Cell Biology Membrane Proteins Quiz

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Questions and Answers

What percentage of sequenced genes encode membrane proteins?

30% (correct)

40%

10%

20%

Which of the following diseases is associated with compromised folding of membrane proteins?

Diabetes

Heart Disease

Asthma

Cystic Fibrosis (correct)

What signaling mechanism is involved in the topology determination of single-pass membrane proteins?

Endoplasmic reticulum retention

Hydrophobic signal only

Exocytosis pathway

Positive-inside rule (correct)

What is primarily transported through vesicular traffic in cells?

Both soluble and membrane proteins Signup and view all the answers

Which type of vesicle coat is known to form football-like structures and aids in vesicle budding?

Clathrin Signup and view all the answers

What is the main fate of membrane proteins that enter the endoplasmic reticulum?

They remain in the ER via retention signals. Signup and view all the answers

In the secretory pathway, what is the typical flow of material?

Toward the exterior for modification and storage Signup and view all the answers

What is the primary role of the protein coat on vesicles?

To provide shape and capture transport molecules Signup and view all the answers

What is the primary function of peroxisomes?

Oxidation of fatty acids Signup and view all the answers

Which type of endoplasmic reticulum is primarily involved in the synthesis and processing of secretory proteins?

Rough endoplasmic reticulum Signup and view all the answers

How are proteins imported into peroxisomes?

By synthesis with PTS and translocation through a membrane channel Signup and view all the answers

What are the two types of ribosomes involved in protein synthesis?

Free ribosomes and membrane-bound ribosomes Signup and view all the answers

What is the lumen of chloroplasts referred to as?

Stroma Signup and view all the answers

What distinguishes co-translational translocation from post-translational translocation?

Co-translational starts at the ER with a signal sequence Signup and view all the answers

Which of the following compartments requires additional signal sequences for its functions?

Thylakoid Signup and view all the answers

What is a characteristic feature of peroxisomes?

They possess a single membrane and lack DNA Signup and view all the answers

What initiates the recognition process required for vesicle transport?

Rab proteins Signup and view all the answers

What is the primary function of SNARE proteins in vesicle transport?

Induce membrane fusion Signup and view all the answers

Which of the following processes begins in the endoplasmic reticulum (ER)?

Protein glycosylation Signup and view all the answers

Which sequence is correctly followed in the secretory pathway?

ER --> Golgi Apparatus --> Plasma Membrane --> External Milieu Signup and view all the answers

What triggers the retention or degradation of misfolded proteins in the ER?

Chaperones Signup and view all the answers

How does glycosylation contribute to protein functionality?

It alters protein structure, protection, and folding Signup and view all the answers

Which structure is responsible for the specificity of vesicle docking at the targeted membrane?

t-SNAREs Signup and view all the answers

What is the role of motor proteins in the transport of vesicles?

Transporting vesicles along the cytoskeleton Signup and view all the answers

What is the default behavior of proteins that enter the endoplasmic reticulum (ER)?

They move on towards the Golgi Apparatus by default. Signup and view all the answers

Which sequences are recognized as retention signals for proteins in the ER?

KDEL or KKXX Signup and view all the answers

How are proteins retrieved back to the ER if they escape to the Golgi Apparatus?

Receptors recognize them and shuttle them back. Signup and view all the answers

What is the primary function of the Golgi Apparatus?

Modification of proteins, primarily glycosylation. Signup and view all the answers

What characterizes constitutive secretion?

It is a continuous process present in all cells. Signup and view all the answers

What is the primary function of secretory vesicles in cells?

To store and release concentrated proteins Signup and view all the answers

Which component of the Golgi Apparatus faces the endoplasmic reticulum (ER)?

Cis-side Signup and view all the answers

What is the role of different enzymes in the compartments of the Golgi Apparatus?

To modify proteins as they pass through. Signup and view all the answers

What type of endocytosis is characterized by the uptake of large particles?

Phagocytosis Signup and view all the answers

Which process involves the binding of macromolecules to receptors before their uptake?

Receptor-mediated endocytosis Signup and view all the answers

Regulated secretion differs from constitutive secretion in that it is:

Dependent on a specific stimulus. Signup and view all the answers

During which process does a clathrin-coated pit lead to the formation of a vesicle?

Endocytosis Signup and view all the answers

What occurs to LDL after it is taken up through receptor-mediated endocytosis?

It dissociates from its receptor due to low pH and is transferred to lysosomes Signup and view all the answers

What is the purpose of phagocytosis in immune cells like macrophages?

To defend against pathogens and remove cellular debris Signup and view all the answers

Which of the following correctly describes ordinary pinocytosis?

It involves indiscriminate continuous uptake of fluids and solutes Signup and view all the answers

How is the increase in cell membrane volume during exocytosis compensated?

By endocytosis Signup and view all the answers

What is the role of signal sequences in protein transport?

They target proteins to a specific organelle. Signup and view all the answers

How does the nuclear pore facilitate transport?

It enables active transport of proteins and RNA. Signup and view all the answers

What is the evolutionary significance of mitochondria and chloroplasts?

They are remnants of ancient prokaryotic cells through endosymbiosis. Signup and view all the answers

What type of transport mechanism is used for large molecule movement between the cytosol and the nucleus?

Large pores Signup and view all the answers

Which organelle is involved in both protein synthesis and degradation?

Cytoplasm Signup and view all the answers

What type of proteins are imported into mitochondria?

Proteins synthesized in the cytosol and partially within mitochondria Signup and view all the answers

Which statement about organelles is correct?

Organelles have specific positions and functions in every cell. Signup and view all the answers

What is the primary function of the endoplasmic reticulum (ER)?

Protein modification and sorting Signup and view all the answers

Study Notes

Intracellular Transport Lecture Aims

Students will gain insight into how proteins and lipids are transported within a cell to reach their destinations.
Students will appreciate general principles of protein and lipid trafficking.
Students will gain mechanistic insight into the biogenesis of membrane proteins.
Students will understand the relationship between protein trafficking problems and diseases.

Course Aims

Students will be able to explain the relationship between a cell's shape and its function.
Students will be able to explain how cells combine to form tissues, using the digestive system as an example.
Students will be able to analyze histological preparations using light microscopy.
Students will be able to draw and explain the structure of organelles within a cell and their functions.
Students will be able to analyze the ultrastructure of a cell using electron microscopy data.
Students will be able to explain how intracellular proteins and lipids are transported to their designated subcellular locations.
Students will be able to describe the various signal transduction pathways and layers of organization that govern cellular processes.
Students will be able to model the connectivity of signal transduction pathways mathematically.

Lectures/Workgroups: Intracellular Transport and Exam Material

Required reading material: Essential Cell Biology (Alberts), Chapter 15 in full, and Chapter 11, pages 369-374 (4th ed.) or 375-380 (5th ed.) or 390-396 (6th ed.). Additional figures from other books may be necessary (check canvas for HC_luirink_2024).
Required workgroup preparation: Questions_workgroup_Luirink.2024.doc (on canvas).
Required workgroup reading: Nobel Prize commentaries from 1999, 2013, 2017, and 2024 (on canvas).
Required workgroup viewing: Relevant videos.

Separation of Cellular Functions

Large enzyme complexes are found in both prokaryotes and eukaryotes.
Eukaryotic cells compartmentalize enzymes within membrane-bound organelles.
How do proteins/lipids reach organelles? (Signals/receptors)
How do proteins/lipids move between organelles?
How do proteins cross organelle membranes?
How do proteins fold within an organelle?
How do proteins insert in a membrane, fold, and function within the membrane?
How is the quality of these processes controlled?

Intracellular Transport in Prokaryotes and Eukaryotes

Proteins and lipids are synthesized in the cytosol of prokaryotes, and proteins are targeted to specific locations by signal sequences.
Eukaryotic cells compartmentalize cellular functions within various organelles utilizing transport mechanisms like channels and vesicles.
Different organelles exist: chloroplast, mitochondrion, peroxisome, nucleus, endoplasmic reticulum, and Golgi complex.

Cell Organelles (EM)

Nucleus: Site of RNA/DNA synthesis.
Cytoplasm: Contains cytosol (protein synthesis/degradation) and organelles (with specialized functions).

Cell Organelles (scheme)

Organelles possess a lumen and membrane.
Lumen and membrane contain specific lipids and proteins.
Organelles have similar functions in all cells.
Organelles have distinct locations within cells.
Abundance of an organelle relates to the cell type.

Evolution of Organelles

Endoplasmic reticulum (ER), Golgi apparatus, endosomes, lysosomes, nucleus, and peroxisomes originated from the plasma membrane of anaerobic archaea by pinching off.
Mitochondria and chloroplasts originated from aerobic bacteria engulfed by anaerobic eukaryotic cells.

Transport Mechanisms

Large pores (e.g., nuclear pores) facilitate transport between the cytosol and nucleus.
Narrow channels facilitate transport across membranes between the cytosol and other organelles (ER, mitochondria, chloroplast, peroxisome).
Vesicles transport materials between the ER, Golgi apparatus, and endosomes/lysosomes/plasma membrane.

Roadmap of Protein Traffic

Proteins travel through various stages from the cytosol to the cell exterior.
Proteins travel via gated transport, transmembrane transport, or vesicular transport to their destinations.

Signal Sequences

Signal sequences (3-30 amino acids long) are targeting signals that guide proteins to specific organelles.
These signal sequences (targeting/sorting signals) are recognized by receptors in the cell, leading the protein to its destination.
These signals are necessary and sufficient for sorting.

Signal Sequence Switching

Signal sequences can be switched, allowing for the transfer of proteins between the cytoplasm and the ER.

Roadmap to Nucleus

Proteins follow a pathway from cytosol to nucleus.
The pathway involves mitochondria, peroxisomes, ER, Golgi, late endosome, lysosomes, and early endosome before reaching the cell exterior.

Import in Nucleus

Prospective nuclear proteins (cargo) are recognized through nuclear localization signals.
Nuclear import receptors bind to and transport cargo through the nuclear pores.
The nuclear pore complex transports these proteins to the nucleus.

Roadmap to Mitochondria and Chloroplasts

Proteins destined for mitochondria and chloroplasts follow a path from cytosol, nucleus, peroxisomes, and plastids to the cell exterior.

Transport into Mitochondria

Mitochondria synthesize some proteins but import others from the cytosol.
They are derived from bacteria, still containing DNA and ribosomes.
The proteins use specialized translocators in the outer and inner membranes for import.
A post-translational process is involved in translocation into the matrix and further sorting.

Import in Mitochondria

Synthesis of mitochondrial proteins occurs in the cytosol, with specific signal sequences ("mit. ss") directing proteins to the mitochondria.
Chaperones bind to these proteins, helping them to their receptor in the outer membrane.
Their signal sequence directs translocation at contact sites between the outer and inner membranes.
The protein is then pulled into the matrix by chaperones, the chaperone proteins facilitate folding within the mitochondrial matrix, and the signal sequence is removed.

Signal Sequences (Mitochondria and Chloroplasts)

The examples of signal sequences in the text represent the typical import sequences of the proteins into the cells.

Subcompartments in Chloroplasts

The lumen inside the chloroplast is called stroma.
A separate compartment called the thylakoid is present.
Different mechanisms and additional sequence signals are essential for proper targeting to the subcompartments within chloroplasts.

Roadmap to Peroxisomes

Proteins follow a pathway from cytosol, nucleus, mitochondria, and plastids to the peroxisomes, followed by the endoplasmic reticulum, Golgi, secretory vesicles, late endosome, lysosomes, and early endosome before reaching the cell exterior.

Peroxisomes

Peroxisomes are responsible for oxidizing fatty acids.
They have a single membrane that protects the cytosol, and they contain enzymes for various metabolic processes.
They contain no DNA or ribosomes.

Peroxisomal Import

Peroxisomal proteins are synthesized in the cytosol with PTS (peroxisomal targeting signals).
PTS binds to receptors in the cytosol.
The receptor-bound protein is transported through the membrane channel.
The cytosolic receptor is recycled to the cytosol.
The transport involves folded proteins.

Signal Sequences (Peroxisomes)

These examples represent the signal sequences required for targeting proteins to peroxisomes.

Roadmap to ER

Proteins follow a pathway from cytosol, nucleus, mitochondria, peroxisomes, and plastids to ER, and Golgi, late endosome, lysosomes, early endosome, and then the cell exterior.

Endoplasmic Reticulum (ER) Network

The ER forms a continuous network within the cell.

Two Types of ER

RER (rough endoplasmic reticulum): Site of protein and lipid synthesis, recognizable for its ribosomes.
SER (smooth endoplasmic reticulum): Specialised functions like detoxification, steroid hormone production, and calcium storage.

Two Sites of Protein Synthesis

Free ribosomes synthesize proteins for the cytosol, mitochondria, chloroplasts, and peroxisomes using post-translational processes.
Membrane-bound ribosomes synthesize proteins for the secretory pathway (ER, Golgi, lysosomes, endosomes, plasma membrane), with co-translational processes.

Co- versus Post-Translational Translocation

Co-translational translocation (all proteins for the secretory pathway, ER, Golgi, lysosomes, endosomes, and plasma membrane) begins at the ER with an ER signal sequence.
Post-translational translocation (proteins for mitochondria, chloroplasts, and peroxisomes) occurs after synthesis.
The process lacks an ER signal sequence.

Insertion of Single-Pass Membrane Proteins (2 signals)

A signal sequence targets the protein to the ER and a stop-transfer sequence anchors the protein in the ER membrane.
This kind of protein is inserted into the ER membrane through protein translocators.
Final topology: N-terminal in the ER lumen & C-terminal in the cytosol.

Insertion of Single-Pass Membrane Proteins (1 signal)

A single signal sequence targets the protein to the ER and anchors it in the membrane.
The topology is determined by the positive-inside rule, with the inside of the protein relating to a cytosolic location.

Insertion of Double-Pass Membrane Proteins

A hydrophobic start-transfer sequence targets the protein to the ER, followed by a hydrophobic stop-transfer sequence, allowing the protein to span the membrane twice.

Topology of Multi-Pass Membrane Proteins

Multi-pass transmembrane proteins have multiple hydrophobic segments alternating with hydrophilic segments, which act as start and stop signals.

Fate of ER Proteins

Soluble and membrane proteins residing in the ER may either remain in the ER or continue their journey through the secretory pathway.

Roadmap of Vesicular Traffic

Transport between various organelles occurs via vesicles, navigating from ER to Golgi, secretory vesicles, late endosome, lysosomes, and eventually to the cell exterior.

Two Directions in Vesicular Traffic

Endocytic pathway: Uptake of molecules from the outside.
Secretory pathway: Transport towards the outside.

Exocytosis and Endocytosis

Exocytosis: Release of molecules outside the cell.
Endocytosis: Uptake of molecules into the cell.

Characteristics of Vesicular Traffic

Transport of various proteins (soluble and membrane-bound) uses different vesicle types to ensure precise targeting.
Transport must be controlled for accuracy.

Vesicle Budding

Vesicles possess protein coats that facilitate budding and cargo selection through shaping and molecule capture.

Coat Gives Shape

Clathrin forms spherical structures ("round baskets") crucial for shaping budding vesicles.
Clathrin consists of triskelions that combine to form the framework of the coat.

Coat Selects Cargo

Specific adaptins in the clathrin coat help select cargo molecules suitable for transport.

Specificity of Transport (where do the naked vesicles go)

Vesicles move along cytoskeleton by motor proteins, directed by Rab proteins and recognized by tethering proteins.
SNAREs provide specificity for precise vesicle docking and fusion with target membranes.

SNAREs induce membrane fusion

SNAREs (v-SNARE and t-SNARE) facilitate fusion between transport vesicles and target membranes.

The 2013 Nobel Prize in Physiology or Medicine

Awarded to James E. Rothman, Randy W. Schekman, and Thomas C. Südhof for their discoveries related to vesicle transport.

Secretory Pathway

The secretory pathway begins at the ER, travels through the Golgi, then to the plasma membrane, and ultimately releases its contents outside the cell.
Transport in the pathway is executed by vesicles.
The transport involves modifications like folding, glycosylation, and quality control.

Modification, f.i. Glycosylation in Lumen of ER

Precursor oligosaccharides are attached to proteins with Asn-X-Ser/Thr motifs during protein synthesis inside the ER lumen.
Oligosaccharides are further modified and processed in the ER and Golgi, affecting protein structure.

Quality Control in the ER

The ER verifies protein folding and releases only correctly folded proteins.
Misfolded proteins remain bound to chaperones and can either become refolded or degraded.
This quality control process can be defective in diseases like cystic fibrosis.

Unfolded Protein Response (UPR)

The UPR detects unfolded proteins, triggering responses to enhance protein folding capacity in the ER.

Sorting

Proteins in the ER can either remain there or proceed to other destinations.
Proteins may remain in the ER if they have retention signals.
Proper sorting also prevents these proteins from being mistakenly packaged in vesicles.
Retention in ER occurs if the protein has targeting signals for retention (e.g., KDEL or KKXX).

Retrieval of ER Resident Proteins

ER resident proteins have KDEL or KKXX signals, allowing their retrieval from the Golgi back to the ER.

Roadmap from ER to GA

A roadmap illustrating the pathway of proteins from the ER (endoplasmic reticulum) to the Golgi.

The Golgi Apparatus, Structure

Golgi apparatus consists of stacked cisternae (flattened sacs) and tubules.
It's polarized; the cis face faces the ER, and the trans face faces the plasma membrane.

The Golgi Apparatus, Function

The Golgi primarily modifies proteins (e.g., trimming of sugars, glycosylation).

Functional Compartmentalization of the GA

The Golgi apparatus has different compartments with specialized enzymes for modifying proteins, especially glycosylation.
The CGN (cis Golgi network) and TGN (trans Golgi network) serve as sorting stations.

Roadmap of Exocytosis

Roadmap indicating the pathway for exocytosis, starting at the ER, progressing through the Golgi, and then transporting material to the cell exterior via either secretory pathway or regulated secretion.

Two Pathways of Exocytosis

Constitutive exocytosis: continuous release of proteins and lipids.
Regulated exocytosis: release triggered by specific signals delivered to the surface membrane proteins.

Secretory Vesicles

Secretory vesicles store concentrated proteins destined for extracellular release and use specific mechanisms for fusion with the plasma membrane.

Roadmap of Endocytosis

Roadmap depicting the pathway of endocytosis, beginning at the cell exterior and progressing through early endosomes, late endosomes, and eventually, lysosomes.

Endocytosis and Degradation

Phagocytosis: Uptake of larger particles.
Pinocytosis: Uptake of solutes or fluid.
Receptor-mediated endocytosis (RME): Specific uptake of molecules via receptor binding.

Endocytosis: Phagocytosis

Phagocytosis refers to the uptake of larger particles, often by specialized cells like macrophages.
The mechanism involves the binding of particles to receptors, followed by engulfment and degradation in lysosomes.

Endocytosis: Pinocytosis

Ordinary pinocytosis is a continual and nonspecific uptake of fluids and membrane into the cell.
Receptor-mediated endocytosis (RME) is a specific uptake mechanism utilizing receptors that bind to specific molecules for uptake into the cell.

Sorting in Endosomes

Early endosomes fuse and mature into late endosomes, which may merge with lysosomes.
The decreasing pH within endosomes facilitates receptor recycling and degradation of enclosed macromolecules.
Cargo is typically degraded within lysosomes.

Roadmap to Lysosomes

Proteins follow a pathway that may lead to lysosomes, starting at the ER and Golgi complex, moving to late endosome and early endosome before reaching the cell exterior.

Lysosomes

Lysosomes contain acid hydrolases for degrading macromolecules.
They maintain an acidic interior (pH ~5) to optimize the activity of these hydrolases.
They receive materials from various pathways, including endocytosis and autophagy, before degrading them.

4 Entry Pathways for Lysosomes

Materials can enter lysosomes through pinocytosis/endocytosis, phagocytosis, autophagy, and vesicular traffic from the Golgi apparatus.

Vesicular Traffic from GA to Lysosomes

Lysosomal hydrolases are tagged with M6P (mannose-6-phosphate), which targets them to lysosomes in the Golgi apparatus.
Membrane proteins in vesicles containing the lysosomal hydrolases are transported using receptors.
The phosphate is removed in the lysosome, activating the enzyme.

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Description

Test your knowledge on membrane proteins, their functions, and the processes involved in their synthesis and transport. This quiz covers key topics such as vesicular traffic, signaling mechanisms, and various protein types related to cell biology. Perfect for students studying advanced cell biology concepts.