Chapter 15: How damage to DNA that is not correctly repaired leads to mutations in DNA sequence that can alter the characteristics of organisms

Mutations definitiion

permanent change in the DNA sequence, therefore, a transient change to the DNA sequence is not considered a mutation

Does DNA damage always lead to mutation?

No, because if accurate DNA repair occurs before the DNA sequence is permanently changed, the mutation was avoided

do mutations always have to be in a gene?

No, although, we are more likely to notice them (see a phenotypic change) if the mutations are occurring in a gene

What are the categories of mutation sources?

1. Naturally occurring: spontaneous mutations

2. Caused by external agents: induced mutations

What are the causes of natural forms of mutations?

1. errors in replication

2. spontaneous chemical changes in the bases

3. naturally occurring recombination errors

What are the causes of induced mutations

1. chemical mutagens that cause base substitutions or indels

2. UV irradiation

3. X-rays or ionizing radiation

What do naturally occurring errors in replication lead to?

base substitutions and indels

what do spontaneous chemical changes in bases lead to?

depurination, deamination, or oxidation —> base substitutions

What do naturally-occurring recombination events lead to

chromosomal rearrangements

what do chemical mutagens result in?

base substitutions or indels

What does UV irradiation result in?

pyrimidine dimers → base substitutions

What do X-rays or ionizing radiation lead to?

chromosome breakage → chromosomal rearrangements; alternatively, base damage deamination, or oxidation → base substitutions

What are the two purines?

AG

What are the two pyrimidines

TC

What nucleotide is this

Deoxyadenosine 5’ monophosphate

What nucleotide is this?

Deoxyguanosine 5’ monophosphate

What nucleotide is this?

Deoxycytidine 5’ monophosphate

What nucleotide is this?

Deoxythymidine 5’ monophosphate

base substitutions

change one nucleotide to another without changing the number of nucleotides in the DNA

indels

insertions and/or deletions of nucleotides and by definition they are changing the number of nucleotides in the DNA

Transition

changes between purines or between pyrimidines

Is A ←>G a transition or a transversion

transition

Is C → T a transition or a transversion

transition

is T→ C a transition or a transversion

transition

Is A → T a transition or a transversion

transversion

Is T → A a transition or a transversion?

transversion

Is A → C a transition or a transversion

transversion

Is G → T a transition or a transversion

transversion

IS G→ C a transition or a transversion

transversion

transversions

changes in nucleotides between purines and pyrimidines

Are transitions or transversions more distorting?

transversions

What is the Cap on mRNA and what is its function (in eukaryotes)

7-methylguanosine attached to the 5’ end of the mRNA with three phosphate groups; protects the RNA from degradation and is required for translation in eukaryotes

silent mutation, AKA…

Change of the DNA that does not influence the gene’s function; synonymous mutation

Missense mutation, AKA…

nonsynonymous mutation; changes in the DNA that influences the genes function

nonsense

early addition of a stop codon

What do you cause a missense mutation that results in now encoding and amino acid that has similar properties as the original amino acid

conservative missense mutation

What do you cause a missense mutation that results in now encoding and amino acid that has different properties than the original amino acid

nonconservative

do mutations have to occur in a protein coding region to have a phenotypic outcome?

no

examples of mutations in a non-protein coding region that results in a phenotype

point mutations in transcription enhancer or promoter elements can change the binding site of transcription factors or RNA pol complex, respectively; point mutations in the UTR can affect translation and or gene regulation by affecting the binding of miRNAs; point mutations in splice sites/A branch point can affect the binding of snRNPs and therefore affect splicing

Explain the basis of the Luria Delbruck fluctuation test

System: phage attacked bact, but some survived due to REM

Question: were the mutations induced by the phage or were they there before?

Dependent Variable: percent of the cultures that are resistant

In the luria delbruck fluctuation test, what result would you expect to see if the phage resistance mutation was induced?

the same number of resistant colonies in each assay

In the luria delbruck fluctuation test, what result would you expect to see if the phage resistance mutation was spontaneous?

You would see variation in the number of resistant colonies

In what number of occasions does DNA pol not use proofreading

very very rare, <1 in 10^9 occasions

Which nucleotides have keto groups involved in hydrogen bonds

G and T

Which nucleotides have amino groups involved in hydrogen bonds

A and C

What happens if you lose the keto groups of G/T or if you lose the amino groups of A/C

loss of hydrogen bonds, no base pairing

Tautomerization of DNA bases

the spontaneous isomerization of a ntirogen or oxygen base to an alternative hydrogen-bonding form

How does the conversion of a keto group to an enol group on Thymine change what the nucleotide can pair with?

now pairs with G (three hydrogen bonds)

How does changing the amino group on a cytosine to an imino group change what the nucleotide can pair with?

now pairs with A (two hydrogen bonds)

Does DNA pol recognize differences in bases that are caused by tautomerization?

no

What is the predominant form of A

amino

What is the predominant form of T

keto

What is the predominant form of G

keto

What is the predominant form of C

amino

What is the rare tautomer of A, and what does it pair with, # of hydrogen bonds

imino, C, 2

What is the rare tautomer of T, and what does it pair with, # of hydrogen bonds

enol, G, 3

What is the rare tautomer of G, and what does it pair with, # of hydrogen bonds

enol, T, 3

What is the rare tautomer of C, and what does it pair with, # of hydrogen bonds

imino, A, 2

Do tautomeric changes cause transitions or transitions

transitions because the nature of the base is changed, i.e., a purine stays a purine and a pyrimidine stays a pyrimidine

How can wobble contribute to DNA pol errors

In this process, there is no chemical change to the bases. The bases mispair due to a slight shift in their position

DNA pol wobble leads to the following atypical base pairs:

AC and TG

Does DNA pol wobble lead to transitions or transversions

transitions only

How do you get insertion in replication slippage

in the new strand, an extra base slips out, the loop is stabilized by repetitive DNA sequences, during the next round, a Pair is _________

How do you get deletion in replication slippage

in the template strand, extra bases loops out, the loop is stabilized by repetitive sequences, during the next round of replication, a base pair is ___________

What is an example of the impact of replication slippage

CCG expansion in fragile X that results in the most common form of an inherited intellectual disability

What is CCG expansion in Fragile X syndrome caused by molecularly?

the number of trinucleotide repeats positively correlates with methylation in the 5’ UTR of the FMR1 gene —> when methylation is high, FMR1 is silenced → this results in disease

Do all nucleotide expansions that cause disease lead to gene silencing?

No. Some result in disease because they affect coding sequence and created repeats of amino acids that are deleterious for the function of the protein

Depurination

spontaneous loss of G or A by breakage of glycosidic bond with deoxyribose → leading to random base substitution

Deamination

naturally-occurring conversion of a C to a U → transition mutation of GC to AT

Oxidation of bases

naturally-occurring oxygen radicals attack G&T and alter their structures —>results in transversions

Which bases can depurination occur on

A or G but are more common on G

Why does depurination lead to problems for DNA pol

DNA pol does not have a base to read on the template strand; often causes DNA pol to be able to pass through this area

Does depurination directly affect the DNA backbone

no