Genomic Regulation Flashcards
What are the 3 roles of the nucleus?
Cell regulation
Proliferation
DNA transcription
Describe the central dogma of genetics.
DNA -> RNA -> Protein
DNA –> RNA (transcription)
RNA –> Protein (translation)
Which part of the central dogma does RNA virus such as HIV affect? What is the enzyme this virus utilizes?
DNA –> RNA (Transcription)
Reverse Transcriptase
Why are mitotic chromosomes condensed 500 times more than interphase chromosomes?
To prevent physical damage to the DNA as chromosomes are separated and passed on to daughter cells.
How is DNA packaged? (Hint: What kinds of bonds are used, there are 3 of them)
DNA hydrogen bonds with the histone octamer in each nucleosome.
2 other bonds include hydrophobic interactions and Salt linkages
______ _____ are highly conserved across species.
Histone proteins
Theres only a 2 amino acid difference between a pea and a cow histone H4
What is the charge of histones? Why is this important?
Positive, this is important because DNA is negative and therefore binds to positively charged histones
Histones have many Lysine and Arginine Amino acids
Which part of the histone is targeted for post-translational modifications?
Lysine residues
____ are the basic unit of chromosome packing
Nucleosomes
Proteins that bind to DNA are made up of what two classes?
Histones
Non-histone chromosomal proteins (transcription factors)
Each nucleosome core particle consists of a complex of ____ ____ ____
Eight histone proteins
What are the 2 components of a chromatin? What does this form?
Protein and DNA
This forms beads on a string
TF Euchromatin is often under active transcription
True
What two places of the chromosome are heterochromatins concentrated?
At the centromeres and telomeres
Long Terminal Repeats (LTRs) are formed by what enzyme?
What are they used for?
Reverse Transcriptase of retroviral RNA
Used by viruses to insert their genetic material into the hosts genomes
What does DNA polymerase require to begin the replication process?
DNA Polymerase requires a free 3’ -OH group to begin the replication process
During replication, which strand is synthesized continuously and which in segments?
Leading strand is synthesized continuously
Lagging strand is synthesized in segments
What is the function of Single-Stranded DNA Binding Proteins (SSBP)? What does this prevent the formation of?
They bind cooperatively to exposed ssDNA and stabilize them. This prevents the formation of hairpins.
During DNA replication, the replication fork creates an un-winding problem for the parental helix. What enzyme is utilized to relieve this stress?
what enzyme is this called in bacteria?
Topoisomerase relieves this supercoil
AKA as DNA Gyrase in bacteria
How can Topoisomerase Inhibitors be used to prevent cancers?
What does do Topoisomerase Inhibitors lead to?
Without Topoisomerases activity, the cell cycle is blocked and generates single and double stranded breaks, which harms the integrity of the genome.
This leads to apoptosis and death of the cancer cell
Does DNA Polymerase have the ability to proofread DNA?
Yes
Differentiate between Germ cells and Somatic cells in terms of mutation rates and how this affects the organism.
Germ cells have low mutation rates in order to maintain the species
Somatic cells have low mutations rates to avoid cancer
What is the function of Histone Deacetylase (HDAC)?
What is the function of Histone Acetylase (HAT)?
Histone Deacetylase (HDAC) is used to repress gene expression by compacting the chromatin
Histone Acetylase is used to activate gene expression by opening the chromatin and making it transcriptionally active
What kinds of modifications do histone proteins undergo?
Post-Translational Modifications
What are the 4 components of a histone?
H2A
H2B
H3
H4
Which 2 components of the histone protein have long tails protruding from the nucleosome?
H3 and H4
What are the 7 types of Post-Translational Modifications?
Methylation Acetylation Phosphorylation Ubiquitination SUMOylation Citrullination ADP-ribosylation
Differentiate between the 2 types of spontaneous DNA damage, Depurination and Deamination?
Depurination- losing a Guanine or an Adenine
Deamination- oxidizing an amino side chain. Can be Adenine -> Hypoxanthine, Guanine to Xanthine, or Cytosine to Uracil** (main one)
What are the repercussions following depurination and deamination?
Depurination- If an adenine is removed, after DNA replication the mutated strand will cut out the Thymine therefore causing an A-T nucleotide pair to be deleted and shortening the sequence by 1bp. The conserved sequence will fix the damage by adding another adenine.
Deamination- If a cytosine is changed to a uracil, after DNA replication occurs the mutated strand will have a Uracil bound to an Adenine when the proper pair should be Cytosine bound to Guanine.
What is the problem with methylated cytosine residues in Cytosine-phosphate-Guanine (CpG) islands? How is this fixed and what nucleotide is the methylated cytosine converted into?
Methylation of CpG islands stably silences genes (whether they be cancer or DNA repair genes)
Methylated Cytosine is deaminated to produce Thymine that is mismatched with Guanine.
DNA glycosylase removes the Thymine.
Define the type of damage that is repaired by the process Direct Repair.
Pyrimidine dimers are repaired through this process.
Define the type of damage that is repaired by the process Base Excision Repair.
Single-base mismatches
Non-distorting Alterations (Ex. Depurination)
Define the type of damage that is repaired by the process Nucleotide Excision Repair. What disease does this cause?
Removing the entire nucleotide
Xeroderma Pigmentosum
Define the type of damage that is repaired by the process Mismatch Excision Repair. What are the enzymes involved? What disease does this cause?
Mismatched daughter strand
MutS and MutL, DNA Polymerase, and DNA Ligase
Hereditary Nonpolyposis Colorectal Cancers
Define the type of damage that is repaired by the process Recombination Repair (Both non-homologous and homologous recombination). What disease does this cause?
Double stranded breaks and interstrand cross-linking
Leads to BRCA1/2 breast cancer (Homologous Recombination only)
Define the type of damage that is repaired by the process Transcription-Coupled Repair. What disease does this lead to?
Stalled RNA polymerase during transcription (Note-not during replication***)
Causes Cockayne Syndrome
What does Xeroderma Pigmentosum cause? What process is affected?
Skin cancer and UV sensitivity
Nucleotide Excision Repair is affected
What does Ataxia Telangiectasia cause? What is defective in patients suffering from this?
Causes Leukemia, Lymphoma, gamma-ray sensitivity
ATM protein (a protein kinse activated by double strand breaks) is mutated
ATM stands for Ataxia Telangiectasia Mutated protein
What does BCRA2 cause? What is the repair process defective?
Breast, Ovarian, and Prostate Cancer
Repaired by homologous recombination
What does Fanconi Anemia cause? What is the repair process affected?
Congenital abnormalities, Leukemia
DNA interstrand cross-link repair (remember that this is from both non-homologous and homologous combination)
Describe the process of Direct repair to correct Thymine Dimers.
Thymine dimer occurs on DNA strand
Photolyase excises the dimer
Describe the Base Excision Repair process. Be sure to note key enzymes.
Deaminated Cytosine is converted to a Uracil, which is wrongly base paired to Guanine
Uracil DNA Glycosylase removes the Uracil base
AP Endonuclease and Phosphodiesterase remove the Sugar Phosphate
DNA Polymerase adds the new, correct nucleotide
DNA Ligase seals the nick in the double helix
Describe the Nucleotide Excision Repair process. Be sure to note key enzymes.
Pyrimidine Dimer forms on one side of the DNA strand
Excision Nuclease creates a nick on either side of the Pyrimidine Dimer (note that this incorporates a few nucleotides on either end to ensure the whole dimer is removed)
DNA Helicase unzips the pyrimidine dimer and extra nucleotides and removes it from the DNA strand
DNA Polymerase and DNA Ligase lay down the correct nucleotides and fill in the gaps
*Note that this is similar to Direct Repair, but this process does not act directly on the Pyrimidine Dimer, but instead on the DNA strand surrounding the dimer
Describe the Mismatch Excision Repair (MER) process. Be sure to note key enzymes.
DNA-Dependent DNA Polymerase proofreads the DNA and removes (almost all) errors missed
MutS binds with MutL and scans for nicks within the DNA strand and if one is found it triggers degradation of the nicked strand
DNA Polymerase and DNA Ligase lay the correct nucleotides and fills in the gaps
Note that MER only occurs for incorrectly paired bases for the newly synthesized daughter strand
What are the 3 causes of double stranded breaks?
Ionizing radiation
Replication errors
Oxidizing agents
What are the 2 mechanisms used to repair double stranded breaks?
Non-homologous End Joining- Nick in the ds leads to nucleotides being lost in both directions from each nick and then these nucleotides are ligated together. This leads to a deletion in the DNA sequence.
Homologous Recombination- Nicks in the ds lead to the loss of nucleotides due to degradation from both ends of the each nick. The sister chromatic is then used to provide the information to correctly repair the missing nucleotide pieces. End result is a completely repaired chromosome.
Describe the Transcription-Coupled Repair process.
What 2 types of repair process utilizes this?
What disease is associated with this repair process?
If there is an issue with the DNA strand, cells can direct RNA Polymerases to stall at the issue and repair the machinery there.
The two process that utilize this type of repair is:
Base Excision Repair
Nucleotide Excision Repair
Cockaynes Syndrome is associated with this repair process- due to RNA Polymerase permanently being stalled at sites of damage in important genes
What are the 3 checkpoints of the cell cycle?
G1 to S Phase
S Phase
G2 to M Phase
What is the function of Histone Deacetylases (HDACs)?
Enzymes that remove acetyl groups from the lysines on core histones
How does DNA Methylation affect gene transctription?
Where do they typically occur? Hint: What kind of sites?
It represses gene transcription when at the gene promoter
Usually occurs within CpG sites, which are typically proximal to the start of transcription
What amino acid residue does Ubiquitin attach to on target proteins?
Lysine
What are the 3 types of chemical agents that cause DNA damage?
Cross-linking agents
Alkylating agents
Intercalating agents (Ex. Thalidomide)- found in the major groove of DNA
