BioSc1940 Molecular Biology — Exam 1 Vocabulary Flashcards

Vocabulary practice flashcards covering all major terms, molecular biology techniques, histone modifications, cell cycle regulators, replication factors, and repair pathways from BioSc1940 Exam 1.

Gel electrophoresis

A technique used to separate DNA or RNA fragments by size, taking advantage of the negative charge of nucleic acids to drive migration toward a positive electrode.

SDS-PAGE

A technique used to separate proteins by size, where sodium dodecyl sulfate (SDS) denatures proteins and coats them with a uniform negative charge.

Western blot

A technique to detect a specific protein in a sample by transferring gel-separated proteins onto a membrane and probing them with a specific antibody.

Immunoprecipitation (IP)

A method that uses a specific antibody to isolate and pull down a target protein along with its associated binding partners from a cell lysate.

ChIP (Chromatin Immunoprecipitation)

A technique used to map where a specific protein (such as a modified histone or transcription factor) binds to DNA genome-wide by immunoprecipitating protein–DNA complexes.

Immunofluorescence

A technique that uses fluorescently labeled antibodies to visualize the subcellular localization of proteins within cells or on chromosomes.

PCR

An in vitro enzymatic reaction that exponentially amplifies a specific DNA sequence using primers, a DNA polymerase, dNTPs, and thermocycling.

qPCR

A specialized PCR technique used to quantify the starting amount of DNA or cDNA in real time during amplification.

Site-directed mutagenesis

A PCR-based technique used to introduce specific, targeted nucleotide sequence changes or mutations into a DNA molecule.

Gibson assembly

An isothermal, single-tube cloning method that joins multiple overlapping DNA fragments without requiring traditional restriction endonuclease digestion and ligation.

MNase-seq

A technique that maps nucleosome positions by using micrococcal nuclease (MNase) to digest un-protected linker DNA between nucleosomes.

5′-RACE

A technique used to determine the exact $5'$ end of an RNA transcript, beginning with reverse transcriptase synthesizing cDNA from the RNA template.

Topoisomerase I

An enzyme that breaks one strand of DNA to relieve supercoiling without requiring ATP hydrolysis.

Topoisomerase II

An enzyme that induces double-strand DNA breaks to relieve supercoiling or disentangle DNA molecules in an ATP-dependent manner.

Bacterial gyrase

A bacterial Type II topoisomerase that uses ATP to actively introduce negative supercoils into DNA.

Nucleosome

The basic repeating unit of chromatin, consisting of $\sim 146\,\text{bp}$ of DNA wrapped in a left-handed superhelix around a histone octamer.

Histone octamer

The protein core of a nucleosome comprising two copies each of core histones H2A, H2B, H3, and H4.

Histone H1

The linker histone that binds linker DNA outside the nucleosome core particle to form a chromatosome and promote higher-order chromatin compaction.

H3K4me3

A histone modification mark (trimethylation of lysine 4 on histone H3) that is characteristically associated with transcriptionally active promoters.

H3K27ac

A histone modification mark (acetylation of lysine 27 on histone H3) associated with active promoters and enhancers.

H3K27me3

A repressive histone modification mark (trimethylation of lysine 27 on histone H3) linked to Polycomb-mediated developmental gene silencing.

H3K9me3

A repressive histone modification mark (trimethylation of lysine 9 on histone H3) characteristic of constitutive heterochromatin.

Histone code hypothesis

The concept that specific combinations of post-translational histone modifications dictate unique chromatin structure states and are recognized by specific reader proteins.

H3K36M

An oncogenic histone mutation (lysine to methionine at position 36) that acts in a dominant-negative manner to poison and inhibit histone methyltransferases globally.

CENP-A

A specialized histone H3 variant that selectively replaces canonical H3 at centromeric nucleosomes to specify centromere identity.

LacO/LacI system

A bacterial operon system adapted as a synthetic molecular tool to tether proteins or isolate specific genomic regions tagged with LacO operator repeats.

Restriction point ("Start")

The key commitment point in late G1 phase of the eukaryotic cell cycle, after which a cell is committed to undergoing DNA replication and division.

Cyclins

Regulatory proteins whose concentration levels oscillate across the cell cycle to bind and activate Cyclin-dependent kinases (Cdks) and dictate substrate specificity.

Cyclin-dependent kinases (Cdks)

Serine/threonine protein kinases present at constant levels that require binding to a regulatory cyclin protein for activation and cell-cycle progression.

Rb (Retinoblastoma protein)

A tumor suppressor protein that binds and inhibits the transcription factor E2F until it is phosphorylated by G1 Cyclin-Cdk complexes.

SCF complex

An E3 ubiquitin ligase that drives the G1 to S phase transition by targeting phosphorylated substrates (such as Cdk inhibitors) for degradation.

APC (Anaphase-Promoting Complex)

An E3 ubiquitin ligase activated during mitosis that targets cohesin-inhibiting proteins and cyclins for proteasomal degradation to promote anaphase and mitotic exit.

DNA Primase (DnaG)

A specialized RNA polymerase that synthesizes short RNA primers required for DNA polymerases to initiate synthesis.

β-sliding clamp

A ring-shaped homodimeric protein in E. coli that encircles DNA and docks DNA polymerase III to promote high processivity.

Clamp loader (γ-complex)

A multi-subunit AAA+ ATPase complex that utilizes ATP to assemble and disassemble sliding clamps onto DNA at primer-template junctions.

Tus protein

A bacterial termination protein that binds ter sites in an orientation-specific manner to block replication fork movement.

SeqA

An E. coli protein that specifically binds hemimethylated GATC sequences at oriC to temporarily block DnaA binding and delay re-initiation.

ORC (Origin Recognition Complex)

A multi-subunit initiator complex in eukaryotes that binds replication origins throughout the cell cycle and recruits helicase loaders in G1.

Mcm2-7

A eukaryotic heterohexameric helicase consisting of six distinct subunits that unwinds DNA at the replication fork.

Fen1 (Flap endonuclease 1)

A eukaryotic structure-specific endonuclease responsible for removing displaced 5′ RNA flaps during Okazaki fragment maturation.

Shelterin

A six-protein complex that binds eukaryotic telomeric repeats to protect chromosome ends from being recognized as double-strand DNA breaks.

Telomerase

A ribonucleoprotein reverse transcriptase carrying its own intrinsic RNA template to extend the $3'$ single-stranded overhangs of linear telomeres.

Condensin

An SMC-family protein complex that utilizes ATP hydrolysis to extrude DNA loops and drive mitotic chromosome condensation.

Cohesin

An SMC-family protein complex loaded in G1 phase that physically holds sister chromatids together from S phase until anaphase cleavage.

Separase

A cysteine protease that cleaves the kleisin subunit of centromeric cohesin at the metaphase-to-anaphase transition, triggering sister chromatid separation.

Spindle assembly checkpoint (SAC)

A mitotic surveillance mechanism that sequesters Cdc20 via Mad2 at unattached kinetochores to prevent premature APC activation.

Base Excision Repair (BER)

A repair pathway initiated by DNA glycosylases that excise single damaged bases to generate an AP site for subsequent cleavage and replacement.

Nucleotide Excision Repair (NER)

A repair pathway (mediated by UvrA, UvrB, UvrC, and UvrD in E. coli) that recognizes and removes bulky, helix-distorting DNA lesions as single-stranded oligonucleotides.

Translesion synthesis (TLS)

A DNA damage tolerance pathway utilizing specialized, low-fidelity polymerases (e.g., Pol IV/V) to bypass lesions that stall high-fidelity replicative polymerases.

Mismatch repair (MMR)

A post-replication repair mechanism that recognizes mismatched base pairs and preferentially repairs the unmethylated or newly synthesized daughter strand.

Transposon

A mobile genetic element encoding a transposase flanked by inverted repeats that can excise or copy itself and insert into target DNA sites.