Problem Set 14 RNA Transcription, Processing, & Translation

Problem Set 14RNA Transcription, Processing, &amp, TranslationECOL 320: Genetics, F 2011Name: 1. The box below contains portions of a gene sequence in the box below. IUPAC codes denote each ofthe nucleotide bases as follows: A = adenineC = cytosineG = guanineT = thymineDNAU = uracilR = G or A (purine)Y = T or C (pyrimidine)K = G or T (keto)M = A or C (amino)S = G or CW = A or TB = C or G or TD = A or G or TH = A or C or TV = A or C or GN = A G C T (any)5’ —–TATAAA——-YYANWYY——ACCATGG——-MAGGTRAGT——A—–CAGG—-TGA——AATAA—-3’ABCDEFGHa. Under the letters A-H, label the function of each of the sequence motifs. b. Above the sequence, mark the transcription start site with a +1, indicate the location of the 3’ UTRand the 5’ UTR, and draw an arrow at the 3’ cleavage site. c. Is this sequence from a eukaryote or prokaryote? How can you tell?12. DNA from a eukaryotic gene was isolated, denatured, and hybridized to the mRNA transcribed from the gene. The hybridized structure was then observed with the use of an electron microscope. The following structurewas observed. a. How many introns and exons are there in this transcript?b. On the diagram above, identify the location of each of the following: i. The ‘AG’ of the 3’ splice site of the last intronstii. Branch point on the 1 introniii. Promoteriv. 5’ capv. 3’ consensus sequence that signals polyadenylationc. What is the molecular consequence of a mutation that renders the snRNPs found in this cell nonfunctional?23. The following sequence represents the DNA template strand of the first intron of a gene: a. Give the sequence of the mRNA sequence transcribed from this DNA strand and, using thegenetic code, give the amino acid sequence of the polypeptide it encodes. Label the amino andcarboxyl ends. (Note: Do not put ‘stop’. A stop codon does not make anything called ‘stop’. )b. For each of the following codons, give all possible tRNAs. Indicate directionality. Codon 2-Codon 4-Codon 5-c. Give the amino acid sequence of the polypeptide encoded by this sequence after the followingDNA mutations have occurred: For each mutation, go back to the original DNA sequence (i. e. donot assume these are cumulative mutations. )i. a transition at nucleotide #10ii. a transition at nucleotide #12iii. a transition at nucleotide #13iv. an insertion of a “G” immediately following nucleotide #1034. A DNA sequence is shown below. Capital letters indicate the consensus sequence (TATA) or codingsequence (ATG…TAG). The expression of the protein requires the transcription factor p53. The function ofthe protein requires all the specific amino acids in the ORF shown. There is no splicing. sta. In the chart below, enter ‘YES’ or ‘NO’ or ‘Reduced’ in each of the 1 three columns. Enter thenumber of amino acids assembled in the last column. MutationWildtype (no mutation)i. YesYes?Transversion of C at +19v. Yes# Amino AcidsTransition of C at +14iv. Functional?Transversion of A at +5iii. Translated?TATAaa to TTTAccii. Transcribed?Insertion of T between14C &amp, 15Ab. Briefly explain how a transition at +14 (part iii above) would affect function. c. Briefly explain what would happen to the mRNA transcript and/or polypeptide after translation ifthere were an insertion of a T between 14C and 15A (part v in the chart above). 45. A protein domain is a part of protein sequence that can evolve, function, and exist independently of the rest ofthe protein chain. Consider the domain structures and the phenotypes of mutants in the gene shown below. The three domains are shown (amino acids 20-220 for the rectangle, 250-350 for the oval, and 400-450 forthe triangle). The gene has two functions, one in smelling and one in tasting. The gene has no introns. Cells(wt or “wildtype” = normal, mutant 1, mutant 2) are homozygous for each allele. a. Mutant 1 is a deletion that removes the oval domain joining the two domain regions shown. Is thisdeletion likely an in frame or out of frame deletion. Explain. b. What is a likely molecular consequence and phenotype of a frameshift mutation in the oval domain?Explain. c. What is a likely molecular consequence and phenotype of a missense mutation between codons 150and 180 in which an alanine is mutated to a glycine. Explain. d. What is a likely molecular consequence and phenotype of a nonsense mutation at codon 350?5

Problem Set 14 RNA Transcription, Processing, & Translation

Question
Problem Set 14
RNA Transcription, Processing, & Translation
ECOL 320: Genetics, F 2011

Name:

1. The box below contains portions of a gene sequence in the box below. IUPAC codes denote each of
the nucleotide bases as follows:
A = adenine
C = cytosine
G = guanine
T = thymine

DNA

U = uracil
R = G or A (purine)
Y = T or C (pyrimidine)
K = G or T (keto)

M = A or C (amino)
S = G or C
W = A or T
B = C or G or T

D = A or G or T
H = A or C or T
V = A or C or G
N = A G C T (any)

5’ —–TATAAA——-YYANWYY——ACCATGG——-MAGGTRAGT——A—–CAGG—-TGA——AATAA—-3’

A

B

C

D

E

F

G

H

a. Under the letters A-H, label the function of each of the sequence motifs.
b. Above the sequence, mark the transcription start site with a +1, indicate the location of the 3’ UTR
and the 5’ UTR, and draw an arrow at the 3’ cleavage site.
c.

Is this sequence from a eukaryote or prokaryote? How can you tell?

1

2. DNA from a eukaryotic gene was isolated, denatured, and hybridized to the mRNA transcribed from the gene.
The hybridized structure was then observed with the use of an electron microscope. The following structure
was observed.

a. How many introns and exons are there in this transcript?

b. On the diagram above, identify the location of each of the following:
i. The ‘AG’ of the 3’ splice site of the last intron
st
ii. Branch point on the 1 intron
iii. Promoter
iv. 5’ cap
v. 3’ consensus sequence that signals polyadenylation
c.

What is the molecular consequence of a mutation that renders the snRNPs found in this cell nonfunctional?

2

3. The following sequence represents the DNA template strand of the first intron of a gene:

a. Give the sequence of the mRNA sequence transcribed from this DNA strand and, using the
genetic code, give the amino acid sequence of the polypeptide it encodes. Label the amino and
carboxyl ends. (Note: Do not put ‘stop’. A stop codon does not make anything called ‘stop’.)

b. For each of the following codons, give all possible tRNAs. Indicate directionality.
Codon 2-

Codon 4-

Codon 5-

c.

Give the amino acid sequence of the polypeptide encoded by this sequence after the following
DNA mutations have occurred: For each mutation, go back to the original DNA sequence (i.e. do
not assume these are cumulative mutations.)
i. a transition at nucleotide #10

ii. a transition at nucleotide #12

iii. a transition at nucleotide #13

iv. an insertion of a “G” immediately following nucleotide #10

3

4. A DNA sequence is shown below. Capital letters indicate the consensus sequence (TATA) or coding
sequence (ATG…TAG). The expression of the protein requires the transcription factor p53. The function of
the protein requires all the specific amino acids in the ORF shown. There is no splicing.

st

a. In the chart below, enter ‘YES’ or ‘NO’ or ‘Reduced’ in each of the 1 three columns. Enter the
number of amino acids assembled in the last column.
Mutation
Wildtype (no mutation)
i.

Yes

Yes

?

Transversion of C at +19

v.

Yes

# Amino Acids

Transition of C at +14

iv.

Functional?

Transversion of A at +5

iii.

Translated?

TATAaa to TTTAcc

ii.

Transcribed?

Insertion of T between
14C & 15A

b. Briefly explain how a transition at +14 (part iii above) would affect function.

c.

Briefly explain what would happen to the mRNA transcript and/or polypeptide after translation if
there were an insertion of a T between 14C and 15A (part v in the chart above).

4

5. A protein domain is a part of protein sequence that can evolve, function, and exist independently of the rest of
the protein chain. Consider the domain structures and the phenotypes of mutants in the gene shown below.
The three domains are shown (amino acids 20-220 for the rectangle, 250-350 for the oval, and 400-450 for
the triangle). The gene has two functions, one in smelling and one in tasting. The gene has no introns. Cells
(wt or “wildtype” = normal; mutant 1, mutant 2) are homozygous for each allele.

a. Mutant 1 is a deletion that removes the oval domain joining the two domain regions shown. Is this
deletion likely an in frame or out of frame deletion. Explain.

b. What is a likely molecular consequence and phenotype of a frameshift mutation in the oval domain?
Explain.

c.

What is a likely molecular consequence and phenotype of a missense mutation between codons 150
and 180 in which an alanine is mutated to a glycine. Explain.

d. What is a likely molecular consequence and phenotype of a nonsense mutation at codon 350?

5