DNA Repair Mechanisms and Nuclear Structure

Flashcards covering DNA repair pathways (BER, NER, MMR, translesion synthesis), mutation types, PCR methods, and nuclear structural components.

With proofreading and repair mechanisms operating, the DNA replication mistake rate drops from $1/10^5\text{ bases}$ to __________.

$$1/10^9\text{ bases}$$

The five endogenous and exogenous causes of DNA damage designated by the mnemonic RICCU are Replication Errors, Ionizing Radiation, Chemical Exposure, Cellular Mechanisms, and __________.

UV radiation

During endogenous deamination, a cytosine ($C$) base is converted to a uracil ($U$) base by replacing an $-NH_2$ group with an __________.

$$O$$

When UV radiation strikes two adjacent thymines in DNA, they form covalent bonds that produce a __________ ring.

cyclobutane

Chemical exposure leading to DNA adducts includes benzene rings attaching to guanine, which can occur as a product of smoke from __________.

vaping or smoking

Base Excision Repair (BER) is a cellular repair pathway specifically dedicated to removing a __________ from the DNA backbone.

single damaged base

In the Base Excision Repair (BER) pathway shown below, the enzyme that cleaves the damaged base from deoxyribose to generate an AP site is __________.

DNA glycosylase

Following base cleavage during BER, the phosphodiester bond adjacent to an apurinic or apyrimidinic site is cut by the enzyme __________.

AP endonuclease

If an AP site is not properly repaired, an endonuclease can digest both strands, producing damaged DNA molecules with __________ ends that lack single-stranded overhangs.

blunt-ended

Tissues with high rates of cellular replication, such as __________ cells, have a strong requirement for Base Excision Repair.

epithelial

In the general Nucleotide Excision Repair (NER) mechanism shown below, the single-stranded segment containing the lesion released after helicase action is the __________.

excised oligonucleotide

Nucleotide Excision Repair can function as transcription-coupled repair, which is specifically dedicated to correcting lesions located within __________ genes.

actively transcribed

In the eukaryotic NER complex shown below, the general transcription factor containing the helicase subunits XPB and XPD is __________.

TFIIH

In the dual incision step of eukaryotic NER shown below, the endonuclease heterodimer responsible for cleavage on the $5'$ side of the DNA lesion is __________.

XPF/ERCC1

Xeroderma Pigmentosum (XP) is an inherited __________ condition caused by defects in NER genes, leading to extreme photosensitivity and high skin cancer risk.

autosomal recessive

Among the five XP gene products involved in NER, the enzyme responsible for providing $3'$ nuclease activity is __________.

XPG

In bacterial Mismatch Repair (MMR), the repair machinery identifies the newly synthesized strand because it lacks __________ present on the template strand.

hemimethylation

In the bacterial Mismatch Repair pathway shown below, the mismatch is initially detected and bound by the protein pair __________.

MutS and MutL

In the eukaryotic Mismatch Repair pathway shown below, mismatched bases on both the leading and lagging strands are recognized by the MutS and MutL homologs designated as __________.

MSH and MLH

When the replication machinery bypasses past a DNA lesion and corrects it later, the process is known as __________ synthesis.

translesion

A point mutation that replaces a codon specifying an amino acid with a stop codon is termed a __________ mutation.

nonsense

Unlike mutations in germ cells, mutations acquired in __________ cells (such as skin cancer caused by UV exposure) cannot be inherited by future generations.

somatic

In the Polymerase Chain Reaction (PCR) cycle shown below, primer annealing to template strands is carried out at __________.

$$55^\circ\text{C}$$

During the denaturation step of a PCR cycle, double-stranded template DNA is separated into single strands by heating to __________.

$$95^\circ\text{C}$$

The thermostable enzyme that extends primers by synthesizing complementary DNA strands during PCR at $72^\circ\text{C}$ is __________.

Taq polymerase

In reverse transcriptase PCR (RT-PCR), gene expression levels are quantified by first using reverse transcriptase to convert __________ into cDNA.

RNA

The nuclear __________, a lattice-like meshwork of fibrous proteins lining the inner nuclear membrane, provides structural integrity to help the nucleus withstand pressure.

lamina

In the nucleus, transcriptionally active and relaxed chromatin is called euchromatin, whereas transcriptionally inactive and tightly condensed chromatin is called __________.

heterochromatin

The specialized compartment inside the nucleus responsible for the synthesis of ribosomal RNA (rRNA) is the __________.

nucleolus

The fluid-filled region separating the inner and outer membranes of the nuclear envelope is known as the __________ space.

perinuclear