Reference no: EM132579305

1. In the case of a transmembrane protein (see https://mfrlab.org/teaching/stbc2012/): a computer program that is designed to find a transmembrane helix given a protein sequence will need to have the following features:

A. Be able to read in a PDB structure
B. Be able to read in a sequence
C. Be able to identify a stretch of 35 hydrophobic residues
D. Be able to identify a stretch of 23-25 hydrophobic residues
E. Be able to identify alternating hydrophobic and hydrophilic residues

2. As a guide refer to: https://mfrlab.org/teaching/stbc2012/. A computer program has identified a series of alternating hydrophobic and hydrophilic residues when it was processing a sequence input. Which of the following are possible for that sequence (select all that apply):

A. The sequence is a beta strand that is on the surface of a water soluble protein.
B. The sequence is a transmembrane helix.
C. The sequence is a transmembrane beta strand.
D. The sequence is located at the core of a hydrophobic protein.
E. The sequence is a beta strand that is on the surface of a transmembrane pore with one side facing the membrane bi-layer and the other side facing a water channel.

3. Using the sequence of the BPSL1549 protein - carry out an NCBI BLAST search using an appropriate BLAST program for the type of input sequence and restrict your search to the non redundant protein sequences (nr) database. What does the list of significant alignments tell you? Select all that apply.

A. Most of the hits appears to belong mainly in the genus Burkholderia.
B. There appears to be a B. mallei homolog that has an acceptable E value but only has a query coverage of 18%.
C. There is one significant homolog of the protein from Skemanella stibiiresistens.
D. The protein in theory could be used as a drug against cancer cells although it hasn't been proven.
E. The protein is possibly a toxin.

4. A recent journal article has identified an important toxin found in many bacterial pathogens. You have just received the sequencing data for the genome of a bacterial pathogen that was isolated from a patient. How do you proceed with confirming that the pathogen that you have the sequence data for also has the important toxin that was reported?

A. Run BLAST: use the protein sequence as input for a tblastn search against the new genome as the database.
B. Carry out a multiple sequence alignment of the toxin sequence against the new genome sequence.
C. Run BLAST: use protein sequence as the input for a blastx search against the new genome as the database.
D. Carry out a multiple sequence alignment of all the genes in the newly sequenced genome.
E. Run BLAST: use the new genome sequence as input for a tblastx search against the protein sequence as the database.

5. As a guide refer to: https://mfrlab.org/teaching/stbc2012/. Human growth hormone and bacteriorhodopsin both have a similar arrangement of helix bundles. However, the surface of the growth hormone protein is composed of primarily hydrophilic residues while the sequence of bacteriorhodopsin is composed of mostly hydrophobic residues. Select ALL true statements from the list below that can explain this observation.

A. Human growth hormone is water soluble / in an aqueous environment.
B. Bacteriorhodopsin is in a hydrophobic environment.
C. Human growth hormone is in a hydrophobic environment.
D. Bacteriorhodopsin is in a hydrophilic environment.
E. The entropy that drives protein folding forces the folding of the bacteriorhodopsin because it is in a water soluble environment.

6. You have carried out a multiple sequence alignment of 7 gene sequences. A defect in the protein sequence of this gene can cause a deadly disease called disease DD. One of the 7 genes belongs to a patient with the DD disease. The other 6 belong to individuals who do not have DD disease. After receiving the alignment results, you were able to identify several SNPs in the alignment. However, after you had translated all the genes, they appeared to be synonymous mutations - in other words, although the nucleotide sequences had differences, the protein sequences turned out to be the same. What are possible explanations for your observation? Select ALL answers that apply.

A. The DD disease in this case is a result of epigenetics - where nucleotide modifications may result in deficiencies in producing the protein.
B. It is common for sequence alignments to not be able to detect similarity at the protein level when there are differences at the nucleotide level.
C. A factor located elsewhere that is involved in regulating the production of this gene is faulty thus causing the protein to not be produced.
D. It doesn't matter that no differences were detected at the protein level because the SNPs can already cause a change in the protein conformation.
E. The SNPs result in a truncated protein thus it does not matter that there are no differences between the protein sequences.

7. The method of alignment that is suitable for aligning closely related sequences is:

A. paired-neighbours alignment
B. global alignment
C. local alignment
D. statistical alignment
E. matrix alignment

8. The type of alignment that tries to align the entire sequence is:

A. paired-neighbours alignment
B. global alignment
C. local alignment
D. statistical alignment
E. matrix alignment

9. The procedure used to align many sequences at the same time is called:

A. diversity sequence alignment
B. multiple sequence alignment
C. local alignment
D. multiple statistical alignment
E. substitution matrix alignment

10. The method of alignment that tries to align regions with high level matches without considering the alignment of the rest of the sequence is called:

A. global alignment
B. multiple sequence alignment
C. local alignment
D. multiple statistical alignment
E. high level matching alignment

11. The type of sequence alignments that is most suited for finding conserved patterns in DNA or protein sequences is called:

A. global alignment / multiple sequence alignment
B. local multiple alignment
C. local alignment / multiple polymorphism search
D. multiple statistical alignment
E. high level matching alignment

12. Your research group has just completed the genome sequencing for a new bacterial species named V. novela. This newly sequenced genome has not yet been annotated. Your colleague has been studying the VTOX protein in E. modeli for many years and is interested in finding out whether a homolog for the VTOX protein can be found in the bacterial species V. novela. Select the options that are TRUE that can be used to provide an answer to your colleague.

A. Carry out a blastn against the PDB database.
B. Use the blastp program with the VTOX protein as the query to search the UniProt database.
C. Use the VTOX protein sequence as a query for the tblastn program to search the V. novela genome as the database.
D. Search the E. modeli database using tblastn and the VTOX protein as the query.
E. Carry out a gene prediction for the V. novela genome and use the resulting genes as blastx queries to search a protein sequence database.