Genomic Regulation Flashcards
What is the central dogma of genetics?
***DNA transcribes to RNA which translates to proteins
DNA can replicate via mitosis
RNA can be reverse transcribed into DNA
DNA is double-stranded and anti-parallel. These strands are connected ________ bonds.
Hydrogen bonds
What does the backbone of DNA consist of?
Sugar-Phosphate
Mitotic chromosomes are condensed 500 times when compared with interphase chromosomes. Why?
To prevent physical damage to the DNA as chromosomes are separated and passed on to daughter cells
DNA is wound around what proteins?
Histones
Approximately 20 percent of histone protein amino acid residues are either _______ or _______. A lot of positive charges, which attract to the negatively charged backbone.
Lysine
Arginine
Lysine residues in histone proteins are the target of what?
Post-translational modifications (PTMs)
How many proteins make up a histone?
8 (octamer)
These are the basic unit of chromosome packing. Includes core histone particle and linker DNA.
Nucleosomes
Protein and DNA make up what?
Chromatin (“beads on a string”)
This is the lightly packed form of chromatin and is highly enriched in genes. Often (but not always) under active transcription.
Euchromatin
This is very condensed chromatin thought to be late replicating and genetically inactive.
Heterochromatin
In Feb. 2001 the sequence of the human genome was announced, but it was only 90 percent of sequence. It was finished in 2004. It involved 2000 people at the cost of 1 billion dollars. This project was called…
The Human Genome Project
About how many genes are in the genome?
26,000
What percentage of the genome is responsible for coding?
1.5 percent
People usually have 1,000 differences in their genome, which are called…
Copy number variations (CNVs)
CNVs are the basis for our differences and for disease states. How are they detected?
Comparative genome hybridization
In ________ ________ ________, we probe human genome CHIP with DNA from one person and with DNA from a ‘normal’ reference DNA. Then it detects copy number variation. Used now clinically.
Comparative genome hybridization
This is the term for the biological process in which RNA molecules inhibit gene expression, or translation by neutralizing targeted mRNA molecules.
RNAi (RNA interference)
This is the term for identical sequences of DNA that are repeated hundreds or thousands of times. They’re found at either end of retrotransposons (proviral DNA) and are formed by reverse transcription of retroviral RNA.
LTRs (Long terminal repeats)
What are long terminal repeats (LTRs) in viruses used for?
To insert their genetic material into the host genomes
This type of RNA is responsible for preventing gene expression by blocking translation or degrading the mRNA.
miRNA
This enzyme is responsible for cutting miRNA into shorter segments.
Dicer
This enzyme unwinds the DNA helix.
Helicase
This enzyme relieves overwound supercoils (called DNA gyrase in bacteria).
Topoisomerase
This enzyme helps stabilize the unwound DNA. It prevents the formation of hairpins, but keeps the DNA bases exposed.
Single-stranded DNA-binding protein
This enzyme synthesizes RNA-DNA primer.
DNA polymerase alpha
This enzyme synthesizes new DNA chain in the 5’-3’ direction.
DNA polymerases d and e
This enzyme fills in gap in DNA replication.
DNA polymerase d
This enzyme seals nicks in DNA replication.
DNA ligase
Because DNA synthesis involves the formation of 3’-5’ phosphodiester bonds, nucleoside analogues that lack the _______ group act as drugs that inhibit DNA replication. Such nucleosides need to be converted to _______ before they can act as inhibitors of DNA polymerase.
3’ -OH
dNTPs
***Correlation Box: Nucleoside analogue inhibitors (324)
Give some examples of nucleoside analogue inhibitors of DNA synthesis.
ara-C – used in leukemia treatment
Acyclovir – used in chicken pox, herpes, shingles, etc.
AZT – used in HIV therapy
This histone modification can activate or deactivate (loosen or tighten) DNA, but if this is done directly to DNA then it is deactivated.
Methylation
***Added to cytosine and adenine on DNA molecule
This histone modification relaxes their association with DNA, making DNA available for transcription.
Acetylation
This histone modification is a critical intermediate step in chromosome condensation during cell division, transcriptional regulation, and DNA damage repair.
Phosphorylation
DNA polymerase synthesizes DNA in what direction?
5’ to 3’
DNA polymerase requires a primer with a free _______ to begin processing.
3’ -OH
The _______ strand has continuous synthesis, and the _______ strand has discontinuous synthesis in DNA replication.
Leading
Lagging
The lagging strand creates fragments called…
Okazaki fragments
DNA helicase is a protein with 6 identical subunits and binds and hydrolyzes ______ to propel itself forward like a rotary engine.
ATP
Pharmaceutical drugs that target this enzyme of DNA replication, are used as anti-cancer agents.
DNA topoisomerase
Why are topoisomerase inhibitors used as anti-cancer agents?
- Block the cell cycle
- Generate single and double stranded breaks
- Harms the integrity of the genome
- Leads to apoptosis and cancer cell death
_______ cells have low mutation rates – maintain species.
Germ
_______ cells have low mutation rates – avoid uncontrolled proliferation/cancer.
Somatic
If there is a mutation in replication, we have “spell check” or proofreading thanks to what enzyme?
DNA polymerase
What enzyme is responsible for deacetylation of histones?
Histone Deacetylase (HDAC)
***Represses gene expression
What enzyme is responsible for acetylation of histones?
Histone Acetyl Transferase (HAT)
***Activates gene expression
Genes can be repressed by deacetylation blocking the ________ _______ signal from its appropriate ligand. Acetylation removes this block and allows the ligand to bind, stimulating the gene.
Nuclear receptor
Histone proteins H3 and H4 have long protruding tails from the nucleosome that often are the target for what?
Post-Translational Modification (PTM)
DNA damage can occur from exposure to reactive forms of _____ in the cell or chemicals in the environment.
O2
This type of DNA damage is due to UV radiation from the sun, which can produce a covalent linkage between two adjacent _________, called _______ _______.
Pyrimidines (T-T or C-T)
Pyrimidine dimers
DNA damage via UV radiation is also called…
Non-ionizing radiation
Ionizing radiation (i.e., X-rays) and the resulting reactive oxygen species can induce what changes in DNA?
- Strand breaks
- 40-60 chemical modifications of bases
- DNA-protein cross-links (i.e., Thymine-Tyrosine cross-link)
Depurination and deamination are examples of what type of DNA damage?
Spontaneous
In ________, the purine base is removed from the nucleotide via hydrolysis of the N-glycosidic bond between the base and the deoxyribose group. Creates a sugar-phosphate by itself. 5000 purines lost per day.
Depurination
In ________, the amino group of purine or pyrimidine base is hydrolyzed such that adenine is converted to hypoxanthine, guanine is converted to xanthine, and cytosine is converted to uracil, which forms an unnatural deoxyuridine.
Deamination
What are the possible outcomes of spontaneous DNA damage?
- DNA replication ensues
- - Base deletion or substitution
The methylation of ______ ______ can stably silence genes (cancer/DNA repair genes). However, the deamination of these can produce a mismatched _____ with _____.
CpG islands
T
G
This is an epoxide that is considered a carcinogen. It is due to well-done grilled meats.
BPDE
What is the pro-carcinogen that forms BPDE?
benzo[a]pyrene
List some of the cross-linking agents.
Nitrogen mustard
Cisplatin
Mitomycin C
List some alkylating agents.
Diemthylsulfate (DMS)
Methylmethanesulfonate (MMS)
List some intercalating agents.
Ethidium bromide
Thalidomide (caused major birth defects)
Doxorubicin
Xeroderma pigmentosum is a disease caused by a defect in what kind of repair mechanism?
Nucleotide excision repair
The skin of people with this disease is extremely sensitive to sunlight, and they are prone to developing melanomas and squamous cell carcinomas. The UV component of sunlight causes thymine dimers to form in the DNA. These can be removed by NER in normal individuals, but defects in certain proteins in the NER complex exhibit the disease.
Xeroderma pigmentosum
Hereditary nonpolyposis colorectal cancers are due to a defect in what kind of repair mechanism?
Mismatch excision repair
This type of disease is caused my mismatch excision repair, which normally fixes a mismatched base in the daughter strand. Individuals with inherited mutations in one of the alleles of genes in the MER complex have an increased chance of getting disease. An acquired mutation in the remaining good gene would then render the MER system nonfunctional, allowing the disease to occur. Autosomal dominant.
Hereditary nonpolyposis colorectal cancers
This type of recombination repair is responsible for the BRCA1/2 gene in breast cancer.
Homologous recombination
What are the types of recombination repair that fix double-strand breaks and inter strand cross-linking?
NHEJ (Non-homologous end joining)
Homologous recombination
This type of repair mechanism will also fix pyrimidine dimers.
Direct repair (enzymatic repair)
This type of repair mechanism will fix single-base mismatches and non distorting alterations (i.e., depurination).
Base excision repair (BER)
This disease occurs by a defect in transcription-coupled repair. Normally, TCR will fix a stalled RNA polymerase during transcription. However, the genes ERCC6 and ERCC8 become mutated, which would usually help in TCR of DNA. This disease causes developmental and neurologic delays, photosensitivity, and progeria. Autosomal recessive.
Cockayne syndrome
BRCA1/2 are (ONCOGENES/TUMOR SUPPRESSORS). Mutations of these genes cause a fivefold increase in women’s risk of developing breast and/or ovarian cancer before menopause.
Tumor suppressors
This type of repair mechanism will fix unprepared thymine dimers or apurini AP sites.
Translation synthesis (bypass synthesis)
This type of repair mechanism will fix stalled RNA polymerase during transcription (not replication).
Transcription-coupled repair (TCR)
In mismatch excision repair, proofreading is done by DNA-dependent ______ ______, which removes almost all errors missed. ______ binds while ______ scans for the nick and triggers degradation of nicked strand.
DNA polymerase
MutS
MutL
In this type of recombination, the broken ends of DNA are brought together and rejoin by DNA ligation. One or more nucleotides are lost.
NHEJ
What happens A, G, and C are deaminated, respectively?
Forms Hypoxanthine, Xanthine, and Uracil
What happens when a depurination occurs?
Cut out A/G
Ionizing radiation often causes what in DNA?
Strand breaks
This is what tags proteins to be degraded. It attaches to lysine residue on target proteins.
Ubiquitin
This process is analogous to ubiquitin, but it does not “tag” proteins for degradation. The protein will bind when the final four proteins are cleaved from C-terminus.
SUMOylation
