Cycle 4 Flashcards
A mechanism for correcting errors made by DNA polymerase during replication
Mechanism of proofreading
A mechanism for correcting errors made during replication that escapes proofreading
Mechanism of mismatch repair
Mehcniamss for correcting various kinds of DNA damage, such as those caused by chemical and radiation
Mechanism of excision repair
2 main sources of DNA Damage
Exogenous and Endogenous
When each mechanism is most likely to be used
1) Proofreading:
2) Mismatch repair:
3) Excision repair:
1) During DNA replication
2) Immediately after DNA replication
3) Anytime during the cell cycle but usually in response to DNA damage
Endogenous (______ the cell)
within
Exogenous (sources ______ the cell)
outside
Exogenous EX: (3)
UV light, chemicals, ionizing radiation
Exogenous: Damages coming from the _______
environment
When UV hits your DNA, you get bonds formed between ___ (shouldn’t be formed bases in the same strand)
T-T
Less or more ROS as you age
More
_____ can cause a single-strand or double-strand break in DNA
Chemicals
We have ____ that will take care of the electron
enzymes
______ is the final electron acceptor (but if a single electron is given to O. will produce free radical)
Oxygen
O2 is normal, O2- (______) is free radical with extra e- {TYPE OF ROS}, not stable
superoxide
Metabolism {______ _______ _______ (ROS)}
Reactive oxygen species
electrons usually travel in pairs, but in ____ transporting them singularly
ETC
Dangour because can produce ______ (UNPAIRED ELECTRON in outer orbital) when misplaced
free radicals
____ Are highly reactive molecules
Has to give an electron to become stable, sp targets DNA, RNA, or protein (causes mutations)
ROS
________ react with this to convert to safe molecule
Antioxidants
Can use ____ in positive way, but for the most part if it starts to accumulate, not a good thing
ROS
O2- to H2O2 (nonfree radical ROS) to ____
H2O
Lead to errors while polymerase is making ______-strand
second
H2O can be converted to ____ (is a free radical ROS)
OH (hydroxyl)
Accidnelty add the _____ base
wrong
Substitution mutation also called
____ mutation it is when one base pair has been changed
Point
DNA replication errors:
The process occurs in the __ phase
S
Normal sequence = ____ type
wild
If the mismatch goes unchecked, becomes a _____ OR
mutant OR DNA slippage either forward or backward (can cause insertion or deletion mutations)
_____(codon changes, codes for a different amino acid)
Missense
_____ (premautre stop)
Nonsense
_____ (leads to same amino acid, because of redundancy in codon)
Silent
_______
Delete bases
Deletion
DNA Damage or Mutation:
Single-stranded change
DNA Damage
______
The sequence is exactly the opposite
Inversion
DNA Damage or Mutation:
-Double-stranded change
-Complementary base pairing
Mutation
Repair mechanisms: (2)
proofreading, mismatch repair
Proofreading:
Done by ______ itself
Detects ______ in the backbone
Then starts moving backward: 3’-5’ exonuclease activity
Removes (as removing nucleotides), then starts moving forward once done
polymerase
distortion
3’-5’
Cause of double-strand breaks:
Radiation damages DNA
Double-strand breaks are repaired through:
Non-Homologous End Joining (NHEJ)
Repair of double strand break: ____ pieces the DNA back together but introduces errors
NHEJ
_______
Extra bases that aren’t supposed to be there
Insertion
NHEJ is slopping and can result in ______
mutation
Repair enzymes:
____ done by polymerase alone
Requires the help of ______ ______ that will then come and cut the distorted part
Cuts it out, and then _____ repairs the gap
Sealed by ____
Not
repair enzymes
polymerase
ligase
Slip backward (causes ____) and forms a little loop thinks it has not synthesized that part yet
insertion
Some Mutagens are tautomerically unstable base “______”
analogues
Hard to put it back as it was before: leads to ______ ______ or ______
Deletion, insertion, inversion
Can also bring it back to wild type: a very high or low possibility?
LOW
Delation is by _____ slippage
forward
Spontaneous ______ shifts change base pairing “partners”
tautomeric
InDel (insertion or deletion) Mutations due to DNA polymerase ________
Slippage
Transposable Elements: the “______ Genes”
Jumping
Transversion vs Transition: ______ are interchanges of two-ring purines (A G), or of one-ring pyrimidines (C T): they therefore involve bases of similar shape. ______ are interchanges of purine for pyrimidine bases, which therefore involve exchange of one-ring & two-ring structures.
Transitions, Transversions
Spontaneous tautomeric shift: Different preferred partner
YES OR NOT COMPLEMENTARY BASE PAIRING?
NOT
More TE = Higher __ value
C
Active TEs have evolved to insert into_______ ______ in the genome
safe heavens
Transposable elements are Another way to get mutations
Another way to get mutations
Are TE Present in every single organism?
YES
___ of the human genome contains TEs
50%
Most are:
dead/inactive
The host ____ more active TEs
Put into _____ regions
silences, intron
___ most common TE
Alu
_______: Structural changes to the DNA, such as strand breaks or base modifications, which can be repaired.
DNA damage
______: A permanent alteration in the DNA sequence that isn’t repaired and is passed on during replication.
Mutation
___: often neutral but can be linked to disease.
SNP Single base substitution;
___: Insertion or deletion of one or more nucleotides, potentially altering the reading frame.
InDel
Discovered by ________ in maize, transposable elements (or “jumping genes”) are DNA sequences that move within the genome.
Barbara McClintock
Why transposable elements can be considered biological mutagens.
They can insert into or near genes, disrupting function, leading to mutations, or altering gene regulation.
What is the difference between DNA damage and a mutation?
A) DNA damage is when bonds in the DNA backbone are disrupted, and a mutation is when there are changes in the sequence of nitrogenous bases.
B) DNA damage is not heritable because it occurs when the DNA sequence in somatic cells is changed. A mutation is inheritable because it occurs when the DNA sequences in germline cells are Changed.
C) DNA damage is a single-stranded change in DNA sequence, while a mutation is a double-stranded change in DNA sequence
D) DNA damage occurs when exogenous sources cause a change in DNA sequence, while mutations occur when endogenous sources cause a change in DNA sequence.
C
In addition to being an integral component in the synthesis of new strands of DNA, the enzyme DNA polymerase III also has exonuclease activity that enables it to repair any mismatch errors it may make. What is the directionality of the exonuclease activity in DNA polymerase III?
A) Always 5’ to 3’
B) Always 3’ to 5’
C) 3’ to 5’ on the synthesized strand and 5’ to 3’ on the template strand
D) 5’ to 3’ on the synthesized strand and 5’ to 3’ on the template strand
B
Which of the following enzymes are capable of cutting out short segments of DNA bases as part of a repair process?
1. Excision repair enzymes
2. Enzymes that conduct non-homologous end joining
3. Mismatch repair enzymes
4. DNA polymerase III 1.
A) 2 and 3
B) 1 and 3 (Excision repair enzymes and mismatch repair enzyme are able to cut through the phosphodiester bonds in the DNA backbone. * DNA polymerase III only removes one base at a time.)
C) 2 and 4
D) 4 only
E) All of 1, 2, 3, and 4 are correct.
B
Which of the following statements about ROS is correct?
A) Low levels of ROS can increase the oxidative stress levels in the cell.
B) ROS can achieve stability by stealing electrons from DNA.
C) The highly electronegative nature of ROS allows them to stabilize the genome.
D) ROS can increase the lifespan of an organism.
B
