Mutations, DNA damage, DNA repair review

What would happen if there was a problem with DNA polymerase II, IV, and V?

DNA polymerase II,IV and V repair and do checks on the DNA that is replicated. They can cut out problems and add if needed. If any of these three polymerase are damaged or cannot work properly, mistakes will not be fixed and mutations and damages would accumulate.

Which of the following is a single base change in DNA? A. Alkylation B. Deamination C. Endonucleases D.Methyl guanine methyltransferase E. A & B

e

What would be a consequence if there was a nonsense mutation while making a polypeptide?

A nonsense mutation is where a STOP codon is produced due to a change in the DNA sequence. As a result of this, a polypeptide would be stopped before it is fully made. This could lead to a myriad of problems. Some examples would be, the polypeptide could be folded incorrectly, there could be a change in what could bind, and the polypeptide may not form its desired function because it is shorter than it should be.

You are a genetics counselor that got handed the case of Patient A. It was found that Patient A has a silent mutation, and you have to break the news to him. Explain whether the silent mutation will have a big effect, no effect, or slight effect on the DNA sequence of Patient A.

A silent mutation is just a change in the DNA sequence with no change in amino acid sequence. For example, if Patient A had the codon UGU and the silent mutation changed the codon to UGC, there wouldn't be an effect because the codons code for the same amino acid (cys). So, Patient A really has nothing to worry about as the silent mutation will not have little to no effect on his DNA sequence.

You are examining DNA from a person that spends a lot of time in the sun. You notice that there is a slight bulge on some of the DNA where two identical bases next to each other have covalently bonded together. What is most likely the identity of the bases, what most likely caused it and how can it be repaired.

Because the person spent a lot of time in the sun, the 2 bases are most likely Ts. The mutation was most likely caused by UV exposure and it would be corrected by Nucleotide Excision Repair.

Explain what would happen if DNA photolyase could not reduce (FAD) to (FADH-)?

If DNA Photolyase could not reduce (FAD) to (FADH-) the enzyme would no longer be able to transfer an electron to break up the Covalently bonded dimers in a Damage DNA strand. This would cause the dimers to go along unfixed. This would be particularly problematic in cells exposed to the sun in prokaryotes and non-placental mammalian eukaryotes.

What and how would something remove a methyl group from guanine?

Methyl guanine methyltransferase is a large enzyme that would bind to the minor groove and rotate the methylated guanine out into the major groove. Now that it is rotated out, the methyl guanine methyltranserase will remove the methyl group and release it.

Sickle Cell Disease is caused by a type of mutation on the 6th Codon in a 20 Codon sequence in the patient's DNA. The sequence of this amino acid prior to the identification of Sickle Cell Disease is stated below along with the sequence of this amino acid after the identification of Sickle Cell Disease. 6th Codon without Disease: GAG (Glutamic Acid) 6th Codon with Disease: GTG (Valine) What kind of mutation caused this adaptation of this amino acid?

Missense Mutation because the adenine is mutated into a thymine which changes the codon to translate from Glutamic Acid to Valine.

Are there any benefits of mutations? Explain.

Mutations can be beneficial in helping organisms to better adjust to their environment, they can lead to evolution, variability in populations, humans can develop immunities to certain diseases, HIV being an example of one.

An organism has a mutation that leaves proofreading exonucleases severely malformed. What are some of the consequences that could accompany this mutation?

Presumably the proofreading exonucleases are malformed enough to not work or at least work with less efficiency. Errors in DNA would likely increase from 1 in 10 million (with proofreading) to somewhere closer 1 in 10 thousand (mistakes with just polymerases). With fewer chances to fix mistakes along the replicated DNA more mutations would be present.

Ammonia's molecular formula is NH3, which of the single base changes that we've talked about in class could create this molecule? Where does this base change arise from (how does the process work)? What are the potential problems associated with this?

The mentioned single base change would be Deamination. This is the process of having a Cytosine lose its amine group for an oxygen which turns it into a U. Unless it happens to be fixed, the DNA will continue to replicate with an incorrect nucleotide. Other than having ammonia loose in our body and those related issues. It would lead to any potential nucleotide change problem (silent, missense, and nonsense). Where either no changes would arise and the amino acid wouldn't change as degenerative codons would save the individual, the nucleotide change would result in a different amino acid which would disrupt the secondary and tertiary structure of the protein potentially causing it to take a potentially different function, or it could result in a premature stop codon which would be very detrimental if early on in the amino acid chain synthesis (unless it was a negative protein then it wouldn't be detrimental, it would be a good thing for it to be removed).

You are looking at a piece of DNA in the lab that is shown to have damage on it. After evaluating the DNA you see that it has a slight bulge and that there are two Thymines covalently bonded to each other. What can you assume caused the damage to the DNA?

This form of damage is an example of structural distortion. It is cause by too much UV radiation.

During DNA replication, what could a possible result be if the proofreading exonuclease is damaged, and cannot function?

There are a few different possibilities that could result. Since the proofreading exonuclease is damage, then an error within the strand would not be fixed, causing either a beneficial mutation, or one that hinders the organism, (or does nothing at all). However, if there is no damage/error to the strand in the first place, then the lack of a proofreading exonuclease would cause no changes to occur.

A mutagen has been shown to alter one base of a certain stretch of DNA, the DNA sequence on the template strand changes from TACAATTTTACCCTCATT to TACAATTTTACTCTCATT. What type of mutation is this and what possible effects could be seen from this change? (if this question was asked, you would be given a codon table)

This would be a nonsense mutation because the sequence is changed from coding for Trp to a STOP codon. This may not have a huge effect on the final because only two amino acids were stripped from the amino acid sequence. However, these two deletions will have some effect on the overall shape and functioning of the protein. Most likely the change will be detrimental and will result in the protein not being able to complete its intended purpose.

Suppose a genetic mutation in children causes their cells to lack XP repair proteins. Based on this information, what behavior would likely be recommended to minimize the impact of this mutation?

When DNA is damaged by UV radiation, it can cause 2 Thymines to covalently bind to each other which causes a structure distortion in the DNA strand. For placental mammals to fix this Thymine dimer caused by UV radiation, the structure must first be recognized by the XPC. The THIID (XPB and XPD) complex will then bind, and will begin unwinding the DNA (helicase action) to allow endonucleases to bind and cut DNA. Endonucleases XPG will cut 6 nucleotides away from the damage on the 3' side, while XPF will cut 20 nucleotides away from the damage on the 5' side, resulting in a 25-30 nucleotide strand cut away. Polymerase will then come in an fill the gaps in the DNA, and Ligase will fill in the nicks in the backbone.

Xeroderma Pigmentosum (XP) is a rare skin condition where there is a deficiency in ability to repair DNA damage caused by UV radiation from the sun. What DNA repair mechanism would be deficient in an individual with XP?

XP could possibly be caused by a deficiency in the nucleotide excision repair mechanism, since this mechanism is the primary way that placental mammals fix UV damage.

Which of the following molecules/molecule complexes are involved in the mismatch repair system of DNA by identifying the error? a. XPF, XPC, XPD complex b. MutSalpha/MutLalpha c. HXG d. EXO1

b

Which type of mutation would likely be the most deleterious for an organism? A) Silent B) Nonsense C) Missense D) Transition

b

3. Which is NOT true of mutations a. They can be beneficial b. They provide genetic variation c. They must be caused by a mutagen d. They help drive evolution

c

A mutation that causes nucleotides after it to shift to the left is referred to as a ________ mutation. a) frameshift; insertion b) point mutation; transition c) frameshift; deletion d) point mutation; transversion

c

A nonsense mutation has occurred in the DNA segment which codes for "protein A". After it has been transcribed and translated, what is the most likely product formed from this mutated region? A) A product that differs in only a single amino acid from "protein A" B) A product that differs in only a single base pair from "protein A", but with entirely different amino acids C) A small, truncated, nonfunctional "protein A" D) A normally shaped, fully functional "protein A"

c

Frameshift mutations... A) Adds one or two bases B) Changes one or two bases to another C) Removes one or two bases D) A+C E) All of the above

c

In Eukaryotes, what is the order of binding of transcription factors? A. TFIID,TFIIE,TFIIF,TFIIB,TFIIH B.TFIIE,TFIIB,TFIIH,TFIIF,TFIID C.TFIID,TFIIB,TFIIF,TFIIE,TFIIH D.TFIIH,TFIIE,TFIIB,TFIIF,TFIID

c

What method does an Owl use to repair UV damage? A) Nucleotide Excision Repair B) Base Excision Repair C) Photoreactivation D) A&C E) B&C

c

What type of mutation would have the largest impact on an an entire nucleotide sequence? A. Silent Mutation B. Point Mutation C. Frameshift Mutation D. Missense Mutation E. Nonsense Mutation

c

Why are transerversion DNA mutations worse than transition? A.) One base changes to a different one B.) Affect every codon from there after C.) More likely to cause a change in amino acid sequence D.) Cannot be fixed

c

Two individuals are under observations for possible mutations. We come to realize that they both have mutations in their hair color production. Individual X has a mutation but expresses no physical changes while individual Y hair color changes from brown to white. What, if any, has happened to these two different individuals?

if we know that a mutation has taken place with these two people, we have to determine what kind it is. For X, we know a mutation has taken place but no physical change has taken place, so here we know a silent mutation has taken place. On the other hand, Y has had a missense mutation since it has had a affect on the phenotypic display of this individual.