MAMMALIAN GENETICS BCH5413 EXAM 4
LATEST UPDATE
DNA can be both replicated and transcribed into mRNA, which can
be translated into protein - ANSWER What is the central dogma of
molecular biology?
True (this is due to intrastrand crosslinking, in which adjacent
nucleotides basepair, causing bubbling) - ANSWER T/F: the addition
of bulky aromatic rings and/or exposure to UV light can cause the
DNA to "bubble."
True - ANSWER T/F: chemotherapy can cause both single and
double-stranded breaks in DNA.
Damaged DNA can lead to incorrect base pairing, which can lead to
mutations (permanent changes in the DNA sequence) - ANSWER Why
is it very important that damaged DNA is repaired?
Guanine with a new -C=O bond in place of the original =C-H2 bond -
ANSWER What is 8-oxyguanine?
8-oxyguanine flips over, causing it to hydrogen bond with adenine
(instead of cytosine) and become a thymine in the next round of DNA
replication - ANSWER What happens to GC base pairing when
guanine is converted to 8-oxyguanine?
2 (instead of guanine's normal 3) - ANSWER How many hydrogen
bonds does 8-oxyguanine have with its partner nucleotide?
An agent used in chemotherapy that has lots of bulky side chains -
ANSWER What is cisplatin?
Bulky adducts (DNA "bubbles") caused by the addition of large
sidechains and/or intrastrand crosslinking caused by cisplatin
binding to 2 adjacent guanines - ANSWER What type of DNA damage
,can be caused by cisplatin?
The addition of cisplatin causes damage to DNA, so introducing it to
cancer cells can help damage/kill them - ANSWER Why is cisplatin an
effective treatment for cancer?
Silent mutation - ANSWER What type of mutation occurs when a
single basepair is changed, but the amino acid stays the same?
Missense mutation - ANSWER What type of mutation occurs when a
single basepair is changed, changing the amino acid?
Nonsense mutation - ANSWER What type of mutation occurs when a
single basepair is changed, causing the formation of a stop codon?
False (mutations in the active site are more detrimental than
mutations in outer regions of the protein) - ANSWER T/F: mutations in
any part of a protein's sequence can be equally damaging.
Frameshift mutation - ANSWER What type of mutation occurs when a
single basepair is inserted or deleted?
A single-stranded break in the DNA - ANSWER What kind of DNA
damage is recognized by the BER repair proteins?
Each type of glycosylase recognizes a different type of DNA damage
- ANSWER Why is it necessary to have multiple types of
glycosylases?
Mono-functional glycosylases will only cleave an incorrect base;
bi-functional glycosylases will cleave both an incorrect base and the
DNA's backbone - ANSWER How does BER differ if a mono-functional
vs. a bi-functional glycosylase is used?
False ("short-patch" DNA repair is when only 1 base is removed and
replaced) - ANSWER T/F: "Short-patch" DNA repair refers to multiple
bases being removed and replaced along a short section of DNA.
FEN1 (cleaves the "flap" of incorrect bases) - ANSWER What is the
additional enzyme that's required for "long-patch" DNA repair before
,ligase can seal up the nick?
(1) To cut the DNA backbone at the 5' end; (2) to proofread for
mistakes by DNAP-beta - ANSWER What are the 2 functions of APE1?
No ligase has been added, so the fragments are not able to be
connected, giving the short band only (21 bp) - ANSWER Functions of
APE1 experiment: why is only 1 short band visible in the control lane?
DNA ligase is added, causing the 2 fragments to be connected and
be located higher on the gel (40 bp) - ANSWER Functions of APE1
experiment: how does the short band become a long band (21 bp ->
40 bp)?
If the base pairing before a nick is CORRECT, ligase can easily seal it
back up; if the base pairing before a nick is a MISMATCH, ligase
requires the help of APE1 and DNAP-beta to efficiently seal the nick
(low efficiency if ligase acts alone) - ANSWER Functions of APE1
experiment: why does adding ligase to lane 3 (correct A/T pairing)
cause robust formation of the long band while adding ligase to lane 8
(G/T mismatch) only results in a small amount of the long band?
DNAP-beta is not able to remove the incorrect base pair before
replacing it, as it requires APE1 to do so - ANSWER Functions of
APE1 experiment: why does the addition of DNAP-beta in lane 9 not
improve the efficiency of forming the long band?
APE1 is able to remove the mismatched base pair, allowing
DNAP-beta to easily add a new base and ligase to seal the nick -
ANSWER Functions of APE1 experiment: why does the addition of
APE1 in lane 10 improve the efficiency of long band formation?
True (ligation efficiency is dependent on APE1 concentration) -
ANSWER T/F: the more APE1 added to nicked DNA, the more
efficient the ligation is.
False (APE1 is required for efficient ligation) - ANSWER T/F: ligation
, after DNA repair can be efficient without APE1 (only with ligase and
DNAP-beta).
Since glycosylases target many different types of DNA damage,
having certain ones be defective can result in many different
consequences - ANSWER Why are there a wide variety of
consequences if BER enzymes are defective?
Bulky adducts in DNA ("bubbles" caused by intrastrand crosslinking)
- ANSWER What kind of DNA damage is recognized by the NER repair
proteins?
GG-NER is for inactive genes while TC-NER is for genes being
actively transcribed - ANSWER What is the basic difference between
the GG-NER pathway and the TC-NER pathway?
False (oligonucleotide excision involves a long piece of damaged
DNA being removed, while "long-patch" DNA repair involves only
removing a few bases) - ANSWER T/F: oligonucleotide excision is the
same as "long-patch" DNA repair.
It uses its beta-sheet "finger" to flip the 2 correct bases (across from
the dimerized bases) out of the helix, allowing it to stabilize and act
as a scaffold for other proteins - ANSWER GG-NER: how does XPC
become stabilized at typical DNA damage by bulky adducts?
False (while DNA glycosylases flip out the damaged base for
removal, XPC flips out the CORRECT bases that are across from the
dimerized bases) - ANSWER T/F: DNA glycosylases and XPC both flip
the damaged bases out of the helix for removal.
XPC requires the help of DDB (damaged DNA-binding) protein to flip
out the correct bases and stabilize - ANSWER GG-NER: how does
XPC become stabilized at harder-to-detect DNA damage (extra bulky
adducts)?
During transcription, RNAP will automatically stall at areas of DNA
damage - ANSWER TC-NER: how does the DNA damage get
recognized?
LATEST UPDATE
DNA can be both replicated and transcribed into mRNA, which can
be translated into protein - ANSWER What is the central dogma of
molecular biology?
True (this is due to intrastrand crosslinking, in which adjacent
nucleotides basepair, causing bubbling) - ANSWER T/F: the addition
of bulky aromatic rings and/or exposure to UV light can cause the
DNA to "bubble."
True - ANSWER T/F: chemotherapy can cause both single and
double-stranded breaks in DNA.
Damaged DNA can lead to incorrect base pairing, which can lead to
mutations (permanent changes in the DNA sequence) - ANSWER Why
is it very important that damaged DNA is repaired?
Guanine with a new -C=O bond in place of the original =C-H2 bond -
ANSWER What is 8-oxyguanine?
8-oxyguanine flips over, causing it to hydrogen bond with adenine
(instead of cytosine) and become a thymine in the next round of DNA
replication - ANSWER What happens to GC base pairing when
guanine is converted to 8-oxyguanine?
2 (instead of guanine's normal 3) - ANSWER How many hydrogen
bonds does 8-oxyguanine have with its partner nucleotide?
An agent used in chemotherapy that has lots of bulky side chains -
ANSWER What is cisplatin?
Bulky adducts (DNA "bubbles") caused by the addition of large
sidechains and/or intrastrand crosslinking caused by cisplatin
binding to 2 adjacent guanines - ANSWER What type of DNA damage
,can be caused by cisplatin?
The addition of cisplatin causes damage to DNA, so introducing it to
cancer cells can help damage/kill them - ANSWER Why is cisplatin an
effective treatment for cancer?
Silent mutation - ANSWER What type of mutation occurs when a
single basepair is changed, but the amino acid stays the same?
Missense mutation - ANSWER What type of mutation occurs when a
single basepair is changed, changing the amino acid?
Nonsense mutation - ANSWER What type of mutation occurs when a
single basepair is changed, causing the formation of a stop codon?
False (mutations in the active site are more detrimental than
mutations in outer regions of the protein) - ANSWER T/F: mutations in
any part of a protein's sequence can be equally damaging.
Frameshift mutation - ANSWER What type of mutation occurs when a
single basepair is inserted or deleted?
A single-stranded break in the DNA - ANSWER What kind of DNA
damage is recognized by the BER repair proteins?
Each type of glycosylase recognizes a different type of DNA damage
- ANSWER Why is it necessary to have multiple types of
glycosylases?
Mono-functional glycosylases will only cleave an incorrect base;
bi-functional glycosylases will cleave both an incorrect base and the
DNA's backbone - ANSWER How does BER differ if a mono-functional
vs. a bi-functional glycosylase is used?
False ("short-patch" DNA repair is when only 1 base is removed and
replaced) - ANSWER T/F: "Short-patch" DNA repair refers to multiple
bases being removed and replaced along a short section of DNA.
FEN1 (cleaves the "flap" of incorrect bases) - ANSWER What is the
additional enzyme that's required for "long-patch" DNA repair before
,ligase can seal up the nick?
(1) To cut the DNA backbone at the 5' end; (2) to proofread for
mistakes by DNAP-beta - ANSWER What are the 2 functions of APE1?
No ligase has been added, so the fragments are not able to be
connected, giving the short band only (21 bp) - ANSWER Functions of
APE1 experiment: why is only 1 short band visible in the control lane?
DNA ligase is added, causing the 2 fragments to be connected and
be located higher on the gel (40 bp) - ANSWER Functions of APE1
experiment: how does the short band become a long band (21 bp ->
40 bp)?
If the base pairing before a nick is CORRECT, ligase can easily seal it
back up; if the base pairing before a nick is a MISMATCH, ligase
requires the help of APE1 and DNAP-beta to efficiently seal the nick
(low efficiency if ligase acts alone) - ANSWER Functions of APE1
experiment: why does adding ligase to lane 3 (correct A/T pairing)
cause robust formation of the long band while adding ligase to lane 8
(G/T mismatch) only results in a small amount of the long band?
DNAP-beta is not able to remove the incorrect base pair before
replacing it, as it requires APE1 to do so - ANSWER Functions of
APE1 experiment: why does the addition of DNAP-beta in lane 9 not
improve the efficiency of forming the long band?
APE1 is able to remove the mismatched base pair, allowing
DNAP-beta to easily add a new base and ligase to seal the nick -
ANSWER Functions of APE1 experiment: why does the addition of
APE1 in lane 10 improve the efficiency of long band formation?
True (ligation efficiency is dependent on APE1 concentration) -
ANSWER T/F: the more APE1 added to nicked DNA, the more
efficient the ligation is.
False (APE1 is required for efficient ligation) - ANSWER T/F: ligation
, after DNA repair can be efficient without APE1 (only with ligase and
DNAP-beta).
Since glycosylases target many different types of DNA damage,
having certain ones be defective can result in many different
consequences - ANSWER Why are there a wide variety of
consequences if BER enzymes are defective?
Bulky adducts in DNA ("bubbles" caused by intrastrand crosslinking)
- ANSWER What kind of DNA damage is recognized by the NER repair
proteins?
GG-NER is for inactive genes while TC-NER is for genes being
actively transcribed - ANSWER What is the basic difference between
the GG-NER pathway and the TC-NER pathway?
False (oligonucleotide excision involves a long piece of damaged
DNA being removed, while "long-patch" DNA repair involves only
removing a few bases) - ANSWER T/F: oligonucleotide excision is the
same as "long-patch" DNA repair.
It uses its beta-sheet "finger" to flip the 2 correct bases (across from
the dimerized bases) out of the helix, allowing it to stabilize and act
as a scaffold for other proteins - ANSWER GG-NER: how does XPC
become stabilized at typical DNA damage by bulky adducts?
False (while DNA glycosylases flip out the damaged base for
removal, XPC flips out the CORRECT bases that are across from the
dimerized bases) - ANSWER T/F: DNA glycosylases and XPC both flip
the damaged bases out of the helix for removal.
XPC requires the help of DDB (damaged DNA-binding) protein to flip
out the correct bases and stabilize - ANSWER GG-NER: how does
XPC become stabilized at harder-to-detect DNA damage (extra bulky
adducts)?
During transcription, RNAP will automatically stall at areas of DNA
damage - ANSWER TC-NER: how does the DNA damage get
recognized?
