INFORMATION
DNA → RNA → protein
Transcription makes RNA using DNA as a template. Translation uses mRNA to assemble a polypeptide. DNA does not leave the nucleus to visit a ribosome. Some RNA molecules function without being translated.
Expanded interactive edition / cell and molecular biology
Inside the cell.
Structure becomes function.
Explore cellular microanatomy, inspect organelle components in 3D, and follow the processes that copy chromosomes, express genes and power a cell. Use the step controls or move the timeline yourself; every model and animation is included in this file.
Ready for offline use. All models, graphics and simulations are embedded in this file. Only the external reading links need internet access.
Spatial organization
Explore the cellular interior
Rotate the cutaway and click an organelle, or choose its name. Selection opens a dedicated 3D inspector with component labels and expanded biological explanations. Turn off automatic inspection to study the whole-cell view without opening a dialog.
ANIMAL CELL / EXPLANATORY CUTAWAY
Preparing embedded surface geometry...Mouse, touch and keyboard controls
Follow a protein destined for secretion
An enlarged marker follows cargo from rough ER to Golgi to the plasma membrane in the animal-cell model.
1 / Rough ER
2 / Transport
3 / Golgi
4 / Vesicle
5 / Exocytosis
A ribosome translates mRNA, and a signal sequence can direct the growing polypeptide into the rough ER. The moving marker represents secretory cargo, not a protein leaving the nucleus.
This pathway is one destination, not the route taken by all proteins. Many proteins are translated on free ribosomes and remain in the cytosol or are imported into other compartments. OpenStax: endomembrane system.
Organelle microanatomy
Go beyond the outer surface
Open an organelle to rotate a dedicated close-up, click its component surfaces, and connect its architecture to a biological process. These are new explanatory cutaways, not simply larger copies of the whole-cell model.
Labels, cut surfaces and molecular components are enlarged for learning. Models are not specimen reconstructions or atomic structures. Structure references are included in each inspector.
A shared foundation, different solutions
Compare cell types
Cells share a plasma membrane, genetic material, cytoplasm and ribosomes. A nucleus and membrane-bound organelles distinguish typical eukaryotic cells from prokaryotic cells.
| Feature | Typical animal cell | Photosynthetic plant cell | Typical bacterium |
|---|---|---|---|
| Nuclear compartment | DNA enclosed by a nuclear envelope | DNA enclosed by a nuclear envelope | No membrane-bound nucleus; DNA in a nucleoid region |
| Outer boundary | Plasma membrane; no cell wall | Plasma membrane plus a cellulose-rich wall | Plasma membrane; most have a peptidoglycan wall |
| Energy conversion | Mitochondria support aerobic ATP production | Mitochondria plus chloroplasts in photosynthetic cells | Respiratory or photosynthetic membranes, depending on the species |
| Internal organization | ER, Golgi, lysosomes and other compartments | ER, Golgi, plastids and a prominent central vacuole | No ER or Golgi; internal organization is not simply random |
| Protein synthesis | Cytosolic ribosomes and ribosomes in mitochondria | Cytosolic ribosomes; also in mitochondria and chloroplasts | Ribosomes present, despite the absence of a nucleus |
Introductory comparison; there are specialized exceptions. For example, mature mammalian red blood cells lack a nucleus, and many nonphotosynthetic plant cells lack chloroplasts. Prokaryotic cells · Eukaryotic cells.
ENERGY
ATP links cellular work
ATP hydrolysis can be coupled to energetically unfavorable processes. Cells regenerate ATP rather than store an unlimited supply. Mitochondria are important, but glycolysis also produces ATP in the cytosol.
ARCHITECTURE
Membranes separate environments
A phospholipid bilayer has water-facing polar heads and a hydrophobic interior. Membrane proteins provide transport, signaling and anchoring. A compartment can maintain conditions different from the surrounding cytosol.
Observe real biological material
Models are not microscope images
Compare an isolated cell with a stained tissue section. The imaging method determines what a bright, dark or colored feature means. Do not assume that every visible patch is a named organelle.
Quantitative phase imaging
Stained tissue section
Observation task: distinguish a single-cell boundary from a tissue-level arrangement. Then explain why these two images cannot be treated as successive magnifications of the same specimen.
Experiment with a membrane
Diffusion and osmosis laboratory
Diffusion concerns the movement of particles. Osmosis is the net movement of water across a selectively permeable membrane. Compare them without confusing solute transport with cell swelling.
Left compartment130 particles
Right compartment30 particles
Total particles160
Track the redistribution
LeftRight
Particles move randomly in both directions. With a permeable boundary, an initial imbalance tends to decrease. Equal particle counts represent equal concentrations here because the compartments have equal volumes.
This stochastic, two-dimensional teaching model conserves 160 solute particles. Equal concentrations mean no sustained net flux, not that molecular motion stops. The simulation does not model electrochemical forces, pumps or specific protein channels.
Relative volume1.00 ×
Inside concentration300 mOsm/L
Net water tendencyNo net flux
Water responds to an osmotic difference
The initial inside concentration is 300 mOsm/L. At the same outside concentration, water still exchanges, but there is no net volume change.
Assumptions: water can cross; the modeled solute cannot; the outside is a large reservoir; the amount of intracellular solute is fixed. Thus Cinside = 300/V. The displayed volume limits are graphical limits, not experimentally determined lysis thresholds. Real cell mechanics and volume regulation are omitted.
OpenStax: passive transport, osmosis and tonicity. Active transport can move a substance against its electrochemical gradient using an energy source; that mechanism is outside these two passive-transport experiments.
Growth and DNA-copying context
Cell-cycle overview
A simplified diploid cell with 2n = 4 makes it possible to follow every chromosome. DNA replication doubles DNA content; it does not immediately double the number of chromosomes counted by centromeres.
Continue to the detailed mitosis and meiosis animations →
Explanatory diagram. Colors distinguish chromosome sets, not stains. Nuclear envelope and spindle details are simplified; stage durations are not to scale.
G1 / cell growth
Chromosomes
DNA content
Cell count
Centromere rule: an X-shaped replicated chromosome is one chromosome containing two sister chromatids. After the sisters separate, each is a daughter chromosome. Cytokinesis partitions the cytoplasm.
Chromosome choreography
One division or two?
Watch chromosomes move continuously rather than switching between static pictures. Both laboratories start after DNA replication with a small diploid teaching cell: 2n = 4, meaning two homologous pairs. Human chromosome numbers are not being modeled.
Mitosis: preserving the chromosome set
Follow condensation, spindle attachment, alignment, sister-chromatid separation, nuclear re-formation and cytokinesis.
One homologous originThe other originSpindle microtubulesLong pair A / short pair B
Counting rule: a joined pair of sister chromatids is one replicated chromosome. After sister separation, each chromatid is a daughter chromosome. C denotes DNA relative to one unreplicated haploid genome. The model illustrates an animal cell with centrosomes and a cleavage furrow; plant cytokinesis instead builds a cell plate.
Meiosis: making haploid products
Pair homologs, exchange corresponding DNA segments between nonsister chromatids, separate homologs in meiosis I, then separate sisters in meiosis II.
Homolog origin 1Homolog origin 2Mixed-color chromatid = exchanged segment
One S phase, two divisions: there is no new DNA replication between meiosis I and II. Crossing-over is shown at one site per homologous pair, and the two orientations are selected examples rather than all possible assortment outcomes. Four equal-sized products are a conceptual model, not a depiction of asymmetric egg formation. In plants and fungi, meiosis can produce spores rather than gametes.
| Question | Mitosis | Meiosis |
|---|---|---|
| How many divisions follow DNA replication? | One | Two; no S phase between them |
| What aligns first? | Individual replicated chromosomes | Homologous pairs in meiosis I |
| What separates in the first division? | Sister chromatids | Homologous chromosomes, still replicated |
| Outcome in this 2n = 4 model | Two cells, each 2n = 4 and 2C DNA | Four haploid products, each n = 2 and 1C DNA |
| Why do products differ? | Normally preserve the parental chromosome complement, aside from mutations or errors | Crossing-over and independent assortment redistribute genetic material |
Do not equate X shape with a chromosome: an unreplicated chromosome is still a chromosome. The X-like form represents two joined sisters after replication and condensation.
DNA to RNA to protein
Read, process, translate
These three linked laboratories distinguish transcription from RNA processing and translation. Track strand direction and base identity, then follow codons into a polypeptide. The workbench uses a short synthetic coding fragment, not a complete gene.
Sequence workbench
Only A, C, G and T are accepted. Spaces are ignored. This input is the template strand, not the coding strand. The initial example produces AUG CCU GAA UCG CGU UAA.
Coding DNA / 5′ to 3′
Transcription: making an RNA copy
RNA polymerase opens a small DNA region and builds a complementary RNA strand. The coding and template strands remain DNA; neither is converted into RNA.
Coding DNATemplate DNANew RNA
Direction matters: polymerase reads template DNA 3′ to 5′ and synthesizes RNA 5′ to 3′, adding to its 3′ end. This is a schematic nuclear RNA polymerase II example; promoter architecture and downstream termination are condensed. A translation stop codon is not a transcription termination signal. The workbench fragment omits untranslated regions, introns and regulatory DNA.
RNA processing: preparing a mature message
Follow 5-prime capping, intron removal, exon joining, 3-prime polyadenylation and export. Switch the splice pattern to compare two hypothetical RNA isoforms.
Exons retained in the chosen isoformIntrons removedBlock lengths are not sequence measurements
Not a rigid schedule: the steps are separated here so you can see them. Capping and much splicing can occur while transcription is still underway. The poly(A) tail is added enzymatically after cleavage; it is not simply copied from a long DNA run of T bases. Exons can contain untranslated regions as well as protein-coding sequence. This block diagram is a separate hypothetical gene, not the workbench sequence.
Translation: decoding RNA into a polypeptide
Watch ribosome assembly, codon recognition, tRNA entry, peptide extension and release at an in-frame stop codon. This laboratory uses the RNA derived from the workbench.
mRNARibosomal subunitsPolypeptide
Another direction change: the ribosome reads mRNA 5′ to 3′ and the polypeptide grows from its N terminus toward its C terminus. tRNA anticodons are antiparallel to codons. Release factors, not a stop-codon tRNA, recognize stop codons. This uses the standard nuclear genetic code; the first AUG is an instructional start rule, not a complete eukaryotic initiation model. Folding and post-translational processing are not simulated.
Try a mutation: replace the template's second triplet GGA with ATT. The second RNA codon becomes UAA. Compare the resulting polypeptide with the original example. This is a deliberately early stop in a synthetic fragment; it is not a prediction about a person's health.
Copy before you divide
DNA replication is not transcription
Replication copies DNA to DNA before division. Each new duplex contains one parental strand and one newly synthesized strand. Follow a single right-moving replication fork and notice why the two daughter strands are assembled differently.
Replication fork: leading and lagging strands
Unwind parental DNA, extend the leading strand toward the fork, build lagging-strand fragments away from the fork, then replace primers and join the fragments.
Parental DNANew DNARNA primer
Both new strands grow 5′ to 3′. The leading strand is continuous relative to this fork; the lagging strand is assembled from Okazaki fragments. Primer removal and gap filling precede ligation. Only one fork is shown; real origins commonly launch forks in both directions, and eukaryotic chromosomes use many origins. Enzyme identities and proofreading are simplified.
Energy across a membrane
Why the mitochondrial membrane folds
A membrane can store an electrochemical difference. In mitochondria, respiratory electron transfer helps establish a proton gradient; proton flow through ATP synthase can drive ATP production. Follow these related but distinct flows.
Oxidative phosphorylation: coupling a gradient to ATP synthesis
Trace electron transfer, proton pumping and proton return through ATP synthase in a magnified inner-membrane segment.
H+ / protonsElectron-transfer markersMembrane proteins
Separate the carriers: electrons flow through respiratory carriers, while protons cross the membrane. Complexes I, III and IV contribute to proton pumping; complex II does not. ATP synthase permits proton return toward the matrix and couples that flow to ATP synthesis. Oxygen is reduced to water at the end of the respiratory chain. The animation compresses stoichiometry, carrier steps and timing; it does not compute ATP yield per glucose.
Predict before pressing play
Investigations for the expanded laboratory
Why is an X still one chromosome?
Pause at mitotic metaphase. Count four replicated chromosomes, each comprising two sisters. At anaphase the sisters separate, so the still-undivided cell briefly contains eight daughter chromosomes. Each daughter eventually receives four.
Can chromosome number halve without DNA amount reaching 1C?
Yes. After meiosis I, each product in this model has n = 2 chromosomes, but both are still replicated: its DNA content is 2C. Meiosis II separates sisters and produces n = 2, 1C products.
What changes when pair B is reversed?
At metaphase I, reverse pair B. Track which A and B homologs arrive together. Independent orientation changes combinations without changing the chromosome number in each product.
How do you check an RNA sequence?
Enter a 3-prime-to-5-prime DNA template. Pair A with U, T with A, G with C and C with G. The RNA should match the displayed coding DNA apart from U replacing T. Do not reverse the already oriented template a second time.
Does removing exon 2 remove it from the DNA?
No. The splice example removes a segment from the RNA product. Genomic DNA remains unchanged. Whether an alternative RNA produces a stable functional protein depends on its actual sequence and regulatory context.
How would an impermeable inner membrane help make ATP?
Low uncontrolled proton permeability helps preserve a gradient. ATP synthase provides a coupled return route. A large uncoupled leak could dissipate the gradient instead of capturing its energy as ATP.
Guided investigations
Try, predict, explain
Identify before reading
- Choose the animal cell and rotate it.
- Find a mitochondrion by its folded interior.
- Compare it with the Golgi stack and rough ER.
Check your explanation
Mitochondria contain cristae in an inner membrane. Golgi cisternae form a stack; rough ER has ribosomes on its cytosolic face. Shape supports identification, but a real specimen requires appropriate imaging.
Change a boundary condition
- Run diffusion with a permeable membrane.
- Reset; make the membrane impermeable.
- Predict the long-term counts before advancing.
Check your prediction
With permeability, counts tend toward roughly equal values but fluctuate. With an impermeable boundary, counts remain 130 and 30. Both compartments still contain moving particles.
Count chromosomes, not arms
- Compare G1 with G2.
- Advance to metaphase, then anaphase.
- State chromosomes per daughter after division.
Check your count
G1 and G2 each have four chromosomes, but G2 has twice the DNA. During anaphase there are eight daughter chromosomes in the still-undivided cell. After cytokinesis each daughter has four chromosomes and 2C DNA.
Knowledge check
Check your understanding
Twenty questions span organelles, membrane transport, mitosis, meiosis, replication and gene expression. Grade to reveal explanations. Responses remain in this page and are not transmitted.
Vocabulary
A working cell-biology vocabulary
CytosolThe aqueous phase inside a cell, excluding membrane-enclosed organelle interiors.
CytoplasmIn a eukaryotic cell, the region inside the plasma membrane but outside the nucleus, including cytosol and organelles.
OrganelleA specialized cellular structure; many, but not every use of the term, refer to membrane-bound compartments.
Selective permeabilityA boundary allows some substances to cross more readily than others.
ChromatinDNA associated with proteins; its organization changes through the cell cycle.
Sister chromatidsThe two replicated copies of a chromosome, joined before separation during division.
Molecular vocabulary
Terms you can now visualize
- Homologous chromosomes
- Chromosomes with corresponding gene loci, one inherited through each parental lineage; their alleles can differ.
- Sister chromatids
- Replicated copies of one chromosome that remain associated before sister separation.
- Centromere and kinetochore
- A centromeric chromosome region supports assembly of the kinetochore, a protein complex that attaches to spindle microtubules.
- Haploid and diploid
- One chromosome set (n) versus two sets (2n). This is different from whether each chromosome has been replicated.
- Crossing-over
- Exchange of corresponding DNA between nonsister chromatids of paired homologs during meiotic prophase I.
- Exon and intron
- Exons are retained in a particular mature RNA; introns are removed by splicing. Not every exon base is translated.
- Template strand
- The DNA strand used to guide a complementary RNA or DNA copy, read 3-prime to 5-prime during synthesis.
- Codon and anticodon
- An mRNA triplet and its antiparallel tRNA recognition sequence; the standard code includes stop codons recognized by release factors.
- Okazaki fragment
- A short stretch of newly synthesized DNA on the lagging strand, later joined to neighboring stretches.
- Chemiosmosis
- Coupling ion movement down an electrochemical gradient to work such as ATP synthesis.
- Crista and thylakoid
- A crista is a mitochondrial inner-membrane fold. A thylakoid is a photosynthetic membrane compartment; they are not interchangeable terms.
- Checkpoint
- A regulatory control that helps coordinate progression with conditions such as DNA integrity and chromosome attachment.
Read further
Cellular biology resources
Eukaryotic cells
Review nuclei, mitochondria, plastids and other compartments in a free introductory textbook.
Open resource →The endomembrane system
Connect rough ER, Golgi, transport vesicles and secretory destinations.
Open resource →Passive transport and osmosis
Revisit diffusion, selective permeability, water movement and tonicity.
Open resource →The cell cycle
Review DNA replication, mitosis and cytokinesis with additional explanations.
Open resource →NIGMS image gallery
Explore biological microscopy and illustrations; read each image's method and credit.
Open resource →HeLa cells: cytoskeletal imaging
A multiphoton image identifying actin, microtubules and nuclei by distinct fluorescence labels.
Open resource →Golgi and actin in epithelial cells
Compare stained nuclei and actin with targeted fluorescent labeling of the Golgi.
Open resource →Quantitative phase image
Read the calibration, provenance and reuse terms for the single-cell image embedded here.
Open resource →Immunohistochemical tissue image
Read the staining method and provenance for the colonic gland sample.
Open resource →Meiosis and recombination
Homolog pairing, reductional division and genetic diversity.
Open resource →Transcription
RNA polymerases and nuclear gene transcription.
Open resource →RNA processing
Capping, splicing and polyadenylation.
Open resource →Translation
Ribosomes, tRNAs and protein synthesis.
Open resource →DNA replication
Copying eukaryotic DNA and coordinating replication.
Open resource →Cellular respiration
Electron transport, proton gradients and ATP synthase.
Open resource →NIH organelle tour
A student-oriented starting point for cellular compartments.
Open resource →NHGRI genetics glossary
Definitions of chromosome, gene, RNA and related genetic terms.
Open resource →