Construct a multiple protein sequence alignment using human HOXD13 and 9 other orthologues of human HOXD13. In the figure legend, describe what is being shown, and specify the size (start and stop number of amino acid) and location of conserved domain(s) in HOXD13 level: UNI
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- Sequence: CCACCTGTACCCGGACACACCCTGGTGTCC What human disease has been connected to this gene? Calculate molecular weight (kiloDalton, kD) and calculated pI (the pH where the protein carries no net electrical charge) of the protein.Which of the sequences below do you think would most likely be found in an intrinsically disordered protein? GSSKSSKKREPS MVLITTEVKAT MVLITTEVIIAA All of these could be found in an intrinsically disordered proteinA common strategy for identifying distantly relatedhomologous proteins is to search the database using a shortsignature sequence indicative of the particular proteinfunction. Why is it better to search with a short sequencethan with a long sequence? Do you not have more chancesfor a “hit” in the database with a long sequence?
- Shown below is a portion of a DNA sequence ( 31 base pairs long ) that encodes the last amino acids of a protein : The first three underlined base pairs indicate the frame and include the coding region . 123456789 A. Write the peptide sequence of the last 6 amino acids of the protein . Label both ends of the peptide . B. A insertion of one base pair causes the protein to decrease in length by 5 amino acids . With respect to the sequence given above , where does this insertion occur , and what base pair will you insert ? C. An change of one base pair leads to the protein to increase in length by one amino acid. With respect to the sequence given above , which base pair would you change ? How would you change this base pair for the protein to increase in length by one amino acid ?A comparison of the aligned amino acid sequences of two proteins each consisting of 150 amino acids reveals them to be only 8% identical. However, their threedimensional structures are very similar. Are these two proteins related evolutionarily? Explain1. For each of the sequences given below, list what type of secondary structural element, if any is most likely to be formed by that amino acid sequence. 1a. SEGEWQLVLHVWA 1b. GKGPPGPPGPRGPC 1c. CHSRHPGDFSC 1d. ASVRMNLGF
- A very common molecular biology research method is to analyze cell or tissue homogenates by SDS-polyacrylamide gel electrophoresis and immunoblotting (Western blot). What can we learn about a protein of interest from this type of analysis? More than one answer is correct. Options: Determine the tertiary structure of the protein of interest. Determine or verify the molecular weight of the protein of interest. Compare the levels of the protein of interest in two different cell types. Determine the amino acid sequence from the product ion spectrum. Determine the intracellular binding partners of the protein of interest.Below is a sequence of 540 bases from a genome. What information would you use to find the beginnings and ends of open reading frames? How many open reading frames can you find in this sequence? Which open reading frame is likely to represent a protein- coding sequence, and why? Which are probably not functioning protein-coding sequences, and why? Note: for simplicitys sake, analyze only this one strand of the DNA double helix, reading from left to right, so you will only be analyzing three of the six reading frames shown in Figure 19.4.Describe the planar sections of the primary sequence, their influence on the shape of the protein backbone, and identify these sections given a drawing of the primary sequence.
- How many binary sequences of length n contain at most five 1 digits? The genetic code specifies an amino acid through a sequence of three nucleotides. Each nucleotide can be of one of the four types T, A, C and G, beingrepetitions allowed. How many amino acids can be encoded in this way?And if there are n types. CompareShown below are two homologous lengths of the alpha and betachains of human hemoglobin. Consult a genetic code dictionary and determine how many amino acid substitutionsmay have occurred as a result of a single nucleotidesubstitution. For any that cannot occur as a result of a singlechange, determine the minimal mutational distance. Alpha: ala val ala his val asp asp met proBeta: gly leu ala his leu asp asn leu lysYou discovered a (tiny) novel protein and figured out that the protein sequence was: Met-Ala-Arg-Gly-Trp-Ala-Pro Work backwards (showing your work) to identify 2 possible DNA sequences that might encode your protein. Sequence 1: ______________________________________________________________________ Sequence 2: ______________________________________________________________________ Based on these sequences, is there anything you could infer about where this organism might live? Could the DNA in your possible sequences be beneficial for any particular environments?