Functions and Dysfunctions of Genomic Regulation Flashcards
How does histone protein bind to DNA?
Hydrophobic Interactions and Salt Linkages
~20% of histone protein amino acid residues are Lysine (Lys) or Arginine (Arg).
Positive charges bind to negative backbone of DNA
Proteins that bind to DNA are divided into what two classes?
Histone Proteins
Non-histone chromosomal proteins (Transcription Factors)
How many histone proteins per nucleosome core particle?
Eight
_____ is protein in which DNA is wound.
What are the protein and DNA together referred to as?
Histone octamer
Protein + DNA = Chromatin
The lightly packed form of chromatin, highly enriched in genes and often under active transcription.
What percentage of the human genome is this type?
Chromatin
92%
What is very condensed chromatin, containing very few active genes?
Where is this found?
Heterochromatin (thought to be late replicating and genetically inactive)
Found at the centromeres and telemeres
What is the position effect?
Activity a gene depends on relative position on chromosome
Actively expressed genes will be silenced if relocated near heterochromatin
Why are mice great genetic models? What accounts for their differences?
90% amount of mouse genome is the same
99% of mouse genes have human analogues
Major proteomic differences
A lot of alternative splicing
What percentage of the genome is exons?
1.5%
What is comparative genome hybridization?
Detection of Copy Number Variations (1000 differences)
CGH is done through probing Human Genome CHIP with DNA from one person and comparing it to normal reference.
Being used clinically now and can detect copy number variation.
What are long terminal repeats and how do Virus’s utilize them?
Identical sequences of DNA repeat hundreds or thousands of times
Found at either end of retrotransposons (proviral DNA)
Formed by reverse transcription of retroviral RNA
Used by viruses to insert their genetic material into the
host genomes
How are ~100,000 proteins encoded by only 26,000 genes
Alternative splicing
15% of mutations affect this
What do 99% of introns begin and end with?
…GT…….AG…
How are histones activated?
How are they deactivated?
Acetylation - Histone Acetyl Transferases (HATS)
Deacetylation - Histone Deacetylase (HDAC)
How do HDACs and HATs directly regulate gene expression?
A ligand binds to a receptor and recruits a coactivator (HATs) after displacing a corepressor (HDACs).
This upregulates transcription factor associated proteins that acetylate the DNA
What on histones stands out for Post Translational Modification
Histone protein tails
How does DNA Methylation occur and on what DNA bases?
Methyl groups added to cytosine and adenine by methyltransferase enzymes
Represses Gene when at gene promoter.
What does DNA topoisomerase do?
Reversible enzyme
Breaks a phosphodiester bond
Changes superhelicity
Relieves supercoiling
Why are gene promoter CpG islands considered in carcinogenesis?
Acquire abnormal hypermethylation
Transcriptional silencing
Can be inherited by daughter cells following cell division
Methylation resulting in chromosomal instability and loss of imprinting.
Hypomethylation
What happens with Hypermethylation?
Associated with gene promoters
Can arise secondary to an oncogene suppressor promotor resulting in its suppression
Can be a epigenetic target for therapy
DNA polymerase requires ______ to begin processing.
a primer with a free 3’ -OH
What is DNA Helicase do?
Binds and hydrolyzes ATP
Pries apart DNA at 1000bp/sec
What do SSBP do?
Helps stabilize the unwound DNA
Prevents the formation of hairpins
What are the type one topoisomerase inhibitors and what do they do?
Inhibit topoisomerase I during the S phase
Irinotecan/Folfori- used in colorectal cancer
Type II Inhibitors of topoisomerase do what?
Etoposide, anthracyclines, doxorubicin, and daunorubocin
Etoposide causes secondary leukemias (dose dependent)
Anthracyclines cause cardiotoxicity (dose dependent)
What is a pyrimidine dimer and how is it formed?
UV radiation, produces covalent linkage between two adjacent pyrimidines (T-T or C-T)
What kind of damage can Ionization radiation cause?
Double-stranded breaks
What is Depuration and how often does it occur?
5000 purines lost per day
A purine is lost to an OH group.
Can lead to base deletion
What is deamination and how often does it occur?
A change from C to U, 100 Bases a day
Can lead to point mutations
Methylation of CpG Islands does what
Stably silences genes “some are related to cancer” and produces a T mismatched with a G
What removes the mismatched pairs due to CpG methylation?
A special glycosylase recognizes and removes the T
DNA repair is relatively ineffective in this case however
What percentage of C nucleotides are mutated?
How many point mutations does this account for?
3%
1/3 of all point mutations
Why are well-done meats dangerous?
Benzo(a)pyrene a procarcinogen and become BPDE (Carcinogen)
What crosslinking agents can cause DNA Damage
Nitrogen mustard
Cisplatin
Miomycin C
Carmustin
“NCMC”
What are the alkylating agents that can cause DNA damage?
Dimethyl sulfate
Methyl methanesulfonate
What Intercalating agents can cause cancer?
Thalidomide
Photoreactivation of thymine dimer
Photolyase corrects this with light
First step of Base Exclusion repair
The altered base is detected by DNA glycosylases
DNA glycosylase removes the base (hydrolyzes N-glycosidic bond)
Second Step of Base Exclusion repair
AP Endonuclease cuts phosphodiester bond
AP lyase removes deoxyribose phosphate
Third step of Nucleotide excision repair
DNA polymerase replaces the existing nucleotide
DNA ligase seals nick
NER complex does what
Is involved in Nucleotide excision repair (NER). Removes DNA segment, polymerase/ligase reform.
Faulty NER can cause what?
Xanderma pigmentosum, cockayne syndrome
What is MER?
Mismatch excision repair
The mismatch is recognized and daughter strand is cut out to remove it.
MutS and MutL excise DNA.
How are new strands distinguished in MER?
E.Coli uses methylation to distinguish strand
Eukaryotes use Okazaki fragments
Autosomal dominant mutation in MER causes this disease.
Hereditary nonpolyposis colorectal cancer.
Nonhomologous vs homologous recombination
Nonhomologous leads to end joining.
Homologous leads to using the sister chromatid as a template.
A drug that binds to the B subunit of RNA polymerase in bacterial cells
Rifampicin
What are the checkpoints that ensure the completion of one stage in the cell cycle before the next begins
Damage Delays
- G1 into S phase blocked
- Slows progression in S
- Blocks transition from G2 to M phase
What disease is characterized by a defective ATM protein, a protein kinase activated by double-strand breaks?
Ataxia telangiectasia
Leukemia, lymphoma, y-ray sensitivity
Defect in BRCA2 causes what?
Repair by homologous recombination compromised
Breast, ovaria, and prostate cancer
Caused by Defect in DNA interstrand cross-repair
Fanconi anemia froups A-G
Post-transcriptional mods can compete for action on _______
Lysine
A mechanism for regulating gene activity independent of DNA sequence that determines which genes are turned on or off.
What influences it?
Epigenetics
Precurser SUMO is turned into Mature SUMO how?
Sentrin proteases chop an XX domain on the enzyme, leaving a GG tail.
