MP2: How are proteins processed? Flashcards
What are caspases?
Caspases are a family of proteases (enzymes that break down proteins) that play a crucial role in programmed cell death, also known as apoptosis. They are a group of cysteine proteases, named for their ability to cleave after an aspartic acid residue in their target proteins.
What’s the difference between initiator and effector caspases?
Initiator: activated in response to specific signals and cleave and activate effector caspases.
Effector: cleave and activate other downstream targets, ultimately leading to the death of the cell.
How are caspases activated from zymogens? Why is this important?
Caspases are initially synthesized in cells as inactive zymogens, which require proteolytic cleavage for activation. Cleavage of the inactive zymogen forms the p10 and p20 fragments which associate together to form the active caspase enzyme.
This ensures that caspases are not activated prematurely, which could lead to unwanted cell death.
What is the apoptosome?
a platform that activates procaspases in response to intrinsic cell death signals such as release of cytochrome c from the mitochondria
What is the function of apoptosis? What does it involve?
- Eliminate unwanted or damaged cells in a controlled and programmed manner.
- Helps shape and sculpt tissues and organs during development.
- Role in the immune system response.
It involves:
1. activation by intracellular/extracellular signals
2. execution by effector caspases
3. clearance of apoptotic bodies by phagocytic cells through recognition of PS on the outer leaflet (serves as an ‘eat me’ sign)
What is necroptosis? Describe what happens.
Unlike apoptosis, necroptosis is a type of cell death that’s accompanied by a pro-inflammatory response, which can lead to tissue damage and inflammation. It’s a form of traumatic cell death that results from acute cellular injury.
Formation of the necrosome results in disruption of the plasma membrane and release of intracellular contents, including DAMPs to activate an inflammatory response.
What are inhibitors of apoptosis (IAPs)? How do they inhibit? Give one example.
IAPs block the activity of caspases. They’re characterized by one or more BIR domains, which are responsible for their anti-apoptotic activity.
They inhibit through ubiquitination of caspases, targeting them for degradation.
e.g., XIAP
How can IAPs be inhibited? (i.e., apoptosis be promoted.) Give two examples and therapeutic uses.
The BIR domains on IAPs can be bound by IAP inhibitors, which are activated when cytochrome c is released.
e.g., SMAC and XIAP-binding protein.
SMAC is released from the mitochondria during apoptosis. XIAP BP competes with caspases for binding to XIAP, thereby promoting caspase activity and cell death.
IAP inhibitors have been developed as potential cancer therapies to promote apoptosis of cancer cells.
Give the writer, reader, and eraser for acetylation.
Writer: histone acetyltransferase (HAT)
Reader: bromodomain
Eraser: deacetylase (HDACs and Sirtuins)
What is the role of acetylation in epigenetics?
Acetylation of lysine residues on histones is found in enhanced transcription of target genes because it removes lysine’s positive charge. This reduces the interaction with the negatively charged DNA.
Give the writer, reader, and eraser for methylation.
Writer: methyl transferase
Reader: tudor, PHD and chromodomains
Eraser: demethylase
What is used as the acetyl source for acetylation?
Acetyl CoA
What is used as the methyl source for methylation?
SAM
What is the role of methylation in epigenetics?
Both activation and repression e.g., H3K4me3 activates whilst H3K27me3 represses.
What is the tubulin code? Give an example of such a code in this context.
The tubulin code refers to a set of post-translational modifications that occur on microtubules. The tubulin code is believed to regulate microtubule stability, dynamics, and function.
For example, acetylation of lysine residues on tubulin has been shown to promote microtubule stability. Others aren’t completely understood.
Give the writer, reader, and eraser for ubiquitination.
Writer: ubiquitin ligase (E1, E2 and E3)
Reader: Ubiquitin binding domains
Eraser: deubiquitinating enzymes (DUBs)
What are E1, E2 and E3 ubiquitin ligases?
E1, E2, and E3 are the three main classes of enzymes involved in the ubiquitination pathway, which is a process by which ubiquitin, a small protein, is covalently attached to target proteins.
E1: activate Ub and transfer them to E2
E2: attach Ub to the target
E3: recognize the target and facilitate Ub transfer from E2
What is the ubiquitin code? Give examples of what different ‘codes’ can lead to.
Ubiquitin contains 7 internal lysine residues that can also be ubiquitinated. The formation of different Ub chains gives rise to the ubiquitin code.
E.g., Lys48 polyubiquitination = degradation
Met1 = innate immune signaling
Describe the structure and function of E1 ubiquitin ligase.
Structure:
- multiple domains and subunits
- flexible domain (key to function)
Function:
- activates ubiquitin and transfers to E2
Describe the structure and function of E2 ubiquitin ligase.
Structure:
- small protein
- single catalytic domain
- Ub binding site for backside binding to form polyubiquitination chains
- conserved cysteine residues to form thioester bonds with Ub from E1
Function:
- transfers Ub from E1 to the target protein
Describe the structure and function of E3 ubiquitin ligase.
Can be divided into two main classes based on their structure:
- HECT - contain a HECT domain with a catalytic cysteine
- RING - contain a RING domain, but no catalytic residue
Function:
- recognize and bind specific target proteins and facilitate transfer of Ub from E2 to the protein.
As RING ligases don’t have catalytic residues, they function by positioning Ub-E2 in the right place with the target protein.
How is ubiquitination associated with Parkinson’s disease?
Parkin is an E3 HECT ligase that is associated with protein-degradation pathways and mitophagy.
Mutations in the parkin gene disrupts its function, leading to impaired mitophagy and accumulation of damaged mitochondria in cells. This has been associated with Parkinson’s disease.
Describe the process of mitophagy.
- Damaged mitochondria prevents PINK1 transport for degradation, resulting in accumulation of PINK1 on the mitochondrial membrane.
- PINK1 promotes recruitment of Parkin.
- Parkin attaches Ub to mitochondrial proteins, marking them for degradation.
- Autophagosome forms an engulfs the damaged mitochondria.
What are cullin RING ligases?
A family of E3 ubiquitin ligases that play a key role in the regulation of protein degradation pathways. e.g., APC.
The cullin protein serves as a scaffold for the assembly of the complex, while the RING finger protein interacts with E2 ligases.
What are anaphase promoting complexes?
A large multi-subunit protein complex that acts as an E3 ubiquitin ligase to target specific proteins for degradation in the cell cycle. It’s a member of the cullin RING superfamily.
What is the isoleucine 44 patch on ubiquitin?
A hydrophobic surface on ubiquitin that allows for recognition and binding of ubiquitin by various ubiquitin-binding proteins.
The hydrophobic nature of the Ile44 patch allows for specific interactions with complementary hydrophobic pockets, leading to the formation of stable protein complexes that facilitate the transfer of ubiquitin from E2 to the target protein.
What is the function and structure of the proteasome?
The proteasome is a large protein complex found in cells that is responsible for the degradation of proteins. It is a multi-subunit complex composed of two main components: the 20S core particle and one or two 19S regulatory particles.
Core: proteolytic chamber
Regulators: ATPases to unfold and translocate proteins, as well as removing Ub tags for recycling.
What are ubiquitin-like proteins? Give two examples and their functions.
Ubiquitin-like proteins (UBLs) are a family of proteins that share structural and functional similarities with ubiquitin.
- SUMO: involved in the DNA damage response
- Nedd8: cullin RING ligase regulator
Like ubiquitin, UBLs are conjugated to target proteins through a series of enzymatic reactions involving E1, E2, and E3 enzymes, and can also be removed by deconjugation enzymes.
Give the writer, reader, and eraser for phosphorylation. On what residues can phosphorylation occur?
Writer: kinase
Reader: SH2 domains, 14-3-3 proteins
Eraser: phosphatases
Occurs on polar residues and histidine.
What is the role of the beta-grasp fold in ubiquitin?
The beta-grasp fold in ubiquitin is responsible for binding to target proteins and is essential for ubiquitination.
What is the kinome?
The complete set of protein kinases encoded by an organism’s genome. The human kinome consists of over 500 protein kinases that are classified into different families based on their properties.
