Cells, Central Dogma, and Gene Regulation

Vocabulary practice flashcards covering cell structure, organelles, the endomembrane system, cytoskeleton, Central Dogma, gene expression, operons, and molecular genetics laboratory techniques.

Light Microscope (LM)

An optical instrument in which visible light is passed through a specimen and then through glass lenses, which refract the light to magnify the image.

Scanning Electron Microscope (SEM)

An electron microscope that focuses a beam of electrons onto the surface of a specimen, creating detailed images that appear three-dimensional.

Transmission Electron Microscope (TEM)

An electron microscope that directs an electron beam through a thin specimen to study the internal ultrastructure of cells.

Cell Fractionation

A laboratory procedure that breaks open cells and separates organelles and other subcellular components by centrifugation based on size and density.

Nucleoid

A dense, non-membrane-enclosed region in a prokaryotic cell where the genetic material (bacterial chromosome) is concentrated.

Surface Area to Volume ($SA/V$) Ratio

A geometric relationship that constrains cell size, where volume grows with the cube of the radius ($V = \frac{4}{3}\\times \frac{4}{3}\,\pi r^3$) while surface area increases only with the square of the radius ($A = 4\,\pi r^2$).

Endomembrane System

A collection of intracellular membranes related through direct physical continuity or vesicular transport, consisting of the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and plasma membrane.

Smooth Endoplasmic Reticulum (SER)

The ribosome-free portion of the endoplasmic reticulum that functions in lipid synthesis, carbohydrate metabolism, calcium ion storage, and drug/poison detoxification.

Rough Endoplasmic Reticulum (RER)

The ribosome-studded portion of the endoplasmic reticulum that manufactures secretory glycoproteins, produces transport vesicles, and serves as a membrane factory.

Golgi Apparatus

An organelle of flattened membranous sacs (cisternae) with distinct polarity ($cis$ receiving face and $trans$ shipping face) that modifies, sorts, and packages macromolecules for delivery.

Lysosome

A membrane-bound sac containing hydrolytic digestive enzymes that function optimally at acidic $\text{pH}$ to digest food particles and intracellular debris.

Autophagy

A lysosomal catabolic recycling process whereby damaged organelles and cytosolic macromolecules are enclosed in vesicles and digested for cell reuse.

Central Vacuole

A prominent cellular organelle found in mature plant cells that stores water, inorganic ions, and organic compounds, functioning in plant cell enlargement and turgidity.

Endosymbiont Theory

The evolutionary model proposing that mitochondria and chloroplasts originated as symbiotic oxygen-using and photosynthetic prokaryotes engulfed by an ancestral host cell.

Peroxisome

A specialized metabolic compartment enclosed by a single membrane that produces hydrogen peroxide ($\text{H}_2\text{O}_2$) as a byproduct of oxidation and subsequently decomposes it into water.

Microtubules

Hollow cytoskeletal cylinders measuring $25\,\text{nm}$ in diameter with a $15\,\text{nm}$ lumen, composed of $\alpha$-tubulin and $\beta$-tubulin dimers, that resist compression, organize chromosomes, and direct intracellular vesicle movements.

Microfilaments

Thin cytoskeletal fibers measuring $7\,\text{nm}$ in diameter, composed of two intertwined strands of actin, that support tension, facilitate cell motility, and support muscle contraction.

Intermediate Filaments

Cytoskeletal fibers measuring $8\text{--}12\,\text{nm}$ in diameter, composed of coiled fibrous proteins (such as keratins), specialized for bearing tension and anchoring the nucleus and nuclear lamina.

Dynein

An ATP-powered motor protein that moves vesicles and organelles unidirectionally along microtubule cytoskeletal tracks.

Chromatin

The structural complex consisting of eukaryotic DNA associated with histone proteins that condenses to form visible chromosomes prior to cell division.

Nucleolus

A dense structure within the non-dividing eukaryotic nucleus responsible for synthesizing ribosomal RNA ($\text{rRNA}$) and assembling ribosome subunits.

Central Dogma

The core molecular biological principle that cellular genetic information flows sequentially from $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{protein}$.

Transcription

The enzymatic synthesis of an RNA molecule using a DNA strand as a template, catalyzed by RNA polymerase in the $5' \rightarrow 3'$ direction.

Translation

The ribosomal assembly of a polypeptide chain based on the triplet codon sequence found in an mRNA transcript.

Codon

A sequence of three adjacent nucleotide bases in mRNA, read in the $5' \rightarrow 3'$ direction, that designates a specific amino acid or a termination signal.

Wobble Effect

Flexible, non-standard base pairing at the third base ($3'$ end) of an mRNA codon that allows a single tRNA species to pair with multiple synonymous codons.

Promoter

A specific nucleotide sequence in DNA that binds RNA polymerase and related transcription factors to designate the transcription start site.

TATA Box

A conserved eukaryotic promoter DNA sequence situated approximately $25\,\text{nucleotides}$ upstream from the start point that organizes the transcription initiation complex.

Transcription Factors

Regulatory proteins that bind specific DNA sequences or RNA polymerase to regulate or mediate the transcription of target genes.

Transcription Initiation Complex

The full macromolecular assembly consisting of transcription factors and RNA polymerase II positioned on a eukaryotic promoter.

Polyadenylation Signal Sequence

A conserved hexanucleotide sequence (AAUAAA) in eukaryotic pre-mRNA that directs RNA endonuclease cleavage $10\text{--}35\,\text{nucleotides}$ downstream.

$5'$ Cap

A modified guanine nucleotide added to the $5'$ end of eukaryotic pre-mRNA that facilitates export, protects against degradation, and aids ribosome attachment.

Poly-A Tail

A continuous tract of $50\text{--}250$ adenine residues attached to the $3'$ end of eukaryotic pre-mRNA that promotes stability and nuclear export.

Introns

Noncoding intervening segments of nucleic acid in eukaryotic pre-mRNA that are excised during RNA splicing before cytoplasmic translation.

Exons

Coding nucleotide sequences in a gene and primary RNA transcript that are preserved during splicing and expressed as mature mRNA.

Spliceosome

A large ribonucleoprotein complex composed of proteins and small nuclear ribonucleoproteins (snRNPs) that excises introns and ligates exons.

Ribozyme

An RNA molecule displaying catalytic enzymatic activity, capable of self-cleavage or splicing without requiring protein enzymes.

Alternative RNA Splicing

A regulatory mechanism where primary transcripts are processed into distinct mature mRNAs by selecting different combinations of exons.

Transfer RNA (tRNA)

An adaptor RNA molecule containing an anticodon loop and an amino acid attachment site that delivers specific amino acids to a translating ribosome.

Anticodon

A specialized base triplet on a tRNA molecule that base-pairs with a complementary triplet codon on an mRNA molecule.

A Site (Aminoacyl-tRNA Site)

The ribosomal binding pocket that receives the incoming aminoacyl-tRNA bearing the subsequent amino acid for the growing polypeptide.

P Site (Peptidyl-tRNA Site)

The ribosomal binding cavity that anchors the tRNA holding the growing nascent polypeptide chain.

E Site (Exit Site)

The ribosomal site from which deacylated, discharged tRNAs are released from the translation complex.

Release Factor

A cytosolic protein shaped like a tRNA that binds the stop codon at the ribosomal A site and hydrolyzes the completed polypeptide from the peptidyl-tRNA.

Signal-Recognition Particle (SRP)

A cytosolic protein-RNA complex that binds an emergent signal peptide, halts translation, and targets the ribosome to a rough ER receptor.

Polyribosome (Polysome)

An array of multiple ribosomes simultaneously engaged in translating a single mRNA molecule in a linear cascade.

Point Mutation

A genetic mutation involving an alteration, substitution, insertion, or deletion of a single nucleotide base pair within a gene.

Silent Mutation

A base substitution that alters a codon without changing the encoded amino acid due to degeneracy within the genetic code.

Missense Mutation

A nucleotide-pair substitution that alters a codon to specify a different amino acid, potentially altering protein structure or function.

Nonsense Mutation

A nucleotide substitution that prematurely converts an amino acid codon into a termination codon, leading to truncated polypeptides.

Frameshift Mutation

A mutation caused by the insertion or deletion of nucleotide pairs not divisible by three, displacing the downstream codon reading frame.

Operon

A prokaryotic genetic regulatory unit composed of a promoter, an operator, and a cluster of coordinately transcribed structural genes.

Operator

A regulatory DNA sequence positioned within or adjacent to a bacterial promoter that serves as the binding site for an active repressor protein.

Repressor

A sequence-specific regulatory DNA-binding protein that inhibits the transcription of an operon by physically impeding RNA polymerase.

Corepressor

A small allosteric effector molecule (such as tryptophan) that binds and activates an aporepressor to switch off transcription.

Inducer

A small metabolite (such as allolactose) that binds to and inactivates an active repressor protein, turning on operon transcription.

Catabolite Activator Protein (CAP)

A bacterial transcriptional activator that binds cyclic AMP ($\text{cAMP}$) when glucose is deficient, stimulating RNA polymerase binding to the lac promoter.

Histone Acetylation

The covalent addition of acetyl groups to lysine residues on histone tails, diminishing basic charges, relaxing chromatin, and promoting transcription.

DNA Methylation

The covalent enzymatic addition of methyl groups to cytosine bases in DNA, typically leading to long-term transcriptional silencing and chromatin condensation.

Enhancers

Clusters of distal control elements situated upstream, downstream, or within introns that bind transcriptional activators to enhance gene transcription.

Bicoid

A maternal effect morphogen in fruit flies whose localized anterior concentration gradient establishes head and thoracic structures.

microRNAs (miRNAs)

Short, single-stranded endogenous noncoding RNA molecules that bind complementary sequences on mRNAs to trigger their degradation or halt translation.

RNA Interference (RNAi)

A gene-silencing pathway in which double-stranded RNA molecules trigger the targeted degradation or translational repression of matching mRNAs.

CRISPR/Cas9

A bacterial adaptive immune mechanism adapted for precise genome editing that pairs a custom guide RNA with the Cas9 endonuclease to introduce double-strand DNA breaks.

Complementary DNA (cDNA)

Double-stranded DNA generated in vitro from a mature mRNA template using reverse transcriptase and DNA polymerase, lacking noncoding introns.

DNA Microarray Assay

A high-throughput slide or chip arrayed with thousands of microscopic single-stranded DNA fragments used to assess simultaneous global gene expression profiles.

Fluorescent In Situ Hybridization (FISH)

A molecular cytogenetic technique utilizing fluorescently labeled single-stranded nucleic acid probes to visualize the cellular location of specific DNA sequences or mRNAs in intact tissue.