BCH 5413 EXAM 4 STUDY GUIDE | 240
QUESTIONS AND CORRECT ANSWERS
(VERIFIED ANSWERS) | ALREADY GRADED A+ |
LATEST UPDATE 2025-2026
What is the function of DNA-PK in NHEJ? - ANSWER -DNA-dependent protein
kinase
-phosphorylates Ku to activate its helicase activity
-a second DNA-PK phosphorylates each other to dissociate from DNA
APE1 - ANSWER AP Endonuclease 1: skilled nucleic acid surgeon
Two major functions:
1. AP-site incision: DNA backbone cleavage activity at AP sites
2. 3'-5' exonuclease: proofread 3' mismatches inserted by pol beta during BER and
remove 3' DNA end damage at single strand breaks
Examples of endogenous cellular processes that damage DNA - ANSWER -
Oxidation, alkylation, or hydrolysis (depurination/depyrimidation) of bases
-Bulky adduct formation
-Mismatch of bases due to erros in DNA replication
Examples of exogenous sources that damage DNA - ANSWER -UV, X-ray
-Ionizing radiation
-Industrial chemicals
-Even oxygen
,spontaneous deamination - ANSWER removal of an amino group generates
mutagenic lesions such as uracil, hypoxanthine, and xanthine
deamination of cytosine produces - ANSWER Uracil
deamination of adenine produces - ANSWER hypoxanthine
deamination of guanine produces - ANSWER xanthine
Depurination - ANSWER -Hydrolysis of the N-b-glycosyl bond linking a purine
base to the sugar-phosphate backbone
-elevated temperature increases the rate of depurination
Alkylation of bases occurs when: - ANSWER electrophilic substances seek the
negative centers in DNA, attack them and add a carbon-containing group (alkyl
group)
Emethanesulfonate (EMS) - ANSWER -Chemotherapeutic agent causes
alkylation of guanine O6 resulting in pairing with thymine.
-DNA alylation interferes with transcription and DNA replication
-cytotoxic
oxidative DNA damage - ANSWER highly reactive oxidative radicals (chemical
substances with unpaired electrons) that are generated as a byproduct of cellular
,respiration (endogenous) or OS (exogenous) can react with different parts of DNA
structure
Guanine Oxidation - ANSWER -results in 8-oxoGuanine
-most common oxidative DNA base damage
-highly mutagenic
-plays a critical role in carcinogenesis
-Hoogsteen base pairing with adenine
Two forms of ionizing radiation - ANSWER gamma rays and x-rays
nonionizing radiation - ANSWER Ultraviolet rays
UV-B DNA damage - ANSWER cross-link adjacent pyrimidines, resulting in
formation of pyrimidine dimers which distort DNA and base-pairing and block
replication
UV-A DNA damage - ANSWER creates mostly free radicals
Gamma and X-rays - ANSWER -Ionize molecules around the DNA (e.g. water)
-Cause single-strand and double-strand breaks in DNA backbone
-can alter bases (oxidative damage)
, nonsense mutation - ANSWER A mutation that changes an amino acid codon
to one of the three stop codons, resulting in a shorter and usually nonfunctional
protein.
missense mutation - ANSWER A point mutation in which a codon that specifies
an amino acid is mutated into a codon that specifies a different amino acid.
Mechanism of DNA polymerase proofreading - ANSWER If wrong nucelotide is
incorporated during DNA synthesis, polymerase pauses and transfers the 3' end of
the growing strand to the 3'-5' exonuclease site where the mis-paired base is
removed then then 3' end flips back to the polymerase site and replication
continues
mismatch repair - ANSWER Repairs base mismatches and loops (small
insertion/deletions)
Basic steps of MMR - ANSWER -mismatch detection
-excision
-re-synthesis by DNA polymerase
-ligation by DNA ligase
MutS - ANSWER -E. coli MMR protein
-Mismatch detection
-Binds to DNA mismatch and small single-stranded loops, known as sliding clamp
ATPase
MutL - ANSWER -E. coli MMR protein
QUESTIONS AND CORRECT ANSWERS
(VERIFIED ANSWERS) | ALREADY GRADED A+ |
LATEST UPDATE 2025-2026
What is the function of DNA-PK in NHEJ? - ANSWER -DNA-dependent protein
kinase
-phosphorylates Ku to activate its helicase activity
-a second DNA-PK phosphorylates each other to dissociate from DNA
APE1 - ANSWER AP Endonuclease 1: skilled nucleic acid surgeon
Two major functions:
1. AP-site incision: DNA backbone cleavage activity at AP sites
2. 3'-5' exonuclease: proofread 3' mismatches inserted by pol beta during BER and
remove 3' DNA end damage at single strand breaks
Examples of endogenous cellular processes that damage DNA - ANSWER -
Oxidation, alkylation, or hydrolysis (depurination/depyrimidation) of bases
-Bulky adduct formation
-Mismatch of bases due to erros in DNA replication
Examples of exogenous sources that damage DNA - ANSWER -UV, X-ray
-Ionizing radiation
-Industrial chemicals
-Even oxygen
,spontaneous deamination - ANSWER removal of an amino group generates
mutagenic lesions such as uracil, hypoxanthine, and xanthine
deamination of cytosine produces - ANSWER Uracil
deamination of adenine produces - ANSWER hypoxanthine
deamination of guanine produces - ANSWER xanthine
Depurination - ANSWER -Hydrolysis of the N-b-glycosyl bond linking a purine
base to the sugar-phosphate backbone
-elevated temperature increases the rate of depurination
Alkylation of bases occurs when: - ANSWER electrophilic substances seek the
negative centers in DNA, attack them and add a carbon-containing group (alkyl
group)
Emethanesulfonate (EMS) - ANSWER -Chemotherapeutic agent causes
alkylation of guanine O6 resulting in pairing with thymine.
-DNA alylation interferes with transcription and DNA replication
-cytotoxic
oxidative DNA damage - ANSWER highly reactive oxidative radicals (chemical
substances with unpaired electrons) that are generated as a byproduct of cellular
,respiration (endogenous) or OS (exogenous) can react with different parts of DNA
structure
Guanine Oxidation - ANSWER -results in 8-oxoGuanine
-most common oxidative DNA base damage
-highly mutagenic
-plays a critical role in carcinogenesis
-Hoogsteen base pairing with adenine
Two forms of ionizing radiation - ANSWER gamma rays and x-rays
nonionizing radiation - ANSWER Ultraviolet rays
UV-B DNA damage - ANSWER cross-link adjacent pyrimidines, resulting in
formation of pyrimidine dimers which distort DNA and base-pairing and block
replication
UV-A DNA damage - ANSWER creates mostly free radicals
Gamma and X-rays - ANSWER -Ionize molecules around the DNA (e.g. water)
-Cause single-strand and double-strand breaks in DNA backbone
-can alter bases (oxidative damage)
, nonsense mutation - ANSWER A mutation that changes an amino acid codon
to one of the three stop codons, resulting in a shorter and usually nonfunctional
protein.
missense mutation - ANSWER A point mutation in which a codon that specifies
an amino acid is mutated into a codon that specifies a different amino acid.
Mechanism of DNA polymerase proofreading - ANSWER If wrong nucelotide is
incorporated during DNA synthesis, polymerase pauses and transfers the 3' end of
the growing strand to the 3'-5' exonuclease site where the mis-paired base is
removed then then 3' end flips back to the polymerase site and replication
continues
mismatch repair - ANSWER Repairs base mismatches and loops (small
insertion/deletions)
Basic steps of MMR - ANSWER -mismatch detection
-excision
-re-synthesis by DNA polymerase
-ligation by DNA ligase
MutS - ANSWER -E. coli MMR protein
-Mismatch detection
-Binds to DNA mismatch and small single-stranded loops, known as sliding clamp
ATPase
MutL - ANSWER -E. coli MMR protein
