Function & Dysfunction of Genomic Regulation Flashcards
1
Q
(GENOMIC ALTERATION)
Transposons
A
- “jumping genes”
- mobile sequences of DNA that change position within the genome of a single cell
- copy/cut -> paste
- can reverse mutations that are there or create new ones
2
Q
(GENOMIC ALTERATION)
SNPs
A
- common inherited change in 1 BP
- not actually a mutation but can present as one
- used as markers in mapping of genomes - indicates increase risk of a certain disease
- polymorphisms (changes in SNPs) may be associated with increase susceptibility to disease
- can be used in drug development
3
Q
What type of DNA repair mechanism is responsible for the repair of double stranded breaks?
A
Recombination Repair
4
Q
(DNA REPAIR)
Base Excision Repair
A
- used for small, single base problems
- spontaneous depurination and deamination
- repair process:
(1) altered base recognized by DNA Glycosylasas
(2) DNA Glycosylases remove base, AP Endonuclease cuts phosphodiester bond, AP Lyase removes deoxyribose phosphate
(3) DNA Polymerase β replaced excised nucleotide
(4) DNA Ligase seals nick
5
Q
(DNA REPAIR)
Nucleotide Excision Repair (NER)
A
- used for damage due to: chemical adducts (BPDEguanine adducts, cisplatin adducts), alteration in DNA shape in the local area, UV damage
- repair process:
(1) NER complex recognizes distortions and nicks DNA on both sides of damage sites
(2) Removal of stretch of damaged DNA
(3) DNA Polymerase ε fills in gaps
(4) DNA Ligase seals nick
6
Q
(DNA REPAIR)
Mismatch Excision Repair (MER)
A
- damage occurs during DNA replication when the wrong nucleotide gets inserted into newly synthesized daughter strand
- repair process:
(1) MER Complex binds to DNA and recognizes mismatch in daughter strand
(2) Removal of damaged section of daughter strand by MER complex
(3) DNA Polymerase δ fills gap
(4) DNA Ligase seals nick
7
Q
(DNA REPAIR)
Recombination Repair
A
- repairs double strand breaks and radiation/chemical damage
- 2 types: non-homologous end joining, homologous recombination
8
Q
What type of genetic mutation results in the formation of a stop codon?
A
Nonsense
9
Q
What are the 4 major types of genomic alterations?
A
The Cats Get Snuggles
- Transposons
- Chromosomal mutations
- Gene amplification
- Single nucleotide polymorphisms (SNPs)
10
Q
What disease is caused by a transposon genomic alteration?
A
Hemophilia A
- hereditary bleeding disorder caused by a lack of blood clotting factor VIII
- transposon L1 is inserted into factor VIII gene which renders factor VIII ineffective
11
Q
(GENOMIC ALTERATION)
Chromosomal Mutations
A
- includes: deletions (chromosome segment lost), translocation (segment from chromosome is transferred to another), duplication (segment from one chromosome transferred to its homologous chromosome which gives it a duplicate of some genes), inversion
- Ex: translocations can cause down syndrome – translocated chromosome 21
12
Q
(GENOMIC ALTERATION)
Gene Amplification
A
- typically occurs in S phase when one gene gets duplicated – results in 4 copies of gene so when cell divides each daughter cell will have 2 copies of the gene
- can be a result of all the other genomic alterations
- also can be caused by impaired replication
- can be good: more copies of gene means less mutational effects in evolution
- can be bad: cancer, cancer therapy resistance
13
Q
What are the 3 major ways DNA is damaged?
A
- Spontaneous
- Physical agents: Radiation
- Chemical agents
14
Q
Spontaneous DNA Damage
A
- happens daily
- most frequently happens thru depurination (purine removed from nucleotide and now only have backbone) or deamination (lose an amine on nucleotide, impacts transcription)
15
Q
What are the two type of physical agents that lead to DNA Damage?
A
- Ionizing Radiation
- Non-ionizing Radiation
16
Q
Ionizing Radiation
A
- due to gamma radiation
- leading cause of double strand break
17
Q
Non-Ionizing Radiation
A
- due to UV light (requires NER for repair of DNA)
- leading cause of pyrimidine dimers – esp thymine dimer
18
Q
What are the two types of chemically induced DNA damage?
A
- Agents that act DIRECTLY to modify DNA
- Agents that require metabolic activation (INDIRECT)
19
Q
Direct Chemical DNA Damage
A
- agent integrates itself into DNA
- cross-linking agents: nitrogen mustard, CISPLATIN, mitomycin c, carmustine
- alkylating agents: DMS, MMS
- intercalating agents: ethidium bromide, thalidomide, doxorubicin, daunomycin
20
Q
Indirect Chemical DNA Damage
A
- damage often due to the highly toxic material produced that can interact with DNA
- associated agent: BPDEguanine adducts
21
Q
General Scheme of DNA Repair
A
(1) RECOGNIZE damage DNA strand
(2) REMOVE damaged DNA sequence
(3) REPAIR of strand via DNA polymerase
(4) RELIGATE by DNA Ligase
22
Q
What are the 5 different DNA Repair Mechanisms?
A
- Base Excision Repair (BER)
- Nucleotide Excision Repair (NER)
- Transcription-Coupled Repair (TCR)
- Mismatch Excision Repair (MER)
- Recombination Repair
23
Q
(DNA REPAIR DISORDER)
Cockayne Syndrome
A
- results from mutation in TCR – genes ERCC6 and ERCC8 are mutated
- sxs: neurologic delay, photosensitivity, progeria (premature aging), hearing loss, eye abnormalities
24
Q
(DNA REPAIR DISORDER)
Xeroderma Pigmentosum
A
- genetic disorder associated with mutations in NER
- sxs: high sensitivity to light, pigmentary skin changes
- prone to developing melanomas and squamous cell carcinomas (due to UV light exposure)
- autosomal recessive
25
Q
(DNA REPAIR DISORDER)
Hereditary Non-Polyposis Colorectal Cancers
A
- known as Lynch Syndrome
- results from mutations in one of the alleles of genes in the MER complex
- accumulation of unrepaired DNA damage leads to genomic instability = cancer
26
Q
(DNA REPAIR)
TCR
A
- transcription coupled form of NER
- occurs when damage causes lesion in the DNA that is unrecognizable by RNA Polymerase – RNA Polymerase stalls at lesion -> TCR proteins called ERCC6 and ERCC8 recognize the stalled RNA Polymerase and recruit other repair proteins (NER)
- repair process is the same as NER
27
Q
Non-homologous End Joining (NHEJ)
A
- type of recombination repair
- error prone repair that leads to loss of genetic information
- leads to chromosomal translocation which causes neoplastic chromosomal rearrangements
- repair process:
(1) double strand break in DNA
(2) DNA Protein Kinase binds to each end of broken DNA and recruits protein Artemis which cuts off single stranded ends
(3) DNA Ligase seals nick
28
Q
Homologous Recombination (HR)
A
- occurs during G2 of cell cycle which is after replication but before cell division (have double of everything in this stage b/c preparing to divide)
- requires template
- essentially what happens is double strand break is repair by using sister chromatid
- more reliable repair mechanism compared to NHEJ b/c uses sister chromatid as template so no lose of nucleotides
- repair process:
(1) double strand break in DNA
(2) MRN protein complex binds to each end of broken DNA and recruits exonucleases to remove nucleotides from one strand of the DNA
(3) one of the broken ends is placed near homologous sequence of sister chromatid
(4) broken strand pairs up with complementary strand of intact homologous sequence result in formation of a loop in the homologous DNA
(5) DNA polymerase binds and creates nucleotides to extend broken end of DNA until reaches sequence that is complementary to the other broken end of DNA
(6) broken strand releases from sister homologous strand and binds its new nucleotides to the other end of broken DNA
(7) DNA Polymerase fills in any gaps
(8) DNA Ligase seals bond
29
Q
Homologous Recombination (HR) in Breast Cancer
A
- hereditary breast cancer associated with mutations in BRCA1 and BRCA2
- genes two genes encode proteins that facilitate homologous recombination
- five-fold increase in risk of developing breast cancer and other cancers if mutation in either of these genes
30
Q
Mutations in coding region (ORF) of DNA lead to different AAs being incorporated into protein. What are the 4 key mutations associated with this?
A
- Silent
- Missense
- Nonsense
- Frameshift
31
Q
Missense Mutation
A
- codon containing the changed base may code for a different AA
- Ex. if serine codon UCA is given a different C to become CCA then it will code for proline instead
- result of substitution of incorrect AA
32
Q
(GENETIC DISEASE/DISORDER)
Sickle Cell Anemia
A
- MISSENSE MUTATION in the β-globin gene in which glutamate is changed to valine and gives rise to HbS
- alters conformation of Hb
- mutated hemoglobin aggregates, forming rigid structures which causes deformation of RBCs into sickle like shape
- associated w/ poor oxygen carrying capacity and tends to clog capillaries
- sxs: anemia, frequent pain, frequent infections, delayed growth or puberty
33
Q
Nonsense Mutation
A
- codon containing the changed base becomes a stop codon
- produces truncated protein
34
Q
(GENETIC DISEASE/DISORDER)
Bo Thalassemias
A
- NONSENSE MUTATION
- premature stop signals located at codons 17 (exon 1) and 39 (exon 2)
- results in lack of production of β-globin protein
35
Q
Frameshift Mutation
A
- occurs when one or two nucleotides are either deleted from or added to the coding region of a message sequence, thus altering the reading frame
- can result in a product with radically different AA sequence or a truncated produce if premature creation of stop codon
36
Q
(GENETIC DISEASE/DISORDER)
Cystic Fibrosis
A
- FRAMESHIFT MUTATION
- occurs when there is a deletion of 3 nucleotides from the coding region of a gene, resulting in the loss of phenylation at the 508th postion in the protein encoded by that gene
- mutation prevents normal folding of CF transmembrane conductance regular (CFTR) protein
- CFTR normally functions as Cl channel in epithelial cells -> loss of this results in production of thick, sticky secretions in lungs and pancreas -> lung damage and digestive deficiencies
37
Q
Epigenetics
A
- changes that do not change DNA sequence of the genome
- affected by environment
- alterations in gene expression that are stably inherited
- two main types of modification: gene methylation, histone modification
38
Q
Gene Methylation
A
- methyl group directly added to nucleotide base in DNA
- renders a gene nonfunctional
39
Q
Imprinting
A
- when silencing of genes on chromosomes is a result of gene methylation
- genes are said to be “imprinted” or have the ability to be turned on or off depending on which parent contributed the gene that has bene silenced
40
Q
Fragile X Syndrome
A
- result of imprinting
- caused by mutation in FMRI gene on the long arm of the X chromosome
- full mutation has >200 CGG trinucleotide repeats (normally the gene only has 55 CGG repeats) which causes hypermethylation of FMRI gene
- FMRI gene is inactivated so unable to undergo transcription and translation
- sxs: ASD, intellectual disability, abnormal facial features (large ears, long face, prominent jaw), large testicles
41
Q
Histone Modification
A
- lysine residue acetylation (adds negative charge) weakens interaction with DNA (positively charged) and makes DNA more accessible to factors needed for transcription
- histone deacetylation is associated with gene silencing
42
Q
HATs
A
enzymes that catalyzes histone acetylation
43
Q
HDACs
A
enzymes that catalyze histone deacetylation
44
Q
___ cells may use epigenomic modifications for therapy resistance
A
Cancer
- silencing of pro-apoptotic genes (death genes) such as Bax and Bak
- use of epigenetic drugs as effective treatment for cancer
