(L11) Genomic Regulation Flashcards
What is the effect of histone acetylation and deacetylation? L11 S55
Acetylation: Activate Deacetylation: Deactivates
What is non-ionizing radiation and what does it cause L11
Sunlight is the main non-ionizing radiation. Pyrimidine (thymine) cylobutane dimers, or 6-4 covalent linkage.
Explain nuclear receptor signaling.
When a ligant binds to a nuclear receptor: causes a confromational shift which will then allow the complex to bind to DNA and regulate DNA expression as it is a TF.
-Example: When a ligand is added, a co repressor (HDAC) WILL LEAVE and a co activatior (HAT) will enter and acteylate the histone
What is the effect of ionizing radiation on DNA? L11 S65
What are the affects of UV radation?
Double stranded breaks, Base modification, DNA-protein cross-links (thymine tyrosine cross links)
Pyrimidne dimers
What are the main types of spontaneous DNA damage? L11 S67
Depurination: -loss of G/A base leaving only sugar and phosphate -results in loss of base pair (frame shift) in one of the strands
Deamination: -loss of amine group from C to form U -results in change of G to an A during DNA replication
What are CpG islands and what is significant about methylated CpG islands? L11 S71
Adjacent C and G nucleotides Found around 70% of promotors and, when methylated, stably silence genes
What are DNA cross-linking agents? L11 S74
-nitrogen mustard -cisplatin -mitomycin C -carmustine
What are alkylation agents? L11 S74
-dimethyl sulfide (DMS) -methyl methanesulfonate (MMS)
What are intercalating agents? L11 S74
-ethidium bromide -thalidomide
What is base excision repair? What proteins are involved? L11 S81
- DNA glycosolases (multiple types) look for altered bases
- base is “flipped out” and glycosyl bond is cleaved
- AP (apurininc/apyrimidinic) endonuclease and phosphodiesterase remove backbone
- DNA polymerase and ligase fill and seal gap
What is nucleotide excision repair? What proteins are involved? L11 S83
- enzyme complex looks for lesions/distortions in the double helix (pyrimidine dimer)
- backbone is cleaved on either side of the damage by an excision nuclease (ner complex)
- helicase “peels” the damaged DNA off
- DNA polymerase and ligase fill and seal the gap
Defect in NER complex can cause xeroderma pigmentosum or cockayne syndrome
What is mismatch excision repair? What proteins are involved? L11 S85
Removes most of the mismatched base pairs that were missed by proofreading.
-MutS (also known as MER complex proteins) (MSH2/6) binds newly synthesized DNA at sites of mismatch.
MutL scans for nicks further along on the DNA (nicks indicate newly synthesized strand vs. original strand).
The newly synthesized strand is removed and resynthesized.
-defects in MER cause hereditary nonpolyopsis collerectal cancers (autosomal dominant)
What is nonhomologous end joining? What changes are made to the DNA sequence? L11 S89
Ends of break are degraded and are ligased back together. This results in a loss of the degraded DNA sequences.
brca1/2 breast cancer
What is homologous recombination? What changes are made to the DNA sequence? L11 S88
Ends of break are degraded and sister chromatid is used as template to resynthesize missing segment. This doesn’t NOT result in a loss of the degraded DNA sequences.
if enzyme is deffienct you will get breast cancer
What is the result of failure to repair a double stranded break? L11 S90
Portion of a chromosome would no longer have a centromere and origin of replication. It would also lack protection (telomeres) on the broken ends and would be vulnerable to DNase activity.
What is transcription coupled repair? What is significant about where it can detect damage? L11 S91
RNA polymerase stall at lesions in DNA and will direct DNA repair mechanisms to the site. Can only detect damage on the strand being transcribed, damage on the other strand will go undetected.
-if this is not working: cockanye syndrome
What are the main types of post-translational modification of DNA proteins? L11 S103
-phosphorylation -acetylation -ubiquitination -SUMOylation -methylation
What is the difference between CpG islands and sites? L11 S112-113
Found primarily in promoter regions and are in high frequency CpG sites occur by happenstance
What is the mechanism behind hereditary nonpolyposis colorectal cancer? What repair mechanism is it associated with? L11 S88 Panini pg. 333
Inherited defect in mismatch excision repair (MER) genes MSH2/6 (mutS). Risk factor for tumor growth. Loss of heterozygosity of functional gene allows tumor development.
What is the mechanism behind xeroderma pigmentosum? What repair mechanism is it associated with? Panini pg. 333
The XP protein is used in nucleotide excision repair (NER), most notably of thymine dimers caused by UV exposure. Results in UV sensitivity and significantly increased of risk of skin cancer. Typically have a very freckled appearance
What is the mechanism behind Cockayne syndrome? What repair mechanism is it associated with? Panini pg. 334
Caused by ERCC-6/8 protein which is involved in transcription-coupled repair (TCR). Results in developmental/neurological delays and photosensitivity.
What is the DNA repair method associated with breast cancer? Panini pg. 334
Caused by BRCA1/2 (breast cancer susceptibility protein 1/2) which are involved in homologous recombination. 5X increased risk of breast cancer and increased rate of other types of cancer as well.
Both HAT and HDAC are _____.
Drug targets
Non ionizing radiation can cause?
Thymine thyime cross links or thyinme 6-4 covalent linkage on thymine
Depurination vs Deamination
Depurination: loss of a purine
deaminiation: C to U change , Adenine to hypoxanthine, guanine to xanthine, 5 metyl C to T
Xeroderma pigmentosum
- SKIN CA, uv sensitivity, neuro abromailites
- NER IS AFFECTED
Describe how metabolism can produce caringoens
Benzyoprynes (pro carcinogen, from burnt meat) can make BPDE via cyp.
BPDE can form an adduct with a guanine
Direct repair
photolyase will remove a thyimine dimer and light will seal it up
defects in recomniation repair, non homologus end joining and homologus recombination cause what?
bRACA1/2
BREAST CANCER
aTAXIA TENGIECTASIA
-CAUES LUKEMIA, LYMPOMA, PROBLEMS WITH atm PROTEIN, A PROTIEN THAT IS ACTIVATED BY DS breaks
MSH2, 3,6 MLH 1 AND PMS2 give rise to what?
Colon cancer, affects miss match repair
Brac2
breast, ovarian, and prostate cancer
-caused by errors in reparr of homologus recomination
fanconi anemia groups a-6
- causes lukemia
- erros in DNA interstrand cross link repair
Cancer cells are very sentivite to inhibitors of what?
HLysine deacetylases (HDAC ihibitors) include vorinostat, valproic acid
Rifampicin ihibits?
Bacterial rna synth
epigenetics is what?
Mechanism that regulates gene activity. Can be stimulated by disease state, stress, enrovioment and more.
Writers: enzymes that add histone modifications
readers: enzymes that remove histone mods
readers: proteins that bind to hitone and alter gene activity and production
DNA methylation
methylates A and C which repress gene tranascriton when at gene promoter (at CPG islands)
- assocaited with x chromsomal inactivation, genomic impritining and more
- can be inheritied by daughter cells after cell division
Epigenetics is the combination of what?
Methylation, sumolation, unqiniation, histone acetylation (all regulate lysine) and phsoporylation (serine and threoninie)
Central Dogma of molecular biology
DNA RNA protein
RT
uses reverse transcriptase to generate complementary DNA (cDNA) from RNA
How is DNA packaged
tthrough DNA protein interactions: hyrdophobic interactions and salt linkages between DNA and the histone octemer in each nucleosome
-histones are converved across species
Decribe histone proteins
(20%) lots of lysine and argnine in histones thus a lot of positive charges
- attaches well with negativley changed DNA backbone
- lysines are targets of post translational modifications
What is a nucleosome
eukaryotic chromosome, consisting of a length of DNA coiled around a core of histones.
- has the octmer histone protiens and non histone chromsomal proteins
- 2H2A, 2H2B, 2HC 2 H4
Eurochromatin vs heterochromatin
-euro: lighly packed, highly enriched in genes and ofthen being transcribed
92% of our genome is eurochromatin
hetro: condensed, and stained dark, found in centromeres and telomeres
What is the position effect
Activity of gene depends on its location
-activley expressed genes will be silenced if relocated near hetrerochromatin
What are RNAi
miRNA inhibit gene expression or translation by neutralizaing mRNA molecules
(also known as rna interference)
Long terminal repeats
- Long sequences of identical DNA
- found at either end of retrotransposons
- formed by RT of retroviral DNA
- used by viruses to insert their gene material in our host genome
Alternative splicing
- can make more than one protein from one gene
- all introns bein with GT and end with AG
15% OF mutations affect RNA splicing
DNA replication
DNA polymerase makes new DNA in 5’ to 3’ direction
- you need a primer with a free 3’ OH
- DNA rep is semi concerevative
DNA replication enzymes are:
DNA helicase - unwinds DNA (NEEDS ATP)
dna GYRASE (bacteria), topoisomerase (humans): breaks phosphodiester bond and relives supercoiling (used as a ihbibitor in anti cancer agents)
- DNA primase
- DNA ligase
What happened in 1953?
Watson and crick found structre of DNA
What happened in 1966
found genetic code
what is the percentage of DNA sequences in exons?
1.5
Histone methylation vs demethylation
Metylation condenses
-de metylation does relaxes
Histone phosporylation
Helicase
Topoisomerase
DNA ligase
DNA poly
SSBP
- UNZIP GENE
- REDUCE SUPERCOILS
- LIGAGATES OKAZAKI FRAGMENTS
- SYNTH DNA
- Prevents formation of haripoinds and DNA bases remain exposed
Azidothymidine
nucleoside alaog inhibitor, used in HIV, ihbibit DNA replication
arabinosylcytosine
ara-c nuclsoside analogue ihibitor: used in lukemia
acyclovir
used in herpies
Thymine modifications
Demaniation of methyl C produces T miss matched with G
Cockane Syndrome
caused by errors in transcriton coupled repair ERCC6 and ERCC8 proteins)
Polymerase Proof reading
“A 3′→ 5′ proofreading exonuclease domain is intrinsic to most DNA polymerases, allowing excision of mismatched nucleotides as DNA is being made
Post translational covalent mods of chromatin on gene transcripton:
- metylation
- sumolation
- ubinitination
- histone acetylation and deacetylation
- phosporylation
- metylation: supresses
- sumolation: tags for degredation
- ubinitination: tags for degretation
- Histone acetyl: unrwaps it (all act on lysine)
- phos: more transcripton (serine, threonine)
