3. DNA Damage And Repair

Question 1

Mutation

Answer 1

Describes both a process that produces altered DNA sequences and the outcome of that change

Can have diff consequences:

Normal phenotype (height)
Disease phenotype
No obvious effect on phenotype
Very rare, beneficial effect 

Originat as a result of changes in our DNA that are not corrected by cellular DNA repair systems

Changes are occasionally are induced by radiation and chemicals in our environment - MOSTLY arise from endogenous sources

Question 2

Scale of Genetic variation and its consequences

Answer 2

Change in copy number of whole nuclear DNA molecules are almost always harmful (trisomy, deletion)

Most common are SNP on small scale (point mutations) and have no obvious effect on phenotype - neutral mutations

Question 3

Single nucleotide variants / polymorphism

Answer 3

Most common type of genetic variation in human genome

Account for 75% of DNA changes

1 SNP per 1000 base pairs - 3 million SNPs per individual

Question 4

Functional genetic variation

Answer 4

ABO blood group - different surface antigens on RBCs

In a normal person a number of genes are inactivated

Most genetic variation has a neutral effect on phenotype but a small fraction are harmful

Question 5

Examples of functional genetic variation

Answer 5

ABO blood group

Immune system:

Genes of immune system are polymorphic - undergo somatic rearrangements to produce different variants

Genes involved in identifying microbial pathogens - constant positive selection to maximize diversity in proteins involved in antigen recognition

Question 6

Origins of DNA sequence variation

Answer 6

Recombination - hot spot regions where recombination is more likely such as in subtelomeric regions

Independent assortment of paternal and maternal homologs

Various mutational elements
Endogenous chemical damage to DNA
Chemical damage to DNA caused by external mutagens
DNA replication errors
Chromosome segregation and recombination errors

Question 7

Endogenous chemical damage to DNA

Answer 7

Hydrologic damage -

Disrupt covalent bonds that hold bases to sugars, cleaving that base from sugar to produce abasic site (depurination)

Oxidative damage -

from normal cellular metabolism, most significant are superoxide anions (O2-) hydrogen peroxide (H2O2) and hydroxyl radicals (OH-)

Aberrant DNA methylation

Inappropriate methylation by SAM to methylated DNA to produce harmful bases

Question 8

Chemical damage to DNA by external mutagens

Answer 8

UV radiation (sunlight) -

covalent bonding between pyrimidines

High energy irradiation (x-rays) -

generate ROS - breaking DNA strands

Mutagenic chemicals (cigarette smoke, automobile fumes) -

bulky DNA adducts - distortion of the double helix

Question 9

DNA repair single strand

Answer 9

minor DNA damage - an altered base

DNA cross linking - may block DNA replication or transcription

Base excision repair (BER)
DNA mismatch repair (MMR)
Nucleotide excision repair (NER)

Question 10

Base excision repair (BER)

Answer 10

Repair on single strand

Lesions where single base has either been modified or excised by hydrolysis to leave an abasic site

DNA glycosolyse cleaves sugar base bond to delete the base to create abasic site

For abasic sites the residual sugar-phosphate residue is removed by endonuclease and phosphodiesterase

Gap is filled by a DNA polymerase and DNA ligase

Available throughout the cell cycle

Question 11

DNA mismatch Repair (MMR)

Answer 11

Repair on a single strand - colorectal non-polyp

Repairs erroneous insertion, deletion, mis-incorporation of bases that occurs during DNA replication

Mismatch on the daughter DNA strand is recognized and fully excised along with the surrounding nucleotides

Generates a gap that is repaired by DNA polymerase and DNA ligase

Question 12

Nucleotide excision repair (NER)

Answer 12

Repairs of single strand damage - Xeroderma

Allows the repair of bulky, helix- distorting DNA lesions (UV induced diners)

After lesion is detected damage site is opened and out

DNA is cleaved some distance away on either side of the lesion generating an olionucelotide of about 30 nucleotides containing the damaged site- which is discarded

More important in G1, but not restricted to only G1

Question 13

Repair of DNA lesions affecting both DNA strands

Answer 13

Homologous recombination (HR)

Non-homologous end joining (NHEJ)

Question 14

Homologous recombination (HR) - mediated DNA repair

Answer 14

Repair affecting both strands

Highly accurate repair mechanism - required homologous intact DNA strand to be available to act as template strand

Operated in S and G2 (before mitosis) using a DNA strand from undamaged sister chromatid as a template to guide repair

Question 15

Non-homologous end joining (NHEJ)

Answer 15

Repair affecting both strands -SCID

No template strand is needed broken ends are fused together

Specific proteins bind to the DNA ends are recruit a special DNA ligase (DNA ligase IV) to rejoin broken ends

NHEJ is always available to cells - most important for repair in G1 phase before DNA has replicated

Question 16

Xeroderma Pigmentosum

Answer 16

Autosomal recessive disorder

Inability to repair damage caused by UV light (NER is defective)

Malfunction of excision repair - thymine diners much remain and block production

Predisposition to skin cancer - Leads to basal cell carcinomas and other skin malignancies - by 10 years old

Signs appear in infancy or early adult hood - dry skin, freckles, loss of hearing, movement disorder, decrease life spoon

Question 17

Hereditary Non-polyps is Colorectal cancer

Answer 17

Autosomal dominant - caused by mutations in genes involved in DNA mismatch and repair (MMR proteins)

Most common form of hereditary colorectal cancer - 50-70% risk of developing colorectal and other cancers

Propensity to develop predominantly right-sided, flat adenomas at a young age

Develop adenomas at the same rate as the general population BUT more likely to progress to cancer

Question 18

Severe combined immunodeficiency (SCID)

Answer 18

X-linked autosomal recessive inheritance

Deficiency in both B and T lymphocytes functions with remarkeably low IgG, IgA, IgE levels - have neither cell mediated or antibody mediated immunity

Most cases- mutation in gene encoding common gamma chain (yc) a protein that is shared by the receptors for interluekins

Most severe form - defects in the pathway for double-strand break repair called non-homologous DNA end joining or NHEJ

If given bone marrow transplant by 3 months after birth = good prognosis

Question 19

Bloom syndrome

Answer 19

Autosomal recessive pattern of inheritance

Characterized by short stature, butterfly task, high pitched voice and distinctive facial features: long narrow face, small lower jaw and prominent nose and ears

High risk of developing cancer

Mutation in BML gene

Defective RecQ helicases

Defective unwinding of DNA

Defective DNA repair

Question 20

• Identify the type of DNA repair available to the cell during each phase of the cell cycle.

Answer 20

HR - S G2 
NHEJ - most important in G1 always available
NER - G1 but not resticted 
BER- throughout cell cycle
MMR - ??

Question 21

Base mismatches caused by replication errors

Answer 21

MMR

Question 22

Small insertions/deletions due to replication slippage

Answer 22

MMR

Question 23

Small scale single base modification

Answer 23

BER

Question 24

Single base deletion - an abasic site resulting from hydrolysis

Answer 24

BER

Question 25

Bulky helix distorting DNA lesions - large DNA adducts, DNA instrastrand crosslinking and so on

Answer 25

NER

Question 26

Single stranded DNA breaks other then DNA nicks

Answer 26

BER