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CMMB 413 Study Guide - Final Guide: Polypyrimidine Tract, Chromodomain, Azacitidine

Cellular, Molecular and Microbial Biology
Course Code
CMMB 413
Christopher Wang
Study Guide

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1. As shown in homozygosity mapping, why does
the amount of identity to the original
chromosome diminish with each succeeding
- Recombination happens such that that region that was initially linked to mutation
gets smaller in each generation, such that affected individuals in the last
generation are homozygous for all the alleles of the markers that flank the
disease gene
2. Autonomy in Medical Ethics - It is the patient's right to self governance
- Involves informed consent, making decisions free of coercion, right to
confidentiality and privacy
3. Azacitidine (Vidaza) - Modifies epigenome to treat cancer
- C is methylated in cytosines, this drug puts a nitrogen in this position, which
cannot be methylated
- This drug is given to leukemia patients
- During replication, wherever a C should go, this drug goes in. So you're
incorporating residue with N instead of C. In the next round, p53 gene cannot be
methylated, so it turns on
- Prolongs overall survival in elderly patients with acute myeloid leukemia
- Data: in the cohort treated with azacitidine, see rapid decline, possibly because
of cytotoxicity of the drug because it is hitting every cell in your body, so it is
turning every gene in your body that should be off, on
4. Beneficence in Medical Ethics - It is to do good
- Involves considering the patient's best interest
- Can involve removing or reducing harm
5. BRAF (activating variant ) - Somatic activating variants in BRAF are found in 50% melanoma cases
- When you have an SNV that changes amino acids, the BRAF gene becomes
continually on, no matter what happens before BRAF is activated in the normal
6. Burkitt lymphoma - Endemic variant in regions endemic with malaria (eg. Africa)
- Sporadic in regions where malaria is not endemic (eg. Canada)
7. Cancer results from the ________. - Somatic variants in the genome
8. CCR5 gene - Encodes receptor that HIV uses to enter the white blood cell
- Mutant recessive allele results in a non-functional protein
- Homozygous recessive individuals are resistant to HIV infections due to a lack
of receptors
9. Chromodomain helices DNA-binding protein 7
- Chromodomain was initially found in polycomb genes
- Depending on the cell, complex is involved in turning on or off genes
10. Codeine - Has to be metabolized to morphine
- Between 5-15% of the dose you're taking gets activated in your body
- Balance of activating and deactiviting mediate how you respond to a drug
11. Codine is metabolized by the ___________ of
enzymes in the __________.
- Cytochrome family ; liver
12. Components of an intron - The last 2 nucleotides of an exon are usually an A or G (purine purine)
- Invariant sites: must be those sequences, that if the gene is influenced, the cell
cannot recognize it
- Branch site: where intron loops around during termination
- -1 and -2 positions must be AG (invariant sites of splice acceptor site)
- Polypyrimidine tract
13. Constitutional chromosome instability - Bialleic
- Childhood onset
- Recessive
- Severe
- Result from complete loss of DNA repair enzymes
CMMB 413 Final Exam
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14. CpG islands - Regions of high CG content
- 60% of mammalian promoters are found in CpG islands
15. DNA damage - 10 000 to 1 000 000 bases per day per cell are damaged
- Damage can occur by natural processes such as deamination (removal of an amine group),
depurination, UV light (thymine dimers) or by mutagens
16. DNA methylation - Inherited without sequence change (epigenetic modification)
- In the semi-replicative model of replication, the mother strand is methylated and the daughter
strand isn't because its newly synthesized
17. DNase1 digestion data - If you overlay the sequence of the DNA, see most of the genes have DNase1 hypersensitivity
- The genes that don't have hypersensitivity are the ones that are not expressed in the cell line
18. DNase1 hypersensitive sites
mark regulatory DNA
- DNase1 is a naturally occurring enzyme that cuts free DNA. It doesn't cut DNA that is circling
nucleosomes, or DNA that is protected by proteins
- Quick exposure to DNase1 will give you fragments which you can sequence to find all the
pieces of DNA that are not protected
- DNase1 hypersensitive sites at promoters are depicted as peaks in ENCODE data
19. DNA sequence changes in which
regions of an intron always
affect splicing?
- Positions: +1, +2, -2, -1
20. Dynamic mutations (repeat
expansions) (Fragile X)
- Fragile X syndrome is caused by a repeated (CGG)n element near the promoter of the FMR1
- Most people in the general population will have 6-54 CGG repeats in this gene
- People with the syndrome have 200-1000 repeats in this gene, and their phenotypically normal
moms are known as pre-mutation, because they have risk of child that will have the disease,
however, they don't have it themselves
21. Exon-level duplications or
- One or more exons is duplicated (rare) or deleted
- Most common cause of X-linked Duchenne muscular dystrophy
22. Format for writing DNA change
of a specific nucleotide? (exons)
c. position#(letter it should be) > (letter it is now)
- Example: c.1A>C
- Translates to: cDNA nucleotide ____ at position ____ is now _____
23. Format for writing DNA change
of a specific nucleotide?
c. (last exon nucleotide position #) +/- (nucleotide change position #)(nucleotide it should be) >
(nucleotide it is now)
- Example: c.90+5G>C
- Translates to: cDNA 5th nucleotide in intron after 90th nucleotide in exon changed from G to C
24. Frequencies in Hardy Weinberg - Frequency of recessive genotype (aa) = q^2
- Frequency of the recessive allele (a) = q
25. The frequency of which alleles
in a population cannot be
measured directly?
- Recessive alleles
26. Gain of function variants - Mutations that enhance normal protein function
- Associated with dominant disorders
- Example: achondroplasia
- Condition in which protein activity is not seized when needed
27. Gene components and products - Promoter: tells the gene when and where to be expressed, it drives transcription
- Pre-mRNA: contains the entire transcribed product (introns, exons, and UTRs)
- Mature mRNA: contains only exons, has 7mG (at 5' end), PolyA tail (at 3' end)

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28. Gene dosage - Extra copies of normal gene (especially dosage-sensitive genes) products have the
potential to cause disease
- Imbalances in gene dosage can lead to dominant disorders
- Variable penetrance and expressivity
- Related to haploinsufficiency
29. Gene inversions - Genes with inverted repeats can pair improperly during meiosis, so its best to get an
inversion of a gene that is in the middle
30. Haploinsufficiency - An individual who is heterozygous for a variant is clinically affected because one
normal gene copy is not enough for normal function
- Inherited as dominant disorders, often with vairable expressivity
- Can be inherited or de novo variants
31. Hardy-Weinberg calculation p + q = 1
- p = frequency of the dominant allele
- q = frequency of the recessive allele
- The chance of a fertilized egg being homozygous was p^2 or q^2 (carrying similar
- The chance of a fertilized egg being heterozygous was 2pq (carrying different
32. Hardy Weinberg Equation p^2 + 2pq + q^2 = 1
33. Hardy Weinberg Law of Equilibrium - A simple relationship exists between allele frequencies and genotype frequencies in a
- Ideal population: allele and gentoype frequencies remain constant between
34. Herceptin (Trastuzumab) - Herceptin blocks the signalling cascade of HER2, which is amplified in 20-30% of
invasive breast cancers
- Marks the cell the immune system to die
- Not curative because not every cell that's expressing HER2 will be marked
35. Histone Code hypothesis: histone
modification cross-talk
- Modifications work synergistically
- There multiple levels of regulation
- Cross-talk is mediated by readers
36. How are allele frequencies in a
population measured?
- Hardy Weinberg (holds true only under certain, specified conditions)
37. How are genetic markers and alleles
- One a chromosome, a marker is a region, and an allele is what is actually there
38. How are start codon variants disease
- Protein doesn't start where it needs to be
- Example: if due to a change, the next start codon happens 100 downstream from
original site, the overall protein would be affected
39. How are start codon variants written? p. Met (new start codon happens at codon #)(new amino acid)
- Example: p.Met1Val
- Translates to: methionine in protein is now changed to valine
40. How can codominant allele frequencies
be measured?
- Directly, by counting phenotypes
41. How can you delineate the putative
location of the disease gene?
- By genotyping other markers linked to the original marker
42. How can you identify tumour variants for
targeted therapy?
- Sequence both tissue types (unaffected and affected) and try to determine what is
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