Cell Biology: Proteins, Organelles, and Transport Mechanisms Flashcards

Vocabulary flashcards covering protein structure, bioenergetics, mitochondrial function, nuclear transport, organelle protein sorting, vesicular trafficking, and protein degradation.

Peptide Bond

A planar, trans covalent bond formed between the carboxyl group of one amino acid and the amino group of another through a dehydration reaction, stabilized by resonance.

Primary Structure

The linear sequence of amino acids in a polypeptide chain.

Alpha-helix ($\alpha$-helix)

A common secondary protein structure stabilized by hydrogen bonds within the polypeptide backbone, with side chains projecting outward from the helix axis.

Beta-sheet ($\beta$-sheet)

A secondary protein structure formed by hydrogen bonds between backbone atoms of adjacent extended polypeptide strands.

Tertiary Structure

The overall three-dimensional spatial conformation of a single polypeptide chain.

Quaternary Structure

The three-dimensional arrangement formed by the assembly of multiple distinct polypeptide subunits.

Domain

A distinct structural and functional unit within a single polypeptide chain that can fold and function independently.

Subunit

An individual polypeptide chain that interacts with other chains to form a quaternary protein complex.

Porin

A channel protein found in the outer mitochondrial membrane that permits free diffusion of molecules smaller than approximately $1000\,\text{daltons}$.

Chemiosmotic Theory

The concept proposed by Peter Mitchell stating that ATP synthesis is driven by an electrochemical proton ($H^+$) gradient generated across a membrane by electron transport.

ATP Synthase ($F_1F_0$ ATPase)

A reversible membrane protein complex consisting of a transmembrane proton carrier ($F_0$) and a catalytic head ($F_1$) that converts an electrochemical proton gradient into ATP.

Endosymbiont Hypothesis

The evolutionary proposal that mitochondria originated approximately 2 billion years ago when an early anaerobic eukaryote engulfed an aerobic prokaryote.

TOM Complex

The Translocase of the Outer Membrane that recognizes N-terminal presequences and translocates proteins across the outer mitochondrial membrane.

TIM Complex

The Translocase of the Inner Membrane responsible for importing proteins across or inserting them into the inner mitochondrial membrane.

Peroxisome

A single-membrane organelle containing enzymes involved in oxidation and detoxification reactions, such as the breakdown of hydrogen peroxide ($H_2O_2$), alcohol, and fatty acids.

Signal Hypothesis

The model proposing that protein targeting to the endoplasmic reticulum requires an N-terminal signal sequence and occurs co-translationally.

Signal Recognition Particle (SRP)

A cytosolic ribonucleoprotein complex that binds the ER signal sequence, temporarily arrests translation elongation, and targets the ribosome-nascent chain complex to the ER membrane.

Translocon

The membrane-bound protein-conducting channel through which nascent polypeptide chains pass into the ER lumen or membrane.

Stop-Transfer Signal

A hydrophobic \n\alpha-helical sequence that stops translocation through the translocon and anchors the polypeptide as a transmembrane domain.

BiP (ER Hsp70)

An ER lumenal chaperone protein that assists in the folding and refolding of newly translocated proteins.

Protein Disulfide Isomerase (PDI)

An ER enzyme that catalyzes the formation, cleavage, and reshuffling of covalent disulfide ($S-S$) bonds to achieve proper tertiary structure.

Dolichol Phosphate

A specialized lipid carrier in the ER membrane on which a 14-sugar oligosaccharide precursor is assembled before transfer to an asparagine residue.

ER-Associated Degradation (ERAD)

A quality-control mechanism wherein persistently misfolded ER proteins are retro-translocated into the cytosol, ubiquitinated, and degraded by the proteasome.

Unfolded Protein Response (UPR)

A cellular stress signaling pathway triggered by the accumulation of unfolded or misfolded proteins in the ER, leading to increased transcription of ER chaperones.

Flippase (Scramblase)

An ER membrane enzyme that translocates phospholipids bidirectionally between lipid bilayer leaflets to maintain symmetric membrane growth.

KDEL Signal

A C-terminal amino acid sequence (Lys-Asp-Glu-Leu) that targets soluble lumenal ER proteins for retrieval from the Golgi back to the ER.

Mannose-6-Phosphate (M-6-P)

A specific carbohydrate modification added in the cis-Golgi network that targets acid hydrolases to lysosomes.

Clathrin

A coat protein with a triskelion structure that self-assembles into a polyhedral cage to drive vesicle budding during endocytosis and Golgi export.

Dynamin

A GTPase protein that forms a ring around the neck of a budding coated pit and pinches off the transport vesicle.

Rab Proteins

A family of small monomeric GTPases that act as molecular tags on transport vesicles to ensure correct targeting and docking with target membranes.

SNARE Proteins

A family of complementary membrane proteins (v-SNAREs and t-SNAREs) that interact to form helical bundles, driving membrane fusion.

Lysosome

A membrane-bound organelle containing acid hydrolases maintained at acidic pH ($\approx 5$) by an ATP-driven proton pump, responsible for degrading macromolecules.

Autophagy

A degradation pathway where damaged organelles or cytosolic regions are sequestered in an ER-derived autophagosome and delivered to lysosomes.

Nuclear Envelope

A double-membrane barrier enclosing the nucleus, composed of inner and outer nuclear membranes separated by a perinuclear space and pierced by nuclear pores.

Nuclear Lamina

A fibrous meshwork underlying the inner nuclear membrane composed of lamin intermediate filaments, providing mechanical support and chromatin attachment sites.

Hutchinson-Gilford Progeria

A genetic condition caused by a deletion in exon 11 of the LMNA gene that leads to aberrant splicing, accumulation of mutant lamin A, and premature aging.

Nuclear Localization Signal (NLS)

A specific amino acid motif, such as the basic PKKKRKV sequence in SV40 T-antigen, that directs proteins for import into the nucleus.

Importin

A nuclear transport receptor that binds NLS-containing cargo proteins in the cytoplasm and facilitates their entry through the nuclear pore complex.

Ran GTPase

A small monomeric GTPase whose GDP/GTP bound state dictates the binding and release of cargo by importins and exportins across the nuclear pore.

Chaperones

Proteins that assist in the correct folding of un-folded or misfolded polypeptide chains by binding exposed hydrophobic regions.

Chaperonin (GroEL/ES System)

A large, barrel-shaped chaperone complex (Hsp60-like) that isolates unfolded proteins inside a central cavity to allow ATP-dependent refolding.

Prion

An infectious protein that can induce normal PrP proteins to adopt a misfolded, toxic, self-propagating conformation without involving nucleic acids.

Ubiquitin

A conserved 76-amino-acid protein attached covalently to target proteins as a marker for degradation.

E3 Ubiquitin Ligase

An enzyme in the ubiquitination pathway that recognizes specific degradation signals on target proteins and mediates the transfer of ubiquitin from E2.

Proteasome

A barrel-shaped cytosolic protease complex that recognizes polyubiquitinated proteins and degrades them into short peptides in an ATP-dependent manner.