylation patterns, which contributes to the differences in gene expression in different cell types.
Methylation makes DNA less likely to be transcribed
The Barr body of the second X chromosome in females is highly methylated. Once a gene is methylated, it stays methylated even when the cell divides. The daughter cells will keep the genes methylated. This is called genomic imprinting and the gene remains inactive.

13. The role of enhancers and transcription factors.
a. Transcription factors bind to the promoter region (TATA box) for the RNA polymerase to attach.
b. Inducer regions which may help transcription factors to bind.
c. DNA site control elements even further upstream (thousands of nucleotides away) called a enhancers.
DNA enhancers can work by a protein (activator) attaching to the enhancer.
The DNA then loops the DNA back on itself to attach to the promoter region.

14. Role of Transcription Factors
The enhancers attract activators. These activators and the region of the DNA they are attached to are attracted to the promoter region of the DNA gene. It causes actual folding of the DNA gene which, in turn, attracts more transcription factors and the attachment of RNA polymerase.

15. Role of Transcription Factors and Activators
This illustrates how different cells have different activators which activate different genes.
The liver cells need the protein albumin and not the protein crystallin and the lens cells do not need albumin but do need crystallin.
Note how each cell has a unique set of activators and transcription factors that interact with only certain genes in the cell.

16. Post-Transcriptional Control Alternative Splicing
Once the immature mRNA is made, it could be processed in different ways to give rise to different mature mRNA and thus different proteins.
Fot example,. In Drosophila there is a gene that is called a "double--sex" gene because the mRNA can be processed two different ways depending on the presence of a tra gene product. The "double-sex" gene has 6 exons and in females the tra gene product is present. It causes exon 3 to be linked to exon 4 but the remaining exons are deleted. In males the tra gene product is absent. This causes exon 3 to be linked to 5 and 6, skipping # 4 altogether. Once the mRNA is made, it will lead to development of either a male or female.

17. Second Example
In Drosophilia there is a gene called Tropin T. There are enough exons and introns in the gene that the mRNA from this gene can be spliced over 17,000 ways giving rise to 17,000 different proteins. These unique proteins are found on different nerve cells in Drosophilia.

18. Example of Alternative Splicing the Same Gene in Humans
Current estimates from the Human Genome Project show that there are about 23,700 protein-coding genes in the human genome; BUT they are responsible for producing about 160,000 different proteins. This is possible due to alternative splicing during RNA Processing. Each protein coding gene has an average of 7 different products. 95% of human genes undergo alternative splicing.
An average human gene is 36,000 base pairs (bp) long, but contains 6 introns that are about 5700 bp each and 7 exons that are about 300 bp each. So, the actual coding region is only 2100 bp for a 36,000 bp gene. (a bit of trivia: by bp number, if we include the introns, 25% of your genome is composed of protein-coding genes, but if we only count the exons, then only 1.3% of your genome codes for protein)
CGRP (calcitonin gene related peptide) is a hormone that 37 is amino acids long and produced in the hypothalamus. This molecule interacts with receptors in nervous tissue. It is a potent peptide vasodilator and can function in the transmission of pain. It is thought to be a part of the cause of migraine headaches.
Calcitonin which is produced by the thyroid gland is formed from the alternative splicing of the same gene as CGRP (calcitonin/CGRP gene). This located on chromosome 11. Calcitonin increases the concentration of calcium in the blood when secreted from the thyroid gland.
There are 23,700 protein-coding genes in the human genome; BUT they are responsible for producing about 160,000 different proteins. This is possible due to alternative splicing during RNA Processing. Each protein coding gene has an average of 7 different products. 95% of human genes undergo alternative splicing.

19. Post-translational control- Ubiquitin
Proteins that need to be degraded are tagged with a protein called ubiquitin. Once tagged, a protein complex called a proteasome breaks down the protein. The ubiquitin molecules are recycled and the small polypeptide fragments are further degraded by other enzymes.