MBOD Block II: Comprehensive Study Questions
Nickalus Khan
Dr. Nishimoto: Transcription I, II , III, RNA Processing
1) What is transcription?
2) What types of RNA are needed for translation?
3) Are genes expressed into RNA at similar rates?
4) How is the structure of RNA different from DNA?
5) What property of RNA gives rise to its ability for secondary structure?
6) How is the coding strand of DNA related to RNA?
7) How is the template strand of DNA related to RNA?
8) What direction is RNA synthesized?
9) What is mRNA used for?
10) What is tRNA used for?
11) What is rRNA used for?
12) What is small RNA used for?
13) Does most of DNA encode for RNA?
14) What is a promoter sequence?
15) What is a terminator sequence?
16) What protein factor is used for promoter recognition in bacteria?
17) What is this replaced by in Eukaryotes?
18) How far upstream are the bacterial RNA pol. Promoters?
19) In bacteria how many RNA pol’s are there?
20) Is mRNA modified before translation in bacteria?
21) Are translation and transcription coupled in bacteria?
22) Do bacteria contain introns?
23) How many RNA’ pol’s are there in eukarya?
24) What are the functions of each eukaryotic RNA pol?
25) How is eukaryotic RNA modified ?
26) Is DNA in eukaryotes monocistronic or polycistronic?
27) What is the half-life of mRNA in eukaryotes and prokaryotes?
28) How is transcription regulated in prokaryotes?
29) In regards to the lac operon if glucose is present and lactose not present will transcription
occur?
30) If glucose is absent and lactose absent will transcription occur?
31) If glucose is absent and lactose present will transcription occur?
32) What are some common features of gene regulatory proteins?
33) Which domain regulates the activity of the gene switch?
34) What are some common motif’s of DNA binding regions?
35) What part of DNA do the dna binding domains interact with?
36) How do proteins interact with DNA?
37) In eukaryotes gene regulation is geared for what?
38) What is the flow of genetic information?
39) What is produced by each eukaryotic RNA pol?
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
40) Where is rRNA made?
41) What makes 45S RNA?
42) What makes 5S RNA?
43) Describe the formation of 80S Ribosome
44) What is responsible for the modifications in formation of the 80S ribosome?
45) Why is the assembly complex for Pol. I and III stable?
46) Why is pol. II regulated?
47) What is required for assembly of RNA Pol.II?
48) What does TBP do ?
49) What does phosphorylation of RNA Pol. II do?
50) What is the assembly point for transcription factors?
51) What chromatin structures can enhance transcription?
52) What are some gene regulatory processes?
53) Can gene regulatory proteins work at a distance?
54) Do all cells types contain the same DNA?
55) What signals in embryonic development determine cell fates?
56) Are genetic expression patterns remembered in daughter cells?
57) What signal converts a fibroblast to a muscle cell?
58) What are the inducer molecules mentioned in class ? (spatial signals)
59) What are the two ways to establish a gradient of spatial signals?
60) How do cells remember patterns of gene expression?
Dr. Nelson, Epigenetics
61) What is epigentics?
62) Where does DNA methylation take place?
63) In general DNA methylation turns genes ____.
64) 5-methyl is only added to cytosine in a __________ pair.
65) What enzyme methylates any newly made strand to match toe parental strand?
66) Abnormalities in maintenance DNA methyltransferase could result in?
67) What does methylation typically turn genes off?
68) Why do humans have low amounts of CpG pairs?
69) What enzymes establish new methylation patterns once the pattern is reset at birth?
70) How are methylated cytosines found (experimentally)?
71) What are some ways histones are modified?
72) What does histone acetylation do?
73) What is DNa reprogramming?
74) What is RNA interference?
75) What are miRNA’s produced by?
76) What is the main component of RISC?
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
Dr. Albritton, Translation I & II
77) What is the smallest unit that encodes AA?
78) What occurs during translation?
79) How many codons are there?
80) How many specify AA?
81) There are multiple codons for all amino acids except for which two?
82) All proteins begin with the codon for which AA?
83) What is the start codon?
84) What are the stop codons?
85) A change in DNA sequence is called ?
86) What is a silent mutation?
87) What is a missense mutation?
88) What is a nonsense mutation?
89) What are the two major differences between eukaryotic and prokaryotic DNA?
90) What is the function of tRNA?
91) What are the enzymes that catalyze the charging of tRNA ?
92) The AA is attached to what part of the tRNA molecule?
93) Is the Eukaryotic or prokaryotic ribosome larger?
94) What are the three steps in protein synthesis?
95) The small subunit of the prokaryotic ribosome always recognizes?
96) What is always 5-10 spaces down from the shine delgarno sequence?
97) How does the eukaryotic ribosome bind?
98) What step occurs after the ribosome binds?
99) In elongation step, what molecule brings in the tRNA?
100) What factor moves the ribosome down the mRNA by one codon?
101) What is the enzyme that catalyzes the formation of a peptide bond?
102) What residue catalyzes peptide bond formation?
103) What is the mechanism of diphtheria toxin?
104) What is the mechanism of ricin toxin?
105) Why can we tolerate low levels of ricin toxin?
Dr. Cox, Cytoskeleton I,II,III
106) Is the cytoskeleton found in eukaryotes or prokaryotes?
107) What are the functions of the cytoskeleton?
108) What are the three main components of the cytoskeleton?
109) What molecules are microtubules composed of?
110) How many protofilaments are typically in a microtubule?
111) What gives microtubules their polarity?
112) T or F: Microtubles can be both permanent and transient
113) What accounts for the transient nature of microtubules?
114) Where do microtubules usually originate from within a cell?
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
115) What end of the microtubule attaches to the centrosome?
116) Why are nucleation sites needed?
117) What are nucleation sites formed by?
118) What is dynamic instability of microtubules due to?
119) What subunit of tubulin does the GTP bind to?
120) T or F: Movement along microtubules is bidirectional.
121) What is the + end directed motor protein?
122) What is the – end directed motor protein?
123) The head domains of these proteins bind what?
124) The tail domains bind what?
125) How many tubulin dimers does each motor protein translocate per step?
126) How many ATP molecules are required per step?
127) What molecular motor pulls the ER toward the periphery of a cell?
128) What motor protein pulls the golgi adjacent to the nucleus?
129) Flagella and Cilia are formed by what array of microtubules? What are they attached to?
130) What attaches between doublets?
131) What could lead to immotile cilia syndrome?
132) What do primary cilia lack?
133) What molecules do primary cilia associate with?
134) What happens during prometaphase?
135) How are microtubules different in mitosis than interphase?
136) What proteins destabilize microtubules in mitosis?
137) What proteins stabilize microtubules in mitosis?
138) Microtubules attach at what plate on chromosomes?
139) Microtubles are popped off one at a time from the kinetochore plate by?
140) What happens in anaphase A?
141) Anaphase B?
142) What does vinblastine, vincristine drugs do?
143) What does the drug taxol do?
144) What does the drug colchichine do?
145) What are microfilaments mainly composed of?
146) Does actin have polarity?
147) What type of actni is found in skeletal muscle?
148) What regulates the assembly and disassembly of actin molecules?
149) Does dynamic instability apply to actin?
150) T or F: Microtubules are more stable than actin
151) What is the function of cytochalasins?
152) What is the function of phalloidins?
153) What is the function of Gelsolin?
154) What is the function of thymosin?
155) What is the function of profilin?
156) What is the function of myosin?
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
157) What is the function of tropomyosin?
158) T or F: Actin forms stress fibers in cells
159) What does fibroblast movement depend on?
160) What is cell adhesion dependent on during cell movement?
161) Fillopdia contain what types of actin arrays? Lamellopodium?
162) What complex are lamellipodia dependent on?
163) What forms as a dimer that binds to the + end of actin and promotes assembly of actin
monomers?
164) What forms as a monomer that binds to the + end of actin and promotes assembly of actin
monomers?
165) What is responsible for morphogenic changes in cell development?
166) What protein family triggers reorginzation of different microfilament populations?
167) When are rho proteins active?
168) What does Rac protein stimulate?
169) What does cdc42 promote?
170) What end of actin does myosin move towards?
171) What is different between type I and type II myosin?
172) ATP binding results in the movement of myosin of how many actin monomers?
173) T or F: ATP binding reduces myosin binding affinity for actin.
174) What filaments are responsible for forming the contractile ring that cleaves daughter cells
apart?
175) What ends of actin are embedded in the Z disk?
176) T or F: Intermediate filaments are only found in multicellular organisms
177) How are intermediate filaments different from microtubules and actin?
178) Since IF are identified primarly with specific cell types, what can they be used for?
179) Describe the structure of intermediate filaments.
180) Where are vimentin like IF’s found?
181) Where are nuclear lamins found?
182) Where are keratins found?
183) Where are neuronal intermediate filaments found?
184) IF stabilize epithelium by attaching to?
185) Epidermolysis bullosa is due to a defect in?
186) What links IF to other cytoskeletal elements?
187) What is unique about the IF’s involved in nuclear lamins?
188) What is the ER retention signal?
189) What type of signal is needed for transport into the mitochondria?
190) What type of signal is needed for import into the nucleus?
191) What type of signal is needed for import into the peroxisomes?
192) T or F: Gated transport is only in the nucleus
193) Proteins made on free ribosomes in the cytosol are destined for?
194) What are the three mechanisms for moving proteins between cellular compartments?
195) What do all nuclear proteins contain?
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
196) T or F: Nuclear transport requires Ran-GTP
197) Proteins destined for the mitochondria are folded or unfolded?
198) What maintains proteins in unfolded state during transport to the mitochondria?
199) T or F: signal sequence is cleaved once the mitochondrial protein enters the mitochondira
200) Proteins destined for the nucleus are folded or unfolded?
201) What is the function of a peroxisome?
202) T or F: peroxisomal protein import requires ATP.
203) Proteins in folded or unfolded state In peroxisomal transport?
204) What peroxisomal targeting sequence is found on the c terminus?
205) What peroxisomal targeting sequence is found on the N terminus?
206) Are c terminal signals ever cleaved?
207) What disease is correlated with protein transport into peroxisomes?
208) Where is the predominant site of phospholipid synthesis?
209) What kind of signal targets protein to the ER?
210) What is the mechanism of co-translational transport into the ER?
211) What enzyme cleaves the ER signal after the protein is translocated?
212) In relation to the topology of proteins in the ER membrane, positively charged amino acids are
typically found where?
213) What is the function of the golgi apparatus?
214) Where does N-linked sugar modficiations occur?
215) Describe the process of N-linked modifications.
216) What catalyzes the formation of disulfide bonds in ER?
217) What assists in proper folding of proteins for export out of ER?
218) What happens to misfolded proteins in the ER?
219) What does the accumulation of misoflded proteins in the ER trigger?
220) Movement of proteins from the ER to the golgi occurs via?
221) What helps direct these vesicles?
222) What vesicles are covered by clathrin?
223) What vesicles are covered by COP I ?
224) What vesicles are covered by COP II?
225) Clathrin ______ form a basket-like structure.
226) What pinches off clathrin coated vesicles?
227) What is adaptin 1 protein used for?
228) What is adaptin 2 protein used for?
229) Where are v-snares located?
230) Where are t-snares located?
231) How do v and t snares interact?
232) What are vesicles recognized by at the plasma membrane?
233) Retrieval of ER cargo receptors and missorted ER proteins occurs via what protein coat?
234) What does the COPI coat bind to for retrieval of transmembrane ER proteins (AA sequence)?
235) What is the ER retrieval sequence (aka ER retention signal)?
236) In absence of a sorting signal proteins are targeted for where?
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
237) Describe the release of secretory vesicles.
238) What is used as an enzyme marker for lysosomes?
239) How is the pH maintained in lysosomes?
240) What signaling tab targets vesicles from the trans golgi to lysosomes?
241) What enzyme adds this tag ?
242) What is I cell disease due to?
243) What causes Tay Sach’s?
244) What does phagocytosis require?
245) What does the phagosome fuse with?
246) What is fluid phase endocytosis called?
247) Is pinocytosis specific ?
248) Is receptor mediated endocytosis saturable?
249) What internalizes extracellular molecules such as lipids?
250) Describe the process of receptor mediated endocytosis.
251) What is one cause of familial hypercholesterolemia?
252) Are EGF receptors recycled ?
253) Describe the method of diphtheria toxin entry into cells.
254) How does cholera toxin enter cells?
255) How are viral genetic elements released, such as in influenza, into the cytosol?
256) Does HIV require endocytosis?
Dr. Senogles, Signal Transduction
257) What is signal transduction?
258) What are the four major types of signals within cells?
259) ____ signals have widespread effects.
260) ____ signals have local effects only.
261) ____ signals are delivered long distance to specific targets.
262) ____ signals make direct contact with neighboring cells.
263) What limits the amount of signals a cell can receive from its extracellular environment?
264) How does one agonist have a diverse effect on target cells?
265) What is a first messenger?
266) What is a second messenger?
267) Proteins are ____ switches for transduction of signal.
268) How can proteins integrate multiple signals? Describe NOT, AND, OR, NOR conditions.
269) What are the two broad distinction of receptors?
270) Which type of receptor typically receives hydrophilic signals?
271) Which type of receptor typically receives hydrophobic signals?
272) What are the criteria for a physiological receptor?
273) What are receptors classified by?
274) Define: Ligand
275) Define: Agonist
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
276) Define: Antagonist
277) In a linear saturation isotherm, what does specific binding equal?
278) What is Kd?
279) Describe a competition assay.
280) What the EC50?
281) How is EC50 related to Kd?
282) T or F : The lower the EC50 the more potent the ligand
283) In GPCR’s is the N terminus extracellular or intracellular?
284) What subunits is a G protein composed of?
285) What is the inactive state of a G protein?
286) How is a G protein activated?
287) What does the alpha subunit associate with after GTP has been hydrolyzed to GDP again?
288) Activated alpha subunit can associate with what enzyme to produce cAMP?
289) What does cAMP activate?
290) What controls the degradation of cAMP?
291) What amino acids does PKA phosphorylate?
292) What are the two separate ways PKA regulates cellular activity?
293) What is the function of the Beta-Gamma subunit when activated?
294) Describe the activation of Protein kinase C (PKC).
295) What part of a phospholipid does Phospholipase C cleave?
296) What amino acids does PKC phosphorylate?
297) What are the three ways GPCR’s are regulated?
298) In desensitization what phosphorylates the agonist occupied receptor?
299) What binds to the phosphorylated GPCR?
300) What is the method of sequesteration in regulation of GPCR function?
301) What are the two types of receptor tyrosine kinases?
302) How many transmembrane helices does each receptor tyrosine kinase domain have?
303) What do tyrosine kinases phosphorylate?
304) T or F: Phosphorylation can make a target enzyme more or less active.
305) What are the three parts of a Receptor Tyrosine Kinase?
306) Receptor tyrosine kinases _____ after binding to an extracellular signal.
307) After dimerization what occurs?
308) What is the purpose of adaptor proteins?
309) What is SH2/SH3?
310) What is the amino acid sequence of the terminal end for SH2 domains?
311) What type of sequences do SH3 bind?
312) What is Grb2?
313) What is SOS?
314) What is Ras?
315) What is the function of Ras after activation?
316) Is the JAK-STAT system have intrinsic receptor kinase activity?
317) Describe the sequence of the Jak-Stat system.
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
318) What sequence do JAK bind to?
319) What does STAT use to dimerize?
320) Is a steroid receptor typically a extracellular receptor?
321) What is the base structure of most of the intracellular signaling molecules ?
322) What does the activated nuclear receptor protein bind to in the nucleus?
323) What is an estrogen antagonist used in chemotherapy of estrogen responsive breast cancer?
324) What is a progesterone receptor antagonist that can be used to induce abortion?
325) What is an antagonist of a gluccocorticoid receptor, aids in anti-inflammatory response?
326) What is an antagonist to the androgen receptor, used for treatment of prostate cancer?
327) What three things do all steroid receptors have?
328) What motif does the DNA binding element of steroid receptors typically contain?
329) What makes a gene responsive to cortisol?
330) What does GRE, ERE stand for?
331) Steroid receptors that form heterodimers are always found where?
332) Steroid receptors that form homodimers are trapped where?
333) What are some of the effects of gluccocorticoid binding to its steroidal receptor?]
334) Is nitric oxide (NO) a 2nd messenger?
335) How is NO formed?
336) What does NO cause? (smooth muscle)
337) What does NO do on a molecular basis in the cell?
338) What is cGMP formed and degraded by?
339) How does Viagra work?
340) What has been used for treatment of Angina historically and why?
341) Where is the retina?
342) Does light travel through the inner or outer layers of the retina first?
343) Describe the pathway of light through the eye.
344) What two segments can the retina be divided into?
345) How many neuronal layers are there?
346) What does the outer nuclear layer contain?
347) What does the inner nuclear layer contain?
348) What does the ganglion cell layer contain?
349) What does the inner segment of a photoreceptor contain?
350) How is the inner segment of a photoreceptor connected to the outer layer?
351) What do the outer segments contain?
352) What type of light do rod cells process?
353) How often is the outer segment of a rod replaced (phagocytosis mechanism)?
354) What is the synaptic extension of a rod called?
355) What type of light do the cone cells process?
356) What are the three types of cones?
357) What is the synaptic terminus of a cone called?
358) Opsins of which cones are carried on the x chromosome?
359) In humans ____ and ____ opsins are linked
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
360) What is below the photoreceptor layer?
361) Cones and rods undergo ________ in response to light.
362) Describe how a photoreceptor functions in the dark.
363) Describe how a photoreceptor functions in the light.
364) Opsin is a ________ pass transmembrane helical protein.
365) What is rhodopsin composed of?
366) What part of rhodopsin absorbs light?
367) After 11-cis retinal absorbs light what does it isomerizes into?
368) What is activated rhodopsin called?
369) What does it mean to say rhodopsin is bleached?
370) Activated rhodopsin causes the G protein ________ to exchange GTP for GDP, an amplification
step.
371) The ___ subunit of transducin disasscociates from beta-gamma subunits and activates
____________.
372) T or F: cGMP phosphodiesterase is an alpha-beta,gamma heterotetramer
373) The inhibitory subunit of cGMP phosphodiesterase _________ is removed so PDE can
hydrolyze cGMP from the cytosol.
374) How does a decrease in cGMP effect sodium channels?
375) How is rhodopsin deactivated?
376) How is rhodopsin recycled?
Re, Cell Cycle
377) What is the cell cycle?
378) What are the universal properties of each cell?
379) What are the four phases of the Cell cycle?
380) What is the phase in G1 in which cells become quiescent?
381) Is the length of M phase constant for all cells?
382) Is the length of G1 constant?
383) At what point can the cell cycle become arrested?
384) What does G1 checkpoint check for?
385) If the environment is unfavorable in G1 what happens?
386) What does the G2 checkpoint check for?
387) What does the metaphase checkpoint check for?
388) What three things were mentioned as targets for agents that could disrupt the cell cycle?
389) How do Microtubule interfering agents inhibit the cell cycle?
390) What are the microtubule interfering agents mentioned in lecture?
391) How do microfilament interfering agents inhibit the cell cycle?
392) What was the microfilament interfering agent mentioned in lecture?
393) How do DNA interfering agents cause an interruption in the cell cycle?
394) What protein family does the cell cycle depend on for control?
395) What do these proteins phosphorylate (which specific amino acids)?
396) What protein switches Cdks on and off?
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
397) Does cyclin have enzymatic activity?
398) What three factors control the activity of Cdks?
399) What type of cyclin is M-Cdk associated with?
400) What type of cyclin is S-Cdk associated with?
401) What type of cyclin is G1-Cdk associated with?
402) What type of cyclin is G1-S cdk associated with?
403) What controls entry into M phase?
404) When does M-cyclin begin being produced?
405) What components form M-Cdk?
406) What protein does M-Cdk phosphorylate that provides its positive feedback loop?
407) What does M-Cdk phosphorylate that promotes breakdown of the nuclear envelope?
408) What does M-Cdk phosphorylate that promotes condensation of chromosomes?
409) What does M-Cdk phosphorylate that promotes formation of the mitotic spindle?
410) T or F : M-Cdk is only active in mitosis
411) What determines the accumulation of cyclin molecules?
412) Other than cyclin, what causes M-Cdk to be maximally active?
413) What kinase adds the activating phosphate group to M-Cdk?
414) What is the kinase that adds the inhibitory phosphate group to M-Cdk?
415) What is the phosphatase that removes the inhibitory phosphate group from M-Cdk?
416) How does the positive feedback loop for M-Cdk activation work?
417) If you inhibit Wee1 what can happen?
418) What accounts for the explosive nature of switching from G2 to mitosis?
419) How is M-Cdk inactivated?
420) What complex is responsible for separating sister chromatids?
421) How does incomplete replication of DNA inhibit M-Cdk?
422) If chromosomes are not attached properly to kinetochores how does this affect M-Cdk?
423) How is M-Cdk kept inactivated during G1?
424) Movement out of G1 to S phase requires what extracellular signal?
425) Describe the mitogen cascade
426) What does phosphorylation of Rb do?
427) When Cdk phosphorylates Rb?
428) What proteins are transcribed through activation of the E2F protein?
429) After the cell transcribes these genes, this is known as the _______ point.
430) What is the DNA damage sensor?
431) What is p53 normally complexed with?
432) What gene does p53 cause transcription of?
433) How is p53 activated?
434) How can excessive mitogen activation result in cell death?
435) How does S-Cdk initiate s phase?
436) When does the pre replication complex assemble?
437) What causes activation of the pre replication complex?
438) How is the pre-replication complex disassembled?
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
439) What is apoptosis?
440) What is apoptosis triggered by?
441) What is apoptosis mediated by?
442) Caspases cleave at _____ sites and have ______ in their active sites.
443) What are the two types of caspases discussed in lecture and what are their functions?
444) T or F : Caspases are proenzymes
445) What protein to lymphocytes produce that bind to a death receptor on a target cell?
446) What molecules does this receptor recruit?
447) What do mitochondria release that causes apoptosis?
448) What family of proteins helps regulate caspases?
449) Describe the anti-apoptotic members of this family
450) Describe the pro-apoptotic members of this family
Re, Oncogenes
451) What does the term neoplastic mean?
452) What does the term malignant mean?
453) T or F: cancer usually has a monoclonal origin.
454) T or F: multiple mutations are required for cancer to ensue.
455) What are some properties involved in converting normal cells to cancer cells?
456) T or F: Oncogenes act in a recessive fashion at the cellular level.
457) Define Tumor suppressor genes.
458) What is a proto-oncogene?
459) How do proto-oncogenes become oncogenic?
460) What are the three steps of cancer development?
461) Why does cancer incidence increase with age?
462) Describe the clonal evolution of cancer cells.
463) What was the first oncogene found?
464) What did this gene encode for?
465) Normal cells contained the gene c-src which was identified as ?
466) What was the first discovered human oncogene?
467) What are typically the functions of proteins encoded for by proto-oncogenes?
468) Retinoblastoma results from ?
469) Li-fraumeni syndrome results from?
470) What are some methods for inactivation of the remaining tumor suppressor gene?
471) What are the two classes of tumor suppressor genes?
472) What is the function of APC?
473) What happens when APC is not present?
474) What inhibitor was discovered to treat chronic myelogenous leukemia in mice?
475) What are three similarities between stem cells and cancer cells?
476) What are the causes for the heterogeneity of cancer stem cells?
477) What marker protein identifies breast cancer?
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MBOD Block II: Comprehensive Study Questions
Nickalus Khan
478) Mutations in which genes are specifically related to colorectal cancer?
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