Term
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Definition
| The process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes. During transcription, a DNA sequence is read by RNA polymerase, which produces a complementary, antiparallel RNA strand. As opposed to DNA replication, transcription results in an RNA complement that includes uracil (U) in all instances where thymine (T) would have occurred in a DNA complement. |
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Term
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Definition
| A protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to mRNA. Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific genes. |
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Term
| T or F: Only alterations in genes themselves(coding SNPs)account for differences in health among individuals. |
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Definition
| False! Alterations in gene expression levels (regulatory SNPs)can account for these differences. |
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Term
| What are the polymerases that exist in eukaryotic cells? |
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Definition
1) RNA polymerase I (Pol I) - Transcribes most rRNA genes.
2) RNA polymerase II (Pol II) - Transcribes all protein-coding genes, plus some genes for small RNAs (e.g., those in spliceosomes).
3) RNA polymerase III (Pol III) - Transcribes tRNA genes, 5S rRNA gene, and genes for some small structural RNAs. |
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Term
| What is transcribed by RNA polymerase I? |
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Definition
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Term
| What is transcribed by RNA polymerase II? |
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Definition
| All protein-coding genes, plus some genes for small RNAs (e.g., those in spliceosomes). |
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Term
| What is transcribed by RNA polymerase III? |
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Definition
| tRNA genes, 5S rRNA gene, and genes for some small structural RNAs. |
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Term
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Definition
| An enzyme that produces RNA. In cells, RNAP is needed for constructing RNA chains from DNA genes as templates, a process called transcription. |
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Term
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Definition
| A region of DNA that facilitates the transcription of a particular gene. Promoters are located near the genes they regulate, on the same strand and typically upstream (towards the 5' region of the sense strand). In order for the transcription to take place, the enzyme that synthesizes RNA, known as RNA polymerase, must attach to the DNA near a gene. Promoters contain specific DNA sequences and response elements which provide a secure initial binding site for RNA polymerase and for proteins called transcription factors that recruit RNA polymerase. These transcription factors have specific activator or repressor sequences of corresponding nucleotides that attach to specific promoters and regulate gene expressions. |
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Term
| What is required by RNA polymerase II at the promoter? |
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Definition
| General transcription factors (e.g. TFIID, TFIIA, TFIIB, TFIIE, TFIIF, TFIIH, and others). However, although necessary, this is not sufficient; gene specific regulatory proteins are also required. |
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Term
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Definition
| A DNA sequence (cis-regulatory element) found in the promoter region of genes. Considered to be the core promoter sequence, it is the binding site of either general transcription factors or histones (the binding of a transcription factor blocks the binding of a histone and vice versa) and is involved in the process of transcription by RNA polymerase. Simply put, it's a DNA sequence that indicates the point at which a genetic sequence can be read and decoded. |
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Term
| TATA-binding protein (TBP) |
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Definition
| A transcription factor that binds specifically to a DNA sequence called the TATA box. This DNA sequence is found about 35 base pairs upstream of the transcription start site in some eukaryotic gene promoters. TBP, along with a variety of TBP-associated factors, make up the TFIID, a general transcription factor that in turn makes up part of the RNA polymerase II preinitiation complex. As one of the few proteins in the preinitiation complex that binds DNA in a sequence-specific manner, it helps position RNA polymerase II over the transcription start site of the gene. TBP is involved in DNA melting (double strand separation) by bending the DNA by 80° (the AT-rich sequence to which it binds facilitates easy melting). The TBP is an unusual protein in that it binds the minor groove using a β sheet. |
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Term
| Transcription (pre)initiation complex |
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Definition
| A large complex of proteins that is necessary for the transcription of protein-coding genes in eukaryotes. The preinitiation complex helps position RNA polymerase II over gene transcription start sites, denatures the DNA, and positions the DNA in the RNA polymerase II active site for transcription. Typically the PIC is made up of six general transcription factors: TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH. |
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Term
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Definition
| A short region of DNA that can be bound with proteins (transcription factors) to enhance transcription levels of genes. An enhancer may be located upstream or downstream of the gene that it regulates. Furthermore, an enhancer does not need to be located near to the transcription initiation site to affect the transcription of a gene, as some have been found located in several hundred thousand base pairs upstream or downstream of the start site. Enhancers do not act on the promoter region itself, but are bound by activator proteins. These activator proteins interact with the mediator complex, which recruits polymerase II and the general transcription factors which then begin transcribing the genes. |
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Term
| How do gene regulatory proteins (aka transcription factors) work? |
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Definition
Transcription factors work through two general mechanisms:
1) By helping to recruit Pol II machinery (via contacts with “Mediator complex” to bring Pol II transcription machinery to promoter).
2) By helping recruit chromatin modifying enzymes to "open up" chromatin. |
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Term
| How do transcription factors help recruit Pol II machinery? |
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Definition
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Term
| T or F: Transcription factors necessarily upregulate a gene's expression. |
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Definition
| False. Transcription factors can either upregulate or downregulate a gene's expression. For example, certain transcription factors can block the binding of RNA polymerase to the DNA strand. |
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Term
| Activator proteins (gene specific transcription factors) help recruit Pol II machinery (cartoon). |
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Definition
[image]
An activator protein bound in proximity to promoter attracts RNA polymerase complex and general transcription factors to the promoter. Looping of the DNA permits contact between the activator protein bound to the enhancer and the transcription complex bound to the promoter. In the case shown here, a large protein complex called the mediator serves as the go-between. |
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Term
| What are the two major classes of modifying enzymes used to “open up” chromatin to allow transcription? |
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Definition
1)Histone modifying enzymes - covalently modify amino acid side chains of histones.
2) ATP-dependent remodeling enzymes - evict or translocate nucleosomes. |
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Term
| How do histone modifying enzymes (e.g. histone acetylase (HAT)) allow transcription? |
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Definition
Histone tails are normally positively charged due to amine groups present on their lysine and arginine amino acids. These positive charges help the histone tails to interact with and bind to the negatively charged phosphate groups on the DNA backbone. Acetylation, which occurs normally in a cell, neutralizes the positive charges on the histone by changing amines into amides and decreases the ability of the histones to bind to DNA. This decreased binding allows chromatin expansion, permitting genetic transcription to take place.
Oversimplification: histones carry + charge, DNA a - charge. Acetylation of histones makes them less positive, and they stick less well to DNA. |
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Term
| How do histone deacetylase prevent gene transcription? |
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Definition
| Histone tails are normally positively charged due to amine groups present on their lysine and arginine amino acids. These positive charges help the histone tails to interact with and bind to the negatively charged phosphate groups on the DNA backbone. Acetylation, which occurs normally in a cell, neutralizes the positive charges on the histone by changing amines into amides and decreases the ability of the histones to bind to DNA. This decreased binding allows chromatin expansion, permitting genetic transcription to take place. Histone deacetylases remove those acetyl groups, increasing the positive charge of histone tails and encouraging high-affinity binding between the histones and DNA backbone. The increased DNA binding condenses DNA structure, preventing transcription. |
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Term
| How do ATP-dependent remodeling enzymes alter chromatin structure to allow for transcription? |
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Definition
| They use the energy of ATP hydrolysis to locally disrupt or alter the association of histones with DNA. |
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Term
| Rubinstein-Taybi syndrome |
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Definition
A specific pattern of physical features
and developmental disabilities which
occur together in a consistent fashion.
Individuals with Rubinstein-Taybi
syndrome have short stature,
developmental delay, similar facial
features, and broad thumbs and first
toes. Approximately 1 out of 300,000
persons has the Rubinstein-Taybi
syndrome. The condition occurs with
equal frequency in males and females. The identified affected gene is called
“CAAT-enhancer Binding Protein” (CBP),
a HAT enzyme that binds CREB, a key
transcription activator for learning and
memory genes in hippocampus cells. |
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Term
| T or F: Both mechanisms of transcription factor function(Pol II recruitment; chromatin structure alteration)likely operate at the same promoter. |
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Definition
| True. They do. They just do. |
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Term
| T or F: Repressors and operators like those found in bacteria (e.g. Trp operon- Lec 2-6) are generally observed in eukaryotes. |
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Definition
| False. Repression in eukaryotes often acts via chromatin and is often referred to as “transcriptional silencing” |
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Term
| What is the difference between general transcription factors and gene regulatory proteins? |
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Definition
| General transcription factors assemble on all promoters transcribed by Pol II. Gene regulatory proteins are specific to a gene and serve to fine-tune expression levels. |
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Term
| What is one major way in which bacterial and eukaryotic cells differ in terms of DNA transcription? |
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Definition
| Bacterial RNA polymerases can initiate transcription without the help of additional proteins (e.g. trp operon) whereas eukaryotic RNA polymerases can't-- they require the help of general transcription factors. |
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Term
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Definition
| Toxin present in the poisonous mushroom Aminita sp. Affects RNA polymerase II activity. |
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Term
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Definition
| A general transcription factor that is a protein kinase. Its action of phosphorylation is thought to help the polymerase disengage from the promoter so RNA synthesis can begin. |
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Term
| How is transcription of a eukaryotic gene initiated by RNA polymerase II? |
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Definition
1)The promoter contains a DNA sequence called the TATA box, which is located 25 to 30 nucleotides away from the site where transcription is located.
2) The TATA box is recognized and bound by transcription factor TFIID, which then enables the adjacent binding of TFIIB.
3) The rest of the general transcription factors as well as the RNA polymerase itself assemble at the promoter.
4) TFIIH then uses ATP to phosphorylate RNA polymerase II, changing its conformation so that the polymerase is released from the complex and is able to start transcribing. |
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Term
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Definition
| The entire expanse of DNA involved in regulating transcription of a gene. (Includes promoter and regulatory sequences.) |
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Term
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Definition
| A segment of DNA where regulatory proteins such as transcription factors bind preferentially. These regulatory proteins bind to short stretches of DNA called regulatory regions, which are appropriately positioned in the genome, usually a short distance 'upstream' of the gene being regulated. By doing so, these regulatory proteins can recruit another protein complex, called the RNA polymerase. In this way, they control gene expression and thus protein biosynthesis. |
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Term
| What is the difference between a promoter, regulatory sequence, and an enhancer? |
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Definition
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Term
| What is the benefit of having so many gene regulatory proteins? |
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Definition
Gene regulatory proteins allow for fine-tuned expression levels. Specifically:
- Gene regulatory proteins allow individual genes of an organism to be turned on or off specifically.
- Different selections of gene regulatory proteins are present in different cell types and thereby direct the patterns of gene expression that give each cell type its unique characteristics.
- Each gene in a eukaryotic cell is regulated differently from nearly every other gene. |
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Term
| What is the main function of gene activators? |
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Definition
To attract, position, and modify the general transcriptions factors and RNA polymerase II at the promoter so that transcription can begin. They do this by:
1) Acting directly on the transcriptional machinery itself, and
2) Changing the chromatin structure around the promoter. |
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Term
| T or F: DNA-bound activator proteins typically increase the rate of transcription by up to 1000-fold. |
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Definition
| True. Yup, better believe that shit! |
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Term
| Histone acetyltransferases (HAT) |
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Definition
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Term
| Histone deacetylases (HDAC enzymes) |
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Definition
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Term
| What sort of enzymes activate gene expression? |
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Definition
| Histone acetyltransferases (HAT enzymes). |
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Term
| What sort of enzymes inhibit gene expression? |
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Definition
| Histone deacetylases (HDAC enzymes). |
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Term
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Definition
| Caused by a deficit in a protein called MeCP2. The MeCP2 protein has two major functional domains: the methyl-binding domain (MBD) which binds specifically to DNA at methylated CpGs, and a transcription repression domain (TRD) that is responsible for recruiting other proteins that mediate transcription repression, such as HDAC enzyme. This results in the deacetylation and condensation of chromatin, which is now not accessible to the transcription to the transcription machinery. Thus, genes in the region of DNA that MeCP2 binds are not expressed. |
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Term
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Definition
| The phenomenon of eukaryotic gene regulatory protein networks, rather than functioning individually to turn a gene on or off, working as part of a “committee” of regulatory proteins, all of which are necessary to express the gene in the right cell, in response to the right conditions, at the right time, and at the required level. This principle of cooperativity allows eukaryotic promoters to act as binary switches; that is, all conditions for expression of the respective gene must be met before the promoter will fire. There are thought to be, on average, between four and eight qualitatively different inputs (i.e. transcription factors/complexes) per human gene. The human genome encodes ~1,850 distinct transcription factors (PNAS, 2002, 99:546). Enhancers tell genes which ones to listen to. Some activators for a given gene function by “polymerase recruitment”, while others alter chromatin structure, or else recruit chromatin structure-altering enzymes. The combination of these effects leads to transcription initiation. |
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Term
| T or F: The same transcription factors assemble to regulate expression of all genes. |
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Definition
| False. Although the general transcription factors that assemble at the promoter are the same for all genes transcribed by polymerase II, the gene regulatory proteins and the locations of their binding sites relative to the promoters are different for different genes. The effects of multiple gene regulatory proteins combine to determine the rate of transcription initiation. |
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Term
| How does repression happen in eukaryotic cells? |
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Definition
| Repression acts via chromatin structure (e.g. through the activities of HDAC). |
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Term
| What are the two basic domains of a transcription factor? |
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Definition
1) The activation domain - provides function.
2) The DNA-binding domain - provides specificity. |
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Term
| Where do most gene regulatory proteins interact with DNA? |
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Definition
| Most often they fit into the major groove of DNA and form tight associations with a short stretch of base pairs. |
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Term
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Definition
| Stable folding patterns often assumed by proteins responsible for gene regulation in order to (most often) interact with the major helix of DNA. |
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Term
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Definition
[image]
A structural motif in many DNA-binding proteins. It consists of three linked alpha helices, which are shown as cylinders in this figure. Most of the contacts with the DNA bases are made by helix number 3 (which is seen end-on in [B]). The asparagine (Asp) in this helix contacts an adenine in the manner shown.
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Term
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Definition
[image]
Built from an alpha helix and a beta sheet (the latter shown as a twisted arrow) held together by a molecule of zinc (indicated by a sphere). Zinc fingers are often found in clusters covalently joined together to allow the alpha helix of each finger to contact the DNA bases in the major groove. The illustration here shows a cluster of three zinc fingers. |
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Term
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Definition
[image]
This DNA- binding motif is formed by two alpha helices, each contributed by a different protein molecule. Leucine zipper proteins thus bind to DNA as dimers, gripping the double helix like a clothes pin on a clothes line. These three motifs are found in gene regulatory proteins in virtually all eukaryotic organisms, where they are responsible for controlling the expression of thousands of different genes. |
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Term
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Definition
| The alpha-helix of the gene regulatory protein contacting the major groove of DNA. |
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Term
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Definition
| A structural motif capable of binding DNA. It is composed of two α helices joined by a short strand of amino acids and is found in many proteins that regulate gene expression. It binds to the major groove of DNA through a series of hydrogen bonds and various Van der Waals interactions with exposed bases. The other α helix stabilizes the interaction between protein and DNA, but does not play a particularly strong role in its recognition. |
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Term
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Definition
A protein structural motif that characterizes a family of transcription factors. The motif is characterized by two α-helices connected by a loop. In general, transcription factors including this domain are dimeric, each with one helix containing basic amino acid residues that facilitate DNA binding. In general, one helix is smaller, and, due to the flexibility of the loop, allows dimerization by folding and packing against another helix. The larger helix typically contains the DNA-binding regions.
Helix-loop-helix motifs are related to the leucine zipper. |
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Term
| Helix-turn-helix (cartoon) |
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Definition
[image]
Each white circle denotes the central carbon of an amino acid. The C-terminal α helix (red) is called the recognition helix because it participates in sequence-specific recognition of DNA. As shown in (B), this helix fits into the major groove of DNA, where it contacts the edges of the base pairs. The N- terminal α-helix (blue) functions primarily as a structural component that helps to position the recognition helix. |
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Term
| Helix-loop-helix (cartoon) |
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Definition
[image]
The two monomers are held together in a four-helix bundle: each monomer contributes two α helices connected by a flexible loop of protein (red). A specific DNA sequence is bound by the two α helices that project from the four-helix bundle. |
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Term
| If different gene regulatory proteins use one of a limited number of motifs, how then do they recognize different nucleotide-pair sequences? |
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Definition
| Although the motifs are the same, they vary in amino acid sequence and hence, recognize different nucleotide-pair sequences. This is called sequence specificity. |
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Term
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Definition
| The recognition helices of different gene regulatory proteins with identical motifs vary in amino acid sequence and hence, recognize different nucleotide-pair sequences. |
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Term
| Dimerization (as it relates to DNA binding proteins) |
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Definition
| DNA-binding proteins bind in pairs (dimers) to the DNA helix. Dimerization roughly doubles the area of contact with the DNA, thereby increasing the strength and specificity of the protein-DNA interaction. Because even two different proteins can also be combined in pairs (“heterodimerization”), dimerization makes it possible for many different DNA sequences to be recognized by a limited number of proteins. |
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Term
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Definition
| The pairing of two different proteins to bind with the DNA helix. |
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Term
| What does it mean when someone says that most gene activator proteins have a "modular design"? |
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Definition
| Gene activator proteins have a design consisting of at least two distinct domains. One domain usually contains one of the structural motifs discussed above that recognizes a specific regulatory DNA sequence. DNA-binding domains alone, however, are necessary but insufficient for activator function. A second domain, sometimes called the activation domain, accelerates the rate of transcription initiation. Activation domains function by various mechanisms, one of which involves protein-protein interactions with one or more components of the RNA polymerase II transcriptional machinery. |
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Term
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Definition
| Recognize a specific regulatory DNA sequence. DNA-binding domains alone, however, are necessary but insufficient for activator function. |
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Term
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Definition
| Provide function; accelerates the rate of transcription initiation. Activation domains function by various mechanisms, one of which involves protein-protein interactions with one or more components of the RNA polymerase II transcriptional machinery. |
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Term
| T or F: Gene regulatory proteins are influenced only by signals outside the cell. |
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Definition
| False. Gene regulatory proteins are also influenced by signals from outside the cell, which can make them active or inactive in a variety of different ways. Thus, the pattern of gene expression in a cell can be viewed as the result of a complicated molecular computation that the intracellular gene control network performs in response to information from the cell’s surroundings. |
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Term
| What are 7 ways in which transcription activators are controlled by signals outside the cell? |
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Definition
1) Protein synthesis
2) Ligand binding
3) Protein phosphorylation
4) Addition of second subunit
5) Unmasking
6) Stimulation of nuclear entry
7) Release from membrane |
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Term
| Protein synthesis (method of controlling gene regulatory proteins) |
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Definition
[image]
The protein is synthesized only when needed and is rapidly degraded by proteolysis so that it does not accumulate. |
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Term
| Ligand binding (method of controlling gene regulatory proteins) |
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Definition
[image]
Activation by ligand binding. |
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Term
| Protein phosphorylation (method of controlling gene regulatory proteins) |
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Definition
[image]
Activation by phosphorylation. |
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Term
| Addition of second subunit (method of controlling gene regulatory proteins) |
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Definition
[image]
Formation of a complex between a DNA-binding protein and a separate protein with a transcription-activating domain. |
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Term
| Unmasking (method of controlling gene regulatory proteins) |
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Definition
[image]
Unmasking of an activation domain by the phosphorylation of an inhibitor protein. |
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Term
| Stimulation of nuclear entry (method of controlling gene regulatory proteins) |
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Definition
[image]
Stimulation of nuclear entry by removal of an inhibitory protein that otherwise keeps the regulatory protein from entering the nucleus. |
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Term
| Release from membrane (method of controlling gene regulatory proteins) |
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Definition
[image]
Release of a gene regulatory protein from a membrane bilayer by regulated proteolysis. |
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Term
| If all cells contain the same chromosomes, what accounts for specialized cell types? |
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Definition
| The specialized cell types in a multicellular organism differ by virtue of the different sets of RNA and protein molecules made. Different gene regulatory proteins are present in different cell types and thereby direct the patterns of gene expression that give each cell type its unique characteristics. |
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Term
| What governs differential synthesis of such RNAs and proteins over space (tissue-specificity) and time (developmental control)? |
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Definition
| It involves a combination of the cell’s internal programming and developmental history, as well as the presence at any given moment of particular spatial cues and environmental signals, all of which impinge on the function of regulatory proteins and RNA polymerase II at gene control regions unique to each gene. |
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Term
| Of a cell's ~25,000 genes, how many are expressed at any one time in any given cell? |
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Definition
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Term
| How many gene-specific transcription factors are encoded in the human genome? And why so many? |
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Definition
| Approximately 2,000. This large number allows specificity because gene regulatory proteins allow individual genes to be turned on or off individually. |
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Term
| Are any 2 genes in a eukaryotic cell regulated the same way? |
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Definition
| No, each gene is regulated differently. |
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Term
| Gene expression profiling (transcriptional profiling) |
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Definition
| The classification of disease state based on gene expression profile of patient. This involves the measurement of the activity (the expression [of mRNA abundance as measured by DNA microarray]) of thousands of genes at once, to create a global picture of cellular function. These profiles can, for example, distinguish between cells that are actively dividing [or between cancerous vs. non-cancerous cells of an individual], or show how the cells react to a particular treatment. Many experiments of this sort measure an entire genome simultaneously, that is, every gene present in a particular cell. |
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Term
| How are genes expressed at the right time (during development) and in the right place (cell, tissue type)? |
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Definition
| "It involves a combination of the cell's internal programming and developmental history, as well as the presence at any given moment of particular spatial cues and environmental signals, all of which impinge on the function of regulatory proteins and RNA polymerase II at gene control regions unique to each gene." - Alberts |
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Term
| How does testosterone promote or inhibit a given set of genes? |
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Definition
| Steroid hormones (e.g. cortisol, estradiol, testosterone) are hydrophobic signal molecules which are plasma membrane-permeable and which bind to intracellular receptors. The receptors for these hormones are gene regulatory proteins that are present in an inactive form in the unstimulated cell. When its hormone binds, the receptor protein undergoes a large conformation change that enables it to bind to its corresponding regulatory sequence in the DNA; it can then promote or inhibit the transcription of a selected set of genes. There are different receptor proteins for each type of hormone; each receptor acts at a different set of regulatory sites and thus regulates a different set of genes. |
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Term
| Describe the essential role of the steroid hormone receptors in the mediation of a given effect of that steroid. |
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Definition
| The essential role of the steroid hormone receptors is illustrated by the dramatic consequences of a lack of the receptor for testosterone in humans. The male sex hormone testosterone acts in the fetus and at puberty as a signal for development of male secondary sexual characteristics. Some very rare individuals are genetically male (that is, they have one X and one Y chromosome) but lack the testosterone receptor as a result of a mutation in the corresponding gene: they make the hormone, but cells cannot respond to it (called “androgen insensitivity syndrome” or “testicular feminization”). The consequence is that they develop, to all outward appearances, as females. This demonstrates the key role of the hormone receptor in the action of testosterone, and also shows that the receptor is required not just in one cell type to mediate one effect, but in many cell types to produce the whole range of features that distinguish men from women. |
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Term
| Describe the effect of a single gene regulatory protein on differentiation using muscle cells as an example. |
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Definition
A human skeletal muscle cell is highly distinctive cell type. It is typically an extremely large cell that is formed by the fusion of many muscle precursor cells called myoblasts (and therefore contains many nuclei). The mature muscle cell is distinguished from other cells by the production of a large number of characteristic proteins, such as actin and myosin, which make up the contractile apparatus.
Genes encoding such proteins are switched on coordinately when myoblasts begin to fuse. Key gene regulatory proteins, expressed only in potential muscle cells, coordinate the gene expression by binding to sites present in their regulatory regions and are thus crucial for muscle cell differentiation. These key gene regulatory proteins can convert nonmuscle cells to muscle by activating the changes in gene expression typical of differentiating muscle cells. When the gene for one of these gene regulatory proteins, MyoD, is introduced into fibroblasts (connective tissue cell type) , the fibroblasts start behaving as myoblasts and fuse to form muscle-like cells. It appears that the fibroblasts, which are derived from the same broad class of embryonic cells as muscle cells, have already accumulated all the other necessary gene regulatory proteins required for the combinatorial control of the muscle-specific genes, and that addition of MyoD completes the unique combination that directs the cells to become muscle. |
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Term
| Describe the idea of complex transcriptional regulation found in the human ß-globin gene. |
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Definition
| Hemoglobin is a telemetric protein abundant in RBCs that is comprised of two ß-globin chains plus two α-globin chains. The ß-globin gene has two enhancers, one upstream and one downstream of the gene. A complex array of gene regulatory proteins controls expression of the ß -globin gene, some acting as activators and others as repressors. The concentrations (or activities) of many of these gene regulatory proteins is thought to change during development, and only a particular combination of all the proteins triggers transcription of the gene. The human ß-globin gene is part of a cluster of highly-homologous (but non-identical) globin genes; this cluster is known as the ß-like globin gene cluster. On another chromosome there is an analogous cluster of α-like globin genes (which are more similar to each other than to the ß-like globin genes), but we will confine our discussion to the ß-like globin gene cluster. The five genes of the ß-like cluster are transcribed exclusively in erythroid cells (red blood cell lineage). Moreover, each gene is turned on at a different stage of development and in different organs: the ε-globin gene is expressed in the embryonic yolk sac, γ in the yolk sac and fetal liver, and δ and ß primarily in the adult bone marrow. Each of the ß- like globin genes has its own set of regulatory proteins that are necessary to turn the gene on at the appropriate time and tissue. In addition to the individual regulation of each of the globin genes, the entire cluster appears to be subject to a shared control region called the locus control region (LCR). The LCR lies far upstream from the gene cluster. In cells where the globin genes are not expressed (such as brain or skin cells), the whole gene cluster appears tightly packed into a heterochromatin-like structure. In erythroid cells, by contrast, the higher order packaging of the chromatin has become decondensed. This change occurs even before the individual globin genes are transcribed, suggesting that there are two steps of regulation. First, the chromatin of the entire globin locus becomes decondensed, which is presumed to allow additional gene regulatory proteins to access the DNA. Second, the remaining gene regulatory proteins assemble on the DNA and direct the expression of individual genes. Unfortunately, the mechanism of switching from one ß-like globin gene to another during development is not understood in any detail. |
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Term
| Locus control region (LCR) |
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Definition
| Defined by the ability to enhance the expression of linked genes to physiological levels in a tissue-specific and copy number-dependent manner at ectopic chromatin sites. The concept derives from the idea that developmental and cell lineage-specific regulation of gene expression relies not only on gene-proximal elements such as promoters, enhancers, and silencers, but also on long-range interactions of various cis-regulatory elements and dynamic chromatin alterations. |
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Term
| What is the appearance of the human ß-globin gene cluster in cells where the globin genes are not expressed? In erythroid cells? |
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Definition
| The whole gene cluster appears tightly packed into a heterochromatin-like structure. In erythroid cells, by contrast, the higher order packaging of the chromatin has become decondensed. |
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Term
|
Definition
| The LCR appears to act by controlling chromatin condensation/decondensation, but the manner in which it does this is poorly-understood. |
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Term
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Definition
| A severe form of inherited anemia where in a certain subset of patients, the ß-globin locus is found to have undergone deletions that remove the LCR, and although the ß-globin gene and its nearby regulatory regions are intact, the gene remains transcriptionally silent even in erythroid cells. In other ß–thalassemic patients, the gene region between the δ and ß-globin genes, which contains the upstream enhancer for the ß– globin gene, is deleted, thereby preventing expression of adult ß-globin. An origin of replication happens to be located near the ß–globin enhancer, but this point is peripheral to the problem at hand. Be aware that other mutations arising in the ß-globin locus can also cause ß-thalassemia (such as splice site mutations in the ß -globin gene). |
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