DNA Damage
When is a mutation a problem? Before or after replication?
After replication.
What is the difference between a chemical and physical mutagen?
Why we are concerned about mutagens.
A chemical mutagen is a chemical that binds to and damages the DNA.
A physical mutagen is an ionizing or non-ionizing radiation that can damage DNA.
We are concerned about mutagens because they can damage DNA which can lead to mutations.
What is direct DNA repair?
The DNA is repaired directly at the damaged site by enzymes.
Ex: Photolyase.
What is a silent mutation?
The protein is not different even though the codon is slightly different.
What is in an operon?
Promoter
Operator
Two or more genes
Terminator
What is depurination? What is lost/changed?
How does it happen?
A purine leaves (G and A). (More likely to happen to purines than pyrimidines.)
The purine reacts with water and leaves the DNA.
If it is not caught, there is a 75% chance of the DNA polymerase adding the wrong base.
Do some genes have locations within the chromosome that make them more susceptible to mutations?
If true, what nucleotide is most commonly found to cause trouble in hot spots?
Yes.
Cysteine.
What is base excision repair?
The bases around the damaged site are removed and replaced. The backbone is nicked but is otherwise not removed in the first step. Then, an endonuclease recognizes the site, takes out a section, and then Pol I replaces it.
What is a missense mutation?
A different amino acid is coded for but can affect protein function depending on which new amino acid is coded for.
Give an example of a cis-element in an operon.
Operator.
Promoter.
Enhancer and silencer sites.
What is deamination? What is lost/changed?
How does it happen?
An amino group is lost from a base and changes into another base.
Most often happens to Cs.
Normal Cs turn into Us.
5-methylated Cs turn into Ts.
Can happen spontaneously or due to environmental mutagens.
What is a base modifier? What does it alter?
How does it happen?
The chemical structure of the base.
It binds to the base and chemically alters it.
What is nucleotide excision repair?
Several whole nucleotides around the damaged site are removed and replaced.
What is a nonsense mutation?
A different amino acid is coded for and it does affect protein function.
What is the inducer for the lac operon?
Allolactose.
What is a tautomeric shift? What is lost/changed?
How does it happen?
An H+ group is lost or added to bases and this changes their structure so that they hold more or fewer hydrogen bonds.
Can happen to all bases but most often to Cs.
Can happen spontaneously or due to environmental mutagens.
What is a base analog? What does it alter?
It is a chemical that looks chemically similar to a normal base.
It mimics a normal base.
What is mismatch repair?
After replication but before the daughter strand is methylated, the mismatch repair system scans the DNA for any mismatches. If it finds one, it removes the wrong base from the daughter strand. It knows which one is the daughter strand because that one is not methylated yet.
Reads in the 3’ to 5’ direction to be ahead of the methylation.
What is a frameshift mutation?
A nucleotide or two are duplicated or deleted that changes the reading frame.
When lactose and glucose are both present in a cell, what sugar does the cell want to deal with first? So, how is the lac operon regulated in this situation?
When lactose and glucose are present: CAP is not bound, lac repressor is not bound.
What is the difference between a paracentric and pericentric inversion?
Paracentric inversion leads to a reversal of DNA w/o the centromere being involved.
Pericentric inversion leads to a reversal of DNA with the centromere being involved.
What are intercalating agents? What does it alter?
It sticks in between the bases. This makes the DNA brittle and it cannot get into the double helix.
It binds to the DNA between the bases.
Can result in deletions or duplications.
What is nonhomologous end joining?
After a double-strand break, pieces of DNA are put back together. This is done so that the lone piece of DNA is not degraded but can result in a translocation, inversion, and most likely a deletion. The DNA had a double-strand break so most likely some DNA was lost.
What is a trinucleotide repeat mutation (TNRE) and what are the two unusual characteristics of the disorder?
The RNA polymerase stutters and adds extra triplets of nucleotides.
Once the TNRE gets long enough, it is associated with disease symptoms.
What is trp attenuation?
When trp is plentiful, the tRNAs for trp come quickly and an inhibitory mRNA stem-loop is formed.