Cancer Flashcards
True or false cancer cells have abnormal gene expression
True
Is a group of cells or tumor that stays in the tissue that they belong where it belongs cancerous?
No, it is known as a benign tumor, and it will stay that way as long as it does not go beyond the tissue that it belongs
When is cell becomes invasive, It is still benign true or false.
False it is now cancerous because the cells have accumulated enough mutations to cause them to break barriers between where they belong and new tissues
When a cell colonizes a new site in the body, what is that called?
Metastatic cancer
The new mass in a different part of the body is actually a clone of the original tumor
What happens when a cancer cell promotes angiogenesis?
The cancer cell secretes growth factors and force blood vessels to grow to it
The tumor is rapidly growing and dividing so it will need lots of nutrients/fuel and so it requires blood vessels to do that
Cells are not normally able to do this, but these particular cancer cells gain mutations that allow them to secrete growth factors
Normal cells require signals that are neuronal or hormonal to get them to grow and divide and also they need extrinsic signals from our body that are anti growth signals to tell the cells to stop growing and dividing what cancer cells do?
They secrete growth factors, and they also express their receptor for that growth factor so basically they’re telling themselves to grow and divide independent of the rest of the body and then if the body is telling them to stop growing via anti growth signals, they ignore them
How do cancer cells avoid apoptosis?
They accumulate mutations in proteins involved in apoptosis, or they accumulate mutations in proteins involved in signaling for apoptosis like P 53, which is mutated a lot in cancers
Therefore, the cancer cell avoids apoptosis by inactivating those pathways
Cancer cells can indefinitely divide true or false
True
What causes abnormal chromosomal rearrangements that we see in cancer?
Single stranded and double stranded breaks
Examples: aneuploidies
What are rearrangements of the chromosomes that result in aneuploidies?
Deletions
Duplications
Inversions
Insertions
Translocation’s
What is the inversion rearrangement of chromosomes?
Where a piece of DNA is completely flipped around in the chromosome
What is the translocation rearrangement of chromosomes?
It is a mutual exchange of information between two chromosomes
Example part of chromosome four goes on chromosome 20 and part of chromosome 20 goes on chromosome four
What do insertion rearrangements of chromosomes entail?
It is an exchange of genetic information between two chromosomes
It basically takes a part of one chromosome and puts it on another so example part of chromosome four gets inserted in chromosome 20
What region are the pro growth genes of cells that are constantly growing and dividing located in?
A euchromatin region , because it is very easy to access the DNA and transcribe these pro-growth genes
Therefore cells with high turnover have pro growth genes in these regions
In cells where there isn’t high turnover, what are the regions where you would find pro growth genes?
In heterochromatin regions - so it is very difficult to access DNA and therefore to mutate genes that are never expressed
Example is wisdom, tooth, enamel, intercostal, skeletal muscles, internal intestinal cells, Achilles tendon, heart, muscle cells, cerebellum, Gre8 matter, Hippocampal neurons, and the visual cortex
Why do epigenetic modifications influence cancer development?
Because epigenetic modifications, alter gene expression
What are the mutations that help cancer to develop?
Mutations and genes that regulate the cell cycle that determine if we are undergoing DNA replication and cell division
What two things should a normal healthy cell have?
A balance of gas and brakes so proto-oncogenes should be working, which encode a protein that favorite cell growth and tumor suppressor genes should be working which encodes inhibitory proteins that stop a cell from growing 
What are proto-oncogenes?
They are pro growth genes in a normal cell that doesn’t have mutations. They encode, normal pro growth, gene pro growth proteins.
How do proto-oncogenes become oncogenes?
They gain activation, mutations that cause pro growth protein to be overly active or overly expressed
So either the pro growth gene is being produced way too much or the pro growth protein is overly active
What gene develop loss of function mutations?
Tumor suppressor genes
These loss of function mutations cause pro growth proteins not to be expressed anymore or when the pro growth proteins are expressed the protein itself doesn’t work anymore
What is the difference between a quiescent phase and a senescence phase?
This is referring to G0 phase where when cells are quiescent they are not growing and dividing, but when there are in senescence, then they are permanently in the G0 phase and they won’t get out of it
What does the phase of the cell cycle we’re going to be in depend upon?
Activity of Kinase complexes called Cyclin CDK’s
What are the two subunits of the Cyclin-CDKs?
- Cyclin - Regulatory subunit
- CDK - it is a kinase. It has a place for ATP to bind
—all kinases need ATP to function
When is the only time a cyclin dependent kinase sub unit is active?
When it’s regulatory subunit, the cyclin is bound to it
How do we regulate the activity of the kinases?
We have to vary the expression of the cyclins
These different kinase activities give us different phases of the cell cycle
What are the 4 CDKs and 4 cyclins we have ?
CDK 4, CDK 6, CDK 2, CDK 1
Cyclin D, Cyclin E, Cyclin A, Cyclin B
Why do different kinase activities give us different phases of the cell cycle?
Because all the kinases have different targets that are needed in different phases of the cell cycle
How do we regulate the activities of kinases to give us oscillations or rhythms of activity?
The oscillations are the result of:
1. CDK phosphorylation or dephosphorylation
2. Controlled degradation of the cyclin subunit
3. Periodic synthesis of CDKs and cyclins
4. The action of specific CDK-inhibiting proteins
True or false in the G0 phase there are no cyclins
True
There are no active kinase complexes here because we are not growing and dividing
When a cell gets signal to grow and divide what will it do?
It will produce the first cyclin, which is cyclin D
Next, it will bind to its CDK (regulated through phosphorylation / de phosphorylation)
—— there is an amino acid (usu. tyrosine 15) that is phosphorylated in inactive CDK…… this phosphorylation blocks the ATP binding site of the CDK subunit
- once we dephosphorylate that amino acid to open up the ATP binding site
- next you have to phosphorylate the threonine 160 on the other side of the protein in order for CDK to be active
— now, you have an active CDK complex
What happens when we receive anti-growth signaling to the cell?
We have to turn off the Growth
Therefore we activate s a protein called DBRP (destruction box recognizing protein) which destroys the cyclin
It does this by binding to the cyclin ubiquitinates it which targets it for degradation by the proteasome
—- the cyclin will therefore be degraded which will put the CDK in an inactive conformation
When a cell needs to grow and divide where should it receive it signals from only?
From the body
-the signals will tell those cells to start producing cyclin proteins so that if they are in the G0 phase, then they will enter the G1 phase where they will undergo DNA replication and cellular division
What kind of signaling will signal to cells to start growing and dividing?
Hormones specifically, peptide hormones or steroid hormones
Those hormones will attach to the receptors that are expressed by the cells that they need to affect which will tell them they need to grow and divide starting a cascade of events that’s going to get the cell ready for cellular growth, and division
Why are the receptors for peptide hormones located in the cellular membrane?
Because peptide hormones cannot cross the plasma membrane
—-when the peptide hormone binds to the receptor, it will change the shape (conformation) of that receptor, and that change is relayed to the inside of the cell
—— then secondary messengers will be made that will activate transcription factors changing transcription and getting the cell ready for cellular division
Why are steroid hormones able to cross the plasma membrane?
Because they are mainly hydrophobic, so the receptors for our steroid hormones actually exist on the inside of the cell
Once active, the nuclear hormone receptors act as transcription factors to change gene expression in order to get the cell ready for cellular growth, and division
What are the receptors that steroid hormones bind to?
Nuclear hormone receptors
How do steroid hormones work taken into account an example of one which is estrogen?
- They are released from females ovaries during puberty and travels through the body to the memory epithelial cells that express the estrogen receptor
- Once estrogen binds to the receptor of the memory epithelial cells, they will then grow and divide Which leads to the development of the mammory gland at puberty
- Once estrogen enters the cell and attaches itself to the estrogen receptors which are each monomer they will dimerize, becoming an active transcription factor.
- The newly formed dimer will then go into the nucleus and bind to its particular DNA sequences, therefore promoting transcription of a lot of pro-growth genes (ex Jun)
Do you estrogen receptors exist on the inside of the cell?
Yes, because estrogen is a steroid hormone, and therefore can cross the plasma membrane to get to the estrogen receptor
True or false when the estrogen receptor is in its inactive state, it exists as a monomer
True and when the estrogen binds to it, it is going to dimerize. Meaning two subunits come together and form an active transcription factor.
What is Jun?
It is a pro growth gene that will act as one part of a transcription factor needed to make our first cyclin in activating the cell cycle related to cellular growth and division of the mammary gland
What does the estrogen receptor which is a nuclear hormone receptor contain that allows it to act as a transcription factor?
A DNA binding domain
Since it is a nuclear hormone receptor, it has a zinc finger motif within its DNA binding domain which allows it to bind DNA in a sequence specific manner
so
the estrogen receptor has zinc finger DNA binding domains.
What happens to the estrogen receptor in some types of cancers?
It will remain active, even when there is no estrogen around
So mutations in the estrogen, receptor will cause it to dimerize, even if estrogen is not around
Once a dimmer rises, it will activate transcription of the pro growth genes even though the cell is not receiving signaling to grow and divide
What targeted treatment do we use for patients that are ER positive?
ER positive means the estrogen receptors are contributing to cancer
Therefore, we use a drug called Tamoxifen
How does Tamoxifen work?
It is an estrogen antagonist, so it is going to go into the cell and bind to the estrogen receptor competing for the estrogen finding site
When it binds the estrogen receptor Tamoxifen causes it to be inactive
—-therefore the mutated ER can no longer stimulate pro growth pathways, which will help stop the cancer from growing and dividing
What is an example of a peptide hormone pathway and how does it work?
RAS dependent pathway is a peptide hormone pathway which is at the heart of the cell cycle stimulating these pro-growth pathways
*** Remember that because peptide hormones cannot cross the plasma membrane their receptors are in the plasma membrane
So, the Receptor Tyrosine Kinase (RTK) is in the plasma membrane
The peptide hormone will bind to the RTK and the signal is going to be relayed to the inside of the cell.
- The peptide hormone binds to RTK.
- RTK phosphorylates itself on those tyrosine amino acids that it has which become binding sites for other proteins that are needed in this pathway.
- SOS will bind to RAS (its target protein and main switch for this pathway) which is inactive and tell RAS to let go of its GDP in exchange for SOS’s GTP.
- RAS is now active
- RAS will now stimulate the rest of the pathway to change gene expression in order to promote this growth pathway
- Eventually, the cell is going to receive signals telling it to stop growing and dividing.
- So we need to turn off this pathway.
- RAS will bind to GAP which will cause it to hydrolyze GTP into GDP which will put RAS back into its inactive state
What is SOS?
It is a guanine nucleotide exchange factor meaning it’s going to bind to a target protein, and tell that protein to let go of the guanine nucleotide it’s holding in order to bind another guanine nucleotide
When there is no more signaling and no more recruitment of SOS one what does the cell need to do?
It needs to put RAS back into the inactive state.
1.
True or false RAS is a GTPase that can hydrolyze GTP by itself
False although RAS is a GTPase that can hydrolyze GTP. It cannot do it by itself.
It will need to be bound to a GTPase Activating Protein aka GAP
Why is RAS usually inactive in our cells?
Because most of our cells are not growing and dividing, so there’s no need for RAS
What is the difference between the active and inactive state of RAS?
When RAS is bound to a GTP molecule the gamma phosphate of the GTP interacts with the amino acids on the RAS‘s arms
This particular confirmation allows RAS to bind the next protein in the pathway
However, when RAS hydrolyzes GTP to GDP, the Gamma phosphate of that GTP is no longer there so the bonds it formed with the amino acids of RAS‘s arms also disappear, and therefore those arms will splay out——> meaning RAS can no longer bind the next protein in the pathway ——>meaning RAS is inactive
What happens when RAS is activated?
It signals a signaling cascade
- In its active conformation RAS binds the next protein which is RAF (a kinase)
—— RAF has many cytoplasmic targets that are involved in getting ready for the cell cycle (this increase nutrient uptake, changes in cell morphology, etc) - RAF phosphorylates MEK (another kinase)
—- MEK will now phosphorylate different cytoplasmic targets than RAF that are involved in pro-growth pathways - MEK will phosphorylate ERK (another kinase)
—— ERK will phosphorylate a lot of other cytoplasmic targets that are different than MEK
——It will also phosphorylate some transcription factors - ERK phosphorylates ELK (transcription factor)
—- ELK has DBD’s (DNA binding domains) so when it binds DNA it upregulates transcription of a lot of pro-growth genes (ex FOS) - So, ELK binds the DNA in the nucleus which produces FOS which is the 2nd half of this important transcription factor needed to create Cyclin
So what are we doing with the signaling cascade of the RAS dependent pathway?
- We are activating the kinases in the signaling cascade in order to amplify the original signal, and we are also ❤️ 2. diversifying that original signal because we are phosphorylating and activating a number of different things involved in all the processes needed for cell growth and division❤️
How do we turn off all the kinases in the RAS dependent pathway when we need to turn off the pathway completely?
We use protein phosphatases to remove phosphate groups from the kinases
True or false the RAS dependent pathway is full of proto-oncogenes
True
What transforms RAS into RAS oncogene?
RAS mutations occur in a large percentage of pancreatic colorectal and non-small cell lung cancers
Normally, the glycine in an RAS gene mutates glycine at position 12, G 12 (very important for RAS’s GTPase activity) which is found in its GTP binding site
The mutation is :
G12C meaning G is the wild type and C in this case is the mutant amino acid that the G changes into and in the middle of the wild type and mutant we put the position so in this case we have G12C
—— therefore with C being there instead of G that means RAS cannot hydrolyze GTP ——>means once RAS binds to GTP, it stays active because it cannot hydrolyze GTP to go back to its inactive state——> this then contributes to the development of cancer because RAS will continue to stimulate pro-growth pathways even when it should not be
How does the RAS inhibitor work?
It only binds to RAS’s that have a C at the 12 position (only binds to the mutated RAS)
It will trap RAS in the inactive state bound to GDP … this will keep RAS from ever exchanging it for GTP … which will keep it from ever being activated…. Therefore it cannot stimulate pro-growth pathways
Where is the mutation of RAS’s G 12 amino acid normally found?
A lot of lung cancers
What is licensing?
It prevents an origin from being used more than once during a round of replication
What results in amplification?
Sometimes an origin bypasses licensing and is used more than once so a region of DNA is duplicated more than it should be.
If the cell’s don’t remove this extra piece of DNA then amplification can happen
What is amplification?
This is where the number of the gene copy increases
We should only be getting two copies one from mom and one from dad
But when you have more copies like five copies 10 copies or 20 copies, each copy will be producing pro growth, protein and so this protein is going to be way over expressed in cells
What is an example of amplification?
HER2 - it is a Receptor Tyrosine Kinase (RTK) that can activate the RAS dependent pathway
It exists in the plasma membrane of cells that are not growing or dividing
—- so a normal one of these cells should have a very low level of HER2
HER2 exists in the plasma membrane as a monomer in the plasma membrane and binds its target molecule…. Once it does that it dimerizes and activates the RAS dependent pathway
So when there are so many HER2’s in an abnormal cell they will run into each other and dimerize and therefore activate RAS dependent pathway even when they shouldn’t because there is no target there
What is the targeted treatment for HER2 positive breast cancer?
Herceptin which is a synthetic antibody
It finds the cancer cells expressing HER2 and it will bind to a monomer of HER2 and trap it in its monomeric state meaning it won’t be able to dimerize …. Meaning it won’t be able to activate the RAS dependent pathway
Because it is a synthetic antibody the cells will have much of the Herceptin antibodies on their cell surface which will activate the patient’s immune system….
The Killer T cells will see this and destroy the cell layered with the antibodies
25% of breast cx are HER2 + so Herceptin is useful and results in a 84% survival rate
What are the checkpoints for in the cell cycle and what are they caused by?
They are meant to check if the DNA is OK and ready to replicate before progression in the cell cycle
The inhibitors are what stops the cell cycle at these checkpoints
What are the two things we need in order to leave G0 and go into the G1 phase of the cell cycle?
We need cellular signaling such as what comes from the RAS dependent pathway and a very special transcription factor called activating protein or AP1
What is AP1 made of?
Two subunits: JUN and FOS (both activated by the RAS dependent pathway)
AP1 Will bind to its specific DNA sequence located in lots of pro growth genes
—-this will help activate their transcription
Which gene will AP1 activate that is needed to go from G0 to G1?
Cyclin D (the first cyclin needed to enter the cell cycle)
When are we officially in the G1 phase?
Once AP1 is activates transcription of cyclin D, and it is produced, we are officially in the G1 phase
What is AP1 DNA binding domain and what does it allow it to do?
It is a leucine zipper and it gives it the ability to bind DNA in a sequence specific manner
FOS makes up one alpha helix and JUN makes up the other alpha helix
—-both he will see is dimmer eyes and that allows AP1 to bind to DNA in a sequence specific manner
So, AP1 is able to bind to genes upregulating them
What is MYC up regulated by and what is MYC? What does it do?
MYC is histone acetyl transferase or HAT that is upregulated by AP1
As a HAT it will go to the pro growth proteins and acetylate their histone tails which will open up their chromatin structures, making it easy to transcribe these pro-growth genes….. this will then help with the progression through the cell cycle.
So MYC and AP1 up regulate cyclin D gene (progrowth gene) transcription which starts the cell cycle
True or false once we are in the G1 phase, we are committed to DNA replication and cellular division
False. In order to get into S phase where we have DNA replication. The cell must overcome the restriction point in G1 which is a checkpoint
So we are going to have to make enough pro growth proteins to get over the restriction point which is a wall of several tumor suppressor genes of inhibitors
Once we are over that wall, we are committed to DNA replication and we are going to enter S phase
What is the restriction point of G1 made up of?
Tumor suppressor genes of inhibitors of the cell cycle
So what specifically makes up the restriction point?
It is made up of inhibitors of our CDK complexes (which blocks the cell cycle from progressing)
What is driving the cell cycle?
CDK complexes which pushes us into the next phases of the cell cycle via their activities
What are the two types of CDK inhibitors?
- INK4 or Inhibitor of CDK4 proteins - it will bind the CDK subunit (half of the whole complex), blocking the cyclin from binding
Remember if a CDK can’t find its cyclin it won’t be an active kinase
- CDK interacting protein or CIP: binds to the whole cyclin CDK complex and inhibits it’s kinase action
Commonly these two types of CDK inhibitors are used to inhibit these kinases from phosphorylating things from progressing to the next stage of the cell cycle
So these are the inhibitors that we have to outcompete by building up a large concentration of cyclin CDK’s
—-meaning there will be so many cyclins and CDK‘s in the cell that there’s not enough inhibitors to inhibit all of them…. allowing us to move past the restriction point and start the S phase.
So how is a normal cell supposed to get from G1 to S phase when it has a double stranded break and it’s DNA or any kind of DNA damage?
Well, the transcription factor P53 will be activated and it will stimulate the transcription of DNA repair genes, but also cell cycle inhibitor proteins
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P53 will then up regulate the gene called P21, which is a CIP inhibitor
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CIP inhibitor will bind to the CDK cyclin complexes to block their activity and therefore blocking progression through the cell cycle
⬇️
Once the DNA damage is fixed, then P53 will no longer be activated, and P21 will no longer be produced
⬇️
The kinase complexes will be active and they will phosphorite the pRb/E2F (stimulates itself as well) complex, which will activate our replication proteins, officially moving us past the restriction point into the S phase, which now commits us to DNA replication and cellular division… meaning we are not going back
What DNA replication genes will E2F
Stimulate transcription of ? And what prevents it from doing so?
1) cell machinery genes: It will activate more cyclins and CDK‘s that we need for S phase
2) pro growth transcription factors and genes which includes itself (so it is stimulating its own activity) and MYC HATS that open up chromatin structure,
3) components of DNA replication machinery: replisomes
4) genes encoding structural proteins of chromatin : stimulate transcription of our histone genes because it is instrumental in duplicating the genome to give us double the number of histones for the other genome we are creating
What is pRB to E2 F?
It is retinoblastoma protein that acts as a co-repressor that binds the transcription activation factor E2F which arrests cell division
What is retinoblastoma Rb?
It is cancer of the retina
Sporadic retinoblastoma: patient inherits two copies of Rb gene … leads to sporadic tumor in one eye
- both copies of good Rb gene have to be inactivated for this to happen
Familial Retinoblastoma: they inherit one bad copy (defective copy) of Rb either from mom or dad
—- they are starting life with every single cell of their body only having one good Rb gene
—- they have two independent tumors bcuz there risk of developing retinoblastoma is much higher than in sporadic retinoblastoma
What is the two hit hypothesis?
It says in order to get lots of function of a tumor suppressor gene. You must have two hits one in each copy of the gene.
One hit causes you to only have one tumor suppressor gene to stop the progression of cancer
Which tumor suppressor gene is mutated in about 50% of all human cancers?
P53
Because it is central to stopping the cell cycle
A first hit to the p53 gene due to a mutation from a deletion, nonsense, missense or epigenetic silencing can cause heterozygosity meaning it has one good gene and one bad gene…. Meaning it is still able to function to keep the cell normal
2nd hit from mutations or epigenetic silencing causes loss of heterozygosity which results in both bad genes and contributes to the development of cancer
**remember when there is DNA damage p53 will be activated , and since it is a transcription factor it has a DBD which is a zinc finger so it will bind to genes involved in cell cycle arrest, DNA repair, and if bad enough it will activate genes involved in senescence and apoptosis
What kind of ligamer is P53?
It is a tetramer —— binds to the DNA with four copies or subunits of p53
—— when it is phosphorylated then it is active
—- it will activate genes involved in repair or cell cycle arrest
What is the exception to the two hit hypothesis?
1 hit can destroy all p53
This is a missense mutation in the zinc finger DBD which causes it to misfold and therefore no longer bind DNA
So in the cell youll have a bad copy that cant bind dna and a good one that can (wild type)
But because p53 binds as a tetramer these two types will randomly mix to form tetramers
If just one of these subunits is a mutant the entire tetramer cannot bind DNA and therefore there will be no activation of transcription
How many mutations does it take in oncogenes and tumor suppressor genes before cancer begins?
6 - 12 mutations
