BIO230 Self Final Notes
Lecture 12: Cancer
Clonal origin: one cell -> mutation -> tumor / progeny of the cell -> more mutation -> % success inc
Screening -> Early detection
Carcinoma (epithelial cell), Sarcoma (skin &muscle cell), Leukemia (Blood)
Tumor cell: cell survives, grows, divides independently -> can get a mutation, cell division (proliferation) inc, cell survival, inc, cell death dec.
Cancer cells: malignant tumor cells -> decreased cell-cell adhesion, invade the basal lamina.
Metastasis: cells spread via blood or lymph -> secondary tumor / only small % survive to form metastases
Tumor -> mutation -> inc cell division, dec apoptosis / can evade apoptosis -> body instead of lumen => metastasis, recruit other cells (microenv)
Mutations in cancer cells -> inc genetic instability -> inc accumulation of further mutations
Mutagens exposure: inc mutation probability / not all chemicals are mutagens (Aflatoxin B1)
Ames test -> Salmonella strain, bacteria plated on histidine-free medium -> growth = mutation / should test w and without liver (homogenized
liver modifies the chemicals that might cause mutations)
Viruses can also cause mutation (HPV) -> contribute to cancer.
Cancer-critical genes: oncogene (all gas, gain of function, inc protein) and tumor-suppressor gene (no brake, loss of function, dec or no protein)
Proto-oncogene: normal version, promotes cell survival, growth, division – mutation -> oncogene (dominant mutation – one copy enough)
Oncogene overactivity mutations -> deletion, point, regulatory, gene amplification, chromosome rearrangement, epigenetic
➔ Deletion (overreactive receptor): survival receptors, growth factor receptors, mitogen receptors.
➔ Point mutation (Ras gene): Can’t hydrolyze GTP -> signaling pathway always ON.
➔ Myc oncogene: inc G1-Cdk activity, inc G1-Cdk expression, inc E2F, dec Rb activity, inc S-Cdk, inc phosphorylation.
➔ Chromosomal rearrangements: Abl normally good, Bcr-Abl (Philadelphia chromosome) -> hyperactive Abl (C.M.C)
Gleevec: Mutation in the binding site of Bcr-Abl kinase activity.
Tumor-suppressor genes: underactive or inactive, recessive mutations (need both copies), repress survival-growth-division.
➔ Loss of Rb function => tumor progression: Hereditary (good + bad) = multiple tumors in both eyes (common) / Non-hereditary (good
+ good) = mutation in one eye with a secondary mutation (1 in 30000)
Loss of p53 function -> dec apoptosis => tumor
➔ p53: transcriptional regulator, activity leads to inc Cdk inhibitor activity, ubiquitination decreases p53 activity.
p53 should be inhibited before the cells with high Myc can develop into cancer.
Bad Rb (cell proliferation, cell cycle entry), bad p53 (tolerance to DNA damage, cell survival), bad Ras (dec cell growth, cell cycle) => tumor
Multiple mutations are typically required for cancer progression (mutation in just p53 just not enough to get cancer -> multiple mutations!!!)
Question: Mutation in HPV gene E7 that inhibits Rb (bad), treatment? Inhibit p27 (bad), Activate E2F (bad), Activate G1-Cdk (bad), Inhibit S-
Cdk (good)
Combined question with lecture 9: If Gleevec belongs to the class of drugs as kinase inhibitors: An EGFR inhibitor (EGFR is a receptor tyrosine
kinase)
Caspase-8 is inactivated by protein cleavage.
M-cyclin is inactivated by ubiquitin-mediated degradation (APC/C and Cdc20)
Question: A high number of histidine-independent bacteria can be counted. In the presence of liver extract, histidine-independent bacteria cannot
be found -> chemical is dangerous, but if you eat it, your liver will decrease toxicity.
The direct target for S-Cdk (S phase) -> DNA helicase inside the nucleus (responsible for DNA unwinding)
,Lecture 11: Programmed Cell Death (PCD)
PCD: embryonic development (separating hand and feet), metamorphosis (tadpole in frog), immune system function
➔ Apoptosis: regulated, reproducible (dec cell adhesion, DNA fragmentation, engulfment, cytoskeleton disassembly, surface lipid
exchange)
➔ Necrosis (accidental, causes inflammation)
Caspase: synthesized as inactive -> requires cleavage to become active -> trigger apoptosis.
➔ Some can activate (initiator 8,9) and activate others (executioner 3,6,7) = caspase cascade
Executioner caspase: indirectly causes DNA breakdown (cleaved iCAD), alters surface lipid composition (cleaves flipasses, activates
scramblase = more lipid @ outer layer -> signal for phagocytosis)
Apoptosis can be triggered by:
➔ Extrinsic pathway: extracellular signal molecules activate executioners and cascade -> activation via death receptor on cell surface
such as Fas.
➔ Intrinsic pathway: intracellular receptors -> cytochrome c release (UV light)
➔ The signal from the triggering molecule crosses a membrane in each case, the first proteins recruited are not caspases in either case,
the initiator caspase has an additional protein domain in each case, and the complex formed for extrinsic activation is different from
the one formed for intrinsic activation.
Extrinsic pathway: caspase-8, FADD, death domains -> Fas death receptor binds to Fas ligand on a killer receptor and triggers apoptosis.
➔ Decoy receptors: Prevents apoptosis by binding death ligands without transmitting death signals -> binds to Fas ligand but does not
initiate caspase activation, thus preventing apoptosis (no DISC assembles).
Intrinsic pathway: Cytochrome c binds to Apaf-1, facilitating the formation of the apoptosome, which then activates caspase-9 to begin the
caspase cascade (exposition of CARD domain, oligomerization domain on Apaf-1) -> cell with mutant Apaf-1 that lacks CARD domain (Apaf-1
will bind to cytochrome c from mitochondria but will not associate with caspase 8)
➔ Mitochondria actions in apoptosis: proteins Bak & Bax are important for mitochondrial outer membrane permeabilization (MOMP),
which allows the release of cytochrome c.
Bcl2 & Bcl-xL: antiapoptotic proteins (binds to Bak & Bax and inhibits them) (dec apoptosis).
➢ Bad: Proapoptotic protein which promotes apoptosis by neutralizing Bcl2 & Bcl-xL (inc apoptosis).
Inhibitors of apoptosis (IAPs): blocks both caspases to prevent unintended apoptosis -> XIAP directly binds and inhibits caspases, blocking
apoptosis even if upstream signals have been activated (antiapoptotic – dec apoptosis).
➔ MOMP releases anti-IAP proteins (Omi, Smoc) which are proapoptotic (inc apoptosis).
Cells require survival factors to survive -> apoptosis if not supported by survival factors.
➔ Survival factors can activate antiapoptotic proteins (can inhibit apoptosis): Signaling cascade -> inc Bcl2 -> Bcl2/BclxL block
Bak/Bax -> MOMP blocked -> apoptosis stop.
➔ Survival factors can inactivate proapoptotic proteins (can inhibit apoptosis): Signaling cascade-> Akt kinase activated and
phosphorylates Bad = inactive so it cannot inhibit Bcl2 & BclxL -> they block MOMP -> apoptosis stop.
Inappropriate cell death -> death
Question: Inc apoptosis: Inc Fas decoy receptor (dec), dec [IAPs] (inc), inc Bad phosphorylation (dec by SFs), inc Akt kinase (dec by SFs).
Trigger apoptosis: Dec Fas, the release of cytochrome c to the cytosol from mitochondria, Dec Bcl2, Dec IAP
Question: Inc apoptosis: dec Bcl2, inc anti-IAPs, dec Akt kinase activity, decreased Hid phosphorylation (Hid is proapoptotic)
Roles of apoptosis: Can eliminate cells that escape their protective environment. Plays a key role in regulating cell numbers. Can be triggered by
killer lymphocytes via extrinsic pathway. It is controlled cellular breakdown, not leading to inflammation.
Fas is signaling contact-dependent signaling.
, Lecture 10: The Cell Cycle
Green lights for cell cycle progression:
➔ Cyclin synthesis / Cdk activity:
Stimulated by growth factors and mitogens.
Myc: A transcription factor upregulated by mitogenic signals that promote cyclin synthesis.
E2F release (Rb phosphorylation): Following Rb phosphorylation, E2F activates the transcription of genes for cyclin synthesis.
➔ Cdk activation:
CAK (Cdk-Activating Kinase): Phosphorylates and activates Cdks.
Cdc25 Phosphatase: Removes inhibitory phosphates from Cdks, promoting activation.
➔ Cyclin-Cdk complex formation:
Cyclins binding to Cdks: Different cyclins bind to their respective Cdks, forming active complexes that drive the cell cycle
forward.
➔ Degradation of inhibitory proteins:
Ubiquitination and proteasomal degradation: Targets specific inhibitors of cyclin-Cdks for destruction.
➔ Positive feedback loops (happening all together):
M-Cdk activation of Cdc25 (M-Cdk activity): Active M-Cdk can phosphorylate and activate Cdc25, enhancing its activation.
Inhibition of Wee1 by M-Cdk: Active M-Cdk can also phosphorylate Wee1, inhibiting the kinase that adds inhibitory phosphates
to Cdks.
Red lights for cell cycle progression:
➔ Inhibition of cyclin-Cdk activity:
Cdk inhibitor proteins (CKIs) (p21 and p27):
➢ P21 and p27: Bind to and inhibit cyclin-Cdk complexes. Synthesis is often induced by DNA damage via p53 activation.
Wee1 kinase: Adds inhibitory phosphates to Cdks.
➔ Cyclin degradation:
APC/C and Cdc20: E3 ubiquitin ligases that target cyclins for degradation, particularly M-cyclin during mitotic exit. This
process is crucial for the cell to exit mitosis and reset the cell cycle.
➔ Inhibitory phosphorylation of Cdks:
Wee1 kinase: Phosphorylates Cdks at inhibitory steps, preventing their activation.
Inhibition of Cdc25 phosphatase counteraction: Maintains the Cdk in an inactive state by preventing the removal of inhibitory
phosphates. (must be phosphorylated to be active)
➔ DNA damage response:
P53 activation: In response to DNA damage, p53 activates the transcription of CKIs like p21, halting the cell cycle (S phase).
➔ Retinoblastoma protein (Rb) Function:
Rb inhibition of E2F: When not phosphorylated, Rb binds and inhibits E2F, preventing transcription of S phase genes.
➔ Mitogen withdrawal:
Decreased Myc: Without mitogenic signals, Myc levels fall, leading to reduced cyclin synthesis and thus, decreased cyclin-Cdk
activity.
➔ Protein phosphatase 2A (PP2A): Acts in opposition to Cdk activation by dephosphorylating proteins, including Cdks and their
substrates, effectively reversing the phosphorylation events that promote cell cycle progression.
➔ M-cyclin polyubiquitylation
Question: Cdk inhibitor (red light): Cyclin under expression (red), p27 upregulation (red), M-cyclin polyubiquitylation, no Cdc25 phosphatase
activity (red)
Cell cycle: During cell growth, all molecules in the cell are NOT produced together over the same time (e.g. polyubiquitylation of cyclin).
Different cell cycle stages CAN BE DIRECTED BY THE SAME CDKs. Different cell cycle stages CAN NOT BE DIRECTED BY THE SAME
CYCLINS. Active and inactive Cdks can have a phosphate group at the Cdk-activating kinase phosphorylation site.
Question comparing cyclins and Cdks in vertebrates versus budding yeast is most accurate: The downstream effects of yeast cyclin-Cdk
complexes must be specified solely by the cyclin present. => Yeast has less cyclin diversity. Cyclin is the regulatory subunit. Cdk is a catalytic
subunit. -> cyclin-Cdk activity is more reliant on which cyclin is present because the Cdk part of the complex is more constant.
Most likely to promote cell cycle progression: A mutation that inhibits Cdk interaction with p27.
Least likely to promote tumor growth: Mutations in both copies of Polo kinase leading to loss of Polo function (disrupt cell cycle progression)
Removal of the corresponding cyclin will always inhibit a CDK’s activity (Cyclin-dependent kinase)
Lecture 12: Cancer
Clonal origin: one cell -> mutation -> tumor / progeny of the cell -> more mutation -> % success inc
Screening -> Early detection
Carcinoma (epithelial cell), Sarcoma (skin &muscle cell), Leukemia (Blood)
Tumor cell: cell survives, grows, divides independently -> can get a mutation, cell division (proliferation) inc, cell survival, inc, cell death dec.
Cancer cells: malignant tumor cells -> decreased cell-cell adhesion, invade the basal lamina.
Metastasis: cells spread via blood or lymph -> secondary tumor / only small % survive to form metastases
Tumor -> mutation -> inc cell division, dec apoptosis / can evade apoptosis -> body instead of lumen => metastasis, recruit other cells (microenv)
Mutations in cancer cells -> inc genetic instability -> inc accumulation of further mutations
Mutagens exposure: inc mutation probability / not all chemicals are mutagens (Aflatoxin B1)
Ames test -> Salmonella strain, bacteria plated on histidine-free medium -> growth = mutation / should test w and without liver (homogenized
liver modifies the chemicals that might cause mutations)
Viruses can also cause mutation (HPV) -> contribute to cancer.
Cancer-critical genes: oncogene (all gas, gain of function, inc protein) and tumor-suppressor gene (no brake, loss of function, dec or no protein)
Proto-oncogene: normal version, promotes cell survival, growth, division – mutation -> oncogene (dominant mutation – one copy enough)
Oncogene overactivity mutations -> deletion, point, regulatory, gene amplification, chromosome rearrangement, epigenetic
➔ Deletion (overreactive receptor): survival receptors, growth factor receptors, mitogen receptors.
➔ Point mutation (Ras gene): Can’t hydrolyze GTP -> signaling pathway always ON.
➔ Myc oncogene: inc G1-Cdk activity, inc G1-Cdk expression, inc E2F, dec Rb activity, inc S-Cdk, inc phosphorylation.
➔ Chromosomal rearrangements: Abl normally good, Bcr-Abl (Philadelphia chromosome) -> hyperactive Abl (C.M.C)
Gleevec: Mutation in the binding site of Bcr-Abl kinase activity.
Tumor-suppressor genes: underactive or inactive, recessive mutations (need both copies), repress survival-growth-division.
➔ Loss of Rb function => tumor progression: Hereditary (good + bad) = multiple tumors in both eyes (common) / Non-hereditary (good
+ good) = mutation in one eye with a secondary mutation (1 in 30000)
Loss of p53 function -> dec apoptosis => tumor
➔ p53: transcriptional regulator, activity leads to inc Cdk inhibitor activity, ubiquitination decreases p53 activity.
p53 should be inhibited before the cells with high Myc can develop into cancer.
Bad Rb (cell proliferation, cell cycle entry), bad p53 (tolerance to DNA damage, cell survival), bad Ras (dec cell growth, cell cycle) => tumor
Multiple mutations are typically required for cancer progression (mutation in just p53 just not enough to get cancer -> multiple mutations!!!)
Question: Mutation in HPV gene E7 that inhibits Rb (bad), treatment? Inhibit p27 (bad), Activate E2F (bad), Activate G1-Cdk (bad), Inhibit S-
Cdk (good)
Combined question with lecture 9: If Gleevec belongs to the class of drugs as kinase inhibitors: An EGFR inhibitor (EGFR is a receptor tyrosine
kinase)
Caspase-8 is inactivated by protein cleavage.
M-cyclin is inactivated by ubiquitin-mediated degradation (APC/C and Cdc20)
Question: A high number of histidine-independent bacteria can be counted. In the presence of liver extract, histidine-independent bacteria cannot
be found -> chemical is dangerous, but if you eat it, your liver will decrease toxicity.
The direct target for S-Cdk (S phase) -> DNA helicase inside the nucleus (responsible for DNA unwinding)
,Lecture 11: Programmed Cell Death (PCD)
PCD: embryonic development (separating hand and feet), metamorphosis (tadpole in frog), immune system function
➔ Apoptosis: regulated, reproducible (dec cell adhesion, DNA fragmentation, engulfment, cytoskeleton disassembly, surface lipid
exchange)
➔ Necrosis (accidental, causes inflammation)
Caspase: synthesized as inactive -> requires cleavage to become active -> trigger apoptosis.
➔ Some can activate (initiator 8,9) and activate others (executioner 3,6,7) = caspase cascade
Executioner caspase: indirectly causes DNA breakdown (cleaved iCAD), alters surface lipid composition (cleaves flipasses, activates
scramblase = more lipid @ outer layer -> signal for phagocytosis)
Apoptosis can be triggered by:
➔ Extrinsic pathway: extracellular signal molecules activate executioners and cascade -> activation via death receptor on cell surface
such as Fas.
➔ Intrinsic pathway: intracellular receptors -> cytochrome c release (UV light)
➔ The signal from the triggering molecule crosses a membrane in each case, the first proteins recruited are not caspases in either case,
the initiator caspase has an additional protein domain in each case, and the complex formed for extrinsic activation is different from
the one formed for intrinsic activation.
Extrinsic pathway: caspase-8, FADD, death domains -> Fas death receptor binds to Fas ligand on a killer receptor and triggers apoptosis.
➔ Decoy receptors: Prevents apoptosis by binding death ligands without transmitting death signals -> binds to Fas ligand but does not
initiate caspase activation, thus preventing apoptosis (no DISC assembles).
Intrinsic pathway: Cytochrome c binds to Apaf-1, facilitating the formation of the apoptosome, which then activates caspase-9 to begin the
caspase cascade (exposition of CARD domain, oligomerization domain on Apaf-1) -> cell with mutant Apaf-1 that lacks CARD domain (Apaf-1
will bind to cytochrome c from mitochondria but will not associate with caspase 8)
➔ Mitochondria actions in apoptosis: proteins Bak & Bax are important for mitochondrial outer membrane permeabilization (MOMP),
which allows the release of cytochrome c.
Bcl2 & Bcl-xL: antiapoptotic proteins (binds to Bak & Bax and inhibits them) (dec apoptosis).
➢ Bad: Proapoptotic protein which promotes apoptosis by neutralizing Bcl2 & Bcl-xL (inc apoptosis).
Inhibitors of apoptosis (IAPs): blocks both caspases to prevent unintended apoptosis -> XIAP directly binds and inhibits caspases, blocking
apoptosis even if upstream signals have been activated (antiapoptotic – dec apoptosis).
➔ MOMP releases anti-IAP proteins (Omi, Smoc) which are proapoptotic (inc apoptosis).
Cells require survival factors to survive -> apoptosis if not supported by survival factors.
➔ Survival factors can activate antiapoptotic proteins (can inhibit apoptosis): Signaling cascade -> inc Bcl2 -> Bcl2/BclxL block
Bak/Bax -> MOMP blocked -> apoptosis stop.
➔ Survival factors can inactivate proapoptotic proteins (can inhibit apoptosis): Signaling cascade-> Akt kinase activated and
phosphorylates Bad = inactive so it cannot inhibit Bcl2 & BclxL -> they block MOMP -> apoptosis stop.
Inappropriate cell death -> death
Question: Inc apoptosis: Inc Fas decoy receptor (dec), dec [IAPs] (inc), inc Bad phosphorylation (dec by SFs), inc Akt kinase (dec by SFs).
Trigger apoptosis: Dec Fas, the release of cytochrome c to the cytosol from mitochondria, Dec Bcl2, Dec IAP
Question: Inc apoptosis: dec Bcl2, inc anti-IAPs, dec Akt kinase activity, decreased Hid phosphorylation (Hid is proapoptotic)
Roles of apoptosis: Can eliminate cells that escape their protective environment. Plays a key role in regulating cell numbers. Can be triggered by
killer lymphocytes via extrinsic pathway. It is controlled cellular breakdown, not leading to inflammation.
Fas is signaling contact-dependent signaling.
, Lecture 10: The Cell Cycle
Green lights for cell cycle progression:
➔ Cyclin synthesis / Cdk activity:
Stimulated by growth factors and mitogens.
Myc: A transcription factor upregulated by mitogenic signals that promote cyclin synthesis.
E2F release (Rb phosphorylation): Following Rb phosphorylation, E2F activates the transcription of genes for cyclin synthesis.
➔ Cdk activation:
CAK (Cdk-Activating Kinase): Phosphorylates and activates Cdks.
Cdc25 Phosphatase: Removes inhibitory phosphates from Cdks, promoting activation.
➔ Cyclin-Cdk complex formation:
Cyclins binding to Cdks: Different cyclins bind to their respective Cdks, forming active complexes that drive the cell cycle
forward.
➔ Degradation of inhibitory proteins:
Ubiquitination and proteasomal degradation: Targets specific inhibitors of cyclin-Cdks for destruction.
➔ Positive feedback loops (happening all together):
M-Cdk activation of Cdc25 (M-Cdk activity): Active M-Cdk can phosphorylate and activate Cdc25, enhancing its activation.
Inhibition of Wee1 by M-Cdk: Active M-Cdk can also phosphorylate Wee1, inhibiting the kinase that adds inhibitory phosphates
to Cdks.
Red lights for cell cycle progression:
➔ Inhibition of cyclin-Cdk activity:
Cdk inhibitor proteins (CKIs) (p21 and p27):
➢ P21 and p27: Bind to and inhibit cyclin-Cdk complexes. Synthesis is often induced by DNA damage via p53 activation.
Wee1 kinase: Adds inhibitory phosphates to Cdks.
➔ Cyclin degradation:
APC/C and Cdc20: E3 ubiquitin ligases that target cyclins for degradation, particularly M-cyclin during mitotic exit. This
process is crucial for the cell to exit mitosis and reset the cell cycle.
➔ Inhibitory phosphorylation of Cdks:
Wee1 kinase: Phosphorylates Cdks at inhibitory steps, preventing their activation.
Inhibition of Cdc25 phosphatase counteraction: Maintains the Cdk in an inactive state by preventing the removal of inhibitory
phosphates. (must be phosphorylated to be active)
➔ DNA damage response:
P53 activation: In response to DNA damage, p53 activates the transcription of CKIs like p21, halting the cell cycle (S phase).
➔ Retinoblastoma protein (Rb) Function:
Rb inhibition of E2F: When not phosphorylated, Rb binds and inhibits E2F, preventing transcription of S phase genes.
➔ Mitogen withdrawal:
Decreased Myc: Without mitogenic signals, Myc levels fall, leading to reduced cyclin synthesis and thus, decreased cyclin-Cdk
activity.
➔ Protein phosphatase 2A (PP2A): Acts in opposition to Cdk activation by dephosphorylating proteins, including Cdks and their
substrates, effectively reversing the phosphorylation events that promote cell cycle progression.
➔ M-cyclin polyubiquitylation
Question: Cdk inhibitor (red light): Cyclin under expression (red), p27 upregulation (red), M-cyclin polyubiquitylation, no Cdc25 phosphatase
activity (red)
Cell cycle: During cell growth, all molecules in the cell are NOT produced together over the same time (e.g. polyubiquitylation of cyclin).
Different cell cycle stages CAN BE DIRECTED BY THE SAME CDKs. Different cell cycle stages CAN NOT BE DIRECTED BY THE SAME
CYCLINS. Active and inactive Cdks can have a phosphate group at the Cdk-activating kinase phosphorylation site.
Question comparing cyclins and Cdks in vertebrates versus budding yeast is most accurate: The downstream effects of yeast cyclin-Cdk
complexes must be specified solely by the cyclin present. => Yeast has less cyclin diversity. Cyclin is the regulatory subunit. Cdk is a catalytic
subunit. -> cyclin-Cdk activity is more reliant on which cyclin is present because the Cdk part of the complex is more constant.
Most likely to promote cell cycle progression: A mutation that inhibits Cdk interaction with p27.
Least likely to promote tumor growth: Mutations in both copies of Polo kinase leading to loss of Polo function (disrupt cell cycle progression)
Removal of the corresponding cyclin will always inhibit a CDK’s activity (Cyclin-dependent kinase)
