Basic molecular biology Flashcards
Why are nucleosomes covalently modified?
- Modifications affect gene transcription by making the chromatin more or less condensed
What 3 ways can histones be covalently modified?
1) Acetylation of lysines
2) Phosphorylation of serine 10 in histone H3
3) Methylation of lysines and argenines in core histone N-terminal tails
What is heterochromatin?
- Densely/condensed packed, ‘closed’ chromatin
- Repressors bound to the chromatin
- Hypoacetylated
What is euchromatin?
- Loosely packed/accesible, ‘open’ chromatin
- Activators bound
- Hyperacetylated
How does methylation of DNA BLOCK transcription? (2 ways)
1) Direct blocking of TFIID binding (a TATA binding protein)
2) Recruitment of histone deacteylases
How is transcription controlled?
By expressing specific proteins such as transcription factors in different cell types
How are the 8 ways in which gene expression can be controlled?
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
What is alternative splicing?
- 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
What are the 3 choices of a stem cell?
1) Self- renewal
- Making a copy of itself
- Involves the cell cycle
2) Differentiation
- Changes in gene expression
3) Death
What are the phases of the cell cycle?
G1
S
G2
M (mitosis)
- Prophase
- Prometaphase
- Metaphase
- Anaphase
- Telophase
- Cytokinesis
What makes up ‘interphase’ in the cell cycle?
G1, S and G2 stages
What happens during G1 in the cell cycle?
- Cells increase in size
- Ribosomes, RNA produced
- Preperation for DNA synthesis
What happens during S in the cell cycle?
- DNA synthesised
- Chromosomes duplicated
What happens during G2 in the cell cycle?
- Cell checks fidelity (quality of faithfullness) of DNA
- Preparation for nuclear division
What are the cell cycle checkpoints?
G1 (start)
G2 (enter to mitosis)
Metaphase to anaphase
What are the questions ‘asked’ in the G1 checkpoint?
1) Is the cell big enough?
2) Is the environment favourable
3) Is there any DNA damage?
What are the questions ‘asked’ in the G2 checkpoint?
1) Is all DNA replication
2) Is the cell big enough?
3) Is the environment favourable?
What are the questions ‘asked’ in the metaphase to anaphase checkpoint?
Are all the chromosomes attached to the spindle?
What are the 3 principle components of the cell cycle?
1) Cyclin dependent kinases (CDK)
- Serine/threonine kinases
- Constitutively expressed (all of the time)
- Cyclins
- Periodic synthesis and degradation - CDK inhibitor proteins
- Non-kinase inhibitors
what are 2 examples of CDK inhibitor proteins?
INK4 family and KIP family
In mammalian cells how many cyclins are there and how many CDK?
- Cyclins A-T
- CDK 1-9
What does cyclin A bind to?
CDK 1/2
- S and G2
What does cyclin B bind to?
CDK 1
- G2/M
What does cyclin D bind to?
CDK 4/6
- G1
What does cyclin E bind to?
CDK2
- G1/S
What is the expression of each cyclin limited to?
A specific cell cycle phase
What does cyclin D promote?
- Self- renewal
- Is the direct link between the extracellular environment and the cell cycle
How do most growth factors act?
Directly up-regulating cyclin D expression
What is the key transition point in the mammalian cell cycle and what happens here\?
- 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
What is the G1/S restriction point progession?
- 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
Describe the INK4 inhibitor protein family
Inhibitor of CDK4/6
- Binary inhibitors
- Prohibit cyclin binding
- In G
Describe the KIP inhibitor protein family
CDK2 inhibitor protein
- Ternary inhibitors
- Prevent cyclin-CDK activation
- In G1/S/G2
What does PSC stand for?
Pluripotent stem cell
What is different between somatic and PSC cell cycle?
PSC
- Longer S
- Shorter G1
- Self-renewal maintained in S/G2
What is G0 and what happens here?
- Resting (quiescent) state
- Cells can withdraw from the cell cycle and dismantle the regulatory machinery
- CDKs and cyclins disappear
What happens to hepatocytes in G0?
Enter temporarily and divide infrequently
What happens to neurons in G0?
Differentiated, spend their life in G0
What 2 things can cause cancer?
1) Fundamental alterations in the genetic control of cell division
2) Normal cell cycle regulatory mechanisms are lost
What are 6 typical features of stem cells?
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
What 5 does the malfunction of apoptosis lead to?
1) Cancer (TNF produced by macrophages activates the extrinsic pathway)
2) Neurodegenerative diseases
3) AIDS
4) Ischemic stroke
5) Autoimmune disease
What happens if there is too much apoptosis in disease?
Neurodegeneration
What happens if there is too little apoptosis in disease?
Cancer
Atherosclerosis
What happens if there is too much apoptosis within stem cells?
Loss of stem cells
Problems with regeneration
What happens if there is too little apoptosis within stem cells?
Too many stem cells
Problems with regeneration and function
What is apoptosis?
Programmed cell death
What is necrosis?
Lethal cell injury from accidental cell death in the living oraganism
What are 5 features of apoptosis?
- 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
What are 7 features of necrosis?
- 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
Why is apoptosis important in development and morphogenesis?
1) Eliminates excess cells
2) Eliminates non-functional cells
Why is apoptosis important in adults?
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
What cells represent a threat to the integrity of the organism?
1) Cells infected with viruses
2) Cells of the immune system after a mediated response
3) Cells with DNA damage
4) Cancer cells
What makes a cell decide to commit suicide?
1) Withdrawal of positive signals
2) Presence of negative signals
What does the suvival of a cell require?
- Continuous stimulation from other cells
- Continued adhesion
What are 3 examples of negative signals?
1) Increase levels of free radicals and oxidants
2) DNA-related inducers (eg. UV light)
3) Physiological activators (eg. growth factor withdrawal)
What are the 4 stages of apoptosis?
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
3 assays to detect apoptotic cells?
1) DNA fragmentation
- Electrophoresis
2) Morphological changes
- Nuclear blebbing
- Cell shrinkage
3) Loss of plasma membrane integrity
- Loss of dye exclusion
What are caspases and what are they involved in?
Cleave proteins, involved in:
- Inhibiting apopsosis
- DNA repair
- Cell cycle
- Nuclear structure
What is the intrinsic apoptosis pathway?
1) Triggered by DNA damage and p53
2) Mitochondria release cytochrome C
3) Recruitment of initiator caspase 9
4) Effector caspase 3
5) Apoptosis
What is the extrinsic pathway of apoptosis?
1) Triggered by death ligands
2) Activated death receptors
3) Initiator caspase 8
4) Effector caspse 3
5) Apoptosis
What does self-renewal of a stem cell require?
Growth factors which stimulate growth (increase in cell size)
- By promoting synthesis
AND - Inhibiting degredation of macromolecules
What is cell death mediated by?
Death factors - promote apoptosis
Suvival factors - Suppresss apoptosis
When does a stem cell decide what fate to endure?
- Process the information flow in cells
- Change gene expression accordingly to either;
Self-renew
Differentiate
Die
What defines the ‘state’ of a stem cell?
What is the stem cell state maintained by?
- Genes that are expressed from the stem cell
- Actively maintained by receiving external signals such as:
- Soluble ligands for receptors
- Internally generated signals
What must happen within a cell for it to differentiate?
Must turn genes on/off
Lock in changes
Chromatin must be altered to allow or close down transcription
What parts of a DNA sequence is excluded from the primary transcript?
1) Enhancer
2) Promoter
3) Termination region
What binds at the TATA box?
General transcription factors
Histones
What is the relationship between GTFs and histones at the TATA box?
They block each other from binding
What defines a cell type/
- 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
What is the ‘mediator complex’ and how is it involved in transcription?
- 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
What structure is important for controlling cell fate decisions?
3D structure
What drives expression differently in different cell types and times?
Tissue-specific enhancers
What kinases are CDKs?
Serine/ threonine
What occurs at the restriction point with Rb?
- 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
What is an example of a positive growth factor?
EGF
What is and example of a negative growth factor?
TGF-beta
In the cell cycle, where are cells most sensitive to different signals?
G1
In the cell cycle, where are the self-renewal controls?
G2
