Functions/Dysfunctions of Genomic Regulation Flashcards
central dogma
dna-rna-protein
reverse transcriptase turns rna to dna
only mrna becomes protein
retroviruses can turn rna to DNA
DNA composition
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’
the two DNA strands are aligned
antiparallel, form the right handed B form via hydrophobic bases in the interior and hydrophilic sugar backbones in the exterior
base pairing
AT with two H bonds
GC with three H bonds
Eukaryotic Packaging
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
mitotic chromosomes are condensed 500 times when compared with interphase chromosomes. Why?
to prevent physical damage to the DNA as chromosomes are spearated and passed on to daughter cells
142 H bonds between DNA and the histone octamer in each nucleosome as well as
hydrophobic interactions and salt linkages
histone proteins are highly conserved across species
only 2 AA different between pea and cow H4
proteins that bind DNA are made of two classes
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
only ___ of proitein coding sequence in DNA
1.5%
Euchromatin
loosely packed, easily accesible, transcriptionally active found in nondividing cells
heterchromatin
tightly packed, dense, inaccesibly, transcriptionally inactive
posttranslation modifications happen on
histone tails.
the core histone H2A and H2B can also be modified
combinations of moidifcations constitute the histone core
methyltion/demethylation
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
acetylation
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
deacetylation
represses genes by compacting the chromatin, uses HDACs
Phosphorylation
associated with local chromatin opening and transcriptional acitvation
linked with chromatin condensation during mitosis
important for regulation of DNA damage repsonse
semiconservative DNA replication
each parental strand of DNA is the template for the daughter
each replicated molecule contains one parent strand and one new strand
bidirectional DNA replication
replication of DNA in a eukaryotic chromosome (goes in both directions)
semidiscontinuous DNa replication
both new DNA strands are synthesized in teh 5-3 direction.
leading strand is made continuously wherase lagging strand is made with Okazaki framgents
DNA polymerase
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
DNA helicase
melts H bonds and unwinds DNA
topoisomerase
releives coil strain ahead of replication fork
ssDNA binding protein
keeps template strands separated
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
DNA ligase
seals nicks
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
both acyclovir and AZT lack 3OH thus
arresting viral DNA synthesis by acting as chain terminators
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
deaminiation of the bases A, G and C make
hypoxanthine, xantine, uracil
ionizing radiation
xrays, results in ROS and cause base famage, break strands, cross link DNA protein
nonionizing radiation
UV light damages DNa by indicating the formation of covalent linkages between adjacent pyrimidine bases, forming thymine dimers and 6-4 linkages
depurination
5000 purine lost/bases per day
example guanine gets hydrolyzed off and only sugar P left
deamination
C to U changes, 100 bases per day. In DNA this is bad for replciation
left with a sugar phpshate
AGT can be deaminated and adenine will turn into hypoxanthine which increases
uric acid and gout
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
polymerase proofreading
double checks the bases match?
direct repair
enzymatic
repairs pyrimidine dimers
6 methylguanine
uses DNA photolyase, methylgianine methyltransferase
base excision repair
repairs single BASE mismatches, nondistoring alterations like depurination
involves DNA glycolysis, AP endonuclease, AP lyas, DNA polymerase, DNA ligase
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
mismatch repair
repairs mismatched base in daughter strand
involves MER complex, helicase, endonuclease, DNA polymerase D, DNA ligase,
dz is hereditary nonpolyposis, colorectal cacners
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
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
transcription coupled repair
repairs stalled RNA polymerase during transcription (not replication)
dz is cockayne
translation synthesis
bypases synthesis
repairs unprepared thymine dimers
involves DNA polymerase (reduced fidelity polymerases)
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
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 `
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
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
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
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
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)
CpG islands
adjacent C-phosphate-G assocaited with inactive genes
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
Benzoapyrene becomes
BPDE (burnt meat carcinogen)
examples of cross linking agents
nitrogen mustard gas, cisplatin, mitomycin C, carmustine (joins Aa to proteins or N)
examples of alkylating agents
diomethyl sulfate, methyl methamsulfinate
intercalating agents
ethidum bromide, thalidomide, doxorubicin, daunomycin, intterupts the base pairs
Defect: MSH2, 3, 4, MLH1, PMS2
colon cancer
mismatch repair
defect: Xeroderma pigmentisum, grousp A-G
skin cancer, UV sensitivity, neuro issues
nucleoride excision repair
defect: ataxia telangeictasia
leukeima, lymphoma y ray sensitivity, genomic instabilirt
ATM protein, a protein kinase, activated by DS breaks
BRCA 2
breast, ovarian, prostate cancer
repair by homologous recombination
Fanconi Anemia groups A-G
congenital annomalies, leukemia, genome instbaility
cross link repair, DNA interstrand
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
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
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
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
adopted orphan nuclear receptor superfamily
PXR-xenobiotics
cytochrome p450 catalyze
oxidation reactions
hypermethylation
dchromsomal instability, loss of imprinting
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)
ubiquination and SUMO
go toegher to repair damage from stress
