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BIOL3006 > Module 6 > Flashcards

Module 6 Flashcards

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1
Q

What are Type II CRISPR-Cas systems?

A

Bacterial systems that provide adaptive immunity to viruses and plasmids.

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2
Q

What does CRISPR stand for?

A

Clustered Regularly Interspaced Palindromic Repeats.

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3
Q

What is the role of Cas9?

A

CRISPR Associated Protein 9, crucial for gene editing.

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4
Q

How efficient is CRISPR/Cas9 gene editing?

A

Up to 80% of targeted cells can have modifications.

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5
Q

What is a single guide RNA (sgRNA)?

A

A chimeric RNA combining CRISPR RNA (crRNA) and trans-activating CRISPR RNA (tracrRNA).

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6
Q

What is PAM in CRISPR/Cas9?

A

Protospacer Adjacent Motif, typically the sequence NGG, essential for target recognition.

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7
Q

How can CRISPR/Cas9 be used for gene correction?

A

By creating stop codons or introducing specific mutations using guide RNAs.

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8
Q

What is the role of BCL11A in beta-thalassaemia?

A

A negative regulator of the gamma globin gene; targeting it can increase fetal hemoglobin (HBF).

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9
Q

What is the impact of mutations in beta-globin?

A

Can lead to beta-thalassemia, resulting in symptoms like severe anemia and jaundice.

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10
Q

What is the endoplasmic reticulum (ER)?

A

A complex network of membranous sacs and tubules essential for protein and lipid synthesis.

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11
Q

What are the two types of ER?

A

Rough Endoplasmic Reticulum (RER) and Smooth Endoplasmic Reticulum (SER).

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12
Q

What characterizes the Rough ER (RER)?

A

It is studded with ribosomes and primarily synthesizes proteins for secretion and organelle transport.

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13
Q

What is the function of Smooth ER (SER)?

A

Involved in lipid synthesis, detoxification, and calcium storage.

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14
Q

What role do chaperones play in protein folding?

A

Assist in proper folding and prevent misfolding or aggregation of proteins.

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15
Q

What are disulfide bonds, and why are they important?

A

Stabilize protein structures; formed in the oxidizing environment of the ER.

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16
Q

What is glycosylation?

A

The addition of carbohydrate chains to proteins, critical for their folding and function.

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17
Q

What is the Golgi apparatus’s role?

A

Refines, stores, and distributes products from the ER, modifying proteins in distinct compartments.

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18
Q

How is insulin processed in the ER?

A

Synthesized as preproinsulin, then converted to proinsulin before being cleaved into insulin.

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19
Q

What are GPI anchors?

A

Glycolipid modifications that attach proteins to the plasma membrane, synthesized in the ER.

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20
Q

What is the significance of the cellular stress response?

A

It is a universal mechanism that promotes survival in response to macromolecular damage and can elicit programmed cell death.

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21
Q

What are the two types of reactions in the fight or flight response?

A

Fight reactions aim to limit the stimulus’s effects, while flight reactions involve cell motility to escape harmful stimuli.

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22
Q

What is the effect of acute stress on homeostasis?

A

Acute stress activates protective responses to return to homeostasis.

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23
Q

What can chronic stress lead to?

A

Chronic stress can cause permanent changes and an inability to adapt, resulting in system breakdown.

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24
Q

List the five main types of cellular stress.

A
  1. Oxidative Stress 2. Genotoxic Stress 3. Hypoxic Stress 4. Nutrient Stress 5. Endoplasmic Reticulum Stress
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25
Define oxidative stress.
A condition where free radical production exceeds the body's ability to neutralize them, leading to cellular damage.
26
What are the consequences of oxidative stress?
DNA damage, protein damage, lipid damage, inflammation, and cell death.
27
What agents can cause genotoxic stress?
Free radicals, reactive oxygen species, DNA replication errors, ionizing radiation, chemical agents, environmental pollutants.
28
What types of DNA damage can occur from genotoxic stress?
Single-strand breaks, double-strand breaks, and base modifications.
29
What are the cellular responses to DNA damage?
Activation of DNA repair mechanisms, cell cycle arrest, and apoptosis if damage is irreparable.
30
Define hypoxic stress.
A condition characterized by insufficient oxygen availability to meet cellular metabolic demands.
31
What are the effects of hypoxia on cellular function?
Increased anaerobic glycolysis, enhanced ROS production, activation of stress response pathways, and potential cell death.
32
What is nutrient stress?
A condition that occurs when cells lack essential nutrients, affecting their viability and functionality.
33
What are the consequences of nutrient stress?
Impaired cell growth and division, DNA damage, cell death, diminished cell function, and increased susceptibility to infection.
34
What is endoplasmic reticulum (ER) stress?
A condition where the ER cannot fold proteins properly due to an overload of misfolded proteins.
35
What happens when cells experience ER stress?
Increased production of unfolded proteins, activation of the unfolded protein response (UPR), and potential cell death if stress is prolonged.
36
What is the unfolded protein response (UPR)?
A cellular stress response activated by ER stress that helps protect the cell and promotes survival.
37
What are the three main outcomes of the UPR?
Decreased protein translation, restoration of protein folding, and degradation of misfolded proteins (ERAD).
38
How is the IRE1 pathway activated?
When the ER is overloaded with unfolded proteins, leading to RNA cleavage and spliced mRNA production (XBP1).
39
What triggers the ATF6 pathway?
The inability of the ER to maintain calcium levels, leading to unfolded protein accumulation and activation of ATF6.
40
How does the UPR affect inflammation?
It can activate transcription of pro-inflammatory cytokines and ROS production, which may trigger inflammatory responses.
41
What is the primary purpose of protein degradation?
To remove damaged or misfolded proteins, recycle amino acids, regulate protein levels, and respond to cellular stress.
42
Why is it important to remove damaged or misfolded proteins?
They can interfere with normal cell function and be toxic.
43
What is ER-associated protein degradation (ERAD)?
A cellular pathway that targets misfolded or unfolded proteins in the endoplasmic reticulum (ER) for degradation by the proteasome.
44
What role does the ERAD pathway play in disease?
It maintains protein quality and is involved in diseases like neurodegenerative disorders, cancer, and autoimmune diseases.
45
What is the first step in the ERAD process?
Recognition of misfolded proteins in the ER by proteins such as calnexin, calreticulin, Grp78 (BiP), EDEM, and HRD1.
46
What is the function of calnexin and calreticulin?
They stabilize misfolded proteins and prevent aggregation by binding to N-glycans on glycoproteins.
47
What is retro-translocation in the context of ERAD?
The process of moving misfolded proteins from the ER into the cytosol for degradation.
48
Which proteins are involved in the retro-translocation process?
Sec61, Derlin-1, HRD1, and p97.
49
What occurs during ubiquitin-dependent degradation by the proteasome?
Misfolded proteins are tagged with ubiquitin, forming a polyubiquitin chain, leading to recognition and degradation by the proteasome.
50
What is the function of the ERAD-C and ERAD-L checkpoints?
ERAD-C monitors the folding state of cytosolic domains, while ERAD-L checks the folding of luminal domains to prevent accumulation of misfolded proteins.
51
Define autophagy.
A cellular process of self-digestion that maintains homeostasis and protects against starvation and microbial invasion.
52
What are the three types of autophagy?
1. Macroautophagy 2. Microautophagy 3. Chaperone-mediated autophagy
53
Describe the process of macroautophagy.
It involves the formation of an autophagosome that engulfs damaged organelles or proteins, which then fuses with lysosomes for degradation.
54
What occurs during microautophagy?
The lysosome engulfs small components of cytoplasmic material directly through invagination of its membrane.
55
How does chaperone-mediated autophagy differ from other types?
It specifically recognizes proteins via a chaperone (hsc70) that facilitates direct translocation of substrates into lysosomes without membrane reorganization.
56
What triggers the initiation of macroautophagy?
Nutrient starvation or growth factor-mediated starvation.
57
What is the role of mTOR in autophagy?
mTOR is involved in regulating the initiation and execution of macroautophagy by sensing nutrient availability.
58
How does autophagy contribute to the immune response?
It degrades pathogens and promotes antigen presentation to T cells, aiding both innate and adaptive immunity.
59
Provide an example of how autophagy combats infection.
It helps clear intracellular bacteria like Mycobacterium tuberculosis and controls the inflammatory response to infections.
60
What is endoplasmic reticulum (ER) stress?
A condition where the ER's capacity to fold proteins is overwhelmed, leading to an accumulation of misfolded proteins.
61
What triggers ER stress?
Factors like nutrient deprivation, oxidative stress, viral infections, and abnormal protein aggregation.
62
What is the unfolded protein response (UPR)?
A cellular response activated by ER stress to restore normal function by halting protein translation, degrading misfolded proteins, and enhancing protein folding capacity.
63
What diseases are associated with chronic ER stress?
Inflammatory bowel disease (IBD), cystic fibrosis (CF), metabolic diseases, neurodegenerative diseases.
64
How does ER stress contribute to inflammatory bowel disease (IBD)?
By disrupting intestinal epithelial homeostasis, leading to increased inflammation and impaired mucosal healing.
65
What is the role of ER stress in cystic fibrosis (CF)?
CFTR mutations cause protein misfolding, leading to chronic inflammation and lung disease.
66
How does ER stress relate to metabolic diseases?
It contributes to insulin resistance and dysregulated lipid metabolism, promoting conditions like obesity and type 2 diabetes.
67
In neurodegenerative diseases, how does ER stress play a role?
It is linked to the accumulation of misfolded proteins (e.g., in Alzheimer’s and Parkinson’s diseases), leading to neuronal apoptosis.
68
How do viral infections relate to ER stress?
Many viruses exploit ER stress responses for replication, while causing additional stress through the accumulation of viral proteins.
69
What are potential therapeutic implications of targeting ER stress?
Modulating ER stress pathways could lead to treatments for IBD, CF, metabolic diseases, and neurodegenerative conditions.

BIOL3006 (8 decks)

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