genomic functions Flashcards
What is the base excision repair mechanism?
For single base mismatches that don’t distort (DNA polymerase does this)
DNA glycosylase detects and removes the mismatched base.
AP endonuclease cuts the phosphodiester bond
AP lyase removes the deoxyribose phosphate
DNA polymerase Beta replaces the nucleotide
DNA ligase seals the nick
What is the mechanism for nucleotide excision repair? (often chemically induced damage like thiamine dimers)
NER complex recognizes distortions and nicks DNA on both sides of the distorting adduct.
DNA polymerase then fills the gap
DNA ligase seals the nick
Describe transcription-coupled repair
When RNA polymerase is stalled at lesions in DNA it directs repair machinery to it.
Describe Mismatch repair
MER complex binds to DNA, recognizes mismatch in daughter strand, then cuts the segment
DNA polymerase and ligase fill and seal the gap.
How is DNA packaged and unwound by histones?
Lys and Arg are positive (1/5 of histone), DNA negative charge
Histone acetylation: loosely packed for transcription by removing positive charge
Histone methylation: loosely packed for transcription by physical interference
describe how histones are modified
HIstones have tails upon which various enzymes work.
Writer enzymes add modifications
Eraser enzymes remove them
Reader enzymes bind to the modification to further alter gene activity
Helicase
unwinds DNA helix
ATP fuels it
Topoisomerase
Relieves over-wound supercoils;
reversible
DNA polymerase a
In complex with primase.
Synthesizes RNA-DNA primer
DNA polymerase d and e
Synthesize new DNA chain in the 5to3 direction
Flap endonuclease 1
REmoves RNA primers
DNA polymerase d
Fills in gaps
DNA ligase
seals nicks
What enzyme is inhibited during DNA replication?
Topoisomerase is inhibited by
Etoposide in eukaryotes
Flouroquinolones in prokaryotes
What is the relationship between telomeres and telomerase?
telomeres are the primers for replication. When the primer runs out then the cell cannot replicate more DNA
Telomerase restores the lost primer each division. It has a RNA template for reverse transcription. One step that cancer must accomplish is further activation of telomerase
What causes pyrimidine dimers?
UV radiation causes adjacent pyrimidines to form covalent bonds
What is the problem involving methylated cytosines?
If C is methylated then it often spontaneously is converted to T. In CpG islands there is a high frequency of methyl-C. This methylation silences Cancer/DNA repair genes. If converted to T often in the island then silencing is ineffective.
Name some cross linking agents
Nitrogen mustard, Cisplatin, Mitomycin C, Carmustine
Name some alkylating agents:
Dimethyl sulfate (DMS) Methyl mehanesulfonate (MMS)
Name some Intercalating agents.
Ethidium bromide
Thalidomide
Doxorubicin
Daunomycin
Direct repair
pyrimidine dimer repair and methylguanine repair
DNA photolyase
Methylguanine methyltransferase
Base excision repair enzymes
DNA glycolases, AP endonuclease, AP lyase, DNA polymerase, DNA ligase
Nucleotide excision repair enzymes
NER protein complex, DNA polymerase, DNA ligase
Mismatch excision repair enzymes
MER complex, helicase/endonuclease, DNA polymerase, DNA ligase
Recombination repair enzymes
BRCA1/2
a bunch of enzymes
Transcription-coupled repair enzymes
depends on the cause of the lesion in the DNA
Translesion synthesis enzymes
DNA polymerases;
repairs thymine dimers or apurini AP sites
Describe Xeroderma pigmentosum
Mutation in the NER complex makes it so UV damage cannot be fixed. Pts easily sunburn, have dry and scaly skin, prone to develop squamous cell carcinomas
describe hereditary nonpolyposis
Mutation to one of the alleles in the MER complex have and increased susceptibility to hereditary nonpolyposis colorectal cancers.
A mutation to the remaining allele would render MER nonfunctional=tumor
describe cockayne syndrome
Mutation of genes involved in TCR of DNA repair.
describe BRCA
Mutation in tumor suppressor genes involved with treatment.
Describe alternative splicing
Alternative splicing, or differential splicing, is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA
snRNA
small nuclear RNA part of splicosomes (splicing)
scRNA
involved in protein synth and transport,
associated with SRP (ER and making transmembrane proteins)
RNaseP
catalytic RNA involved in cleavage and removal of extra RNA sequences of tRNAs
siRNA
short, derived from transposons, complementary to mRNA, inhibit translation of mRNA and enhance their degradation in RNA-induced silencing complexes (RISCs)
miRNA
like siRNA, short, involved in posttranscriptional regulation of gene expression
describe transposons
A transposable element (TE or transposon) is a DNA sequence that can change its position within a genome, sometimes creating or reversing mutations and altering the cell’s genetic identity and genome size.
Describe LTR retrotransposons
RNA is transcribed, then it is reverse transcribed into new DNA, then that DNA is inserted at another location on the DNA
Describe non-LTR retrotransposons
RNA is transcribed, then it is reverse transcribed directly into the genome.
Heterochromatin vs euchromatin
hetero-packed, less active;
eu; unpacked, more active
heterochromatin features
stains darkly, highly concentrated at centromeres and telomeres,
What residues on the histone complex interact with DNA?
Lysine and Arginine (1/5 of histone compilation; positive charge)
Histones are conserved?
histones are highly conserved, any mutation would likely be lethal
Describe HDAC
histone de-acetylase i think. These close the chromatin.
Inhibited by vorinostat, entinostat;
counteracts p53 by not allowing the trans factor to create p21
Which direction does DNA polymerase synthesize new DNA?
5’ to 3’;
it synthesizes in a bi-directional manner
describe cross linking and intercalating
intercalating is a positioning of an agent covalently between the base pairs
cross linking just links them?
Xeroderma pigmentosum is correlated with a defect in which repair mechanism?
Nucleotide excision repair NER
Hereditary nonpolyposis non-colorectal cancer is associated with a defect in which DNA repair mechanism
MER mismatch excision repair
BRCA1/2 breast cancers are associated with a defect in which DNA repair mechanism?
Recombinant repair
Cockayne syndrome is associated with a defect in which repair mechanism?
TCR transcription-coupled repair
Describe DNA glycosylases
at least six different types
each recognizes a specific type of altered base and catalyzes it’s removal
after base is removed then nuclease, lyase, polymerase, then ligase complete removal and replacement
DNA polymerase have with repair mechanisms attached to it?
DNA glycosylase and mismatch repair functions
