Download set 3

Biology 105/Summer 2013
PROBLEM SET #3
7/24/13
I.
A. The bacterium E. coli uses the "standard" codon assignments given in the genetic code table
in the textbook.
In E. coli there is only a single form of tRNACys and a single form tRNATrp.
What are the expected anticodons for these tRNA's?
tRNACys
3' __ __ __ 5'
tRNATrp
3' __ __ __ 5'
B. In mammalian mitochondria we find a variant of the standard code that exhibits several
alternate codon assignments as given below:
CODON
5' UGU 3'
5' UGC 3'
5' UGA 3'
5' UGG 3'
Cys
Cys
Trp
Trp
That is, 5’ UGA 3’ is a sense codon, not a termination codon in this variant.
Similar to E. coli, there is a single form of tRNATrp in mammalian mitochondria.
What is the probable anticodon sequence of tRNATrp in mammalian mitochondria?
tRNATrp
3' __ __ __ 5'
C. Briefly describe the nature of the mutation (location, and identity of nucleotides involved) that
would account for the change from Stop to Trp for the UGA codon in the mitochondrial code.
REFERENCE:
Different pattern of codon recognition by mammalian mitochondrial tRNAs
Proc. Natl. Acad.Sci.USA Vol.7,No.6,pp.3164-3166,June1980
http://www.pnas.org/content/77/6/3164.full.pdf
Biology 105/Summer 2013
PROBLEM SET #3
7/24/13
II.
The table below represents the DNA sequence of a short region within a gene, the sequence of
the RNA transcript, the anticodon sequences of the tRNA’s that decode the mRNA and the amino
acid sequence of the protein product.
The identities of some nucleotides and amino acid/s are given, but most boxes are left blank. You
must fill in all the blank boxes with the appropriate nucleotide or amino acid. In some cases there
may be several possible choices, in which case you must supply ALL possibilities.
You must also fill in the boxes on the left with the appropriate designations of strand polarity (5’,
3’, NH2, COOH). DO NOT assume that any rows are given according to a standard left-right
convention for writing polarities in texts and diagrams. However, you should assume that the
polarity of a given row is consistent with the other rows, with respect to structural and mechanistic
principles.
Make up a few of these problems for yourself and friends using the template below:
Polarity
DNA
Doulbe Helix
mRNA
tRNA
protein
Biology 105/Summer 2013
PROBLEM SET #3
7/24/13
III.
The diagram represents a segment in a larger DNA molecule, where a base mismatch (G with T)
has resulted from the misincorporation of a nucleotide durimg replication. The diagram also
shows a nearby GATC sequence.
1.
Which of the bases in the mismatch is erroneous?
2.
Use an arrow to indicate the approximate location of strand cutting by the endonuclease
MutH.
3.
If the mismatch is not repaired, the overall mutation that would result is:
AT ---> GC
GC ---> AT
AT ---> TA
GC ---> CG
AT --->CG
GC ---> TA