DNA Replication and Repair Flashcards

Flashcards covering vocabulary related to DNA replication and repair.

Antiparallel

The two strands of DNA are in opposite polarities with a five prime end and a three prime end, where the five prime end of one strand lines up with a three prime end of the other and vice versa.

Processivity

Maintaining contact between the DNA polymerase and the DNA strand as it is synthesizing DNA so that it synthesize a long stretch of DNA without falling off.

Leading Strand

The continuous strand that's running in the correct direction during DNA replication.

Lagging Strand

The strand where the DNA polymerase would have to run-in the wrong direction, requiring the formation of Okazaki fragments.

Okazaki Fragment

Short stretches of DNA synthesized on the lagging strand due to the discontinuous nature of replication in that direction.

DNA Helicase

A hexameric complex that hydrolyzes ATP to rotate on the DNA and pry apart the DNA strands.

Sliding Clamp

A clamp that holds the DNA polymerase in contact with the DNA, allowing it to let go of the DNA to move forward one nucleotide but prevents complete separation from the DNA strand.

Topoisomerases

Enzymes that relieve the torsional stress on DNA during unwinding by either nicking and swiveling (Type I) or using a gating mechanism (Type II).

Nick and Swivel

The mechanism used by topoisomerase I where a tyrosine residue performs a nucleophilic attack on the sugar-phosphate backbone of one DNA strand, creating a nick and allowing the strands to rotate independently.

Origin of Replication

Specialized regions of DNA where DNA synthesis initiates, typically having high AT content.

DNA adenine methylase (dam methylase)

A methylase in prokaryotes that methylates adenines within the GATC sequence at the origin of replication, required for initiating DNA replication.

Origin Recognition Complex (ORC)

A complex in eukaryotes that binds to the origin of replication and is key for initiating DNA replication.

Telomerase

A specialized enzyme that synthesizes telomeres at the ends of linear chromosomes to prevent shortening during replication, containing an RNA component and a protein component (reverse transcriptase).

Hayflick Limit

The number of times a normal human cell population will divide until cell division stops due to the shortening of telomeres.

Exonucleolytic Proofreading

A secondary error-correction mechanism of DNA polymerase in which it checks the most recently added nucleotide, excising it if it is incorrectly paired.

Strand Directed Mismatch Repair

A mechanism used to detect mutation errors due to DNA damage, where a complex of proteins binds to the area where the DNA is distorted and removes the incorrect nucleotides.

Replication Fork

The area where the parental DNA strands are separated and new daughter strands are being synthesized during DNA replication.

Primase

An enzyme that synthesizes short RNA primers to provide a starting point for DNA polymerase to begin replication.

Single-Stranded Binding Proteins (SSBPs)

Proteins that bind to single-stranded DNA to prevent it from re-annealing or forming secondary structures during replication.

DNA Ligase

An enzyme that catalyzes the formation of phosphodiester bonds to join Okazaki fragments on the lagging strand or to seal nicks in DNA.

Telomeres

Repetitive nucleotide sequences at the ends of linear chromosomes that protect the coding regions from degradation and shortening during DNA replication.

Reverse Transcriptase

A DNA polymerase enzyme that synthesizes DNA from an RNA template as seen in retroviruses and telomerase.

Mismatch Repair System

A DNA repair system that recognizes and corrects mismatched base pairs that were not corrected by the proofreading activity of DNA polymerase.

Base Excision Repair (BER)

A DNA repair pathway that removes damaged or modified bases from the DNA, followed by replacement of the correct base.

Nucleotide Excision Repair (NER)

A DNA repair pathway that removes bulky, helix-distorting lesions such as thymine dimers or chemically modified bases from the DNA.