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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
Q

topoisomerase

A

relieves the overwound supercoils in bacteria

breaks a phosphodiester bond, changes superhelicity

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26
Q

DNA gyrase

A

DNA topoisomerase in bacteria

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27
Q

Irinotecan

  • used to treat what
A

topoisomerase inhibitor

used to treat colorectal cancer

28
Q

Etoposisde

  • used to treat what
A

topoisomerase inhibitor

anti-cancer drug that can cause secondary leukemias

29
Q

anthracyclines

  • used to treat what
A

topoisomerase II inhibitor

anti-cancer drug that can cause cardiotoxicity

30
Q

how is UV radiation harmful to DNA

A

UV radiation from the sun can produce a covalent linkage between two adjacent pyrimidines (TT or C-T)

pyrimidine dimers

31
Q

depurination

A

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
Q

deamination

A

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
Q

what happens to deamination of methyl-C in CpG islands

A

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
Q

BPDE

A

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
Q

benzo(a)pyrene

A

a pro-carcinogen that can form the metabolite BPDE which is a carcinogen

36
Q 
what do
nitrogen mustard
cisplatin
mytomycin C
carmustine
have in common?
A

they are all cross-linking agents

37
Q 
what do 
dimethyl sulfate (DMS) and methyl methanesulfonate (MMS) have in common
A

they are alkylating agents

38
Q

Thalidomide

A

a intercalating agent

prescribed for pregnant women to treat morning sickness

less to birth defects such as loss of or shortening of limbs

39
Q

Xeroderma pigmentosum

A

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
Q

hereditary nonpolyposis colorectal cancers

A

caused by a mutation in one of the alleles of genes in the mismatch excision repair complex

41
Q

cockayne syndrome

A

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
Q

BRCA mutations

A

BRCA1 and BRCA2 are tumor suppressor genes

increased risk for breast cancer

women: cervical, uterine, pancreatic, colon
men: pancreatic, testicular, early prostate cancer

43
Q

direct repair mechanism (enzymatic repair)

A

repairs pyrimidine dimers

44
Q

base excision repair (BER)

A

repairs single base mismatches

45
Q

nucleotide excision repair (NER)

  • what does it do
  • what does it use
  • disease
A

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
Q

mismatch excision repair (MER)

  • what does it do
  • what does it use
  • disease
A

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
Q

recombination repair

  • what does it do
  • what does it use
  • disease
A

repairs double strand breaks and interstrand cross linking

uses exonucleases, DNA polymerase, MER system

mutations can cause BRCA1/2 breast cancer

48
Q

transcription coupled repair (TCR)

  • what does it do
  • disease
A

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
Q

translesion synthesis (bypass synthesis)

  • what does it do
  • what does it use
A

repairs thymine dimers or apurini AP sites

uses DNA polymerases

50
Q

MSH2, 3, 6, MLH1, PMS2 genetic defects

  • phenotype
  • process affected
A

colon cancer

mismatch repair

51
Q

ataxia telangiectasia (AT)

  • phenotype
  • enzyme affected
A

leukemia, lymphoma, gamma ray sensitivity, genome instability

ATM protein (activated by double strand breaks)

52
Q

BRCA2

  • process affected
A

affects repair by homologous recombination

53
Q

fanconi anemia groups A-G

  • phenotype
  • process effected
A

congenital abnormalities, leukemia, genome instability

DNA interstrand cross-link repair

54
Q

base excision repair

A

replacing missing base in the genome

55
Q

nucleotide excision repair

A

removes distorted DNA segment and replaces it

56
Q

mismatch excision repair

A

MutS and MutL bind and trigger degradation of the nicked strand –> strand removal –> repair DNA synthesis

57
Q

Rifampicin

A

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
Q

DNA methylation in humans

A

occurs at the 5 position of the pyrimidine ring of cytosine

forms 5-methylcytosines

59
Q

ubiquitin

A

marks a protein for degradation

exists in all eukaryotic cells

attached to lysine residues on target proteins

60
Q

SUMOylation cycle

A

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
Q

SUMO-targeted ubiquitin ligases (STUbLs)

A

add the ubiquitin to the protein for degradation

can be mediated by RNF4 gene in humans

62
Q

how do topoisomerase inhibitors act as anti cancer agents (4 ways)

A
  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
Q

intercalating agent

A

inserts molecules between the bases of DNA; causes DNA damage

64
Q

inhibitors of HAT have shown promise in treating:

A

Alzheimer’s disease

Rheumatoid Arthritis

65
Q

inhibitors of HDACs:

  • two examples
  • what are they used for
A

valproic acid
vorinostat

anticonvulsives and anticancer drugs

MCM Exam II (14 decks)

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