Midterm 2 study Q's Flashcards
What are the main reasons why it’s important to have Controls in the Cell Cycle?
- The different processes of the cell cycle have to happen in a specific order, so we need to make sure things start at the correct time.
- It can be catastrophic if there are mistakes in the cell cycle (cancer, etc.)
What exactly is Cyclin, what’s it’s role in the cell cycle?
- it is a protein that helps to regulate the progression of the cell cycle.
*
What are 4 things that cyclin and Cdk (Cyclin-dependant-kinase)
1: DNA replication
2: Mitosis
3: chromosome segregation
4: cell proliferation
What are the 4 major classes of cyclins?
1) G1/S Cyclins: bind cdk near the end of G1 and lead cell into DNA replication.
2) S-cyclins: bind cdk during s phase and are required for DNA replication, control early mitotic events.
3) M-cyclins: promote mitosis
4) G1-cyclins: (in most cells) Promote passage through restriction point in late G1.
Why does apoptosis occur?
Apoptosis occurs as a way to control cell growth, eliminate harmful cells, and ensure proper development.
what is blebbing in apoptosis?
Blebbing is a characteristic feature of apoptosis, where the cell’s plasma membrane forms irregular bulges or protrusions called blebs.
They will detach from the cell body.
They form because the cytoskeleton begins to break down. This disruption weakens the structural support of the cell, allowing the plasma membrane to bulge outward and form blebs.
It is like squeezing a gooey stress ball. They from due to intracellular pressure and a flexible membrane.
how does a macrophage know to mark a cell that has undergone apoptosis to be ‘eaten’ by phagocytosis?
Because of Phosphatidylserine!
Phosphatidylserine (PS) is a type of fat molecule that normally resides on the inside of a cell’s membrane, which is the protective layer surrounding the cell. When a cell is healthy, PS is hidden on the inner side of the membrane. However, when a cell begins the process of apoptosis (programmed cell death), PS flips to the outside of the membrane. This change acts like a “come and eat me” sign for immune cells called macrophages. These macrophages have special receptors that can recognize the PS on the outside of the dying cell. When they bind to PS, it signals the macrophages to engulf and digest the dying cell. This process helps clear away dead cells without causing inflammation, keeping tissues healthy and balanced.
True or false:
When a cell apoptoses, the asymmetric distribution of the plasma membrane is lost.
True!
True or false:
C. elegans has 959 somatic cells, and 131 apoptose every time.
True!
Define Capsases.
What lead to their discovery?
Caspases are a family of enzymes that play a key role in apoptosis, or programmed cell death. They are divided into two main types: initiator caspases, which kickstart the cell death process in response to signals, and effector caspases, which carry out the actual dismantling of the cell. Once activated, caspases cleave various proteins inside the cell, leading to changes like cell shrinkage and fragmentation. This process helps remove damaged or unnecessary cells without harming surrounding tissues. Additionally, some caspases are involved in inflammation by processing proteins that trigger the immune response.
These caspases are proteases—enzymes that break down other proteins—by specifically cutting at an aspartate site using a cysteine residue in their active site. Caspases are essential for most changes observed in cell death, like cell shrinkage and fragmentation, as they cleave many essential proteins inside the cell to help dismantle it. They can even cleave each other, which activates more caspases, amplifying the cell death process. This controlled breakdown ensures that unnecessary or damaged cells are removed efficiently without harming surrounding tissue.
The discovery of the ced-3 gene in C. elegans led to the identification of a similar group of proteins in mammals, which are Caspases.
What happens when Caspases cleave the following?:
- Protein Kinases:
*Lamins:
*Cytoskeleton:
*CAD:
- Protein Kinases: When caspases cleave protein kinases, it disrupts cell adhesion—the proteins and structures that help the cell stick to other cells and its surroundings. This loss of adhesion helps the cell detach, making it easier for the immune system to clear away the remains after apoptosis.
*Lamins: These proteins provide structure to the nucleus. When cleaved, the nucleus breaks down, allowing the DNA to condense.
–> “disassembly of nuclear lamina”
*Cytoskeleton: The cell’s structure collapses as the cytoskeleton is cut apart, leading to cell shrinkage and blebbing (membrane bubbles).
–> “changes in cell shape”.
*CAD: CAD is an enzyme that cuts DNA. Caspases release CAD from its inhibitor, which then fragments the DNA, a final step in breaking down the cell’s internal contents.
What does Procapsase mean?
it is the inactive version of a caspase.
A procaspase is the inactive, precursor form of a caspase enzyme. Caspases start as procaspases to keep them inactive until the right time. During apoptosis, specific signals trigger the conversion of procaspases into active caspases. This is usually done by cleaving off certain sections of the procaspase, causing it to fold into an active shape that can then start breaking down other proteins in the cell. This conversion ensures that caspases only become active when needed for programmed cell death, preventing accidental damage to healthy cells.
Once procaspases are activated, they often become initiator caspases, which can then go on to activate executioner caspases through proteolytic interactions (essentially, by cleaving them). This step-by-step activation amplifies the cell death signal, allowing the apoptosis process to progress in a controlled, cascading manner until the cell is fully dismantled.
–>”These capsases go on to activate executioner caspases by proteolytic interactions (cleavage). “
Recap the step-by-step activation of caspases, starting with the initiator caspases that get activated first and then go on to activate executioner caspases.
1: Initiator Caspases (like caspases 8 and 9) are normally inactive. They consist of two parts: an adaptor-binding domain and a protease domain, which is where the actual cutting happens. These are inactive until they receive a signal to start apoptosis.
2: When an apoptotic signal is received (like damage or stress in the cell), adaptor proteins come in and help two initiator caspase monomers (the inactive form) join together, a process called dimerization. This activates them by cutting or cleaving the caspases at specific sites, turning them into an active caspase.
3: The active initiator caspases then go on to activate executioner caspases (like caspases 3, 6, and 7). They do this by cleaving the executioner caspases, turning them from inactive forms into their active forms.
4: Once activated, the executioner caspases cut up many different proteins in the cell, leading to the breakdown of the cell and the progression of apoptosis.
What are the stages of mitosis? Briefly, what happens in each?
What happens after?
PMAT
P: Prophase – Chromosomes condense, and the nuclear envelope starts to break down.
M: Metaphase – Chromosomes line up in the middle of the cell.
A: Anaphase – Sister chromatids are pulled apart to opposite sides of the cell.
T: Telophase – Two new nuclei form around the separated chromosomes, and the cell starts to split.
After these stages, the cell goes through Cytokinesis, where the cytoplasm divides, creating two separate daughter cells.
(Intracellular Control)
WHY ARE WE LOOKING AT THE CELL CYCLE?
We’re focusing on mechanisms that allow a cell to stay within a phase or transition into the next one; in other words, the mechanisms of control that occur at specific stages
(Intracellular control)
WHY DOES THE CELL CYCLE NEED TO BE CONTROLLED?
The cell cycle is well orchestrated and occurs in a pre-programmed, coordinated sequence
> if otherwise, then that may lead to disastrous consequences
Through binding and phosphorylation, regulatory proteins and biochemical switches control the progression through the cell cycle
The system monitors intracellular and extracellular environments
(intracellular control)
WHAT are CDKs and what do they do?
Cdks are cyclin-dependent kinases, which are important biochemical switches for controlling the cell cycle and other events
> events such as DNA replication, mitosis, chromosome segregation, and cell proliferation
They are dependent on cyclins, which are proteins whose concentrations rise and fall throughout the cell cycle (cyclical concentrations)
With the changes in concentration of the cyclins, the concentrations of Cdk also changes at different phases of the cell cycle
(intracellular control)
HOW ARE CYCLINS CLASSIFIED?
They are classified into 4 major groups
G1/S cyclins: are present when cells are coming out of G1 and enter the S phase. They bind Cdk near the end of G1 and lead the cell into DNA replication
S-cyclins: their increase is required for Cdks to bind and for the S phase of cells. They are needed for DNA replication and they control early mitotic events
> without G1/S cyclins and the increase of S cyclins, DNA replication doesn’t occur
M-cyclins: they rise to promote mitosis, and then decrease to get out of mitosis
G1-cyclins: they allow the cell to pass through the restriction point in late G1
WHAT ARE PROTEIN KINASES AND PHOSPHATASES?
PROTEIN KINASE: A protein kinase is an enzyme that (using ATP) will phosphorylate another protein (ADD PHOSPHATE).
–>((Depending on where the phosphate is attached, since they have multiple binding sites, they can change the structure of the function and either activate or deactivate the protein))
PHOSPHATASE: A protein phosphatase is a protein that removes a phosphate. Depending on the protein it removes the phosphate from, it can either activate or deactivate it
HOW ARE CDKS ACTIVATED?
Cyclin comes in and binds to an inactive Cdk, changing the conformation of its T-loop. The Cdk becomes partly active
The T-loop interacts with the cyclin, causing a conformational change that exposes a phosphorylation site
Another protein kinase called CAK (Cdk-activating kinase) comes in and phosphorylates the Cdk. The Cdk is then fully active, which it has to be in order to control the cell cycle
HOW IS CDK ACTIVITY IN THE CELL CYCLE REGULATED?
How are cyclins regulated?
Cdk activity is regulated by the concentrations of cyclins in the cell
Cyclins, on the other hand, are controlled by ligases that destroy them. Sometimes there are cyclins that are already present in the cytoplasm, but the ligases destroy them, causing their activity to drop. Once ligases are deactivated, cyclin activity rises again, leading to the activation of Cdk
How can CDKs be inhibited?
How is CDK inhibition different from CKD degradation?
There are 2 examples that we look at that can inactivate a Cdk
1) Wee1: it is a kinase that puts an inhibitory phosphate in the inhibitory site of the active Cdk. This prevents Cdk from phosphorylating anything
2) CKI: Cyclin–dependent kinase inhibitors (e.g. p27). p27 interacts with an entire protein complex, preventing it from undergoing conformational changes or interacting with other proteins.
CDK inhibition involves temporarily blocking cyclin-dependent kinases (CDKs) with inhibitors, which pauses their activity without destroying them.
–> CDK degradation, on the other hand, permanently removes CDKs from the cell by breaking them down, usually via the proteasome after tagging with ubiquitin
Tell me about the Ubiquitin Ligase #1: SCF
Tell me about how SCF controls destruction of CKIs, and why is this important?
-SCF breaks down G1/S cyclins {which will inhibit actication of G1/S cdks. (This is needed to allow new cdks to take over after these ones have done their job to allow the cell to pass through the G1/S checkpoint.)}
-It also destroys CKIs (Cdk inhibitors) to activate Cdks when needed.
-SCF is constitutively active, meaning active at all times, regardless of what cell cycle stage it’s in.
-The destruction of CKIs is important because it is a mechanism of inhibiting an inhibitor, which is important for the progression of a cell into S phase.
How SCFs control destruction of CKIs:
> SCFs have an F-box protein that targets CKIs only if they’re phosphorylated, allowing for the application of a polyubiquitin chain
> CKI goes off to the proteasome and it’s destroyed
> Level of active CKI is reduced in the cytoplasm
> Importance: this mechanism prevents the inhibition of Cdk, allowing for high levels of S-Cdk so that the cell can move forward into S-phase. This is a “positive effect” because the cell progresses forward.
What are Ubiquitin Ligases, and how are they involved in protein degradation?
What are the 2 kinds of Ubiquitin ligases?
Ubiquitin Ligase is an enzyme that joins ubiquitin proteins to cyclin proteins, which will mark them for degradation by the proteasome.
Ubiquitin is applied/attached to the target protein through an enzymatic reaction, until a chain of ubiquitin is formed on the target
A protein that’s marked for degradation is taken to the proteasome: a structure found in cells that degrades proteins into amino acids
The ubiquitin takes the protein there and then leaves, and the protein moves through the proteasome and is degraded
Two ubiquitin ligases that are involved in parts of the cell cycle are SCF and APC
Tell me about Ubiquitin Ligase 2: APC
-APC (Anaphase Promoting Complex) is involved in the destruction of securin, so it promotes anaphase.
-It also leads to the destruction of M-cyclin, allowing cell to leave M-phase and progress in the cycle.
- APC requires that another subunit such as Cdh1 or Cd20 binds to it, in order to be activated.
How APCs control M-cyclin destruction:
> Cdc20 binds with the APC, activating it
> A polyubiquitin chain is applied to the cyclin
> The cyclin is destroyed, so Cdk is left alone and deactivated
> The cell can leave M-phase and continue in the cycle
What is a Ligase?
And how does it relate to cyclins?
A ligase is an enzyme that joins two molecules together, often by forming a bond between them, typically using ATP.
In relation to cyclins, a specific type of ligase called the ubiquitin ligase (such as the APC/C complex) tags cyclins with ubiquitin, marking them for degradation. This helps regulate the cell cycle by controlling cyclin levels.
What is Ubiquitin, and how does it relate to cyclins?
Ubiquitin is a regulatory protein that attaches to other proteins to mark them for degradation.
For cyclins, which are proteins that control cell cycle progression, ubiquitination is a key mechanism for regulating their presence. Cyclins need to be degraded at specific points in the cell cycle to allow the cycle to progress correctly. By tagging cyclins with ubiquitin, the cell ensures that they are removed when no longer needed.
True or false:
The ubiquitin ligase will carry around ubiquitin and it will tag cyclins with this ubiquitin for degredation.
True!
The ubiquitin ligase is an enzyme that facilitates the process of tagging proteins (like cyclins) with ubiquitin. It attaches ubiquitin molecules to specific cyclins at the right time, marking them for degradation by the proteasome.
True or false:
The ubiquitin protein itself will degrade the cyclins.
False.
The ubiquitin protein itself does not degrade the cyclins. Instead, ubiquitin tags the cyclins for degradation, signaling them to be broken down by the proteasome, which is the actual machinery that degrades proteins.
Tell me about the proteasome and how it relates to cyclins.
The proteasome is a protein complex that degrades unwanted or damaged proteins in cells. When cyclins are tagged with ubiquitin (by ubiquitin ligase), this signals the proteasome to break them down.
(Intracellular controls)
True or false:
(intracellular controls)
What are CKIs and how do they relate to CDKs?
CKI stands for Cyclin-dependant Kinase Inhibitor.
As you can imagine from the name, it inhibits the activity of CDKs.
Inhibiting CDKs will stop the cell cycle from progressing.
(intracellular controls)
True or false:
SCF is constitutively active: it’s active throughout different phases of the cell cycle, and often present in high activity.
True.
When we say that SCF is constitutively active, it means that this complex remains active at all times, regardless of the specific phase of the cell cycle (G1, S, G2, or M).
(intracellular control)
True or false:
CDKs are inhibitors.
False.
CDKs (Cyclin-Dependent Kinases) are not inhibitors; they are enzymes that promote cell cycle progression when activated by cyclins.
So a CDK is actually an ACTIVATOR essentially. It is what allows the cell cycle to PROGRESS through the checkpoints!
(intracellular controls)
Briefly recap the stages of the cell cycle (G1, S, G2, M, G0)
G1: This is the growth stage occurring in new cells after mitosis. This is also where differentiation will happen for them.
S: Synthesis stage, this is where the DNA will be replicated.
G2: this is the second growth stage, any growth that needs to happen before mitosis, happens here.
M: The Mitosis stage has 4 parts (PMAT): Prophase, Metaphase, Anaphase, Telophase. And then the last step is cytokinesis.
G0: this is a rest stage that a cell can go into after mitosis has occurred. It is a stage of pause, where the cell is just ‘at rest’ in terms of division and stuff. most cells in eukaryotes are in G0 because there’s no need to be divinging all the time.
(Intracellular controls)
Recap the stages of MITOSIS for me.
(PMAT + Cytokinesis)
Prophase: The chromatin condenses into visible chromosomes, and the nuclear envelope begins to break down. The mitotic spindle starts to form.
(Prometaphase: The nuclear envelope completely disappears, and spindle fibers attach to the centromeres of the chromosomes.)
Metaphase: (“Middle”) Chromosomes align along the equatorial plane of the cell, known as the metaphase plate.
Anaphase: (“Away”) Sister chromatids are pulled apart toward opposite poles of the cell as the spindle fibers shorten.
Telophase: The chromatids reach the poles, the nuclear envelope begins to reform around each set of chromosomes, and the chromosomes start to de-condense back into chromatin.
Cytokinesis: Cytokinesis (though not a part of mitosis itself): The cytoplasm divides, resulting in two separate daughter cells, each with a complete set of chromosomes.
(Intracellular control)
What
(intracellular control)
Tell me about the 4 “classes” of cyclins and how the affect CDKs.
(G1/S cyclins, S-cyclins, M-Cyclins, G1-cyclins)
1: G1/S cyclins ~ These binds to the Cdk near the end of G1, and lead it into DNA replication.
{That is why it’s called G1/S because it is allowing the transition from G1 to S.}
2: S-cyclins ~ bind Cdk during the S phase and are required for DNA replication!
(They also control early mitotic events).
3: M-Cyclins ~ Promote events of Mitosis.
4: G1-cyclins ~ promote passage through restriction point in late G1
(in most cells)
(Intracellular controls)
True or false:
Cdks are actually protein kinases. (so they phosphorylate things).
True.
(It’s literally called a Cyclin-Dependant KINASE).
CDKs (Cyclin-Dependent Kinases) are a type of protein kinase, and they phosphorylate specific target proteins to regulate various processes in the cell cycle.
