DNA Organization, Replication, and Repair

A complete set of vocabulary flashcards detailing DNA structure, chromatin packaging, replication enzymes and steps, as well as single- and double-strand DNA repair pathways.

Purines

Nitrogenous bases consisting of Adenine (A) and Guanine (G).

Pyrimidines

Nitrogenous bases consisting of Cytosine (C) and Thymine (T).

Phosphodiester Bond

A covalent bond formed between the $3'\text{-OH}$ of one pentose sugar and the $5'\text{-OH}$ of the next sugar that connects nucleotides into a polynucleotide chain.

DNA Denaturation

The separation of double-stranded DNA into two single strands caused by heat or alkali disruption of hydrogen bonds, leaving phosphodiester bonds intact.

Melting Temperature ($T_m$)

The temperature at which $50\text{\%}$ of double-stranded DNA is present as single strands, which depends on its base composition.

Hybridization

The tendency of single-stranded DNA to bind to complementary sequences of single-stranded DNA or RNA.

Mitochondrial DNA

Circular, double-stranded, GC-rich DNA that lacks histones, contains 37 genes (13 for energy production and 24 for rRNA and tRNA), and is inherited exclusively from the mother.

Centromere

The constricted region of a chromosome that serves as the attachment site for spindle microtubules and is required for correct mitosis.

Telomeres

Structures at the ends of chromosomes consisting of hexanucleotide repeats ($\text{TTAGGG}$ repeated approximately 1000 times) that shorten with each cell division.

Euchromatin

A less condensed form of chromatin located on chromosome arms containing unique sequences and many genes that are frequently transcribed.

Heterochromatin

A highly condensed form of chromatin located at centromeres and telomeres containing repeated sequences and few genes that are infrequently transcribed.

Nucleosome

The basic structural unit of chromatin consisting of a histone octamer core (two molecules each of H2A, H2B, H3, and H4) wrapped by double-stranded DNA.

Histone H1

The linker histone protein that, along with linker DNA, connects adjacent nucleosomes to form the "beads-on-a-string" structure.

Origins of Replication (ori)

Specific DNA sequences where replication begins, with eukaryotes having approximately 100 per chromosome and prokaryotes having 1.

Replication Fork

The Y-shaped region where DNA unwinding and active DNA synthesis occur.

Helicase

An enzyme that separates the two parental DNA strands by breaking hydrogen bonds between complementary base pairs.

DNA Topoisomerase

An enzyme that relaxes supercoiled DNA and unwinds strands ahead of the replication fork.

Single-Stranded Binding Proteins (SSBP)

Proteins that attach to separated single-stranded DNA to prevent reannealing during replication.

Primase

A subunit of DNA polymerase that synthesizes an RNA primer of approximately $15\text{ nt}$ complementary to the parental DNA strand.

DNA Polymerase $\alpha$ (Pol $\alpha$)

A eukaryotic DNA polymerase that contains a primase subunit and initiates DNA synthesis, lacking $3' \rightarrow 5'$ exonuclease proofreading activity.

DNA Polymerase $\delta$ (Pol $\delta$)

The eukaryotic DNA polymerase that elongates Okazaki fragments on the lagging strand and possesses $3' \rightarrow 5'$ exonuclease proofreading activity.

DNA Polymerase $\epsilon$ (Pol $\epsilon$)

The eukaryotic DNA polymerase that elongates the leading strand and possesses $3' \rightarrow 5'$ exonuclease proofreading activity.

DNA Polymerase $\gamma$ (Pol $\gamma$)

The eukaryotic DNA polymerase responsible for replicating mitochondrial DNA, equipped with $3' \rightarrow 5'$ exonuclease proofreading activity.

Leading Strand

The parental strand running $3' \rightarrow 5'$ toward the replication fork, which is replicated continuously in the $5' \rightarrow 3'$ direction.

Lagging Strand

The parental strand running $3' \rightarrow 5'$ away from the replication fork, which is replicated discontinuously as short Okazaki fragments of approximately $200\text{ nt}$.

DNA Ligase

An enzyme that joins adjacent DNA segments by forming a phosphodiester bond between a free $3'\text{-OH}$ group and a free $5'\text{-phosphate}$ group.

Telomerase

A ribonucleoprotein complex containing reverse transcriptase (TERT) and an RNA template (TERC) that adds hexanucleotide repeats ($3'\text{-AAUCCC}-5'$) to extend the $3'$ end of chromosomes.

Direct Damage Reversal

The simplest DNA repair mechanism that removes alkylation damage (such as $O^6\text{-methylguanine}$ via methyltransferase) without making cuts in the phosphodiester backbone.

Base Excision Repair (BER)

An excision repair pathway that corrects small non-distorting base lesions (such as spontaneous depurination or cytosine deamination to uracil) while keeping the sugar-phosphate backbone intact.

Mismatch Repair (MMR)

A repair system that removes mispaired, undamaged bases incorporated during replication that escaped polymerase proofreading; defects cause autosomal dominant Lynch syndrome (HNPCC).

Nucleotide Excision Repair (NER)

An excision repair mechanism that removes bulky lesions that distort the DNA double helix (such as UV-induced thymine dimers or benzo[a]pyrene-guanine adducts); defects cause xeroderma pigmentosum.

Homologous Recombination (HR)

A precise double-strand break repair mechanism active mostly during the S phase of the cell cycle that uses sequence information from the sister chromatid as a template.

Non-Homologous End Joining (NHEJ)

The primary and fastest double-strand break repair mechanism in mammalian cells that directly joins strand breaks without sequence homology, operating mostly in G1 and causing small insertions or deletions.