Flashcards

Structure of Mitochondria

• Outer Membrane

  • Contains porins (proteins that form channels).

• Inner Membrane

  • Impermeable to most solutes.

• Intermembrane Space

  • Similar to the cytosol in composition.

• Matrix

  • Site of the TCA cycle (Krebs Cycle).

• Cristae

  • Invaginations that increase surface area for electron transport.

Role of Transit Sequences in Mitochondria

• Definition: N-terminal signals that direct polypeptides to mitochondria for import.

TOM and TIM Complexes in Mitochondria

• TOM (Translocase of the Outer Membrane): Facilitates the transport of proteins across the outer membrane.

• TIM (Translocase of the Inner Membrane): Transports proteins into the inner membrane and matrix.

Function of Hsp70 and Hsp60 Chaperones

• Hsp70: Binds to proteins to assist in unfolding during import.

• Hsp60: Ensures proper refolding of proteins inside the mitochondrial matrix.

TCA Cycle and Location

• Location: Occurs in the mitochondrial matrix.

• Process: Converts pyruvate to Acetyl-CoA via the pyruvate dehydrogenase complex.

Key Outputs of the TCA Cycle

• Outputs: 3 NADH, 1 FADH, and 1 GTP (which is converted to ATP).

Regulation of the TCA Cycle by NADH, ATP, and Acetyl CoA

• Inhibition: All act as allosteric inhibitors of TCA cycle enzymes.

Electron Transport Chain (ETC) Process

• Function: Transfers electrons from NADH and FADH2 to oxygen, establishing a proton gradient across the inner membrane.

Role of Complexes in the Electron Transport Chain

• Complex I:

  • Transfers electrons from NADH to Fe-S to CoQ.

  • Pumps 4 protons per electron pair.

• Complex II:

  • Transfers electrons from succinate to FADH2 and Fe-S centers to CoQ.

  • Does not pump protons.

• Complex III:

  • Transfers electrons from CoQ to cytochrome c.

  • Pumps 4 protons into the intermembrane space.

• Complex IV:

  • Transfers electrons from cytochrome c to oxygen.

  • Pumps 2 protons per electron pair, generating water.

Proton Gradient Creation by the ETC

• Mechanism: Pumps protons from the matrix into the intermembrane space, producing a proton gradient that drives ATP synthesis.

Components of ATP Synthase

• Fo Subunit:

  • Embedded in the inner membrane, acts as a proton translocator.

• F1 Subunit:

  • Located in the matrix, responsible for ATP synthesis.

Function and Changes of F1 Subunit During ATP Synthesis

• F1 Conformational Changes:

  • β subunits switch between three states: L (loose), T (tight), and O (open).

• c-ring Rotation:

  • Driven by proton flow, facilitates γ subunit rotation necessary for ATP synthesis.

ATP Yield from NADH and FADH2

• NADH: Yields 2 ATP.

• FADH: Yields 1.5-2 ATP.

• Glucose Total Yield: 30-32 ATP produced during cellular respiration.

Endomembrane System Components

• Endoplasmic Reticulum (ER):

  • Involved in protein synthesis and sorting.

• Golgi Apparatus:

  • Responsible for protein processing and sorting.

• Lysosomes:

  • Digest ingested materials and cellular components.

• Peroxisomes:

  • Involve lipid metabolism and scavenging of reactive oxygen species.

Smooth vs. Rough ER

• Smooth ER:

  • Involved in drug detoxification, carbohydrate breakdown, calcium storage, and steroid biosynthesis.

• Rough ER:

  • Responsible for membrane protein synthesis and folding.

Glycogen Breakdown Process

• Pathway:

  • Glycogen is converted to glucose-1-phosphate via glycogen phosphorylase, then transported into the ER luminal side where glucose-6-phosphatase allows glucose release back to cytosol.

Membrane Biosynthesis Process

• Synthesis:

  • Lipids synthesized in the cytosol, transferred via phospholipid translocators (flippases), and facilitated by phospholipid exchange proteins.

ER Signaling Sequence in Protein Targeting

• Function:

  • Essential for directing polypeptides to specific ER destinations, consists of 15-30 amino acids.

Signal Recognition Particle (SRP) Role in Protein Synthesis

• Function:

  • Mediates ribosome-ER contact, halting translation until binding with the rough ER, allowing translation to continue afterward.

Stop Transfer Sequences

• Definition: Hydrophobic sequences that halt protein translocation into the ER lumen, leading to integration into the ER membrane.

Start Transfer Sequences in Membrane Proteins

• Function: Internal sequences for translocating membrane proteins through the ER membrane without needing an ER signaling sequence.

Anterograde Transport

• Definition: Movement of substances towards cell membrane, involving ER membrane fusion with cell membrane to release materials.

Golgi Apparatus and Protein Processing

• Structure: Collection of flattened membrane stacks (cisternae) for glycosylation and sorting of proteins and lipids.

Retrograde Transport

• Function: Movement of vesicles from Golgi cisternae back to ER to balance lipid movement and provide materials for new vesicles.

Glycosylation

• Definition:

  • Attaching carbohydrates to proteins; critical for folding, stability, and functionality.

  • N-linked starts in the ER; O-linked occurs solely in Golgi.

COPI vs. COPII

• COPI: Involved in retrograde transport from Golgi to ER.

• COPII: Responsible for ER to Golgi material movement.

Receptor-Mediated Endocytosis Process

• Mechanism: Ligand binding triggers clathrin-coated pit formation, leading to vesicle pinching and early endosome fusion.

SNARE Proteins Function

• Role: Facilitate vesicle fusion to target membranes by binding v-SNAREs with t-SNAREs, merging lipid bilayers.

Exocytosis Process

• Definition: Moving materials out of the cell via vesicle fusion with the cell membrane to release contents outside.

Lysosomes and Cellular Digestion

• Function: Contain hydrolytic enzymes for macromolecule digestion, maintain acidic pH to activate these enzymes.

Stationary Cisternae Model of Golgi Function

• Concept: Golgi cisternae are stable, while shuttle vesicles transport materials in a cis-to-trans flow.

Mannose-6-Phosphate Role

• Function: Tags proteins for endosome and lysosome transport by binding to specific receptors in the trans-Golgi network.

Glycosylation Process in ER

• Initiation: Begins in ER with dolichol phosphate insertion and addition of mannose and GlcNAc for core oligosaccharide formation.

Unfolded Protein Response (UPR) Significance

• Function: Quality control to prevent misfolded protein accumulation by halting translation.

ARF Role in COPI Vesicle Formation

• Function: GTP-binding protein that recruits COPI coatamer for vesicle formation needed for retrograde transport.

Receptor Maturation in Early Endosomes

• Process: As early endosomes mature and pH drops, receptors separate from ligands, recycling them back to TGN.

v-SNAREs and t-SNAREs in Vesicle Targeting

• Mechanism: Key for specificity in vesicle targeting and fusion; v-SNAREs on vesicles, t-SNAREs on target membranes.

Endocytosis Definition and Mechanism

• Definition: Movement of materials into a cell via inward folding of cell membrane to form endocytic vesicles containing extracellular material.

Importance of Lysosomal Acidic Environment

• Role: Maintains pH 4-5 for hydrolytic enzyme activation for digesting cellular waste.

Cisternal Maturation Model of Golgi

• Concept: Cisternae move from CGN to TGN while unneeded enzymes undergo retrograde transport.

Chaperones in Protein Folding within the ER

• Function: Assist in protein folding and disulfide bond formation for proper structure.

Phagocytosis Process

• Definition: Engulfing of particles creating phagocytotic vacuoles, which fuse with late endosomes to become lysosomes.

Endocytic Vesicles and TGN Interaction

• Mechanism: Fuse with TGN vesicles containing acid hydrolases for material digestion.

Fate of Lysosomes Post-Digestion

• Outcome: Digestive lysosomes can exocytose indigestible materials or retain material contributing to cellular aging.

Role of Motor Proteins in Cellular Transport

• Proteins: Kinesin and dynein walk along microtubules to transport vesicles; kinesin typically moves towards the plus end, dynein towards the minus end.

Kinesins vs. Dyneins Transport Directionality

• Kinesins: Move towards the plus end (anterograde transport).

• Dyneins: Move towards the minus end (retrograde transport).

Axonemal Dyneins Structure and Function

• Structure: Heavy chains with AAA+ domains, enabling sliding of microtubules in the axoneme for bending motion.

Basal Body Significance in Cilia and Flagella

• Function: Modified centrioles templating axoneme formation for cilia and flagella structure.

Axoneme Structure in Cilia and Flagella

• Structure: 9 + 2 structure composed of 9 outer doublet microtubules and 2 central single microtubules.

Nexin's Contribution to Axoneme Movement

• Role: Connects doublets in axonemes allowing for coordinated bending instead of free sliding.

Intraflagellar Transport in Axoneme Growth

• Process: Involves kinesin transporting tubulin to axoneme tip and dynein returning subunits to the base for growth maintenance.

Myosins in Muscle Contraction

• Function: Interact with actin filaments to enable muscle contraction.

Myosins Structure and ATPase Activity

• Structure: Heavy globular head, tail with light chains regulating ATPase activity for actin binding.

Sarcomeres in Muscle Function

• Definition: Repeating units of muscle fibers with thin (F-actin) and thick (myosin) filaments, leading to muscle shortening.

H-Zone Changes During Muscle Contraction

• Observation: H-zone shrinks as thin and thick filaments slide past during contraction.

Difference Between A Bands and I Bands in Muscle Fibers

• A Bands: Dark bands with thick filaments.

• I Bands: Light bands containing only thin filaments.