The sequences below show the first 60 amino acids of onepolypeptide, using the one-letter abbreviations for the aminoacids. An underscore (_) indicates a gap inserted in a sequence tooptimize its alignment with the corresponding sequence inArabidopsis.
Acyrthosiphon (aphid) IKIIIIGSGV GGTAAAARLS KKGFQVEVYEKNSYNGGRCS IIR_HNGHRF DQGPSL__YL Pantoea (bacterium) KRTFVIGAGFGGLALAIRLQ AAGIATTVLE QHDKPGGRAY VWQ_DQGFTF DAGPTV__IT
At how many positions are the amino acids the samebetween the two species?
The sequences below show the first 60 amino acids of onepolypeptide, using the one-letter abbreviations for the aminoacids. An underscore (_) indicates a gap inserted in a sequence tooptimize its alignment with the corresponding sequence inArabidopsis.
Acyrthosiphon (aphid) IKIIIIGSGV GGTAAAARLS KKGFQVEVYEKNSYNGGRCS IIR_HNGHRF DQGPSL__YL Pantoea (bacterium) KRTFVIGAGFGGLALAIRLQ AAGIATTVLE QHDKPGGRAY VWQ_DQGFTF DAGPTV__IT
At how many positions are the amino acids the samebetween the two species?
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Instructions
BACKGROUND
The amino acid sequence for a protein that is associated with the onset of Huntington's Disease in humans is 582 amino acids long and is provided below. This disease is autosomal dominant and results in a prolonged degeneration of nerve cells in the brain.
INSTRUCTIONS
For this assignment, use any method you determine most feasible (i.e. programming in MATlab, R script, Crystal Ball, Witchcraft/Hocus Pocus, etc.) to decipher the amino acid composition of this protein and answer the 15 questions associated with this protein and its associated amino acid structure.
You will be calculating proportions (percentages - %) for this assignment. Calculate all proportions to 1 decimal place and make sure you have rounded up or down correctly. If unsure, use a spreadsheet program such as Excel to display your proportional calculations to 1 decimal place.
Spelling matters (Incorrect spelling will be graded as such - incorrect).
Huntington Disease Associated Protein Amino Acid Sequence
The first amino acid below ('m') represents the amino (NH3) terminus of this protein. The last amino acid in this sequence represents the carboxy (COOH) terminus and is the very last 'c' at the bottom of this protein sequence structure. The amino acids are numbered individually across the rows (left to right) beginning from the amino terminus (#1) to the carboxy terminus (#582).
| mvskreniat | hhlyqawdpv | pslspattga | lisheklllq | inperelgsm | syklgqvsih |
| svwlgnsitp | lreeewdeee | eeeadapaps | spptspvnsr | khragvdihs | csqfllelys |
| rwilpsssar | rtpailisev | vrsllvvsdl | fternqfelm | yvtltelrrv | hpsedeilaq |
| ylvpatckaa | avlgmdkava | epvsrllest | lrsshlpsrv | galhgilyvl | ecdllddtak |
| qlipvisdyl | lsnlkgiahc | vnihsqqhvl | vmcatafyli | enypldvgpe | fsasiiqmcg |
| vmlsgseest | psiiyhcalr | glerlllseq | lsrldaeslv | klsvdrvnvh | sphramaalg |
| lmltcmytgk | ekvspgrtsd | pnpaapdses | vivamervsv | lfdrirkgfp | cearvvaril |
| pqflddffpp | qdimnkvige | flsnqqpypq | fmatvvykvf | qtlhstgqss | mvrdwvmlsl |
| snftqrapva | matwslscff | vsastspwva | ailphvisrm | gkleqvdvnl | fclvatdfyr |
| hqieeeldrr | afqsvlevva | apgspyhrll | tclrnvhkvt | tc | CARBOXY TERMINUS |
I need these decoded in order to answer the following questions:
a.) What is the name of the least abundant amino acid in this protein and what proportion of the total amino acids in the protein does this individual amino acid represent?
b.) What is the proportion of essential amino acids included in this protein sequence?
c.)How many Tryptophan residues are present in this protein sequence?
d.) The amino acid sequence from residues 73-85 is represented by the amino acids EEEWDEEEEEEAD, how would you generally classify this small region of the protein
e.) Two amino acids are present in the same proportion in this protein, which two are those?
f.) How many positively charged amino acids are present in this protein?
g.)Which class of amino acids is the most abundant in this protein?
h.) What amino acid(s) is/are present at locations 572 and 582 in the Huntington Disease protein (Full Amino Acid Name(s))
i.) What type of structure could form between these amino acids that could help stabilize this protein's structure?
j.) How many valine residues are present in this protein?
k.)Which class of amino acids is least abundant in this protein?
l.) How may negatively charged amino acids are present in the Huntington disease protein?
m.) How many Aspartic Acid residues are present in this protein and what proportion do they represent of the total amino acids in this protein?
n.)Summed together, how many hydrophilic amino acid residues are present in this protein?
o.)What is the sequence of amino acids from positions 487-492 (First letters only)?
p.) How would you classify this area of the Huntington protein based on these amino acids?
Below you have the sequence of 33 nucleotides(part of a coding region of gene TTr34) from two different species of birds (Species A and Species B). For simplicity, the amino acids encoded by the codons of Species A is also indicated, and â.â indicates the same nucleotide as the one observed in the first sequence.
| Pro | Gly | Asn | Thr | His | Glu | Ala | Gln | Lys | Ala | Val | |
| Species A | CCT | GGG | AAT | ACT | CAT | GAA | GCA | CAA | AAA | GCC | GTC |
| Species B | . . G | . . T | . . C | . . . | . . . | . C . | . . . | . C . | . . T | A . . | . . T |
Use these two sequences to estimate the molecular distances.
a. How many nucleotide changes produce a change in amino acid (nonsynonymous changes)(use the genetic code)?
b. How many nucleotide changes are synonymous (do not cause a change in amino acid)(use the genetic code)?
c. Calculate the molecular distance for synonymous (Ds) and Nonsynonymous (Da) for this gene region without correction. To estimate the total number of synonymous and nonsynonymous sites, assume that 25% of the sites are synonymous and 75% of sites are nonsynonymous.
* Please show all work and explain. *