Cellular Biology: Energy, Membranes, Transport, and the Cytoskeleton

Comprehensive vocabulary flashcards covering energy metabolism, glycolysis, the citric acid cycle, electron transport and ATP synthesis, membrane structure and dynamics, transmembrane transport mechanisms, and cytoskeletal filaments and motors.

Energy carriers

Molecules that store and transport chemical energy within cells to power cellular processes, such as ATP/GTP for direct currency and NADH or $FADH_2$ for storing energy in high-energy electrons.

Metabolism

The sum of all chemical reactions that occur inside the cells of a living organism to sustain life and manage raw materials, consisting of catabolism plus anabolism.

Catabolism

The metabolic process of breaking down complex molecules into simpler molecules, which is energetically favorable.

Anabolism

The metabolic pathway that turns molecules available in a cell into new molecules needed by the cell, which is energetically unfavorable.

Stepwise glucose oxidation

The sequential harvesting of energy from organic molecules that prevents energy from being released as a single large burst.

Oxidation

The removal of electrons from an atom or molecule.

Reduction

The addition of electrons to an atom or molecule.

$$\Delta G$$

The change in free energy that occurs during a chemical reaction.

$$\Delta G^\circ$$

The standard free energy change under standard conditions, independent of concentration and dependent on the intrinsic characteristics of the reacting molecules.

Spontaneous reaction

An energetically favorable reaction characterized by a negative $\Delta G$.

Nonspontaneous reaction

An energetically unfavorable reaction characterized by a $\Delta G > 0$ that requires an input of energy to proceed.

Glycolysis

A cytosolic pathway that breaks down glucose, utilizing $2\,\text{ATP}$ and producing $4\,\text{ATP}$ to yield a net gain of $2\,\text{ATP}$ and $2\,\text{NADH}$.

Fermentation

A cytosolic anaerobic process occurring after glycolysis that regenerates $NAD^+$ without producing ATP, yielding ethanol and $CO_2$ in yeast or lactate in muscle cells.

Substrate-level phosphorylation

The direct transfer of a phosphate group from a high-energy phosphorylated molecule directly to ADP to form ATP.

1,3-bisphosphoglycerate (1,3-BPG)

A high-energy phosphorylated glycolytic intermediate that transfers a phosphate group to ADP in step 6 of glycolysis.

Citric acid cycle

A metabolic pathway located in the eukaryotic mitochondrial matrix that processes acetyl-CoA, producing $3\,\text{NADH}$, $1\,\text{FADH}_2$, $1\,\text{ATP/GTP}$, and $2\,\text{CO}_2$ per turn.

Acetyl-CoA

A carrier molecule formed during pyruvate oxidation in the mitochondrial matrix that delivers a 2-carbon acetyl group into the citric acid cycle.

Fatty acid cycle

A pathway in the mitochondrial matrix of eukaryotic cells where fatty acyl-CoA enters via the carnitine shuttle to produce $1\,\text{NADH}$, $1\,\text{FADH}_2$, and $1\,\text{acetyl-CoA}$.

Electron transport chain (ETC)

A series of protein complexes that transfer electrons from NADH and $FADH_2$ to oxygen and use the released energy to pump $H^+$ across the inner mitochondrial membrane.

Complex I

The mitochondrial ETC complex that accepts electrons from NADH and pumps protons across the inner mitochondrial membrane.

Complex II

The mitochondrial ETC complex that accepts electrons from $FADH_2$ via succinate dehydrogenase without pumping protons.

Complex III

The protein complex in the ETC that transfers electrons along the chain and pumps protons across the membrane.

Complex IV

The final complex in the ETC that pumps protons as the final electron acceptor $O_2$ is reduced to $H_2O$.

Electrochemical gradient

A dual gradient produced across the inner mitochondrial membrane containing higher $H^+$ and positive charge outside in the intermembrane space and lower $H^+$ and negative charge inside the matrix.

ATP Synthase

A multi-subunit enzyme consisting of a membrane-embedded $F_0$ rotor/channel, a matrix $F_1$ catalytic head, and a stator, which harnesses proton flow to synthesize ATP.

Binding change mechanism

The catalytic cycle of ATP synthase wherein gamma stalk rotation drives beta subunits through Loose (bind ADP and Pi), Tight (synthesize ATP), and Open (release ATP) conformations.

Chemiosmotic model

The principle stating that the electron transport chain builds an $H^+$ electrochemical gradient across a membrane, and this gradient powers ATP synthesis.

Proton ionophores

Uncoupling agents that increase metabolic rate while blocking ATP synthesis by dissipating the essential proton gradient across the inner mitochondrial membrane.

Fluid mosaic structure

A membrane model describing the lipid bilayer as a dynamic, flexible two-dimensional fluid in which proteins float and move.

Exoplasmic face

The extracellular leaflet of the plasma membrane that displays glycolipids and glycoproteins involved in cell recognition, adhesion, and immune signaling.

Cytoplasmic face

The intracellular leaflet of the plasma membrane enriched with negatively charged lipids like phosphatidylserine, phosphatidylethanolamine, and phosphatidylinositols for signaling and cytoskeletal anchoring.

Glycerophospholipid

A membrane phospholipid that contains a glycerol backbone attached to phosphate head groups and two fatty acid tails.

Sphingolipid

A class of membrane lipids possessing a sphingosine backbone rather than a glycerol backbone.

Cholesterol

A rigid steroid ring molecule in animal cell membranes that acts as a fluidity buffer by preventing tight packing at low temperatures and restricting tail movement at high temperatures.

Lateral diffusion

The rapid swapping of positions between adjacent phospholipid molecules within the same membrane leaflet.

Flip-flop

The transverse movement of a phospholipid from one membrane leaflet to the opposite leaflet, typically catalyzed by specific enzymes.

Scramblase

An ATP-independent enzyme that moves any lipid type non-specifically in either direction across the bilayer, dissipating asymmetry during processes like apoptosis and platelet activation.

Flippase

An ATP-dependent enzyme that specifically moves phosphatidylserine (PS) and phosphatidylethanolamine (PE) from the exoplasmic leaflet to the cytosolic leaflet.

Floppase

An ATP-dependent enzyme that specifically transports phosphatidylcholine (PC) and sphingolipids (SL) from the cytosolic leaflet out to the exoplasmic leaflet.

Kennedy (CDP-choline) pathway

The biosynthetic pathway on the cytosolic face of the smooth ER where choline is phosphorylated, conjugated to CTP to form CDP-choline, and reacted with diacylglycerol to produce phosphatidylcholine.

Cardiolipin

A unique membrane lipid synthesized in mitochondria and specifically enriched within the inner mitochondrial membrane.

Endomembrane system

A group of cellular membranes that are either directly connected or continuously exchange materials via vesicle transport.

Integral membrane proteins

Proteins embedded directly in the lipid bilayer, often traversing it as transmembrane structures.

Peripheral membrane proteins

Proteins bound noncovalently to the membrane surface through ionic and hydrogen bonds with lipid headgroups or integral membrane proteins.

Lipid-anchored proteins

Proteins covalently attached to a lipid molecule that inserts into the hydrophobic core of the bilayer.

Transmembrane alpha helix

A common protein motif of 20 to 25 hydrophobic amino acids where internal backbone hydrogen bonding neutralizes polarity to span the hydrocarbon interior of the membrane.

Beta barrel

A transmembrane structure composed of 8 to 22 beta strands rolled into a cylinder, found in outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria.

Glycocalyx

A carbohydrate-rich protective coating on the outer surface of the plasma membrane that aids in cell-cell recognition, adhesion, and mechanical defense.

Simple diffusion

A passive transport process where small, nonpolar molecules (such as $CO_2$ and $O_2$) cross the lipid bilayer down their concentration gradient without transport proteins.

Facilitated diffusion

Passive transport down a concentration gradient that requires transport proteins, such as selective channels or carrier uniporters.

Channel proteins

Multi-pass transmembrane proteins that form open pores allowing rapid transport of water or specific ions without undergoing conformational cycling for each solute.

Transporter (carrier) proteins

Membrane proteins that bind specific solutes and undergo alternating conformational changes to move large or polar molecules across the membrane at a slower rate than channels.

Membrane potential

The electrical voltage difference across the cell membrane, generated and maintained by the unequal distribution of ions like $Na^+$ and $K^+$.

SGLT (sodium-coupled glucose transporter)

A secondary active symporter in the apical membrane of kidney and intestinal epithelial cells that imports glucose against its gradient using energy from the inward $Na^+$ gradient.

GLUT (glucose transporter)

A uniporter carrier protein on basolateral membranes that mediates facilitated diffusion of glucose out of epithelial cells or into metabolizing cells upon insulin stimulation.

$$Na^+/K^+\text{-ATPase}$$

A primary active P-type pump that hydrolyzes one ATP to pump $3\,\text{Na}^+$ out and $2\,\text{K}^+$ in, generating transmembrane ionic gradients and an outward net positive charge.

P-type ATPase

A family of ATP-driven ion pumps that cycle between E1 and E2 conformations and form a transient phosphorylated aspartate intermediate during the transport cycle.

Antiport

A secondary active transport mechanism in which two different solutes move across the membrane in opposite directions.

Symport

A secondary active transport mechanism in which two different solutes move across the membrane simultaneously in the same direction.

$Na^+\text{-}H^+$ exchanger (NHE)

An antiport carrier in animal plasma membranes that uses the $Na^+$ gradient to actively export $H^+$ ions for intracellular pH regulation.

SERCA

A P-type $Ca^{2+}$ ATPase located in the sarcoplasmic reticulum of muscle cells and ER of animal cells that actively imports $Ca^{2+}$ into the lumen using ATP hydrolysis.

Bacteriorhodopsin

A light-driven proton pump found in the plasma membrane of certain bacteria that exports $H^+$ to establish an electrochemical gradient directly from light energy.

Microfilaments

The smallest cytoskeletal filaments, composed of actin polymers organized just under the plasma membrane in the cell cortex to provide shape and drive motility.

Intermediate filaments

Rope-like cytoskeletal polymers composed of twisted protein strands distributed throughout the cytoplasm and inner nuclear envelope to provide mechanical tensile strength.

Microtubules

The largest cytoskeletal filaments, formed as hollow cylinders of 13 protofilaments composed of alpha/beta-tubulin heterodimers radiating from the centrosome.

Treadmilling

A steady-state filament dynamic where actin monomers add continuously to the plus (barbed) end while dissociating from the minus (pointed) end at equivalent rates.

Dynamic instability

The stochastic switching of individual microtubules between phases of polymerization and rapid depolymerization (catastrophe) governed by the presence or loss of a GTP cap.

Keratins

Intermediate filament proteins of epithelial cells, hair, and nails that anchor to desmosomes and hemidesmosomes to distribute mechanical stress across tissue sheets.

Nuclear lamins

Intermediate filament proteins (lamins A, B, and C) forming a structural fibrous meshwork lining the inner nuclear membrane of nucleated cells.

Plectin

A cytoskeletal cross-linking protein that binds intermediate filaments to microtubules, actin filaments, and adhesive junctions such as desmosomes and hemidesmosomes.

Progerin

An abnormal, permanently farnesylated lamin A variant encoded by a mutated LMNA gene that causes nuclear blebbing, mechanical fragility, and Hutchinson-Gilford progeria.

LINC complex

A nuclear envelope bridging complex formed by outer membrane KASH-family proteins and inner membrane SUN-family proteins that couples the cytoskeleton to the nuclear interior.

Microtubule-organizing centers (MTOCs)

Cellular structures such as centrosomes and basal bodies that nucleate and anchor the minus ends of microtubules, dictating their cellular orientation and distribution.

$\gamma$-tubulin ring complex ($\gamma\text{-TuRC}$)

A ring-shaped protein complex located at the MTOC that serves as the nucleation template and minus-end cap for newly polymerizing microtubules.

Kinesin-13

A catastrophe-promoting factor that actively depolymerizes microtubules at their ends.

Kinesins

ATP-driven motor proteins that walk hand-over-hand toward the plus end of microtubules to mediate anterograde transport toward the cell periphery.

Cytoplasmic dynein

An ATP-driven motor protein complex that travels toward the minus end of microtubules to carry out retrograde transport toward the cell center.

$9 + 2$ axoneme

The structural arrangement of cilia and flagella comprising nine outer doublet microtubules encircling a central pair of single microtubules.

Arp2/3 complex

A protein complex that nucleates new actin microfilaments as side branches at approximately 70-degree angles off pre-existing filaments to form branched meshworks.

Formins

Nucleating proteins that promote the assembly of straight, unbranched, parallel bundles of actin microfilaments, such as those found in filopodia.

Capping proteins

Proteins that bind specifically to the plus (barbed) end of actin filaments to block further subunit addition, keeping filaments short and rigid.

Lamellipodia

Broad, sheet-like cellular protrusions driven by Arp2/3-mediated branched actin networks at the leading edge of migrating cells.

Filopodia

Thin, finger-like sensory protrusions driven by parallel bundles of straight actin filaments at the leading edge of a migrating cell.

Myosin I

A single-headed, non-filament-forming actin motor protein with a tail that binds membrane lipids to participate in vesicle movement and cortical membrane attachment.

Myosin II

A two-headed actin motor protein with a long coiled-coil tail that assembles into bipolar thick filaments to drive muscle contraction, cytokinesis, and stress fiber contraction.

Myosin cross-bridge cycle

The cyclical interaction of myosin with actin: rigor attachment without nucleotide, release upon ATP binding, cocking via ATP hydrolysis to ADP + Pi, and power stroke execution upon Pi release.