Lecture 12: Bacterial gene mutations Flashcards
Name the major regions of the bacterial gene.
From 5’ to 3’: Promoter region, antileader, coding region, antitrailer, terminator
Name the major areas on the promoter and what happens at each.
-35: RNA polymerase recognition site
-10: RNA polymerase binding site (also called Pribnow box)
+1: start of transcription
Name the major regions of the transribed mRNA.
Leader (complement to antileader section): start of translation (after AUG)
Trailer (at the end, complement to antitrailer section)
What is a base substitution mutation?
A base pair in the DNA is changed out for the other base pair, i.e. T-A for G-C or vice versa.
What is a deletion mutation?
One or several base pairs are deleted, leaving a shorter piece of DNA.
What is an inversion mutation?
The order of the base pairs is flipped around (from left to right to right to left)
What is a transposition mutation?
New base pairs are inserted into the DNA, leaving a longer piece of DNA.
What is a duplication mutation?
A stretch of base pairs is duplicated, leaving a longer piece of DNA.
What are the two types of morphological mutations? Explain them.
Colonial or cellular. Cellular morphological mutations are when individual cells change shape. Colonial mutations are when the shape of the colony itself changes.
What is a lethal mutation?
This is when the mutation results in the cell being unable to function. For example, if it loses its ability to replicate its DNA.
What is a biochemical mutation?
If one enzyme is mutated, a biochemical pathway might be disrupted and a molecule might not be able to be synthesized.
A biochemical mutation can turn a bacteria from […] to […]
Prototroph, auxotroph
Give an example of a biochemical mutation.
if a cell can no longer produce its own leucine, it must pick it up from the environment. It becomes a leucine auxotroph.
What is an auxotroph?
It is when a cell cannot grow without the specific addition of a molecule.
What is a resistant mutation?
When cells are treated with antibiotics or chemicals, mutations will occur. They will then attempt to mutate in order to resist this, as pressure has been placed on them to evolve.
What is a spontaneous mutation?
It is a mutation that occurs during DNA replication when the DNA polymerase III fails to catch its mistake.
What is a point mutation?
It is when just a single base pair is changed.
What are the 4 types of point mutations? Explain them.
Silent: the change doesn’t change the amino acid it’s coding for
Missense: the change does change the amino acid it’s coding for
Nonsense: the change results in a stop codon and thus a premature stop during synthesis.
Frameshift: There is a deletion or insertion that causes a change in reading frame, thus changing the codons
Give two examples of mutagens that can cause DNA mutations.
Physical: UV, x-rays, gamma rays
Chemical: 5-bromouracil
What is a forward mutation?
It is a mutation with respect to a baseline, the wild-type, that is chosen by you.
What is a reversion mutation?
It is a mutation that yields a back-to-wild phenotype. The codon sequence is not necessarily the same, but the end result is the same.
What are the three types of reversion mutations?
- Original wild-type sequence gets returned
- Silent: new codon but same amino acid
- Missense: new codon but similar amino acid
What is a suppressor mutation?
Similar to a reversion mutation, it undoes forward mutations, but are located in a different location than the original mutation.
What are the two types of suppressor mutations?
Intragenic: same gene, other location
Extragic: different gene
Explain what an intragenic suppressor mutation is.
It is when there is a mutation elsewhere than the original forward mutation, but when the protein is folded in 3D, they both end up at the same catalytic site and the suppressor compensates for it, restoring the cell function to what it was.
Explain what an extragenic suppressor mutation is.
If there is a mutation in a different protein that works in concert with the protein with the original forward mutation, and when they work together this fixes the function of the original protein to bring activity back to 100%.
What conditions lead to slippage?
When there is a long series of A-T bonds that are not very strongly bonded together compared to G-C bonds. This creates potential for slippage leading to an addition or deletion.
Slippage in the […] strand will lead to a […], while slippage in the […] will lead to a […].
New, addition to the new strand, parental, deletion in the new strand
A slippage in the new strand will lead to [more/less] A-T bonds than in the parent strand.
More.
A slippage in the parental strand will lead to [more/less] A-T bonds than in the parent strand.
Less
Explain the cause of thymine dimers and what their effect is on DNA.
UV light from the sun leads to the generation of a double bond between the bases of 2 adjacent thymines. This generates a kink in the DNA, leading to major problems during DNA replication.
Chemical mutations can be induced using […]
5-bromouracil
5-bromouracil has two […] forms: […]. Explain the difference between them.
Totomeric, enol and keto. Enol form can base pair with guanine, while keto form can base pair with adenine.
Explain how 5-bromouracil can be used to induce mutations.
When it keeps switching forms, it can change the corresponding nucleotide in the new strand to G or A, creating mutations.
Name 4 forms of DNA repair.
Proofreading by DNA polymerases, mismatch repair, nucleotide excision repair, base excision repair
What is the purpose of mismatch repair?
It is meant to fix non-complementary base pairs in the DNA, such as G=T
What is the purpose of nucleotide excision repair?
It is meant to fix distorted DNA (e.g. thymine dimer)
What is the purpose of base excision repair?
To fix a missing pyrimidine/purine or to fix damaged or unnatural bases (presence of U in DNA).
The main proteins involved in mismatch repair are […]
MutS, MutL, MutH, DNA polymerase III, ligase
Explain the process of mismatch repair.
MutS scans the DNA after replication and recruits MutL and MutH. MutH differentiates the new strand from the parent strand based on the fact that it is not yet methylated. It makes a cut in the new strand and an exonuclease removes a chunk of the DNA leading up to the mutation. The DNA polymerase III then resynthesizes that area to fix the base pairing. The DNA ligase then seals the ends.
The main proteins involved in nucleotide excision repair are […]
UvrAB, UvrC, UvrD, DNA polymerase I, ligase
Explain the process of nucleotide excision repair.
UvrAB tracks along the DNA in search of damaged DNA. When it finds a distorted section, it releases UvrA and recruits UvrC, allowing it to bind. UvrC makes a cut on either side of the distortion, and then the complex disassembles. UvrD is then recruited to remove the portion of damaged DNA. DNA polymerase I then fills in the gap and DNA ligase seals it.
The major proteins involved in base excision repair are […]
DNA glycosylase, AP endonuclease, DNA polymerase I, DNA ligase
Explain the process of base excision repair.
There are two processes: recognition of unnatural bases and recognition of missing base.
Recognition of unnatural base: the DNA glycosylase recognizes an unnatural base, a ribonucleotide base (U), and cleaves the bond between the base and the sugar, removing it.
Recognition of missing base: the AP endonuclease recognizes that a base is missing and cleaves the DNA backbone on the 5’ side. DNA polymerase I then removes the damaged region and then fills it in with normal DNA. DNA ligase then seals the region.
What are error free systems of DNA repair?
They are ways to repair the DNA without DNA synthesis, as new synthesis still creates the potential for new mistakes to be made. Error-free systems do not involve the DNA polymerase.
Give 3 examples of error free systems of DNA repair (issue and associated enzyme to fix it)
Thymine dimers - photoreactivation, photolyase)
Methyls - methylguanine methyltransferase
Alkyls - alkyltransferase
What protein is involved in recombinational repair?
RecA
Explain how recombinational repair works.
Say there are two problems present at the same position on the DNA. This problem can be resolved when the cell is replicating, when there is a second chromosome available. By recombination, parts of strands with the same sequence can be flipped in order to move one of the mutations onto the other copy of the chromosome. This allows for the separation of the mutations individually.
