Neha Block 3 Genetics TA notes

Biochemical Genetics

I. Unstable Repeat Expansion

a. Expansion of repeating tandem nucleotide units within a gene
i. Mostly triplet but can also have quadruplet & pentuplet
b. General features:
i. Genes associated w/ repeat expansion have polymorphic wild type alleles
ii. Dynamic mutations
1. # of repeats can increase beyond normal phenotypic range
2. Expansion can occur during:
a. DNA replication
3. Genome maintenance (gene repair)slipped mispairing
4. Anticipation-appearance of the disease at an early as it is transmitted
through a family
a. Two examples?
iii. Most common molecular mutational mechanismslipped mispairing DNA
replication
iv. Parental transmission bias
1. Maternal
a. Friedrich’s ataxia AAG
b. Myotonic dystrophy
c. Fragile X
2. Paternal
a. Huntington
c. Primary neurological phenotype
i. Ataxia
ii. Cognitive defects
iii. Dementia
iv. Nystagmus
v. Parkinson’s and spasticity
II. Tetranucleotide repeat expansion diseases
a. Myotonic dystrophy 2- CCTG (close genocopy of Myotonic dystrophy)
i. CCTG
III. Pentanucleotide repeat expansion disease
a. Spinocerebellar atrophy 10
i. ATTCT
IV. Pathogenesis
a. Class I-mutations in 5’UTRimpairing transcription
i. Fragile X
 ii. Freidrich ataxia
b. Class II-mutations in 3’UTRnovel properties of RNA
i. Myotonic dystrophy 1 and 2
ii. Fragile X-associated tremor/ataxia
c. Class III- mutations in coding regionnovel properties of encoded protein
i. Huntington disease
ii. Spinocerebellar ataxia
V. Fragile X syndrome
a. X linked- fragile site where chromatin fails to condense properly during mitosis
i. FMR1 gene; CGG repeat—5’ untranslated region
1. Up to 60 repeats= Normal
2. 60-200= premutation
3. >200hypermethylation of 5’ untranslated region & promoter
a. Interference of replication and chromatin condensation, creates
fragile sites, defects transcription
b. FMR proteinabnormal phenotypic expression
i. FMRP=RNA binding protein
ii. Premutation carriersadult onset of cerebellar dysfunction & neurological
dysfunction—fragile X associated tremor/ataxia syndrome
1. Some female carriersovarian failure by 40
VI. Huntington disease
a. AD; chromosome 4p
b. AGE DEPENDENT PENETRANCE—presents around 40+yrs
i. chorea, dystonia, loss of cognition, progressive loss of motor control,
degeneration of cortex
c. CAG repeats in coding region of HD gene that codes for Huntingtinpolyglutamine
tracts in mutant proteinglutamine residue in Huntingtinneurodegeneration
i. Aggregation of mutant Huntingtin insoluble clusters
ii. Normal-9-35
iii. Premutation-29-35
iv. Some people 36-39= Huntington at advanced age
v. Full mutation= >40
VII. Friedrich Ataxia
a. AR; AAG repeat, FRDA gene
b. commonly inherited spinocerebellar ataxia
i. Normal-5-34
ii. Disease condition-100-1200
c. FRDA genefrataxin; mitochondrial iron binding protein
i. Regulated iron homeostasis in mitochondria
1. Too many AAGimpairs transcriptional elongation, loss of function of
frataxin mitochondrial iron, impaired heme synthesis, reduced
activity of Fe-S cluster in complexes 1-3 of ETC
 d. Incoordination of limbs, speech difficulty, aflexia or hyporeflexia, impairment of
vibration and position sense, cardiomyopathy, scoliosis and foot deformities, Type 2
Diabetes
VIII. Myotonic Dystrophy
a. DMPK (myotonic dystrophy protein kinase),CTGCUG repeats in mRNA
i. CUG repeats bind to RNA binding proteinsinterference in mRNApleiotropic
manifestations
ii. Normal:5-30
iii. Premutations:38-54
iv. >50=disease
v. Chromosome 19qarm
b. Anticipation
c. Pleiotropic, severe myopathy and mental retardation, facial weakness, distal extremity
weakness, neck muscle weakness, cardiomyopathy, frontal baldness, hypogonadism,
insulin resistance-diabetes, cataract

Mitochondrial Disorders

I. Mitochondrial Genome
a. Small DS circular DNA
b. All cells have about 1000 mtDNA/cell cept oocytes which have 100,000
i. Contains
1. 13 genes for subunits of proteins/enzymes of oxidative
phosphorylation
2. 2 rRNA genes
3. 22 tRNA genes
II. Mitochondrial genome and nuclear genome
a. 74 polypeptides of oxidative phosphorylation encoded by nuclear genome
i. Maintenance & expression of mtDNA
ii. Assembly and expression of oxidative complexes
b. Mutations in nuclear genes can show phenotype of mitochondrial diseases
i. Mendelian inheritance for nuclear and MATERNAL for mitochondrial
c. Mutations in mtDNA have distinctive patterns of inheritance
i. Based on:
1. maternal inheritance
2. Replicative segregation
3. Homoplasmy
4. Heteroplasmy
a. Pleitropy
b. Reduced penetrance
c. Variable expression
d. Mitochondrial bottleneck
 i. In oocyte, # of mtDNA molecules reduced before being amplified to
total
1. Clinically affected offspring more likely if mom has more
mutant DNA
a. EXCEPTION
i. If mother has heteroplasmy for deletion
mutation; NOT TRANSMITTED TO
OFFSPRING
2. Mutation is 10x greater than for nuclear DNA
a. LACK OF PROOFREADING IN DNA POLYMERASE
e. Widespread range of clinical disease
i. Predominantly neuromuscular disease
1. 3 types of mutations:
a. Missense; coding regions
i. Change activity of oxidative
phosphorylation
b. Point; tRNA/rRNA genes
i. Impair protein syn
c. Rearrangementsduplications & deletions
2. Deletions in mtDNA
a. Pearson syndrome-
b. Kearns-Sayre syndrome
i. Sporatic somatic mutation
1. B/c affected women have severe
phenotype & can’t reproduce
ii. mtDNA and clonal expansion
1. Loss of dopaminergic neurons in
substantia nigra sporadic form of
Parkinsons
3. Tissues dependent on oxidative phoshorylation generally
affected
a. Pathology:
i. ATP, reactive oxygen species
b. Disorders cause by deletion: 60% express
phenotype
c. Disorders caused by other types of mutations: 90%
express phenotype
f. Phenotypes:
Neuromuscular May also include
Encephalopathy Liver dysfunction
Myopathy Bone marrow failure
Ataxia Pancreatic islet cell def.
 Retinodegeneration Diabetes
LOF external ocular muscles
d. Mutations in tRNAproblems in oxidative phosphorylation(MELAS) mitochondrial
encephalopathy w/ lactic acidosis)
i. 3243AG in tRNA (leu) most common mutation
e. Mitochondrial disorder phenotypes can also be produced due to mutations in nuclear
DNA, e.g.,
i. Autosomally transmitted deletions in mtDNA
1. Presents as chronic progressive external ophthalmoplegia
ii. Mutations in 2 genes
1. Twinkle protein which is a DNA primase or helicase
2. Mitochondrial specific DNA polymerase γ
f. mtDNA depletion syndrome
i. decrease in # of copies of mtDNA
ii. Mutations in any of six genes that encode for proteins
iii. Required to maintain nucleotide pools
iv. Metabolize nucleotides in mitochondria
v. Mitochondrial gastrointestinal encephalomyopathy
vi. Mutations in thymidine phosphorylase
vii. Blood thymidine levels are increased
g. Leber’s Hereditary Optic Neuropathy
i. Generally homoplasmy
ii. Rapid, painless bilateral loss of central vision in adults
1. Reason for optic nerve damage unclear
2. Some recovery of vision may be seen
iii. Increased penetrance of disease in males
1. Could be due to modifier gene on short arm of X chromosome
IX. Alzheimer’s Disease
a. Adult neurodegenerative disorder
i. 6th-9th decade of life
ii. Progressive deterioration of memory and higher cognitive functions
1. Degeneration of neurons in specific regions of cerebral cortex and
hippocampus
iii. 4 genes associated:
1. APPβAPP
2. PSEN1prensilin 1
3. PSEN2prensilin2
4. ApoE (not associated w/ mongenic AD)
a. ε4 allele of ApoE
b. Modestly increases susceptibility to nonfamilial AD; sometimes
influenced age of onset
b. Pathogenesis
 i. Amyloid/senile plaques
ii. Extracellular depositions of mainly Aβ42 and apoE
iii. Neurofibrillary tangles  intracellular (intraneuronal)
1. Hyperphosphorylated Tau proteinAlzheimers
a. MUTATIONfrontotemporal dementia (NOT ALZHEIMERS)
2. Normal Tau- promotes assembly and stability of microtubules
a. Note: Mutations are not associated with AD
3. βAPP  single pass transmembrane protein
a. Has 3 distinct proteolytic fates
b. α-secretase and β-secretase  cell surface secretases
i. no formation of neurotoxic AB peptide
c. γ-secretase  atypical protease
i. Production of either nontoxic Aβ40 or neurotoxic Aβ42
ii. Presenlin 1; cofactor for gamma secretase
1. Mutations =increase production of Aβ42
iii. Presenilin 2
iv. ε4 allele is a major risk factor for development of AD
1. earlier age of onset  10-15 years earlier
2. dose dependent
v. ε2 allele has a protective effect
X. Zellweger Syndrome
a. Very rare peroxisomal biogenesis disorder
i. Defects of import of peroxisomal enzymesperoxisomal matrix
ii. AR inheritance
iii. Severe neurologic deficits,
1. Progressive hepatic and renal dysfunction
2. Skeletal abnormalities
3. Rarely survive their first year
XI. Refsum disease; AR
a. Rare disorder of lipid metabolism
b. Peripheral neuropathy
c. Cerebellar ataxia
d. Retinitis pigmentosa
e. Bone and skin changes.
f. Accumulation of phytanic acid bc of defect in phytanoyl CoA hydroxylase pathway
i. Exclusively dietary in origin
1. Dairy products, meat, fish, phytol
ii. Phytanic acid  branched fatty acid
1. Cannot be oxidized directly in β-oxidation
a. cycles of α-oxidation and β-oxidation
g. Tx: Plasmapheresis, Dietary adjustments
i. Must be continued for life
XII. Wilson’s disease; AR
a. Disorder of copper transport
b. ATP7B located on chromosome 13
i. Codes for a transmembrane pump (P-type ATPase)
1. Transports copper into hepatocyte secretory pathway
2. Incorporation into ceruloplasmin
3. Excretion into bile
c. Impaired excretion into bile
d. Accumulation of Cu2+ in liver  cell deathliver disease
e. Release of Cu2+ into plasma
f. Hemolysis and deposition of copper in extrahepatic tissues
i. Onset of symptoms between ages of 6 and 40.
ii. 'Kayser-Fleischer ring'  copper-colored ring at periphery of cornea
XIII. Neuropsychiatric symptoms in adults
a. Tremors , Speech problems, Abrupt personality change
b. Unexplicable deterioration of school work, Neurosis or psychosis.
c. Dx: Decreased serum ceruloplasmin, Increase in urinary copper, Increase in hepatic
copper concentration
d. Treatment
i. Copper chelation by penicillamine ,Restriction of copper in diet
ii. Must continue as long as patient lives

XIV. Menke’s syndrome

a. X-linked recessive; Mt gene for a P-type ATPase
i. Responsible for the efflux of copper from cells
ii. Copper accumulates in intestine but is deficient in other tissues, especially the
CNS
b. Clinical features  loss of function of cuproenzymes
i. Abnormal hair (reminiscent of steel wool cleaning pads) and pigmentation
ii. Skin laxity of skin
iii. Cerebellar degeneration
iv. Failure to thrive
c. Dx  decreased serum copper and ceruloplasmin
d. Treatment  copper histidine
XV. Hereditary hemochromatosis
a. AR disorder ; HFE gene on chromosome 6
i. Normal gene productbinds to transferring receptormay act by modulating
its affinity for transferring
ii. Abnormal gene product:
1. Impaired cell-surface protein; doesn’t migrate to surface; doesn’t bind
transferring receptorno internalization of transferring into small
intestine cellcompensatory increase in iron absorption
 b. increases iron absorption via intestine
i. Symptoms caused by storage of excess iron as hemosiderin
ii. Normal gene product:
c. Principal organs affected
i. Liver  cirrhosis, hepatoma
ii. Pancreas  Diabetes mellitus
iii. Heart  cardiomyopathy
iv. Endocrine organs  hypogonadism
v. Skin  dark pigmentation
vi. Joints  arthritis

XVI. William’s syndrome

a. Rare Autosomal Dominant congenital disorder
i. Contiguous gene syndrome on chromosome 7
1. Elastin and LIM kinase genes deleted
2. Loss of elastinvascular problems
ii. LIM kinase- strongly expressed in brain
1. Deletion of LIM kinase impaired visuospatial constructive cognition in
Williams syndrome
iii. Physical and development problems.
1. "elfin-like" facial features
2. Heart and blood vessel problems
3. Irritability during infancy
4. Dental and kidney abnormalities
5. Hyperacusis (sensitive hearing)
6. Musculoskeletal problems.
b. Generally low IQ but competence in
i. Language
ii. Music
iii. Interpersonal relations