DNA Replication, Repair, and Gene Expression

A complete set of vocabulary flashcards covering DNA replication, repair mechanisms, transcription, translation, and the RNA world hypothesis.

Meselen-Stahl Experiment

The experiment that determined DNA replication is semi-conservative, using heavy radioactive nitrogen ($16N$) and light radioactive nitrogen ($16N$).

Semi-conservative replication

A mode of DNA replication where each daughter DNA molecule contains one parental DNA strand and one newly synthesized DNA strand.

Replication origin

The specific site where DNA replication begins; bacteria have one, while eukaryotes have numerous origins.

Replication fork

A Y-shaped junction where double-stranded DNA ($dsDNA$) is unwound and DNA replication begins.

5' → 3' direction

The constant direction in which DNA synthesis always occurs.

Leading strand

The DNA strand that is synthesized continuously as the double-stranded DNA ($dsDNA$) is unwound.

Lagging strand

The DNA strand synthesized discontinuously in the direction opposite to the movement of the replication fork.

Okazaki fragments

Short segments of DNA produced during the discontinuous synthesis of the lagging strand.

Helicase

An enzyme that unwinds double-stranded DNA ($dsDNA$) at the replication origin.

SSB proteins

Proteins that bind to single-stranded DNA ($ssDNA$) to prevent it from bonding back together.

Primase

An enzyme that creates a short RNA primer that DNA polymerase can extend.

DNA polymerase

An enzyme that catalyzes the formation of phosphodiester bonds to synthesize DNA and possesses editing (proofreading) ability.

Sliding clamp

A protein that keeps DNA polymerase attached to the DNA template strand.

Clamp loader

A protein complex that locks the sliding clamp onto the DNA; it is needed once on the leading strand and multiple times on the lagging strand.

Nucleases

Enzymes that remove RNA primers so they can be replaced with DNA nucleotides by DNA polymerase.

DNA ligase

An enzyme that creates phosphodiester bonds between Okazaki fragments or repaired DNA segments.

Topoisomerase

An enzyme that creates a single-stranded break to relieve torsional stress caused by the unwinding of DNA by helicase.

Telomerase

An enzyme that replicates the ends of linear chromosomes by extending the template strand using repetitive DNA sequences.

Telomere

Repetitive DNA sequences located at the ends of chromosomes.

Depurination

A type of DNA damage involving the loss of a purine (guanine or adenine), which can cause a single nucleotide deletion if unrepaired.

Deamination

The loss of an amino group that converts cytosine to uracil, potentially leading to a $G \rightarrow A$ mutation.

Thymine dimers

The formation of covalent bonds between two adjacent Thymines caused by UV radiation, creating a kink in the DNA.

Mismatch

A mispaired nucleotide resulting from a mistake by DNA polymerase that was not corrected by proofreading.

Nonhomologous end joining (NHEJ)

A "quick and dirty" repair mechanism for double-stranded breaks that is prone to nucleotide deletions.

Homologous recombination

An accurate repair mechanism for double-stranded breaks that uses an undamaged homologue as a template.

Germ-line cells

Cells that divide via meiosis to produce gametes; mutations in these cells are passed on to all cells in the offspring.

Somatic cells

Non-sex cells where an accumulation of mutations can lead to cancer.

Tumor suppressor genes

Genes involved in the regulation of cell division and apoptosis (cell death).

Gene expression

The process by which a gene is used to make a product, such as a protein or an RNA molecule.

Promoter

A DNA sequence recognized by RNA polymerase and accessory proteins to initiate transcription.

Sigma factor

A protein in bacteria that binds to RNA polymerase to recognize the promoter region.

Transcription factors

Proteins in eukaryotic cells that bind to the promoter region and recruit RNA polymerase.

TATA box

A specific DNA sequence of T and A that makes it easier to unwind double-stranded DNA ($dsDNA$) during transcription initiation.

Template strand

The strand of DNA that runs from $3' \rightarrow 5'$ and is used to produce a complementary RNA transcript.

Coding strand

The DNA strand that runs from $5' \rightarrow 3'$ and has an identical sequence to the RNA transcript, except it contains T instead of U.

5' cap

An atypical nucleotide and a phosphate bridge added to the $5'$ end of eukaryotic mRNA during transcription.

3' poly-A tail

The addition of hundreds of Adenines to the $3'$ end of an mRNA transcript to stabilize it.

Splicing

The process of removing introns from a pre-mRNA transcript.

Introns

Non-coding sequences removed from mRNA prior to translation.

Exons

Regions of mRNA that code for amino acid sequences.

Spliceosome

An assembly of protein and RNA molecules that removes introns from pre-mRNA.

Terminator

A DNA sequence that causes RNA polymerase to halt and dissociate from the DNA template.

Codon

A group of three nucleotides that encodes for a particular amino acid.

Reading frame

The way a genetic code is read based on the starting nucleotide; there are three possible frames for any sequence.

Ribosomes

Complexes of protein and ribosomal RNA ($rRNA$) that synthesize proteins in the cytoplasm or on the rough ER.

Ribozymes

RNA molecules that possess catalytic activity, such as the $rRNA$ forming the catalytic site for peptide bond formation.

A-tRNA-S

Enzymes that perform "charging" reactions to attach the correct amino acid to a tRNA molecule.

Polycistronic

A characteristic of prokaryotic mRNA where one mRNA transcript encodes for multiple different proteins.

Start codon

The sequence (AUG) that codes for methionine ($M$) and signals the beginning of translation.

Stop codon

Sequences (UAA, UAG, or UGA) that signal the ribosome to dissociate without coding for an amino acid.

Polyribosomes

Large cytosolic assemblies where many ribosomes are simultaneously attached to a single mRNA transcript.

Post-translational modifications

Covalent attachments, such as methylation or phosphorylation, that occur after a protein is translated.

Ubiquitination

The covalent attachment of a ubiquitin protein that tags a protein for rapid degradation.

RNA world hypothesis

The theory that in primitive cells, RNA both stored genetic information and catalyzed chemical reactions.

Autocatalysis

The ability to catalyze reactions that lead to the production of more molecules like themselves.