Molecular Biology Fundamentals, DNA Manipulation, and Laboratory Analysis

Vocabulary practice cards covering DNA/RNA structure, chromosome organization, bacterial growth and transformation, DNA repair mechanisms, molecular cloning, gene regulation, and DNA extraction/analytics protocols.

Purines

Double-ring nitrogenous bases found in nucleic acids, specifically Adenine (A) and Guanine (G).

Pyrimidines

Single-ring nitrogenous bases found in DNA, specifically Thymine (T) and Cytosine (C).

Phosphodiester Bond

The chemical linkage connecting the 5' phosphate group of one nucleotide to the 3' hydroxyl ($-\text{OH}$) group of an adjacent nucleotide to form the sugar-phosphate backbone.

G-C Base Pair Stability

A base pair held together by 3 hydrogen bonds (compared to 2 hydrogen bonds in an A-T pair), making G-C rich regions more thermally stable and harder to denature.

3' Carbon

The carbon on the deoxyribose/ribose ring that bears a free hydroxyl group ($-\text{OH}$), serving as the mandatory attachment site for the incoming nucleotide during nucleic acid synthesis.

5' Carbon

The carbon located outside the main deoxyribose/ribose ring structure attached directly to the phosphate group.

Deoxyribose vs. Ribose

Ribose possesses a hydroxyl group ($-\text{OH}$) at the 2' position, whereas deoxyribose possesses a hydrogen atom ($-\text{H}$) at the 2' position.

Telomere

Repetitive DNA sequence caps (TTAGGG in humans) located at the ends of linear chromosomes that prevent degradation and end-to-end fusion.

Centromere

The constricted chromosomal region where sister chromatids attach and the kinetochore complex binds to spindle fibers during mitosis and meiosis.

Origin of Replication (Ori)

A specific DNA sequence where the cellular replication machinery binds and DNA synthesis initiates.

Histone Octamer

A protein core consisting of two copies each of four distinct core histones: H2A, H2B, H3, and H4, around which DNA wraps to form a nucleosome.

Heterochromatin

Tightly packed, transcriptionally inactive and repressed DNA, typically anchored at the nuclear periphery against the nuclear lamina.

Euchromatin

Loosely packed, transcriptionally open and accessible DNA spread throughout the nucleoplasm.

Nucleolus

The dense sub-nuclear site of ribosome biogenesis where genes encoding ribosomal RNA (rRNA) are localized.

Plasmid

A small, extrachromosomal, circular double-stranded DNA molecule that replicates independently of host genomic DNA in bacteria.

TE Buffer

A protective storage solution containing Tris (which buffers pH to ~8.0) and EDTA (which chelates divalent cations like $\text{Mg}^{2+}$ and $\text{Ca}^{2+}$ to disable nucleases).

Bacterial Transformation

The process by which a bacterial cell uptakes foreign, naked DNA from its surrounding environment and integrates or expresses it.

Transformation Efficiency

A quantitative measure of transformation defined as the number of colony-forming units (CFUs) generated per microgram ($\mu\text{g}$) of plasmid DNA used: $\frac{\text{Number of Colonies (CFU)}}{\text{Amount of DNA plated (}\mu\text{g)}}$.

Heat-Shock Transformation

A procedure utilizing ice-cold $\text{CaCl}_2$ to neutralize charge repulsion, a brief $42^{\circ}\text{C}$ pulse to create transient thermal pores for DNA entry, ice recovery, and outgrowth at $37^{\circ}\text{C}$ without antibiotics.

Lysogeny Broth (LB) Media

A nutrient-rich complex growth medium containing tryptone (peptides), yeast extract (vitamins and trace factors), and $\text{NaCl}$ (osmolarity) used for culturing E. coli.

Thymine Dimers

Covalent crosslinks formed between adjacent pyrimidine bases induced by UV radiation damage.

Mismatch Repair (MMR)

A DNA repair pathway that fixes mispaired bases that escaped proofreading by recognizing the unmethylated nascent strand, degrading it, and resynthesizing it.

Base Excision Repair (BER)

A pathway in which DNA glycosylases recognize and cleave damaged individual bases, creating an AP site that is subsequently repaired by AP endonuclease, DNA polymerase, and DNA ligase.

Non-Homologous End Joining (NHEJ)

An error-prone double-strand break repair pathway where Ku proteins bind broken ends and nucleases trim bases before ligation, frequently introducing insertions or deletions (indels).

Homologous Recombination (HR)

An error-free double-strand break repair pathway that utilizes an undamaged homologous chromosome or sister chromatid as a sequence template.

Restriction Enzyme

An endonuclease that recognizes and cuts specific, short, palindromic double-stranded DNA sequences (typically 4–8 base pairs long).

Directional Cloning

A cloning strategy where vector and insert DNA are digested with two different restriction enzymes, enforcing specific insert orientation and preventing vector self-ligation.

Semiconservative Replication

The mode of DNA replication where each daughter double helix retains one intact parental template strand and one newly synthesized strand.

DNA Ligase

An enzyme that seals single-strand nicks in double-stranded DNA by catalyzing a phosphodiester bond between a 3'-OH and an adjacent 5'-phosphate group.

RNA Polymerase II CTD Phosphorylation

Phosphorylation of the C-terminal domain tail of eukaryotic RNA Polymerase II that acts as a switch to drive transcription elongation and recruit 5' capping, splicing, and polyadenylation machineries.

TATA Box

A conserved, A-T rich consensus sequence located in eukaryotic gene promoters that assists in positioning RNA Polymerase II at the transcription start site.

Sigma ($\sigma$) Factor

A bacterial protein that binds the core RNA polymerase enzyme and directs it to specific promoter sequences to initiate transcription.

Operon

A functioning genetic unit found in bacteria consisting of a cluster of genes under the control of a single promoter, operator, and transcribed into a single polycistronic mRNA.

Buffer ATL

A pre-lysis buffer containing Proteinase K used in genomic DNA isolation to break down tough tissues and digest cellular proteins.

Buffer AL

A cell lysis buffer containing Guanidine HCl (chaotropic salt) that lyses cellular membranes and denatures proteins during genomic DNA isolation.

Buffer P1

A resuspension buffer containing RNase A used in alkaline lysis plasmid minipreps to resuspend bacterial pellets and degrade host RNA.

Buffer P2

An alkaline lysis buffer containing SDS (which lyses cell membranes) and NaOH (which denatures both chromosomal and plasmid DNA).

Buffer P3

A neutralization buffer containing Potassium Acetate that restores neutral pH, allowing small plasmids to renature while large genomic DNA precipitates into an insoluble clot.

260/280 Ratio

A spectrophotometric ratio assessing protein contamination; pure double-stranded DNA displays an $A_{260}/A_{280}$ ratio of ~1.8.

260/230 Ratio

A spectrophotometric ratio assessing contamination from organic compounds and chaotropic salts; pure double-stranded DNA typically yields a value between 2.0 and 2.2.

TAE Electrophoresis Buffer

An electrophoresis buffer consisting of Tris (pH buffer), Acetic acid (provides ions for electrical conductance), and EDTA (chelates divalent cations to inhibit nucleases).

Supercoiled Plasmid DNA

The intact, tightly wound topological form of a plasmid that migrates the fastest through an agarose gel matrix.