Expression Regulation

• Gene regulation


  Mechanisms for controlling which genes get expressed at which levels
• Operon


  Cluster of genes under control of a single promoter (all transcribed together) which usually have functions that work together so will have to happen at the same time anyways. Common in prokaryotes but rare in eukaryotes
• Regulatory protein


  Proteins that control how much of an operon is transcribed
• Inducer


  Small molecule capable of turning operons "on" from their usual "off" state
• Corepressor


  Small molecule capable of turning an operon "off"
• Housekeeping genes


  Genes whose products are constantly needed by the cell to maintain essential functions. Have promotors and other regulatory DNA sequences that ensure constant expression
• Lac operon 


  Operon that allows bacteria to use lactose as a fuel source when glucose is unavailable
• Operator


  Overlaps the lac promoter so that when it is there, RNA polymerase cannot bind to it, and so negatively regulates its use
• CAP binding site


  Positive regulator site bound by catabolite activator protein which helps RNA polymerase attach to transcribe proteins when bound
• Lac repressor


  Protein that inhibits the transcription of the lac operon by binding to the operator, which overlaps the promotor. When lactose is present, it loses its ability to bind and floats off, leaving it technically open for transcription
• Allolactose


  Isomer of lactose that is synthesized in small numbers when lactose is present. Inducer that changes the lac repressor shape so that it can no longer bind DNA
• Inducer


  Small molecule that triggers the expression of a gene or operon
• Inducible operon


  Operons that are usually repressed but can be turned on with the presence of an inducer (like the lac operon with allolactase)
• Catabolic activator protein


  CAP
• CAP


  Protein that binds to a region of DNA just before the promoter region that helps guide RNA polymerase attach to it, driving high levels of transcription. Necessary in the lac operon because it's not usually transcribed on its own
• CAP is generally produced in low glucose environments, because it needs cAMP to bind to the DNA. However, when glucose is high, there is less cAMP, so that's why the lac operon (which needs CAP to catalyze more transcription) only kicks in when there is low glucose and lactose available
• cAMP


  Hunger signal made by e coli when glucose levels are low. Needed to bind to CAP to activate the lac operon
• trp operon


  E coli operon used to synthesize its own tryptophan when it's not available in its environment
• Corepressor


  Small molecule like tryptophan that puts a repressor in its active state
• Attenuation


  Mechanism for reducing expression of the trp operon by stopping it from completing translation, even after it's been initiated, when tryptophan levels are high enough
• Chromatic accessibility


  Type of gene regulation where more relaxed chromatin is easier to transcribe than more tightly wound chromatin
• Transcription


  Key regulatory point for many genes where the available transcription factors for specific genes could repress or increase their expression
• RNA processing


  Gene expression regulation that involves different RNAs being made from the same RNA through alternative splicing
• RNA stability


  Gene expression factor that has to do with how long an mRNA floats in the cytosol relating to how many proteins can be synthesized from it. miRNAs play a role too because they can chop up mRNAs if they're excessive
• Translation


  Gene expression factor that has to do with how much an mRNA is turned into proteins. Influenced by regulators that can increase it or decrease it
• Protein activity


  Gene expression factor that has to do with how a protein acts after it's been synthesized (like if it's been tagged or chopped up)
• Transcription factors


  Proteins that help turn genes "on" or "off" by binding to nearby DNA
• Basal transcription factors


  Part of a eukaryotic cell's core transcription toolkit which is needed for RNA polymerase to attach to the promoter on the gene's DNA
• Activators


  Transcription factors that make transcription happen, like by helping basal transcription factors and/or RNA polymerase bind to the promoter
• Repressors


  Transcription factors that inhibit transcription, like by getting in the way of RNA polymerase and/or basal transcription factors so they can't get to promotors and begin transcription
• Binding sites for transcription factors can sometimes be far from the promotor because DNA loops back on itself and folds so that they're essentially next to each other anyways
• A gene that has to be expressed in more than one body part or cell type will probably have enhancers to activate where it needs to be activated and silencers for the opposite
• Tissue specific enhancers


  Enhancers that control a gene's expression in certain parts of the body. Mutations in these cause changes in body form, whereas mutations in the gene itself would probably be fatal
• Combinatorial regulation


  When a gene is controlled by several transcription factors, and so needs several conditions to turn on, like an actual coding logic system. Foe example, only if activators A and B are present but repressor C is absent