Module 11 Flashcards
Major forms of DNA damage
- spontaneous oxidative damage
- hydrolytic attack (more common for PURINES than PYRIMIDINES)
- uncontrolled methylation
all damage to single base
Define DNA damage
any modification of DNA that changes its coding properties or natural function in transcription or replication
Define DNA mutation
an alteration in the nucleic acid sequence of the genome of an organism, virus, extrachromosomal DNA
Main causes of DNA damage
- radio + chemotherapy
- UV –> replication errors
- light –> alkylating agents
What are the types of DNA repair mechanisms?
- double-strand break repair
- nucleotide excision repair
- single-strand base excision repair
- mismatch repair
What happens if a lesion is not repaired?
DNA replication will fail at that point & one part of the DNA will remain single-stranded
loss of a whole bunch of DNA
Explain how the mismatch repair identifies the incorrect base AFTER DNA replication
E coli is methylated on the adenines in GATC sequences
repairs single mismatches ONLY immediately after DNA replication
What is a possible cause of mismatch repair?
error during replication that was not corrected by the polymerase
What kind of proteins identify mismatches?
Mut proteins
What is depurination?
the HYDROLYTIC removal of GUANINE or ADENINE from the #1 carbon of deoxyribose in a DNA strand
What is deamination?
the HYDROLYTIC removal of amino (-NH2) groups from guanine, cytosine, or adenine
Damage to a single base
- could remove a full base, or it could remove an amine group from a base –> deamination
- hydrolytic attack removes AMINE GROUP
- when this happens to cytosine, it becomes uracil (unusual)
5-methylcytosine –> thymine
What 4 enzymes are involved in base excision repair?
1) DNA glycosylase
2) AP endonuclease
3) DNA pol I
4) DNA ligase
What causes a thymine dimer?
UV
What are thymine dimers?
- thymine dimers are 2 adjacent thymine bases that are abnormally linked together by covalent bonds
What is the consequence of thymine dimers?
this dimerization inhibits DNA replication, which may lend to death of organisms
What 4 enzymes are involved in nucleotide excision repair?
1) exinuclease
2) DNA helicase
3) DNA pol I
4) DNA ligase
What are 2 differences between base excision repair & nucleotide excision repair?
1) involves cutting at 2 sections on both sides of lesion
2) also removes the strand of DNA w/ lesion (nucleotide excision repair)
When is base excision repair needed?
a pathway that repairs replicating DNA THROUGHOUT the cell cycle
When is nucleotide excision repair needed?
a pathway that constantly repairs damaging DNA due to UV rays, radiation, & mutagens
DS breaks are . . .
the most biologically significant lesions caused by ionizing radiation
Most DS breaks are repaired within . . .
24 hours, but 25% of the repairs contain errors
ERROR-PRONE PATHWAY OF REPAIR (non-homologous end joining)
Why is NHEJ error prone?
bc there will be a small loss of nucleotides due to the degradation from the ends (due to any nucleases that come into contact w/ them)
4 main regulatory processes in the cell cycle
- protein phosphorylation
- protein degradation
- protein synthesis
- inhibitors
What is special about the G0 phase?
terminally differentiated cells withdraw from the cell cycle at this point indefinitely (however, there is a re-entry point from G0)
What are cyclin-dependent kinases?
- regulates the PROTEINS that carry out cyclical cellular functions
- are heavily regulated
- require binding to a cyclin for activity
Kinase activity is. . .
CYCLICAL
What are cyclins?
- undergo a cycle of protein SYNTHESIS + degradation
- protein levels are cyclical
- essential regulators of CDK activity (G1/S cyclins, S cyclins, G2/M cyclins)
Phosphorylation of Thr160 . . .
in the T-loop ACTIVATES the CDK by allowing TARGET binding
Phosphorylation of Tyr15, near the amino terminus. . .
INACTIVATES CDK2 by BLOCKING the ATP binding site w/ its negative charge
What is DBRP?
destruction box recognizing protein
What is the function of DBRP?
targets the cyclin for degradation
9 amino acid sequence neat the amino terminus
What is ubiquitin?
small protein covalently bonded to proteins as a marker of degradation
What is a proteasome?
large protein complex that degrades proteins back to amino acids
What are the 2 CDK inhibitors?
p21 and p27
What are 2 examples of CDK targets and the phase of the cell cycle at which they act?
1) Nuclear lamins
2) condensins
What are nuclear lamins?
proteins found on inside of nuclear envelope
the breakdown of the nuclear envelope (during transition into mitosis) is assisted by the phosphorylation of the lamins by the CDKs that are controlling entry into mitosis
What are condensins?
proteins that control the condensing of chromosomes
if you mix condensin proteins with DNA, they will naturally condense the DNA in the test tubes
What happens if there are mutations in the condensins?
the cell can no longer condense its DNA
condensins are physically associated with the chromosomes
Explain the importance of checkpoints in maintaining genome integrity
they ensure that a cell’s DNA is intact before permitting DNA replication & cell division to occur
failures in these checkpoints can lead to . . .
an accumulation of damage, which in turn leads to mutations
Why does inactivation of pRB lead to cancer?
riggers uncontrolled cell proliferation
Cells with 2 altered copies of the RB1 gene produce. . .
NO functional pRB and are unable to regulate cell division effectively
retinal cells lacking functional pRB can divide uncontrollably to form cancerous tumours
Describe some of the uses of programmed cell death during embryonic development
1) sculpting
2) refining neural connections
3) refining tissues - destroying self-recognizing B cells
List 3 of the features of a cancer cell, so called “hallmarks of cancer”
- resisting cell death
- avoiding immune destruction
- evading growth suppressors
What causes a tumour?
increased growth
decreased apoptosis
What is necrosis?
not programmed; the cell just bursts & that can lead to an inflammatory response
Most cells don’t express telomerase enzyme. Which ones do?
1) stem cells (to replenish other cells)
2) germ cells (that produce gametes)
What is pRB?
a tumor suppressor & key regulator of the cell cycle
