EBIO 2070 EXAM 3 2024/2025 WITH ACCURATE SOLUTIONS
Substitution - Answer ✔✔One nucleotide replaced by another
Causes of substitutions - Answer ✔✔DNA polymerase errors,
spontaneous deamination, alkylating chemicals, UV light
Spontaneous deamination - Answer ✔✔Turns cytosine into uracil
Alkylating chemicals - Answer ✔✔Alkylating chemicals like ENU and
EMS change the structure of the N-containing bases; used to introduce
substitutions in genetic model systems
How does UV light create substitutions? - Answer ✔✔Indirectly
through DNA repair mechanisms
1. UVB light creates pyrimidine dimers
2. Normal DNA polymerase cannot replicate through them
3. Usually get "undone" by photolyases
4. Second line of defense is nucleotide excision repair - region around
the dimers is removed and replaced
5. When 3 and 4 don't work, translesion synthesis with special DNA
polymerase can occur - this is error prone and can cause substitutions
,Consequences of substitutions - Answer ✔✔1. There are few
consequences for substitutions in non-protein coding sequences (most of
the genome)
2. Substitutions in protein coding exons and important non-protein
coding sequences (enhancers, promoters, etc.) can cause changes in
protein structure and gene expression
3. Loss of splice donor/acceptor sites can interfere with splicing, often
leading to introns being left in
4. Loss of polyadenylation signal can prevent poly-A tail formation
Tyrosinase is an enzyme needed to make the pigment melanin encoded
by two exons, exon 1 and exon 2. A goat has a mutation in its tyrosinase
gene that removes a splice donor site in the tyrosinase transcript. As a
result, the transcript cannot be properly spliced and a 2,000 nucleotide-
long intron remains between exon 1 and exon 2 of the mature tyrosinase
mRNA. What would you predict about the goat's tyrosinase protein? -
Answer ✔✔It is shorter than normal - the ribosome will hit a stop codon
within the intron and not finish the protein
In a random sequence of non-protein coding DNA or RNA on average,
how often would you come across a stop codon? - Answer ✔✔One stop
codon for every 64 nucleotides
Why would you expect substitution mutations in CREs to have little, or
no, effect on gene expression?
A. Because transcription factors don't need exact binding site sequences
to bind enhancers
, B. Because each type of transcription factor binds to several sites in an
given enhancer
C. Because enhancers don't use the genetic code
D. Two of the above are correct
E. a, b, and c - Answer ✔✔E
Which type of repair mechanism will fix UV induced mutations?
A. DNA polymerase proofreading
B. Deamination
C. Nucleotide excision repair
D. Translesion synthesis - Answer ✔✔C and D
Causes of insertions/deletions (indels) - Answer ✔✔Basal slippage
(adds/removes repeats), DNA intercalating chemicals, ionizing radiation
How do DNA intercalating chemicals cause indels? - Answer ✔✔Stuff
themselves into the double helix, disrupting DNA structure during
replication which leads to insertions (ex: ethidium bromide and BaP)
How does ionizing radiation create indels? - Answer ✔✔Indirectly
through DNA repair mechanisms
1. Causes double-stranded breaks in DNA molecules
2. Breaks may be uneven (one strand is longer than the other)
3. To be repaired, both strands must be the same length
Substitution - Answer ✔✔One nucleotide replaced by another
Causes of substitutions - Answer ✔✔DNA polymerase errors,
spontaneous deamination, alkylating chemicals, UV light
Spontaneous deamination - Answer ✔✔Turns cytosine into uracil
Alkylating chemicals - Answer ✔✔Alkylating chemicals like ENU and
EMS change the structure of the N-containing bases; used to introduce
substitutions in genetic model systems
How does UV light create substitutions? - Answer ✔✔Indirectly
through DNA repair mechanisms
1. UVB light creates pyrimidine dimers
2. Normal DNA polymerase cannot replicate through them
3. Usually get "undone" by photolyases
4. Second line of defense is nucleotide excision repair - region around
the dimers is removed and replaced
5. When 3 and 4 don't work, translesion synthesis with special DNA
polymerase can occur - this is error prone and can cause substitutions
,Consequences of substitutions - Answer ✔✔1. There are few
consequences for substitutions in non-protein coding sequences (most of
the genome)
2. Substitutions in protein coding exons and important non-protein
coding sequences (enhancers, promoters, etc.) can cause changes in
protein structure and gene expression
3. Loss of splice donor/acceptor sites can interfere with splicing, often
leading to introns being left in
4. Loss of polyadenylation signal can prevent poly-A tail formation
Tyrosinase is an enzyme needed to make the pigment melanin encoded
by two exons, exon 1 and exon 2. A goat has a mutation in its tyrosinase
gene that removes a splice donor site in the tyrosinase transcript. As a
result, the transcript cannot be properly spliced and a 2,000 nucleotide-
long intron remains between exon 1 and exon 2 of the mature tyrosinase
mRNA. What would you predict about the goat's tyrosinase protein? -
Answer ✔✔It is shorter than normal - the ribosome will hit a stop codon
within the intron and not finish the protein
In a random sequence of non-protein coding DNA or RNA on average,
how often would you come across a stop codon? - Answer ✔✔One stop
codon for every 64 nucleotides
Why would you expect substitution mutations in CREs to have little, or
no, effect on gene expression?
A. Because transcription factors don't need exact binding site sequences
to bind enhancers
, B. Because each type of transcription factor binds to several sites in an
given enhancer
C. Because enhancers don't use the genetic code
D. Two of the above are correct
E. a, b, and c - Answer ✔✔E
Which type of repair mechanism will fix UV induced mutations?
A. DNA polymerase proofreading
B. Deamination
C. Nucleotide excision repair
D. Translesion synthesis - Answer ✔✔C and D
Causes of insertions/deletions (indels) - Answer ✔✔Basal slippage
(adds/removes repeats), DNA intercalating chemicals, ionizing radiation
How do DNA intercalating chemicals cause indels? - Answer ✔✔Stuff
themselves into the double helix, disrupting DNA structure during
replication which leads to insertions (ex: ethidium bromide and BaP)
How does ionizing radiation create indels? - Answer ✔✔Indirectly
through DNA repair mechanisms
1. Causes double-stranded breaks in DNA molecules
2. Breaks may be uneven (one strand is longer than the other)
3. To be repaired, both strands must be the same length
