Functions and Dysfunctions in Genomic Regulation Flashcards
Nucleus:
- % volume in cell
- # in cell
- roles in cell
6%
1
cell regulation, proliferation, DNA transcription
bond between G and C nucleotides
triple bond
why are mitotic chromosomes condensed 500x more than interphase chromosomes
to prevent physical damage to the DNA as chromosomes are separated and passed on to daughter cells
what interactions and linkages are between DNA and its histone octamer in each nucleosome
hydrophobic interactions
salt linkages
20% of histone protein AA residues are what two AA
lysine and arginine
each nucleosome core particle consists of a complex of how many histone proteins
8
protein + DNA =
chromatin
“beads on a string”
euchromatin
loosely packed form of chromatin (DNA, RNA, and protein)
most active part of the genome
92% of human genome
often under active transcription
heterochromatin
very condensed chromatin
late replicating and genetically inactive
highly condensed at centromeres and telomeres
contains very few active genes
will silence a gene if it is relocated in close proximity
position effect
activity of a gene depends on its relative position on a chromosome
what percentage of the genome is responsible for coding
1.5%
comparative genome hybridization
detecting variations in people’s genomes
probes human genome CHPI with DNA from one person and with DNA from a “normal” reference
detects the copy number variation
personalized medicine
RNAi
RNA interference
a biological process in which RNA molecules (miRNA) inhibit gene expression or translation
neutralizes targeted mRNA molecules
“fine tuning gene expression”
long terminal repeats (LTRs)
identical sequences of DNA that are repeated 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 host genomes
microRNA (miRNA)
form of gene expression regulation
forms an miRNA protein complex that can prevent gene expression by either degrading the target mRNA or by blocking its translation
mechanism:
- miRNA folds back on itself and forms H bonds
- Dicer cuts strand into small segments
- one half of small segments is degraded, the other associates with a protein to form the complex
99% of all introns begin with ___ and end with ___
begin with GT
end with AG
histone deacetylase (HDAC)
co-repressor that actively represses gene expression
removes the acetyl group from lysines on core histones and non histone proteins
the chromatin then becomes compact and transcriptionally repressed
“beads are wound tight on the string”
histone acetyl transferase (HAT)
co-activator that actively promotes gene expression
acetylates the chromatin which allows it to become open and transcriptionally active
“the beads are wound loosely on the string”
what does DNA methylation at a gene promoter do
represses the gene transcription
essential for normal development
what do gene promoter CpG islands do
transcriptional silencing
acquire abnormal hypermethylation
can be inherited by daughter cells following cell division
what does hypo methylation cause
chromosomal instability
loss of imprinting
large problem with hypermethylation
can silence oncogene suppressors, causing cancer
what does DNA polymerase require to begin processing
a primer with a free 3’-OH
single stranded DNA-binding protein (SSBP)
binds cooperatively to exposed ssDNA to help stabilize the unwound DNA and prevent the formation of hairpins
topoisomerase
relieves the overwound supercoils in bacteria
breaks a phosphodiester bond, changes superhelicity
DNA gyrase
DNA topoisomerase in bacteria
Irinotecan
- used to treat what
topoisomerase inhibitor
used to treat colorectal cancer
Etoposisde
- used to treat what
topoisomerase inhibitor
anti-cancer drug that can cause secondary leukemias
anthracyclines
- used to treat what
topoisomerase II inhibitor
anti-cancer drug that can cause cardiotoxicity
how is UV radiation harmful to DNA
UV radiation from the sun can produce a covalent linkage between two adjacent pyrimidines (TT or C-T)
pyrimidine dimers
depurination
a type of spontaneous DNA damage; 5000 purine bases can be lost per day
the N terminus of the sugar is cleaved and replaced with an OH group which cannot bind to the base and form a nucleotide
deamination
a type of spontaneous DNA damage which causes C bases to change to U bases; about 100 bases per day
requires H2O input and releases NH3
adenine –> hypoxanthine
guanine –> xanthine
cytosine –> uracil
what happens to deamination of methyl-C in CpG islands
it produces a T mismatched with a G
needs a special DNA glycosylase to recognize this and remove the T
DNA repair is still relatively ineffective however
BPDE
a carcinogenic metabolite formed from benzo(a)pyrene
cross-linking agent and intercalating agents
adduct (N-H) formed between guanine and benzo(a)pyrene to form BPDE; it then acts as a DNA transcription repressor
benzo(a)pyrene
a pro-carcinogen that can form the metabolite BPDE which is a carcinogen
what do nitrogen mustard cisplatin mytomycin C carmustine have in common?
they are all cross-linking agents
what do dimethyl sulfate (DMS) and methyl methanesulfonate (MMS) have in common
they are alkylating agents
Thalidomide
a intercalating agent
prescribed for pregnant women to treat morning sickness
less to birth defects such as loss of or shortening of limbs
Xeroderma pigmentosum
a disease caused by a defect in the nucleotide excision repair complex; patients cannot repair cyclobutane thymine dimers caused by UV sunlight
sx:
- very sensitive skin to sunlight
- prone to developing melanomas
- prone to squamous cell carcinomas
hereditary nonpolyposis colorectal cancers
caused by a mutation in one of the alleles of genes in the mismatch excision repair complex
cockayne syndrome
result of mutations in ERCC6 and ERCC8 that code for ERCC-6 and ERCC-8 proteins that are involved in the TCR of DNA
defect in transcription-coupled repair
sx: neurological delay
- photosensitivity
- progeria (premature aging)
- hearing loss
- eye abnormalities
- death in first two decades
BRCA mutations
BRCA1 and BRCA2 are tumor suppressor genes
increased risk for breast cancer
women: cervical, uterine, pancreatic, colon
men: pancreatic, testicular, early prostate cancer
direct repair mechanism (enzymatic repair)
repairs pyrimidine dimers
base excision repair (BER)
repairs single base mismatches
nucleotide excision repair (NER)
- what does it do
- what does it use
- disease
repairs chemical adducts that distort DNA
- pyrimidine dimers
- BPDE-guanine adducts
- cisplatin adducts
uses NER protein complex, DNA polymerase, DNA ligase
mutations cause xeroderma pigmentosum
mismatch excision repair (MER)
- what does it do
- what does it use
- disease
repair mismatched bases in daughter strand
uses MER complex (MSH2 and MSH6), helicase, DNA polymerase, DNA ligase
mutations can cause hereditary nonpolyposis colorectal cancers
recombination repair
- what does it do
- what does it use
- disease
repairs double strand breaks and interstrand cross linking
uses exonucleases, DNA polymerase, MER system
mutations can cause BRCA1/2 breast cancer
transcription coupled repair (TCR)
- what does it do
- disease
stalls RNA polymerase during transcription (not replication) and repairs it; used on sequences that urgently need repair
works with base excision repair and nucleotide excision repair
mutations can cause Cockayne syndrome
translesion synthesis (bypass synthesis)
- what does it do
- what does it use
repairs thymine dimers or apurini AP sites
uses DNA polymerases
MSH2, 3, 6, MLH1, PMS2 genetic defects
- phenotype
- process affected
colon cancer
mismatch repair
ataxia telangiectasia (AT)
- phenotype
- enzyme affected
leukemia, lymphoma, gamma ray sensitivity, genome instability
ATM protein (activated by double strand breaks)
BRCA2
- process affected
affects repair by homologous recombination
fanconi anemia groups A-G
- phenotype
- process effected
congenital abnormalities, leukemia, genome instability
DNA interstrand cross-link repair
base excision repair
replacing missing base in the genome
nucleotide excision repair
removes distorted DNA segment and replaces it
mismatch excision repair
MutS and MutL bind and trigger degradation of the nicked strand –> strand removal –> repair DNA synthesis
Rifampicin
an antibiotic that inhibits RNA synthesis in bacterial cells; prevents translation
side effects include:
- regulation of hepatic cytochrome P-450 enzymes (CYP-3A4 and (CYP-2C9) and thus an increase in the metabolism of other drugs and hormones
DNA methylation in humans
occurs at the 5 position of the pyrimidine ring of cytosine
forms 5-methylcytosines
ubiquitin
marks a protein for degradation
exists in all eukaryotic cells
attached to lysine residues on target proteins
SUMOylation cycle
Small Ubiquitin Like Modifier
post-translational modification involved in various cellular processes, such as nuclear-cytosolic transport, transcriptional regulation, apoptosis, protein stability, response to stress, and progression through the cell cycle
SUMO-targeted ubiquitin ligases (STUbLs)
add the ubiquitin to the protein for degradation
can be mediated by RNF4 gene in humans
how do topoisomerase inhibitors act as anti cancer agents (4 ways)
- block the cell cycle
- generate single and double stranded breaks
- harm the integrity of the genome
- lead to apoptosis and death
intercalating agent
inserts molecules between the bases of DNA; causes DNA damage
inhibitors of HAT have shown promise in treating:
Alzheimer’s disease
Rheumatoid Arthritis
inhibitors of HDACs:
- two examples
- what are they used for
valproic acid
vorinostat
anticonvulsives and anticancer drugs
