Cell bio (organelles/cytoskeleton/secretion/signaling)

Question 1

What are the key differences between prokaryotes and eukaryotes?

Answer 1

Nucleus, DNA type/location, mitochondria, and ribosomes.

Question 2

List the steps of the nonsecretory pathway:

Answer 2

Synthesis of proteins lacking an ER signal sequence is completed on free ribosomes (step 1 ). Those proteins that contain no targeting sequence are released into the cytosol and remain there (step 2 ). Proteins
with an organelle-specific targeting sequence (pink) are first released into the
cytosol (step 2 ) but are then imported into mitochondria, chloroplasts, peroxisomes, or the nucleus.

Question 3

List the steps of the secretory pathway:

Answer 3

Ribosomes synthesizing nascent proteins in the secretory pathway are directed to the rough endoplasmic reticulum (ER) by an ER signal
sequence (pink; steps 1 and 2 ). After translation is completed on the ER, these proteins can move via transport vesicles to the Golgi complex (step 3 ). Further sorting delivers proteins either to the plasma membrane or to lysosomes.

Question 4

What is the default fate of a nontagged protein?

Answer 4

Unless tagged or targeted, proteins will otherwise stay in the cytosol.

Question 5

What is PTS1?

Answer 5

The Peroxisomal Targeting Sequence (PTS1) is composed of the sequence Ser-Lys-Leu (SKL) at the carboxy terminus. This small tag ensures that the proteins carrying it are shuttled to the peroxisomes, where they will perform their designated functions.

Question 6

What is NLS?

Answer 6

Nuclear Localization Signal (NLS) is characterized by highly basic sequences interspersed with hydrophobic segments. This signal is a targeting motif to the nucleus, guiding proteins through the nuclear pore complexes and into the cell’s command center.

Question 7

What is MTS?

Answer 7

Mitochondrial Targeting Signal (MTS), found at the N-terminus, spans 10 to 70 amino acids and forms an amphipathic helix. This unique structure, with alternating hydrophobic and positively charged amino acids, navigates the protein to the mitochondria.

Question 8

What is the ER signal sequence?

Answer 8

The ER signal sequence or signal peptide. This sequence directs the protein to the endoplasmic reticulum (ER) for proper folding, modification, and transport to other organelles like the lysosomes. The signal peptide is a stretch of 5-30 hydrophobic amino acids at the N-terminus of the nascent protein. The signal peptide is recognized by the signal recognition particle (SRP) during translation in the cytosol, which pauses translation and directs the ribosome-protein complex to the ER membrane. The protein is then translocated into the ER, and the signal peptide is usually cleaved off by signal peptidase.

Question 9

What is the ER retention signal?

Answer 9

KDEL

Lys-Asp-Glu-Leu

Protein tagged KDEL at or near carboxy terminus

Question 10

What is the lysosome targeting signal?

Answer 10

the addition of mannose-6-phosphate

Lysosomal Targeting Signal involves the addition of mannose 6-phosphate (M6P) to proteins in the cis-Golgi.

This modification directs proteins to the lysosomes by binding to mannose-6-phosphate receptors (MPR), which then incorporate the proteins into secretory vesicles for transport

Question 11

Proteins leaving the golgi in clarithryn coated vesicles are typically destined for ____ ?

Answer 11

Endosomes or lysosomes

Question 12

What is the directionality of COP I vesicles?

Answer 12

Retrograde (i.e. Golgi to RER)

o COPI vesicles also mediate retrograde transport between Golgi cisternae.
o This is crucial for maintaining the distinct enzymatic compositions of different Golgi compartments.
o Some proteins, like mannose-6-phosphate receptors, are recycled from endosomes back to the TGN.

Question 13

What is the directionality of COP II vesicles?

Answer 13

Anterograde (RER to Golgi)

Question 14

Where can glycosylation of proteins be made during post-translational modification?

Answer 14

The ER and Golgi

Question 15

What are LDSs (aka LSDs)

Answer 15

Lysosomal storage diseases. Most LSDs are inherited in an autosomal recessive manner, although some, such as Fabry disease and Hunter syndrome (MPS II), are X-linked recessive. The genetic mutations responsible for LSDs affect genes encoding lysosomal enzymes, enzyme activators, membrane proteins, or proteins involved in lysosomal biogenesis.

Question 16

What is I-Cell disease?

Answer 16

The LDS - Mucolipidosis II (I-cell disease),

Question 17

List two disorders that arise from defects in lysosmal membrane proteins?

Answer 17

Danon disease and Cystinosis

Question 18

List the clinical manifestations of LDSs:

Answer 18

The clinical presentation of LSDs can vary widely, even within the same disease, depending on the specific enzyme
deficiency, residual enzyme activity, and the affected organs. Common features include:

a) Organomegaly (hepatosplenomegaly)
b) Neurological symptoms (developmental delay, seizures, ataxia)
c) Skeletal abnormalities (dysostosis multiplex)
d) Ophthalmological issues (corneal clouding, retinal degeneration)
e) Cardiovascular complications (cardiomyopathy, valvular disease)
f) Dermatological manifestations (angiokeratomas in Fabry disease)

Question 19

What LDS(s) arise from the following accumulated substrate?

Sphingolipids

Answer 19

Gaucher disease, Niemann-Pick disease, & Fabry disease

Question 20

What LDS(s) arise from the following accumulated substrate?

Mucopolysaccharides (MPS)

Answer 20

Hurler syndrome (MPS I), Hunter syndrome (MPS II)

Question 21

What LDS(s) arise from the following accumulated substrate?

Oligosaccharides

Answer 21

Pompe’s Disease (abnormal glycogen accumulation)

Question 22

What LDS(s) arise from the following accumulated substrate?

Mucolipids

Answer 22

Mucolipidosis II (I-cell disease), Mucolipidosis III

Question 23

What LDSs are x-linked recessive?

Answer 23

Fabry disease and Hunter
syndrome (MPS II)

Question 24

Most LDSs display what type of inheritance pattern?

Answer 24

Autosomal recessive

Question 25

List the structure and function of microtubules:

Answer 25

• Structure: These are hollow, cylindrical tubes made up of tubulin protein subunits.
• Function: Microtubules are the ‘railways’ of the cell. They provide tracks for the transport of cellular materials using motor proteins like kinesins and dyneins. They also play a crucial role in cell division, helping separate chromosomes during mitosis. Centrioles, which are involved in organizing cell division, are also made up of microtubules.

Question 26

List the structure and function of microfilaments:

Answer 26

• Structure: These are thin, flexible filaments primarily composed of the protein actin. They often appear as intertwined strands, much like two strings twisted together.
• Function: Actin filaments are involved in many cellular movements. They play a role in muscle contraction, cell division, and cell motility. When you see cells “crawling” during wound healing or immune responses, it’s actin filaments at work. They also provide structural support at the cell’s periphery, giving the cell its shape.

Question 27

List the structure and function of intermediate filaments:

Answer 27

• Structure: As the name suggests, these filaments are intermediate in thickness between microtubules and microfilaments. They are made up of various proteins, depending on the cell type.
• Function: Intermediate filaments are the ‘rope’ of the cell. They provide tensile strength, preventing the cell from being torn apart by mechanical stress. They’re particularly abundant in cells that undergo a lot of stress, like skin cells. A classic example of their importance is seen in certain skin blistering diseases, where mutations in intermediate filament proteins lead to weakened skin cells.

Question 28

What are the monomeric units of microtubules?

Answer 28

alpha and beta tubulin

Question 29

Which part of the cytoskeleton is known as the “highway of the cell?”

Answer 29

Microtubules

Question 30

What is the dynamic instability of microtubules?

Answer 30

• Microtubules are not static; they undergo rapid phases of growth and
  shrinkage, primarily at their ‘plus’ end (the end away from the cell
  center). This behavior is termed “dynamic instability.”
• This dynamic behavior allows the cell to reorganize its microtubule
  network in response to changing needs rapidly.

Question 31

What birth defects can arise from mutations in tubulin?

Answer 31

Mutations in tubulin can lead to brain malformations due to issues in neuronal migration, a process heavily reliant on microtubules.

Question 32

How are microtubules associated with cancer therapy and Alzheimer’s disease?

Answer 32

• Cancer Therapy: Many chemotherapy drugs, like taxanes and vinca alkaloids, target microtubules. They either stabilize or destabilize microtubules, disrupting mitosis (microtubules compose the mitotic spindle) and inhibiting cancer cell proliferation.
• Neurodegenerative Diseases: Abnormal microtubule function and tau protein (which stabilizes microtubules) aggregation are implicated in diseases like Alzheimer’s.

Question 33

What is the monomeric unit of a microfilament? Also, describe the polymerization/depolymerization of microfilaments:

Answer 33

• Basic Unit: The primary building block of an actin filament is the actin monomer, also known as G-actin (globular
  actin).
• Polymerization: This is the process by which G-actin monomers join together to form a long chain called F-actin (filamentous actin). This assembly primarily occurs at the ‘plus’ end of the filament. ATP hydrolysis to ADP provides the energy for this process.
• Depolymerization: This is the reverse process, where F-actin disassembles into its constituent G-actin
  monomers. This typically happens at the ‘minus’ end of the filament

Question 34

How do microfilaments aid cell integrity?

Answer 34

• Actin filaments form a dense network just beneath the cell membrane, known as the cell cortex. This network provides structural support, helping the cell maintain its shape. It also resists tension, much like the guy-wires on a tent, ensuring the cell doesn’t get pulled out of shape.

Question 35

What is hereditary spherocytosis?

Answer 35

Alterations in actin dynamics can contribute to conditions like hereditary spherocytosis. In this condition, red blood cells become sphere-shaped due to defects in proteins interacting with actin, making them less flexible and more prone to rupture as they pass through small capillaries.

Question 36

Define the basic structure of an intermediate filament:

Answer 36

An intermediate filament is made of tetramers, which are formed by two
dimers joining in an anti-parallel manner. These tetramers line up side by side
to form a short filament, which then joins end-to-end to form the full-length
filament, providing strength and flexibility.

Question 37

How are intermediate filaments clinically relevant?

Answer 37

1. Epidermolysis Bullosa Simplex (EBS): This is a genetic condition where mutations in the genes encoding keratins 5 and 14 (a type of intermediate filament specific to epithelial cells) lead to skin fragility. Individuals with EBS develop
   painful blisters in response to minor trauma or friction.
2. Amyotrophic Lateral Sclerosis (ALS): Mutations in the gene encoding the
   intermediate filament protein called neurofilament are associated with
   some cases of this neurodegenerative disease.
3. Giant Axonal Neuropathy (GAN): This is a rare neurodegenerative disorder
   caused by mutations in the GAN gene, which encodes a protein involved in
   maintaining the structure and function of intermediate filaments in
   neurons.
4. Hutchinson-Gilford progeria syndrome: Mutations in lamin A can lead to
   accelerated aging.

Question 38

How do mutations in dnynein and kinesin clincally manifest?

Answer 38

• Kinesin-related disorders: Mutations in kinesin family members can lead
  to various neurodegenerative diseases, given their role in axonal transport.
• Dynein-related disorders: Mutations affecting dynein or associated proteins can lead to primary ciliary dyskinesia (PCD). PCD is characterized by respiratory issues, infertility, and, in some cases, situs inversus (a condition where the internal organs are mirrored from their normal positions)

Question 39

What are the roles of IFs, microtubules, and microfilaments during cell division?

Answer 39

• • Microtubules: Form the mitotic spindle to separate chromosomes.
• • Actin Filaments: Form the contractile ring during cytokinesis.
• • Intermediate Filaments: Provide mechanical support during division.

Question 40

What are the roles of IFs, microtubules, and microfilaments during cell migration?

Answer 40

• • Actin Filaments: Push the cell membrane forward.
• • Microtubules: Orient the cell’s organelles and direct intracellular transport.
• • Intermediate Filaments: Provide tensile strength during movement.

Question 41

What are the roles of IFs, microtubules, and microfilaments during intracellular transport?

Answer 41

• • Microtubules: Serve as tracks for motor proteins to transport cellular components.
• • Actin Filaments: Facilitate short-range transport.
• • Intermediate Filaments: Maintain the positioning of organelles and cellular structures.

Question 42

Describe adheren junctions:

Answer 42

• Function: Adherens junctions are cell-cell junctions that provide strong mechanical attachments between adjacent cells.
• Structure: They are formed by cadherin proteins on the cell surface that bind to similar proteins on adjacent cells. The intracellular domain of cadherins is linked to the actin cytoskeleton via catenin proteins.
• Role of Cytoskeleton: The actin filaments provide the structural support to adherens junctions, ensuring cells remain attached to each other, especially during tissue stretching.

Question 43

Describe desmosomes:

Answer 43

• Function: Desmosomes are also cell-cell junctions, but they are more like “spot welds” that provide strong points of adhesion between cells.
• Structure: Desmosomes are formed by desmoglein and desmocollin (types of cadherins) that span the cell membrane and bind with similar proteins on adjacent cells. The intracellular domain of these proteins connects
  to intermediate filaments.
• Role of Cytoskeleton: Intermediate filaments, like keratin, anchor desmosomes inside the cell, providing robust tensile strength to tissues, especially in areas subjected to mechanical stress, like the skin.

Question 44

Describe focal adhesions:

Answer 44

• Function: Focal adhesions anchor cells to the extracellular matrix (ECM), facilitating cell movement and transmitting signals from the ECM to the cell.
• Structure: Integrin proteins on the cell surface bind to ECM components like fibronectin. Inside the cell, integrins connect to actin filaments via a complex of proteins, including talin and vinculin
• Role of Cytoskeleton: The actin cytoskeleton provides the structural backbone for focal adhesions. As the cell moves, focal adhesions form at the front and disassemble at the rear, a process driven by the dynamic nature of
  the actin cytoskeleton.

Question 45

List drugs that interact with the cytoskeleton:

Answer 45

Colchicine:
* Target: Microtubules

• Mechanism of Action: Colchicine binds to tubulin, the protein subunit of microtubules, and inhibits its polymerization. This prevents the formation of microtubules.
• Clinical Implications: Due to its ability to disrupt microtubule formation, colchicine is used in the treatment of gout. In gout, white blood cells move to the joints and cause inflammation. By disrupting microtubules, colchicine
  inhibits the migration of these white blood cells, reducing inflammation. However, it can have side effects like gastrointestinal upset due to its impact on other cells.

Taxol (Paclitaxel):
* Target: Microtubules

• Mechanism of Action: Unlike colchicine, taxol stabilizes microtubules. It binds to the β-tubulin subunit of the microtubule and prevents its depolymerization. This means that once microtubules are formed, they cannot be broken down.
• Clinical Implications: Taxol is used as a chemotherapy drug. Rapidly dividing cancer cells require dynamic microtubules for mitosis (cell division). By stabilizing microtubules, taxol effectively halts cell division, inhibiting
  tumor growth. However, it can also affect normal cells, leading to side effects like neuropathy and hair loss.

Cytochalasin:
* Target: Actin filaments (microfilaments)

• Mechanism of Action: Cytochalasin binds to the plus end of actin filaments and prevents the addition of further actin monomers, thereby blocking actin polymerization.
• Clinical Implications: While cytochalasin itself is not used therapeutically, understanding its mechanism has provided insights into the dynamics of actin filaments. It is often used in cell biology research to study actin function and dynamics