Lecture 10 Flashcards
What is mitosis?
The process going from one ‘mother cell’ to two identical ‘daughter cells’ (also identical to the mother cell)
Why is mitosis needed?
- Growth
- Repair
- Cell replacement
What are somatic cells?
Non-sex cells
What are germline cells?
Sex-cells
What is the result of meiosis?
From one cell to four non-identical sex cells
Describe the cell cycle
- Interphase (G1, S, G2)
- Division: Nuclear division (mitosis), cellular division (cytokinesis)
Describe what happens in each stage of the cell cycle
- G1 phase - cell content duplication
- S phase - DNA replication
- G2 phase - double check and repair
- M phase - mitosis
- Also G0
What is the G0 phase?
Stationary phase or quiescence phase
(comes off G1 stage)
A cells will enter the G0 phase if it doesn’t need to be replicated e.g. neurones after being created will stay in G0 for the rest of its life, e.g. liver cells only divide again i.e. come out of G0 when they are stressed, they then re-enter G1 (growth factors required for this)
G0 is either temporary or permanent
How long does each stage in the cell cycle last?
1 full cell cycle lasts about 24 hours.
- G1 phase
- 10-12 hours
- S phase
- 6-8 hours
- G2 phase
- 3-4 hours
- M phase
<1 hour
What happens if the cell cycle is not controlled?
Can lead to cancer…
Cell cycle control
Extremely complex, lots of factors are involved
How many checkpoints are in the cell cycle?
3
What controls the cell cycle?
Controlled by CDK/cyclin complexes.
CDK stands for Cycle Independent kinesis, there are proteisn that can phosphorylate other proteins. They are activated when paired up with cyclin
Describe the control processes in the cell cycle
- G1 checks for: cell size, nutrients, growth factors, DNA damage
- G2 checks for: DNA damage, DNA replication completeness
- Mitosis: Checks if all chromosomes are properly attached to the mitotic spindles
Why is DNA integrity important at a nucleotide and gene level?
Don’t want the code to be disrupted or damaged
Why is DNA integrity important at chromosome level?
Important as chromosomes are passed from one generation to the next
DNA integrity - could damage…
- Single strand damage (not as bad because the integrity of the molecule is not disrupted)
- Double strand damage (very genotoxic to the cell)
How do DNA mechanisms fit in to DNA repair?
Most damage to DNA is recognised by the body, so is repaired making it healthy again.
However, if damaged DNA is not checked by:
- DNA repair mechanisms = mutation
- DNA repair mechanisms go wrong = mutation
What in DNA can be damaged?
All components of the DNA molecule can be damaged:
- DNA base
- Sugar phosphate backbone
- Any strand
- Sugar
What type of DNA damage could occur?
- Base missing
- Base is U instead of T
- Chemical base change
- Single strand break
- Bulky adducts (bulky bits added to DNA)
- A chemical structure that shouldn’t be there is there
- Cross-link
- Double stranded break
- Insertion
- Deletion
DNA damage (two types of sources)
- Exogenous sources
- Endogenous sources
List examples of exogenous sources and what is the definition of this?
• ionising radiation
• UV
• alkylating agents
• mutagenic chemicals
• anti-cancer drugs
• free radicals
List examples of endogenous sources
Endogenous substances and processes are those that originate from within a system such as an organism, tissue, or cell.
- free radicals
- replication errors
Why are free radicals endogenous source?
- Mitochondria creates free radicals
- Inflammation creates free radicals
What can free radicals do?
Free radicals cell damage DNA
What DNA damage could occur?
- Up to one million molecular lesions damaged per cell per day
- Apurinic site
- Deamination
- Mismatches
- Pyrimidine dimer
- Double stranded breaks
- Intercalating agent
- Interstrand crosslink
- Bulky adduct
- Single-strand break
Define DNA replication stress
Replication stress = Inefficient replication that leads to replication fork slowing, stalling and/or breakage
Replication stress - when replication goes wrong
3 main groups of DNA replication stress
- Replication machinery defects
- Replication fork progression hindrance
- Defects in response pathways
- Replication machinery defects
What could go wrong?
- DNA polymerase
- DNA ligase
- Topoisomerase
- DNA helicase
- DNA primase
- DNA replication fork progression hindrance (another replication stress)
What could hinder the progression of replication fork?
- Limited nucleotides
- DNA lesions (diamer forms)
- Fragile sites
- RNA nucleotide inclusion (U instead of T)
- DNA loops
- Transcription taking place (instead of DNA replication
- Repetitive DNA
What are the two scenerios in fork slippage
- Scenerio 1: An extra ‘A’ nucleotide has been synthesised in a competitive area. Therefore, there is now a ‘bulge’ in the new strand, where there is an extra nucleotide
- Scenerio 2: Can get the same situation in the template strand, this means that the newly synthesised strand will be missing 1 nucleotide
Both are called fork slippage
Fork slippage - Backward slippage
Fork slippage - Forward slippage
What happens in Huntington’s?
Backward slippage
Fork slippage can lead to trinucleotide (3 bases together - CAG, CAG, CAG, CAG, CAG, addded in) expansion e.g. Huntington’s, spinocerebellar ataxia, Fragile X
In Huntington’s this backward slippage has occured over and over again
(Look at other flashcard too)
Huntington’s disease - the types of repeats etc
Huntington’s Disease
• CAG repeats in HTT gene leading to polyglutamine repeats in Huntingtin protein
• Normal 6-39 repeats
• Disease 35-121 repeats
What happens in Huntingtons (symptoms)
- Normal function of Huntingtin protein still unknown
- Mutant Huntingtin protein aggregates in neurons affecting mainly basal ganglia (causes degeneration of neurones)
- Progressive, late onset disease
- Defects in response pathways (DNA replication stress)
These are the pathways that ‘deals’ with all these mutations, e.g. helicase can ‘deal’ with the loops, if there are defects in the response pathway, this can also cause DNA replication stress
Response to DNA damage response
Sensors (signals of damage can be sensed by sensor) -> transducers -> effectors (decide what should happen to the cell - e.g. death, permanent cell cycle arrest, senescene)
What are the three outcomes of a mutation?
- Senescene
- Apoptosis
- Proliferation
If DNA damage levels are too high or persist what is the DNA damage response?
- Senescene = permanent cell cycle arrest (it won’t divide anymore but will still have some function, cells in senescence die sooner)
- Apoptosis = cell death
But the body would rather repair DNA and maintain function
If DNA damage levels are manageable, DNA repair will occur to maintain function
- Proliferation (DNA repair and cell cycle control will occur and then proliferation will occur)
What does the body do during DNA repair? (i.e. slow down, quicken up cell cycle)
May need to slow down the cell cycle during DNA repair (put the cell cycle in temporary arrest whilst DNA repair is occuring)
- DNA repair can take place at any point in the cell cycle
What are the 4 DNA repairs?
- Base-excision repair (single-strand base repair)
- Nucleotide-excision repair (single-strand base repair)
- Mismatch repair (single-strand base repair)
- Recombinant repair (when there is a double strand break)
Different types of DNA damage will have different types of DNA repair mechanism
- DNA repair: Base excision repair (something is wrong with the base)
In example below, U is incorporated instead of a C
- DNA repair: Nucleotide excision repair
- DNA repair: Mismatch repair
Overall characteristics of a single strand break
(includes: base excision, nucleotide excision, mismatch repair)
- relatively simple
- many different mechanisms
- integrity of the DNA molecule intact
- ‘damage’ removed on one strand only
- homology of other strand used to repair the damage on the damaged strand
- not error-free, but not error-prone either (normally successful as it uses the other strand as a template - as DNA has stayed intact on this strand
- DNA repair: Double strand break
Characteristics of this
- complex
- integrity of the DNA molecule lost (loss of DNA integrity)
- more likely error-prone, as not sure if putting the ‘right’ bits together
- use of homology may be possible
What is non-homologous end joining (in DNA repair)
Non-homologous end joining
- broken ends recognised and protected
- complex formed and damaged ends removed (so cut a bit of the double strand ends)
- broken ends ligated (ends put back together)
- error-prone (it is much better to have a mutation (usually) than having a double stranded break. It is error-prone as don’t know if the right bits are being stuck together, always some removal of DNA)
What is homologous-directed repair
Homologous-directed repair
- Remove some of the strands, leaving overhangs in both strands
- The intact DNA strands forms a bubble
- The overhand then ‘invades’ the other DNA helix. The bits circled are complementary as they are joining up
- By invading the other DNA helix, it can then remake the DNA using the other homologous DNA molecule, repairing it perfectly
(do not need to know any more details than this)
Ends up with a perfect repair
It uses the other homologous chromosome to make the repair.
This is much better as it is much less risk prone, but if the cell does not have machinary available for the homologous-directed repair, non-homologous end joining will occur (non-homologous end joining hopes for the best that it will not cause a problematic mutation)
Overview of both double stranded repair types
- Non-homologous end joining
- Homologous-directed repair
Have an understanding that both non-homologous (NHEJ) end joining and homologous-directed repair (HR) occur more at different parts of the cell cycle
- Cause of cancer - Loss of cell cycle control can lead to cancer
When the checkpoints don’t occur correctly
*learn these checkpoints
What is the meaning of a multi-step cancer model?
Mutation accumulation - lots of mutations need to occur before cell becomes cancerous
- Cause of cancer - DNA replication stress stimulates carcinogenesis
Many mutations need to occur before a cell becomes cancerous
DNA replication stress -> induces mutations -> accumulation of mutations -> malignant cells
Example of mutation accumulation
Don’t need to learn details in the picture!
DNA damage response are meant to prevent carcinogenesis (e.g. DNA repair mechanisms like base excision etc)
- Cause of cancer - DNA repair defects stimulate carcinogenesis
e.g. causes by DDR defect, mutated gene, syndrome, cancer predisposition
Remember DNA repair mechanisms include:
- Base excision repair
- Mismatch repair
- Non-homologous end joining
- Single strand break repair
- Nucleotide excision repair
- Homologous dependent repair
- Double strand break repair
(lots of others too, but the above list is what I need to learn)
What is tumour heterogeneity?
Tumour heterogeneity describes the observation that different tumour cells can show distinct morphological and phenotypic profiles, including cellular morphology, gene expression, metabolism, motility, proliferation, and metastatic potential. This phenomenon occurs both between tumours and within tumours.
For example, the tumour attached is made up of 3 different sub-clones
Cancer evolution
The tumour at the end looks very different from the tumour at the beginning (look at the attached picture, to show a tumour timeline)
What does clonal expansion mean?
Multiplication or reproduction by cell division of a population of identical cells descended from a single progenitor. In immunology, may refer to the clonal proliferation of cells responsive to a specific antigen as part of an immune response
(the first step shows clonal expansion in the picture attached)
What is the clonal expansion model?
Heterogenous tumours contain lots of different cancer clones. The make up of the tumour is changing all of the time, because:
- cells are still mutating
- when new cancer cells of a different type form, they are also competing for nutrients and oxygen etc. If they are better at getting these compared to antoehr cancerous clone, they outcompete the other clone. This will cause the ‘less efficient’/’less resourceful’ clone to die and the more resourceful/better competitor to continue multiplying and increasing in numbers.
- *This leads to the clonal expansion model**
Chemotherapy - how does this change the tumour?
The tumour exists of many subclones, each subclone has a different sensitivity to the chemotherapy. (In the diagram attached, can see that chemotherapy is very effective against the red clone as it has reduced in size, however, the purple clone is resistant to chemotherapy). The blue clone keeps proliferating and the tumour comes back = differential sensitivity.
Chemotherapy - how can these sometimes induce mutagenesis?
By trying to kill the cancer through chemotherapy, chemotherapy may actually induce more mutations, e.g. in the diagram attached, one of the red clones has mutated into a black clone which is resistant against chemotherapy
Synthetic lethality strategies
The concept of using synthetic lethality as a therapeutic strategy in cancer: Looking at the diagram below, the loss of gene A or gene B in isolation is compatable with cellular viability (i.e. the cell will survive), however, if both genes are not functional, the cell will die. The diagram attached shows that in the cancer cell, gene B is mutated as part of the cancer anyway, the third cell across shows that it is surviving as gene A is still functional. However, gene A has been targetted by medication, this has now stopped both gene A and gene B from being functional in the cancer, but as only gene B is non-functional in the healthy cell, it can still survive (as it has gene B).
