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DNA, RNA, Amino Acids...oh my!

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DNA, RNA, Amino Acids...oh my!

Postby guanine » Wed Apr 26, 2006 10:25 pm

Hey, been browsing the site and whish I knew about this forum earlier...can anyone explain these to me...I've exhausted 3 text books (Lodish, McMurry, and Pratt) and still am lost :(

1. What is the difference between the standard and the physiological free energy change observed in heart muscle cells?

2. Explain how cells of vertebres recognize mismatched G-T base pairing on DNA and describe how this is repaired in the cell?

3. Why is RNA polymerasese not able to correct base errors during replication or transcription. Describe the biological consequences of the protein that may develop in this case.

4. Given: 5'-CCUUACACAGGAAACACGUAUGACCAUUGAGGCUUGAACAA-3' (found to occur in mRNA molecule)

i) What is the amino acid sequence represented here following its translation?

ii) For the above amino acid sequence, identiy the bases that correspond to the Shine-Dalgarno sequence. Explain.

iii) Describe how the amino acid sequence would change if the 21st base (U) were mutated to G?

I appreciate any help in advance...I losing my hair over these questions
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question 4

Postby haf2006 » Thu Apr 27, 2006 10:31 am

can only help with question 4 i'm afraid, the translated sequence is P V T G N T V D H * G L N aa

the shine delgarno sequence is usually AGG AGG and is part of the signal for protein biosynthesis in prokaryotes.

if the 21st base changed to a G the amino acid would become a stop codon (as * above)
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Postby kiekyon » Thu Apr 27, 2006 1:05 pm

for Q1
standard energy change = under standard condition, 25 C, 1 atm
physiological free energy change = body temperature
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Postby dae » Sat May 06, 2006 1:51 am

In regards to question 2, base pair mismatches in vertebrates can be corrected in two ways (that I know of). First, DNA polymerase has 3' to 5' exonuclease activity that proofreads the daughter strand in the 3' to 5' direction (that is to say, DNA polymerase backpedals). You can find a model for this so I will only elude to it by saying that the newly synthesized strand moves from the P site to the E site of DNA polymerase where the error is corrected. The second methods is "strand-directed mismatch repair." Again, you can research this on your own but in brief, when a mismatch occurs the dsDNA bulges out and disrupts the double helix enough for a mismatch repair enzyme to locate it. Cf. the human disorder "hereditary nonpolyposis colon cancer" (HNPCC) where one of these mismatch repair genes is mutated leading to a drastic increase in the likelihood of cancer due to a buildup of uncorrected errors.

In regards to question 3, RNA polymerase doesn't replicate, it only transcribes. RNA polymerase cannot correct errors it has made because it transcribes in the 5' to 3' direction and does not backtrack - unlike DNA polymerase. A mistake has the possibility to not affect the protein at all (due to the codon-to-amino acid translational process where several codons can code for one amino acid). If this is not the case, an incorrect amino acid could be inserted or the protein could be truncated (because the error formed a stop codon). If the protein was affected, it might behave differently than the wild type protein (you can take it from there).
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