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26 May 2019

Thank you to whoever can help!!

For optimal alignment of 2 sequences, fill in the blanks for the following dot plot:

a) A diagonal move indicates 2 residues are___

b) A vertical move indicates a ___

c) A horizontal move indicates an ___

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Keith Leannon
Keith LeannonLv2
27 May 2019

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Related questions

1) The observed numbers of dominant and recessive offspring in an F2 generation is 53 and 47. This indicates a _______ cross.

2) Using the observed numbers in question 1, what would the expected number be for both dominant and recessive phenotypes?

Please answer both questions and explain if you can this is due today your help is greatly appreciated thank you.

Section A – Edit distance (8 points total)

1. Find the edit distance between ACGAAGTTC and ACCAAGGTGTTC. How do you know it is at most that much? How do you know it is at least that much?

Section B – More on sequence alignment (52 points total)

2. (6 points) Which of the following would be the two most appropriate to assess whether there are regions of homology between two distantly related proteins? Select two.

A) Needleman-Wunsch Algorithm

B) edit distance

C) local sequence alignment

D) global sequence alignment

E) dot plot

3. Consider the following alignment: ACACCAGGTCCCC ACA-----TGACC

a) (3 points) With a match score of +3, and mismatch score of -1, and using a gap penalty of -2, what is the score of the above alignment?

b) (3 points) If we keep the same match score and mismatch score, but use a gap open penalty of -6 and a gap length penalty of -1 per additional residue, what is the score of the previous alignment?

c) (8 points) Using the scoring system used in part b (match +3; mismatch -1; gap open -6 ; gap extension -1), Which of the following alignments is best? Which is worst? How do you know?

A) ACACCAGGTCCC A---CATGA-CC

B) ACACCAGGTCCC ACA---TGACC

C) ACACCAGGTCCC ACATGA----CC

D) ACACCAGGTC-CC ACA-----TGACC

E) ACACCAGGTCCC ACA--TG-ACC

F) ACA---CCAGGTCCC ACATGACC-------

4. Look up the INS gene in Entrez Gene.

a) (2 points) What tag do you put inside square brackets after INS to search for INS as a gene symbol?

b) (2 points) Find the record for the human INS gene. Which chromosome is INS on?

c) (2 points) What is the accession number for the RefSeq record for the shortest mRNA for human INS?

d) (2 points) What is the accession number for the RefSeq record for the human gene’s genomic DNA?

d) (6 points) Using the Needleman-Wunsch program, how could you find the mRNA sequence within the genomic DNA version? Give the best strategy, including the scoring parameters.

e) (4 points) Find the next gene upstream of the INS transcription start site. Which neurotransmitter does the product of this next gene make? How many base pairs separate the two genes?

f) (2 points) Now look up ins-1 as a gene symbol in Entrez Gene. Choose the entry for the worm C. elegans. Which chromosome is it on?

g) (2 points) What is the URL for the Wormbase link on this Entrez Gene record? What is the gene accession number for ins-1 in the C. elegans genome database?

g) (10 points) Perform Needleman-Wunsch alignments between C. elegans INS- 1 protein and Homo sapiens INS preproprotein, using the default parameters, except changing the substitution matrix to PAM10 for one alignment, and PAM50 for the second alignment. Use the following online tool: https://www.ebi.ac.uk/Tools/psa/emboss_needle/ What are the number of identical residues, score, and number of gapped residues for each of the two alignments? What conclusions can you draw about which of the two matrices, PAM10 or PAM50, is more appropriate in this situation?

What is the percent sequence identity between hemoglobin (2HHB) and myoglobin (1A6M)?

A.

93%
B.

39.46%
C.

25.17%
D.

4.08%

QUESTION 2

Which of the following statements is consistent with the sequence similarity parameter?

A.

The abundance of amino acids with similar properties that are arranged in the same order is equal to the abundance of identical amino acids.
B.

These parameters are not related and cannot be compared.
C.

The abundance of amino acids with similar properties that are arranged in the same order is less than the abundance of identical amino acids.
D.

The abundance of amino acids with similar properties that are arranged in the same order is higher than the abundance of identical amino acids.

QUESTION 3

Which of the following statements is consistent with the similarity parameter and visualization of the aligned structures?

A.

Hemoglobin and myoglobin do not have similar structures.
B.

Hemoglobin and myoglobin have only moderately similar structures, as indicated by the large abundance of gray chains.
C.

Hemoglobin and myoglobin have very similar structures.
D.

Hemoglobin and myoglobin are perfectly aligned at every amino acid.

QUESTION 4

Hemoglobin (2HHB) is ___ amino acids shorter than myoglobin; the sequence alignment considers only ___ amino acids, and alignment results show that hemoglobin is missing a contiguous strand of ___ amino acids.

A.

10; 141; 6
B.

10; 141; 5
C.

10; 147; 6
D.

10; 147; 5

QUESTION 5

Which of the following statements best describes the evolutionary relationship between hemoglobin and myoglobin?

A.

The low sequence identity indicates that hemoglobin and myoglobin are not related, as tertiary structure cannot be used to study protein evolution.
B.

Both the high sequence identity and structural similarity suggest that hemoglobin and myoglobin are related.
C.

The difference in sequence identity and similarity values suggests that hemoglobin and myoglobin are related.
D.

The high structural similarity suggests that hemoglobin and myoglobin are related, while the low sequence identity suggests that the genes for each protein have diverged through mutation and deletion of several amino acids.

QUESTION 6

The comparison of sequences and tertiary structures in this exercise indicates that:

A.

only similar amino acid sequences can provide the same tertiary structure.
B.

different amino acid sequences can provide very similar tertiary structures.

QUESTION 7

The structures of deoxyhemoglobin and oxyhemoglobin are derived from the same source, have the same exact amino acid sequence and length, and differ only in the presence of noncovalently bound oxygen.

A.

True
B.

False

QUESTION 8

When using the Sequencing and Structure Alignment tool, the degree of the structural similarity is shown by the superimposition of the backbones. Accordingly, which of the following statement best describes the comparison of deoxyhemoglobin and oxyhemoglobin?

A.

Only slight differences in the backbone traces occur throughout the aligned proteins.
B.

The only differences in the backbone traces occur near the oxygen-binding sites.
C.

The backbone traces of the proteins are drastically different.
D.

The backbone traces of the proteins are identical.

QUESTION 9

The alignment of 2HHB and 1HHO shows that the binding of oxygen results in _______ in the protein.

A.

minor conformational changes at sites proximal and distal to the oxygen-binding site
B.

no conformational change
C.

drastic conformational changes
D.

minor conformational changes only within the oxygen-binding site

QUESTION 10

The alignment of 2HHB and 1HHO shows that the conformation of the Fe-heme group _____ upon oxygen binding.

A.

changes
B.

does not change

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