Cellular Processes: The Nucleus & DNA Replication

Comprehensive vocabulary flashcards covering nuclear structure, chromatin organization, historical discoveries of genetic material, DNA chemistry, and the enzymology and mechanics of DNA replication.

Nucleus

The most conspicuous eukaryotic organelle; stores most cellular genes and coordinates DNA replication and transcription.

Nuclear Envelope

Double phospholipid-bilayer membrane surrounding the nucleus; continuous with the endoplasmic reticulum and pierced by nuclear pores.

Nuclear Pore Complex

Large protein channel (≈100 proteins) that regulates material exchange (e.g., mRNA, ribosomal subunits) between nucleus and cytoplasm.

Nucleoplasm

Specialized fluid matrix inside the nucleus that suspends chromatin and contains the nuclear lamina and matrix.

Nuclear Lamina

Filamentous protein mesh lining the inner nuclear membrane; maintains nuclear shape and organizes chromatin.

Nuclear Matrix

Intranuclear filament network extending throughout nucleoplasm; helps arrange chromatin and supports replication/transcription.

Nucleolus

Dense, membrane-less nuclear body where rRNA is transcribed and ribosomal subunits are assembled.

Chromatin

Eukaryotic DNA complexed with histone proteins; packages genetic material, protects DNA, and regulates expression.

Histone

Positively charged basic protein; DNA wraps around core histone octamers to form nucleosomes.

Core Histones

Eight-protein octamer (two each of H2A, H2B, H3, H4) that forms the nucleosome core particle.

Linker Histone (H1/H5)

Histone that binds linker DNA between nucleosomes and promotes 30-nm fiber compaction.

Nucleosome

“Bead” of ~146 bp DNA wrapped 1.65 turns around a histone octamer; fundamental chromatin unit.

Linker DNA

~50 bp stretch of DNA connecting adjacent nucleosomes in the “beads-on-a-string” fiber.

Euchromatin (10-nm fiber)

Less condensed chromatin form; transcriptionally active and accessible to regulatory proteins.

Heterochromatin (30-nm fiber)

More condensed chromatin form; transcriptionally silent and further compactable into chromosomes.

Condensin

Protein complex that drives further chromatin condensation into mitotic chromosomes.

Transformation (Griffith)

Heritable change in genotype/phenotype caused by uptake of external DNA by a cell.

Avery–MacLeod–McCarty Experiment

1944 study proving DNA—not protein or RNA—is the transforming principle in bacteria.

Bacteriophage (Phage)

Virus that infects bacteria; used by Hershey & Chase to show DNA is genetic material.

Hershey–Chase Experiment

1952 phage study using 32P-DNA and 35S-protein labels to confirm DNA enters host cells.

Chargaff’s Rules

(1) DNA base composition varies among species; (2) A = T and G = C within a species.

Purine

Two-ring nitrogenous base family: adenine (A) and guanine (G).

Pyrimidine

Single six-membered ring bases: cytosine (C), thymine (T), and uracil (U).

Nucleotide

DNA/RNA monomer: nitrogenous base + five-carbon sugar + one or more phosphate groups.

Nucleoside

Nitrogenous base attached to a five-carbon sugar, lacking phosphate.

Phosphodiester Bond

Covalent linkage between 3’-OH and 5’-phosphate of adjacent nucleotides in nucleic acids.

Antiparallel

Orientation of DNA strands running in opposite 5’→3’ directions within the double helix.

5’→3’ Directionality

Only direction in which DNA polymerases synthesize new DNA due to phosphodiester chemistry.

Sense Strand

DNA strand whose sequence matches the resulting mRNA (except T→U); non-template strand.

Antisense Strand

DNA template strand used by RNA polymerase to synthesize complementary mRNA.

Origin of Replication (oriC)

Specific A/T-rich DNA sequence where replication machinery assembles and begins copying.

Replication Fork

Y-shaped region where parental DNA is unwound and new strands are synthesized.

Replication Bubble

Region of duplex separation containing two replication forks expanding in both directions.

Helicase (DnaB)

Enzyme that unwinds parental DNA ahead of the replication fork using ATP.

Single-Stranded Binding Proteins (SSBs)

Proteins that stabilize unwound DNA strands and prevent re-annealing.

Primase (DnaG)

RNA polymerase that synthesizes short RNA primers needed for DNA polymerase initiation.

DNA Polymerase III

Primary bacterial replicative enzyme; adds nucleotides to growing DNA strand and proofreads.

DNA Polymerase I

Bacterial enzyme that removes RNA primers (5’→3’ exonuclease) and fills gaps with DNA.

DNA Polymerase II

Bacterial polymerase mainly involved in DNA repair and additional proofreading.

Beta Clamp

Ring-shaped subunit of Pol III that encircles DNA and confers high processivity.

Gamma Complex (Clamp Loader)

Protein assembly that opens and loads the beta clamp onto primed DNA.

Topoisomerase

Enzyme that relieves supercoiling by cutting, swiveling, and rejoining DNA strands.

Okazaki Fragment

Short DNA segment (1000-2000 bp in bacteria) synthesized discontinuously on lagging strand.

Leading Strand

New DNA strand synthesized continuously in the same direction as fork movement.

Lagging Strand

Strand synthesized discontinuously opposite fork movement via Okazaki fragments.

DNA Ligase

Enzyme that forms the final phosphodiester bond to seal nicks between DNA fragments.

Semi-Conservative Replication

DNA replication model where each daughter helix contains one parental and one new strand.

Conservative Replication

Hypothetical model where parental strands stay together and daughter strands form a new helix.

Dispersive Replication

Hypothetical model with interspersed parental and daughter DNA within each strand.

Meselson–Stahl Experiment

15N/14N density-labeling study that confirmed semi-conservative replication in bacteria.

Supercoiling

Over- or under-winding of DNA ahead of the replication fork; relieved by topoisomerases.

DNA Double Helix

Right-handed, antiparallel, uniform-diameter structure with complementary base pairing.

Base Pairing Rules

A pairs with T via two H bonds; G pairs with C via three H bonds.

GC-Rich Region

DNA segment with high G-C content; exhibits stronger H-bonding and higher melting temperature.

Mg²⁺ in DNA Synthesis

Cofactor that stabilizes nucleotide triphosphate and aids nucleophilic attack during polymerization.

Deoxyribose

Five-carbon sugar lacking a 2’-OH; found in DNA nucleotides.

Ribose

Five-carbon sugar with a 2’-OH; found in RNA nucleotides.

30-nm Fiber

Higher-order chromatin structure formed by H1-mediated nucleosome packing.

Chromosome

Highly condensed DNA-protein structure formed during cell division, derived from chromatin looping.

DNA Polymerase Holoenzyme

Multiprotein Pol III complex containing core enzymes, beta clamp, gamma loader, and associated factors.

RNA Primer

Short RNA segment synthesized by primase to provide a 3’-OH for DNA polymerase.