Comprehensive Cellular Biology, Metabolism, Genetics, and Pathology

Comprehensive vocabulary flashcards covering cell anatomy, microscopy, bioenergetics, stoichiometry of cellular respiration, photosynthesis, meiosis errors, cell cycle dynamics, cancer epidemiology, transport mechanisms, and transport-associated channelopathies.

Eyepiece (Ocular Lens)

The lens at the top of a compound microscope that a viewer looks through, which magnifies the primary image produced by the objective lens.

Condenser

A microscope lens system located beneath the stage that concentrates and focuses light from the illuminator up through the specimen.

Diaphragm (Iris)

An adjustable apparatus beneath the microscope stage that regulates the amount and intensity of light passing through the specimen.

Thermodynamic Efficiency of Aerobic Respiration

The percentage of energy captured from glucose into useful cellular energy ($\text{ATP}$), calculated as $\frac{32 \times 7.3}{686} \times 100 = 34\%$, with the remaining $66\%$ released as thermal heat.

Standard Free Energy of Glucose Oxidation

The baseline energy metrics of cellular respiration where the total energy input released per mole of glucose is $686\,\text{kcal}$, while the useful output captured per mole of $\text{ATP}$ is $7.3\,\text{kcal}$.

Adenosine Triphosphate (ATP)

The primary energy currency of the cell, composed of the nitrogenous base adenine, a 5-carbon ribose sugar, and a chain of three phosphate groups.

Anabolic Pathways

Metabolic pathways in which simple, small precursor molecules are assembled into larger, complex molecules, requiring an input of cellular energy.

Catabolic Pathways

Metabolic pathways that degrade large, complex molecules into smaller units, resulting in a net release of chemical energy.

Glycolysis

A 10-step catabolic pathway occurring in the cytoplasm that breaks down one 6-carbon glucose molecule into two 3-carbon pyruvate molecules, consuming $2\,\text{ATP}$ to yield a net $2\,\text{ATP}$ and $2\,\text{NADH}$.

Pyruvate Oxidation

The conversion of each 3-carbon pyruvate into a 2-carbon acetyl coenzyme A ($\text{acetyl-CoA}$) upon entering the mitochondrial matrix, producing $1\,\text{NADH}$ and releasing one $CO_2$ per pyruvate.

Krebs Cycle (Citric Acid Cycle)

A cyclic metabolic pathway in the mitochondrial matrix where each acetyl-CoA combines with oxaloacetate to generate $3\,\text{NADH}$, $1\,\text{FADH}_2$, $1\,\text{ATP}$, and $2\,\text{CO}_2$ per turn.

Malate-Aspartate Shuttle

A biochemical shuttle mechanism that transports cytoplasmic electrons from glycolysis into the mitochondrial matrix to regenerate $\text{NADH}$, preserving the maximal theoretical yield of $38\,\text{ATP}$ per glucose.

Glycerol Phosphate Shuttle

An electron shuttle mechanism that transfers cytosolic electrons from glycolytic $\text{NADH}$ to mitochondrial $\text{FAD}$, producing $\text{FADH}_2$ and reducing the net theoretical energy yield to $36\,\text{ATP}$ per glucose.

Beta-Oxidation

The catabolic process occurring in the mitochondrial matrix that cleaves fatty acid chains into successive two-carbon units coupled with coenzyme A to form $\text{acetyl-CoA}$.

Lactic Acid Fermentation

An anaerobic pathway occurring in the cytoplasm where pyruvate is reduced directly by $\text{NADH}$ to produce lactic acid and regenerate $\text{NAD}^+$, operating at a thermodynamic efficiency of only $2.1\%$.

Nondisjunction

The failure of homologous chromosome pairs to separate during meiosis I or sister chromatids to separate during meiosis II, leading to aneuploid gametes.

Turner Syndrome

The only known survivable human monosomy ($45,\text{X}$ or $45,\text{X0}$), characterized clinically in females by short stature and sterility.

Klinefelter Syndrome

A sex chromosome trisomy ($47,\text{XXY}$) occurring in approximately 1 in 2000 live male births, characterized by tall stature, sterility, and normal cognitive intelligence.

Autotroph

An organism capable of synthesizing its own complex organic nutrients from inorganic substances using light energy (photoautotrophs) or chemical oxidation (chemoautotrophs).

Thylakoids

Flattened, saclike photosynthetic membranes embedded within chloroplasts that are arranged in stacks called grana and house chlorophyll pigments and the electron transport chain.

Stroma

The enzyme-rich fluid portion of the chloroplast surrounding the thylakoid membranes, serving as the site of the light-independent reactions (Calvin-Benson cycle).

Chlorophyll a

The primary photosynthetic pigment that converts solar energy into chemical energy, showing major absorption peaks in the blue ($430\text{--}450\,\text{nm}$) and red ($660\text{--}680\,\text{nm}$) regions while reflecting green light.

NADP+

Nicotinamide adenine dinucleotide phosphate; an electron acceptor in photosynthesis that accepts two high-energy electrons and one hydrogen ion ($H^+$) to form $\text{NADPH}$.

Photolysis

The light-driven splitting of water molecules ($H_2O$) during the light-dependent reactions of photosynthesis, releasing electrons, protons, and oxygen gas ($O_2$).

RuBisCO

Ribulose-1,5-bisphosphate carboxylase/oxygenase; the planet's most abundant enzyme that catalyzes the initial carbon fixation step attaching atmospheric $CO_2$ to $\text{RuBP}$ at a rate of approximately 3 reactions per second.

Calvin-Benson Cycle

The light-independent stage of photosynthesis occurring in the stroma, consisting of three phases—carbon fixation, reduction of $3\text{-PGA}$ to $\text{G3P}$, and regeneration of $\text{RuBP}$—fueled by $\text{ATP}$ and $\text{NADPH}$.

Interphase

The metabolic stage of the cell cycle encompassing the $G_1$, S, and $G_2$ phases during which the cell grows, accumulates nutrients, duplicates organelles, and replicates its genomic DNA, occupying approximately $90\%$ of cell lifespan.

G0 Phase

A quiescent, non-dividing state exited from the cell cycle where cells perform specialized physiological functions without preparing for cell division.

G1/S Checkpoint

A critical surveillance point located at the end of the $G_1$ phase that evaluates cell size, nutrient reserves, and genomic DNA integrity before committing the cell irreversibly to DNA synthesis.

Cyclin-Dependent Kinases (CDKs)

Constitutively expressed catalytic enzymes that remain inactive until bound by regulatory cyclin proteins, forming active complexes that phosphorylate targets to drive cell cycle progression.

Binary Fission

A form of asexual reproduction in prokaryotes where a single circular DNA molecule replicates simultaneously with cell elongation, pinching the cell into two genetically identical daughter cells without a mitotic spindle.

Cytokinesis

The final physical cleavage of the cytoplasm following mitosis, occurring via an actin contractile ring forming a cleavage furrow in animal cells or a cell plate in plant cells.

Cell Cycle Durations in Cultured Human Cells

The standard 24-hour mammalian cell cycle division of time: $G_1$ phase lasts 11 hours ($45.8\%$), S phase lasts 8 hours ($33.3\%$), $G_2$ phase lasts 4 hours ($16.7\%$), and M phase lasts 1 hour ($4.2\%$).

p53 Protein

A tumor suppressor protein encoded by the TP53 gene known as the 'guardian of the genome,' which arrests the cell cycle or triggers apoptosis upon detecting DNA damage; mutated in over $50\%$ of all human cancers.

Retinoblastoma Protein (Rb)

A tumor suppressor gatekeeper that controls the $G_1\text{-to-}S$ phase transition by sequestering E2F transcription factors until phosphorylated.

Apoptosis

A programmed, orderly physiological process of cellular self-destruction that eliminates damaged, obsolete, or dangerous cells without provoking an inflammatory response.

Palbociclib

A targeted therapeutic drug that selectively inhibits CDK4 and CDK6, restoring the $G_1$ checkpoint block to halt abnormal cell proliferation in breast cancer.

2024 Philippine Cancer Statistics

National health data recording 149,852 total new cancer cases, 86,338 cancer-related deaths, and a $15.3\%$ lifetime risk of developing cancer before age 75.

Lung Cancer Burden in the Philippines (2024)

The most common cancer diagnosed in Filipino males (9,910 cases; $16.2\%$) and the leading cause of overall cancer mortality nationwide (11,715 deaths; $13.6\%$).

Breast Cancer Burden in the Philippines (2024)

The most diagnosed cancer overall and among females (28,124 cases; $31.7\%$ of female cancers), as well as the second leading cause of cancer mortality (11,160 deaths; $12.9\%$).

Phagocytosis

A specialized form of endocytosis ('cellular eating') where immune cells extend pseudopodia to engulf large solid particles, microbes, or cellular debris into a phagosome.

Pinocytosis

A continuous, non-specific form of endocytosis ('cellular drinking') where the plasma membrane invaginates to form tiny vesicles filled with extracellular fluid and dissolved solutes.

Receptor-Mediated Endocytosis

A highly selective bulk transport mechanism where specific extracellular ligands bind to transmembrane receptors clustered in clathrin-coated pits, triggering targeted vesicle internalization.

Phagosome

A membrane-bound intracellular vesicle formed around an engulfed particle during phagocytosis that subsequently fuses with a lysosome for enzymatic degradation.

Exocytosis

An active bulk transport process where secretory vesicles originating from the Golgi apparatus traffic along microtubules and fuse with the plasma membrane to expel cargo into the extracellular space.

Cystic Fibrosis

An autosomal recessive channelopathy caused by mutations in the CFTR gene, disrupting chloride ion transport and resulting in dehydrated, thick mucus accumulation in pulmonary and digestive tracts.

Familial Hypercholesterolemia

A severe genetic transport disorder caused by mutations in the LDLR gene, impairing the receptor-mediated endocytosis of LDL into hepatocytes and causing premature atherosclerosis.

Nephrogenic Diabetes Insipidus

A renal pathology caused by defective vasopressin V2 receptors or Aquaporin-2 water channels in the collecting ducts, preventing water reabsorption and causing profound polyuria.

Niemann-Pick Type C

A lysosomal storage disease caused by mutations in NPC1 that disrupt intracellular lipid efflux, leading to massive cholesterol accumulation in late endosomes/lysosomes and neurodegeneration.

Cell Differentiation

The developmental process by which unspecialized stem cells selectively regulate gene expression to develop distinct morphological structures and physiological functions.

Microvilli

Microscopic, finger-like plasma membrane extensions found on epithelial tissues such as the small intestine and renal tubules that dramatically increase absorptive surface area without increasing cell volume.

Erythrocytes (Red Blood Cells)

Specialized gas-transport cells with a biconcave disc shape that lack a nucleus in mature mammalian form to maximize intracellular space for hemoglobin packaging.

Guard Cells

Paired epidermal plant cells flanking each stoma that regulate stomatal pore aperture through osmotic changes in turgor pressure to control gas exchange and water transpiration.

Chromatophores

Specialized pigment-containing and light-reflecting cells in animals that rapidly expand or contract pigment sacs under neuronal or hormonal control for camouflage, thermoregulation, and signaling.

Squamous Epithelium

A tissue layer consisting of thin, flat, scale-like cells optimized for rapid passive diffusion and filtration, located in sites such as pulmonary alveoli and vascular endothelium.

Columnar Epithelium

A cellular layer composed of tall, column-shaped cells lining the digestive tract that provide physical protection and ample cytoplasmic volume for processing absorbed nutrients.

Selective Permeability

The fundamental property of the plasma membrane that allows specific substances to traverse while restricting the movement of others to maintain stable internal homeostasis.

Membrane Cholesterol

A lipid steroid interspersed within the phospholipid bilayer that modulates fluidity, preventing membranes from becoming overly rigid at low temperatures or excessively fluid at high temperatures.

Osmosis

The passive net movement of water molecules across a selectively permeable membrane from a region of higher water concentration (lower solute) to a region of lower water concentration (higher solute).

Fluid Mosaic Model

A structural model describing the biological membrane as a dynamic, two-dimensional liquid matrix of amphipathic phospholipids embedded with wandering proteins, carbohydrates, and sterols.

Sodium-Potassium Pump (Na+/K+ Pump)

An electrogenic primary active transport protein that hydrolyzes $\text{ATP}$ to pump $3\,\text{Na}^+$ ions out of the cell and $2\,\text{K}^+$ ions in against their steep electrochemical gradients.

Crenation

The cellular shriveling and shrinking that occurs when an animal cell, such as an erythrocyte, is placed in a hypertonic environment, causing rapid osmotic efflux of water.

Hemolysis

The swelling and osmotic lysis of red blood cells caused by excessive water influx when exposed to a hypotonic solution.