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Genetics Eukaryotic gene Expression (Ch 7)

by: Jazmine Burnam

Genetics Eukaryotic gene Expression (Ch 7) BIOL 3451

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Jazmine Burnam

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This is the study guide for Ch 17 gene expression regulation in eukaryotes. This will be covered in Exam 4 which is less than a week away. I've filled out everything in detail and all you guys have...
Dr. Padilla
Study Guide
Genetics, Exam 4, Gene Expression, eukaryotes, Eukaryotic gene expression, Padilla, Pamela Padilla, Spring 2015
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This 14 page Study Guide was uploaded by Jazmine Burnam on Monday April 11, 2016. The Study Guide belongs to BIOL 3451 at University of North Texas taught by Dr. Padilla in Spring 2016. Since its upload, it has received 189 views. For similar materials see Genetics in Biology at University of North Texas.


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Date Created: 04/11/16
Study Guide- Euk Gene expression 1. Describe how the following have a role in or impact gene expression: a. Nuclear territories: are regions of the nucleus preferentially occupied by particular chromosomes.  Where chromosomes reside  DNA not random  Can change depending on cell type and environment  Variability in condensation (how tightly wound the chromosomes are) b. Enhancer Element: regulatory DNA sequences that, when bound by specific proteins called transcription factors, enhance the transcription of an associated gene.  An array short (<10 bp) sequence elements  also bind transcription factors  May be located several to many kb distant.  have the ability to greatly increase the expression of genes in their vicinity c. Silencing Element: A DNA sequence that transcription factors known as repressors can recognize and bind to, thereby (more or less) blocking access to a gene and preventing its transcription  lowers the rate of initiation of transcription of eukaryotic genes  When transcription factors bind to them, expression of the gene they regulate is repressed. d. DNA & histone contact/interaction: e. SWI/SNF complex: an evolutionarily conserved multi-subunit chromatin-remodeling complex, which uses the energy of ATP hydrolysis to mobilize nucleosomes and remodel chromatin. Study Guide- Euk Gene expression f. DNA methylation: a process by which methyl groups are added to DNA. Methylation modifies the function of the DNA  epigenetic mechanism used by cells to control gene expression  Commonly used epigenetic signaling tool that can fix genes in the “off” position. g. Histone deacetylation: removes acetyl groups from histone tails, causing the histones to wrap more tightly around the DNA and interfering with the transcription of genes by blocking access by transcription factors.  Overall result of histone deacetylation is a global (nonspecific) reduction in gene expression.  Is involved in a series of pathway in the living system. h. Histone acetylation complex: For transcription to occur, the area around a prospective transcription zone needs to be unwound.  This is a complex process requiring the coordination of histone modifications, transcription factor binding and other chromatin remodeling activities.  Once the DNA is open, specific DNA sequences are then accessible for specific proteins to bind i. microRNAs: gnomically-encoded, untranslated RNA molecules of approximately 20-25 nucleotides  regulate diverse processes Study Guide- Euk Gene expression j. DNA demethylation: the process of removal of a methyl group from nucleotides in DNA k. cis elements: DNA sequences that regulate the expression of a gene located on the same chromosome l. transcription factors: A DNA binding protein that binds to specific sequences adjacent to or within the promoter region of a gene; regulates gene transcription m. Dispersed promoter: direct initiation from a number of weak transcription start sites located over a 50- to 100 nucleotide region. 2. Give an example of how the post-translational modification of histones plays a role in gene expression?  Can have profound impacts of phenotype (male vs female)  Control of Alternative splicing  Mature RNA  mRNA stability Study Guide- Euk Gene expression  RNA silencing 3. Describe three common structural motifs observed in transcription factors.  Zinc Finger o interacts with amino acids o contains clusters of two cysteines and two histidine’s at repeating intervals o Clusters bind zinc atoms, fold into loops, and interact with specific DNA sequence o  Helix Tuned Helix o Interacts with DNA o Presence of two adjacent alpha helices separated by a “turn” of several amino acids enables the protein to bind to DNA Study Guide- Euk Gene expression  Leucine Zipper o Interacts as 2 individual polypeptides interacting with each other o Allows protein-protein dimerization o When two bZIP containing molecules dimerize, the leucine residues “zip” together o Resulting dimer contains 2 basic alpha helical regions adjacent to the zipper that bind to the phosphate residues and specific bases in their DNA-binding site. 4. What is the role of a transcription factor in gene expression? How does the function of general transcription factors (such as TATA Study Guide- Euk Gene expression binding protein) differ from the role of specific transcription factors (such as SRY protein or MTF1 protein)?  Role: o Help proteins find the DNA (affect various genes) o Regulates gene transcription  How function of general T-factors differ from the role of specific T-factors: o General transcription factors are proteins that help form the pre- imitation complex responsible for the start of transcription in all class II genes. o Specific transcription factors can be a wide variety of proteins involved in modulation of transcription processes, i.e. inhibition, activation and can be classed according to structure and function. Describe in general how gene regulation can occur based on environment. Use the Human metallothionein IIA gene as an example as to how a specific environment can regulate gene expression.  How gene regulation can occur based on environment IIA gene o Gene is expressed at low levels within all cells but high levels when cells are exposed to heavy metals or steroid hormones (glucocorticoids)  Enhancers: (MRE, metal response elements; GRE, glucocorticoid response elements)  Silencers: PZ120 repressor 5. How does alternative splicing impact diversity of gene products? In your answer provide an example. Study Guide- Euk Gene expression  How It Impacts Diversity: o Can generate different forms of mRNA from identical pre-mRNA molecules, so that expression of one gene can give rise to a number of proteins, with similar or different functions o Increases the number of proteins that can be made from each gene  EX: Alternative splicing of the Dscam gene o Encodes a protein that guides axon growth during development o Gene contains various alternatives for exons o Leads to diversity of gene products o Spliced into the mature mRNA in an exclusive fashion so that each exon is represented by no more than one of its possible alternatives 6. How does alternative splicing impact sex differentiation in Drosophila?  Sex differentiation: o Ratio of X chromosomes to autosomes (AA) affects transcription of the Sxl gene o The presence of SXL protein begins a cascade of pre-mRNA splicing events that culminate in female-specific gene expression and production of the DSX-F transcription factor. o In the absence of SXL protein, a male-specific pattern of pre- mRNA splicing results in male-specific patterns of gene expression induced by the DSX-M protein Study Guide- Euk Gene expression However, in male cells it is spliced in such a way that a stop codon remains in the mRNA leading to a nonfunctional TRA protein in male cells. In female cells the TRA protein influences proteins important Sxl will affect splicing of various pre-mRNAs (tra mRNA) in both male and female cells.for female differentiation 7. Given the diagram below- diagram the two potential mRNA products expressed from this gene.  1-2-3-4-Poly A tail (top) red arrow like things indicate removal of introns o Results in the product Calcitonin peptide Study Guide- Euk Gene expression  1-2-3-5-6-poly A tail (bottom) removes the 4 th exon as well as all the introns o Results in the product CGRP peptide (Calcitonin gene related peptide) 8. What does the data, shown in the image below, indicate? In your answer include why these type of experiments are conducted.  Summarizes the transcriptional effects of mutations in the CAAT box and other promoter elements  Dots=nucleotides for which no mutation was tested  Mutations within specific elements have the greatest effects on the level of transcription Each line represents the level of transcription produced in a separate experiment by a single nucleotide mutation at a particular location 9. Describe what the image below is noting in regards to the regulation of the hMTIIA gene.  Contains multiple cis-acting regulatory sites  Transcription factors control basal and induced levels of hMTIIA  hMTIIA codes for a protein that binds to heavy metals (Zinc, Cadmium)  Gene is expressed at low levels within all cells but high levels when cells are exposed to heavy metals or steroid hormones (glucocorticoids) o Enhancers: (MRE, metal response elements; GRE, glucocorticoid response elements) o Silencers: PZ120 repressor  Cellular environment will influence gene expression via signaling pathways 10. Define Spliceopathy. How a DNA mutation (in this case an expansion of a trinucleotide repeat) in a gene that has no functional role in splicing (DM1) impact splicing indirectly.  Spliceopathy: A mutation of splicing that causes the disease known as myotonic dystrophy  Myotonic dystrophy o Defect in alternative RNA splicing o Form of muscular dystrophy (1 in 8000, autosomal dominant) o DM1 and DM2 o Muscle wasting, insulin resistance, cataracts, testicular atrophy, cardiac problems o DM1: caused by expansion of CTG in the 3’ UTR of DMPK Gene; 150- 2000 repeats o DM2: CCTG expansion ZNF9 gene o RNA’s produced, accumulate in nucleus, sequester proteins involved with splicing 11. Think about the multiple mechanisms in which gene expression is regulated in a eukaryotic cell. Is every gene subjected to the same level of regulation? Can you propose how genes that are involved in similar processes may be co-regulated? Is every gene subjected to the same level of regulation o Different cells express different proteins  Example, an individual's neurons will express different proteins than their liver cells. This reflects the different structures, activities and functions of these two very distinct cell types o Even for a single cell, the gene expression pattern may change during the different phases of the cell cycle or in response to extracellular signals o Some genes are expressed in all cells;  For example, those that encode the structural proteins and proteins involved in common cellular pathways such as DNA replication and translation. These are commonly referred to as housekeeping genes. o Other genes encode more specialized proteins that may only be expressed in one cell type  Ex. insulin in the islet cells of the pancreas How genes may be co-regulated o It is thought that genes with similar patterns of mRNA expression and genes with similar functions are likely to be regulated via the same mechanisms o Genes can't control an organism on their own; rather, they must interact with and respond to the organism's environment. 12. How does DNA rearrangement lead to diversity in immune response?  DNA rearrangement o Occurs during development of beta cells o Can regulate gene expression  Mammals capable of producing hundreds of millions of different types of antibodies in response to the presence of a wide variety of antigens  DNA encoding the immunoglobin genes is not fixed but undergoes multiple programmed changes, including deletions, translocations, and random mutations 13. Define microRNAs. How were microRNAs identified? What is the cellular role of microRNAs?  MicroRNAs: o Gnomically-encoded, untranslated RNA molecules of approximately 20-25 nucleotides  How were they Identified: o Victor Ambros and colleagues identified the first miRNA in elegans o The lin-4 gene encoded a small RNA that imperfectly base-paired to complementary sequences on target messenger RNAs (mRNAs) in order to block gene expression o A second miRNA, let-7, was discovered by Gary Ruvkun's group to direct the later stages of C. elegans development o Evolutionarily conserved from flies to humans, implicating a more universal role for these genes in animals  the cellular role of microRNAs: o regulate diverse processes o regulate gene expression by participating in the degradation of mRNAs


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