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SFM Quiz 2 > Functions/Dysfunctions of Genomic Regulation > Flashcards

Functions/Dysfunctions of Genomic Regulation Flashcards

1
Q

central dogma

A

dna-rna-protein

reverse transcriptase turns rna to dna

only mrna becomes protein

retroviruses can turn rna to DNA

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2
Q

DNA composition

A

deoxynucleotitde with PO sugar, missing OH and base

represented in 5’-3’ direction

the 3OH end is connected to a phosphodiester linkage to the 5’ phosphate of the next nucleotide

every DNA strand has a phosphate residue at the 5’ terminus and a free OH at the 3’

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3
Q

the two DNA strands are aligned

A

antiparallel, form the right handed B form via hydrophobic bases in the interior and hydrophilic sugar backbones in the exterior

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4
Q

base pairing

A

AT with two H bonds

GC with three H bonds

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5
Q

Eukaryotic Packaging

A

DNA double helix wraps around pairs of four histones

this forms the nucleoside

H1 histone is attached to linker DNA

nucleosides are further packaged into 30nm fibers and then to chromatin

when cells divide in the M phase, chromatin condenses into chromosomes

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6
Q

mitotic chromosomes are condensed 500 times when compared with interphase chromosomes. Why?

A

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

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7
Q

142 H bonds between DNA and the histone octamer in each nucleosome as well as

A

hydrophobic interactions and salt linkages

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8
Q

histone proteins are highly conserved across species

A

only 2 AA different between pea and cow H4

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9
Q

proteins that bind DNA are made of two classes

A

histone proteins
non histone chromosomal proteins ‘

each nucleosome core particle consists of a complex of 8 HP, histone octamer which DNA winds around.

Protein +DNA is chromatin

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10
Q

only ___ of proitein coding sequence in DNA

A

1.5%

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11
Q

Euchromatin

A

loosely packed, easily accesible, transcriptionally active found in nondividing cells

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12
Q

heterchromatin

A

tightly packed, dense, inaccesibly, transcriptionally inactive

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13
Q

posttranslation modifications happen on

A

histone tails.

the core histone H2A and H2B can also be modified

combinations of moidifcations constitute the histone core

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14
Q

methyltion/demethylation

A

transger 1-3 methyl groups from S-adenosyl-L-methionne to lysine or arginine residues of hostone by histone methyltransferase (HMT)

HMTs control DNA methylation through chromatin transcriptional dependent repressino/activation

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15
Q

acetylation

A

enzymatic addition of an acetyl group from acetyl CoA

involvedin the regulation of many processes, gene silencing, cell cycle, apoptosis

uses aceyltransferases (HATs) which acetylate H3 and H4

H3 acetylation can be increased by unhibition of histone deacetylases and decreased by HAT inhibition

imbalance in acetylation has been assocaited with cancer

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16
Q

deacetylation

A

represses genes by compacting the chromatin, uses HDACs

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17
Q

Phosphorylation

A

associated with local chromatin opening and transcriptional acitvation

linked with chromatin condensation during mitosis

important for regulation of DNA damage repsonse

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18
Q

semiconservative DNA replication

A

each parental strand of DNA is the template for the daughter

each replicated molecule contains one parent strand and one new strand

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19
Q

bidirectional DNA replication

A

replication of DNA in a eukaryotic chromosome (goes in both directions)

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20
Q

semidiscontinuous DNa replication

A

both new DNA strands are synthesized in teh 5-3 direction.

leading strand is made continuously wherase lagging strand is made with Okazaki framgents

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21
Q

DNA polymerase

A

needs a primer to start synthesis

adds in the 5-3 direction
uses free nucleotide triphoshate as substrates

the free 3OH group of the primer attacks the P of the incoming NTP therby releasing the terminal two PP and hydrolysis of the PP drives the reaction

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22
Q

DNA helicase

A

melts H bonds and unwinds DNA

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23
Q

topoisomerase

A

releives coil strain ahead of replication fork

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24
Q

ssDNA binding protein

A

keeps template strands separated

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25
topoisomerase inhibitors as anticancer drugs
block cell cycle, generate single and double stranded breaks, harms the genome, leads to apoptosis and death ex: Type I irinotecan, folfori, etopsiside, anthracyclines
26
DNA ligase
seals nicks
27
Nucleoside analog inhibtors
DNa synthesis involves the formation of 3-5 phosphodiester bonds because of that, nucleoside analogues lack the 3OH group and act as drugs to inhibit DNA repliction these nucleosides need to be converted to dNTPs before they can act as inhibitors of DNA polymerase ex. acyclovir, others
28
both acyclovir and AZT lack 3OH thus
arresting viral DNA synthesis by acting as chain terminators
29
spontaneous damage by endogenous agents
deprivation of adenosine and guanosine via removal of their bases, purination occurs via hydrolysis of N glyucosyl linkage giving rise to abasic/apurininc sites in the DNA strand
30
deaminiation of the bases A, G and C make
hypoxanthine, xantine, uracil
31
ionizing radiation
xrays, results in ROS and cause base famage, break strands, cross link DNA protein
32
nonionizing radiation
UV light damages DNa by indicating the formation of covalent linkages between adjacent pyrimidine bases, forming thymine dimers and 6-4 linkages
33
depurination
5000 purine lost/bases per day example guanine gets hydrolyzed off and only sugar P left
34
deamination
C to U changes, 100 bases per day. In DNA this is bad for replciation left with a sugar phpshate
35
AGT can be deaminated and adenine will turn into hypoxanthine which increases
uric acid and gout
36
Outcomes of DNA damage
unrepared DNA damage can lead to deleterious consequences such as impaired cellular function, programmed cell death and mutations that lead to cancer
37
polymerase proofreading
double checks the bases match?
38
direct repair
enzymatic repairs pyrimidine dimers
39
6 methylguanine
uses DNA photolyase, methylgianine methyltransferase
40
base excision repair
repairs single BASE mismatches, nondistoring alterations like depurination involves DNA glycolysis, AP endonuclease, AP lyas, DNA polymerase, DNA ligase
41
nucleotide excision repair
repairs chemical changes that distort DNA like pyrimidine dimers, BPDE-guanine adductor, cisplatin adducs involves NER protein complex, DNA polymerase E, DNA ligase disease Xeroderma Pigmentosum
42
mismatch repair
repairs mismatched base in daughter strand involves MER complex, helicase, endonuclease, DNA polymerase D, DNA ligase, dz is hereditary nonpolyposis, colorectal cacners
43
recombination: nonhomologous end joining
repairs double strand breaks, interstrand cross linking involves damaged ends that are filled in and joined some base pairs may be mising mulitple proteins and enzymes including DNA ligase
44
recombination: homologous recombination
repairs double strand breaks, interstrand cross linking involves ligases, DNA polyermase, MER system damaged duplex repair using infmration on undamage homologous duplex dz is BRCA 1-2
45
transcription coupled repair
repairs stalled RNA polymerase during transcription (not replication) dz is cockayne
46
translation synthesis
bypases synthesis repairs unprepared thymine dimers involves DNA polymerase (reduced fidelity polymerases)
47
Xeroderma Pigmentsum
skin sensitivity to direct sunlight prone to melanomas causes cyclobutane dimers to form in the DNA can be repaired through NER but that is defective in the XP proteins (A-G) in the NER complex in those with the dz
48
Cockayne Syndrome
rare, autosomal recessive congenital disorder mutant genes invovled are ERCC6 and 8 these genes code for their proteins and are invovled in the TCR of DNA if DNA not repaired, cell death occurs sx include neuro isses, photosensitivity, progeria mutations in ERCC8 and 6 lead to cockayne A and B respectively with B being more common `
49
BRCA 1 and 2
tumor suppresor genes increase risk for breast cancer 5x the norm as well as ovarian cancer before meno men with these mutations have increased resik for breast cancer as well BRCA1 increases cervical cacner, iterine, pancreatic colon in women and pancreatic, testicular, prostate in men men more oftenaffected by BRCA2 with increase risk for melanoma, pancreas, stomach, gallbladder and bile duct for women
50
imprinting
certain genes from mother or father are expressed while other s are silenced impriented allele are silenced such that the gene is expreseed only from the non-imprinted parent epigenetic process that invovles the methylation and histone modification of egg and sperm during formation while genetic seuqence is unchanged duplicated in all somatic cells prader willi
51
epigenetics
mechanism for regualting gene acticity indepdent of DNA sequence that determines which genes are turned off or on in a specific cell in different disease states can be develeoped in childhood, utero, drugs, diet, lifestyle
52
More on Methylation
methyl group from diet can tag DNA and activate or repress gnes added to A or C by methyltrasnferase changes activity of promoter does not change sequence repress gene transcription when at the gene promotor essential for normal development assocaited with normal development, impriinting, x inactivation, aging, tetc
53
More on histone acetylation/deacetylation
HATs acetylate core histones to neutralize positive charge on lysine and help chromatin decondsnse acetylate nonhistones as well like TF inhibtors of HAT show promise in dz tx. HDACs remove acetyl groups from lysine on core histones and non histone proteins cancer cells are very sensitive to inhibitors of lysine deacetylases like vampiric acid (anticancer, anti sz)
54
CpG islands
adjacent C-phosphate-G assocaited with inactive genes
55
deamination of methyl cytosine produces
T mismatched with G methylation of CpG islands stably silemnce genes (which in this case can cause cancer) special DNA glycosylase removes T DNA not very hekpful as only 3% of C nucleotides in uhman feneome are methylated, accounts for 1/3 of all point mutations 5-methyl cytosine is deaminated to thymin dont understand any of this
56
Benzoapyrene becomes
BPDE (burnt meat carcinogen)
57
examples of cross linking agents
nitrogen mustard gas, cisplatin, mitomycin C, carmustine (joins Aa to proteins or N)
58
examples of alkylating agents
diomethyl sulfate, methyl methamsulfinate
59
intercalating agents
ethidum bromide, thalidomide, doxorubicin, daunomycin, intterupts the base pairs
60
Defect: MSH2, 3, 4, MLH1, PMS2
colon cancer | mismatch repair
61
defect: Xeroderma pigmentisum, grousp A-G
skin cancer, UV sensitivity, neuro issues nucleoride excision repair
62
defect: ataxia telangeictasia
leukeima, lymphoma y ray sensitivity, genomic instabilirt ATM protein, a protein kinase, activated by DS breaks
63
BRCA 2
breast, ovarian, prostate cancer repair by homologous recombination
64
Fanconi Anemia groups A-G
congenital annomalies, leukemia, genome instbaility cross link repair, DNA interstrand
65
in nucleotide excision repair the distorted adduct undergoes
recognition by the NER cpmplex and nicks the DNA on both sides of the damage if there is a defect here the dz. XP and Cockayne occur
66
in mismatch excision repair for incorect bases in new daughter starnds, MER complex bind to
DNA and recognizes mismatch in daighter strand, daigher is cut and segment with mismatch is removed. If this is defective, you will get hereditary nonpolyposis colorecetla cacner
67
Cockayne is a defect in
transcription coupled repair causes growth retrdation, sleletal abnormalities, sensitive to light, RNA polymerase permanently stalled at sites of damage in important genes
68
Rifampcin side effects
unregulated hepatic cytochrome P450 enzymes and thus increases in the metabolism of other drugs and hormones by the system transiently imparts the red color to sweat, tears, etc
69
adopted orphan nuclear receptor superfamily
PXR-xenobiotics
70
cytochrome p450 catalyze
oxidation reactions
71
hypermethylation
dchromsomal instability, loss of imprinting
72
ATG is
start of translation (met) there are 7-% promoters conained within CpG islands proximal to the start of transciprtion (multiple methylated CpG ssites in islands make stabiliy silenced genes)
73
ubiquination and SUMO
go toegher to repair damage from stress

SFM Quiz 2 (25 decks)

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