Genomic Regulation Flashcards
What are the three types of DNA damage?
spontaneous, physical agents (radiation) and chemical agents (direct and indirect)
Describe spontaneous DNA damage
The most frequent type happens on a daily basis
Most frequent examples: deamination and depurination
What are the two types of radiation caused DNA damage?
Ionizing and non-ionizing
Describe non-ionizing radiation damage
UV radiation/UV induced DNA damage
Formation of pyrimidine dimers (T-T dimers)
Describe ionizing radiation DNA damage
Have high energy photons (like x or gamma ray)
Damage includes direct (bond breaking) or indirect (H2O hydrolysis and free radical formation)
What are the different types of ionizing radiation induced DNA damage?
Base damage, double and single stranded breaks, intercalation, inter-strand and intra-strand cross linkage, DNA-protein or protein-protein crosslink
What is the most common and most damaging type of ionizing radiation induced DNA damage?
double stranded breaks
What are the two types of chemical agents that can cause DNA damage?
Direct and indirect
What are direct chemical agents?
Agents that act directly to modify DNA
ex. Cross-linking agents, alkylating agents, intercalating agents
What do cross linking chemical agents do to DNA?
makes covalent bonds which prevents the strands from opening
ex. nitrogen gas, cisplatin, mitomycin and camustine
What do alkylating chemical agents do to DNA?
add a methyl group to the DNA bases
ex. dimethyl sulfate, methyl methanesulfonate
What do intercalating chemical agents do to DNA
Kills cancer cells by damaging their DNA (but can be harmful to our cells too)
ex. ethidium bromide, thalidomide, daunomycin, doxorubicin
What are indirect chemical agents?
Agents that require metabolic activation
ex. BPDE and aflatoxin which both turn into epoxides (complexes of benzene rings that form adducts between guanine bases)
Cytochrome P450 takes care of a lot of these
What are the 4 major types of genome alterations?
Chromosomal mutations, transposons, single nucleotide polymorphisms (SNP) and gene amplification
What are the 4 types of chromosome mutations?
deletions, translocation, duplication, and inversion
What is a deletion?
chromosome segment is lost
What is a translocation?
segment of chromosome is transferred to another
What is a duplication?
a segment from one chromosome is transferred to its homologous chromosome giving it a duplicate of some genes
What is an inversion?
Segment of chromosome arm is inverted
What is an example of a chromosome mutation?
Translocations can cause Down Syndrome (4% of pts with Down syndrome)
What are transposons?
Jumping genes
Mobile sequences of DNA that can change position within genome of a single cell
copy, cut and paste
Retrotransposons (reverse transcription) and DNA transposons (section gets cut and pasted in a different spot)
What is an example of a disease caused by transposons?
Hemophilia A which is a hereditary bleeding disorder caused by lack of blood clotting factor 8
W/out enough factor 8 blood cannot properly clot to control bleeding
Transposon L1: inserted into factor 8 gene and makes it ineffective
What are single nucleotide polymorphisms (SNP)?
Not mutations but can act like them
Are uncommon alterations in the DNA
A common inherited change in a single bp that occurs in at least 1-5% of the population
Occurs once every 1000-2000 its
Used to make markers in the mapping of genomes and also in drug development
May be associate with susceptibility to disease
What is gene amplification?
All the 3 previous types of genome alterations can lead to gene amplification
Other cause can be impaired replication
It can be good (more copies of the gene = less selective pressure/less mutational effects in evolution)
In diseases such as cancer and cancer therapy resistance
What are the two main outcomes of DNA repair?
DNA is repaired and normal cell function is repaired
DNA is not repaired or inappropriate response to damage occurs due to defects in DNA repair and/or damage detecting mechanisms
What are the two consequences of DNA not being repaired due to an inappropriate response to the damage or faulty repair mechanism?
Deleterious consequences
No deleterious consequences in which the cell normal cell function is regained
What are the deleterious consequences of faulty DNA repair?
Impaired cell function or cell death which lead to impaired function in the organism
Mutations or genetic instability which leads to cancer
What is the general scheme of action for DNA repair systems?
Recognize damaged DNA strand
Excision of damage
DNA polymerase makes repair
DNA ligase seals nick (religate)
What kind of damage does direct repair fix?
UV damage: adjacent pyrimidines (ex. thymine dimers)
Alkylating mutagens
How does direct repair fix UV damage?
Can be repaired by NER
Photolyase repairs the thymine dimers in other organisms however humans lack this enzyme
How does direct repair fix alkylating mutagens?
Enzyme: methyltransferase
Moves the alkylating methyl from the DNA to itself repairing the DNA
What type of damage is repaired with BER?
Single base mismatches, small non-distorting alterations, spontaneous dupurination and spontaneous deamination, uracil, 8-oxoguanine, 3-methyladenine and basic sites
Describe the process of BER
Altered base detected by DNA glycosylase which then removes the base
AP endonuclease cuts phosphodiester bond
AP lyase removes deoxyribose phosphate
DNA polymerase beta replaced excised nt
DNA ligase seals nick
What type of damaged is repaired in NER?
Chemical adducts, alteration in DNA shape in a local area and UV, BPDE-gaunine adducts as well as cisplatin adducts
What is Xeroderma Pigmentosum?
Genetic disorder of DNA repair in which pts carry mutation in the nt repair enzymes mostly an endonuclease
sx: high sensitivity to light, pigmentary skin changes, prone to developing melanomas and squamous cell carcinomas
Autosomal recessive
Defect in NER complex XP proteins (XP-A thru XP-G)
Describe the process of NER
NER complex recognizes distortions and nicks DNA on both sides of damage site
Remove stretch of DNA w/ damage
DNA pol epsilon fills the gap
DNA ligase seals the nick
What type of damage is repaired with transcription coupled repair (TCR) (a form of NER)?
RNA pol stalled at a lesion in DNA
TCR proteins called ERCC-6 and ERC8: recognize stalled RNA pol and recruit repair proteins
What is Cockanye syndrome?
Autosomal recessive
Mutant genes: ERCC6 and ERCC8 (TCR)
sx: neurologic delay, photosensitivity and progeria (premature aging)
Also common: hearing loss and eye abnormalities
What type of damage is repaired with mismatch repair mechanisms (MER)?
During DNA replication, mismatched nt occasionally gets inserted into the newly synthesized daughter strand
What is hereditary non-polyposis colorectal cancer?
Lynch syndrome
Mutations in one of the alleles of genes in MER complex
Accumulation of unrepaired DNA damage leads to genomic instability –> cancer
What type of damage is repaired with recombination repair mechanism?
Double stranded breaks
Radiation and chemical damage
What are the two types of recombination repair?
NHEJ and homologous repair
What damage is repaired with NHEJ?
Chromosomal translocation and neoplastic chromosomal rearrangements
Explain NHEJ
DNA PK and Ku proteins bind to the double stranded break
Nucleosome removes bases from both ends
Ligase joins ends together
What is homologous recombination (HR)?
Needs a template
Occurs after DNA replication and before cell division
ex. Breast cancer
Explain breast cancer and its association with HR
Susceptibility genes (BRCA1 and 2): associated with hereditary breast cancer encode proteins that facilitate HR 5x increased risk of developing breast cancer and other cancers
What are the exceptions of the genetic code that occur in the mitochondria?
Codons AUA and AUU code for Met instead of Ile
AGA and AGG are stop codons instead of Arg
The standard stop codon UGA codes for Trp instead
Mutations in the coding region (also called open reading frame ORF) lead to what?
To different AAs being incorporated into the protein
To different outcomes categorized into 4 types of point mutations
What are the 4 types of point mutations seen in coding regions?
Silent, missense, nonsense and frameshift mutations
What are silent mutations?
Codon containing the changed base may code for the same AA
ex: serine codon UCA is given a different third base U to become UCU, it still codes for serine
What are missense mutations?
Codon containing changed base may code for a different amino acid
ex. If serine codon UCA is given a different first base C to become CCa it will code for a different aa proline
The substitution of an incorrect amino acid is called a missense mutation
What disease is an example of a missense mutation?
Sickle cell anemia
Describe sickle cell anemia
Missense mutation in B globin gene in which GAG (glutamate) is changed to GTG (valine) giving rise to HbS
Alters conformation of deoxy Hb which aggregates and forms rod like structures
Deformation of RBCs into sickle shape
Poor O2 carrying capacity and tends to clog capillaries, thus restricting blood supply
High prevalence in African Americans
sx: anemia, pain, frequent infections and delayed growth/puberty
What is a nonsense mutation?
Codon containing changed base may become a termination codon
Ex. If serine codon UCA is given a different second base A to become UAA -> new codon causes termination of translation
Production of truncated protein occurs
What disease is due to a nonsense mutation?
Beta thalassemia
What is beta thalassemia?
Lack of production of B globin protein due to nonsense mutations
Homozygous mutation of splice sites + nonsense mutations that introduce premature stop signals at codons
What is a frameshift mutation?
If 1-2 nts are deleted or added to the coding region
Alters the reading frame
Results in a product with a radically different AA sequence or truncated product
What disease is caused by a frameshift mutation?
Cystic fibrosis
What is cystic fibrosis?
Most commonly caused by deletion of 3 nts from coding region -> loss of The in the CFTR protein (in 70% of pt)
Mutation prevents normal folding of CFTR protein which normally functions as Cl channel in epithelium
Production of sticky thick secretions in lungs and pancreas leading to lung damage and GI deficiencies
What are epigenetics?
Changes that do not affect DNA sequence
Affected by environment
Alterations in gene expression are stably inherited
What are the two main types of epigenetic modification?
Direct DNA methylation of the gene
Histone modification by acetylation and deacetylation
What is the major site of DNA methylation in mammals?
A cytosine base in DNA (especially the 5’ cytosine adjacent to gaunosine base) because they tend to cluster close to the promoter regions of the gene
Thought to cause steric hindrance to binding of TFs
What is imprinting?
Silencing of genes on chromosomes by methylated them
Genes are said to be imprinted depending on which parent contributed that gene
What is Fragile X syndrome (FXS)?
Example of imprinting
Caused by mutation of fragile X mental retardation I (FMRI) gene on the X chromosome
Addition of CGG tri-nt repeats causing hyermethylation inactivating FMRI
sx: intellectual disability, problems with social interaction, delayed speech, physical features including long and narrow face, large ears, flexible fingers and large testicles
What is histone modification?
Making DNA more or less accessible to TFs
Lysine residue acetylation weakens the DNA-histone interactions and makes the DNA more accessible to factors needed for transcription
Acetylation vs deacetylation
What is histone acetylation catalyzed by?
Histone acetyltransferases or HATs
Associated with transcriptional activation
What enzyme catalyzes histone deacetylation?
histone deacetylase (HDAC) Associated with gene silencing
Describe the role epigenetic plays in cancer
Silencing tumor suppression genes causes cancer
ex. p16 silenced in many tumors
Cancer cells may use epigenetic mods for therapy resistance
But epigenetics can also be a target for cancer therapy
