Clegg TBP sandbox - Revision history

http://52.214.119.220/wiki/index.php?action=history&feed=atom&title=Clegg_TBP_sandbox Clegg TBP sandbox - Revision history 2026-04-14T11:55:40Z Revision history for this page on the wiki MediaWiki 1.11.2 http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615851&oldid=prev Wally Novak at 16:01, 26 November 2012 2012-11-26T16:01:14Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 16:01, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TATA Binding Protein Overview==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TATA Binding Protein Overview==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC starts with the Tata Binding Protein(TBP) binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘<ref>Regulation of RNA polymerase II transcription., Drapkin R., Merino A., Reinberg D.opin, Cell Biol. 4, 490 (1992).</ref>’ This mechanism/assembly enables the start of transcription. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC starts with the Tata Binding Protein (TBP) binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘<ref>Regulation of RNA polymerase II transcription., Drapkin R., Merino A., Reinberg D.opin, Cell Biol. 4, 490 (1992).</ref>’ This mechanism/assembly enables the start of transcription. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==General Structure of TBP== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==General Structure of TBP== </div></td></tr> </table>

Wally Novak http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615850&oldid=prev Wally Novak at 16:00, 26 November 2012 2012-11-26T16:00:20Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 16:00, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TATA Binding Protein Overview==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TATA Binding Protein Overview==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC starts with the TBP binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘<ref>Regulation of RNA polymerase II transcription., Drapkin R., Merino A., Reinberg D.opin, Cell Biol. 4, 490 (1992).</ref>’ This mechanism/assembly enables the start of transcription. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC starts with the <ins style="color: red; font-weight: bold; text-decoration: none;">Tata Binding Protein(</ins>TBP<ins style="color: red; font-weight: bold; text-decoration: none;">) </ins>binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘<ref>Regulation of RNA polymerase II transcription., Drapkin R., Merino A., Reinberg D.opin, Cell Biol. 4, 490 (1992).</ref>’ This mechanism/assembly enables the start of transcription. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==General Structure of TBP== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==General Structure of TBP== </div></td></tr> </table>

Wally Novak http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615769&oldid=prev Wally Novak at 08:08, 26 November 2012 2012-11-26T08:08:31Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 08:08, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/3'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.961</ref>’ As a result the DNA is partially unwound between the two sets of Phenylalanines causing the minor groove to be widened.‘<ref>X-ray crystallographic studies of eukaryotic transcription initiation factors. Burley SK., Philosiphical Transactions of the Royal Society of London series B-Biol Sci. 1996 April 29 . 51: 1339; 483-489 10.1098/rstb.1996.0046</ref>’A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which <del style="color: red; font-weight: bold; text-decoration: none;">can </del>eventually <del style="color: red; font-weight: bold; text-decoration: none;">lead </del>to transcripton. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/3'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.961</ref>’ As a result the DNA is partially unwound between the two sets of Phenylalanines causing the minor groove to be widened.‘<ref>X-ray crystallographic studies of eukaryotic transcription initiation factors. Burley SK., Philosiphical Transactions of the Royal Society of London series B-Biol Sci. 1996 April 29 . 51: 1339; 483-489 10.1098/rstb.1996.0046</ref>’A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which eventually <ins style="color: red; font-weight: bold; text-decoration: none;">leads </ins>to transcripton. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Wally Novak http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615768&oldid=prev Wally Novak at 08:07, 26 November 2012 2012-11-26T08:07:11Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 08:07, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/3'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.961</ref>’ <del style="color: red; font-weight: bold; text-decoration: none;">The </del>DNA is partially unwound between the two sets of Phenylalanines causing the minor groove to be widened.‘<ref>X-ray crystallographic studies of eukaryotic transcription initiation factors. Burley SK., Philosiphical Transactions of the Royal Society of London series B-Biol Sci. 1996 April 29 . 51: 1339; 483-489 10.1098/rstb.1996.0046</ref>’A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/3'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.961</ref>’ <ins style="color: red; font-weight: bold; text-decoration: none;">As a result the </ins>DNA is partially unwound between the two sets of Phenylalanines causing the minor groove to be widened.‘<ref>X-ray crystallographic studies of eukaryotic transcription initiation factors. Burley SK., Philosiphical Transactions of the Royal Society of London series B-Biol Sci. 1996 April 29 . 51: 1339; 483-489 10.1098/rstb.1996.0046</ref>’A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Wally Novak http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615767&oldid=prev Wally Novak at 08:05, 26 November 2012 2012-11-26T08:05:44Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 08:05, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/3'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.<del style="color: red; font-weight: bold; text-decoration: none;">585</del></ref>’ <del style="color: red; font-weight: bold; text-decoration: none;">A </del>total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/3'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.<ins style="color: red; font-weight: bold; text-decoration: none;">961</ins></ref>’ <ins style="color: red; font-weight: bold; text-decoration: none;">The DNA is partially unwound between the two sets of Phenylalanines causing the minor groove to be widened.‘<ref>X-ray crystallographic studies of eukaryotic transcription initiation factors. Burley SK., Philosiphical Transactions of the Royal Society of London series B-Biol Sci. 1996 April 29 . 51: 1339; 483-489 10.1098/rstb.1996.0046</ref>’A </ins>total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Wally Novak http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615766&oldid=prev Wally Novak at 07:57, 26 November 2012 2012-11-26T07:57:41Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:57, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TATA Binding Protein Overview==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TATA Binding Protein Overview==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC <del style="color: red; font-weight: bold; text-decoration: none;">stats </del>with the TBP binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘<ref>Regulation of RNA polymerase II transcription., Drapkin R., Merino A., Reinberg D.opin, Cell Biol. 4, 490 (1992).</ref>’ This mechanism/assembly enables the start of transcription. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC <ins style="color: red; font-weight: bold; text-decoration: none;">starts </ins>with the TBP binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘<ref>Regulation of RNA polymerase II transcription., Drapkin R., Merino A., Reinberg D.opin, Cell Biol. 4, 490 (1992).</ref>’ This mechanism/assembly enables the start of transcription. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==General Structure of TBP== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==General Structure of TBP== </div></td></tr> </table>

Wally Novak http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615765&oldid=prev Wally Novak at 07:46, 26 November 2012 2012-11-26T07:46:09Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:46, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/<del style="color: red; font-weight: bold; text-decoration: none;">2</del>'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.585</ref>’ A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/<ins style="color: red; font-weight: bold; text-decoration: none;">3</ins>'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Voet, Donald et al. 2008. Fundamentals of Biochemistry. 3rd ed. p.585</ref>’ A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Wally Novak http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615760&oldid=prev Wally Novak at 07:20, 26 November 2012 2012-11-26T07:20:15Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:20, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/2'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref><del style="color: red; font-weight: bold; text-decoration: none;">Crystal structure </del>of <del style="color: red; font-weight: bold; text-decoration: none;">a human TATA box-binding protein/TATA element complex</del>.<del style="color: red; font-weight: bold; text-decoration: none;">, Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley SK, Proc Natl Acad Sci U S A</del>. <del style="color: red; font-weight: bold; text-decoration: none;">1996 May 14;93(10):4862-7</del>. <del style="color: red; font-weight: bold; text-decoration: none;">PMID:8643494</del></ref>’ A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place, caused by van der walls repulsion and hydrogen bonding, resulting in the <scene name='Clegg_TBP_sandbox/Bend/1'>bending</scene> of DNA by 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/2'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref><ins style="color: red; font-weight: bold; text-decoration: none;">Voet, Donald et al. 2008. Fundamentals </ins>of <ins style="color: red; font-weight: bold; text-decoration: none;">Biochemistry</ins>. <ins style="color: red; font-weight: bold; text-decoration: none;">3rd ed</ins>. <ins style="color: red; font-weight: bold; text-decoration: none;">p</ins>.<ins style="color: red; font-weight: bold; text-decoration: none;">585</ins></ref>’ A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Wally Novak http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615759&oldid=prev Wally Novak at 07:19, 26 November 2012 2012-11-26T07:19:21Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:19, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 4:</td> <td colspan="2" class="diff-lineno">Line 4:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TATA Binding Protein Overview==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TATA Binding Protein Overview==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC stats with the TBP binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘<ref><del style="color: red; font-weight: bold; text-decoration: none;">Voet</del>, <del style="color: red; font-weight: bold; text-decoration: none;">Donald et al</del>. <del style="color: red; font-weight: bold; text-decoration: none;">2008</del>. <del style="color: red; font-weight: bold; text-decoration: none;">Fundamentals of Biochemistry</del>. <del style="color: red; font-weight: bold; text-decoration: none;">3rd ed</del>. <del style="color: red; font-weight: bold; text-decoration: none;">pp</del>.<del style="color: red; font-weight: bold; text-decoration: none;">962</del></ref>’ This mechanism/assembly enables the start of transcription. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>In order to initiate transcription in eukaryotes, protein factors, known as general transcription factors (GTF), and RNA polymerase must bind to promoter regions of DNA. When all the GTFs are bound into one complex it is known as the preinitiation complex (PIC). The assembly of the PIC stats with the TBP binding to the promoter, followed by TFIIA and TFIIB, next TFIIF binds RNA Polymerase II and transports it to the complex, and finally TFIIE and TFIIH are recruited to complete the complex.‘<ref><ins style="color: red; font-weight: bold; text-decoration: none;">Regulation of RNA polymerase II transcription.</ins>, <ins style="color: red; font-weight: bold; text-decoration: none;">Drapkin R</ins>.<ins style="color: red; font-weight: bold; text-decoration: none;">, Merino A</ins>.<ins style="color: red; font-weight: bold; text-decoration: none;">, Reinberg D</ins>.<ins style="color: red; font-weight: bold; text-decoration: none;">opin, Cell Biol</ins>. <ins style="color: red; font-weight: bold; text-decoration: none;">4, 490 (1992)</ins>.</ref>’ This mechanism/assembly enables the start of transcription. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==General Structure of TBP== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==General Structure of TBP== </div></td></tr> </table>

Wally Novak http://52.214.119.220/wiki/index.php?title=Clegg_TBP_sandbox&diff=1615758&oldid=prev Wally Novak at 07:07, 26 November 2012 2012-11-26T07:07:51Z

<p></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 07:07, 26 November 2012</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 10:</td> <td colspan="2" class="diff-lineno">Line 10:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==TBP-DNA Interactions==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place and the <del style="color: red; font-weight: bold; text-decoration: none;">DNA strand is </del><scene name='Clegg_TBP_sandbox/Bend/1'><del style="color: red; font-weight: bold; text-decoration: none;">bent</del></scene> 80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>When the TBP binds to the TATA box a conformation change takes place<ins style="color: red; font-weight: bold; text-decoration: none;">, caused by van der walls repulsion </ins>and <ins style="color: red; font-weight: bold; text-decoration: none;">hydrogen bonding, resulting in </ins>the <scene name='Clegg_TBP_sandbox/Bend/1'><ins style="color: red; font-weight: bold; text-decoration: none;">bending</ins></scene> <ins style="color: red; font-weight: bold; text-decoration: none;">of DNA by </ins>80 degrees. This conformational change promotes the recruitment of other general transcription factors such as TFIIA and TFIIB. <ins style="color: red; font-weight: bold; text-decoration: none;">Most of the interaction between the protein and DNA takes place within the minor groove of the DNA. In particular the Phe residues 193, 210, 284, and 301 induce a <scene name='Clegg_TBP_sandbox/Phe/2'>kink</scene>, approximately 44 degrees, within the TATA box.‘<ref>Crystal structure of a human TATA box-binding protein/TATA element complex., Nikolov DB, Chen H, Halay ED, Hoffman A, Roeder RG, Burley SK, Proc Natl Acad Sci U S A. 1996 May 14;93(10):4862-7. PMID:8643494</ref>’ </ins>A total of seven <scene name='Clegg_TBP_sandbox/Lysines/1'>lysine</scene> residues interact with DNA backbone. Four of these residues Lys-204, Lys-214, Lys-295, and Lys 305 allow for the partial charge neutralization within the TATA box. Serveral arginines also interact with the DNA strand these residues include: <scene name='Clegg_TBP_sandbox/Lysines/3'>Arg-192</scene>, Arg-199, Arg-290. The TBP is crucual protien that recognizes the promoter region of DNA and allows for other general transcription factors to bind and form a complex which can eventually lead to transcripton. </div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr> </table>

Wally Novak