Term
| activation domain does what |
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Definition
| recruits the transcription machinery |
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Term
| basic region/leucine zipper (bzip) protein |
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Definition
| is usually found as part of a DNA binding domain in various transcription factors, and are therefore involved in regulating gene expression. Functions as a dimerizaiton domain. Its presence generates adhesion forces in parallel alpha helices. |
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Definition
| One part of the domain contains a region that mediates sequence specific DNA properties and the leucine zipper that is required for the dimerization of two DNA binding regions. |
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| is a distinct pattern of nucleotides with GGCCAATCT consensus sequence that occure upstream by 75-80 bases to the initial transcription site. It signals the binding site for the RNA transcription factor -located upstream from the TATA box (in eukaryotes) |
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Definition
| is the enzyme assisted movement of nucleosomes on DNA. At the core of a chromatin remodeling complexes is an ATPase capable of DNA translocation. By moving nucleosomes, transcription factors can get access to DNA that was unavailable. |
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Term
| DNA affinity chromatography |
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Definition
| a method of separating biochemical mixtures and based on a highly specific biological interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand. |
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| s a short region of DNA that can be bound with proteins (trans-acting factors much like transcription factors) to enhance transcription levels of genes. Enhancers are usually cis acting but it does not need to be particularly close to the genes it acts on., and sometimes not even on the same chromosome. It is typically close to the promoter and the gene. |
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Definition
| is a lightly packed form of chromatin that is rich in gene concentration and is often, but not always, under active transcription. Is the most active portion of the genome within the cell nucleus. |
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Definition
| is a biochemical method used to study gene expression and function in organisms such as the fruit fly. Has two parts, the GAL4 gene, which encodes the yeast transcription activator protein Gal4 and the UAS (upstream activation sequence) a short section of the promoter region to which Gal4 specifically binds to activate gene transcription. |
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Definition
| Is the process of combining two or more sequences that would not normally occur together |
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Definition
| is characterized by two a-helicies connected by a loop. The larger helix typically contains the DNA binding regions. |
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Definition
| is a tightly packed form of DNA which comes in different varieties. These varieties lie on a constitutive and facultative. |
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Definition
| are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl CoA to fomr E-N-acetyl lysine. In general it is linked to transcriptional activation and associated with euchromatin. |
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Term
| histone deacetylase (HDAC) |
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Definition
| are a class of enzymes that remove acetyl groups from an E-N-acetyl lysine amino acid on a histone. It is opposite that of HAT |
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Definition
| is a DNA sequence found within genes that are involved in the regulation of patterns of anatomical development in animals, fungi, and plants. It is about 180 base pairs long and encodes a protein domain (homeodomain) which when expressed can bind DNA. |
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Definition
| is a protein structural domain that binds DNA or RNA and is thus commonly found in transcription factors. Has three alpha helicies and it is the third helix that interacts directly with DNA. |
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Definition
| are genes that determine which parts of the body form what what body parts. |
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Definition
| is a short sequence of DNA within the promoter of a a gene that is able to bind a specific hormone receptor complex and therefore regulate transcription. The sequence is most commonly a pair of inverted repeats separated by three nucleotides which also indicates that the receptor binds as a dimer. |
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Definition
| is a motif that is involved as part of a DNA binding domain in various transcription factors, and are therefore involved in regulating gene expression. It involves parallel alpha helices, with a hydrophobic region running along one side. |
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Term
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Definition
| Ligand binding to a receptor alters the chemical conformation (3-D shape). This affects the functional state of the a receptor. |
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Term
| linker-scanning mutagenesis |
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Definition
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Definition
| are a class of proteins found within cells that are responsible for sensing steroid and thyroid hormones and certain other molecules. These work with other proteins to regulate the expression of specific genes, thereby controlling development, homeostasis, and metabolism of the organism. |
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Definition
| (POU comes from the three transcription factors that are used) are eukaryotic transcription factors containing a bipartite DNA binding domain |
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Definition
| is a complex with the capacity to remodel the structure of chromatin. It exhibits a DNA dependent ATPase activity stimulated by both free and nucleosomeal DNA and a capacity to perturb nucleosome structures. |
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Term
| transcription activator protein do what? |
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Definition
| they help recruit the transcription machinery |
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Term
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Definition
| this utilizes a genetically engineered strain of yeast in which the biosynthesis of certain nutrients (usually amino acids or nucleic acids) is lacking. When grown on a media that lacks these nutrients, the yeast dies. This mutant yeast strain can be made to incorporate foreign DNA in the form of plasmids |
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Term
| upstream activating sequence (UAS) |
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Definition
| is a cis-acting regulatory sequence. It is distinct from the promoter and increases the expression of a neighboring gene. Its binds GAL4 |
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Term
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Definition
| is a protein structural motif that can coordinate one or more zinc ions to help stabilize their folds. They function as interaction modules that bind DNA, RNA, proteins, or small molecules. |
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Term
| What are the types of DNA binding domains? |
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Definition
| Zinc fingers, helix-turn-helix structures, basic region/ leucine zipper proteins and helix-loop-helix motifs. |
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Term
| What has been a key technique in identifying promoter elements |
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Definition
| Linker scanning mutagenesis |
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Term
| What binds just upstream of the core promoter elements to bind specific transcription activator protein? |
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Definition
| Promoter proximal elements |
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Term
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Definition
| They modulate transcription and can act at a great distance from the promoter. |
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Term
| The DNA binding domain of transcription activators make sequence specific contacts with ____ or ______? |
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Definition
| Enhancers or promoter proximal elements |
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Term
| The _____ ______ recruits the transcription machinery |
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Definition
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Term
| Nuclear localization and nuclear export signals do what? |
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Definition
| They permit activator proteins to move into or out of the nucleus. |
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Term
| What can be used to purify activator proteins? |
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Definition
| DNA affinity chromatography. |
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Term
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Definition
| they encode important transcriptional activators called homeobox proteins that help define the body axes during development. |
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Term
| The homeodomain of a homeobox protein contains what? |
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Definition
| a helix-turn-helix motif for DNA binding. |
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Term
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Definition
| Both a homeobox and a POU domain for DNA binding. |
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Term
| What is the classical zinc finger model |
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Definition
| Cys2His2- zinc residues are bound by two Cys and two His residues |
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Term
| Nuclear receptors have ____ ____ motifs. The nuclear receptors have a common structural design and are _____ or _____ with a recognition helix that bind to a hormone response element. |
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Definition
| Zinc Finger, homodimers or heterodimers. |
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Term
| _____ proteins bind to DNA as dimers that are held together through coiled coil interactions. |
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Definition
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Term
| Where do activator proteins with a helix-loop-helix motif bind as dimers? |
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Definition
| To the major groove of DNA |
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Term
| In an activator, what must be bound to a DNA binding domain to stimulate transcription? |
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Definition
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Term
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Definition
| They can work through recruitment of the transcriptional machinery or by inducing a conformational change in the transcriptional machinery. |
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Term
| What is one of the best studied transcriptional activators? What has it shown? |
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Definition
| Gal4- It has been shown that the activation domain cannot stimulate transcription without a DNA binding domain. |
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Term
| Chromatin remodeling factors do what |
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Definition
| They alter histone-DNA or histone-histone interactions to make DNA accessible to the transcription machinery. These complexes work without producing covalent modification in chromatin. |
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Term
| Modifying complexes does what? |
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Definition
| it modifies the histone tails to activate or repress transcription. |
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Term
| What tends to activate transcription? What tends to repress transcription? |
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Definition
| Acetylation by HATs, Histone deacetylation by HDACs. |
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Term
| Chromatin remodeling and chromatin modifying complexes interact how? |
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Definition
| They interact with each other and with the transcription machinery to condense or decondense DNA to silence genes or make genes transcriptionally active |
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Term
| Enhancers differ from other regulatory sequences in what way? |
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Definition
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Term
| Each transcription activator protein has at least two independently folding domains: an activation domain and what |
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Definition
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Term
| Genes that assign positional identities to cells along the anterior posterior axis of an embryo are called ____ genes |
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Definition
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Term
| The helix turn helix motif or homeodomain is required for ____ |
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Definition
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Term
| In a classical zinc finger, zinc ions... |
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Definition
| interact with histidine and methionine residues |
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Term
| Members of the nuclear receptor superfamily are induced to activate transcription by___? |
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Definition
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Term
| One reason that the number of nuclear receptors is greater than the total number of genes encoding nuclear receptors is that____? |
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Definition
| The proteins form heterodimers |
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Term
| Leucine zippers are characterized by ___ |
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Definition
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Term
| Leucine zippers have ____ DNA binding domains? |
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Definition
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Term
| What does the b stand for in bZip of bHLH? |
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Definition
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Term
| Myc, Max, and Mad are transcription factors of the ___ family. |
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Definition
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Term
| Transcription will be stimulated as long as the DNA-binding domain and activation domain____. |
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Definition
| are both present, either covalently or noncovalently linked |
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Term
| What are two possible ways an activator protein can affect transcription? |
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Definition
1. recruits transcriptional machinery
2. induces a conformational change in the transcriptional apparatus that stimulates transcription initiation. |
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Term
| Euchromatin, which contains many _____, is usually ____ accessible to transcription machinery |
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Definition
| protein coding genes; more |
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Term
| Histone deacetlyation lowers transcriptional activity by _____ |
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Definition
| stabilizing compact chromatin structure |
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Term
| What are known post-translational histone modifications |
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Definition
1. Serine phosphorylation
2. lysine methylation
3. lysine ubiquitination |
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Term
| A DNA that serves as a binding site for proteins that create a repressive chromatin environment is called a |
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Definition
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