Cancer biology final exam review

What is a tumor

is a group of cells growing out of control that disrupt the normal morphology of the tissue

What is the fundamental differences between benign and non-benign tumors?

Benign tumors are non-invasive meaning they have not yet breached the basement membrane. The non-benign tumors have breached the basement membrane and have the ability to create metastases by cancer cells enter the blood steam. Non-benign/malignate are more serious, because the metastases can form new tumors in different parts of the body.

Describe the basic epithelia cells tissue architecture

A thin layer of cells that are connect to each other via E-cadhereins and are attached to the basement membrane via hemidesmosomes. The BM separates the epithelial cells from the stromal layer.

How do normal cells work together to maintain tissue architecture

Cells communicate with each other via cell-to cell signaling to maintain their architecture.

What goes wrong in cancer cells leading to tumor formation

Mutations to the genes can cause the cancer cells to act autonomously and start dividing on their own.

Where did the sarcoma virus get v-Src

The virus acquired normal src gene from chicken in the past. The phosphorylation of a substrate caused a mutation of a proto-oncogene to an oncogene.

Explain how energy metabolism of cancer cells is different from normal cells.

In normal cells,


1. glucose enters the cell through the GLUT 1 receptor
2. After glucose enters the cell, it is converted into a 6 carbon sugar that begins the process of glycolysis
3. During the last stage of glycolysis pk-m1 converts pep to pyruvate
4. Pyruvate is then oxidized by the pdh causing pyruvate to be converted to acetyl coa
5. The acetyle coa enters the mitochondria and begins the Krebs cycle

In cancer cells, even in the presence of oxygen.


1. a larger amount of glucose is taken into the cells due to the up-regulation of the GLUT1 receptors (effect of mutations)
2. After glucose enters the cell, it is converted into a 6 carbon sugar that begins the process of glycolysis
3. Due to the genetic mutations, the pk isoform m2 is being expressed. This isoform converts pep to pyruvate.
4. The pkm2 isoform blocks pdh from interacting with the pyruvate, cause pyruvate to stay in the cytosol. Because of this ladh oxidizeses the pyruvate and converts it into lactic acid.

How can that difference be used to identify the presence of metastases in patients

Tumors have a higher metabolism so they take in more glucose than normal cells. Doctors can use radioactive glucose inject that into the patients body and track where an excess amount of glucose is being consumes. They can do this in a PET scan.

What are the fundamental characteristics of cancerous cells

* Increased proliferation
* They are monoclonal
* Increased glucose take in.

Gene

a distinct sequence of nucleotides forming part of a chromosome the order of which determines the order of monomers in a poly peptide or nucleic acid moleucles which a cell may synthesis

Kinase

catalyzes the transfer of a phostphate froup form and ATP to a hydroxyl group

Catalytic domain

Region of the enzyme that catalyzes the chemical reaction (active site)

How is v-src different from c-src

* the loss of the C-terminal region of c-src gene causes v-src to have constitutive kinase activity, also it is missing the auto-inhibitory domain.

How does V-Src transform cells

* the v-src mutation causes an increase of proliferation within the cell.

Virus

agent that can replicate only in a host cell.

* can replicate in a host cell using cellular machinery

Provirus

Majority of viruses

* viruses that integrates its genome into host cell genome.
* Can cause cancer by disrupting gene, insertional mutagenesis.

Retroviruses

* could disturb cellular proto-oncogenes by disturbing them insertional mutagenesis.

Oncogenes

encode proteins that are part of proliferation or apoptosis pathways.

Proto-oncogenes

are converted to oncogenes when they get activation (or gain of function) mutation.

Gene mutation

* causes changes in protien structure and therefore increases in enzyme activity (alters protein function)
* protein structural changes can lead to constitutive activation of pro-growth signals.

Increased in gene expression

* higher quantity of protein product= more enzyme activity
* Myc, HER2

Chromosomal translocation

Myc

is a transcription factor that controls expression of genes needed for cellular growth and replication.

Transcription factors

are proteins that bind gene promoters to facilitate transcription.

Myc gene amplification

* increase in gene copy number, increase in protein amount, and increase in myc transcriptional activity in cell.

Myc provirus intergration

* under control of viral promoter, dysregulation of gene expression.

Myc chromosomal translocation

under control of foreign transcriptional promoter.

What are the series in the EGFR signalling starting from production of the growth factor and ending with transcription.

1. Fibroblasts make EGF ligands.
2. The EGF ligands bind with the EGFR which triggers dimerization and phosphorylation of the tyrosine residues on the cytoplasmic domain of the EGFR.
3. Tyrosine phosphorylation creates a binding site for Grb2 (adapter proteins).
4. The Grb2 creates an molecular bridge and recruits SOS, a GEF.
5. SOS, recruits Ras a small GTPase, this binding causes Ras to release GDP. GTP presence increases in the cell causing it to bind to Ras.
6. Ras’s signaling activity is activated, this allows for Ras to have the conformation to bind to its down stream proteins.
7. Ras then binds to GAP which activates Ras’s enzymic activity. This allows for GTP to be hydrolyzed to GDP which turns of Ras’s signaling activity
8. Ras signals to Raf to start the kinases cascade.
9. The kinase cascade end with ElK2 which is a Transcription factor. ELK 2 enters the nucleus.
10. ELK 2 then binds to its correlated promotor sequence that encodes for signaling proteins.

Explain the role of PDGF and PDGFR in wound healing

1. platelets store PDGF in vesicles
2. exocytosis aids in teh release of the PDGF when wounded
3. The PDGF is translated in RER
4. PDGF-R is responsible for the growth of fibroblasts

What would happen if fibroblast made PDGF

* it would be autocrine signalling, the cell can then act autonomously .

How does a DNA mutation leading to truncation of the ectodomain affect EGFR function

Can be close to a normal EGFR, which binds to a ligand causing ligand independent firing.

How do mutation leading to higher expression of EGFR affect EGFR function

If there is an excess amount of EGFR on the cell surface then the EGFR’s can run into each other and trigger dimerization and phosphorylation of tyrosines without the binding to and EGF ligand.

How can abnormal autocrine signaling lead to out-of-control cell growth.

* a cell produces growth factors and growth factor receptors and the cells own GF binds to its own GFR causing out of control cell signaling.

How does the knowledge of mechanisms of EGFR oncogene activation lead to invention of theraputic strategies for treating cancer.

We can target cells expressing high levels of EGFR, causing for NK cells to trigger degranulation into lytic synapses causing the tumor cells to die by apoptosis.

What are the domains of SH and what do they do

* SH1: Kinase domain, binds to ATP, binds to its substrate(tyrosine)
* SH2: Domain that binds to phosphorylated tyrosine
* SH3: Binds to proline rich domains

How does the binding to GTP or GDP control the downstream signaling from Ras.

* Once Ras binds to a GEF, then this triggeres Ras to release its GDP. Now there is an increase of GTP in the cytosol so it binds to Ras. Ras’s signaling activity is now active allowing for Ras to signal its down stream partners. Ras then binds to a GAP which activates Ras’s enzymic activity. THis activity allows for GTP to be hydorlyzed to GTP shutting down Ras’s signaling activity.

Check points

Controls progression through the cell cycle, dysregulation of checkpoints may lead to cancer

R-point

* most important checkpoint for cancer.
* Controlled by mitogenic growth factors, Rb, and cyclin D.

What are the stages of the cell cycle

1. G1: receives signaling from external GF or other mitogenic signaling pathways, getting the cell ready for DNA synthesis


1. R-checkpoint: determines if the cell will go through the cell cycle.
2. S phase: The phase were new DNA is synthesized


1. Checkpoint: Checks for DNA damage, DNA replication is halted if there is damage to the genome.
3. G2: The cell is getting ready to divide.


1. Checkpoint: checks fore DNA damage, entrance to mitosis is blocked if there is damage to the genome.
4. Mitosis: The division of the cell and formation of two identical daughter cells.


1. Has four subunits


1. Prophase
2. Metaphase
3. Anaphase
4. Telophase.
2. Anaphase is blocked if chromatid are note assembled properly on mitotic spindles.
5. G0: Cell death


1. quiescent: can renter cell cycle
2. senescent: cant re-enter cell.

What is cyclin D and how is its abundance controlled in the cell

Cyclin D is a delayed early gene. Cyclin D abundance is controlled by mitogenic signaling.

What are cyclins and CDK’s and how do they work together to control advancement of the cell cycle.

They are regulatory subunits that keep the cell cycle in check. They bind to each other, cyclins activate/regulate kinase activity of CDKs by directing the substrate specificity of the CDK’s. Cyclins are regulated by ubiquitin ligases to control the phases of the cell cycle.

TGF-Beta

can inhibit cell cycle progression by activation CDI’s

CDI’s

block the ATP binding site of CDKs

pRb

* target of viral oncoproteins
* R-point is controlled by phosphorylation state of this.

What is the role of pRb in managing progression through the cell cycle.

* pRb is a pocket protein that contains E2F. pRb is hypophosphorylated by cyclin D during mitosis. pRB is hyperphosphorylated by Cyclin E during G1 right before R-point. This hyperphosphorylation allows for the E2F transcription factor to be released, E2F binds to its promoter sequence the encodes proteins need for s phase.

What is the mechanism of progression past the R point

1. Elk 1 binds to its promoter sequence that encodes Fos.
2. Fos and Jun come together and bind to the Ap-1 binding site
3. Ap-1 is a transcription factors that encodes for cyclin D
4. Cyclin D is produced and accumulates in the cell.
5. During the last stages of mitosis, Cyclin D/Cyclin D CDK’s hypophosphorylate pRb.
6. Once the cell enters G1 phase, the cyclin E CDI’s begin binding and inhibiting the accumulated cyclin D’s. Allowing for cyclin E/cyclin E CDK’s.
7. The cyclin E/Cyclin E CDK’s hyperphosphorylate the pRb.
8. The hyperphosphorylated pRb then releases the E2F transcription factor.
9. E2F then binds to its correlated promoter sequence, leading to the encoding of proteins needed for s phase.

How would the methylation of the promoter of pRB affect the cell cycle

If the promoter is mehtylated then Rb will not be formed. Thus E2F would not bind to it. E2F will them be able to bind with its promoter freely and go about the cell on checked. This would allow for the cell to continue the cell cycle when it shouldn’t.

What is the role of E2F in the cell cycle.

* E2F is a transcription factor the encodes proteins needed for the s phase.

P53

* is a transcription factor
* targets
* CDI’s (p21)
* Regulators of apoptosis
* Bax, Apaf1
* DNA repair machinery genes
* Its own regulator (MDM2)

What does P53 do?

P53 is a transcription factor and it targets genes that activate apoptosis.

How does P53 work?

* P53 is activated when the cell senses DNA damage.


1. Damaged DNA signals for ATM/ATR kinase activations
2. ATM/ATR kinase activations signals for Chk1/Chk2 kinase activation
3. Chk1/Chk2 kinase activation leads the the phosphorylation of p53


1. the phosphorylation of p53 saves it from MDM2, ubiquitylation and degradtion in proteosomes.
4. The active p53 binds to regulatorly region of the p21 gene.
5. The p21 gene goes through transcription and translation.
6. The p21 CDI is now active in the cell and is shutting down the cell cycle.

What is the consequence to a cell if ARF function is eliminated

There would be no backup plan because Arf inactivates MDM2.

How are levels of p53/activity of p53 controlled

* p53 is techanically controlled by itself. One of the downstream targets of p53 is MDM2. MDM2 is an E3 ubiquitin ligase. MDM2 specifically tags p53 for ubiqulation and degradation by the proteosome.
* MDM2 levels increase if there is an accumulation of p53 in the cell. This occurs because more p53 is hitting the MDM2 promoters.
* MDM2 levels decrease when p53 has a loss of function mutation. This is when p53 loses its transcription function so it is just accumulating in the cell and not signaling any of its downstream targets.

What is a dominant-negative mutation

Is a when the mutated allele is more dominate than the wild-type allele. This means that one mutation of the allele will cause the cell to show the mutated phenotype. p53 is a dominate-negative allele, 1 p53 allele with a loss of function mutation results in 15/16 of the p53 tetramers being dysfunctional.

How many mutated alleles are necessary to lose p53 function in a cell

It only takes one mutated allele for p53 to be a loss of function mutation.

Would you rather have a point mutation or a null mutation of p53

* It would be better to have a null mutation than a point mutation. This is because it is better to express no phenotype than a mutated phenotype.

Extrinsic Apoptosis

* triggers caspase activation via ligation of death receptors expressed on the surface of the cell or encounter with a cytotoxic T cell or NK cell.

Intrinsic Apoptosis

1. Cytochrome C releases from mitochondria via the voltage -dependent anion channel.
2. The Cytochrome C is now in the cytosol forms the apoptosomes, and cleaves pro-caspase 9 to caspase 9.
3. Capase 9 cleave the executioner pro-caspases to executioner caspases.
4. The executioner caspases cleave the death substrates.
5. Actin (a death substrate), starts creating blebs.
6. The blebs break off of the cell and start getting eaten by macrophages

Telomeres

protect the natural ends of chromosomes from being accidently fused by DNA repair enzymes.

Shelterin complex

proteins bind to ends of chromosome and inhibit DNA repair machinery from sticking to each other.

How do cells keep DNA repair machinery from sticking chromosomes together

Shelterin complex.

What is the role of p53 in the breakage-fusion-bridge cycles

p53 is not present in when the breakage-fusion-bridge cycle occurs, p53 would apoptosis the cell before the bfb cycle would occur. So p53 must already be a LOF mutation.

How do cells escape crises

they can elongate their telomeres via telomerase.

Do all cells escape crises

* no, just
* cancer cells
* stem cells
* embryotic cells.

Do cancer cells escape crises

* it is by random mutation
* the BFB cycle
* Genomic crisis
* all of these can cause the activation of telomerase holoenzyme

Telomerase holoenzyme 2 complexes

* hTERT catalytic subunit (protein)
* hTR RNA subunit (template)

Chronic inflammation

leads to cell death, cell replacement, telomere collapse, and BFB cycles.

Mismatched repair

detects errors in newly synthesized strands and repairs them using template strand. (occurs after DNA polymerase)

DNA polymerase

* detects the misincorporated nucleotide,
* the polymerase moves backward and degrades recently synthesized strand
* polymerase move forward again and undertakes once again to synthesize proper sequence.

Stalled replication forks

Very dangerous due to the fragility of ssDNA

* can cause ssDNA to break off so DNA will have to use the template strand for genetic information leading to errors in genomic code.

UV radiation

* causes covalent cross-links between adjacent pyrimidines
* must be fixed by transcription-coupled repair or global genomic repair.
* mutations affects the structure of DNA/
* Pyrimidine dimers prevent normal base-pairings during DNA replication or transcription.
* Aberrations in DNA structure can be detected by DNA repair machinery and fixed.

Metabolites

polycyclic aromatic hydrocarbons have high biological activity.

DNA adducts

large bulky structure covalently bonded to the DNA

Ethanol Metabolites

can be mutagenic and cause DNA adducts.

Aflatoxin

is a DNA adduct, one of the most toxic substances known.

Heterocyclic amines

are formed by cooking food at high temps.

* they form adduct on doxyguanosine

Glutathione

is a mechanism that intercepts chemical carcinogens. Glutathinone s-transferase links electrophilic compounds (carcinogens) to the glutothione detoxifies the compound adn prepares them for the metabolism and excretion.

Benzoapyrine

DNA adduct, polycyclic aromatic hydrocarbon, combustion of organic materials.

Nucleotide Excision Repair

* Transcription coupled repair
* Global genomic repair
* triggered by activation of p53
* DNA is nicked, nucleotides around are removed.
* DNA is closed by ligase.

Error prone repair

bypass polymerase activated when DNA replication fork can’t proceed.

* 1 mistake/100 bp

BRCA

* found in nucleus
* cluster at stalled replication forks
* sites of dsDNA breaks
* no BRCA=improper repair of dsDNA breaks

Homology directed repair

uses sister chromatids as a template to restore the original sequence of bases

Non-homologous end joining (NHEJ)

* repairs ds DNA breaks, but is prone to errors, especially insertions or deletions.

Chromosomes number may change in cancer cells

* chromosome instability
* Deregulation of spindle assembly checkpoint
* Merotely- 2 spindle fiber from opposite centrioles connected to same chromosome
* Multiple centrosomes.

Stromal cells

collaborate with neoplastic epithelial cells.

* Fibroblast
* Macrophages
* Mast cells
* smooth muscles
* monocytes

Heterotypic ligand-receptor signaling

occurs between neoplastic cells and stromal cells in the tumor

Wound healing

is a normal physiological function that relies on heterotypic signaling and epithelial-mesenchymal-transition (EMT).

* tumors resemble wounds that do not heal
* Neoplastic epithelial cells undergo EMT can becomes invasive and migrate to distant sites (metastasize)

What are heterotypic interactions

Interactions between stromal cells and epithelial cells. Wha

The wound healing process

1. platelets release PDGF (a growth factor for fibroblasts) and TGF-beta with promote proliferation of epithelial cells and promote the epithelial to mesenchymal transition (EMT)

Epithelial-Mesenchymal Transition

is when epithelial cells switch their transcriptional program (regulation of gene expression) to express different protein, change in phenotype.

VEGF transcription (HIF-1 Activation)

Normal

* Proline Hydroxylase catalyzes the addition of a hydroxyl group to proline in the presence of a normal O2 concentrations.
* Hydroxylation of proline allows binding to pVHL and subsequent ubiquitination.
* Degradation in proteasome

Hypoxia

* HIF-1 alpha binds to the promoter sequence on the VEGF gene along with HIF-1 Beta, causing transcription of the VEGF gene.

Why don’t we inherit mutated oncogenes

* Oncogenic mutations would cause termination of the fetus.

Methylation of DNA and histones

causes nucleosomes to pack tightly together. Transcription factors cannot bind the DNA and genes are not expressed.

Histone acetylation

results in loose packing of nucleosomes. Transcription factors can bind the DNA and genes are expressed.

Nf1 gene

* Ras Gap
* works together with Ras to hydrolyze the gamma phosphate from the GTP.
* In the absence of Nf1, levels of Ras-GTP rise faster and remain elevated following growth factor stimulation

APC

Encodes a scaffolding protein; colon cancer.

* colons have crypts that protect the epithelial cells that protect the colon. Stem cells divide into transmit amplifying cells and these cells continue to divide and the cells migrate from teh bottom of the crypt up out of the crypt on the regular epithelial and then stop proliferation and die. DNA is very vunerable. APC turns off prolifer ation and it is apart of WnT signaling. APC regulates degradation of beta-catenin. When Beta-catenin is phosphorylated and uqbiquinated adn gets brought to the protesomes to become degrades. Beta-catenin is transcription factor. Trancribed all of the time. is also destroyed all of the time, APC is need to degrade beta-catenin.

Thrombospondin (TSP-1)

* inhibits angiogenesis by triggering Fas L expresssion and apoptosis on newly formed endothelial cells.

Angiogenesis inhibited

* by normal physiologic endogenous inhibitors.

Wound healing in cancer cells

1. promote tumor cell proliferation and survival (EGF)
2. Promote invasion of the basement membrane (MMPs)
3. Promote angiogenesis.

Invasion-metastasis cascade

1. primary tumor formation
2. localized invasion
3. intravasation (interaction with platelets, lymphocytes, and other blood components.)
4. transport through circulation
5. arrest in microvessels of various organs
6. extravasation
7. formation of micrometastasis
8. colonization–formation of a macrometastasis.