Download prokaryotic biology

PROKARYOTIC BIOLOGY
MCB 4403
R. H. REEVES
Project I: A Prokaryotic Gene - SAMPLE
At the bottom of this page is a sequence of DNA that encodes a
typical gene found in the genome of Escherichia coli. The nucleotide
sequence shown represents the “sense” strand which is complimentary to
and in the opposite direction of the template strand. In other words
the given sequence of this DNA is the same as the mRNA sequence.
The
sequence is given in GenBank format; it is presented in lines of 60
nucleotides, separated in groups of ten, and numbered on the left for
easy identification.
Within this sequence is the gene and all the
signals needed for transcription and translation. You are to answer
the questions on the next 2 pages (in the spaces provided) and turn in
the assignment on Friday, October 12.
To locate sequences use the numbering system as indicated on the left.
1
atatggggca tttactacct gtaccctgat aatatctgct attactacct ttccatcccg
61
gtactgatcg tactgcaaag gcacttgaca ccatgctagg agtaccctat aatggactcg
-35
S D
-10
+1
Start ORF
121
ctcacgagtt cataggaggu tcctcccatg agctatttaa cggcaacagt taaccagctg
181
ccgcaaaaac cacgtgctcg caaagttgcg aaaagcaacg tgcctgcgct ggaagcatgc
241
gtacgcaaac gtggcgtatg tactcgtgta tatactacca ctcctaaaaa accgaactcc
301
cgcctgcgta aagtatgccg tgttcgtctg actaacggtt tcgaagtgac ttcctacatc
361
agtggtgaag gtcacaacct gcaggagcac tccgtgatcc tgatccgtgg cggtcgtgtt
421
tttgacctcc cgggtgttcg ttaccacacc gtacgtggtg cgcttgactg ctccggcgtt
481
aaagaccgta agcaggctcg ttccaagtat ggcgtgaagc gtcctaaggc ttaatggttc
541
tccgttaact acgcaaagta ggatcagtcg atcctacttt tttttacgac gacgtaatag
601
cgtactattt tcgtacccgg tttcagactt ttgagactac atacggtttt ctactacccc
661
atatggggca tttactacct gtaccctgat aatatctgct attactacct ttccatcccg
721
ggactactga ccatgactaa gctaggacta gactaccatc atatactacg ccatatgcag
Stop
Terminator
Answer all the following questions:
[5 points each]
TRANSLATION:
1.
Where is the gene, the ORF?
What is its length in
nucleotides and how many amino acids are in its protein
product?
148-531(or 534), 384(387) nucleotides (bp)
128 amino acids
2.
Where is the start codon? What does it code for?
Where is the stop codon? Is it amber, ocher or opal?
3.
What are the codons for amino acids 4, 5 and 6 and what are these
three amino acids?
4.
What is the c-terminal amino acid of this protein?
5.
Locate the Shine-Delgarno Sequence (RBS).
sequence?
6.
You have isolated an E. coli strain with a mutation in your
protein gene. The sequence of this strain has a base change at
position 318, a C to G change. What is the effect of this
mutation on your protein?
7.
Another mutant is isolated with an A inserted between position
420 and 421. What is the effect on the protein produced by this
mutant gene?
What is its nucleotide
TRANSCRIPTION:
1.
Locate the promoter (-35 box to the +1 nucleotide).
the sequence below.
2.
Where is the terminator and what is its sequence?
3.
Is there any evidence for the regulation of this gene.
the evidence and why?
4.
What is the length (how many nucleotides) of the transcript?
10 points extra
Write out
What is
1.
An amber nonsense mutation of this gene found in another E. coli
strain has been located to codon 75. What is the base change for
this mutation (as seen in the mRNA)? What is the base-pair
change in the DNA?
2.
Locate the GenBank entry with the accession number: X76945
What is the source (taxon, genus/species) of this gene?
What does the gene code for?
Where is the gene (ORF) within the entry (Use the numbering
system in the entry.)?
What is the tenth amino acid in the protein, the last amino acid
and what are their codons?
Locate the position and sequence of the Shine-Delgarno sequence
for this gene.