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| This is called the Pribnow box which usually consists of the six nucleotides TATAAT. (absolutely essential for transcription) this is found upstream from the start site in prokaryotes |
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| Usually consists of 7 nucleotides TTGACAT. Its presence allows a very high transcription rate |
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| when referring to DNA transcription, this is the DNA strand which has the same base sequence as the RNA transcript produced (with thymine replaced by URacil) it is the strand which contains codons, |
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| refers to the most common nucleotide or amino acid at a particular position after multiple sequences are aligned. (please check definition |
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| This works by using radioactively end labeled DNA to DNase, which cuts the DNA. Gel Electrophoresis follows for DNA sequencing. Areas of the DNA that were in contact with the protein complexes would be protected from enzymatic cleavage- you would use this to revel where the protein bound to the DNA is and give you a promotor sequence. |
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The simplest application of this technique is to assess whether a protein binds to a region of interest within the DNA molecule.
1. PCR amplify and label the region of interest.
2. Add the protein of interest to a portion of the labeled template DNA (also keep a portion without the protein for comparison)
3. Add cleavage agent to both portions of DNA template.
4. Run polyacrylamide gel electrophoresis. |
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(also called Rho-Independent termination) is found in both eukaryotes and prokaryotes and causes mRNA transcription to be stopped. In this mechanism the mRNA contains a sequence that can base pair with itself to form a stem loop that is rich in C-G pairs. Following the stem loop are a chain of uracil residues
-this is a mechanism underlying the activity of cis-acting RNA regulatory elements |
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| This is when a DNA molecule is opened to allow base pairing and elongation etc. |
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| is the region of DNA that facilitates teh transcription of a particular gene. They are located near the genes they regulate on the same strand and typically upstream (towards the 5' region). They 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. |
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| rho-dependent termination |
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| in this type of termination, a protein factor called "rho" destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex |
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| is a prokaryotic protein involved in the termination of transcription. Rho is a member of the family of ATP dependent hexameric helicases that function by passing nucleic acids through the hole in the middle of the hexamer. It acts on an RNA substrate. Its key function is its helicase activity,for which energy is provided by an RNA dependent ATP hydrolysis. Binds at a region that is rich in cytosine and poor in guanine. |
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| the region where rho binds, it is a single stranded region that is rich in cytosine and poor in guanine upstream of the actual terminator sequence. |
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| is an enzyme that produces RNA. The alpha subunit recognizes an upstream element as well as sigma factors at the -10-35 region. It binds to the DNA and switches from a closed complex to an open complex. This chage ivolves the separation of the DNA strands to form an unwound section of DNA. Base pairing then occurs, (elongation) |
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| RNA polymerase holoenzyme |
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| the sense strand is complementary to the antisense strand, which is the strand of DNA transcribed into mRNA during transcription. |
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| is a prokaryotic transcription initiation factor that enable specific binding of RNA poly, to gene promoters,. Different sigma factors are activated in response to different environmental factors. |
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| this is used as a template for RNA synthesis. As transcription proceeds, the RNA polymerase traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy. |
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| can occur with either rho independent, or rho dependent. basically the |
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