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Show nucleotide FASTA files for 4 bacterial genes

Show amino acid FASTA files for 4 bacterial genes

Annotate the start codons for 4 bacterial genes

Annotate the stop codons for 4 bacterial genes

Find a bacterial promoter sequence

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Casey Durgan
Casey DurganLv2
28 Sep 2019

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Related questions

1. Bacterial transcription initiation

a. What are the major components of a bacterial promoter? Do you understand their nomenclature (i.e. how are they related to the transcription start site)?

b. What is the function of each promoter element during initiation?

c. What sequence-based factors contribute to promoter strength?

d. Why are there multiple sigma factors? How do they function to turn on different genes?

e. Why are short (<10 nt) abortive products possible during transcription intiation? What happens to RNAP when these products are released?

f. What changes in the RNAP holoenzyme occur following promoter escape?

1. You have cloned a human gene along with its promoter and ribosome-binding site in a bacterial cloning vector and then introduced the recombinant plasmid into a bacterial host cell that supports the replication and segregation of the cloning vector. Unfortunately, even though you know the whole human gene sequence is present (by DNA hybridization); you cannot get expression of the gene. Which of the following is NOT a reason why there is no expression?

A. The vector cannot replicate

B. The human promoter is not recognized by the bacterial host cell

C. The ribosome-binding site is not recognized by the bacterial host cell

D. The human gene lacks introns, so it is not transcribed by the host bacterium

2. Restriction endonucleases are:

A. sequence-specific

B. able to recognize any 4-, 6-, or 8-base pair sequence

C. always able to produce single stranded tails

D. only able to cleave bacterial DNA

3. Which of the following is NOT a required characteristic of cloning vectors?

A. Genes for replication of vector DNA and segregation to progeny cells

B. Genes for selection of cells carrying the vector (e.g., antibiotic-resistance)

C. DNA sequence for the introduction of foreign DNA where the integrated DNA does not disable the vector

D. None of the above

4. A poly (T) primer is used to produce cDNA from mammalian mRNA. Which of the following would be used to produce cDNA from bacterial mRNA?

A. A poly (T) primer

B. A random DNA sequence primer

C. A poly (A) primer

D. A poly (GC) primer

a. Download a nucleotide sequence from GenBank for a gene of interest. What gene did you download? Was the sequence published? Where, when, and by whom? What format is your nucleotide sequence in? Why is this gene of interest?

b. Perform a BLAST search with your DNA sequence. What does it match to (show the top 10 hits)? Are they from the same study or different studies? Is your sequence protein coding or not? What is the E-value of hit number 10 compared to hit number 1? What is an E-value?

c. Produce a pdf file with a short fragment (no more than 500 bps) of your sequence and the top 5 hits from your BLAST search showing them in FASTA format plus hits from at least 3 different species. What species are included in your data? List the taxonomic hierarchy of these species?

d. How many characters are in your FASTA file? How much space would you need to store a FASTA file of a human genome? A bacterial genome? A viral genome? How did you calculate this?

e. Translate the following sequence to amino acids (assuming the reading frame starts at the first letter):

ccgtcgtagc accgagcctc agcaccacga aagagattga agtagttcct cggaaagttc ttcgactctt ccttgaaaca tgtcttcctg gagcaaccaa cctgccatgg atgattatgg

What does this sequence encode? From what organism does this sequence come? What is the function of this gene? What are the proportions of polar, non-polar, and charged amino acids (attach a link to or copy of the resource you used to help you determine this)?

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