Pro n Eu Flashcards
What are tell-tale signs of a Prokaryote? [4]
- No membrane-bound organelles
- Has nucleoid instead of a nucleus
- Has circular DNA a./w small amt of histone-LIKE proteins
- Has 70S ribosomes (vs 80s)
Why must the genome in eukaryote be so compact? [3]
- Make long molecule of DNA more compact to fit in nucleus
- To prevent entanglement → prevent DNA breakage or damage → prevent cancer
- Regulation of gene expression → DNA wound around histones prevents GTFs and RNA pol access
to genes that are not needed to be expressed
What are some genomic regulation in Eu [4]
- Chromatin Remodelling Complexes
- DNA Methylation
- Histone (De)acetylation
- Gene amplification
What are the MAIN role of telomeres? [4]
Counteracts end-replication problem, NOT solve it
1. [Define] Telomeres are non-coding tandem repeats sequence found at both ends of linear chromosomes
2. [Describe End-Replication Problem] Each round of DNA replication results in shortening of daughter
DNA molecules at telomeres
3. Because DNA polymerase unable to replace RNA primers with DNA, this is end-replication problem
4. Since telomeres are non-coding, this ensures vital genetic information is not eroded with replication
What are the other roles of Telomeres (3)
Other functions: Protect & Stabilise terminal ends of chr, prevent Apoptosis, Attachment pt for Telomerase
* By forming a loop with 3’ overhang, they protect & stabilise chromosomal ends, preventing fusion of
the ends with those of other chr
* Prevent DNA repair machinery from recognising ends of chr as DNA damage, preventing apoptosis
* 3’ Overhang of telomeres provides attachment point for correct positioning of Telomerase → allow for
elongation of telomeres → (prevent telomeres from reaching critical length
In Cancer, other than proto-oncogenes and Tumour Suppressor Gene mutations, what is another reason that cancer are “immortal”?
Due to the activation of telomerase which extends the length of telomeres, preventing the critical length of telomeres to be reached, hence the cell will NOT undergo normal apoptosis.
How does telomerase work? (4)
Function: Elongate Telomeres → maintain Telomere length & prevent loss of genetic info
* Nucleotides of the telomerase RNA anneals and forms complementary base pairs with single-stranded
overhang at 3’ end of the telomere
* Telomerase complementary C&C to specific telomeric DNA seq. Using telomerase RNA as a
template, telomerase catalyses the formation of phosphodiester bonds* between (incoming)
deoxyribonucleotides (& existing 3’ OH group of existing DNA overhang) elongating the 3’overhang
* Telomerase translocates along telomeric end from 5’ to 3’ to elongate the overhang
* In germ & stem cells: allow them to continuously undergo cell division & will not undergo apoptosis
to pass on genetic info to daughter cells for many generations
What are some non-coding sequences in humans?
Telomeres
Centromeres
Definition of cancer
Uncontrolled Cell Division & spread of abnormal cells due to dysregulation of cell cycle
Define proto-oncogenes
Gene that codes for proteins involved in normal cell
division (always establish in given context that gene
was previously normal)
Define Tumour Suppressor Gene
Gene that codes for proteins that inhibits cell division,
helps prevent uncontrolled cell division by (i) Cell
Cycle arrest, (ii) DNA repair, (iii) Apoptosis
What genes undergo Gain in Function mutation in Cancer & what are the traits of GIF mutations?
Proto-oncogenes
- Gene product produces is hyperactive OR excessive
- Only Single Mutation in 1 allele is needed
- Dominant mutation involved
What genes undergo Loss of Function mutation in Cancer & what are the traits of LoF mutations?
TSG
- Gene product produced is non-functional OR insufficient/not produced
- Mutations in BOTH allele is needed (aka 2 mutates)
- Recessive mutation involved
Outline the development of cancer (8)
- [Effect of agent] Carcinogen increases chances of DNA damage and mutations in the genes which
control regulatory checkpoints of the cell cycle in a single cell - Loss-of-function mutation of TSG in BOTH alleles of ‘__’ causes inability to inhibit cell cycle, repair
damaged DNA and promote apoptosis → potential cancerous cells not removed - Gain-in-function mutation of POG in just 1 alleles of ‘__’→ oncogenes will result in overexpression
of proteins or production of hyperactive/degradation resistant proteins → uncontrolled cell division to
form primary tumour - [Development] Loss of contact inhibition enables cells to grow into a tumour
- Genes coding for telomerase are activated → cells can divide indefinitely
- Angiogenesis occurs within the tumour so that the blood vessels formed can transport oxygen and
nutrients for its growth - [Spread] Resulting in the formation of a malignant tumour capable of metastasizing to other parts of
body to form secondary tumours - Cancer is multi-step process that takes time as it takes years to accumulate these mutations.
Why is cancer a disease of old age? What are some risk factors?
Cancer is multi-step process that takes time as it takes years to accumulate these mutations.
Risk factors includes: smoking (carcinogens), excessive ionising radiation (like X-ray)
What are some cell division checkpoints?
M Checkpoint (M for Mitosis)
G1/G2 checkpoint
How Dysregulation of the checkpoints of cell division may lead to cancer? (3)
Dysregulation of (any 1 checkpoint)
o M checkpoint dysregulated → any cell with chromosomes that are not attached to spindle
fibres continues into metaphase & anaphase to produce genetically mutant cells
o G1/G2 checkpoint dysregulated → damaged DNA not repaired → cells continue into M phase
→ accumulating mutations
o Leading to uncontrolled cell division
How does oncogenes cause cancer?
Mutated form of proto-oncogene → excessive
production of the protein products OR oncogene
codes for a protein with increased activity / more
resistant to degradation ➔ uncontrolled cell division
How does mutated TSG cause cancer?
Mutated form of TSG → no functional gene products
formed → unable to stop cell cycle to allow repair any
damaged DNA, unable to activate DNA repair
mechanism to repair damaged DNA thus
accumulation of mutations, unable to initiate
apoptosis → cell with potential to cause cancer not removed
What is the Ras gene? How is it mutated in Cancer?
A gene involved in cell-signaling for normal cell division. Ras (protein) gene product helps activate downstream molecules to eventually cause cell division.
Mutation → constitutively active ras protein → bind
irreversibly to GTP → increasing frequency of cell
division even in absence of growth factors
What is the a specific gene example of TSG? How is it involved in cancer?
p53 gene (master gene for cell division control)
Mutation → p53 gene products no longer act as
Activator that upregulate genes involved in (i) cell
cycle arrest, (ii) DNA repair, (iii) Apoptosis
What is a sign that the cancer is turning malignant?
Loss of contact-inhibition with excessive angiogenesis
In late stages: metastasis happens causing secondary tumours to be formed elsewhere
What are the types of GENE mutations?
SAID
Substitution
Addition
Inversion
Deletion
What are some impacts of gene mutations?
Frame-shift mutation
Silent mutation
Missense mutation
Nonsense mutation
What does it mean to have a Silent mutation? How does silent mutation happen?
Point mutation that
does not lead to ∆ in a.a
seq [S]
explained by:
1. Degeneracy of the Genetic code: change in codon can still code for the same a.a.
2. Point mutation happened in non-coding region
What does it mean to have a nonsense mutation? What are the results?
Point mutation that
leads to premature
STOP codon
This causes the polypeptide to be terminated earlier
What are the stop codons?
Mnemonic:
- U Are Good (UAG)
- U Are Awesome (UAA)
- U Good & Awesome (UGA)
How can the Chr structure be mutated?
Translocation*
Deletions
Duplications
Inversions
What are some Chromosomal Mutations?
Chromosomal STRUCTURE
Chromosomal NUMBER
What is the case-example of a chromosomal number mutation? What are its typical symptoms?
Trisomy 21 (Down Syndrome)
Short stature, low IQ, facial features
Define non-disjunction of chromosomes (2)
- Homologous chromosomes do not move properly to opposite poles during meiosis I OR
- When sister chromatids fail to separate properly to opposite poles during meiosis II.
Where & when can non-disjunction happen to result in errors like Trisomy 21?
- During mitosis (RARE)
- During Meiosis I
- During Meiosis II
When does nondisjunction of Chr causes more deleterious effect?
In meiosis I
end upwith 2x N+1, 2x N-1
(vs in Meiosis II end up with 2x N, 1x N+1, 1x N-1)
Describe how does Promoters work (3)
Serve as recognition site for
binding of RNA pol, GTFs to
initiate transcription
* TATA box- determines
precise transcription start site
* CAAT & GC boxes- improves
efficiency of promoter by
recruiting GTFs & RNA pol to
promoter
Describe how enhancer region work (2)
Allow STFs called Activators
bind to it → (spacer DNA
bends → allowing activator to
bind to RNA pol & GTFs) →
promoting formation of TIC
* May also recruit Histone
Acetyltransferase & CRC to
decondense chromatin →…
Describe how Silencers work
Allow binding STF called
Repressors → (spacer DNA
bends → allowing repressor to bind to RNA pol & GTFs) → preventing assembly of TIC at promoter
* May also recruit histone
Deacetylase & CRC to
condense chromatin → …
Describe how does Chromatin Remodeling Complexes work
Protein complexes that temporarily alter
nucleosome structure
UPREGULATE: ✓ DNA less tightly wound around histones → allow RNA Pol, GTF to access promoter →
promote assembly of TIC → frequency of transcription increase
DOWNREGULATE: × DNA more tightly wound around histones → … → f(transcription) falls
What is so special about DNA methylation? Describe how does it regulate gene activity.
ONLY for selected cytosine
Addition of Methyl group to selected cytosine
residues on DNA [DNA Methyltransferase]
Mainly DOWNREGULATE
× Prevents GTF from accessing promoter →
prevent assembly of TIC
× Recruit CRCs, DNA Deacetylase & Repressors → prevent assembly of TIC & transcription (chromatin condenses)
Describe how histone Deactylation & Acetylation work
Deacetylation by histone deacetylase removes Acetyl group from histones
Histone Acetyltransferase does the opp. of adding
× Removal of acetyl groups → restoring tighter
electrostatic interaction btwn DNA & histones
→ reducing accessibility of promoter → prevent binding of GTP, RNA pol → prevent formation of TIC
✓ Histone Acetyltransferase…
What are methods of regulation at genomic level
CDH
Chromatin remodelling complex
DNA methylation
Histone Deacetylation
What are the ways of regulation at Transcriptional Level
PES
Promoter (proximal CE)
Enhancer (distal CE)
Silence (distal CE)
How does addition of 5’ cap regulate post-transcriptionally? (3)
Allows cell to recognise
mRNA
✓ Act as Signal to export
mRNA out of nucleus
✓ Stabilize & Protect growing
mRNA from Degradation
by Ribonucleases
Describe how splicing of introns act to regulate at post-transcriptional level (2)
✓ Spliceosome splice introns & join exons → allowing mRNA to produce
functional proteins
✓ Alternative Splicing:
allowing 1 gene to produce
mature mRNA with diff
combi of exons to produce
diff proteins
How does polyadenylation regulate ____ level?
Describe how it works (3)
post-transcriptional level
✓ Addition of 3’ Poly A Tail → act as a Signal to export
Mature mRNA out of
nucleus
✓ Stabilize & Protect Mature
mRNA from degradation by
ribonucleases
✓ Interact with initiation
factors & 5’ cap for
initiation of translation
What are the post-transcriptional level regulation?
CSP
5’ cap addition
splicing introns
polyadenylation
What are the ways translational level regulation happens?
- T1/2 of mRNA
- Formation of TIC regulation
Describe how is the mRNA t1/2 regulated?
Longer poly A tail =
longer t1/2
✓ Ribonuclease
remove poly A tail
until it reaches
critical length where
it triggers removal
of 5’ cap by another
ribonuclease
How is the formation of Translation Initiation Complex regulated? what level is this?
Translational level
- Translation
Repressor bind to
(i) 5’ cap, (ii) 5’
UTR, (iii) 3’ UTR →
prevent small
ribosomal subunit
from binding to 5’
cap of mRNA →
prevent formation of
TIC - Phosphorylation
can activate ETIFs - Anti-sense RNA complementary to
mRNA synthesized to
block translation
OR target it for
degradation by
ribonucleases
What are the post-translation regulation methods?
- Quality = Covalent Modification to form functional proteins
- Quantity of the proteins (gene products) via Phosphorylation AND Degradation of proteins by Proteasome
Describe all the ways that post-translation regulation happens
- Covalent Modification to
form functional proteins
✓ C.mod like Glycosylation,
Disulfide bond formation make proteins functional in
GA, RER - Regulate Protein Activity by Phosphorylation
✓ Phosphorylation
activates proteins →
functional & active - Protein Degradation
✓ Ubiquitin ligase tags
proteins with
Ubiquitin protein →
tagged will enter
Proteasome →
enzymes of proteasome hydrolyse protein into
small peptides
✓ Which is then further
hydrolysed to a.a by
enzymes in cytosol
