Exam 2 Materials Flashcards by Long Nguyen

What does the cell do at Interphase?

Cell duplicates chromosomes.

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What does the cell do at Mitosis?

Cell segregates duplicated chromosomes into two daughter cells.

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How many periods does interphase have? What are they?

3 periods: G1, S, G2

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Why is the restriction point important for the cell?

Big commitment whether it will divide or not.

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What does the cell do at G1 phase? What are the two questions the cell will ask itself?

Cell decides whether to divide or not.
“Have I grown enough to enter the cell cycle?”
“Am I OK?”

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What does the cell do at S phase?

Chromosomes are duplicated

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What does the cell do at G2 phase? What are the two questions the cell will ask itself?

Cell prepares to enter mitosis.
“Have I completed DNA synthesis properly?”
“Am I OK?””

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After the cell passed restriction point, if the cell does not receive enough growth factor, it will stop dividing. True or False

False.
The cell no longer responses to growth factors beyond R point

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What are the two conclusion can you draw from this illutration?

S phase stays at S phase => Cell cycle is unidirectional (cannot be reverse)
G1 phase becomes S phase ==> Something in the cytoplasm of S cell induces G1 cell to enter S phase

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What are the two factors regulate the cell cycle?

Promoting factors.
Checkpoints.

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How many chromatids are attached to microtubules during metaphase of mitosis?

92 chromatids because the chromosomes have already been doubled.

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What will happen if anaphase takes place but only 91 chromatids are attached to microtubules?

Aneuploidy daughter cells.

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Cancer has a high frequency of?

Aneuploidy

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What is the first promoting factor in cycle to be identified?

MPF (mitosis promoting factor)

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What is the problem when we want to study mutants that cannot synthesize proteins?

It is lethal.

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What is the function of cdc28?

Requirement for cells to enter S phase

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What is the different in phenotype between budding yeast cdc28 mutants and wildtype? Why?

cdc28 mutants look bigger and budless because they are stuck at G1 phase.

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Fission yeast is good to study at what transition of the cell cycle? Why?

G2 to Mitosis because you can see the furrow in yeast which indicates they are entering mitosis.

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What is the function of cdc2?

Requirement for cells to enter mitosis

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How can you test if cdc28 and cdc2 are homologs?

Introduce cdc28 WT DNA of budding yeast to (cdc2-) mutant fission yeast, and see whether cdc28 WT can rescue cdc2- or not

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Which type of protein kinase do cdc28/cdc2 encode?

Serine/Threonine kinase

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Why is it hard to study the role of cdc2 in fission yeast in the transition between G1 phase to S phase?

Hard to distinguish the length difference in fission yeast (i.e cannot determine whether it has entered S phase or not)

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How can we test to see if human contain a gene that is homolog to cdc28/cdc2 ?

Create human cDNA library and introduce to cdc28-/cdc2- mutant and look for the result that show mutants rescued by human cDNA => identify the gene.

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PICK THE CORRECT OPTION.

Scientists used (Forward/Reverse Genetic) to isolate cdc mutants in budding yeats by creating (loss-of-function/conditional) mutant.

Forward genetics
Conditional (temperature sensitive)

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# Lecture 10 - Result from Tim Hunt's experiment Suggest two non-opposing hypotheses on causation.

1. Something needs to appear in order for the cell to enter mitosis. 2. Something needs to go away in order for the cell cycle to proceed

# Lecture 10 What factor was found that promotes mitosis based on *Xenopus* studies?

Maturation Promoting Factor (MPF)

# (True or False) Statements 1. Cdc genes are all part of the cell cycle regulatory machinery ("the clock"). 2. Cdc gene encode cyclins. 3. Sea urchin eggs start expressing cyclins upon fertilization. 4. Kinases are a major part to the cell cycle clock.

1. False, there are other genes regulate cell cycle clock. 2. False, cyclins are not encoded by cdc gene 3. True 4. True

What are the components of Maturation Promoting Factor (MPF)?

CDK and Cyclin.

How does MPF become active?

CDKs form heterodimers with Cyclins and become active kinases

What type of protein is MPF?

Kinase

What do G1/S-Cdk complexes do?

Commit the cell to a new cell cycle.

What do S-Cdk complexes do?

Promote S phase

What do M-Cdk complexes do?

Entry into mitosis

# True or False M-Cdk complexes are upregulated throughout the entire process of mitosis.

False. M-Cdk complexes are removed before anaphase

How many CDKs and Cyclins do humans have? What are they?

4 CDKs and 4 Cyclins. CDKs: CDC2, CDK4, CDK6, CDK 2 Cyclins: A, B, D, E

How many CDKs and Cyclins do yeasts have?

1 CDK and several Cyclins

What are the major activators of the cell cycle? In other words, which genes are always upregulated in the cell cycle?

CDKs

Which components of MPF are always expressed in the cell cycle?

CDKs

What are the mechanisms of CDKs regulation?

1. Abundance of Cyclins 2. CDK phosphorylation 3. Binding to CKIs (inhibitory proteins)

# Ubiquitination What is the function of E1?

E1 first bind to ubiquitin and transfer it to E2

# Ubiquitination What is the function of E2?

Transfer ubiquitin to the target protein bound by E3 ligase

# Ubiquitination What is the function of E3?

Bind to the target protein with high specificity.

# Ubiquitination Why does E3 has high specificity to target proteins?

Ensure that we degrade the correct proteins.

What are the two basic E3 complexes that act during the cell cycle?

1. SCF 2. APC (anaphase promoting complex)

What are the components of SCF E3 ligase?

Skp, Cullin, F-box

Which part of the SCF does cdc4 encode?

F box, containing WD40 repeats

# Co-immunoprecipitation (Co-IP) experimental What is the conclusion for this experiment?

Cyclin E physically interacts with CDC4

What is the function of Cyclin E? Which process does it involve?

Initiate the assembly of pre-replication complex. DNA replication

What activates SCF at the right time?

CDK2-cyclin E complex actives SCF

What is the function of SCF?

It degrades cyclin E

Why is it important for the cell cycle that cyclin E-cdk2 complex activates its own degradation pathway?

It ensures that the cell cycle will only go in 1 direction.

What is the key point interaction between different cyclins in the cell cycle?

A cyclin promotes (indirectly) **synthesis** of the **next** cyclin. Some, in turn, promote **destruction** of the **previous** cyclins.

What inhibit the activities of CDKs?

Inhibitory phosphorylation.

Active M-CDK is required for cell cycle. Based on the diagram which gene is proto-oncogene? Why?

Cdc25 Because it removes the inhibitory phosphate which allow M-CDK to be activated and continue the cell cycle. *Think what cancer cells want* *Which gene should I constitutively activate?*

What are the two family of Cdk inhibitor proteins (CKIs)?

- INK4 - Cip/Kip

What is the function of INK4 (p16) family proteins?

Bind to CDK4/6 => blocking cyclin D binding

What is the function of the Cip/Kip (p21,p27) family?

Bind to cyclin-CDK complexes in late G1 through M phase and inactivate them, but promote the assembly of CDK4/6-cyclin D

Which CKI protein is frequently mutated in human tumors? What kind of mutation?

p16. Loss-of-function

What is the function of mitogen?

It activates D-CDK4/6 complex and inhibits CKIs

What is proliferation in simplistic way? (2 words)

Growth and Division

Why does B-CDC2 not promote cyclin D expression to ready for the next cell cycle?

Do not want to start another cell cycle while mitosis is still happening in the cell.

# **True** or **False** Mitogen concentration is not relevant in the cell cycle since the cell just needs the signal to start cell cycle.

False. The cell requires enough mitogens to push the cell cycle through the R-point

What could lead the cell to quiescence?

Without growth signals or sub-threshold levels of enzymes

What is the different between **quiescence** or **senescence**?

Quiescence: cell can continue proliferate if it receives enough signals. Senescence: cell cannot proliferate anymore.

# **True** or **False** The cells constantly requires to be exposed to mitogen to go through each phase of cell cycle.

False. The cell cycle is independent of mitogen after the R point.

What are two categories of tumor supressing genes (TSG)?

1. Gatekeepers 2. Caretakers

What is the function of gatekeepers TSG?

Regulate cell cycle progression

What is the function of caretakers TSG?

Maintain genome integrity

What conclusion can you draw from this graph?

Germ-line mutations (familial) in the Rb gene lead to predisposition to cancer

What is the different between sporadic and familial?

The **sporadic form** of the disease can affect anyone and is dependent on genetic changes aquired during the lifetime of the affected individual. The **familial form** of the disease results when affected individuals inherit a defective copy of the Rb gene from one of their parents.

# Fill-in the blanks Rb tumors are associated with a [...] region in chromosome [...]

Rb tumors are associated with a **deleted** region in chromosome **13**

What hypothesis can explain retinablastoma is inherited as a dominant trait, but it is recessive at the cellular level? Give a brief explanation of the hypothesis.

Kundson's "two-hit" hypothesis. It suggests that the normal gene needs to be mutated in two alleles through variety of mechanisms in order to express the phenotype (e.g retinablastoma)

What is the genotype of the cells of people with familial retinoblastoma?

+/- carry one normal copy and one mutated copy.

What is different in the chance of getting cancer between homozygous Rb+/+ people and heterozygote Rb+/- people?

Heterozygote +/- has a higher chance of developing cancer.

What are two main events explain the likelihood of mutation in the first copy increases the chance of mutation in the second copy?

Mitotic recombination Gene conversion

What is the key feature in tumor progression?

Loss of heterozygosity

What are the chances that two heterozygous parents will have a child that is homozygous for Rb(-/-)? Why?

0% Homozygous Rb (-/-) is lethal

# **True** or **False** Tumor suppression gene is not important during embryogenesis.

False. TSG is required in embryogenesis which control the proliferation rate of stem cells.

What are the chances that two heterozygous parents will have a fertilized oocyte homozygous for Rb(-/-)

25% Keyword: oocytes

# **True** or **False** Cancer is inheritable disease.

False. Cancer cannot be inherited.

Does homozygous Rb +/+ viable offspring the same as heterozygous Rb +/- offspring?

No, heterozygous offspring Rb +/- have predisposition which mean they have higher risk of developing cancer.

What is the general function of Rb? Be specific.

Inhibiting a major transcription factor which prevent the cell from crossing R point.

What are two states of Rb protein where it can bind to the transcription factors of E2F?

Hypophosphorylated or Unphosphorylated

What process inactivates Rb protein?

Hyperphosphorylation of Rb gene.

What happens to the E2F proteins during S phase?

It starts to degrade.

What does Rb gene do when it binds to E2F transcription factors? (2)

1. Inhibibt their transcription activation sites 2. Recruits proteins that will "close" the chromatin down. (e.g histone deacetylase)

What happens after the releasing of Rb from the E2F transcription factors?

1. Release of their transcription activation sites 2. Recruitment of proteins that will " open up" the chromatin

# **True** or **False** Cyclin E-CDK2 can bind to unphosphorylated Rb and cause hyperphosphorylation in Rb.

False. Cyclin E-CDK2 cannot bind to unphosphorylated Rb

# **True** or **False** Cyclin D-CDK4/6 first hypophosphorylates Rb and then hyperphosphorylates Rb.

False. Cyclin D-CDK4/6 can only hypophosphorylates Rb

# Gene that is discussed in class What is one of the targeted genes of E2F that is involved in DNA replication?

Cyclin E gene

What is one common mutated location in the majority of tumors?

R site

What are the reasons that lead to uncontrolled crossing of the R site?

1. Loss of Rb function 2. Loss of CKIs 3. Oncogenic activity of cyclin E and D

If Rb is important, why would we need more mutations to form a tumor?

If the cell does not receive more signals from growth factors (mitogen) then the cell would enter quiescence state (G0) regardless of unfunctional Rb.

What are two conditions that make the cell cycle runs indefinitely?

1. Removal of Rb (remove gatekeeper and enter the R point) 2. Cheat the cell mitogen signaling (prevent from going to G0)

CDKs are always expressed in the cell, and Cyclin E presents in a small amount at the beginning of G1 phase. Why does the cell not response to cyclinE-CDK2 signaling?

1. p27-p21 inhibits cyclinE-CDK2 complex 2. There is no substrate for cyclinE-CDK2 (substrate: hypophosphorylated Rb)