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Cell 402 > A1-A2 > Flashcards

A1-A2 Flashcards

1
Q

omnis cellula e cellula (virchow)

A

all cells come from cells

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2
Q

what is cell birth?

A

one cell becomes two daughter cells that may or may not look/act like the same type of cell

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3
Q

what are the four things that cells can do?

A

-survival/maintain homeostasis
-division (making new cells)
-differentiation (making new types of cells)
-death (apoptosis)

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4
Q

the two processes that necessary for cell birth

A

division and differentiation

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5
Q

common eukaryotes that are used for laboratory research (+ pros and cons)

A

-human (well developed cultures but difficult to study whole animals and ethical concerns)
-mouse (well developed cultures and easy to study whole animals; not exactly the same as humans)
-fish (primary cultures only but genome is 4n; not like humans)
-flies (well developed cultures, short generation times)
-c.elegans (primary cultures only; sex determination is vastly different)
-yeast (short generation times)

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6
Q

what is the difference in cell cycle regulation is yeast vs animals?

A

yeast undergoes cell division only so you get the same type of cells; animals undergoes cell division & differentiation to produce multiple different type of cells so cell division and differentiation are linked processes in terms of animal development and homeostasis

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7
Q

how does nutritional cell cycle control works?

A

-without the control, when nutrition is reduced, the cell cycle continues at the same pace, so as the cell divides, the cells don’t grow as much and the cell mass decreases with successive generations
-with the control, when nutrition is reduced, the cell cycle slows down and the cell grows until optimal mass is reached before dividing. the time it takes for the cell to divide then increases but the mass of the daughter cells remain constant

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8
Q

what are metazoans and where do they come from?

A

multicellular animals that (maybe with a grain of salt; cum grano salis) came from a single celled protozoan ancestor and definitely from single celled zygote

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9
Q

do eukaryotic cells have a single appearance?

A

no, obv, the cells structure differs depending on multiple factors, including species, location, function etc.

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10
Q

what are the phases of the cell cycle?

A

G0 (quiescence)
G1
S (DNA replication)
G2
M (nuclear division)
cytokinesis (cytoplasmic division)

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11
Q

interphase phases

A

G0 (G1)
S
G2

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12
Q

what are the phases of M phase and what are they based on?

A

-Prophase, Metaphase, Anaphase, Telophase
-chromosome morphology and position

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13
Q

how does flow cytometry works?

A

a flow cytometer aka a fluorescence activated cell sorter (FACS); cells are stained with a dye and passed through the machine and the cells are put into a single file and then the laser shoots at cells and fluorescence emitted from stained cells and then measure.

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14
Q

how does flow cytometry indicates cell cycle?

A

cells stained with DAPI (Hoescht stain) and then run through flow cytometer; the amount of DNA indicated cell cell (most cells are in G1, second most in G2)

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15
Q

how BrdU indicate cell cycle?

A

BrdU is incorporated with DNA instead of thymine during S phase (DNA replication), indicates S phase and G2 phase cells, identified with immunofluorescence

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16
Q

what are cyclins?

A

molecules that regulate cell cycle; they are degraded at specific points in the cell cycle

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17
Q

why do cyclins associated with CDKs (cyclin dependent kinases)?

A

cyclins require Cdks to regulate passage between cell cycle stages

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18
Q

MPF and SPF regulate what phases?

A

MPF (Mphase promoting factor) - entry into M phase
SPF (Sphase promoting factor) - entry into S phase

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19
Q

what a.a are phosphorylated with ATP during post-translation modification

A

serine, threonine, tyrosine

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20
Q

what are the 6 things that phosphorylation do to proteins?

A

-change activity
-change localization
-change stability
-change conformation
-interacts with other proteins
-crosstalk with other post-translation modification (PTM)

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21
Q

how does Cdk proteins phosphorylation regulate function? & proteins involved

A

1) (CDK activating kinase) add PO4 to CDK-cyclin to activate them; Wee1 kinase add inhibitory PO4 to CDK-cyclin-PO4, so CDK-cyclin with 2PO4 is inactive
2) Cdc25 phosphatase-PO4 removes inhibitory PO4 and makes CDK-cyclin-PO4 (active)
3) active cyclin-CDK phosphorylate Cdc25 to activate it (+ feedback)
4) active cylin-CDK inhbits Wee1 kinase (- feedback)

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22
Q

how does phosphorylation regulates MPF?

A

Wee1 Kinase (add inhibitory PO4)
Cdc25 phosphatase (removes PO4 to activate MPF)

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23
Q

cyclin-cdk pairing (G1)

A

CDK4/Cyclin D
CDK6/Cyclin D (late)

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24
Q

cyclin-cdk pairing (G1/S)

A

CDK2/Cyclin E

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25
Q

cyclin-cdk pairing (S)

A

CDK2/Cyclin A (SPF)

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26
Q

cyclin-cdk pairing (G2)

A

CDK1/Cyclin A

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27
Q

cyclin-cdk pairing (M)

A

CDK1/Cyclin B (MPF)

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28
Q

what is the start of the cell cycle?

A

G1 restriction point

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29
Q

what are the different cell cycle checkpoints?

A

G1 arrest - is there DNA damage
S arrest - is DNA replicated
G2 arrest - is there DNA damage
M arrest - are spindles formed correctly?

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30
Q

how can p53 control cyclins/cdks & checkpoint factors?

A

excess mitogenic stimulation causes increase p53
p53 inhibits G1/S-Cdk -> prevents entry into S phase

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31
Q

how can APC control cyclins/cdks & checkpoint factors?

A

chromsome unattached into spindle and then inhibits APC and entry into G1

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32
Q

how can unreplicated DNA control cyclins/cdks & checkpoint factors?

A

unreplicated DNA inhibited Cdc25, preventing MPF activation and preventing entry into Mphase and DNA replication

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33
Q

how does the three core subunits of E3 ligases work together?

A

-E1 ubiquitin activating enzyme uses ATP to activate ubiquitin and transfers to E2 enzyme
-E2 ubiquitin conjugating enzyme interacts with E3 ubiquitin ligase to add ubiquitin to target protein to proteasome for degradation
-DUB (deubiquitining enzyme) removes ubiquitin to prevent degradation by proteasome?

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34
Q

what is APC/C?

A

-anaphase promoting complex/cyclosome

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35
Q

how does APC/C work to separate chromosomes?

A

-securin + separase complex prevent dissociation of chromosomes until they properly attached to spindle fibres
-inactive APC adds cdc20 to make it active
-active APC causes the ubiquitylation of securin (causes degradation)
-separase cleaved cohesins between chromosomes during anaphase

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36
Q

how does APC/C work to degrade Cyclin B (M-cyclin)?

A

-inactive APC adds cdc20 to make it active (cdc20 is activated by m-cdk)
-uses E1/E2 ubiquitylation enzymes to add ubiquitin to cyclin and causes degradation by proteasome

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37
Q

APC/C activator form proteolysis in G1? M phases?

A

-Cdh1(degrade cyclin A/B)
-CDC20 (degrade securin, cyclinA/B)

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38
Q

CKIs like p21 & p27 act in what way? wbu INK4A/B?

A

-occupy ATP binding site of cyclin complexes
-bind to CDKs to prevent cyclin from binding to activating sites

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39
Q

p27 other name? p21?

A

Kip1
Cip1

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40
Q

how are CKIs, which can bind to fully active CDK-cylin, removed from the cell?

A

Skp1-cullin-F-box protein complex (SCF) Ubiquitin ligase targeted phosphorylated CKI (p27) for degradation in proteasome

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41
Q

what are the components of Skp1-cullin-F-box protein complex (SCF) Ubiquitin ligase?

A

Cdc34 (E2)
CUL1 (scaffold)
Cdc4 (F-box)- substrate specificity
Rbx-1 (recruits E2/Cdc34)
Skp1 (sphase kinase protein)- bridges CUL1 & Cdc4)

42
Q

p27 and Go

A

helps cells center Go as they terminally differentiate; Cdk2 phosphorylate p27 to cause SCF targeting to degradation

43
Q

p21 & p53

A

expression of p21 gene activated by p53, P21 SUPPRESS g1/s-cdk following DNA damage in G1

44
Q

how can cell stiffness also affects the cell cycle?

A

flattened cells enter S phase more than rounded cells

45
Q

howis cell differentiation linked to the cell cycle?

A

changes in expression of a few genes induce a lot of diversity and regulatory factors are often activated sequentially as cells divide (working in combination)

46
Q

what are the two of the most common regulatory factors?

A

DNA TFs and regulatory RNAs

47
Q

what are three main things that can affect cell cycle?

A

cell shape, location, adhesion

48
Q

what is cell differentiation (in relation to cell cycle)

A

changes in gene expression that is maintained through the cell cycle (S phase) even though the cell still has all the same genes

49
Q

what does the Rb/EF2 TF regulatory complex regulate?

A

the transcription of cell cycle genes (ex. cyclins); it is the central integrators of extrinsic signals that influence cell cycle

50
Q

E2 family TFs activate genes required for what?

A

G1/S transition

51
Q

Cyclin D/CDK 4/6 effect on RB/E2

A

Cyclin D/CDK 4/6 inhibits pRB which inhibits E2F; E2 can then act to cause G1/S transition

52
Q

INK4/CDK 4/6 effect on RB/E2

A

INK4 inhibits CDK 4/6 which inhibits pRB which inhibits E2; so no inhibition of pRB so pRB can inhibit E2F and prevent G1/S transition

53
Q

p21/CDK 4/6 or CDK 2 effect on RB/E2

A

p21 inhibits CDK 4/6 or CDK2 which inhibits pRB which inhibits E2; so no inhibition of pRB so pRB can inhibit E2F and prevent G1/S transition

54
Q

Cyclin E/CDK 2 effect on RB/E2

A

Cyclin E/CDK 2 inhibits pRB which inhibits E2F; so inhibition of pRB means that E2 can then act to cause G1/S transition

55
Q

cell proliferation requires the specific of regulation (activation/repression) of what?

A

multiple genes encoding cell cycle proteins

56
Q

RB stands for

A

retinoblastoma protein

57
Q

why is the regulation of rb critical?

A

its regulation is needed to direct the gene transcription towards division or differentiation

58
Q

what does E2F work with?

A

DP (dimerization protein)

59
Q

what are the five cell cycle things that RB is involved in?

A

DNA replication
Differentiation
Checkpoint control (inhibits either G1/S or G2/M transition)

60
Q

what is the rb core?

A

p16 inhibits CDK4/6 which inhibits RB which inhibits E2F/DP

61
Q

what is p16?

A

a CKI; cyclin-dependent kinase inhibitor 2A, INK4A, multiple tumor suppressor 1

62
Q

what state is RB in when repressing E2F?

A

hypophosphorylated

63
Q

rb core action when cell is non-proliferating?

A

p16 is activated and inhibits CyclinD/CDK4/6; RB is hypophosphorylated and active and inhibits E2F (S phase transition inhibited)

64
Q

rb core action when cell is proliferating?

A

p16 is inactivated and CyclinD/CDK4/6 is active RB is hyperphosphorylated and inactive and E2F is active (S phase transition activated)

65
Q

overexpression of p16 consequence

A

cell cant enter S phase

66
Q

p15/INK4B vs p16/INK4A

A

same type of protein that works through regulation of RB core, same as p16 but different gene (CDKN2B)

67
Q

p14(arf) (human) or p19 (arf) (mouse) vs p16/INK4A

A

same as p16 but regulates RB via MDM2 AND P53 (inhibits MDM2 which inhibits p53 which activates P21which inhibits CDK2 which inhibits RB)

68
Q

P14/P19 other names

A

ARF/INK4D

69
Q

p14/ARF and p16/INK4A (humans) gene

A

expressed from the same gene (CDKN2A) via alternative promoters and alternative mRNA splicing

70
Q

rb is what type of protein and how does it work?

A

-pocket proteins
-phosphorylation of Thr373 drives interdomain docking of amino-terminal domain (RBN) and the pocket domain
-phosphorylation of Ser608 and Ser612 allows binding of pocket loop to pocket domain
-phosphorylation of Thr821 and Thr826 allows binding of carboxy terminal doman (rbc) to pocket domain

71
Q

where is e2f(TD) - transactivation (gene regulation) domain in the pocket protein? wbu DP (MB)?

A

-pocket domain (where E2F binds)
-RBC (carboxy terminal domain) (where DP binds)

72
Q

examples of pocket proteins?

A

pRB, p107, p130

73
Q

binding of chromatin regulator to pRB causes what?

A

covers transactivation domains while RB is hypophosph. to prevents E2F/DP activation of genes , even if they are present at promoters

74
Q

E2F forms can be both activators and repressors. which are which?

A

E2F1/2/3A/3B = activators (has NLS, cyclin A region, leucine zipper, marked box, rb binding region)
E2F4/5/6 = repressors (has NES (except E2F 6) , cyclin A region, leucine zipper, marked box, rb binding region)
E2F 7/8 = atypical repressors (has DNA binding region)

75
Q

different E2Fs are active at different part of the cell cycle?

A

Early G1: 4/5
Mid G1: 1/2/3
S: 6/7/8
G2: 4
exiting cell cycle: 3A
G0: 3B/4/5
entering cell cycle: 4

76
Q

E2F/RB core in flies

A

two RB (F1/F2)
has E2F1 (activating) & E2F2 (repressing) that interacts with dDP (drosophila-dp)

77
Q

Cyclin-CDK mutants in yeast or isolated cells have strong effects on cell cycle but weak phenotypes in animals because of what?

A

redundancy in metazoan cell cycle and cooperation with other cells means that Rb core is stongly influenced by intrinsic and extrinsic factors

78
Q

MYC is a TF. Its carboxy-terminal domain (CTD) contains a _______ region that promotes dimerization with ____ and subsequent ____ binding of MYC–MAX heterodimers.
* The amino-terminal domain (NTD) harbours conserved _______ (MBI and MBII), which are essential for the transactivation of MYC target
genes.
* MYC-interacting proteins might or might not bind simultaneously

A

-basic (b) helix–loop– helix (HLH) and leucine zipper (LZ)
-MAX
-DNA
-MYC Boxes’ I and II

79
Q

what is MIZ1?

A

TF that interact with the CTD of c-MYC; can activate transcription by itself, when bound to Max/myc, miz1 represses transcription of genes

80
Q

TGFB & Miz1

A

TGFB releases Miz1 from Myc-Max complex by downregulating expression of Myc, then Miz1 can bind to p15INK4b promoter along TGFB activated Smad4

81
Q

Myc-max promotes G1-S progression through both gene activation and repression; produces _____

A

cyclin D2 and cdk4

82
Q

miz-1myc-max inhibits _____ transcription

A

p15/p21

83
Q

p53 and cell cycle

A

represses cell cycle by promoting activation of gene (CDKN1A) encoding p21 (Cip1/Waf1)

84
Q

how is p53 stability regulated?

A

MDM2 binds to p53 and targets it for degradation (p53 also regulates MDM2 (target gene) so over time p53 is supressed; cellular stress (oncogene activation induces p14ARF which sequesters MDM2)

85
Q

p53-p21-rb

A

p53 promotes p21 transcription, p21 represses cyclin-cdk complexes, cyclin-cdk can’t phosphorylate rb so hypohosphorylation of rb leads to cell cycle arrest

86
Q

quiescence when cells are not actively transiting the cell cycle is highly controlled by the _____

A

microenvironment (ex. cell-cell contact, soluble factor signaling, extracellular matrix)

87
Q

what is the primary mechanism that regulates quiescence (when cells are out of the cell cycle but still retain the ability to divide)?

A

the activity of CKI (p57/Kip2 or p27/Kip1)

88
Q

Only ______ that is not bound by p21/p27 is able to phosphorylate RB. _____ can function to phosphorylate RB even when (partially) bound by p21/p27. This occurs over time, remember that
some hyperphosphorylation of pocket proteins allows E2F-mediated expression of a few critical genes needed for the cell cycle, and increased expression of _____.
* As E2F levels rise and CKI proteins are inhibited, eventually Cyclin E/CDK2 levels and RB phosphorylation allows sufficient E2F mediated transcription of cell cycle genes that the cell cycle can proceed past the restriction point.

A

-Cyclin E/CDK2
-CyclinD/CDK4 and Cyclin D/CDK6
-E2F

89
Q

_____ are transcription factors that specify a myocyte fate. _____ is a transcription factor that specifies a cardiomyocyte fate. They are all inhbited by _____

A

-MEF2 and MYOD
-GATA4
CDK4/CycD (may not require PO4)

90
Q

In fully (terminally) differentiated myotubes _____ levels are elevated, and this seems to be need for differentiation by an unknown (?) mechanism.

A

Cyclin D3

91
Q

PLKs

A

polo-like kinases

92
Q

PLK1 function? PLK2? PLK4? PL3?

A

-G2 at centrosomes, during pro metaphase and metaphase, it is present at spindle pole and anaphase and telophase, central spindle
-regulates early duplication of centrioles at G1/S
-regulates early duplication of centrioles late events
-dna replication, G1/S, G2/M and cytokineses

93
Q

aurora kinase A? B?

A

formation of bipolar spindle, cytokinesis
-sister chromatid cohesion, kinetochore-microtubule, cytokinesis

94
Q

APC/C (CDH1) & aurora and polo-like kineases?

A

destroyed at telophase/cytokinesis

95
Q

The mammalian MuvB complex consists of the protein subunits ______and ____ (also known as RBBP4)
When cells are not actively dividing, MuvB in the DREAM complex represses ______ genes.
MuvB also forms activator _____complexes together with the
transcription factor B -MYB and ____ that are required for the expression
of the mitotic genes in G2/M.

A

-LIN9, LIN37, LIN52, LIN54,
-RBAP48
-G1/S and G2/M
-MuvB -Myb (MMB)
-FOXM1

96
Q

____ = DREAM

A

DP + Rb + E2F & MuvB

97
Q

G0/G1, dream complex is active leading to ____. in S phase, what is active?

A

-cell cycle repression
-MMB (with YAp1 & TEAD), leading to cell cycle activation

98
Q

DREAM complex represses? RB:E2F?

A

-G1/S and G2/M genes
-G1/S genes

99
Q

E2F1-3 complex expresses? MMB?

A

-G1/S genes
-G2/M genes

100
Q

SCF + FboxW7 (FBXW7), S-phase kinase-associated protein 2 (SKP2) and β -transducin repeats-containing protein (β-TrCP)?

A

they are specificity proteins for SCF E3 ubiquitin ligases
-FBXW7 (targets Myc and Cyclin E/CDK2
-SKP2 (targets p27 and p21)
-β-TrCP (targets Wee1)

101
Q

CDH1 is highest in concentration when? SKP2? β-TrCP?

A

M/G1-S
G2/M
G2/M

Cell 402 (5 decks)

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