Download Investigating the effects of different types of mutations

Investigating the effects of different types of mutations
The Genetic Code
How does information go from a sequence made of the four different bases of DNA (adenine,
guanine, thymine and cytosine) to a protein sequence made up of one of 20 different amino acids?
The sequence of DNA that encodes for a protein is called a gene. Genes encode for all proteinsfrom the enzymes needed in respiration to the tough keratin protein that makes up your fingernails.
The first step in the production of a protein is creating a messenger that can pass from the DNA in
the nucleus to the ribosomes in the endoplasmic reticulum. This messenger is RNA and the process
of making RNA from DNA is called transcription. In the endoplasmic reticulum the RNA binds to a
ribosome which is made of two subunits, large and small. The ribosome moves along the messenger
RNA. At each codon a tRNA with a complementary sequence to the codon and carrying an amino
acid enters the ribosome. The ribosome takes the amino acid and adds it to the growing chain of
amino acids (also known peptide). When the ribosome encounters one of the three stop codons it
releases the completed protein and the RNA message.
http://www.nature.com/nature/journal/v443/n7107/fig_tab/nature05002_F1.html
So from the DNA sequence of a gene it is possible to predict the RNA sequence, and in turn the
primary sequence (the order of the amino acids) of the protein it encodes. Amino acids can be
referred to by name (eg Glycine), by three letter abbreviation (Gly) or by single letter abbreviation
(G).
For example
Step #1: Transcribe DNA  RNA
Remember, RNA does not have thymine, it has uracil instead. So:
AU
TA
CG
GC
For example:
DNA (decode top strand)
ACATCTTATACGTTC
TGTAGAATATGCAAG
UGUAGAAUAUGCAAG
Becomes RNA
Step #2: Translate RNA  Protein (chain of amino acids)
Second Letter
U
C
A
UUU
UAU
UCC
UAC
UGC
UUA
UCA
UAA
UGA
UUG
UCG
UAG
UGG
CUU
CCU
CAU
CUC
CCC
CAC
C
CCA
CAA
CUA
CUG
A
CCG
Proline (P)
CAG
Stop (*)
Histidine
(H)
Glutamine
(Q)
CGA
Asparagine
(N)
AGU
CGG
AAU
AUC
ACC
AAC
ACA
AAA
AGA
AAG
AGG
Serine (S)
ACG
Threonine
(T)
GUU
GCU
GAU
GUC
GCC
GAC
GUA
GCA
GAA
GUG
Valine (V)
Arginine (R)
AGC
Isoleucine (I)
Methionine
(M)
Tryptophan
(W)
CGC
ACU
AUA
Cysteine (C)
Stop (*)
CGU
AUU
AUG
G
Leucine (L)
Serine (S)
UGU
GCG
Alanine
(A)
GAG
Lysine (K)
Aspartic
acid (D)
Glutamic
acid (E)
Arginine (R)
GGU
GGC
GGA
GGG
Glycine (G)
U
C
A
G
U
C
A
G
U
C
A
G
U
C
A
G
Third Letter
First Letter
U
Tyrosine (Y)
G
UCU
UUC
Phenylalanine
(F)
For example:
RNA
Becomes protein
UGUAGAAUAUGCAAG
C
R
I
C
K
What do the following secret DNA messages say?
Message 1
CCGCTTTTACTCTGATAGACGAGT
GGCGAAAATGAGACTATCTGCTCA
Message 2
TCGACATATCTTTTAACGCTT
AGCTGTATAGAAAATTGCGAA
Message 3
CTATTGCGCTAGAGTTTGCTTCGTTGG
GATAACGCGATCTCAAACGAAGCAACC
Message 4
ACCGTAATATACCTC?
TGGCATTATATGGAG
What is one possible DNA sequence that would encode for the protein HELP ME
Mutations
Every now and then the sequence of DNA can change. This can be due to damage to the DNA by
chemicals or radiation such as UV light, or by errors made during transcription. There are a number
of different types of mutation and these mutations have different effects on the protein.
For example, consider the DNA sequence:
ATGATCAGTACCGCGAAAGAA
TACTAGTCATGGCGCTTTCTT
What would the protein sequence be?
Now consider the different mutations in the table below. Work out the sequence of the protein
from the DNA sequence and rate how severe you think the effects of the mutation are from 0 (no
change) to 10 (major change). Note, if you find a stop codon, write a * and don’t decode the rest of
the sequence.
Q
Type of mutation
1
2
3
4
5
Original sequence
Single base change
Single base change
Single base change
Single base
insertion
Single base
deletion
Large insertion
Large insertion
Large deletion
Large deletion
Large deletion
6
7
8
9
10
11
DNA sequence
Protein sequence
ATGATCAGTACCGCGAAAGAA
Severity
0
ATGAACAGTACCGCGAAAGAA
ATGATCAGTACCGCGAAGGAA
GTGATCAGTACCGCGAAAGAA
ATGATCAAGTACCGCGAAAGAA
ATGACAGTACCGCGAAAGAA
ATGATCAGTACCACTAUGGCGAAAGAA
A T G A T C A G A A A A AT A C C G C G A A A G A A
ATGAAAGAA
ATG
ATGATCAGTACCAAAGAA
Q12. Did all single base change mutations have the same in severity? Explain your answer.
Q13. Did all insertion and deletion mutations have the same severity? Explain your answer.
Q14. Most proteins are encoded from genes that are about 3 kbp (3000 base pairs in length). How
long would a typical protein be?
Q15. In general, what sort of mutation (or mutations) would have the greatest effect on the function
of the protein? The least? Justify your answer.
Q16. A 3.3 kbp gene encoding for a protein that produces melanin (hair pigment) in rats has 300
bases deleted from the middle of the sequence. Do you think the protein will still be functional?
Explain your answer.
Q17. If this mutation was in the only functional copy of this gene in the individual (ie, assume the
other copy of this gene on the other chromosome was already non-functional but one normal copy
of the gene is enough for normal melanin production), what do you think the phenotype
(appearance) of the rat will be. Why?
Q18. A 2.5 kbp gene encoding for a protein important for the production of petals in a daisy has a
single base change 369 bp into the gene sequence. Do you think the resultant protein from this
mutated gene will be functional? Explain your answer.
Q19. If this mutation was in the only functional copy of this gene in the plant (ie, assume the other
copy of this gene on the other chromosome was already non-functional but one normal copy of the
gene is enough for a normal flower), what do you think the phenotype (appearance) of the daisy will
be. Why?