Ch. 14: Gene variant and DNA repair

Basis of genetic function

-DNA molecule stores, replicates, transmits, and decodes information

-Changes in DNA sequences give rise to variations: results in phenotypic variability, adaptation to environmental changes, and evolution

-Provide the basis for genetic analysis: act as markers for specific genes

Base substitutions

-are the primary mechanism behind Single Nucleotide Polymorphisms (SNPs) if that represent less than 1% of the gene

-Transitions

-Transversions

Transitions

Pyrimidine replaces pyrimidine or purine replaces purine

Transversions

Purine and pyrimidine are interchanged

Silent variants

base substitution, amino acids are not altered

Frameshift variants

-Result from insertions or deletions of nucleotide

-Loss or addition of nucleotide causes shift in reading frame

-Frame of triplet reading during translation is altered

-Altered triplets may code for stop codon (UAA, UAG, UGA)

Missense variants

Substitution change the codon

Nonsense variants

Converts an amino acid-coding codon into a premature stop codon

Sickle cell disease

due to missense variant

Promoter

may increase or decrease the rate of transcription

Regulatory element/operator site

May disrupt the ability of the gene to be properly regulated

5’-UTR/3’-UTR

May alter the ability of mRNA to be translated; may alter mRNA stability

Splice recognition sequence

May alter the ability of pre-mRNA to be properly spliced

Trinucleotide Repeat Expansions

-Insertion of triplet repeats leads to extra amino acids

-The longer proteins shut down the cells (cell apoptosis)

-Trinucleotide repeat expansion (TNRE) disorders

-Length of repeat increase above a certain critical size

-Number of repeats correlates with earlier onset and more severe phenotype- leading to progressive neurological and neuromuscular degeneration, such as Huntington’s disease (CAG), Fragile X syndrome (CGG), and Fridreich’s ataxia (GAA)

Germ-line variants

-occurs in gametes and are heritable

-Somatic variants occur in somatic cells are not heritable, but often lead to altered cellular function and cancer

-Variants can occur spontaneously or they can be induced

-Spontaneous variants have no known cause and are due to errors in normal biological/chemical processes (DNA replication)

-Induced variants are due to exposure to mutagens (radiation)

Base damage

-Deamination: loss of amino group (NH2)

-Cytosine → Uracil or 5-methylcytosine → Thymine

-Base excision repair (BER)

-Point mutations; cancer hot spots; epigenetic aging

DNA base loss

-Depurination and deamination → loss of nucleotide

-Common causes of spontaneous variants

-Lead to new base pairing and variants

-Result: A=T converted G=C

Depurination

-Loss of nitrogenous bases

-Usually a purine- guanine or adenine- leads to apurinic site (without purine)

Deamination

-Amino group in cytosine or adenine converted to keto group

-Cytosine converted to uracil- adenine converted to hypoxanthine; causes a switch in base pair

Tautomers

-Purines and pyrimidines exist in tautomeric forms- alternate chemical forms

-Same elements but they switch positions

Tautomeric shifts

-Can change the bonding structure, allowing noncomplementary base pairing

-May lead to permanent base-pair changes and variants

-causes an anomalous base-pairing, causing an alternative chemical form that differ by only a single proton shift in the molecule

DNA damage vs. variant

-DNA damage is the change in DNA structure caused by a damaging agent (or mutagen)

-Variant is the change in DNA sequence or coding potential that comes from the resolution of DNA damage

-DNA damage can be resolved without variant! But, more DNA damage leads to higher amounts of variant, constant damage of DNA will cause a variant

Oxidative damage

-Due to by-products of normal cellular processes

-Reactive oxidants

Increase in reactive oxygen species (electrophilic oxidants)

Superoxides (O2-) most active free radical

Hydroxyl radicals (OH) not very reactive

Hydrogen peroxide (H2O2) weak radical that can still cause modification

-Result in modification of bases, loss of bases, and single-stranded breaks

Guanine is very susceptible to…

-oxidative stress, another cause of variants

-8-oxoG base pairs with adenine during DNA replication

-Causes GC pairs to become TA pairs, very common damage of DNA; induced with again, DNA

-Oxidative damage also occurs from environmental exposures

-UV light, X rays, chemicals, pollution, etc

Variants arise from replication

-Replication is imperfect

-DNA polymerase occasionally inserts incorrect nucleotides

-Misincorporated nucleotides persist persist after replication, error may get detected

-Errors not detected may lead to variants

-Bases can take several forms (tautomers); increases change of mispairing during DNA replication

Replication Slippage

-DNA polymerase slips or stutters during replication

-Loop occurs in template strand during replication

-DNA polymerase misses looped out nucleotides- small insertions and deletions occur

-More common in repeat sequences (hot spots)

-Hot spots for DNA variant

-Contributes to hereditary diseases: Fragile-X, Huntington disease

Thymine dimers

-causes by ultraviolet (UV) light

-2 nucleotides that should not be binding bind

-Adjacent thymine bases become crosslinked

-Thymine dimers interfere with transcription and translation

-Sun tanning greatly increases exposure to UV light: can increase risk of skin cancer

DNA Repair Systems

-essential to the maintenance of our genetic integrity and occur thousands and thousands times a day

Base excision repair

-corrects the DNA

Nucleotide excision repair

-Does not cut DNA at the backbone

-Instead leaves the backbone intact and only takes out and replaces the damaged/wrong nucleotide

Xeroderma Pigmentosum

-a rare autosomal recessive disorder that predisposes individuals to skin cancer/and sometimes neurological disorders

-It is caused by variant in at least 8 genes involved in nucleotide excision repair; multiple errors in DNA replication