Protein Modeling C

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Re: Protein Modeling C

Post by platypusomelette » October 20th, 2018, 9:07 am

freed2003 wrote:
luanne wrote:im guessing but: hydrophobic forces, formation of hydrogen bonds and formation of van der waals forces?
I was thinking of disulfide bonds or maybe like enthalpy and entropy but that works too
Wait can you clarify or explain that? Also since thread is dead I'm just gonna say Nano that's the correct answer
1. Give a definition of what CRISPR stands for and what it is
2. Describe the function of the cas 9 protein
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Re: Protein Modeling C

Post by JoeyC » October 23rd, 2018, 4:26 am

I FINALLY CAN ANWER THIS!!!! CRISPR stands for clustered regularly inter spaced short palindromic repeats.In bacterial DNA, it was discovered that in one section there were a bunch of repeats of the same lines of DNA, with different spacers in between each repeat. This DNA is a copy of viral RNA, used by the CRISPR proteins to fight of invading viral DNA.
The Cas9 protein uses a tracer RNA and a CRISPR RNA to identify viral RNA and cut it with its nucleases, killing it. The Cas 9 protein is a helicase, unwinding the RNA, and the CRISPR RNA is a complimentary strand to a certain portion of the RNA, so the RNA will line up with it. TRACR RNA holds the CRISPR in place. Then the Cas9 cuts the viral RNA with its nucleases.
when you forget how to use hidden box..
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Re: Protein Modeling C

Post by platypusomelette » October 23rd, 2018, 5:45 am

JoeyC wrote:I FINALLY CAN ANWER THIS!!!! CRISPR stands for clustered regularly inter spaced short palindromic repeats.In bacterial DNA, it was discovered that in one section there were a bunch of repeats of the same lines of DNA, with different spacers in between each repeat. This DNA is a copy of viral RNA, used by the CRISPR proteins to fight of invading viral DNA.
The Cas9 protein uses a tracer RNA and a CRISPR RNA to identify viral RNA and cut it with its nucleases, killing it. The Cas 9 protein is a helicase, unwinding the RNA, and the CRISPR RNA is a complimentary strand to a certain portion of the RNA, so the RNA will line up with it. TRACR RNA holds the CRISPR in place. Then the Cas9 cuts the viral RNA with its nucleases.
when you forget how to use hidden box..
Pretty much correct - just remember that cas9 "breaks" viral DNA because bacterial proteins attempt to repair double-stranded breaks, but usually end up placing mutations in the process. Your turn
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Re: Protein Modeling C

Post by JoeyC » October 23rd, 2018, 8:27 am

1.) What do scientists use the Cas9 for?
2.) What have viruses created in response?
3.) What does the answer to the previous question do against the CRISPR system?
Pretty basic questions.
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Re: Protein Modeling C

Post by platypusomelette » October 26th, 2018, 10:09 am

JoeyC wrote:1.) What do scientists use the Cas9 for?
2.) What have viruses created in response?
3.) What does the answer to the previous question do against the CRISPR system?
Pretty basic questions.
1. Scientists can use it to disable certain genes to see what side effects would happen, or they could remove the cutting domains and modify the gRNA to recognize whatever sequences they want. Proteins like deaminases or fluorescent proteins can be attached to the cas9 to perform other functions.
2. anti-crispr
3. Occupies cas9's PAM binding site, which makes it unable to track down what sequence it is supposed to find.
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Re: Protein Modeling C

Post by JoeyC » October 26th, 2018, 11:55 am

Correct! Your turn.
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Re: Protein Modeling C

Post by platypusomelette » October 30th, 2018, 5:10 am

JoeyC wrote:Correct! Your turn.
1. What is the PAM and why is it important?
2. Describe the process of CRISPR adaptation / acquisition or how viral DNA is inserted into the CRISPR array.
3. What is the difference between tracrRNA, crRNA, gRNA, and sgRNA?
4. What is the purpose of the palindromic repeats in CRISPR / what happens once they are transcribed?
island trash trees hs
anat: reg 4th
herp: reg 6th
genes: reg 5th
protein: reg 2nd
disease: reg 15th
fossils: reg 4th
2016: a&p 1st, fossils 3rd
2017: a&p 3rd, herp 14th
2018: a&p 1st, microbe 8th, herp 13th :/
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Re: Protein Modeling C

Post by platypusomelette » November 8th, 2018, 5:06 am

Bump
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genes: reg 5th
protein: reg 2nd
disease: reg 15th
fossils: reg 4th
2016: a&p 1st, fossils 3rd
2017: a&p 3rd, herp 14th
2018: a&p 1st, microbe 8th, herp 13th :/
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Re: Protein Modeling C

Post by JoeyC » November 8th, 2018, 7:47 am

platypusomelette wrote:
JoeyC wrote:Correct! Your turn.
1. What is the PAM and why is it important?
2. Describe the process of CRISPR adaptation / acquisition or how viral DNA is inserted into the CRISPR array.
3. What is the difference between tracrRNA, crRNA, gRNA, and sgRNA?
4. What is the purpose of the palindromic repeats in CRISPR / what happens once they are transcribed?
Fine 1.) The PAM is where the crRNA bonds to the CAS9, and if blocked by a protein such as and Acr, the Cas willl not function.
2.) Viral DNA is cut by CAS9, and the segment which was used to find it (by CAS9's adaptability that allows it to cut DNA that doesn't exactly match up to it's crRNA) is taken and inserted into the CRISPR RNA
3.) If I'm correct, tracrRNA holds crRNA, which is used to locate the viral DNA, in place. gRNA means guide RNA, and is any RNA, crRNA or chimera that allows a cas to find viral DNA, and sgRNA is guide RNA that is one stranded; in other words a crRNA and tracrRNA combined, a chimera usually made by scientists using it for gene editing
4.) I believe the repeats give space for the spacers to be inserted in between; once they are transcribed they are code for the creation of a cas? (this one is probably incorrect)
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Re: Protein Modeling C

Post by platypusomelette » November 11th, 2018, 7:24 am

JoeyC wrote:1.) The PAM is where the crRNA bonds to the CAS9, and if blocked by a protein such as and Acr, the Cas willl not function.
2.) Viral DNA is cut by CAS9, and the segment which was used to find it (by CAS9's adaptability that allows it to cut DNA that doesn't exactly match up to it's crRNA) is taken and inserted into the CRISPR RNA
3.) If I'm correct, tracrRNA holds crRNA, which is used to locate the viral DNA, in place. gRNA means guide RNA, and is any RNA, crRNA or chimera that allows a cas to find viral DNA, and sgRNA is guide RNA that is one stranded; in other words a crRNA and tracrRNA combined, a chimera usually made by scientists using it for gene editing
4.) I believe the repeats give space for the spacers to be inserted in between; once they are transcribed they are code for the creation of a cas? (this one is probably incorrect)
1. The PAM is actually a short sequence of the viral DNA that the cas9 recognizes in addition to what's on the crRNA, but is not included in the CRISPR array in order to prevent the cas9 from just recognizing and cutting the DNA in the bacterial CRISPR. Acr does block the PAM recognition site in cas9
2. Correct
3. Correct but the gRNA is specifically the combination of the tracrRNA and crRNA
4. Once the palindromic repeats get transcribed they stick to each other (palindrome means both halves will be complementary with each other) and they form a hairpin loop attached as part of the tracrRNA, which idk why but it probably has some structural reason.
Ok your turn
island trash trees hs
anat: reg 4th
herp: reg 6th
genes: reg 5th
protein: reg 2nd
disease: reg 15th
fossils: reg 4th
2016: a&p 1st, fossils 3rd
2017: a&p 3rd, herp 14th
2018: a&p 1st, microbe 8th, herp 13th :/
pigeon YEA WE MADE STATES

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