Cell Biology: Protein Sorting, Vesicular Transport, and Cellular Bioenergetics

Comprehensive practice flashcards in fill-in-the-blank format covering protein sorting mechanisms, vesicular transport, cellular thermodynamics, activated carriers, glycolysis, the citric acid cycle, oxidative phosphorylation, and photosynthesis.

Small, single-membrane organelles packed with enzymes that produce and degrade hydrogen peroxide are called __________.

peroxisomes

Because sorting requires an instructional signal, a newly synthesized protein that lacks any sorting signal remains in the __________ by default.

cytosol

Because organelle interiors originated by membrane invagination from the cell surface, the lumen of the ER is topologically equivalent to the __________.

outside of the cell (or extracellular space)

Traffic of proteins between the cytosol and nucleus occurs via __________ transport through nuclear pore complexes.

gated

Unlike nuclear import, proteins undergoing transmembrane transport into mitochondria or chloroplasts must __________ to thread through narrow translocator channels.

unfold

Receptors recognise the general physical character of an ER signal sequence, which typically consists of an $N$-terminal stretch of __________ amino acids.

hydrophobic

Unlike ER and mitochondrial signal sequences, a nuclear localisation signal (NLS) is rich in lysine and arginine and is __________ following import.

kept (or retained)

Unidirectional import through nuclear pores is driven by a concentration gradient of the GTPase __________, which is maintained in its GTP-bound state inside the nucleus.

Ran (or Ran-GTP)

During co-translational translocation into the ER, the emerging $N$-terminal signal peptide is recognized by the __________, which binds the ribosome and temporarily halts translation.

signal-recognition particle (SRP)

In single-pass transmembrane proteins, translocation halts when the channel encounters a hydrophobic __________ sequence, which discharges laterally into the lipid bilayer.

stop-transfer

In the mitochondrial import pathway depicted, precursor proteins bind outer membrane receptors and are threaded through the TOM complex and the inner membrane translocator __________.

TIM

Vesicular transport enables material to travel between compartments of the endomembrane system without any cargo ever __________ a membrane.

crossing

The two critical functions of vesicle coat proteins are mechanically shaping the bud and __________ appropriate cargo molecules.

selecting (or choosing)

During clathrin-coated vesicle formation, membrane-associated cargo receptors are linked to the outer clathrin lattice by intermediate proteins called __________.

adaptins

The GTP-binding protein that forms a constricting collar around the invaginated neck of a budding vesicle to pinch it off is __________.

dynamin

A transport vesicle must shed its protein coat almost immediately after budding because the coat covers the cytosolic face and obstructs the __________ and fusion machinery.

tethering

Initial recognition between a transport vesicle and its target membrane occurs when a tethering protein captures an organelle-specific surface marker called a __________ protein.

Rab

Irreversible docking and fusion are driven when a vesicle-bound v-SNARE winds into a tight bundle with a complementary __________ on the target membrane.

t-SNARE

As a quality-control checkpoint, misfolded proteins in the ER lumen are retained by __________ and prevented from budding into transport vesicles.

chaperones

An accumulation of misfolded proteins in the ER triggers the __________, which signals the cell to enlarge the ER and produce more chaperones.

unfolded protein response (UPR)

In secretory mutant B shown in the diagram, transport out of the __________ is defective, leading to accumulation of cargo inside that organelle.

Golgi apparatus

Unlike the continuous default constitutive exocytosis pathway, regulated exocytosis holds concentrated secretory vesicles beneath the plasma membrane until triggered by an extracellular signal such as an influx of __________.

calcium ($\text{Ca}^{2+}$)

Endocytosed cargo uncouples from its receptor inside early endosomes because the internal environment is acidified by an ATP-driven __________ pump.

proton ($\text{H}^+$)

Lysosomes degrade macromolecules using a mixture of acid __________ that function optimally at an internal pH of approximately $5$.

hydrolases

The degradation pathway in which a cell sequesters its own obsolete or damaged organelles within a double-membrane enclosure for lysosomal destruction is called __________.

autophagy

Living cells obey the second law of thermodynamics by exporting disorder to their environment primarily in the form of __________.

heat

In a redox reaction, oxidation is defined strictly as the __________ of electrons, while reduction is the gain of electrons.

loss

A chemical reaction is thermodynamically spontaneous and energetically favourable only when its free-energy change, $\Delta G$, is __________.

negative ($< 0$)

The free-energy change $\Delta G$ dictates the spontaneous direction of a reaction, but provides no information regarding its __________.

speed (or rate)

An enzyme accelerates chemical reactions by lowering the __________, leaving both $\Delta G$ and the equilibrium constant unchanged.

activation energy

In living cells, an energetically unfavourable reaction is driven forward by being __________ to an energetically favourable reaction with a net negative $\Delta G$.

coupled

The three phosphate groups of an ATP molecule are joined to each other by high-energy __________ bonds.

phosphoanhydride

Under standard conditions, the hydrolysis of ATP to ADP and inorganic phosphate releases free energy with a $\Delta G^\circ$ of roughly __________ $\text{kJ/mol}$.

$$-30$$

In driving an uphill condensation reaction, ATP does not merely hydrolyse in solution; it transfers a phosphate group onto a substrate to generate a reactive, high-energy __________.

intermediate

While $\text{NADH}$ collects electrons primarily from catabolic oxidation reactions, $\text{NADPH}$ acts as an electron donor in __________ pathways.

anabolic (or biosynthetic)

Polynucleotide synthesis is driven irreversibly forward because the released __________ is rapidly hydrolysed into two inorganic phosphates.

pyrophosphate

During glycolysis in the cytosol, one six-carbon glucose molecule is broken down into two molecules of the three-carbon compound __________.

pyruvate

The net output of glycolysis per molecule of glucose is $2\,\text{pyruvate}$, $2\,\text{NADH}$, and a net gain of __________ $\text{ATP}$.

$$2$$

In the mitochondrial matrix, pyruvate dehydrogenase decarboxylates pyruvate, releasing one carbon as $\text{CO}_2$ and generating $\text{NADH}$ and __________.

acetyl CoA

Each single turn of the citric acid cycle consumes one acetyl group and produces $3\,\text{NADH}$, $1\,\text{FADH}_2$, $2\,\text{CO}_2$, and one molecule of __________.

GTP

Under anaerobic conditions, muscle or yeast cells perform fermentation not to produce additional ATP, but to regenerate __________ so glycolysis can continue.

$$\text{NAD}^+$$

Fatty acid oxidation yields more energy per gram than carbohydrate oxidation because the carbons in hydrocarbon chains are far more __________.

reduced

The outer mitochondrial membrane is permeable to all metabolites under $5000\,\text{daltons}$ because it is rich in channel-forming proteins called __________.

porins

In mitochondria, the proton-motive force driving ATP synthesis is dominated by the __________ component.

membrane potential (or voltage difference / $\Delta V$)

Electrons from $\text{NADH}$ pass through three proton-pumping respiratory complexes: NADH dehydrogenase, cytochrome c reductase, and __________.

cytochrome c oxidase

The final electron acceptor of the mitochondrial electron-transport chain is molecular oxygen, which accepts electrons and protons to form __________.

water ($\text{H}_2\text{O}$)

In the determined structure of ATP synthase shown, the membrane-embedded proton-carrying turbine is designated as the __________ rotor ring.

$$F_0$$

During chemiosmotic ATP synthesis, one full revolution of the ATP synthase central stalk drives conformation changes that synthesize and release __________ ATP molecules.

$$3$$

In oxidative phosphorylation, the electrons entering via $\text{NADH}$ yield approximately $2.5\,\text{ATP}$, whereas electrons entering via $\text{FADH}_2$ yield approximately __________ $\text{ATP}$.

$$1.5$$

Chemical uncouplers collapse the proton gradient across the inner mitochondrial membrane, causing ATP synthesis to halt while oxygen consumption and electron transport __________.

increase (or speed up)

Photosynthetic electron transport and light capture occur within the __________ membrane of the chloroplast.

thylakoid

In contrast to mitochondria, the electron-transport chain of chloroplasts pumps protons from the stroma __________ the thylakoid space.

into

Light-harvesting antenna complexes transfer absorbed photon energy by resonance transfer to a specialized pair of chlorophylls situated within the __________.

reaction centre

The electrons that replace those ejected from the special pair in photosystem II are extracted from __________ by a water-splitting enzyme.

water ($\text{H}_2\text{O}$)

In the photosynthetic Z-scheme shown, the initial light-activated electron boost occurs at __________, which pumps protons as electrons fall downhill.

photosystem II

In the chloroplast stroma, atmospheric $\text{CO}_2$ is covalently linked to ribulose 1,5-bisphosphate by the abundant enzyme __________.

Rubisco

In the Calvin cycle diagram shown, the net three-carbon sugar output produced per three entering $\text{CO}_2$ molecules is __________.

glyceraldehyde 3-phosphate

To generate a net product of one three-carbon sugar from three $\text{CO}_2$, the carbon-fixation cycle consumes $6\,\text{NADPH}$ and __________ $\text{ATP}$.

$$9$$

While the electrochemical proton gradient in mitochondria relies heavily on membrane potential ($\Delta V$), the gradient in chloroplasts is dominated by the __________ gradient.

$\text{pH}$ (or $\Delta\text{pH}$)

The catalytic $F_1$ head of mitochondrial ATP synthase projects into the matrix, whereas in chloroplasts it projects into the __________.

stroma