BIOL 102 - Fundamentals of Biology: Molecular and Cell Biology Study Notes

First Law of Thermodynamics

The principle that energy can be transferred and transformed across various forms, but it cannot be created or destroyed.

Second Law of Thermodynamics

The principle stating that every energy transfer or transformation increases the total entropy (molecular disorder and energy dispersal) of the universe.

Gibbs Free Energy ($\Delta G$)

The portion of a biological system's energy available to perform work at constant temperature and pressure, defined by $\Delta G = \Delta H - T\Delta S$. Reactions with $\Delta G < 0$ are exergonic and spontaneous, whereas reactions with $\Delta G > 0$ are endergonic and non-spontaneous.

Competitive Inhibition

A mechanism of enzymatic inhibition where a mimic molecule binds directly and reversibly to the active site, physically excluding the substrate. It increases the apparent $K_m$ without altering $V_{\max}$.

Noncompetitive (Allosteric) Inhibition

A mode of regulation where an inhibitor binds to a regulatory site physically distinct from the active site, inducing a conformational shape change that decreases $V_{\max}$ without altering $K_m$.

Glycolysis

A ten-step catabolic pathway occurring in the cytosol that splits $1$ six-carbon glucose molecule into $2$ three-carbon pyruvate molecules without requiring oxygen, yielding a net of $2\,\text{ATP}$ via substrate-level phosphorylation and $2\,\text{NADH}$.

Pyruvate Oxidation

A mitochondrial matrix reaction catalyzed by the pyruvate dehydrogenase complex that converts pyruvate into acetyl-CoA, reducing $\text{NAD}^+$ to $\text{NADH}$ and releasing $\text{CO}_2$.

Citric Acid Cycle (Krebs Cycle)

An eight-step cyclical pathway in the mitochondrial matrix that completely oxidizes acetyl-CoA into $\text{CO}_2$, generating $\text{NADH}$, $\text{FADH}_2$, and ATP (or GTP) via substrate-level phosphorylation.

Proton-Motive Force (PMF)

An electrochemical potential established across the inner mitochondrial or thylakoid membrane through directional proton pumping by electron transport chain complexes.

ATP Synthase

A rotary motor enzyme that utilizes the inward flow of protons down their established electrochemical gradient to catalyze the phosphorylation of ADP and inorganic phosphate into ATP.

Fermentation

An anaerobic metabolic process utilizing solely substrate-level phosphorylation in glycolysis, which recycles accumulated $\text{NADH}$ back to oxidized $\text{NAD}^+$ by transferring electrons directly to pyruvate or its derivatives.

Photolysis

The enzymatic splitting of water ($2\,\text{H}_2\text{O} \rightarrow 4\,\text{H}^+ + 4\,e^- + \text{O}_2$) at the reaction-center complex of Photosystem II, supplying electrons to reduce oxidized $\text{P680}^+$, releasing molecular oxygen, and loading protons into the thylakoid lumen.

Calvin Cycle

A light-independent anabolic pathway in the chloroplast stroma consisting of carbon fixation, reduction, and RuBP regeneration that utilizes ATP and NADPH to synthesize glyceraldehyde 3-phosphate (G3P) from inorganic $\text{CO}_2$.

Rubisco

Ribulose-1,5-bisphosphate carboxylase/oxygenase; the key stromal enzyme that catalyzes the primary fixation of $\text{CO}_2$ onto ribulose bisphosphate (RuBP), but can also mistakenly oxygenate RuBP to initiate photorespiration.

Photorespiration

An energetically expensive metabolic salvage pathway triggered when Rubisco fixes $\text{O}_2$ instead of $\text{CO}_2$, generating toxic glycolate 2-phosphate that must be detoxified across organelles while consuming ATP and releasing previously fixed carbon.

G Protein-Coupled Receptor (GPCR)

A seven-transmembrane cell-surface receptor that coordinates with an intracellular heterotrimeric G protein, catalyzing GDP-to-GTP exchange upon extracellular ligand binding to activate downstream effector enzymes.

Receptor Tyrosine Kinase (RTK)

A plasma membrane receptor that dimerizes upon ligand binding, stimulating cross-autophosphorylation of tyrosine residues on its intracellular tails to activate multiple signal transduction cascades simultaneously.

Second Messenger

A small, non-protein, water-soluble molecule or ion (such as cyclic AMP, $\text{IP}_3$, or $\text{Ca}^{2+}$) that diffuses rapidly through the cytoplasm to relay and amplify an extracellular signal inside the cell.

Maturation-Promoting Factor (MPF)

A regulatory cyclin-Cdk protein complex (Cyclin B bound to Cdk1) that triggers entry into the mitotic (M) phase past the $G_2$ checkpoint by phosphorylating target proteins.

Mitosis

An equational nuclear division process that partitions replicated chromosomes into two genetically identical daughter nuclei with preserved ploidy ($2n \rightarrow 2n$).

Meiosis I

The reductional division phase of meiosis wherein homologous chromosome pairs align, undergo crossing over, and segregate into separate daughter cells, reducing chromosomal ploidy from diploid ($2n$) to haploid ($n$).

Crossing Over

The reciprocal exchange of non-sister chromatid DNA segments between paired homologous chromosomes during prophase I of meiosis at visible crossover points called chiasmata.