Chapter 20 Flashcards
(108 cards)
1
Q
True or false: in one way or another, all diseases are related to our genetics in some way.
A
True.
2
Q
What can be said about cancer in relation to genetics?
A
It is certainly linked to our genetics.
3
Q
Define what a tumor is.
A
A tumor is the result of rapid cell growth compared to the nearby cells.
4
Q
What is the difference between benign and malignant tumors?
A
Malignant tumor cells do NOT communicate properly with neighboring cells - they may travel in the blood to other tissues.
Benign tumor cells DO still communicate properly with other tissues, meaning they will stay where they are.
5
Q
How are the cell cycles of normal cells different from those of tumor cells?
A
Normal cells have a balanced cell cycle with equal time spent in each phase, regulated by functional checkpoints.
Tumor cells, however, have shortened G1 and G2 phases due to defective checkpoints, a slightly longer but error-prone S phase, and often bypass G0, leading to continuous, unchecked proliferation.
6
Q
What prevents cells from ‘wandering’?
A
Cadherin proteins are cell adhesion molecules that form junctions between cells that are the same type.
7
Q
In regards to signal transduction, what do cadherins allow cells to do if say a liver cell linked to another by a cadherin bumps into a kidney cell?
A
It will allow cells to communicate with each other via signal transduction pathways to downregulate genes that contribute to proliferation - stop growth of cells in inappropriate places.
8
Q
What is it called when a cell moves to another part of the body?
A
Metastasis
9
Q
What happens to malignant cells in regards to other cells and their respective systems?
A
Malignant cells lose their ability to care about signals from other cells and they also oftentimes lose their ability to make proteins that keep them in their respective systems.
10
Q
How does cancer kill you?
A
When cancer starts to affect an important organ; cells that normally keep you alive in these organs can get displaced by cancer cells.
11
Q
In G1 and likely G2 and S phase, cyclins are _______________ made.
A
progressively
12
Q
If the cell wanted to make a particular cyclin how would that happen?
A
RNA Polymerase would bind to the TATAA box up stream of the gene for the specific cyclin and after the mRNA is made it would need to be processed and then translated.
13
Q
True or false: only a few cyclin are needed to progress into the cell cycle.
A
False, a lot of cyclins need to be made to have enough to bind to enough CDKs for progression to happen - it takes a little while for this to happen.
14
Q
Take for example, cyclins being made during G1 to promote the progression of the cell into S phase.
What do the CDK’s do that are being turned on by these cyclins?
A
They are phosphorylating activators that will push the cell to make proteins that we will need during S-phase: DNA ligase, DNA poly, ss binding proteins etc.
In other words, the cell does not go into S phase and then decide to make proteins it needs for replication.
15
Q
What are proto-oncogenes?
What is one mutation that could occur that won’t cause cancer?
What is one that could cause cancer?
A
They are genes whose products promote the forward movement of the cell cycle.
If the gene undergoes a mutation that makes it not work, that would not cause cancer.
If the gene undergoes a mutation that gives it a more stable half-life, that could cause cancer.
16
Q
True or false: Mutations in proto-oncogenes always result in an oncogene.
A
False
17
Q
When it is said that proto-oncogenes act in a dominant fashion, what does this mean?
A
Even if only one of the genes for a particular proto-oncogene becomes oncogenic, we have issues.
More progression than is normally granted will happen.
18
Q
What are tumor suppressor genes?
A
They are genes whose protein products will slow or inhibit the cell cycle.
19
Q
If a certain mutation of a tumor suppressor caused a lack of function within the protein product, would this be harmful?
A
Yes, any mutation that breaks or denatures the protein is no bueno.
20
Q
When it is said that tumor suppressor genes are recessive, what does this mean?
What did we call this in cancer bio?
A
It means that both alleles for the gene must be mutated for it to be certainly harmful.
This idea is called Knudsen’s two hit hypothesis.
21
Q
True or false: miRNA genes typically only act like proto-oncogenes.
A
False.
They can act as either proto-oncogenes or tumor suppressor genes.
22
Q
What are mutator genes?
What would happen to other cancer genes without mutator genes?
A
They are genes whose protein product acts to repair damaged DNA.
Without these, tumor suppressors and proto-oncogenes would be more prone to mutations.
23
Q
What is an example of a mutator gene that you can think of from Cancer Bio?
A
BRCA 1
ATM kinase
the genes involved in coding proteins involved in mismatch repair or otherwise
24
Q
Explain the EGFR signalling pathway as it was described in cancer bio in the context of proto-oncogenes.
What are the possibilities of consequences that mutation could have on this pathway?
A
In response to a growth factor, the EGFRs will dimerize and auto-phosphorylate each other.
This creates docking sites for signalling molecules like Grb2, which bind to the EGFR intracellular domain via its own SH2 domain. Grb2 then recruits SOS, which will activate RAS by exchanging GTP for GDP.
Active Ras has a GTP bound to it. Ras has the ability to self regulate, but with the help of GAP it can do so more efficiently.
Active Ras will turn on the MAPK pathway on by activating Ras, Ras to Mek, Mek to MAPK.
As this is happening, Src protein is also recruited to the EGFR upon its activation, and acts to amplify and diversify the signal.
MAPK will then enter the nucleus and activate transcription factors for something like cyclins or E2F.
Mutations within this pathway can cause it to be “on all the time - constituent - and always turn genes involved in proliferation on even without a growth factor signal.
25
If you are born with a mutation (germline mutation) on one of your alleles for Rb, why would it be more likely for you to get a second hit vs. someone else how simply obtained a mutation on one of their alleles on a somatic cell?
There is just a much higher relative chance for you to get another mutation on the other allele if you have a germline mutation because that is in every cell.
It would be very unlikely for you to get another mutation on the same exact cell that obtained the mutation in the first place.
26
What is pRb?
This is the protein product of Rb gene.
27
What does pRb normally do?
It has the normal function of binding to E2F and preventing the progression of the cell cycle from G1 to S
28
What must happen to pRb so that it will "let go of" E2F?
It must be phosphorylated by a CDK
29
What does E2F do?
E2F is an activator that binds to enhancer sequences and mediator, thereby activating the genes associated with progression of the cell cycle to S phase.
30
Would E2F be considered an proto-oncogene or a tumor suppressor?
If it is able to bind to an enhancer sequence and mediator, it would be a proto-oncogene.
31
What would happen if someone was recessive for pRb?
It would mean that no functional pRb could be made, and that cells would have no way of preventing a G1 to S transition.
32
What does Mdm-2 normally do within the cell?
It normally stimulates the degradation of p-53 in the cell.
33
What happens when DNA damage is induced to the cell?
Both p-53 and Mdm-2 get phosphorylated.
This phosphorylation prevents Mdm-2s ability to bind, mark and degrade p-53, so we get an accumulation of it in the cell.
34
With p-53 now free to roam, what will it act as?
P-53 will act as an activator for various genes.
35
What safety mechanism that p-53 is involved in is listed as really good for when DNA damage happens?
P-53 will bind to an promoter region of the WAF1 gene, which will activate its transcription, leading to the mRNA that will be translated into P-21.
36
What does P-21 act to do within the cell?
It acts to bind to the Cyclin-CDK complex and prevent the CDK from phosphorylating pRb, giving the cell time to fix the mutation/damage.
Specifically CDK 4 and Cyclin D
37
What safety mechanism that p-53 is involved in is listed as pretty good for when DNA damage occurs?
p-53 will bind to a promoter region upstream of the gene for promiscuous DNA Poly, which will activate its transcription.
38
True or False: the gene for promiscuous DNA Polymerase could be deemed a mutator gene.
True
39
What does promiscuous DNA Poly do?
It helps to repair the DNA to an extent, even though it is not as accurate as the other polymerases.
*ASK DR. C ABOUT THIS*
40
What is the safety mechanism that involves p-53 is listed as poor?
This is when p-53 binds to a promoter for the gene Bax, thereby activating its transcription.
41
What is Bax responsible for?
Bax is responsible for binding to and neutralizing BCL2.
An inactive BCL2 will stimulate apoptosis.
42
What are BRCA-1 and
BRCA- 2 gene mutation associated with?
They are associated with an increased risk of breast cancer.
Women how have a germline mutation in these genes have a much higher rate of breast cancer and cervical cancer.
43
What is BRCA-1 gene involved with?
What will happen when there is no function of BRCA1?
It is involved with fixing DS breaks.
Without BRCA to assist in fixing DS breaks, there will be breaks in tumor suppressors, breaks in proto-oncogenes
44
Walk through the steps of homologous recombination as they were stated in Cancer Bio during the fixing of a double strand break.
1. When a double strand break happens, ATM kinase is activated.
2. ATM kinase activates RAD 50 complex, which creates clean 3’ ends that have overhang, which is important in later steps.
3. Then BRCA 1/2 will transport RAD 51 to the nucleus which, with the help of RAD 52 will bind to the exposed overhung ends.
4. Then, the RAD 51 attached single strands will invade the duplicate sister chromatid and exchange the homologous sequence. The sequence from the sister chromatid acts as a template for repair.
5. Now, with the additional repaired sequence on each single strand from the initial break, other enzymes called resolvases will restore the junctions that were made.
This leaves two copies of intact DNA at the end of the process.
45
Why can miRNA be considered either a tumor suppressor or a proto-oncogene?
Because miRNA can either degrade mRNA transcribed by genes that are responsible for suppressing tumors or for promoting the cell cycle.
46
What is Let-7?
What does it do?
It is an miRNA that is considered a tumor suppressor gene product.
It forms a RISC complex that degrades RAS, which is a G-coupling protein in the EGF pathway.
47
What happens in regards to Let-7 to many people who have cancer?
It could have a mutation that causes it to be missing.
The result: No RAS mRNA is degraded and we see way too much RAS
48
Describe the domino effect that not degrading any RAS has on the rest of the EGF signalling pathway.
Because RAS is a G-coupling protein in many different pathways, we see an amplified RAS signal
Just a few examples from the EGF pathway would include
1. More RAF activated (MAPK)
2. More MEK (MAPKK)
3. More ERK (MAPK)
4. More transcription of target genes.
49
What is the mechanism for treatment for people who have no expression of Let-7?
The goal is to deliver Let-7 to those people's cells.
This is a growing area of research.
50
What is Quantitative Reverse Transcriptase - PCR or (qRTPCR)?
Helps us identify the amount of mRNA in cells.
51
What is the first step in qRTPCR?
You take cancer cells that are expressing high levels of Ras or another analog.
1. In one group you insert the Let-7 in a fat globule into the cells.
In another group you insert just the fat globule
52
What is the second step in qRTPCR (the RNA isolation), and how does it work?
2. After some time, you isolate the mRNA from those cells, by first isolating the RNA and then running that through a column that has Thymines inside of it so that the poly A tails may stick to it. After throwing out the stuff that moves through you elute what you want.
53
What is the third step in qRTPCR (the RT step), and how does it work?
3. Then you take the mRNA that was isolated and you use RT to get ds DNA from it.
To do this you add a primer to the mRNA (usually at the poly A tail) and insert the RT enzyme.
Then, a nicking enzyme is used to introduce ss breaks in the cDNA to allow strand displacement, improving primer access and preparing the template for efficient PCR amplification.
54
What is the fourth step in qRTPCR (the PCR step), and how does it work?
4. This step is the normal PCR reaction of the Ras gene(ex) with a forward primer and reverse primer.
a. 95 degrees celsius denature
b. 55 degrees celsius annealing (just the primers)
c. 72 degrees celsius extension
55
Walk through how the results from PCR are analyzed (quantity) which is the fifth step.
The use of the thermal cycler is very important in this:
With SYBR green in the tubes inside the thermal cycler, which will bind to the dsDNA, after each step the cycler will analyze the amount of glow that we get.
Because we are running two different PCR reactions, we can look at the difference of glow we get per step.
56
What becomes an issue in qRTPCR regarding the number of cells that we took the RNA from initially?
If we had a variable amount of cells in each case (control/experimental), then how would we know if the group without the Let-7 just had more cells and more mRNA was taken as a result.
57
How do we combat the fact that we don't really know how many cells we had in each case?
We introduce an internal control.
This includes GAPDH primers which will facilitate PCR of genes that are called housekeeping genes.
Housekeeping genes are genes that all cells use at the same rate.
58
Now that we have chosen an internal control, what should we do?
We complete the steps the same exactly way, with the primers for the housekeeping gene added INTO each case to also give us a look at the amount of gene that was made in the PCR for each step, which also gives a relative size of the population of cells for the control and the experimental case.
59
If the control had twice the amount of GAPDH PCR product for each step, what does this tell us?
If we had much less of the RAS protein in the experimental step, and much more of that protein in the control, and this seemed to be a great success, say 40 to 8 by the 3rd step,
It tell us that because there was 2 times as many cells in the control, we still had success, but not successful as we thought.
60
Is miRNA 373/372 a tumor suppressor or a proto-oncogene?
What does it do?
It is a proto-oncogene.
It degrades LATs mRNA
61
How do we get such an increase in miRNA 373/372?
There is a point mutation within the enhancer region of miRNA 373/372 so that the activator for it sticks better.
62
What does LATS act normally?
Because it normally acts to chew up LATS mRNA, but if we have way TOO much of 373,372 miRNA, it chews up all of the LATS.
Now, LATS acts to bind the repressor protein of p-53 which is usually present in the cell in high conc. - this results in the repressors NORMALLY being bound by LATS so that p-53 may be transcribed
63
Why is 373+372 mRNA considered a proto-oncogene?
This is because when miRNA 373 and 372 is made way to much, for reasons described earlier, we see it chewing up all the LATS mRNA, resulting in p-53 being highly repressed.
I.E the LATS protein is not present, it cannot bind the p-53 repressor, and the unbound repressor may bind to the silencer region, of DNA for the p-53 gene, and no GTFs will be assembled.
64
Why are mutator genes so important?
They are supposed to fix DNA, but if they are not functioning correctly, (dimers for example) can accumulate and cause tumor suppressors to not work, or turn proto-oncogenes to oncogenes.
65
Describe the step-wise nature of cancer formation.
We have cells that are dividing, and one of them obtains a mutation.
From that cell on, we see an accumulation of mutations that cause an array of problems each time, until we get a cell that can grow uncontrollably.
Essentially, the more accumulation of issues that we have, the better the chance that a cell from its progeny will lose another control mechanism.
66
What is normally in place to kill cells that mutations that give them advantages?
What do cancer cells need to do to grow rapidly and avoid immune destruction?
The immune system is in place to destroy cancerous cells.
To grow rapidly, cells need to produce other types of proteins that give the friendly signal to the cells of the immune system.
67
Do all types of viruses cause cancer?
What percentage of cancers are caused by viruses?
No only a low percentage.
15%
68
Describe the two classes of viruses.
1. Retroviruses - all retroviruses are viral in origin, but they DO NOT carry cancer causing genes, instead they carry genetic info that gets inserted into the genome, and cause mutations in TSGs and proto-oncogenes.
2. DNA Viruses - very small percentage of these - called DNA Tumor viruses - do carry viral oncogenes (genes that trigger cancer)
69
Describe the structure of a Retrovirus and what is contained inside.
Enclosed in a lipid bilayer called the viral envelope. and contains proteins called caspid protein that protects the viral RNA genome.
Also has spike proteins that interact with/stick to something on our cells.
Also contains reverse transcriptase and Integrase.
70
Explain the typical events that would occur in a retrovirus infecting a host.
The spike proteins on the virus would attach to the host cell. (attachment)
The nucleic acid gains entry (there are several ways) and along with it comes the enzymes that were mentioned including RT and integrase.
Then we see RT of the viral RNA and integration of the ds DNA into the cell's genome at a random location by integrase.
71
What is the virus called once it has been RTed and is integrated into the DNA?
This is called the pro-virus.
72
What is it called when the virus is actively reproducing - making new virus via transcription and translation of viral DNA?
This is called the lytic phase.
Immune system notices and kills those cells.
73
What is the latent phase?
Does everything in the process up to the provirus.
This allows the surrounding immune cells to think the host cell is fine, because it is not producing any viral proteins.
74
Talk about the progeny of the cells that contain pro-virus.
Why does this make sense evolutionarily?
Each progeny of the infected cell will contain pro-virus as it is apart of the genome now.
The mechanism makes a lot of sense because they are very very successful at propagation which gives the provirus time to spread.
75
What happens over time as the virus goes from latent to lytic phase?
More and more genes will get interrupted allowing our genome to get more and more interruption of tumor suppressors / proto-oncogenes / mutator genes.
76
How can a RNA virus cause cancer?
1. The provirus could be inserted right next to a human gene, so that the viral promoter controls the human gene.
2. It could also be that the RNA virus now obtains a human gene that will be present in the provirus.
Both these ways can result in more / overexpression of a proto-oncogene.
77
Explain the idea of a transforming virus.
The genetic components that make up a pro virus that encodes 6 genes of which 4 make up the viral fragment (the pieces required to physically make a new virus), and two that make up a tyrosine kinase (Src) get transcribed and translated to form a new virus during the lytic phase.
This goes on to infect other cells, which already contain the src gene. The provirus makes its way in the DNA at a random location and now the cell contains another copy of the src gene.
78
What determines the specifics of a virus?
How much nucleic acid that it can carry.
79
How are DNA tumor viruses different than RNA viruses?
They carry viral oncogenes on their own and rarely integrate into a host's genome.
80
What is contained in a DNA tumor virus?
1. Spike proteins
2. Capsid proteins
3. Viral protein
4. E6 protein
5. E7 protein
81
What does E6 do?
It sequesters the action of p-53
82
What would happen if E6 sequestered the action of p-53 regarding the proliferation of cells?
The cell would not be able to pause when there is DNA damage.
mdm2 usually marks and degrades p-53, but when DNA damage happens, they both get phosphorylated and p-53 accumulates, acting as an activator for p-21 that bind various cyclin-cdk complexes making them inactive.
83
What does E7 do?
It sequesters the action of pRb, so pRb never sticks to E2F and the cell can always proliferate into S-phase.
84
Describe the process of how the immune system recognizes a virus that is in the lytic phase and kills cells producing viral proteins via cytotoxic T-cells.
When foreign proteins invade the cell and are taken in as a phagosome, then fused with a lysosome, they form a phagolysosome.
The parts of the particles contained in the phagolysosome are presented on the surface of the cell in MHCI and MHC II complexes.
Cytotoxic T-cells will interact with the antigen presented on the MHCI complex via their t-cell receptor in coordination with CD8 co-receptor.
They will then proliferate and recognize cancer cells that are presenting this antigen on their surface, to force cells to undergo apoptosis.
T-regulatory cells then come in and shut down the immune system.
The immune system then saves a bunch of the OG cytotoxic T-cells and stores them in our lymph nodes.
85
What about the immune system acting via T-helper cells?
T-helper cells will bind via their unique t-cell receptor and by the CD4 co-receptor. Binding causes the T-helper cells to release cytokines that stick to B-cells.
B-cells have unique gang signs or (B-cell receptors) and they can:
1. Become plasma cells (make antibodies)
2. Become memory B-cells that get stored in our immune system.
86
Generally speaking what are the 3 types of method for treating cancer that we talked about?
1. Traditional
-Chemotherapy
-Radiation
2. Targeted
3. Immunotherapy
87
Describe what the basics of chemotherapy entail.
In chemotherapy we are going out of our way to create mutations either using base analogs (things that look like normal bases but will cause mass mutations) as well as base modifying agents, which modify tons of the DNA and cause mass mutations
The result of this is that the issues will either be resolved meaning that during S-phase, base excision repair should happen and we make good DNA, have good genes and good proteins, OR that the issues are not resolved and the cell should undergo apoptosis.
88
Explain the reasoning behind chemotherapy and why it is successful.
Healthy cells will have lower relative cell death rate because their cell cycle gives them time to pause during G1 and G2 to carry out base excision repair, nucleotide excision repair, and mismatch repair to fix the mutations.
Cancer cells will have higher relative cell death rates because they divide quicker, have a quicker s-phase, etc.
89
What allows healthy cells to have a higher survival rate during chemotherapy?
When we purposefully damage DNA, the cells will see an increase in p-53 because both it and mdm2 were phosphorylated upon detection of damage.
p-53 will act as an activator for p-21, which binds cyclin cdk complexes, arresting the cell in G1, giving us time to repair the cell.
90
What are the three proteins that are the basis for the diagnosis of triple negative breast cancer?
1. Estrogen receptor
2. Progesterone receptor
3. Human epidermal growth factor receptor (HER-2)
91
What does having triple negative breast cancer mean in regard to targeted therapy?
There are no targeted therapy options for patients.
92
What are TSAs?
aka (tumor specific antigens)
These are proteins that are only expressed on cancer cells (in adults)
93
What are TAAs?
aka tumor associated antigens
These are proteins that are expressed in high levels in cancer cells and low levels in normal cells.
94
What is the reasoning for why we would have genes that express proteins only when they are on cancer cells?
The real reason why that gene might exist is because they were needed at some point.
*those genes should never have been turned back on, but cancer cells will do this when they want to grow quickly.
95
What is Chondroitin Sulfate A?
It is a TSA that triggers blood vessel development which allows for more blood flow to the tumor.
96
Where would we normally see CSA upregulated in healthy tissue?
We might see it upregulated in placental cells.
97
Explain the process in which an antibody for say a random TSA is made.
1. Insert said TSA into a rabbit or something with a robust immune system.
2. Inside the rabbit's body the foreign proteins will be taken up in a dendritic cell (or a macrophage) via a phagosome and fused with a lysosome to form a phagolysosome. This then gets displayed on both MHC1 and MHCII complexes on the surface of the cell. This display on MHCII complexes will get recognized by T-helper cells via their T-cell receptor with help of the CD4 co-receptor. T-helper cells then release cytokines that will stick to B-cells and cause them to proliferate and differentiate into plasma cell that create antibodies for the rabbit in high amounts.
3. Now that we have a rabbit with a bunch of antibodies that recognize the different parts of the TSA. So now, we take blood from the rabbit and put into a column that has protein Kinase A (a bacterial protein) that sticks to all antibodies at the shoulder part.
4. Then we can take those different antibodies shown with different gang signs because they could have been made from different B-cells that differentiated into plasma cells with something radioactive. We don't really need a whole lot of radiation b/c it will only bind to cells that have the TSA.
98
What are the two ways that cancer has been viewed as historically?
1. Cancer is a result of when every individual has 70 trillion cells and one of them become cancerous and that spreads within that person to be a tumor.
2. We frequently have cells that could become cancerous, but the immune system will recognize and destroy them.
99
How does the immune system achieve this?
1. The cancer cell expresses a protein that is NOT normally seen in adult cells, and the B-cells and T-cells will recognize this.
100
Where do B-cells reside?
They reside in the bone marrow, bouncing around with their unique gang signs, coming into contact with all kinds of proteins made in the body.
101
How do we prevent autoimmune diseases normally?
If a B-cell has a unique gang sign that binds to something in the bone marrow, it will undergo apoptosis - we don't want B-cells out and about making ourselves sick of self proteins.
102
How long do B-cells last, and how is it permitted to enter the rest of the body?
They usually last around 3 weeks, and if it does not bind to our self-proteins, it is allowed in the body.
*If a tumor is only in the body, not in the bone a marrow, a B-cell could bind a tumor
103
Explain the process by which B-cells fight cancer.
It is the same process that we have described before, where the TSA expressed by the cancer will be taken up by a macrophages / dendritic cell and displayed on MHC II and MHC I complexes.
Blah blah blah, the B cells that are activated by cytokines released by T-helper cells interacting with MHCII complexes will bind different parts of the TSA and create antibodies unique to their gang signs once they are plasma cells.
These antibodies will bind to the cancer cells that are producing the TSA and this will recruit Natural Killer Cells to bind at the shoulder region, that will release toxins to fight the tumor.
104
How do T-cells fight cancer?
T-cell do the same thing as B-cells in this context, but in a little different way.
These are the cytotoxic T-cells that have a t-cell receptor that is very diverse, but not as diverse as antibodies.
They mature in the thymus - same idea as B-cells.
These will bind to MHCI complexes and via their T-cell receptor and release cytokines that will fight tumor cell.
105
How does a cancer cell periodically escape?
They produce proteins that are not normally produced and some of these proteins can cause our immune system to shut off.
106
How do Cancer cells trick our immune system?
All types of T-cell will have what is called PD1 receptor.
Some cancer cells will express a protein called PDL -1 which stands for ligand because it will bind to the PD-1 and send a signal that says "I'm a friend, I'm one of you"
The result is that T-cell will stop releasing cytokines.
107
What is immunotherapy?
We generate an antibody that covers up either the PD-1 or PDL-1 that prevents the cells from sticking together.
108
