Functions and Dysfunctions of Genomic Regulation

Question 1

What are the 3 types of DNA damage?

Answer 1

1. spontaneous: metabolic activity and DNA replication is not perfect, basal mutation rate (2x10^-6 mutations/bp/replication)
2. physical agents: radiation (ionizing and non-ionizing)
3. chemical agents: direct and indirect

Question 2

• type of DNA damage that only happens to bases
• most frequent examples: adenosine and guanosine depurination (removal of adenine and guanine)
• most frequent examples: deamination of adenine to hypoxanthine, guanine to xanthine, and cytosine to uracil

Answer 2

spontaneous DNA damage

Question 3

• type of DNA damage
• caused by energy that is emitted from a body or source that is transmitted through an intervening medium or space and absorbed by another body (transmission is in the form of waves)
• two types: ionizing and non-ionzing

Answer 3

radiation DNA damage

Question 4

• type of radiation DNA damage
• radiation is longer wavelength, lower frequency, lower energy
• sources: infrared, microwaves, radio, heat lamp
• cause: thermal burns

Answer 4

non-ionizing radiation

Question 5

• type of radiation DNA damage
• short wavelength, high frequency, high energy
• significant damage can result including damage to DNA and denaturation of proteins
• sources: ultraviolet, x-ray, gamma rays, tanning

Answer 5

ionizing radiation

Question 6

UV-induced DNA damage causes the formation of __________ dimers between __ and __ nucleotides

Answer 6

pyrimidine, T, C

Question 7

What are the __ types of ionizing radiation induced DNA damage?

Answer 7

1. protein-protein crosslink
2. DNA-protein crosslink
3. single-strand break
4. double-strand break
5. base damage
6. intercalation
7. specific binding site
8. intra-strand crosslink
9. inter-strand crosslink

Question 8

What are the 2 types of chemical induced DNA damage?

Answer 8

1. agents that act directly to modify DNA
2. agents that require metabolic activation

Question 9

What are the 3 types of direct chemically induced DNA damage?

Answer 9

1. cross-linking agents: nitrogen mustard, cisplatin, mitomycin C, camustine
2. alkylating agents: dimethyl sulfate (DMS), methyl methanesulfonate (MMS)
3. intercalating agents: ethidium bromide, thalidomide, doxorubicin, daunomycin

Question 10

What are 3 examples of indirect chemically induced DNA damage?

Answer 10

1. cytochrome P-450 enzymes
2. benzo(a)pyrene > BPDE (an epoxide)
3. aflatoxin B1 > aflatoxin B1-epoxide

Question 11

What are the 4 main types of genomic alterations?

Answer 11

1. chromosomal mutations
2. gene amplification
3. transposons
4. single-nucleotide polymorphisms

Question 12

• type of genomic alteration
• 4 sub-types: deletions, translocations, duplications, and inversions

Answer 12

chromosomal mutations

Question 13

What are the 4 types of chromosomal mutations and what are their effects?

Answer 13

1. deletions: chromosome segment lost
2. translocation: segment from chromosome is transferred to another (can cause trisomy, like down syndrome)
3. duplication: segment from one chromosome is transferred to its homologous chromosome, giving it a duplicate of some genes
4. inversion: segment of chromosome arm is inverted

Question 14

• type of genomic alteration
• jumping genes
• mobile sequences of DNA that can change position within the genome of a single cell
• copy/cut > paste

Answer 14

transposons

Question 15

• hemophilia A is a hereditary bleeding disorder caused by lack of blood clotting factor VIII, without enough factor VIII, the blood cannot clot properly to control bleeding
• what type of genomic alteration is hemophilia A associated with?

Answer 15

transposons

transposon L1 inserted into the factor VIII gene renders factor VIII ineffective

Question 16

• type of genomic alteration
• common inherited change in a single base pair that occurs in at least 1-5% of the population
• not a mutation, but can act as one
• occur once every 1000 to 2000 nucleotides
• used as markers in the mapping of genomes
• may be associated w/ increased susceptibility to disease
• can also be used in drug development (certain individuals may need higher doses of drugs, lower doses, or need to avoid drug all together due to toxicity)

Answer 16

single-nucleotide polymorphisms (SNPs)

Question 17

• type of genomic alteration
• can be caused by chromosomal mutations, transposons, SNPs, or impaired replication
• causes an aberrant replication fork that creates extra DNA and a two free DNA strand loop structure
• can be good: more copies of the gene and less selective pressure (less mutationals effects) in evolution and environmental adaptation
• can be bad: can cause diseases such as cancer and cancer therapy resistance

Answer 17

gene amplification

Question 18

What are the general 4 steps in repairing damaged DNA?

Answer 18

1. recognize damaged DNA strand
2. remove/excision of damage
3. DNA polymerase makes repair
4. DNA ligase seals nick

Question 19

• type of DNA repair mechanism
• does not require a template
• two main types: UV light and alkylating agents

Answer 19

direct DNA repair

Question 20

• direct DNA repair
• direct reversal through photoreactivation (photolyase) can inverse this dimerization reaction by utilizing light energy for the destruction of the abnormal covalent bond between adjacent pyrimidine bases. This type of photoreactivation does not occur in humans

Answer 20

UV light direct DNA repair

Question 21

• direct DNA repair
• methylation of guanine bases produces a change in the structure of DNA by forming a product that is complimentary to thymine rather than cytosine, the protein methyl guanine methyl transferase (MGMT) can restore the original guanine by transferring the methylation product to its active site

Answer 21

alkylating agents direct DNA repair

Question 22

• DNA repair mechanism
• damage: single-base mismatches and small, nondistorting alterations; spontaneous depurination and spontaneous deamination; uracil, 8-oxoguanine, 3-methyladenine, and abasic sites
• mechanism: altered base detected by DNA glycosylases, DNA glyosylase removes base (hydrolyzes N-glycosidic bond), AP endonuclease cuts phosphodiester bond, AP lyase removes deoxyribose phosphate, DNA polymerase β replaces excised nucleotide, DNA ligase seals nick

Answer 22

base excision repair (BER)

Question 23

What is the mechanism of base excision DNA damage repair?

Answer 23

• altered base detected by DNA glycosylases
• DNA glyosylase removes base (hydrolyzes N-glycosidic bond), AP endonuclease cuts phosphodiester bond, AP lyase removes deoxyribose phosphate
• DNA polymerase β replaces excised nucleotide, DNA ligase seals nick

Question 24

• DNA repair mechanism
• damage: chemical adducts; alteration in DNA shape in the local area; UV, BPDE guanine adducts, and cisplatin adducts
• mechanism: NER complex recognizes distortions and nicks DNA on both sides of damage site, removes stretch of DNA with damage, DNA polymerase ε fills in gap, DNA ligase seals nick

Answer 24

nucleotide excision repair

Question 25

• autosomal recessive genetic disorder of DNA repair in which patients carry mutations in the nucleotide repair enzymes mostly an endonuclease
• high sensitivity to sunlight, pigmentary skin change
• prone to developing melanomas and squamous cell carcinomas
• defects in the NER complex XP proteins (XP-A through XP-G)

Answer 25

xeroderma pigmentosum

Question 26

• DNA repair mechanism
• damage: lesion in DNA that causes RNA polymerase to stall
• mechanism: RNA polymerase stalls at a lesion in the DNA, TCR proteins called ERCC-6 and ERCC-8 recognize the stalled RNA polymerase and recruit other repair proteins

Answer 26

transcription-coupled repair (TCR) (form of NER)

Question 27

• autosomal recessive disease involving transcription-coupled repair
• mutant genes: ERCC6 and ERCC8
• sx: neurologic delay, photosensitivity, progeria (premature aging), hearing loss, eye abnormalities

Answer 27

cockayne syndrome

Question 28

• DNA repair mechanism
• damage: incorrect matching nucleotides that get synthesized into new daughter strand
• mechanism: MER complex proteins (MSH2 and MSH6) binds to DNA and recognizes mismatch in daughter strand, daughter strand cut out, segment with mismatch removed, DNA polymerase δ fills gap, DNA ligase seals nick

Answer 28

mismatch excision repair (MER)

Question 29

• mutations in one of the alleles of genes in the MER complex
• accumulation of unrepaired DNA damage lead to genomic instability > cancer
• ex: Lynch syndrome

Answer 29

hereditary nonpolyposis colorectal cancers

Question 30

• DNA repair mechanism
• damage: double strand breaks, radiation and chemical damage
• two types: nonhomologous end joing (NHEJ) and homologous recombination (HR)

Answer 30

recombination repair

Question 31

• type of recombination repair
• damage: chromosomal translocation, neoplastic chromosomal rearrangements
• mechanism: DNA PK and ku proteins bind the ends of double stranded breaks, nuclease removes bases from both ends, ligase joins ends together

Answer 31

nonhomologous end joining (NHEJ)

Question 32

• type of recombination repair
• needs template, after DNA replication and before cell division
• mechanism: DNA with breaks adjacent to undamaged homologous DNA, broken DNA is digested leaving 3’ overhand, overhang of lower broken strand invades undamaged homologous DNA to base pair with lower undamaged strand, invading broken strand is extended and top undamaged strand based pairs with 3’ overhand of top broken strand, DNA polymerase extends repositioned broken strands, ligate ends of top broken strand and lower broken strand, cleave phosphodiester bonds and ligate alternative ends

Answer 32

homologous recombination

Question 33

• breast cancer susceptibility genes (BRCA1 and BRCA2) are associated with hereditary cancer when mutated
• they are key players in encoding proteins that facilitate _________ ___________
• five-fold increase risk of developing breast cancer and other cancers if these genes are mutated

Answer 33

homologous recombination

(suggests homologous recombination plays a role in preventing development of cancer)

Question 34

What are the 4 types of genetic code mutations?

Answer 34

1. silent mutation
2. missense mutation
3. nonsense mutation
4. frameshift mutation

Question 35

• type of genetic code mutation
• codon containing changed based codes for the same amino acid as original codon

Answer 35

silent mutation

Question 36

• type of genetic code mutation
• codon containing the changed base codes for a different amino acid
• example: sick cell anemia

Answer 36

missense mutation

Question 37

• disorder caused by missense mutation in the β-globin gene in which GAG, a glutamate, is changed to GTG, a valine, giving rise to HbS
• alters conformation of hemoglobin to the deoxy form
• mutated hemoglobin molecules aggregate, forming rigid rod-like structures and cause deformation of red blood cells into sickle-like shape
• the deformed RBC’s have poor oxygen-carrying capacity and tend to clog capillaries, thus restricting blood supply to various tissues
• high prevalence in African Americans
• sx: anemia, episodes of pain, frequent infections, delayed growth/puberty

Answer 37

sickle cell anemia

Question 38

• type of genetic code mutation
• codon containing changed base becomes a termination codon
• causes production of truncated protein
• example: β-thalassemia

Answer 38

nonsense mutation

Question 39

• disorder caused by nonsense mutation
• lack of prod of β-globin protein due to nonsense mutations giving rise to truncated transcripts that decay rapidly
• homozygous mutations of splice sites (GU and AG dinucleotides) and nonsense mutations that introduce premature stop signals at codons 17 (exon 1) and 39 (exon 2) result in this condition

Answer 39

β-thalassemia

Question 40

• type of genetic code mutation
• one or two nucleotides are added/deleted in the coding region of a message sequence
• can result in a product with a radically different amino acid sequence or a truncated production due to creation of termination codon
• example: cystic fibrosis

Answer 40

frameshift mutation

Question 41

• disorder cause by a frameshift mutation
• most commonly caused by a deletion of three nucleotides from the coding region of a gene, resulting in the loss of phenylalanine at the 508th position in the protein (ΔF508) encoded by that gene
• over 70% of patients, the ΔF508 mutation is the cause of the disease
• mutation prevents normal folding of the CF transmembrane conductance regulator (CFTR) gene
• CFTR normally functions as a chloride channel in epithelial cells, and its loss results in the production of thick, sticky secretions in the lungs and pancreas, leading to lung damage and digestive deficiencies

Answer 41

cystic fibrosis

Question 42

• changes that do not affect the DNA sequence of genome
• affected by the environment
• alterations in gene expression that are stably inherited
• two main types: gene methylation (direct DNA methylation) and histone modification by acetylation and deacetylation

Answer 42

epigenetics

Question 43

• the major site of this in mammals is on a cytosine base in DNA, especially the 5’ cytosine adjacent to a guanosine base (5’-CG-3’)
• 5’-CG-3’ residues tend to cluster in the promoter regions of genes
• important for tissue specific gene expression
• thought to cause steric hindrance to the binding of proteins (transcription factors) that influences gene expression
• methylation of a gene is called imprinting

Answer 43

gene methylation (direct DNA methylation)

Question 44

• when silencing of genes on chromosomes is a result of gene methylation
• these genes are said to be _______ or have the ability to be turned on or off depending on which parent contributed the gene that was silenced
• example: fragile X syndrome

Answer 44

imprinting

Question 45

• caused by a mutation of the FMRI gene on the long arm of X chromosome
• FMRI normally has 5 to 55 CGG trinucleotide repeats and can potentially expand during meiosis in oocytes
• “full mutation” is characterized by >200 CGG trinucleotide repeats, which causes FMRI hypermethylation
• DNA methylation inactivates FMRI, preventing transcription and production of _______ __ mental retardation protein
• sx: mild to moderate intellectual disability, problems with social interactions, delayed speech, long and narrow face, large ears, flexible fingers, large testicles

Answer 45

fragile X syndrome

Question 46

• type of epigenetics that makes DNA more or less accessible to transcription factors
• lysine residue acetylation weakens the DNA-histone interactions and makes the DNA more accessible to factors needed for transcription
• acetylation catalyzed by histone acetyltransferase or HATs > a/w transcription activation
• deacetylation catalyzed by histone deacetylase or HDAC > a/w gene silencing

Answer 46

histone modification by acetylation and deacetylation

Question 47

How do epigenetics contribute to cancer etiology?

Answer 47

• one major cause of cellular transformation is silencing of tumor suppressor genes (ex: p16 (cell cycle inhibitor/tumor suppressor gene) is epigenetically silenced in many tumors)
• cancer cell environment is highly dynamic with genomic and metabolic changes that affect gene epigenetic mods
• cancer cells may use epigenomic mods for therapy resistance (i.e. silencing of pro-apoptotic genes such as Bax and Bak)
• epigenetics can be a target for therapy (many epigenetic drugs, DNA methyltransferase enzyme (DNMT) inhibitors and deacetylase (HDACs) have been approved by FDA as effective drugs for cancer treatment)