FirstAid: Biochem Molecular/Cellular/Genetics

Loss of heterozygosity: Definition, examples

1. Definition: Cancer requires mutations in both alleles. 2. Examples: Retinoblastoma, Lynch syndrome (HNPCC), Li-Fraumeni syndrome

Pleiotropy: Definition, example

1. Definition: One gene contributes to multiple phenotypic effects. 2. Example: Autosomal dominant diseases (Example: bones, hair, skin are all affected)

Li-Fraumeni syndrome: Genetics/due to, Sx

1. Due to: Autosomal dominant P53 disorder 2. Sx: SBLA cancer syndrome (sarcoma, breast, leukemia, adrenal gland)

Osteogenesis imperfecta: Genetics/due to, Sx

1. Due to: Autosomal dominant mutation resulting in decreased production of normal type I collagen 2. Sx: (A) Fractures (B) Blue sclera (C) Hearing loss (broken ossicles) (D) Tooth abnormalities (sometimes) (teeth that wear easily)

Marfan syndrome: Due to, chromosome

1. Due to: Defective fibrillin (scaffold for elastin) 2. Chromosome: FBN1 gene mutation on chromosome 15

Kartagener syndrome: Due to, Sx

1. Due to: Dynein arm defect (immotile cilia) (autosomal recessive) 2. Sx: (A) Male and female infertility (immotile sperm and dysfunctional fallopian tube cilia). Ectopic pregnancy. (B) Bronchiectasis (C) Recurrent sinusitis (D) Situs inversus (dextrocardia on CXR)

Lesch-Nyhan syndrome: Due to, Sx, genetics, Tx

1. Due to: HGPRT deficiency 2. Sx: HGPRT: (A) Hyperuricemia (B) Gout (C) Pissed off (aggression, self mutilation) (D) Retardation (intellectual disability) (E) Dystonia 3. Genetics: X linked recessive 4. Tx: Allopurinol or febuxostat (2nd line)

McCune-Albright syndrome: Due to, Sx

1. Due to: Somatic mosaic mutation affecting G-protein signaling 2. Sx: (A) Unilateral café-au-lait spots (B) Polyostotic fibrous dysplasia (fibrous dysplasia of more than one bone) (C) Precocious puberty/endocrine abnormalities

Alport syndrome: Definition, Sx

1. Due to: X-linked dominant mutation in type IV collagen causing thinning and splitting of glomerular basement membrane. 2. Sx: "can't see, can't pee, can't hear a bee." (A) Eye problems (eg, retinopathy, lens dislocation), (B) Glomerulonephritis (C) Sensorineural deafness

Which direction along the microtubule does dynein move? Kinesin?

1. Dynein moves: Retrograde (+ to -) 2. Kinesin moves: Anterograde (- to +)

*What inhibits RNA pol in Euk*? Prok? Both Euk and Prok?

1. Euk: α-amanitin (found in Amanita phalloides, death cap mushrooms, *inhibits RNA polymerase II* and causes severe hepatotoxicity) 2. Prok: Rifampin 3. Prok and Euk: Actinomycin D

Menkes disease: Genetics, due to

1. Genetics: X-linked recessive disease 2. Due to: (A) Defective Menkes protein (ATP7A) (B) Impaired copper absorption and transport (C) Decreased activity of lysyl oxidase (copper is a cofactor)

Ehlers-Danlos: Types (3)

1. Hypermobility type (join instability): Most common type 2. Classical type (joint and skin Sx): Mutation in type V collagen 3. Vascular type (vascular and organ rupture): Deficient type III collagen Note: Associated with joint dislocation, berry and aortic aneurysms, organ rupture

Prader-Willi syndrome: Sx

1. Hyperphagia 2. Obesity 3. Intellectual disability 4. Hypogonadism 5. Hypotonia Fat-stupid-weak-tiny testis

X linked dominant diseases: Examples

1. Hypophosphatemic rickets 2. Rett syndrome 3. Fragile X 4. Alport

AngelMan syndrome: Sx

1. Inappropriate laughter (*"happy puppet"*) 2. *Seizures*, ataxia, and severe intellectual disability

What is the initial RNA transcript? What does the initial transcript become?

1. Initial transcript: heterogeneous nuclear RNA (hnRNA). 2. hnRNA is modified and becomes mRNA

How does p53 inhibit the cell cycle? (5 steps)

1. p53 activates p21 2. Inhibits CDKs 3. Hypophosphorylation of Rb 4. Rb binds to and inactivates transcription factor E2F 5. Inhibition of G1-S progression.

Li-Fraumeni syndrome: Due to, results in

1. p53 mutation 2. Results in unrestrained cell division. SBLA cancer syndrome (sarcoma, breast, leukemia, adrenal gland)

DesMin: Use

Muscle tumors (eg, rhabdomyosarcoma)

Neurofibromatosis type 1 (von Recklinghausen disease): Mutation/Chromosome affected

NF1 gene on Chromosome 17; Note: 17 letters in "von Recklinghausen." 100% penetrance, variable expression.

Neurofibromatosis type 2: Mutation/Chromosome affected

NF2 gene on chromosome 22 Note: type 2 = 22.

RNA modification: polyadenylation signal

~200 NT's with the sequence: AAUAAA (Poly-A polymerase does not require a template)

Mitochondrial myopathies: Muscle biopsy

Ragged red fibers

What are anti snRNP antibodies (anti-Smith antibodies) specific for?

SLE

When should we clinically consider uniparental disomy?

In an individual manifesting a recessive disorder when only one parent is a carrier.

Alport syndrome: EM features

"Basket-weave" appearance

Function of clathrin, COPI, COPII

1. Clathrin: (A) Carries protein from trans-golgi to cell membrane and lysosome. (B) Carries protein from cell membrane to endosome (LDL receptor) 2. COPI: Carries protein retrograde from Golgi to RER (or trans-golgi to cis-golgi) 3. COPII: Carries protein anterograde from ER to cis-golgi

What is a Euk promoter region made of?

1. CAAT box 2. TATA box

Menkes disease: Sx

1. *Brittle kinky hair* 2. Growth retardation 3. *Hypotonia*

I- cell disease (inclusion cell disease/mucolipidosis type II): Sx (5)

1. *Coarse facial features* 2. Clouded corneas 3. *Restricted joint movement* 4. High plasma levels of lysosomal enzymes 5. Often fatal in childhood

Adenosine deaminase deficiency: ADA function, effect of deficiency, genetics

1. ADA is required for degradation of adenosine and deoxyadenosine. 2. Deficiency causes: dATP toxicity in lymphocytes. SCID. 3. Autosomal recessive

Autosomal recessive diseases (9)

1. Albinism 2. Autosomal recessive polycystic kidney disease (ARPKD) 3. Cystic fibrosis 4. Glycogen storage diseases/mucopolysaccharidoses (except Hunter syndrome)/Sphingolipidoses (except Fabry disease) 5. Hemochromatosis 6. Kartagener syndrome 7. Phenylketonuria 8. Sickle cell anemia/Thalassemias 9. Wilson disease

MOA of drugs that inhibit pyrimidine and purine synthesis: Leflunomide, methotrexate, trimethoprim, pyrimethamine, 5-FU, 6-MP, mycophenolate, ribavirin, hydroxyurea

1. Leflunomide: Inhibits dihydroorotate dehydrogenase 2. MTX/TMP/pyrimethamine: Inhibits dihydrofolate reductase 3. 5-FU: Inhibits thymidylate synthase 4. 6-MP: Inhibits purine synthesis 5. Mycophenolate/ribavirin: Inhibit inosine monophosphate dehydrogenase 6. Hydroxyurea: Inhibits ribonucleotide reductase

What cells are rich in SER?

1. Liver hepatocytes 2. Adrenal cortex 3. Gonads

What diseases are transmitted through mitochondrial inheritance? How do you Dx these disorders?

1. Mitochondrial myopathies 2. Dx: Muscle biopsy often shows "ragged red fibers." Note: Rare disorders

Function of golgi: 1. What does it do to asparagine? 2. What does it do to serine and threonine? 3. What does it do to proteins that need to be trafficked to lysosomes?

1. Modifies N-oligosaccharides on asparagine. 2. Adds O-oligosaccharides on serine and threonine. 3. Adds mannose-6-phosphate to proteins for trafficking to lysosomes.

What cells are rich in RER? (2)

1. Mucus-secreting goblet cells of small intestine 2. Antibody-secreting plasma cells

McCune-Albright syndrome: What happens if the mutation occurs before fertilization? What happens if the patient has mosaicism?

1. Mutation before fertilization (all cells affected): Death 2. Mutation with mosaicism: Survivable

Locus heterogeneity vs. allelic heterogeneity

1. Mutations at different loci can produce a similar phenotype. (Albinism) 2. Different mutations in the same locus produce the same phenotype. (β-thalassemia)

Sx of mitochondrial myopathies?

1. Myopathy 2. Lactic acidosis 3. CNS disease (stroke/encephalopathy) Note: MELAS syndrome: mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes are 2° to failure in oxidative phosphorylation.

Autosomal polycystic kidney disease: Two types and chromosomes involved

1. PKD1: Chromosome 16 (most common) 2. PKD2: Chromosome 4

*Collagen synthesis: What step is deficient in scurvy? Osteogenesis imperfecta? Ehlers-Danlos? Menkes disease?*

1. Scurvy: Hydroxylation 2. Osteogenesis imperfecta: Forming procollagen (Glycosylation/forming triple helix) 3. Ehlers-Danlos: Cross-linking 4. Menkes disease: Cross-linking

Somatic mosaicism vs. gonadal mosaicism

1. Somatic mosaicism: Mutation arises from mitotic errors after fertilization and propagates through multiple tissues or organs. 2. Gonadal mosaicism: Mutation only in egg or sperm cells.

*What are the steps in collagen synthesis? (6)*

1. Synthesis 2. Hydroxylation (Requires vitamin C) 3. Glycosylation (Error causes osteogenesis imperfecta) 4. Exocytosis 5. Proteolytic processing 6. Cross-linking (Error causes Ehlers-Danlos/Menkes)

What is elastin composed of?

1. Tropoelastin with fibrillin scaffolding (forms a sheath around elastin) (Rich in in nonhydroxylated proline, glycine, and lysine residues) 2. Cross links

What are all the immunohistochemical stains for intermediate filaments?

1. Vimentin (mesenchymal tumors) 2. Desmin (muscle tumors) 3. Cytokeratin (epithelial tumors) 4. GFAP (Neuroglial stain: Astrocytoma and glioblastoma) 5. Neurofilaments (Neuronal tumors)

Rett syndrome: Due to, Epidemiology, onset, Sx

1. X-linked dominant disorder 2. Epidemiology: Girls only (affected males die in utero or shortly after birth). 3. Onset: 1-4 4. Sx: Regression characterized by: (A) Loss of development (verbal abilities, intellect, ataxia) (B) *Stereotyped hand-wringing*

Lesch-Nyhan syndrome: Blood smear features

Megaloblastic anemia with hypersegmented neutrophils Note: Guanine and hypoxanthine is lost so B12 and folate are used to regenerate them which leads to the anemia

What is the most common lethal genetic disease in the caucasian population? Which chromosome is it on? What is the most common kind of genetic mutation in this disease?

CF (CFTR gene mutation on chromosome 7, most commonly involving a deletion of Phe508)

Axonemal dynein

ATPase that links peripheral 9 doublets and causes bending of cilium by differential sliding of doublets.

What disease is due to a defect in type IV collagen?

Alport and Goodpasture syndrome Note: Defective in Alport, targeted by antibodies in Goodpasture

GFAP: Use

Astrocytoma, glioblastoma

What DNA repair mechanism is important in repair of spontaneous/toxic deamination?

Base excision repair Note: Base-specific glycosylase removes altered base and creates AP site, apurinic/apyrimidinic. One or more nucleotides are removed by AP-endonuclease, which cleaves the 5′ end. Lyase cleaves the 3′ end. DNA polymerase-β fills the gap and DNA ligase seals it. Occurs throughout cell cycle.

Basal body: Definition

Base of a cilium below the cell membrane, consists of 9 microtubule triplets with no central microtubules.

Marfan syndrome: Sx (3)

CT disorder affecting skeleton, heart and eyes: 1. Skeleton: Tall with long extremities, pectus excavatum, hypermobile joints and long tapering fingers and toes (arachnodactyly) 2. CV: Cystic medial necrosis of aorta (aortic incompetence and dissecting aortic aneurysm), floppy mitral valve 3. Lens: Subluxation of lenses, typically upward and temporally

What can osteogenesis imperfecta be confused with?

Child abuse

What chromosome is defective in Prader-Willi and Angelman syndrome?

Chromosome 15

Familial adenomatous polyposis: Chromosome involved

Chromosome 5q (APC gene) Note: 5 letters in the word "polyp"

What are the wrinkles of aging due to?

Decreased collagen and elastin production

*Hereditary hemorrhagic telangiectasia (Osler-Weber-Rendu syndrome): Sx (2)*

Disorder of blood vessels causing: 1. Telangiectasias +*AV malformations* 2. Bleeding: *Skin discolorations* , Recurrent epistaxis (*nose bleed*), GI bleeding (poop bleed), Hematuria (pee bleed)

What is mutated in ataxia telangiectasia and Fanconi anemia

Double strand break repair pathway: Nonhomologous end joining Note: Brings together 2 ends of DNA fragments to repair double-stranded breaks. No requirement for homology. Some DNA may be lost.

Neurofibromatosis type 2: Sx (3)

Ears-Eyes-Brain: 1. *Bilateral acoustic schwannomas* 2. Juvenile cataracts 3. Meningiomas and ependymomas.

Cytokeratin: Use

Epithelial tumors (eg, squamous cell carcinoma)

Dominant negative mutation

Exerts a dominant effect. A heterozygote produces a nonfunctional altered protein that also prevents the normal gene product from functioning.

Ehlers-Danlos: Due to

Faulty collagen synthesis

Flow cytometry

Fluorescent labeled antibody binds to cell marker of interest. Purpose is to quantify the number of cellular markers.

What amino acids are necessary for purine synthesis?

GAG: Glycine, Aspartate, Glutamine

Uniparental disomy: What does heterodisomy indicate?

Heterodisomy (heterozygous) indicates a meiosis I error.

Use of southwestern blot?

Identifies DNA-binding protiens

I-cell disease (inclusion cell disease/mucolipidosis type II): Due to

Inherited lysosomal storage disorder: 1. Defect in *N-acetylglucosaminyl-1-phosphotransferase* 2. Failure of the Golgi to phosphorylate mannose residues (ie. mannose-6-phosphate) on glycoproteins 3. Proteins are secreted extracellularly rather than delivered to lysosomes.

Ouabain: MOA

Inhibits K+ site on Na+/K+ ATPase

Cardiac glycosides digoxin and digitoxin: MOA

Inhibits Na-K+ ATPase (indirect inhibition of Na+/Ca2+ exchange leading to an increase in calcium and increased cardiac contractility)

Uniparental disomy: What does isodisomy indicate?

Isodisomy (homozygous) indicates a meiosis II error or postzygotic chromosomal duplication of one of a pair of chromosomes, and loss of the other of the original pair.

Prader-Willi syndrome: Definition

Maternal imprinting: gene from mom is normally silent and Paternal gene is deleted/mutated. Note: 25% of cases due to maternal uniparental disomy (two maternally imprinted genes are received; no paternal gene received).

What gene is MEN 1 associated with?

MEN1 gene

Gene expression modifications: Cre-lox system

Manipulating genes at specific developmental points

What disease is caused by a defect in fibrillin?

Marfan

Vimentin: Use

Mesenchymal tumors (eg, sarcoma), but also many other tumors (eg, endometrial carcinoma, renal cell carcinoma, and meningiomas)

Defect in Lynch syndrome (hereditary nonpolyposis colorectal cancer, HNPCC).

Mismatch repair (Newly synthesized strand is recognized, mismatched nucleotides are removed, and the gap is filled and resealed. Occurs predominantly in G2 phase of cell cycle)

What are anti-U1 RNP antibodies highly associated with?

Mixed connective tissue disease (MCTD)

What drugs act on microtubules? (5)

Mnemonic: Microtubules Get Constructed Very Poorly: 1. Mebendazole (antihelminthic) 2. Griseofulvin (antifungal) 3. Colchicine (antigout) 4. Vincristine/Vinblastine (anticancer) 5. Paclitaxel (anticancer)

Neurofilaments: Use

Neuronal tumors (eg, neuroblastoma)

Defect in xeroderma pigmentosum

Nucleotide excision repair: Pyrimidine dimer repair from UV exposure. (Occurs in G1 of cell cycle and uses endonucleases)

Tuberous sclerosis: Sx

Numerous benign hamartomas Note: Neurocutaneous disorder with multi-organ system involvement. Variable expression.

von Hippel-Lindau disease: Sx

Numerous tumors, both benign and malignant

X linked recessive disorders (11)

Oblivious Female Will Often Give Her Boys Her x-Linked Disorders: 1. Ornithine transcarbamylase deficiency 2. Fabry disease 3. Wiskott-Aldrich syndrome 4. Ocular albinism 5. G6PD deficiency 6. Hunter syndrome 7. Bruton agammaglobulinemia 8. Hemophilia A and B 9. Xtra: PDC deficiency, Menke's, Chronic granulomatous disease 10. Lesch-Nyhan syndrome 11. Duchenne (and Becker) muscular dystrophy

Uniparental disomy: Definition

Offspring receives 2 copies of a chromosome from 1 parent and no copies from the other parent.

What disease is due to a defect in type I collagen?

Osteogenesis imperfecta

AngelMan syndrome: Definition

Paternal imprinting: gene from dad is normally silent and Maternal gene is deleted/mutated. Note: 5% of cases due to paternal uniparental disomy (two paternally imprinted genes are received; no maternal gene received).

Heteroplasmy

Presence of both normal and mutated mtDNA, resulting in variable expression in mitochondrially inherited disease.

Mosaicism: Definition

Presence of genetically distinct cell lines in the same individual

What gene is MEN 2A and 2B associated with?

RET gene

Neurofibromatosis type 1 (von Recklinghausen disease): Sx (3)

Skin-Eyes-Adrenal 1. Café-au-lait spots and cutaneous neurofibromas 2. Optic gliomas and Lisch nodules (pigmented iris hamartomas) 3. Pheochromocytomas

Linkage disequilibrium

Tendency for certain alleles at 2 linked loci to occur together more or less often than expected by chance. Measured in a population, not in a family, and often varies in different populations.

What disease is due to a defect in type III collagen?

Vascular type of Ehlers-Danlos

von Hippel-Lindau disease: Mutation/Chromosome

VHL gene deletion on chromosome 3 Note: VHL = 3 words

Hypophosphatemic rickets: Definition

X-linked dominant disease resulting in increased phosphate wasting at the PCT

Gene expression modifications: RNA interference

dsRNA is synthesized that is complementary to the mRNA sequence of interest. When transfected into human cells, dsRNA separates and promotes degradation of target mRNA, "knocking down" gene expression.

RNA production: *P-bodies (function and contents)*

mRNA quality control in cytoplasm Note: Contain exonucleases, decapping enzymes, microRNAs; mRNAs may be stored in P-bodies for future translation.