Exam 3: 31 DNA Repair (missing CLICKER) Flashcards
- Direct repair of a DNA pyrimidine induced by exposure of UV-light relies on the DNA photolyase activities. There are two key cofactors in the DNA photolyase: 5-MTHF and FADH2.
What are the functions of these two cofactors in the enzyme?
A) 5-MTHF acts as an antenna to capture the photon in the range of 300 – 500 nm and passes the excitation energy to FADH-, forming FADH*-
B) FADH2 passes electrons to 5-MTHF
C) FADH2 provides hydrogens to pyrimidine dimer to break the carbon-carbon bonds.
D) All the above
A) 5-MTHF acts as an antenna to capture the photon in the range of 300 – 500 nm and passes the excitation energy to FADH-, forming FADH*-
Example diagram:
MTHF -(light 300-500nm)-> MTHF -(excitation energy transfer)-> + (FADH-)-> FADH-
Why other options are incorrect:
B) FADH2 passes electrons to 5-MTHF: The sources describe the opposite – energy transfer from 5-MTHF to FADH2.
C) FADH2 provides hydrogens to the pyrimidine dimer to break the carbon-carbon bonds: The mechanism involves electron transfer from the excited FADH*-, not hydrogen transfer.
True or False:
5-MTHF acts as an antenna to capture photons and passes excitation energy to FADH-, forming FADH*-.
True
What are the main factors that lead to DNA damage?
Replication errors
Spontaneous chemical changes
Reactive metabolites
Radiation
Environmental Substances
What is Deamination?
A) the loss of amino group (NH2) from a molecule, commonly affecting cytosine bases, converting them to uracil (a hydrolysis reactions)
B) the loss of purine base (adenine or guanine) from the DNA backbone (hydrolysis rxn)
A) the loss of amino group (NH2) from a molecule, commonly affecting cytosine bases, converting them to uracil (a hydrolysis reactions)
What is Depurination?
A) the loss of amino group (NH2) from a molecule, commonly affecting cytosine bases, converting them to uracil (a hydrolysis reactions)
B) the loss of purine base (adenine or guanine) from the DNA backbone (hydrolysis rxn)
B) the loss of purine base (adenine or guanine) from the DNA backbone (hydrolysis rxn)
- Methylated Cytosine nucleotides (mC) in DNA are common sites for mutations in vertebrate DNA. This is because:
A) There is no special DNA glycosylase that recognizes a mismatched T-G (T, Thymine, results from deamination of C, Cytosine)
B) Deamination of a regular C (Cytosine) results in a U (Uracil)
C) Three hydrogen bonds between base pair mCG
D) None of the above
D) None of the above
Deamination: Cytosine, whether methylated or not, is susceptible to spontaneous deamination, a process where the amino group is lost and replaced with an oxygen atom. This converts cytosine to uracil.
Thymine Formation: When methyl-C undergoes deamination, it produces thymine rather than uracil.
T:G Mismatch: The conversion of methyl-C to thymine results in a T:G mismatch, which poses a challenge for repair mechanisms.
Inefficient Repair: The sources indicate that the repair of T:G mismatches arising from deaminated methyl-C is relatively inefficient in vertebrates. This suggests that the specific DNA glycosylase responsible for recognizing and removing this mismatch is not as effective as other glycosylases involved in base excision repair.
- Xanthine glycosylase is responsible for removing Xanthine (resulting from Guanine deamination) in the chromosomal DNA, in cells without functional Xanthine glycosylase, the GC content of their chromosomal DNA will___________
A) Increase
B) Decrease
C) Remain the same over time
D) Fluctuate
B) Decrease
- DNA mismatch repair (MMR) is a system for recognizing and repairing erroneous insertions, deletion, and misincorporation of bases that arise during DNA replication and recombination, as well as repairing of some forms of DNA damage. In prokaryotes, a special set of proteins is required. These proteins include:
A) uvrA/uvrB complex that recognizes the mismatched DNA
B) uvrC, a nuclease, which cuts the damaged strand
C) uvrD, a DNA helicase, which peels the damaged segment of the strand and removes it.
D) None of the above
D) None of the above
The proteins listed in options A, B, and C are involved in Nucleotide Excision Repair (NER), not Mismatch Repair (MMR). NER is a DNA repair system that deals with lesions that cause significant structural changes in the DNA, such as pyrimidine dimers.
The proteins required for MMR in prokaryotes are:
MutS: Scans for mismatches.
MutL: Locates the closest GATC sequence based on methylation status to distinguish the newly synthesized strand.
MutH: Functions as an endonuclease, generating a cut on the newly synthesized strand at the unmethylated GATC sequence.
Are the following proteins required for Mismatch Repair (MMR) or Nucleotide Excision Repair (NER)?
MutS: Scans for mismatches
MutL: locates closest GATC sequence
MutH: Endonuclease, cuts newly synthesized strand at methylated GATC sequence
Mismatch Repair (MMR)
Are the following proteins required for Mismatch Repair (MMR) or Nucleotide Excision Repair (NER)?
uvrA/ uvrB: recognizes pyrimidine dimers
uvrC: nuclease, cuts damaged strand
uvrD: helicase, removes damaged segments
Nucleotide Excision Repair (NER)
(Question from discussion)
Both deamination of cytosine and depurination are caused by ______ on DNA, and both can be repaired by________.
A) oxidative damage; nucleotide excision repair
B) hydrolytic attack; base excision repair
C) uncontrolled methylation; nucleotide excision repair
D) hydrolytic attack; nucleotide excision repair
B) hydrolytic attack; base excision repair
Deamination and depurination are the most common types of DNA damage and both are a hydrolytic process.
Deamination involves the hydrolysis of the amino group, changing cytosine to uracil.
Depurination is the loss of a base, creating an AP site.
Base Excision Repair (BER) is a DNA repair pathway that repairs damaged or abnormal bases, including uracil (resulting from cytosine deamination) and AP sites (resulting from depurination).
BER involves the following steps:
The damaged base is recognized and removed by a DNA glycosylase, creating an AP site.
The AP site is removed by AP endonuclease and phosphodiesterase.
DNA polymerase adds a new nucleotide, and DNA ligase seals the break.
BER does not require a helicase.
Let’s examine why the other answer choices are incorrect:
A) Oxidative damage; nucleotide excision repair: Oxidative damage is a separate category of DNA damage caused by reactive oxygen species. While it can be repaired by nucleotide excision repair (NER), this pathway is not the primary mechanism for repairing deamination and depurination.
C) Uncontrolled methylation; nucleotide excision repair: Uncontrolled methylation is another type of DNA damage. While NER can repair some types of methylation damage, it is not the primary mechanism for repairing deamination and depurination.
D) Hydrolytic attack; nucleotide excision repair: As explained above, BER, not NER, is the primary pathway for repairing deamination and depurination.
(Question from discussion)
Base excision repair primarily repairs ____/____, and nucleotide excision repair primarily repairs ________. The two pathways differ in that base excision repair does not require _______.
A) Depurination/ mismatch repair; pyrimidine dimers; DNA polymerase
B) Depurination/ pyrimidine dimers; Deamination: Helicase
C) Depurination/ deamination; Mismatch repair; DNA polymerase
D) Depurination/ deamination; pyrimidine dimers; Helicase
D) Depurination/ deamination; pyrimidine dimers; Helicase
Base Excision Repair (BER):
primarily repairs depurination and deamination. Both of these processes are common types of DNA damage caused by hydrolytic attack. BER is a DNA repair pathway that specifically targets damaged or abnormal bases. For example, BER can repair uracil, which results from the deamination of cytosine, and AP sites, which are created by depurination.
Nucleotide Excision Repair (NER):
primarily repairs pyrimidine dimers. Pyrimidine dimers are a type of DNA damage caused by UV light exposure, where adjacent pyrimidine rings form covalent bonds. These dimers distort the DNA structure and can block transcription and replication. NER is a more complex repair pathway that involves removing a larger chunk of nucleotides, including the dimer, and replacing them with the correct sequence.
Base Excision Repair (BER):
does not require a helicase. . In contrast, NER does require a helicase (uvrD) to unwind the DNA and remove the damaged segment.
(HW 31)
A nucleotide pairing between A (adenine) and T (thymine) in the original DNA strand is miscopied during DNA replication. On one strand of DNA, A correctly pairs with T. However, on the other strand, T pairs with G (guanine) instead of A. This mistake is not corrected, and the double strand with the mistake is incorporated into a new cell during cell division. The double strand with the G-T mistake is later replicated without mistakes.
What nucleotide pairs will be found in the two new double strands at the site of the G-T mistake?
A) One new strand will have a G-T pair, and the other strand will have an A-C pair.
B) One new strand will have a G-C pair, and the other strand will have an A-T pair.
C) Both new strands will have a G-T pair.
D) Both new strands will have a G-C pair.
B) One new strand will have a G-C pair, and the other strand will have an A-T pair.
To achieve faithful replication, each strand within the parent double helix acts as a template for the synthesis of a new DNA strand with a complementary sequence. In this case, the error is the pairing of T (thymine) with G (guanine), a pairing that is not a Watson–Crick complement. However, when this aberrant strand is replicated again, the strands are separated, and DNA polymerase makes a copy for each strand with the proper Watson–Crick complement. As a result, one new strand has a G–C pair (from the strand with the G), and the other new strand will have an A–T pair (from the strand with the T).
Both new strands will not have the same pair because the strands are separated and copied individually during DNA replication. Because the double strand with the G–T mistake is later replicated without additional mistakes, the new strands will not have a G–T pair nor an A–C pair
(HW 31)
What strategies do cells use to ensure that newly replicated DNA does not contain errors?
(pick all correct choices)
A) Enzymes proofread the DNA after the DNA has been replicated and replace any mismatched nucleotides.
B) Enzymes find misshapen DNA sequences prior to replication and remove and resynthesizes those sequences.
C) DNA polymerase replaces the newly replicated DNA on any chromosomes on which there are mistakes.
D) Enzymes repair mistakes in the new DNA double helix after the new double helix separates from the original double helix.
E) As DNA polymerase synthesizes new DNA, the DNA polymerase finds and corrects misplaced nucleotides.
