DNA Repair

Ultraviolet radiation can alter DNA structure by creating _______ ______

Thymine dimers

High-energy radiation can cause _______ in DNA strands

Breaks

DNA damage can be caused by interaction with _______ compounds like tobacco smoke

Harmful

Byproducts of normal metabolic processes like _______ ________ _______ can damage DNA

Reactive oxygen species

DNA replication is naturally prone to _______; however, cells possess intrinsic repair mechanisms to correct these during the process

Errors

The cell halts the division process to assess and repair damage

Cell cycle checkpoints

The cell may alter _______ _______ in response to damage

Gene expression

A mutated protein can alter _____ ________, changing how the cell functions or communicates

Cell signaling

Simple chemical reversal of damage of DNA

Direct reversal

Removes small, non-helix-distorting base lesions

Base excision repair

Repairs bulky lesions (like those from UV light)

Nucleotide excision repair

Corrects errors that escaped proofreading during replication

Mismatch repair

Accurate repair for double-stranded break using a sister chromatid as a template

Homologous recombination

Glues double-stranded broken ends back together (more prone to error)

Non-homologous end joining

Programmed cell death

Apoptosis

Apoptosis often occurs when DNA damage is beyond _______

Repair

Apoptosis is a ________ process, distinct from necrosis (which is uncontrolled cell death due to injury)

Controlled

DNA Polymerase is responsible for _____ building the DNA strand and checking it for errors during replication

Both

The active site of DNA polymerase where new nucleotides are added to the growing primer strand

P Site

A separate site on DNA polymerase responsible for “proofreading”; if mismatch is detected, the strand moves to this site to be corrected

E Site

As DNA is synthesized, DNA polymerase checks the base pairing, if incorrect, it _______, removes the wrong nucleotide (at the E site) and then resumes synthesis

Pauses

Specialized repair enzymes scan newly synthesized DNA and specifically correct errors in base pairing

Mismatch repair

Used to fix damaged structures of DNA; bulky lesions or physical damage

Nucleotide excision repair

In nucleotide excision repair, a ______ enzyme cuts out the damaged segment

Nuclease

During nucleotide excision repair, a ____ _______ fills the gap with the correct nucleotides using the undamaged strand as a template

DNA Polymerase

In nucleotide excision repair, _____ _______ seals the nick in the sugar-phosphate backbone (makes the covalent bond) to complete the strand

DNA Ligase

________ arise from rare copying errors or accidental damage

Mutations

Mutations in ________ cells are passed to the next generation (inherited)

Germ-line

A single amino acid __________ can drastically change protein structure and function

Substitution

Caused by a mutation that causes Glutamic Acid to be replaced by Valine

Sickle Cell Anemia

In sickle cell anemia, the altered _________ protein shape causes blood cells to sickle, leading to clogged blood vessels and disease

Hemoglobin

Often associated with errors at the polymerase E site

Base-pair mismatch

Chemical changes to the nucleotide structure including Depurination and Deamination

Covalent modification of bases

Dimerization occurring either within a single strand or connecting two opposite strands

Covalent cross-links

Double-stranded breaks are classified as the most _________ type of damage

Dangerous

The loss of a nitrogenous base (specifically Adenine or Guanine) from the nucleotide

Depurination

In depurination, the ________ bond holding the base to the sugar is cleaved

N-glycosidic

In depurination, the sugar-phosphate backbone remains ______, but it is left with a “missing” base (an apurinic site)

Intact

When the replication machinery encounters a depurination site, it may skip that position resulting in a nucleotide __________ in the new strand, causing a frameshift mutation

Deletion

The spontaneous loss of an amino group from a nitrogenous base

Deamination

In deamination, a _________ reaction occurs where water is added and ammonia is released

Hydrolysis

Deamination converts cytosine to ________

Uracil

In deamination, the modified base pairs _________-

Incorrectly

It unrepaired, deamination can result in base-pair ________ in the daughter strands

Substitution

The resulting bases in deamination are considered ________ within DNA

Unnatural

Because these bases are distinct from the standard four DNA bases, DNA repair machinery can easily recognize and excise them to reverse the damage

Deamination

This is caused by exposure to UV light

Covalent cross-linking

Covalent cross-linking forms _______ ________ on the same DNA strand

Thymine dimers

Thymine dimers cause a ______ in the DNA structure

Bulge

Covalent cross-linking stalls the replication machinery, DNA cannot be copied past the _______

Damage

If covalent cross-linking is unrepaired, it can lead to _________

Melanoma

A genetic disorder where the body lacks the mechanism to repair this UV damage

Xeroderma Pigmentosum

To repair thymine dimers, the repair mechanism targets the entire ________ area, not just the damaged base, and fills it back in

Surrounding

A break in the DNA strand can occur when _________ creates a nick to relieve tension but fails to reseal it

Topoisomerase

Radiation and reactive chemicals can cause _______ in DNA

Breaks

Replication stops at a DNA _____ and results in the loss of genetic material

Stops

Due to DNA breaks, because the gene is incomplete, the resulting protein is ______ and usually non-functional

Truncated

Occur in non-coding regions; these are the most common type of mutation overall because most DNA is non-coding

Silent mutations

The mutation changes the codon but creates the same amino acid

Synonymous

The mutation results in a different amino acid (e.g., Sickle Cell Anemia); this is the second most common mutation type

Missense

The mutation creates a stop codon instead of an amino acid

Nonsense

Nonsense mutations result in translation ending _________, creating a truncated, non-functional protein

Prematurely

The addition or removal of nucleotides; usually leads to a frameshift mutation

Indel

Includes direct reversal, base excision repair, and nucleotide excision repair

Repairing damaged bases

Includes non-homologous end joining and homologous end joining/recombination

Repairing double-stranded breaks

This mechanism regenerates the normal base from the damaged DNA without cutting the DNA backbone

Direct reversal

Direct reversal uses __________ to remove alkyl groups specifically from the O6 position of Guanine

Alkyltransferases

In direct reversal, the alkyltransferase transfers the alkyl group from the DNA to ______

Itself

Alkyltransferases for direct reversal are ___ time use only and then become inactivated

One

Direct reversal mechanisms are easily ________ because a new enzyme molecule must be synthesized for every single repair event

Saturated

Used primarily for correcting small, non-bulky damage to specific bases

Base excision repair

Used in base excision repair; recognizes the specific damaged base and cleaves the bond attaching it to the sugar, removing the base

DNA Glycosylase

Base excision repair; cuts the phosphate backbone at the site where the base is missing

AP Endonuclease

Base excision repair; inserts the correct nucleotide into the gap

DNA Polymerase beta

Base excision repair; seals the remaining “nick” in the backbone to complete the repair

DNA Ligase

Used for bulky lesions that distort the DNA helix (e.g., pyrimidine dimers caused by UV light)

Nucleotide excision repair

In nucleotide excision repair, a ________ complex scans the DNA and identifies distortion in the helix

Multi-enzyme

In nucleotide excision repair, the phosphate ________ is cleaved on both sides of the damage

Backbone

In nucleotide excision repair, ________ unwinds the DNA and removes a segment containing the lesion (approximately 12-13 nucleotides long)

Helicase

In nucleotide excision repair, _____ _________ fills in the resulting gap using the undamaged strand as a template

DNA Polymerase

In nucleotide excision repair, ____ ________ seals the final nick in the backbone

DNA Ligase

A mechanism for repairing double-strand DNA breaks; it is described as quick and dirty

Non-homologous end joining

In non-homologous end joining, proteins identify the _____ DNA ends and additional proteins are recruited to hold the DNA strands together

Broken

In non-homologous end joining, the ends are processed and _______ so nucleotides are often removed

Trimmed

This is an error-prone process because it happens randomly without a template; generally results in a deletion of nucleotides (loss of genetic information)

Non-homologous end joining

A precise method for repairing double-strand breaks, usually utilized for smaller problems

Homologous recombination

In homologous recombination, exonuclease activity degrades the 5’ end of the DNA, creating a 3’ _________

Overhang

In homologous recombination, ____ proteins guide the single-stranded overhang to invade a homologous DNA sequence (specifically the sister chromatid)

Rad

In homologous recombination, the _______ chromatid is used as a template for DNA polymerization to replace missing nucleotides accurately

Sister

In homologous recombination, the double-strand break is accurately repaired with no loss of ________ _________

Genetic information

This condition is a result of a genetic translation (a non-homologous end-joining error in recombination) associated with Chronic Myelogenous Leukemia

Philadelphia chromosome

Philadelphia chromosome is the result of a reciprocal translocation between these two chromosomes

Chromosome 9 and 22

The Philadelphia chromosome creates a _________ fusion gene

BCR-ABL

The Philadelphia Chromosome results in a hyperactive _______ _______ protein

Tyrosine kinase

The Philadelphia chromosome hyperactive tyrosine kinase leads to __________ cell signaling, preventing apoptosis and causing increased WBC counts

Uncontrolled

Tyrosine Kinase inhibitor that inhibits the fusion gene product and stops the signal for uncontrolled cell proliferation; prescribed only after a biopsy confirms the presence of the Philadelphia chromosome

Imatinib