5. Using the scores in BLOSUM-62 matrix, and assuming the score of indel is -4, provide the score for the following alignments. Which alignment is relatively better. HARF-L |:: | -AFHIL HARF--L | | | -A-FHIL Is there a indel score value that would make the two alignment scores relatively comparable?
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- Compute the PERCENT IDENTITY for the following pairwise sequence alignment. ACTGATGGGGG--AGACGTA ||||| ... I ||||||| ACTG--AAAAGCTAGACGTA1.8 Calculations for the Purification of a Recombinant Protein The purification of a recombinant protein is carried out starting with 100 liters of a clarified cell lysate (i.e., the cells have been lysed, and the cell debris has been removed to give a clarified solution), which has a total protein concentration of 0.36 mg/ml and a recombinant protein con- centration of 2.2 U/ml, where U denotes units of biological activity of the recombinant protein. It is known that the completely pure recombinant protein has a specific activity of 40.0 U/mg. Purification is continued until a chromatography step that yields 2.0 liters of a fraction containing the protein, with a total protein concentration of 1.11 mg/ml and a recombinant protein concentration of 43.2 U/ml.For the recombinant protein, calculate the starting and ending purity, the starting and ending specific activity, and the percentage yield and fold purification through the chromatography step.Compute the percent identity of the following pairwise sequence alignment: -TGAGACTTAGAGT |..|... | | | | | ATAGGAGCGAGAGT
- Below are 9 possible primer pairs. ● Determine which primer pair is the best choice by considering the following: 1. primers should be 18-24 bases in length; 2. base composition should be 45-55% (G+C); 3. primers should end (3') in a G or C, or CG or GC: this prevents "breathing" of ends and increases efficiency of priming; 4. Tms tween 55-70°℃ are preferred (Tas, annealing temperatures, are approximately 5°C lower than the Tm); 5. the Tm for your primer pair should be within 2 degrees of each other, though ideally the same; 6. runs of three or more Cs or Gs at the 3'-ends of primers may promote mispriming at G or C-rich sequences (because of stability of annealing), and should be avoided; 7. 3'-ends of primers should not be complementary (i.e. base pair), as otherwise the formation of primer dimers will result; 8. primer self-complementary (ability to form secondary structures such as hairpins) should be avoided. • Explain why the other primers are not good choices. ● Underline or…Calculate the dynamic programming matrix and the optimal local and global alignment for the DNA sequences a: GAATTC and b: GATTA, scoring +2 for a match, -1 for a mismatch, and using a linear gap penalty function WL) = -2L thank youYou have purified a recombinant form of the p53 protein from E. coli and determined the A280 to be1.35. Calculate the molar and mass concentration of the purified protein if the extinction coefficientand molecular weight of p53 is 35,410 M-1 cm-1 and 43,653 Da, respectively (l = 1 cm).
- Using the Dynamic Programming algorithm for pairwise local alignment we covered in class, construct the dynamic programming score table for a local alignment of the following two sequences, using the following scoring parameters: match score = +5, mismatch score = -3, gap penalty = -2.: ACGTATCGCGTATA GATGCTCTCGGAAAWhat is score of the best local alignment between these two sequences? Show the alignment of these sequences. asapX The phosphates that make up the phosphodiester bonds in DNA have pKa≈ 2. The genome of the blue crab is 800 million-base-pairs long. What is its total charge on the blue crab genome in aqueous buffer solution when the pH is equal to 2.25?In BLOSUM62 matrix, a conserved Tryptophan position has score S(W,W) = 11, but a conserved Leucine position has score S(L,L) = 4. Give at least one reason why these values differ.
- What is the principle behind the very specific sequence in donning and doffing PPEs? ExplainSDS-PAGE and Agarose gel electrophoresis can both be used to separate proteins or protein- complexes based on their size. Separation of a multi-subunit protein complex by SDS-PAGE resulted in two bands with molecular weights of 86 KDa and 136 KDa, while separation of the same complex using Agarose gel electrophoresis resulted in two bands with molecular weights of 222 KDa and 444 KDa. Based on this information, which of the following statements is most likely to be correct? O The complex has a molecular weight of 222 KDa O The complex exists as a dimer of homo-dimers O The complex exists as a dimer of hetero-dimers SE O The complex exists as a trimer, but the individual protein subunits are covalently crosslinked to each otherWhat is the length in AA’s of the LilP protein? Assume fMet is NOT CLEAVED. Enter just the number, nothing else! Write out the sequence of the polypeptide in AA: use the three letter notation, e.g. Met-Ser-Pro- A lilP mutant called lilPXS is isolated that produces a truncated polypeptide of only 6 AA in length. Describe a single basepair DNA change that would lead to this truncated version of the protein. Multiple options are possible (100 words max.)