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Unit 9: Regulation of Gene Expression

Last updated

May 14, 2022
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- 8.8: rII Locus of T4
- 9.1: Regulation of Gene Expression in Bacteria

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9.1: Regulation of Gene Expression in Bacteria
This page discusses gene expression regulation in E. coli, focusing on the lac operon, which metabolizes lactose through a repressor mechanism. When lactose is present, it enables transcription by detaching the repressor. The page also covers the dual control by Catabolite Activator Protein (CAP), which requires cAMP for DNA binding, allowing prioritization of glucose over lactose.
9.2: The Tryptophan Repressor
This page explains the regulation of tryptophan synthesis in E. coli, which involves five enzymes from a clustered operon. When tryptophan is abundant, it binds to the Trp repressor, a homodimer that attaches to the operator of the operon, inhibiting transcription of the genes for enzyme production. This mechanism ensures that enzymes are not synthesized when tryptophan is already present, effectively regulating the metabolic pathway.
9.3: Regulation of Gene Expression in Eukaryotes
This page discusses human eukaryotic cells, which have about 21,000 genes. Some genes are constantly active (housekeeping genes), while others are regulated based on conditions. Gene expression regulation mainly occurs through transcription rate changes, but also involves RNA processing and translation. Eukaryotes use core promoters, enhancers, silencers, and insulators for gene control; insulators prevent errant activation, and enhancers coordinate gene expression.
9.4: Steroid Response Elements
This page presents a stereoscopic view of the glucocorticoid response element and its receptor, focusing on the structural features of DNA and the glucocorticoid receptor, a zinc-finger transcription factor important for gene regulation.
9.5: Epigenetics
This page discusses epigenetics, which involves heritable phenotype changes without DNA sequence alteration. It covers cellular differentiation, X-inactivation, and imprinting. Converting differentiated cells to induced pluripotent stem cells faces challenges in reversing epigenetic changes. DNA methylation and histone modifications lead to stable gene expression changes, regulated by key players known as "writers," "erasers," and "readers" that modify or recognize epigenetic marks.
9.6: Visualization of Transcription and Translation in Bacteria
This page describes an electron micrograph illustrating simultaneous transcription and translation in E. coli, highlighting polysomes formed by mRNA and ribosomes on the chromosome. It explains that RNA polymerase is responsible for transcription, while ribosomes carry out translation. This simultaneous coordination in bacteria contrasts with eukaryotes, where these processes occur separately in the nucleus and cytosol.
9.7: Footprinting
This page explains the technique of footprinting, which is used to identify DNA sequences where DNA-binding proteins attach. It involves cloning the DNA with the binding site, labeling it, and digesting it with DNase I to create radioactive fragments. Protein-bound regions, such as the lac repressor, remain undigested, resulting in gaps on an autoradiogram. By comparing these gaps to a DNA sequencing ladder, the specific base sequence of the operator can be determined.
9.8: Chromatin Immunoprecipitation
This page discusses DNA-binding proteins such as transcription factors that bind to specific DNA sequences in gene promoters and enhancers through reversible interactions. It highlights the chromatin immunoprecipitation (ChIP) technique for identifying these binding sites, which involves fixing protein-DNA interactions, fragmenting DNA, isolating complexes with antibodies, and analyzing the purified DNA fragments using methods like PCR, Southern blotting, or sequencing.
9.9: Isolating Transcription Factors
This page discusses the isolation of rare transcription factors, highlighting that they exist in low quantities within cells (e.g., E. coli's lac repressor). It explains the use of affinity chromatography, where DNA sequences specific to the repressor are attached to beads to capture and purify these factors, allowing for effective study amid a plethora of other proteins.
9.10: Palindromes
This page explains palindromes, which read the same forwards and backwards, and highlights their significance in DNA. It discusses how palindromes serve as target sequences for restriction enzymes and the role of inverted repeats in transcription factor binding. Additionally, it notes the presence of inverted repeats in transposons, retroviral genes, and the human Y chromosome, where they may improve gene repair through homologous recombination.
9.11: Cell-specific gene expression
This page discusses gene expression study methods, particularly using transgenic techniques in Drosophila with the even-skipped gene and beta-galactosidase for visualization. It highlights green fluorescent protein (GFP) for real-time monitoring in living cells and advancements in DNA chip technology for analyzing thousands of genes simultaneously.
9.12: Imprinted Genes
This page discusses imprinted genes, which have parent-specific expression, with around 80 identified in mammals and angiosperms. Examples include the paternal activation of IGF2 and maternal repression of IGF2r. Imprinting occurs during gamete formation via DNA methylation and can lead to disorders like Prader-Willi and Angelman syndromes, as well as cancers if misregulated.
9.13: Ribozymes
This page discusses ribozymes, RNA molecules with catalytic properties, which were discovered two decades ago, shifting the focus from proteins as the sole enzymes. It highlights their role in RNA processing, particularly in tRNA, rRNA, and mRNA, often through self-splicing. Key examples include ribonuclease P and Group I and II introns. Additionally, it touches on spliceosomes and viroids, noting that viroids can infect plants and exhibit self-splicing capabilities similar to ribozymes.

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