CBG quizlet cards

What is the process of isolating cells and growing them in culture called?

In vitro cell culture

What is the purpose of transformation in protein production?

To introduce a plasmid containing a gene of interest into bacteria.

How do we select bacteria that contain the plasmid?

By using antibiotic resistance as a selection marker.

What is the first step in protein production after selecting bacteria?

Grow bacteria in a liquid suspension.

What is the purpose of cell lysis in protein purification?

To isolate the bacteria and release the proteins.

What is the final step in protein purification?

Analyze the purity of the protein.

What is GFP and its significance in cell biology?

Green fluorescent protein used to track bacteria and study protein interactions.

What is the role of the nucleus in a cell?

To isolate and protect the genome.

What occurs in the nucleolus?

Ribosome biogenesis.

What is the difference between rough and smooth endoplasmic reticulum?

RER has ribosomes and synthesizes proteins; SER lacks ribosomes and synthesizes lipids.

What is the function of the Golgi apparatus?

To sort, package, and send proteins and lipids to their destinations.

What is the role of lysosomes in a cell?

To act as the waste disposal center, containing enzymes to break down proteins.

What do endosomes do?

Sort proteins for degradation and recycling.

What is the function of peroxisomes?

To perform oxidative reactions using molecular O2 and produce hydrogen peroxide.

What are plastids and their function?

Double membrane-bound organelles involved in generating ATP.

What is the nuclear pore complex?

A structure that regulates transport in and out of the nucleus.

What is the Ran cycle's role in nuclear transport?

It controls the transport of proteins through the nuclear pore complex.

What is gated transport?

Transport through the nuclear pore complex that is selective for specific molecules.

What are importins and exportins?

Proteins that bind cargo and shuttle it through the nuclear pore.

What is the significance of the nuclear localization signal (NLS)?

It is required for proteins to be imported into the nucleus.

What happens to Ran GTP in the cytoplasm?

It is hydrolyzed to Ran GDP by Ran GAP.

What is transmembrane transport?

Movement of proteins from the cytosol to specific organelles via membrane-bound translocators.

What is the role of signal sequences in protein transport?

They direct proteins to their specific locations within the cell.

What happens to proteins that do not have signal sequences?

They remain in the cytosol.

What is the secretory pathway?

The pathway through which proteins are synthesized in the ER and secreted from the cell.

Who discovered intrinsic signal sequences in proteins?

Gunter Lobo.

What is the primary function of the rough endoplasmic reticulum?

To synthesize and modify proteins destined for secretion or membrane insertion.

What is the role of karyopherins in nuclear transport?

They are nuclear transport receptors that recognize nuclear localization signals.

What are signal sequences?

Contiguous or discontiguous sequences that direct proteins to the endoplasmic reticulum (ER).

What is the role of signal peptides?

They direct the synthesis of polypeptide chains to the endoplasmic reticulum.

What is the significance of the N-terminal in signal sequences?

It is typically hydrophobic and polar, indicating the protein's destination to the ER.

What is co-translational translocation?

The process where protein synthesis occurs simultaneously with its translocation into the ER.

What is post-translational translocation?

The process where the polypeptide chain is synthesized in the cytosol and then directed to the ER.

What is the function of the signal recognition particle (SRP)?

It recognizes the signal sequence and pauses translation until the ribosome is directed to the SRP receptor.

What is the SEC translocon?

A protein complex that facilitates the translocation of polypeptides across the ER membrane.

What is the role of BIP in post-translational translocation?

BIP binds to the nascent polypeptide chain in its ADP-bound state to prevent degradation and assist in translocation.

What are the characteristics of the SEC translocon pore?

It is heterotrimeric, has a passive pore, an aqueous channel, and is lined with hydrophobic residues.

How does the signal sequence affect membrane protein integration?

The N-terminal ER signal sequence initiates translocation, while a stop-transfer sequence discharges the protein into the lipid bilayer.

What are the two models of protein movement through the Golgi apparatus?

The vesicular transport model and the cisternal maturation model.

What is the purpose of KDEL signal sequences?

They direct proteins back to the ER to prevent depletion of ER resident proteins.

What is the function of chaperone proteins in the ER?

They assist in folding luminal ER membrane proteins and ensure proper exit signals are recognized.

What are the three types of vesicle coats?

COPII (from ER), COPI (from Golgi), and clathrin (from plasma membrane).

What initiates the bending of the ER membrane during vesicle budding?

The binding of SAR1 to GTP causes a conformational change that alters membrane curvature.

What happens during vesicle fusion?

The vesicle membrane fuses with the target compartment, releasing its contents.

What is the role of coat proteins during vesicle budding?

They concentrate cargo, create mechanical forces for membrane curvature, and select cargo for transport.

How does the translocon interact with the ribosome during translocation?

Binding of the translocon to the ribosome causes a conformational change that opens the pore for the polypeptide chain.

What is the significance of the helical plug in the SEC translocon?

It blocks the pore when closed, preventing passage until the translocation process begins.

What is the function of the SEC 63 complex?

It hydrolyzes ATP to assist in the translocation of polypeptides through the SEC translocon.

What is the role of the start-transfer sequence in membrane proteins?

It initiates the translocation process and is cleaved off by a peptidase after integration.

What is the importance of the first transmembrane helix?

It determines the orientation of the polypeptide chain as it passes through the SEC translocon.

What happens to proteins lacking a signal sequence?

They remain in the cytoplasm and do not enter the endoplasmic reticulum.

What is the function of the helical signal sequence during translocation?

It allows the signal to pass laterally into the membrane for processing.

What is the purpose of tracking experiments with VSVDG?

To understand the post-translational modifications and trafficking pathways of proteins.

What is the outcome of GTP hydrolysis in vesicle transport?

It triggers the encoding of the inner and outer coat of the vesicle.

What is the role of GDP and GTP in the protein SAR1?

The exchange of GDP for GTP causes a conformational change in SAR1, triggering ER membrane deformation and vesicle budding.

What is the structure of Clathrin?

Clathrin is composed of triskelions, which consist of heavy and light chains that associate to form a spider-like structure.

What process does dynamin facilitate during vesicle budding?

Dynamin wraps around the neck of the vesicle and, powered by GTP hydrolysis, constricts to pinch off the vesicle.

Why is vesicle fusion energetically unfavorable?

Vesicle fusion requires breaking lipid barriers to mix contents, which is energetically demanding.

What is the main protein machinery responsible for vesicle fusion?

Snares (v-SNAREs and t-SNAREs) are responsible for vesicle fusion and ensuring specificity.

How do Snares ensure specificity in vesicle fusion?

Snares have highly specific interactions that prevent mixing and matching, ensuring correct vesicle targeting.

What is the role of alpha-SNAP in recycling Snares?

Alpha-SNAP binds to the helical complex of Snares and, powered by ATP hydrolysis, frees the v-SNARE and t-SNARE.

What initiates the assembly of vesicle coats?

GTPase proteins, specifically Sar1 and Arf1, initiate the assembly of vesicle coats.

What are the four major roles of the cytoskeleton?

Cell shape, intracellular traffic, cell division, and motion.

What are the three core filaments of the cytoskeleton?

Intermediate filaments, microfilaments (actin), and microtubules.

What is dynamic instability in microtubules?

Dynamic instability refers to the rapid assembly and disassembly of microtubules, requiring GTP.

What is the function of myosins?

Myosins are motor proteins that move along actin filaments.

What is treadmilling in actin filaments?

Treadmilling is the process where actin filaments grow faster at the positive end and disassemble at the negative end.

What is the significance of polarity in filament dynamics?

Polarity allows for directional growth and stability in filament assembly and disassembly.

What is the role of kinesins and dyneins in microtubule transport?

Kinesins move toward the plus end, while dyneins move toward the minus end of microtubules.

What is the structure and function of intermediate filaments?

Intermediate filaments are 10 nm, elongated, rope-like structures that provide mechanical strength and flexibility.

What is keratin's role in epithelial cells?

Keratin provides strength and absorbs mechanical stress in epithelial cells.

What is the extracellular matrix?

A complex network of polysaccharides, glycan, and proteins secreted by cells to strengthen tissue.

What types of cell junctions are there?

Tight junctions, adherent junctions, gap junctions, desmosomes, and hemidesmosomes.

What are cadherins and integrins?

Cadherins are adhesion molecules that mediate cell-cell adhesion, while integrins mediate cell-extracellular matrix adhesion.

What is the basal lamina?

A layer of the extracellular matrix that provides structural support and anchorage for epithelial cells.

What is the significance of the apical and basal faces of epithelial cells?

The apical and basal faces have different biochemical environments, allowing for polarized functions.

What is the role of actin-binding proteins?

Actin-binding proteins stabilize actin filaments and regulate their assembly and disassembly.

How does ATP binding affect motor protein movement?

ATP binding initiates movement by causing conformational changes in the motor protein's structure.

What is the role of accessory proteins in actin dynamics?

Accessory proteins like profilin and cofilin regulate actin polymerization and depolymerization.

What are tight junctions?

Seals neighboring cells together in an epithelial sheet to prevent leakage of molecules.

What is the function of adherens junctions?

Joins an actin bundle in one cell to a similar bundle in a neighboring cell.

What do desmosomes do?

Join intermediate filaments in one cell to those in a neighboring cell.

What is the role of gap junctions?

Forms channels that allow small water-soluble molecules, including ions, to pass from cell to cell.

What do hemidesmosomes anchor?

Anchor intermediate filaments in a cell to the basal lamina.

What are cell adhesion molecules (CAMs)?

Proteins that mediate adhesion between cells, such as cadherins and integrins.

How do cadherins function at adherens junctions?

They bind calcium-dependent, rigidifying cadherin oligomers and connect to the actin cytoskeleton.

What is the structure of integrins?

Transmembrane proteins made up of alpha and beta subunits, existing in two conformations.

What happens to integrins upon ligand engagement?

They change conformation to an elongated shape, impacting the separation of cytoplasmic tails.

What is the role of collagen in connective tissue?

Provides tensile strength and is produced in fibroblasts.

What is the structure of collagen?

Triple-stranded helical structure rich in proline and glycine.

What do fibronectin and integrin do?

Help attach the cytoskeleton to the extracellular matrix.

What are proteoglycans?

Extracellular proteins linked to negatively charged polysaccharides that help resist compression forces.

What are the four major routes for cell signaling?

Autocrine, juxtacrine, paracrine, and endocrine.

What is autocrine signaling?

Self-stimulation, e.g., interleukin-2 from a stimulated T cell.

What is juxtacrine signaling?

Direct contact signaling via membrane-bound ligands.

What is paracrine signaling?

Local signaling between neighboring cells.