Cycle 4 Flashcards by Diya Vyas

A mechanism for correcting errors made by DNA polymerase during replication

Mechanism of proofreading

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A mechanism for correcting errors made during replication that escapes proofreading

Mechanism of mismatch repair

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Mehcniamss for correcting various kinds of DNA damage, such as those caused by chemical and radiation

Mechanism of excision repair

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2 main sources of DNA Damage

Exogenous and Endogenous

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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

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Endogenous (______ the cell)

within

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Exogenous (sources ______ the cell)

outside

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Exogenous EX: (3)

UV light, chemicals, ionizing radiation

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Exogenous: Damages coming from the _______

environment

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When UV hits your DNA, you get bonds formed between ___ (shouldn’t be formed bases in the same strand)

T-T

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Less or more ROS as you age

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_____ can cause a single-strand or double-strand break in DNA

Chemicals

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We have ____ that will take care of the electron

enzymes

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______ is the final electron acceptor (but if a single electron is given to O. will produce free radical)

Oxygen

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O2 is normal, O2- (______) is free radical with extra e- {TYPE OF ROS}, not stable

superoxide

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Metabolism {______ _______ _______ (ROS)}

Reactive oxygen species

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electrons usually travel in pairs, but in ____ transporting them singularly

ETC

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Dangour because can produce ______ (UNPAIRED ELECTRON in outer orbital) when misplaced

free radicals

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____ Are highly reactive molecules
Has to give an electron to become stable, sp targets DNA, RNA, or protein (causes mutations)

ROS

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________ react with this to convert to safe molecule

Antioxidants

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Can use ____ in positive way, but for the most part if it starts to accumulate, not a good thing

ROS

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O2- to H2O2 (nonfree radical ROS) to ____

H2O

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Lead to errors while polymerase is making ______-strand

second

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H2O can be converted to ____ (is a free radical ROS)

OH (hydroxyl)

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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

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

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.

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

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.

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.