The Endomembrane System, Protein Sorting, and Aerobic Respiration

Comprehensive practice flashcards in vocabulary format covering Chapter 12 (The Endomembrane System and Protein Sorting) and Chapter 10 (Chemotrophic Energy Metabolism: Aerobic Respiration) from Becker's World of the Cell.

Endomembrane System

An interconnected network of internal eukaryotic membranes—including the endoplasmic reticulum, Golgi complex, endosomes, and lysosomes (as well as peroxisomes, which receive membrane from the ER)—that functions in protein and lipid synthesis, trafficking, processing, and degradation.

Rough Endoplasmic Reticulum (RER)

The subdomain of the endoplasmic reticulum studded with ribosomes on its cytosolic surface, responsible for the cotranslational synthesis and processing of membrane-bound and soluble proteins, multimeric assembly, chaperone-assisted folding, and initial N-linked glycosylation.

Smooth Endoplasmic Reticulum (SER)

The ribosome-free subdomain of the endoplasmic reticulum specialized for drug and xenobiotic detoxification via hydroxylation, carbohydrate metabolism (hydrolysis of glucose-6-phosphate by glucose-6-phosphatase), calcium storage, and steroid/cholesterol biosynthesis.

Molecular Chaperones

A family of proteins (also known as heat shock proteins, including Hsp70 and Hsp60) that facilitate the proper folding of nascent or misfolded polypeptide chains into their functional three-dimensional conformations through cycles of substrate binding and ATP hydrolysis.

BiP (Binding Protein)

An abundant member of the Hsp70 chaperone family residing in the ER lumen that binds to exposed hydrophobic regions of nascent polypeptides to prevent premature aggregation and uses ATP hydrolysis to drive polypeptide translocation into the ER lumen via a ratchet-like mechanism.

Unfolded Protein Response (UPR)

An ER quality control signaling pathway activated when sensor molecules in the ER membrane detect accumulated misfolded proteins, resulting in a general shutdown of protein translation alongside selective transcriptional upregulation of chaperones and degradation machinery.

ER-Associated Degradation (ERAD)

A quality control mechanism that detects improperly folded or unassembled proteins in the endoplasmic reticulum, exports (retrotranslocates) them across the ER membrane into the cytosol, and targets them for ubiquitination and degradation by proteasomes.

Proteasome

A large ($720\,\text{kDa}$) cylindrical multicatalytic protein complex located in the cytosol (free or attached to the rough ER) and nucleus that recognizes polyubiquitinated target proteins, cleaves off ubiquitin for recycling, and hydrolyzes the target polypeptide into short peptides.

Cytochrome P-450

Family of enzymes located in the smooth ER catalyzes the degration of hydrophobic drugs and xenobiotics to increase excretion in the urine.

Phospholipid Translocators (Flippases)

Membrane-bound enzymes that flip newly synthesized lipids from the cytosolic to the lumenal of the membrane, maintaining lipid asymmetry between membrane leaflets.

Phospholipid Exchange Proteins

Carrier proteins that recognize and convey specific phospholipid molecules through the aqueous cytosol from the ER to organelles that do not receive vesicles directly, such as mitochondria, chloroplasts, and peroxisomes.

Golgi Stack

A localized series of usually three to eight flattened, membrane-bounded cisternae organized with distinct polarity into a Golgi network for sequential protein processing, sorting, and packaging.

Anterograde Transport

The directional vesicular movement of lipids and membrane proteins from the rough ER, through the cis- to trans-cisternae of the Golgi complex, toward the plasma membrane or secretory granules.

Retrograde Transport

The backward flow of transport vesicles from Golgi cisternae back to earlier cisternae and the ER, balancing membrane flow toward the plasma membrane and retrieving escaped ER-resident proteins and vesicle-forming components.

Cisternal Maturation Model

A model of intra-Golgi trafficking proposing that individual Golgi cisternae gradually mature and progress physically from the cis-Golgi network to the trans-Golgi network, while resident Golgi enzymes are continuously shuttled backward via retrograde transport vesicles.

N-Linked Glycosylation

The addition of a pre-assembled oligosaccharide core to the nitrogen atom of an asparagine residue on a nascent polypeptide, which begins in the rough ER and is subsequently trimmed and modified in the Golgi apparatus.

O-Linked Glycosylation

The posttranslational addition of carbohydrate units to the oxygen atom of the hydroxyl group of specific serine or threonine residues within a polypeptide, occurring primarily in the Golgi complex.

Dolichol Phosphate

A long-chain polyisoprenoid lipid embedded in the rough ER membrane that serves as the membrane carrier upon which the core oligosaccharide (consisting of N-acetylglucosamine, mannose, and glucose) is assembled before transfer to a protein.

Protein Splicing

A posttranslational modification wherein internal peptide sequences called inteins are excised autocatalytically from a polypeptide precursor, and the flanking sequences called exteins are ligated together to form a mature, functional protein.

Preproinsulin

The primary translation precursor of insulin containing an N-terminal signal sequence (pre-amino acids) that is cleaved upon translocation into the ER to yield proinsulin, which undergoes disulfide bond formation before the internal pro-amino acids (C-peptide) are cleaved to produce mature insulin.

Cotranslational Import

The mechanism by which ribosomes synthesizing polypeptides destined for the endomembrane system or cell export attach to the ER membrane early during translation, threading the elongating polypeptide across the membrane through a translocon as synthesis occurs.

Posttranslational Import

The uptake of completed polypeptides synthesized on free cytosolic ribosomes into organelles—such as mitochondria, chloroplasts, peroxisomes, or the nuclear interior—mediated by specific organelle-targeting signal sequences after translation is finished.

Signal Recognition Particle (SRP)

A cytosolic ribonucleoprotein complex consisting of six proteins and an RNA that recognizes and binds the hydrophobic N-terminal ER signal sequence of a nascent polypeptide, arrests translation, and docks the ribosome to an SRP receptor on the ER membrane.

Stop-Transfer Sequence

A hydrophobic internal sequence of amino acids in a nascent polypeptide that halts its translocation through the ER translocon and diffuses laterally into the lipid bilayer, anchoring the protein as a permanent single-pass or multi-pass transmembrane segment.

KDEL Sequence

A conserved carboxyl-terminal tetrapeptide retrieval sequence (Lys-Asp-Glu-Leu) present on soluble lumenal ER-resident proteins that triggers their binding to KDEL receptors in the Golgi complex for retrograde vesicular return to the ER.

Mannose-6-Phosphate (M6P) Tag

A phosphorylated carbohydrate sorting tag added to soluble lysosomal hydrolases within the Golgi complex that is recognized by mannose-6-phosphate receptors (MPRs) in the TGN, directing their delivery into late endosomes and lysosomes.

Transit Sequence

A specialized targeting sequence located at the N-terminus of nuclear-encoded polypeptides destined for mitochondria or chloroplasts that directs posttranslational import across the organellar membranes before being cleaved by an internal transit peptidase.

Polarized Secretion

The spatially restricted exocytosis of secretory vesicle contents to a specific surface domain of an asymmetric cell, such as the exocytosis of digestive zymogens from pancreatic acinar cells strictly into the duct leading to the intestine.

SNARE Proteins

Complementary membrane-anchored proteins (vesicle v-SNAREs and target t-SNAREs) that interlock into a four-helix coiled-coil bundle to drive vesicle docking and lipid bilayer fusion, which are later dissociated by NSF and SNAPs.

Phagocytosis

A specialized form of endocytosis by which solid particles or invasive microorganisms are engulfed by cell surface pseudopods to form large phagocytic vacuoles (phagosomes), which mature into lysosomes for enzymatic breakdown.

Clathrin Triskelion

The three-legged multimeric protein complex consisting of three clathrin heavy chains and three light chains radiating from a central vertex that polymerizes into hexagonal and pentagonal lattices to sculpt flat membranes into coated transport vesicles.

Dynamin

A cytosolic GTPase that polymerizes into a helical collar around the invaginating neck of a coated pit at the plasma membrane, constricting and severing the membrane upon GTP hydrolysis to release the coated vesicle.

Transcytosis

A vesicular trafficking process in which internalized receptor-ligand complexes bypass degradation in lysosomes and are instead transported across the cytoplasm to fuse with the opposite plasma membrane surface, releasing their cargo into a different extracellular compartment.

Autophagy

The cellular degradation pathway that breaks down aged, excess, or damaged intracellular components and organelles, either by enveloping them in an ER-derived double membrane (macrophagy to form an autophagosome) or directly enclosing small volumes (microphagy) prior to lysosomal fusion.

Acrosome

A specialized lysosome-derived organelle covering the head of a sperm cell that releases digestive acid hydrolases during the acrosome reaction to degrade the outer protective coats of the oocyte during fertilization.

Peroxisome

A single-membrane-bounded organelle containing oxidases that generate toxic hydrogen peroxide ($\text{H}_2\text{O}_2$) during the catabolism of fatty acids, D-amino acids, and xenobiotics, and abundant catalase to degrade $\text{H}_2\text{O}_2$ into water and oxygen.

Catalase

The defining peroxisomal enzyme that catalyzes the decomposition of hazardous hydrogen peroxide into molecular oxygen and water via the reaction $2\text{H}_2\text{O}_2 \rightarrow \text{O}_2 + 2\text{H}_2\text{O}$, thereby protecting the cell against oxidative damage.

Aerobic Respiration

The complete oxidation of organic fuel molecules to $\text{CO}_2$ coupled to the transfer of electrons through a membrane-bound respiratory chain to molecular oxygen ($\text{O}_2$) as the terminal electron acceptor, driving oxidative phosphorylation to generate up to $38\,\text{ATP}$ per glucose.

Porins (Mitochondrial)

Transmembrane channel proteins localized in the outer mitochondrial membrane that form large aqueous pores, allowing unrestricted passive diffusion of small hydrophilic molecules, metabolites, and ions up to a molecular weight of approximately $5000\,\text{Da}$.

Cristae

Extensive invaginations of the inner mitochondrial membrane connected to the inner boundary membrane via narrow cristae junctions, which provide a high surface area rich in electron transport chain complexes and $F_oF_1$ ATP synthases.

Pyruvate Dehydrogenase (PDH) Complex

A massive multienzyme complex (~$4.6\times 10^6\,\text{Da}$) in the mitochondrial matrix composed of three catalytic enzymes ($E_1, E_2, E_3$), five coenzymes, and regulatory proteins that converts pyruvate, $\text{NAD}^+$, and $\text{CoA-SH}$ into acetyl CoA, $\text{CO}_2$, and NADH.

Citric Acid Cycle (TCA / Krebs Cycle)

An eight-step cyclic pathway in the mitochondrial matrix that oxidizes the two-carbon acetyl group of acetyl CoA to two molecules of $\text{CO}_2$, conserving liberated energy as three NADH, one $\text{FADH}_2$, and one ATP (or GTP) per turn.

Amphibolic Pathway

A metabolic pathway that operates in both energy-yielding catabolic breakdown and biosynthetic anabolism; for example, the citric acid cycle oxidizes fuels while supplying intermediates such as $\alpha$-ketoglutarate, oxaloacetate, and succinyl CoA for amino acid and heme synthesis.

Beta-Oxidation (beta-oxidation)

A cyclic pathway in the mitochondrial matrix that breaks down fatty acyl CoA by successively cleaving two-carbon units from the carboxyl end as acetyl CoA, generating one molecule of $\text{FADH}_2$ and one molecule of NADH per cycle.

Coenzyme Q (Ubiquinone)

The only non-protein electron carrier in the mitochondrial electron transport chain; a hydrophobic, lipid-soluble benzoquinone that diffuses freely within the inner mitochondrial membrane to collect electrons from Complexes I and II and shuttle them to Complex III.

Standard Reduction Potential ($E_0^{\prime}$)

A quantitative electrochemical measure in volts ($\text{V}$) of the affinity of a redox pair for electrons under standard biological conditions, calibrated against the reference half-cell reaction $2\text{H}^+ + 2e^- \rightarrow \text{H}_2$ ($0.00\,\text{V}$ at $\text{pH } 0.0$, $-0.42\,\text{V}$ at $\text{pH } 7.0$).

Respiratory Complex I (NADH-Coenzyme Q Oxidoreductase)

An inner mitochondrial membrane respiratory assembly containing 43 polypeptides, FMN, and iron-sulfur (Fe-S) centers that accepts $2\,e^-$ from NADH, passes them to coenzyme Q, and pumps $4\,\text{H}^+$ from the matrix into the intermembrane space.

Respiratory Complex II (Succinate-Coenzyme Q Oxidoreductase)

An inner mitochondrial membrane respiratory complex containing succinate dehydrogenase, bound FAD, and Fe-S centers that transfers $2\,e^-$ from succinate to coenzyme Q without any accompanying proton translocation across the membrane.

Respiratory Complex III (Coenzyme Q-Cytochrome c Oxidoreductase)

An 11-polypeptide inner mitochondrial membrane complex containing cytochromes $b$ and $c_1$ and an Fe-S center that accepts electrons from $\text{CoQH}_2$ via the Q cycle and delivers them to cytochrome $c$, translocating $4\,\text{H}^+$ per electron pair across the membrane.

Respiratory Complex IV (Cytochrome c Oxidase)

The terminal respiratory complex composed of 13 polypeptides, cytochromes $a$ and $a_3$, and two copper centers that passes four electrons from reduced cytochrome $c$ to molecular oxygen ($\text{O}_2$) to form two $\text{H}_2\text{O}$, while pumping $2\,\text{H}^+$ per electron pair into the intermembrane space.

Chemiosmotic Coupling Model

The fundamental concept formulated by Peter Mitchell in 1961 proposing that the exergonic transfer of electrons down the respiratory chain drives directional proton pumping across a selectively impermeable membrane, generating an electrochemical proton gradient (proton-motive force) that drives ATP synthesis.

Respiratory Control

The physiological mechanism by which the rate of mitochondrial electron transport and substrate oxidation is tightly regulated by the cellular availability of ADP, stimulating electron flow when ADP concentrations are high and suppressing it when ADP is low.

Fo Complex

The hydrophobic, oligomycin-sensitive transmembrane domain of ATP synthase that acts as a proton translocator, composed of a static component (one $a$ subunit forming two proton half-channels and two $b$ stator subunits) and a rotating ring of 10 $c$ subunits.

F1 Complex

The hydrophilic catalytic headpiece of ATP synthase that projects into the mitochondrial matrix, consisting of a catalytic ring of alternating $\alpha$ and $\beta$ subunits ($\alpha_3\beta_3$) immobilized by the $\delta$ stalk, surrounding a central rotating stalk made of $\gamma$ and $\varepsilon$ subunits.

Binding Change Model

Paul Boyer's rotary catalysis model explaining that proton translocation through $F_o$ forces the central $\gamma$ subunit to rotate within the $\alpha_3\beta_3$ ring, driving sequential conformational transitions (Open [O], Loose [L], and Tight [T]) in the three catalytic $\beta$ subunits to synthesize and release ATP.