Cell Biology Exam 2 Study Guide

Comprehensive vocabulary flashcards covering DNA structure, replication, repair, eukaryotic chromosome architecture, transcription, RNA processing, gene regulation, translation, and protein trafficking from the Cell Biology Exam 2 Study Guide.

Deoxyribonucleic Acid (DNA)

A double-stranded nucleic acid macromolecule that stores hereditary genetic information, structured as a right-handed double helix with two antiparallel polynucleotide strands wrapped around a central axis.

DNA Backbone

The structural outer framework of DNA composed of alternating sugar (deoxyribose) and phosphate groups joined covalently by phosphodiester bonds.

DNA Polarity

The distinct chemical orientation of a polynucleotide strand defined by a $5'$ end with a free $5'$-phosphate group and a $3'$ end with a free $3'$-hydroxyl group.

Antiparallel Strands

The arrangement of two paired DNA strands running in opposite chemical directions ($5'\rightarrow 3'$ paired with $3'\rightarrow 5'$), which enables complementary bases to form stable hydrogen bonds in a uniform double helix.

Deoxyribonucleotides

The monomer building blocks of DNA, each composed of a nitrogenous base, a 5-carbon deoxyribose sugar, and a phosphate group linked to the $5'$ carbon of deoxyribose.

Purines

Two-ring nitrogenous base structures found in nucleic acids, consisting of Adenine (A) and Guanine (G).

Pyrimidines

Single-ring nitrogenous base structures, consisting of Cytosine (C) and Thymine (T) in DNA, and Uracil (U) in RNA.

Complementary Base Pairing

The specific pairing rule where Adenine pairs with Thymine via 2 hydrogen bonds and Guanine pairs with Cytosine via 3 hydrogen bonds, maintaining a uniform double helix width of $2\,\text{nm}$.

DNA Thermal Stability

The physical resistance of DNA to thermal denaturation; DNA higher in G-C content is more stable than A-T rich DNA due to having 3 hydrogen bonds per pair and more favorable base-stacking thermodynamic interactions.

Genes

Specific segments of DNA containing nucleotide sequences that provide instructions for functional RNAs or proteins.

Mutations

Permanent alterations in DNA nucleotide sequences that may result in neutral, beneficial, or harmful consequences.

Bacterial Transformation (Griffith, 1928)

The experimental discovery that hereditary genetic information could be transferred from heat-killed pathogenic bacteria to living non-pathogenic bacteria.

Avery-MacLeod-McCarty Experiment (1944)

The experiment demonstrating that DNase, but not other degrading enzymes, destroys the transforming principle, proving DNA is the hereditary genetic material.

Hershey-Chase Experiment (1952)

The experiment that used $^{32}\text{P}$-labeled DNA and $^{35}\text{S}$-labeled protein coats in bacteriophages to confirm that only viral DNA enters bacterial host cells.

Nucleosomes

Repeating structural units of eukaryotic chromatin formed by DNA wrapping around an octamer of histone proteins.

Chromatin

The functional nuclear complex composed of eukaryotic DNA associated with structural proteins, primarily histones.

Interphase Chromosomes

Extended, decondensed, flexible chromosome threads dispersed throughout the nucleus that permit access for transcription and replication machinery.

Mitotic Chromosomes

Fully condensed, compact, rod-like chromosomal structures (46 in human karyotypes) designed to prevent tangling or breakage during spindle-mediated segregation.

Sister Chromatids

Two identical copies of a duplicated chromosome held together by cohesin protein complexes.

Centromere

A constricted DNA locus that physically tethers sister chromatids together and serves as the assembly site for the kinetochore.

Kinetochore

A multiprotein complex assembled at the centromeric DNA of each chromosome that captures and binds spindle microtubules during mitosis.

Telomeres

Repetitive, non-coding DNA caps located at the terminal ends of linear eukaryotic chromosomes that protect them from degradation and end-joining.

Heterochromatin

Highly condensed, transcriptionally inactive interphase DNA regions situated mainly along the nuclear periphery.

Euchromatin

Decondensed, open interphase DNA accessible to transcription factors and actively engaged in RNA transcription.

Nucleolus

A prominent, dark nuclear subcompartment where ribosomal RNA (rRNA) is transcribed by RNA Polymerase I and assembled with proteins into small and large ribosomal subunits at Nucleolar Organizer Regions (NORs).

DNA Replication

The semi-conservative, bidirectional duplication of the genome during S phase where nucleotides are added to the $3'\text{-OH}$ group ($5'\rightarrow 3'$ synthesis), powered by the hydrolysis of pyrophosphate cleaved from incoming dNTPs.

DNA Helicase

An enzyme that unwinds and unzips the parental double-stranded DNA helix ahead of the replication machinery.

Single-Strand DNA-Binding (SSB) Proteins

Proteins that coat transiently exposed single-stranded DNA templates to prevent them from re-annealing or forming secondary hairpins.

Topoisomerase

An enzyme that relieves torsional overwinding and structural supercoiling strain generated ahead of advancing replication forks.

Primase

An RNA polymerase that synthesizes short RNA primers required to provide free $3'\text{-OH}$ groups for DNA polymerases to initiate synthesis.

DNA Polymerase

The primary enzyme responsible for catalyzing the synthesis of new complementary DNA strands strictly in the $5'\rightarrow 3'$ direction.

DNA Ligase

An enzyme that covalently catalyzes the formation of phosphodiester bonds to seal single-strand nicks in the sugar-phosphate backbone.

Leading Strand

The daughter DNA strand synthesized continuously in the $5'\rightarrow 3'$ direction toward the opening replication fork.

Lagging Strand

The daughter DNA strand synthesized discontinuously in the $5'\rightarrow 3'$ direction away from the replication fork as a series of short Okazaki fragments.

Okazaki Fragments

Short stretches of newly synthesized DNA generated discontinuously on the lagging template strand that are subsequently ligated together.

Mismatch Repair

A post-replication surveillance system that selectively identifies and repairs replication errors on the newly synthesized daughter strand (identified by nicks or unmethylated markers) without altering the parental template.

Excision Repair (Damage Repair)

A repair pathway that directly recognizes and cuts out chemically altered or abnormal bases on whichever DNA strand has sustained structural damage.

Non-Homologous End Joining (NHEJ)

An error-prone double-strand break repair pathway active across all cell cycle phases ($\text{G}_1$, S, $\text{G}_2$) that directly ligates broken DNA termini together, frequently generating insertions or deletions (indels).

Homologous Recombination (HR)

A high-fidelity, error-free double-strand break repair pathway restricted to late S and $\text{G}_2$ phases that uses an undamaged sister chromatid as a homologous template.

Transcription

The synthesis of a complementary single-stranded RNA ($5'\rightarrow 3'$) using a DNA template strand ($3'\rightarrow 5'$), catalyzed by RNA Polymerase beginning at a gene's promoter (+1 site).

Ribozymes

Catalytically active RNA molecules capable of folding into specific tertiary 3D conformations to catalyze biochemical reactions.

Messenger RNA (mRNA)

Single-stranded RNA transcripts that carry genetic coding sequences from nuclear DNA to the ribosome to direct protein translation.

Ribosomal RNA (rRNA)

Structural and catalytic RNA molecules that constitute the functional core of the ribosomal subunits.

Transfer RNA (tRNA)

Small adapter RNA molecules that carry specific amino acids and match their anticodon loops to complementary mRNA codons during protein synthesis.

Small Nuclear RNA (snRNA)

Non-coding RNA molecules that associate with proteins to form snRNPs within the spliceosome to catalyze pre-mRNA splicing.

5' Capping

The covalent addition of a 7-methylguanosine residue to the $5'$ end of eukaryotic pre-mRNA to enhance transcript stability and facilitate ribosomal binding.

3' Polyadenylation

The enzymatic post-transcriptional addition of a continuous stretch of adenine residues (poly-A tail) to the $3'$ end of eukaryotic pre-mRNA to protect it from rapid exonucleolytic degradation.

RNA Splicing

The enzymatic removal of non-coding intervening sequences (introns) and the precise ligation of protein-coding segments (exons) performed by spliceosomes.

Coupled Transcription-Translation

The simultaneous occurrence of mRNA transcription and polypeptide translation within the cytoplasm, characteristic of prokaryotic organisms lacking a nuclear envelope.

Cell Differentiation

The developmental specialization process whereby uncommitted cells express defined subsets of their genes to adopt cell-specific structures and functions.

Genomic Equivalence

The concept establishing that almost all somatic differentiated cells retain the complete set of genetic instructions present in the fertilized egg, as demonstrated by somatic nuclear transfer experiments.

Operon

A functional bacterial genetic unit containing a cluster of polycistronic genes transcribed under the control of a single promoter and regulatory operator.

Tryptophan (Trp) Operon

A repressible bacterial operon that turns off when abundant tryptophan binds and activates a repressor protein to block RNA polymerase, and turns on when low tryptophan leaves the repressor inactive.

RNA Polymerase I

The specialized eukaryotic RNA polymerase that transcribes major ribosomal RNA (rRNA) precursors in the nucleolus.

RNA Polymerase II

The eukaryotic enzyme responsible for transcribing all messenger RNAs (mRNAs) as well as various regulatory snRNAs and miRNAs.

RNA Polymerase III

The eukaryotic enzyme that transcribes transfer RNAs (tRNAs), $5\text{S}\text{ rRNA}$, and small structural RNAs.

Enhancers

Distant non-coding cis-regulatory DNA sequences that bind activator transcription factors and loop chromosomal DNA to stimulate transcription initiation at promoters.

Combinatorial Control

The regulatory strategy where combinations of multiple distinct transcription factors interact collectively to establish precise levels and spatial patterns of gene expression.

Translation

The ribosome-mediated decoding of nucleotide sequences on an mRNA molecule into a specific sequence of amino acids to generate a polypeptide chain.

Codon

A specific sequence of three consecutive nucleotides oriented in the $5'\rightarrow 3'$ direction on mRNA that specifies a single amino acid or a translational stop signal.

Reading Frame

One of three potential ways to parse an unbroken sequence of nucleotide triplets in single-stranded mRNA, determined specifically by the placement of the AUG start codon.

Aminoacyl-tRNA

An activated tRNA molecule covalently coupled to its cognate amino acid at its $3'$ terminus by aminoacyl-tRNA synthetase via an ATP-dependent reaction.

Wobble Hypothesis

The principle describing non-standard, flexible base-pairing at the third ($3'$) position of an mRNA codon, enabling a single tRNA species to recognize multiple synonymous codons.

Genetic Code Redundancy

The structural degeneracy of the genetic code wherein 61 sense codons specify only 20 standard amino acids, allowing several codons to code for the same amino acid.

Ribosomal A Site (Aminoacyl Site)

The binding site in the ribosome that accommodates an incoming charged aminoacyl-tRNA whose anticodon matches the exposed mRNA codon.

Ribosomal P Site (Peptidyl Site)

The ribosomal pocket that holds the tRNA carrying the nascent, growing polypeptide chain (initially occupied by initiator formylmethionine/methionine tRNA).

Ribosomal E Site (Exit Site)

The transient staging site within the ribosome that retains the deacylated (uncharged) tRNA prior to its dissociation.

Peptidyl Transferase

The catalytic RNA ribozyme embedded within the large ribosomal subunit that catalyzes peptide bond formation using GTP hydrolysis energy.

Polysomes (Polyribosomes)

Functional complexes formed when multiple individual ribosomes bind and simultaneously translate a single messenger RNA strand in the cytoplasm or on the rough ER.

Signal Sequences

Short amino-terminal or carboxy-terminal amino acid peptide motifs that direct proteins to their intended subcellular organelle or secretory target.

Nuclear Import

The transport mechanism where fully folded proteins bearing nuclear localization signals pass post-translationally through open nuclear pore complexes assisted by importins.

Co-Translational Translocation

The coordinated import pathway where a nascent polypeptide displaying an N-terminal signal sequence is recognized by SRP and threaded directly into the ER lumen while being translated.

Signal Recognition Particle (SRP)

A cytosolic ribonucleoprotein complex that recognizes and binds emerging N-terminal signal peptides, arrests translation, and docks the ribosome to an ER membrane SRP receptor.

Stop-Transfer Sequence

A stretch of hydrophobic amino acids that arrests translocation through the ER translocon and shifts laterally into the lipid bilayer to anchor a transmembrane domain.

Trans-Golgi Network (TGN) Sorting

The sorting process at the exit face of the Golgi complex that packages modified proteins into distinct transport vesicles for delivery to the plasma membrane, secretory pathway, or lysosomes.