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BMS 114: Stem cells and society > Basic molecular biology > Flashcards

Basic molecular biology Flashcards

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1
Q

Why are nucleosomes covalently modified?

A
  • Modifications affect gene transcription by making the chromatin more or less condensed
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2
Q

What 3 ways can histones be covalently modified?

A

1) Acetylation of lysines
2) Phosphorylation of serine 10 in histone H3
3) Methylation of lysines and argenines in core histone N-terminal tails

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3
Q

What is heterochromatin?

A
  • Densely/condensed packed, ‘closed’ chromatin
  • Repressors bound to the chromatin
  • Hypoacetylated
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4
Q

What is euchromatin?

A
  • Loosely packed/accesible, ‘open’ chromatin
  • Activators bound
  • Hyperacetylated
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5
Q

How does methylation of DNA BLOCK transcription? (2 ways)

A

1) Direct blocking of TFIID binding (a TATA binding protein)

2) Recruitment of histone deacteylases

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6
Q

How is transcription controlled?

A

By expressing specific proteins such as transcription factors in different cell types

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7
Q

How are the 8 ways in which gene expression can be controlled?

A

1) Chromatin modifications
2) Control of transcription
3) Alternative splicing
4) Degredation of mRNA

5) Blockage of translation
- siRNA
- miRNA

6) Protein processing and transport
7) Control of enzyme activity by effectors and inhibitorss
8) Proteasome degredation of ubiquitin- tagged proteins

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8
Q

What is alternative splicing?

A
  • Regulated process during gene expression
  • Results in a single gene coding for multiple proteins.
  • Particular EXONS of a gene may be excluded from the final gene product
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9
Q

What are the 3 choices of a stem cell?

A

1) Self- renewal
- Making a copy of itself
- Involves the cell cycle

2) Differentiation
- Changes in gene expression

3) Death

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10
Q

What are the phases of the cell cycle?

A

G1

S

G2

M (mitosis)

  • Prophase
  • Prometaphase
  • Metaphase
  • Anaphase
  • Telophase
  • Cytokinesis
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11
Q

What makes up ‘interphase’ in the cell cycle?

A

G1, S and G2 stages

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12
Q

What happens during G1 in the cell cycle?

A
  • Cells increase in size
  • Ribosomes, RNA produced
  • Preperation for DNA synthesis
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13
Q

What happens during S in the cell cycle?

A
  • DNA synthesised

- Chromosomes duplicated

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14
Q

What happens during G2 in the cell cycle?

A
  • Cell checks fidelity (quality of faithfullness) of DNA

- Preparation for nuclear division

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15
Q

What are the cell cycle checkpoints?

A

G1 (start)

G2 (enter to mitosis)

Metaphase to anaphase

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16
Q

What are the questions ‘asked’ in the G1 checkpoint?

A

1) Is the cell big enough?
2) Is the environment favourable
3) Is there any DNA damage?

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17
Q

What are the questions ‘asked’ in the G2 checkpoint?

A

1) Is all DNA replication
2) Is the cell big enough?
3) Is the environment favourable?

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18
Q

What are the questions ‘asked’ in the metaphase to anaphase checkpoint?

A

Are all the chromosomes attached to the spindle?

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19
Q

What are the 3 principle components of the cell cycle?

A

1) Cyclin dependent kinases (CDK)
- Serine/threonine kinases
- Constitutively expressed (all of the time)

  1. Cyclins
    - Periodic synthesis and degradation
  2. CDK inhibitor proteins
    - Non-kinase inhibitors
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20
Q

what are 2 examples of CDK inhibitor proteins?

A

INK4 family and KIP family

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21
Q

In mammalian cells how many cyclins are there and how many CDK?

A
  • Cyclins A-T

- CDK 1-9

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22
Q

What does cyclin A bind to?

A

CDK 1/2

  • S and G2
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23
Q

What does cyclin B bind to?

A

CDK 1

  • G2/M
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24
Q

What does cyclin D bind to?

A

CDK 4/6

  • G1
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25
Q

What does cyclin E bind to?

A

CDK2

  • G1/S
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26
Q

What is the expression of each cyclin limited to?

A

A specific cell cycle phase

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27
Q

What does cyclin D promote?

A
  • Self- renewal

- Is the direct link between the extracellular environment and the cell cycle

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28
Q

How do most growth factors act?

A

Directly up-regulating cyclin D expression

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29
Q

What is the key transition point in the mammalian cell cycle and what happens here\?

A
  • G1/S restriction point
    1) Integration of internal (growth rate/ cell size) and external (proliferative) cues

2) The cell is committed to complete the remainder of the cell cycle (proceed to S phase)
- Point of no return

OR
2) Exit the cycle into G0

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30
Q

What is the G1/S restriction point progession?

A
  • E2f is transcription factor
  • Associated with pRb (retinoblastoma protein)
  • Phosphorylated by DCDK4
  • Then, phosphorylation by E CDK2 as pass through the restriction point
  • Completes triphosphorylation
  • Releases E2F transcription factor
  • Drives gene transcription
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31
Q

Describe the INK4 inhibitor protein family

A

Inhibitor of CDK4/6

  • Binary inhibitors
  • Prohibit cyclin binding
  • In G
32
Q

Describe the KIP inhibitor protein family

A

CDK2 inhibitor protein

  • Ternary inhibitors
  • Prevent cyclin-CDK activation
  • In G1/S/G2
33
Q

What does PSC stand for?

A

Pluripotent stem cell

34
Q

What is different between somatic and PSC cell cycle?

A

PSC

  • Longer S
  • Shorter G1
  • Self-renewal maintained in S/G2
35
Q

What is G0 and what happens here?

A
  • Resting (quiescent) state
  • Cells can withdraw from the cell cycle and dismantle the regulatory machinery
  • CDKs and cyclins disappear
36
Q

What happens to hepatocytes in G0?

A

Enter temporarily and divide infrequently

37
Q

What happens to neurons in G0?

A

Differentiated, spend their life in G0

38
Q

What 2 things can cause cancer?

A

1) Fundamental alterations in the genetic control of cell division
2) Normal cell cycle regulatory mechanisms are lost

39
Q

What are 6 typical features of stem cells?

A

1) Cannot arrest in G0
2) Loss of G1/S restriction point control
3) Failure to respond appropriately to positive or negative growth factor signals
4) Cells don’t have a limited life span
5) Loss of contact inhibition
6) Unrestrained cell proliferation

40
Q

What 5 does the malfunction of apoptosis lead to?

A

1) Cancer (TNF produced by macrophages activates the extrinsic pathway)
2) Neurodegenerative diseases
3) AIDS
4) Ischemic stroke
5) Autoimmune disease

41
Q

What happens if there is too much apoptosis in disease?

A

Neurodegeneration

42
Q

What happens if there is too little apoptosis in disease?

A

Cancer

Atherosclerosis

43
Q

What happens if there is too much apoptosis within stem cells?

A

Loss of stem cells

Problems with regeneration

44
Q

What happens if there is too little apoptosis within stem cells?

A

Too many stem cells

Problems with regeneration and function

45
Q

What is apoptosis?

A

Programmed cell death

46
Q

What is necrosis?

A

Lethal cell injury from accidental cell death in the living oraganism

47
Q

What are 5 features of apoptosis?

A
  • No loss of integrity
  • Aggregation of chromatin at the nuclear membrane
  • Shrinking of cytoplasm and nuclear/ chromatin condensation
  • Mitochondria release death signals
  • ‘Budding’ forming apoptotic bodies
48
Q

What are 7 features of necrosis?

A
  • Loss of membrane integrity
  • Swelling of the cytoplasm and mitochondria
  • Cell becomes leaky (blebbing)
  • Total cell lysis
  • Disintegration of organelles
  • No vesicle formation
  • Causes inflamation
49
Q

Why is apoptosis important in development and morphogenesis?

A

1) Eliminates excess cells

2) Eliminates non-functional cells

50
Q

Why is apoptosis important in adults?

A

1) Tissue remodelling/ maintenance
2) The loss of the endometrium at the start of mensturation
3) Maintains organ size and function by balancing out proliferation (liver, intestine)
4) Destroys cells that represent a threat to the integrity of the organism

51
Q

What cells represent a threat to the integrity of the organism?

A

1) Cells infected with viruses
2) Cells of the immune system after a mediated response
3) Cells with DNA damage
4) Cancer cells

52
Q

What makes a cell decide to commit suicide?

A

1) Withdrawal of positive signals

2) Presence of negative signals

53
Q

What does the suvival of a cell require?

A
  • Continuous stimulation from other cells

- Continued adhesion

54
Q

What are 3 examples of negative signals?

A

1) Increase levels of free radicals and oxidants
2) DNA-related inducers (eg. UV light)
3) Physiological activators (eg. growth factor withdrawal)

55
Q

What are the 4 stages of apoptosis?

A

1) Death signal to a healthy cell resulting in commitment to die (reversible)
2) Execution to dead cell (irreversible)
3) Engulfment of the dead cell
4) Degradation of the dead cell

56
Q

3 assays to detect apoptotic cells?

A

1) DNA fragmentation
- Electrophoresis

2) Morphological changes
- Nuclear blebbing
- Cell shrinkage

3) Loss of plasma membrane integrity
- Loss of dye exclusion

57
Q

What are caspases and what are they involved in?

A

Cleave proteins, involved in:

  • Inhibiting apopsosis
  • DNA repair
  • Cell cycle
  • Nuclear structure
58
Q

What is the intrinsic apoptosis pathway?

A

1) Triggered by DNA damage and p53
2) Mitochondria release cytochrome C
3) Recruitment of initiator caspase 9
4) Effector caspase 3
5) Apoptosis

59
Q

What is the extrinsic pathway of apoptosis?

A

1) Triggered by death ligands
2) Activated death receptors
3) Initiator caspase 8
4) Effector caspse 3
5) Apoptosis

60
Q

What does self-renewal of a stem cell require?

A

Growth factors which stimulate growth (increase in cell size)

  • By promoting synthesis
    AND
  • Inhibiting degredation of macromolecules
61
Q

What is cell death mediated by?

A

Death factors - promote apoptosis

Suvival factors - Suppresss apoptosis

62
Q

When does a stem cell decide what fate to endure?

A
  • Process the information flow in cells
  • Change gene expression accordingly to either;
    Self-renew
    Differentiate
    Die
63
Q

What defines the ‘state’ of a stem cell?

What is the stem cell state maintained by?

A
  • Genes that are expressed from the stem cell
  • Actively maintained by receiving external signals such as:
  • Soluble ligands for receptors
  • Internally generated signals
64
Q

What must happen within a cell for it to differentiate?

A

Must turn genes on/off

Lock in changes

Chromatin must be altered to allow or close down transcription

65
Q

What parts of a DNA sequence is excluded from the primary transcript?

A

1) Enhancer
2) Promoter
3) Termination region

66
Q

What binds at the TATA box?

A

General transcription factors

Histones

67
Q

What is the relationship between GTFs and histones at the TATA box?

A

They block each other from binding

68
Q

What defines a cell type/

A
  • The cell-type specific gene expression (only a certain repertoire of genes are switched on)
  • Expression of specific proteins such as transcription factors which mediate transcription initiation
69
Q

What is the ‘mediator complex’ and how is it involved in transcription?

A
  • It is a transcription associated complex
  • Present between the transcriptional activator proteins at the cis- acting sequence and the TIC complex
  • Stabilises the complex, allowing transcription to occur
70
Q

What structure is important for controlling cell fate decisions?

A

3D structure

71
Q

What drives expression differently in different cell types and times?

A

Tissue-specific enhancers

72
Q

What kinases are CDKs?

A

Serine/ threonine

73
Q

What occurs at the restriction point with Rb?

A
  • Before the restriction point, cyclin D is synthesised and complexes with CDK4
  • Phosphorylates Rb (which is in a complex with E2F)
  • As cross over into the restriction point, cyclin E synthesised and when complexed with CDK2 completes the triphosphorylation of Rb
  • E2F released (is a transcription factor)
  • Bind to gene and allows gene transcriptiom
74
Q

What is an example of a positive growth factor?

A

EGF

75
Q

What is and example of a negative growth factor?

A

TGF-beta

76
Q

In the cell cycle, where are cells most sensitive to different signals?

A

G1

77
Q

In the cell cycle, where are the self-renewal controls?

A

G2

BMS 114: Stem cells and society (15 decks)

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