Chapter+18+and+19+Prokaryotic,+Eukaryotic+and+Viral+Gene+Regulation

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Chapter 18 Gene Expression & Chapter 19 Viral Genetics Chapter 18 Gene Expression > Positive gene regulation facilitates a more efficient binding of RNA polymerase and the operon's promoter. To help illustrate the process, //E. Coli// bacteria will be used as a model. When glucose levels are low in the //E. Coli cell,// the bacteria must compensate with the catabolism of lactose. The regulatory protein CAP (catabolite activator protein) functions as an activator in the process by binding to DNA promoter and stimulating the transcription of a gene. However in order to assume its active shape, the CAP requires the attachment of the small organic molecule cAMP (cyclic AMP). Once the CAP is attached to the promoter, RNA polymerase can efficiently access and transcribe the //lac// protein which aids in the breakdown of lactose for energy. Once glucose levels return to normal, the cAMP levels decrease thereby inactivating the CAP protein and allowing the bacterial cell to resume its normal breakdown of glucose for energy. -AHC The **transcription initiation complex** is essentially a cluster of proteins that assemble on the promoter sequence at the "upstream" end of the gene. One of these proteins, RNA polymerase II, then proceeds to transcribe the gene, synthesizing a primary RNA transcript (pre-mRNA). RNA processing includes enzymatic addition of a 5' cap and a poly-A tail, as well as splicing out of introns, to yield a mature mRNA. Associated with most eukaryotic genes are multiple **control elements**, segments of noncoding DNA that serve as binding sites for the proteins called transcription factors, which in turn regulate transcription. Control elements and the transcription factors that bind are critical to the precise regulation of gene expression seen in different cell types. [] --Sabrina and Joanne > Kellen   and   Ella ==== non-coding RNA becoems both tRNA and rRNA. (1)Transfer RNA is crucial in the the translation process by carrying specific amino acids to the ribosomes. (2)Ribosomal RNA is what makes up the ribosomes, made of two subunits, it codes for every synthesized protein. (3)Micro RNA acts to silence and degrade teh synthesized trascript, in an attempt to control/limit the amount of protein produced in one period. Some ncRNA function as parts of spicesosomes in between transcription and translation, while others aid in the mRNA degradation process. ====
 * 1) Explain the operon model and its role in protein synthesis in prokaryotes- The operon model is a functioning nit of genomic DNA whose genes work together and are controlled by a promoter and an operator. The promoter and operator synthesize proteins, but do not code for it. When the promoter and operator overlap, the starting and stopping of transcription are determined. RNA polymerase synthesizes for RNA during transcription in prokaryotic cells.
 * 2) Explain in detail negative gene regulation in prokaryotes. Use the Lac operon and the Trp as examples
 * 3) Explain in detail positive gene regulation in prokaryotes.
 * 1) Identify 3 types of gene regulation that take place in eukaryotes.
 * 2) Compare and contrast histone acetylation and DNA methylaton and its effect on transcription
 * 3) Describe in detail the role of the transcription initiation complex, the control elements and how they come together to influence transcription
 * 1) Explain how RNA processing, mRNA degradation, translation initiating factors, protein processing and degradation regulate gene expression. RNA processing involved the addition of a poly-A tail to the 3' end and a cap to the 5' end. Introns are spliced out while extrons are spliced together, finally forming mRNA. The purpose of RNA processing is to convert primary transcripts into functional, mature mRNA. As such, RNA processing impacts translation efficiency, stability, and the potential diversity of the genome by splicing out introns and leaving extrons. Only the genetic information carried in the extrons is actually expressed and thus splicing, part of RNA processing, helps impact gene expression. mRNA degradation involves ribonucleases and cofactors. The 3' poly-A tail protects from RNA degradation by exonucleases. Ultimately, however, RNA degradation impacts gene expression because the genetic information carried in RNA is degraded and no longer able to be fully expressed. If RNA degradation impacts a non-coding region, the effect is minimal, but genetic errors may result from RNA degradation that targets coding regions of RNA. The effect is particularly pronounced on smaller RNA molecules. Translation initiating factors  regulate gene expression. In certain mRNAs, regulatory proteins can block translation initiation by binding to structures on the untranslated region at the 5' to 3' end. This causes ribosomes to not attach to the mRNA strand, so protein synthesis cannot occur. After translation, protein processing can regulate gene control. Gene regulation can occur during cleavage of the initial insulin polypeptide, during phosphorylation/dephosphorylation, and also during transport of cell-surface proteins to their target destinations. Proteasomes, giant protein complexes, degrade proteins after the cell attaches ubiquitin to the protein. This is recognized by a proteasome, which then degrades the protein.[]
 * 1) Decsribe the 3 different types of ncRNA’s and their function in gene expression

-Philip and Emily
A cell undergoing determination is an undifferentiated cell that is being committed to its final fate as a specific type of cell. In other words, a determined cell is one that is committed to its final fate, and will later undergo differentiation. This process may be influenced by the genome of the cell as well as the extracellular environment in which the cell exists. Based on its determined fate, the cell will produce tissue specific proteins. Example: muscle cell. Many decisions lead up to the determination of the fate of somatic cells. Based on events before, during, and after gastrulation, certain somatic cells become precursor cells for skeletal muscles. These specific somatic cells travel into the regions where there fate will be realized; in this case, the cells travel into regions of limbs. At this point, the cells do not have the necessary contractile proteins to function as skeletal muscle cells. They soon start to produce vast amounts of muscle tissue-specific proteins. These cells have been determined since they have made the "choice" to function as muscle cells rather than other connective tissue-specific cells.
 * 1) What does it mean for a cell to be undergoing determination? Give a specific example of this process.

10. Describe how specific proto-oncogenes become oncogenes. A proto-oncogene is a group of genes that can cause normal genes to become cancerous when mutated. The mutated form of a proto-oncogene is an oncogene. Proto-oncogenes usually affect the genes that code for cell growth, stimulation, and programmed death, so you can see how a mutation turning a proto-oncogene into an oncogene could cause cancer. Different mutations that can cause a proto to become and onco are point mutations, extra chromosomal copies of the gene, and second genes being formed through chromosome translocation that cause relocation. Below is a picture...Danny G. a.k.a. G3

Mutations to the BRAC 1 and 2 gene stops the repair of DNA errors. These are tumor suppressor genes that code for proteins to make certain repairs. Without proper repair of damaged DNA, the risk of cancer increases. If cancer develops it will occur in the breasts and ovaries. Gene mutation is genetic and can be passed on to lineage.
 * 1) Describe how mutations in tumor-supressor genes like BRCA I & II can lead to cancer.

[] -Jason Weiss

Chapter 19 The Genetics of Viruses 12. List and describe the structural components of viruses. 13. Describe bacterial defenses against phages and distinguish between the lytic and lysogenic reproductive cycles, using phage lambda as an example. //In lytic reproduction, the viruses replicate until the host cell bursts, releasing the new viruses. In lysogenic reproduction, the viral DNA is incorporated into the host cell's genome, so viruses can be made using the cell's organelles without the cell inhibiting anything.// //[] (animation of both reproductive cycles)//

//Restriction modification systems, CRISPR defense, physical barriers such as the excretion of mucus or formation of complex outer-membrane sugar structures to block phage adsorption, and modifications of phage receptors are some of the ways in which bacteria cells defend themselves against phages.//-Andrew H. 14. Describe the reproductive cycle of an enveloped virus. Use specific examples. 15. List some characteristics that viruses share with living organisms and explain why viruses do not fit our usual definition of life. Similarities: grow, move, breathe, reproduce Different: Viruses can't replicate their genes or generate their own ATP.

why viruses don't fit our definition of life: []

EMILY H

16. Describe the evidence that viruses probably evolved from fragments of cellular nucleic acids.

===Because they do not form fossils, the origin of viruses if often difficult to determine. However, there exist several theories about the origin of viruses, and one of the most prominent theories is that viruses probably evolved from fragments of cellular nucleic acids. One strong piece of evidence that suggests that viruses may have evolved from fragments of cellular nucleic acids is the fact that eukaryotic virus genes are more similar to eukaryotic genes, and prokaryotic virus genes are more similar to prokaryotic genes. Also, viruses do not have a membrane as all other cells do, and rely on host cells to survive. Viruses can be thought of as sub-cellular parasites which infect living cells and then take over the cell's metabolic processes to produce more viruses. Viruses are not cells but they contain substances characteristically found only in living cells.===

-Tom Haile

Article Source: http://EzineArticles.com/2508355

17. Explain how viral infections in animals cause disease. ====viral infections enter the body, and weaken the immune system. This weakening prohibits the body from being able to protect itself against disease. [|WATCH!]==== Hannah 18.1Describe the mechanisms by which new viral diseases emerge. ==== There are 3 main mechanisms by which new viral diseases emerge. First, the mutation of existing viruses is considered to be the most critical mechanism. Various mutations are known to change existing viruses into brand new genetic strains that can cause disease, even to those who are said to be immune to the ancestral virus (ex. - flu / new strains of influenza). The next mechanism known comes from the dissemination of a viral disease from a small and isolated human population (ex. - AIDS). In the case of AIDS, the human population carried it via travel, blood transfusions and the abuse of drugs. The last possible mechanism in humans is the movement of viruses from other animals, as animals are able to transmit a virus but can be unaffected by the very virus that they transmit. (ex. - Swine flu from pigs) - Daniel Kogan ====