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MCM Exam II > Functions and Dysfunctions in Genomic Regulation > Flashcards

Functions and Dysfunctions in Genomic Regulation Flashcards

1
Q

Nucleus:

  • % volume in cell
  • # in cell
  • roles in cell
A

6%
1
cell regulation, proliferation, DNA transcription

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2
Q

bond between G and C nucleotides

A

triple bond

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3
Q

why are mitotic chromosomes condensed 500x more than interphase chromosomes

A

to prevent physical damage to the DNA as chromosomes are separated and passed on to daughter cells

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4
Q

what interactions and linkages are between DNA and its histone octamer in each nucleosome

A

hydrophobic interactions

salt linkages

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5
Q

20% of histone protein AA residues are what two AA

A

lysine and arginine

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6
Q

each nucleosome core particle consists of a complex of how many histone proteins

A

8

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7
Q

protein + DNA =

A

chromatin

“beads on a string”

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8
Q

euchromatin

A

loosely packed form of chromatin (DNA, RNA, and protein)

most active part of the genome

92% of human genome

often under active transcription

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9
Q

heterochromatin

A

very condensed chromatin

late replicating and genetically inactive

highly condensed at centromeres and telomeres

contains very few active genes

will silence a gene if it is relocated in close proximity

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10
Q

position effect

A

activity of a gene depends on its relative position on a chromosome

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11
Q

what percentage of the genome is responsible for coding

A

1.5%

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12
Q

comparative genome hybridization

A

detecting variations in people’s genomes

probes human genome CHPI with DNA from one person and with DNA from a “normal” reference

detects the copy number variation

personalized medicine

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13
Q

RNAi

A

RNA interference

a biological process in which RNA molecules (miRNA) inhibit gene expression or translation

neutralizes targeted mRNA molecules

“fine tuning gene expression”

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14
Q

long terminal repeats (LTRs)

A

identical sequences of DNA that are repeated hundreds or thousands of times

found at either end of retrotransposons (proviral DNA); formed by reverse transcription of retroviral RNA

used by viruses to insert their genetic material into host genomes

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15
Q

microRNA (miRNA)

A

form of gene expression regulation

forms an miRNA protein complex that can prevent gene expression by either degrading the target mRNA or by blocking its translation

mechanism:

  • miRNA folds back on itself and forms H bonds
  • Dicer cuts strand into small segments
  • one half of small segments is degraded, the other associates with a protein to form the complex
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16
Q

99% of all introns begin with ___ and end with ___

A

begin with GT

end with AG

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17
Q

histone deacetylase (HDAC)

A

co-repressor that actively represses gene expression

removes the acetyl group from lysines on core histones and non histone proteins

the chromatin then becomes compact and transcriptionally repressed

“beads are wound tight on the string”

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18
Q

histone acetyl transferase (HAT)

A

co-activator that actively promotes gene expression

acetylates the chromatin which allows it to become open and transcriptionally active

“the beads are wound loosely on the string”

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19
Q

what does DNA methylation at a gene promoter do

A

represses the gene transcription

essential for normal development

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20
Q

what do gene promoter CpG islands do

A

transcriptional silencing

acquire abnormal hypermethylation

can be inherited by daughter cells following cell division

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21
Q

what does hypo methylation cause

A

chromosomal instability

loss of imprinting

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22
Q

large problem with hypermethylation

A

can silence oncogene suppressors, causing cancer

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23
Q

what does DNA polymerase require to begin processing

A

a primer with a free 3’-OH

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24
Q

single stranded DNA-binding protein (SSBP)

A

binds cooperatively to exposed ssDNA to help stabilize the unwound DNA and prevent the formation of hairpins

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25
topoisomerase
relieves the overwound supercoils in bacteria breaks a phosphodiester bond, changes superhelicity
26
DNA gyrase
DNA topoisomerase in bacteria
27
Irinotecan - used to treat what
topoisomerase inhibitor used to treat colorectal cancer
28
Etoposisde - used to treat what
topoisomerase inhibitor anti-cancer drug that can cause secondary leukemias
29
anthracyclines - used to treat what
topoisomerase II inhibitor anti-cancer drug that can cause cardiotoxicity
30
how is UV radiation harmful to DNA
UV radiation from the sun can produce a covalent linkage between two adjacent pyrimidines (TT or C-T) *pyrimidine dimers*
31
depurination
a type of spontaneous DNA damage; 5000 purine bases can be lost per day the N terminus of the sugar is cleaved and replaced with an OH group which cannot bind to the base and form a nucleotide
32
deamination
a type of spontaneous DNA damage which causes C bases to change to U bases; about 100 bases per day requires H2O input and releases NH3 adenine --> hypoxanthine guanine --> xanthine cytosine --> uracil
33
what happens to deamination of methyl-C in CpG islands
it produces a T mismatched with a G needs a special DNA glycosylase to recognize this and remove the T DNA repair is still relatively ineffective however
34
BPDE
a carcinogenic metabolite formed from benzo(a)pyrene cross-linking agent and intercalating agents adduct (N-H) formed between guanine and benzo(a)pyrene to form BPDE; it then acts as a DNA transcription repressor
35
benzo(a)pyrene
a pro-carcinogen that can form the metabolite BPDE which is a carcinogen
36
``` what do nitrogen mustard cisplatin mytomycin C carmustine have in common? ```
they are all cross-linking agents
37
``` what do dimethyl sulfate (DMS) and methyl methanesulfonate (MMS) have in common ```
they are alkylating agents
38
Thalidomide
a intercalating agent prescribed for pregnant women to treat morning sickness less to birth defects such as loss of or shortening of limbs
39
Xeroderma pigmentosum
a disease caused by a defect in the nucleotide excision repair complex; patients cannot repair cyclobutane thymine dimers caused by UV sunlight sx: - very sensitive skin to sunlight - prone to developing melanomas - prone to squamous cell carcinomas
40
hereditary nonpolyposis colorectal cancers
caused by a mutation in one of the alleles of genes in the mismatch excision repair complex
41
cockayne syndrome
result of mutations in ERCC6 and ERCC8 that code for ERCC-6 and ERCC-8 proteins that are involved in the TCR of DNA defect in transcription-coupled repair sx: neurological delay - photosensitivity - progeria (premature aging) - hearing loss - eye abnormalities - death in first two decades
42
BRCA mutations
BRCA1 and BRCA2 are tumor suppressor genes increased risk for breast cancer women: cervical, uterine, pancreatic, colon men: pancreatic, testicular, early prostate cancer
43
direct repair mechanism (enzymatic repair)
repairs pyrimidine dimers
44
base excision repair (BER)
repairs single base mismatches
45
nucleotide excision repair (NER) - what does it do - what does it use - disease
repairs chemical adducts that distort DNA - pyrimidine dimers - BPDE-guanine adducts - cisplatin adducts uses NER protein complex, DNA polymerase, DNA ligase mutations cause xeroderma pigmentosum
46
mismatch excision repair (MER) - what does it do - what does it use - disease
repair mismatched bases in daughter strand uses MER complex (MSH2 and MSH6), helicase, DNA polymerase, DNA ligase mutations can cause hereditary nonpolyposis colorectal cancers
47
recombination repair - what does it do - what does it use - disease
repairs double strand breaks and interstrand cross linking uses exonucleases, DNA polymerase, MER system mutations can cause BRCA1/2 breast cancer
48
transcription coupled repair (TCR) - what does it do - disease
stalls RNA polymerase during transcription (not replication) and repairs it; used on sequences that urgently need repair works with base excision repair and nucleotide excision repair mutations can cause Cockayne syndrome
49
translesion synthesis (bypass synthesis) - what does it do - what does it use
repairs thymine dimers or apurini AP sites uses DNA polymerases
50
MSH2, 3, 6, MLH1, PMS2 genetic defects - phenotype - process affected
colon cancer mismatch repair
51
ataxia telangiectasia (AT) - phenotype - enzyme affected
leukemia, lymphoma, gamma ray sensitivity, genome instability ATM protein (activated by double strand breaks)
52
BRCA2 - process affected
affects repair by homologous recombination
53
fanconi anemia groups A-G - phenotype - process effected
congenital abnormalities, leukemia, genome instability DNA interstrand cross-link repair
54
base excision repair
replacing missing base in the genome
55
nucleotide excision repair
removes distorted DNA segment and replaces it
56
mismatch excision repair
MutS and MutL bind and trigger degradation of the nicked strand --> strand removal --> repair DNA synthesis
57
Rifampicin
an antibiotic that inhibits RNA synthesis in bacterial cells; prevents translation side effects include: - regulation of hepatic cytochrome P-450 enzymes (CYP-3A4 and (CYP-2C9) and thus an increase in the metabolism of other drugs and hormones
58
DNA methylation in humans
occurs at the 5 position of the pyrimidine ring of cytosine forms 5-methylcytosines
59
ubiquitin
marks a protein for degradation exists in all eukaryotic cells attached to lysine residues on target proteins
60
SUMOylation cycle
Small Ubiquitin Like Modifier post-translational modification involved in various cellular processes, such as nuclear-cytosolic transport, transcriptional regulation, apoptosis, protein stability, response to stress, and progression through the cell cycle
61
SUMO-targeted ubiquitin ligases (STUbLs)
add the ubiquitin to the protein for degradation can be mediated by RNF4 gene in humans
62
how do topoisomerase inhibitors act as anti cancer agents (4 ways)
1. block the cell cycle 2. generate single and double stranded breaks 3. harm the integrity of the genome 4. lead to apoptosis and death
63
intercalating agent
inserts molecules between the bases of DNA; causes DNA damage
64
inhibitors of HAT have shown promise in treating:
Alzheimer's disease | Rheumatoid Arthritis
65
inhibitors of HDACs: - two examples - what are they used for
valproic acid vorinostat anticonvulsives and anticancer drugs

MCM Exam II (14 decks)

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