Genomic Regulation Flashcards
Which residues in histone proteins are the target of post-translational modifications?
Lysine
How many histone proteins are in each nucleosome?
8 histone proteins
______ actively represses gene expression
Histone Deacetylation
______ actively promotes gene expression
Histone Acetylation
What kind of bonds are formed between DNA and the histone octamer?
Hydrogen bonds: hydrophobic interactions and salt linkages.
Which amino acid in histone proteins is the target of post-translational modifications?
Lysine
Protein+DNA=?
Chromatin
What variations are the basis for our differences and for disease states?
How to detect them?
Copy Number Variations (CNVs)
Comparative Genome Hybridization
almost all Introns begin with___ and end with___ nucleotide sequence
GT———AG
Which histone proteins have long tails protruding from the nucleosome?
H3 and H4 histones
Where are Methyl groups added to the DNA Molecules during DNA Methylation?
When does it repress gene transcription?
Cytosine and Adenine.
It represses gene transcription when at gene promoter.
What energy does DNA Helicase use to unwind DNA?
Hydrolyzes ATP. Enzyme consists of 6 subunits.
Which proteins help stabilize the unwound DNA and prevents the formation of hairpins during DNA Replication?
SSBP (Single Stranded DNA Binding Protein)
Which enzyme synthesizes RNA-DNA primer?
DNA Polymerase alpha(in complex with Primase)
Which enzyme(s) synthesize new DNA chain in the 5-3 direction? What is it called in prokaryotes?
DNA polymerase Gamma and e. DNA Pol III in Prokaryotes.
Which enzyme removes DNA Primer in eukaryotes? What about in prokaryotes?
Flap endonuclease 1 (FEN1). DNA Pol I in Prokaryotes.
Which enzyme fill sin gaps in Eukaryotes? Prokaryotes?
DNA Polymerase Gamma. DNA Pol I in prokaryotes.
What kind of bonds do DNA Topoiomerase break during the unwinding of DNA?
Phosphodiester bonds.
_______ acts as an competitive inhibitor of DNA Polymerase to stop DNA synthesis. Also used in treatment of Leukemia.
Arabinosylcytosine (Ara-C)
Which nucleoside analogs lack the 3’ OH group and act as chain terminators? Which one is used in treatment of HIV?
AZT and Acycloguanosine (acyclovir). AZT is used in treatment of HIV.
UV Radiation is considered a non-ionizing radiation. What kind of DNA Damage does it cause?
Pyrimidine dimers: example: Thymine dimers.
What are the 2 kinds of Spontaneous DNA Damage?
Depurination and Deamination.
What are the 3 nucleotides that get Deaminated? What is the final product for each one?
Adenine—–Hypoxanthine
Guanine—–Xanthine
Cytosine—–Uracil.
Deamination of Methyl-C converts into____? What enzyme fixes this problem?
Thymine. This will be mismatches with G.
A special DNA Glycosylase recognizes and removes the T.
Thymine Dimer is corrected by which DNA Repair mechanism?
Direct Repair: Photoreactivation. Used photolyase and light to remove the Thymine-Thymine bond.
What repair mechanism fixes single-base mismatches, and non distorting alterations? What enzymes does it use?
Base Excision Repair: DNA Glycosylase hydrolyzes the N-glycosidic bond for the altered base.
AP endonuclease cuts phosphodiester bond. DNA Pol beta replaces excised nucleotide and DNA Ligase seals nick.
What repair mechanism fixes chemical adduce that distort DNA (example Pyrimidine dimers)?
Nucleotide Excision Repair. NER complex recognizes distortions and nicks DNA on both sides of damage site.
Xeroderma Pigmentosum have defective proteins in which complex?
NER complex. This is utilized in the Nucleotide Excision Repair Mechanism.
What are the 2 enzymes in Mismatch Excision Repair and describe their function
MutS binds while MutL scans for the nick and triggers degradation of nicked strand.
Which gene is mutated in the Hereditary Nonpolyposis colorectal Cancer(HNPCC)
Also, how is this inherited?
There is an inherited mutation in the MER gene. HNPCC is inherited in an Autosomal Dominant Manner.
What are the 2 ways DNA is fixed during the Double Strand Break Repair?
Nonhomologous end joining and Homologous Recombination.
Name the disease caused by a defect in the the Transcription-coupled Repair?
Cockayne’s Syndrome.
What are the symptoms of Cockayne’s Syndrome?
Growth retardation, skeletal abnormalities, sensitivity to sunlight.
Name 2 HDAC inhibitors
Vorinostat, Valproic Acid
Where are CpG Islands usually found?
On the promoter region of the gene.
What kind of silencing occurs during hypermethylation of CpG Islands?
Transcriptional Silencing
Topoisomerase I Inhibitor
Irinotecan
Topoisomerase II Inhibitor
Etoposisde.
Which type of RNA molecules inhibit gene expression or translation?
miRNA
