BS Hard-to-Remember updated 6/9

Arrow = SMOOTH ER (SER) = network of membranous sacs, vesicles + tubules continuous with the RER but lacking ribosomes

* enzymes involved in biosynthesis of phospholipids, TGs, sterols (e.g. steroid hormones) ABUNDANT IN CORPUS LUTEUM active synthesizers female sex hormones

ADRENALS (steroid hormone synth)

*detox rxns (glycogen degredation, gluconeogenesis, lipoprotein particle assembly)

lots in liverMT: 9 doublets + 2 (ciliary axoneme) +2 dynein arms)

RER ("parallel arrays of membrane-Bound cisternae populated with

multiple electron-dense dots

Cell undergoing mitosis (HETEROCHROMATIN – condensed, tightly wrapped around histones vs. loosely- packed transcriptionally active euchromatin)

1. Gene X is on opposite strand

sequence will run in opposite direction

2. start codon ATP7B is "near first exon gene X" 5'UTR region ATP7B gene is thus either immediately upstream of its translation start codon or immediately downstream gene X exon 1 opposite Gene X 1st intron (see below)

Different receptor types

ARTERIOLlongitudinal x-sectionA= endothelial cell intima B = PMN in vesselC = basal lamina underlying endothelium D = arteriolar adventitia E = smooth muscle cell in media (b/c this section is longitudinal, the normally "fusiform, spindle-shaped" SM cell appears round BUT STILL SHOULD ID THIS EASILY given it's LOCATION b/w ADVENTITIA + INTIMA (e.g. thus = media)

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DO GEL READINGS QUICKLY – if given a gel and asked for the complementary sequence look at the TOP (which is negative side + therefore the end part of the given gene but we want complementary so this will be start of that) + then just switch to complementary NT (eg AT) – only do for as much as needed to find answer in choicesimmediately look at the last NT in sequence = G Complementary will start with opposite of this = C so know strand starts C, T (vs. G, A)

MISSENSE mutation = MC MUTATION TYPELarge segment deletion – alpha thalassemia

BIOCHEM

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Chronic arthritis, black urine Alkaptonuria

- Tyrosine

Liver and kidney dz 2/2 AA issue Tyrosinosis

Albinism Tyrosine def. melaninPale hair + ↑r/o melanoma/skin ca

Pale hair + skin, MR, musty smell Phenylketonuria (AR)

Phenyalaninetyrisone deficient (phenyl enzyme or TB4 coenzyme)

Branched AAs IsoleucineLeucineValineMaple syrup urine dz – CNS, MR, death, sugar-smell diaper)*"I Love Vermont maple syrup"

MR, osteoporosis, marfinoid-habitus, lens subluxation Homocysteinuria↑↑methionine/↓↓cysteine (cysteine becomes essential AA)

What RBC changes would you expect in a female who presents with an inherited hemolytic anemia

Inherited HEMOLYTIC anemia = 1. G6PD deficiency or 2. PK deficiency If woman, unless information given to suggest x-linked (and then receiving 2 “bad” x’s), most likely pyruvate kinase since this is not sex-linked (AR)

NO Heinz (these are in G6PD – RBC denaturation) RIGHT SHIFT in oxygenation curve – if PK, then glycolytic intermediates back up alternate pathway includes 2,3 BPG affinity for O2 (more offloading, LESS pickup - (REMEMBER, fetal Hgb, HbF has 2,3BPG to allow for affinity/more pickup from mom)

Heritability familial hypercholesterolemia AD

MOLECULAR + CELL BIORER secretory/exported proteins – protein folding here

N-linked oligosacch addition Nissl bodies in neurons ChAT enzyme that makes Ach; peptide NTs ↑GI goblet cells (mucous secretion), plasma cells (Ab-secretion)

Chaperones Class of specialized proteins that function to assist proper folding newly synthesized proteins (properGolgiplasma mem etc.)

If they are dysfunctional + poor folding protein is polyubiquinated lysosome for degredation

Will detect protein IN RER BUT WON'T find receptor (the protein) on membrane (e.g. all is good until RER)

Ex – calnexin, calreticulin

SER STEROID synth DETOX rx, poison ↑ hepatocytes (detox) + adrenal ctx (produces steroid hormones)

Golgi Proteins/lipids ERplasma membrane + vesicles Modifies N-oligos on nitrogen of asparagine Adds O-oligos on serine + threonine Add MANNOSE-6-phos for traffic to lysosomes

o FYI : I-CELL DISEASE – don't tag with mannose secrete enzymes OUTSIDE cell instead of lysosome

Coarse face, clouded corneas, restricted jts, ↑↑plasma lysosomal enzymes

Fatal in chldhood

COPI retrograde, GolgiER

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COPII anterograde, RERcis-Golgi

Endosome outside or Golgi lysosome or Golgi

Clathrin Trans-Golgi lysosomes, Plasma membrane endosomes R-mediated endocytosis (forms coat)

Peroxisome membrane-enclosed organelle for catabolism very LCFAs + AAs

Proteins destined for peroxisome incorporation synthesized on free polysomes (ribosomes?)

Proteosome = degradation damaged/unnecessary proteins tagged by UBIQUITIN

Microtubule – general action, processes - Cilia (details below), flagella- Mitotic spindle- Axonal trafficking- Centrioles

*arranged with neg ( - ) end near centrosome (MTOC) + pos (+) radiates OUT

Microtubules - dynein vs. kinesin - Alpha + B-tubulin dimers, each with 2 GTP- DYNEIN = RETROGRADE (+ -) e.g. toward NUCLEUS = NEGATIVE

(hannahs home-made mnemonics – "I'm DYNING IN tonight" (coming to the home/nucleus)

**CLINICAL CORRELATE herpes, polio, rabies viruses + tetanus toxin are all exogenous substances that affect neuron cell bodies via RETROGRADE axonal transport

(Im "DYing over here", regressing –retrograde")

- KINESIN = ANTEROGRADE ( - +) e.g. away from nucleus

Tubulin Monomeric unites that comprise MT (necessary for movement cargo within cell)

Disease caused by defect in microtubule polymerization and fusion of phagosome with lysosome

Chediak-Hagashi – MT polmerization defect ↓↓ fusion phagosomes+lysosomes Recurrent pyogenic infection Partial albino Peripheral neuropathy

Cilia structure 9+2 MT arrangementAxonal dynein-ATPase links peripheral 9 dblts cilium bending

Disease caused by immotile cilia (and cause of immotility) KARTAGENERS – immotile cilia d/t dynein arm defect Male/female infertility Bronchiectasis Recurrent sinusitis Situs inversus Retrograde axonal transport dysf

Drugs acting on microtubules to treat fungus? To treat worms? To treat cancer (2)? To treat gout?

Mebendazole/thiabendazole – anti-helminth

Griseofulvin – anti-fungal

Vincristine, Vinblastine – anti-CA

Paclitaxel – anti-breast CA

Colchicine – anti-gout

Actin/Myosin – general actions - *Microvilli- Muscle ctx- Cytokinesis- Adherens junctions

Location where processing "goes wrong" in cystic fibrosis CFTR protein is misfolded in endoplasmic reticulum

- d/t ΔF508 mutation (deletion phenylalanine) interference folding + post-translational processing of oligosaccharide side chiains

- degraded by proteosome instead of membrane translocation

DNA ligase Catalyzes formation phosphodiester bond b/w 3' OH of DNA fragment with adjacent DNA 5'-monophosphate grp

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DNA Polymerase I Read 3' 5' (e.g. start at OH grp and read toward phos grp)Synth 5'3' (adding new NT's phospho grp on to the free OH grp of growing strand "hydroxyl attack" + energy from new NTs phos grp)Both polymerization NTs and processing/repair mechs

Polymerase III Prokaryote onlyPart of multiprotein complex, major replicating enzyme e. coli

Topoisomerase and Abx - swivel points in DNA to relieve strain at replication (cut+reseal DNA)

Quinolones interfere here

Cytosine deamination = URACIL if intact DNA repair mechanisms, these will be repaired (mismatch repair genes will eliminate via base excision)

Dolichol Substrate for forming branched "carbohydrate trees" that are transferred to proteins in synthesis glycoproteins (mostly protein w/ some attached sugars)

- on RER- goes to golgi, then either plasma membrane/lysosome/secreted protein

"scientist wants to characterize the carbohydrate chains that will be transferred to protein component of albumin. Which molecule functions for synthesis of these chains?*N-linked carbohydrate chains that will be transferred to protein component of albumin are assembled in RER + attached to colichol phosphate

transferred to nitrogen of asparagine to form glycoproeins

- secreted = albumin- retained in membrane = insulin-R- targeted to lysosome = hexosaminidase A (tay-sachs)

Arachidonic acid Precursor of:

- PGs- Thromboxanes- Leukotrienes

FA in phospholipid membrane released by phospholipase A2

Ceramide Parent sphingolipid from which sphingomyelin, cerebrosides, gangliosides are derived (think LYSOSOMAL STORAGE DISORDERS e.g. niemann-pick genetic deficiencies of lysosomal enzymes that should digest these spingolipids cause the diseases)

Dermatan sulfate GAG (glycosaminoglycan)-precursor of proteoglycan (carbs w/ small proteins remember if protein>>carb component = glycoprotein)- part of ECMTypes: chondroitin sulfate, hyaluronic acidRemember *dermatan + heparan sulfates are substrates to enzymes deficient in HURLER (Worse, corneal cloud) + HUNTER dz

Tetracycline Binds ribosomal 30s subunit (prokaryotic small subunit – euk = 40s)prevents aminoacyl-tRNA attachment

Aminoglycoside Streptomycin, gentamycin, tobramycin, amikacin

Inhibits eIFs = elongating initiation factors that help assemble 30s ribosomal subunit with initiatior tRNA

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Ribosome formation, translation 30+50s = 70s prok40+60=80s euyk

ATP activates tRNA (A=activatation)GTP = initiation, translocation, holding on to tRNA (G=gripping, going places)

A site – incoming aminoacyl-tRNAP – growing polypeptide chainE = empty tRNA AA has been transferred to growing molecule on P site (exit)

Ribosome advances 3 NTs toward 3' end mRNA (e.g. toward end whose last NT has free OH)

- This moves peptidyl RNA to P site = translocation

Chloramphenicol 2 MOAs at 50S ribosome

1. Inihibits 50S peptidyltransferase (this is the "top part" ribosome complex 2. Blocks peptide bond formation (so does clinda)

RIBOZYME RNA molecule that has catalyst (E.g. enzymatic – "yme") activityRibosomal rRNA catalyzes peptide bond formation, transfers growing polypeptide to AA in A site (which then moves to P site when ribosome moves 3NTs forward)

Hammerhead Ribozyme Catalyzes sequence-specific cleavage RNA PDE bonds d/t 2° structure they form (looks like head of hammer)- possible use as treatment of "activating" mutated genes (e.g. SOD1 in ALS) synthetic hammerhead RNA w/ complementary sequence to mutant SOD1 mRNA could potentially bind specifically to mutant + destroy via catalyzing PDE bond cleavage"removes mRNA without direct inhibition of translation initiation" – it's a destruction rather than inhibition

Macrolides Erythromycin, azithromycin, clarithro – static (Vs. cidal)

50S inhibitor blocks translocation – this uses GTP normally*(CHLORAMPHENICOL is also acting at 50S but blocking PEPTIDYLtransferase)

Clindamycin Same as second MOA chloramphenicol – block peptide bond formation at 50S ribosome

"Buy AT 30, CCELL (sell) at 50" 30SAminoglycosides (Strepto, genta, tobra) – bacteriocidalTetracycline – bacteriostatic

50SChloramphenicol, Clindamycin – staticErythromycin (macrolide) – staticLincomycin – staticLinezolid (variable static vs. cidal)**Linezolid is for VREs

Mutation in early post-translational modification collagen Ehler-Danlos – skin + msk abnormalities

DNA methylation associated dz Fragile XThis in addition to TRI-NT repeat EXPANSION

CGG triNT repeat in FMRI gene ↑r/o CHROMOSOMAL BREAK- 2 nd MCC MR (1st = Down’s)- MACROCHORDISM (big testes), long face, LARGE + everted ears, autism,

MVP* (Fragile X = Xtra larges teses/jaws/ears)

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Thick gums, large tongue, hip dislocation, clubbing feet, relative immobility extremities and abnormal inclusions in fibroblasts

I-CELL dz Def. N-acetylglucosamine-1-phosptransferase = defect in addition mannose-6-phosphate moiety to lysosomal enzymes released to extracellar space so culture medium will contain lysosomal enzyme activity

- Coarse facies, skeletal abnll, psychomotor retardation- Type 1 – complete def., death in childhood- Type 3 – partial deficiency = milder dz (pseudo-Hurler) survives to adulthood

Incorrect splicing introns associated with what hematologic disorder

B-THALASSEMIA

- B-globin gene (chr 11, HBB gene) incorrectly spliced to give B- or Bo (small function)

Hematologic dz caused by missense pt mutation HbS – Sickle cellChange A-->T at position 6 allows glutaminevaline

HbC = modified version this error (glutaminelysine)

- less serious and Asx if HbC/A but heterozygous HbS/C can act like HbSS and homozygote HbCC gives hemolytic anemia

Transition vs. transversion pt mutation Transition is substitution within same "class" purinepurine / pyrpyr (same ring "type")

Transversion = switch b/w purine/pyr (A-T T-A or C-G)

(remember Purine – PURe As Gold = Glutamine, adenosine; pyrimidine – CUT the PY = cytosine, thymidine, uracil in proks)

Tautomerism switch point mutation Switch single vs. double bond via migration H+

Tautomers are isomers (structural isomers) of organic compounds that readily interconvert by a chemical reaction called tautomerization.[1][2]This reaction commonly results in the formal migration of a hydrogenatom or proton, accompanied by a switch of a single bond and adjacentdouble bond. The concept of tautomerizations is called tautomerism.Because of the rapid interconversion, tautomers are generally considered to be the same chemical compound. Tautomerism is a special case of structural isomerism and can play an important role in non-canonical base pairing in DNA and especially RNA molecules.

Significance of cytosine deamination CU – this is the only deamination rxn that can be CORRECTED via uracil-DNA glycosylase (this can be missed in mismatch repair – HNPCC, endometrial CA)*STEPS REPAIR: 1.Uracil-DNA glycosylase generates Abasic site = AP2. DNA AP endonuclease sees newly formed Abasic site breaks PDE bond3. DNA Polymerase sees break and creates nick + fills 4. DNA Ligase reforms seal with PDE bond

- ALSO CAN RECOGNIZE related deaminase rxn of METHYLATED cytosine (methylated in regulation gene transcription – epigenetics)

o 5methylcytosinethymine + ammonia (MC single NT mutation) – corrected via thymine-DNA glycosylase – fixes cystine—thymine pt mutation in daughter cell

o **Remember, thymine is a methylated uracil so it makes sense that CU would have methyl-CT

- all others NOT recognizedo Adeninehypoxanthine (this now prefers cytosine instead of

thymidine)o Guaninexanthine (this now prefers thymidine instead of

cytosine)

*recall – deamination = removal of amino grp from molecule

NT base with ketone Guanine

NT base with methyl grp Thymine

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Alkylating agents Cross-link guanine NTs in DNA damaging it enough to stop divisionCisplatinCarboplatin

Base analog agents Incorrectly incorporate the analog into DNA but chemically different enough to not make targeted protein, e.g. mismatch at base-pairing causes daughter DNA mutated

BrdU – find replicating cells for research

Methylating agents Transfer methyl grps to DNA NT bases (not used for cancer Rx since it doesn't lead to cell death)*MGMT = methylguanine methyltransferase repairs

EMS = ethyl methanesulfonate – guanine alkylation that can induce high rates of mutations used in genetic screens/assays to induce mutations to be studied

Antimetabolite 5-FU (fluorouracil) – pyrimidine analog; "suicide inhibitor" – irreversible inhibition thymidylate synthase

Antipurine – azathioprine (cleaved to 6-MP), thioguanine

Antifolate – MTX (analogue that binds, inhibiting DHFR and formation THF), TMP, pyrimethamine, pemetrexed

DNA intercalating agent Insert b/w 2 NT pairs ΔDNA transcription/replication

Fluorescent dye – Ethidium BromideCancer Rx – Doxorubicin, DaunorubicinAflatoxin = AspergillisThalidomide – teratogen with strict use policy for last resort anti-inflammatory (leprosy) + salvage chemo in MM (With dexamethosone)

Birth defect = PHOCOMELIA (horrible limb deformities as well as other body regions)

DNA cross-linking agents Form covalent bond b/w DNA NT bases –can't replicate/transcribe

Platinum

Free radicals Highly active in presence of unpaired electrons

- Age-related cell damage

SuperoxideH2O2Hydroxyl radicals

Ionizing mutagens + UV UV = ↓wavelenth/↑energy vs. normal length covalent adjacent thymine bond formed THYMINE DIMER (r/o skin ca)

Ionizing radiation – radioactive materials with high energy that REMOVE electron from molecule/atom damage/death

Mutagens requiring repair via base excision Xrays O2 radicals Alkylating agents Spontaneous rxns

uracil abasic sites created (AP sites) or single strand break (MCC = CU deamination)

DNA glycosylase + AP endonuclease remove/repaire, polymerase+ligase fill in

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Errors of replication A-G mismatchT-C mismatchInsertionDeletion

Mismatch repair (hMSH/hMLH)

Recombinational repair One damaged strand has some replication – use as templateNonhmologous end-joining (ALWAYS MUTAGENIC) – DNA ligase complexes join separate ends dbl helix

N-terminal hydrophobic signal sequence added on during synthesis via cytoplasmic ribosomes

Sequence = "signal recognition particle" (SNP)– attaches growing peptide + ribosomal complex to RER opens up channel allowing peptide to thread into ER lumenWill be on any protein destined to be secreted / membrane-bound / lysosomalIf absent protein would be UNABLE TO enter RER in first place (pre-folding error)

Lysosomes Contain enzymes (made in RER) that degrade sugars (glycosidases) + proteins (proteases)

Intermediate filament stains – vimentin Connective tissue

Intermediate filament stains – desmin Muscle*note – connects cytoplasmic bodies to membrane dense plaques in actin filament structure of smooth muscle; cardiac + skeletal myopathies associated w/ mutations in this protein

Intermediate filament stains – cytokeratin Epithelial cells

Intermediate filament stains – GFAP neuroGLIAL cells – astrocytoma, ependymal cells**REMEMBER – GFAP only marks astrocytomas, for prognosis use Ki-67

Intermediate filament stains – neurofilaments Neurons

Drugs that act on microtubules Mebendazole/thiabendazole – anti-helminthGriseofulvin – anti-fungalVincristine, Vinblastine – anti-CAPaclitaxel – anti-breast CAColchicine – anti-gout

Dynein arm defects KARTAGENERS – immotile cilia d/t dynein arm defect

Male/female infertility Bronchiectasis Recurrent sinusitis Situs inversus

Partial albinism, peripheral neuropathy and recurrent pyogenic infections 2/2 molecular bio issue

Chediak-Hagashi – MT polmerization defect ↓↓ fusion phagosomes+lysosomes

Recurrent pyogenic inection Partial albino Peripheral neuropathy

Kinesin vs. Dynein DYNEIN = RETROGRADE (+ -) e.g. toward nucleus

KINESIN = ANTEROGRADE ( - +) e.g. away from nucleus

Make-up of microvilli actin/myosin – NOT microtubules

Actin, myosin, MT roles in replication Actin/myosin = cytokinesisMicrotubules = mitotic spindle, centrioles

Plasma membrane composition leading to decreased fluidity and higher melting temp

MORE cholesteroal and/or MORE long saturated FAs

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RER activity + what cells have more - secretory/exported proteins- N-linked oligosacch addition- Nissl bodies in neurons ChAT enzyme that makes Ach; peptide NTs- ↑GI goblet cells (mucous secretion), plasma cells (Ab-secretion)

SER activity + what cells STEROID synth DETOX rx, poison ↑ hepatocytes (detox) + adrenal ctx (produces steroid hormones)

Mitosis order InterphaseProphaseMetaphaseAnaphaseTelophase

"PMAT" or "People Meet And Talk"

Hand action mnemonicProphase = fingers linked together in the middleMetaphase = MIDDLE (flat hands)Anaphase = pulled APART (hands apart)Telophase = TWO (close fingers to two fists)

Sign and significance of tripolar mitoses = 3 clusters of chromosomes seen on telophase

Signifies malignancy in tumor

2 drugs that act on Na/K ATPase channel directly (not neuro) Ouabain – binds K+ siteDigoxin/digitoxin (glycosides) – direct inhibit Na/K = indirect inhib Na/Ca (true target) ↑[Ca2+]in = ↑contract

Na/K pump activation Phosphorylated = ACTIVEATPADP (donates phos)

Collagen types I – IV "Be (So Totally) Cool, Read BooksI = Bone, Skin, tendon

Type ONE = BONE

II = cartilage (with hyaline), vitreous body + nucleus pulposus

Type TWO = carTWOlage

III = Reticulin = skin, vessels, uterus, fetal tissue, granulation tissue

Type III = ThreE D defective in Ehlers-Danlos

IV = Basement membrane (Easy, think goodpastures)

"Four = Under the Floor"

Disease a/w DEFECT in Type 1 collagen Osteogenesis imperfecta ("BRITTLE BONE") – COL1A1/2

The one that looks like child abuse Multiple fx w/ minimal trauma BLUE SCLERA (translucent CT over choroid) Hearing loss (ABNL MIDDLE EAR BONE) DENTAL lack dentin

*rememberI = Bone, Skin, tendon

Type ONE = BONE

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Disease a/w DEFECT in Type 3 collagen Ehlers-Danlos – COL3A1 collagen + lysine hydroxylase gene mutations

Hyperextensible skin Easy BRUISING/Bleeds Hypermobile jts

**6 types w/ varying inheritance/severity (AD or AR)

TYPE 4 (rare) = MENKE's dz (x-linked depigmented, lusterless KINKY hair with many facial/ocular/vascular/cerebral manigestations, copper transport defect and ↓activity copper-depndent enzymes LYSYL OXIDASE –REMEMBER, THIS IS CU-DEPENDENT ENZYME that crosslinks pre-collagein in ECM to form mature collagen)

+/- associated with:

Joint dislocation BERRY ANEURYSM Organ rupture

*rememberIII = Reticulin = skin, vessels, uterus, fetal tissue, granulation tissue

Type III = ThreE D defective in Ehlers-Danlos

Disease a/w DEFECT in Type 4 collagen Alport Syndrome (goodpasture = autoimmune not defect)

hereditary GN ESRD HEARING LOSS +/- ocular disturbances MC type = X-LINKED RECESSIVE (BOYS)

*remember IV = Basement membrane (Easy, think goodpastures)

Collagen – 4 steps within fibroblasts + location 1. Synthesis (RER)o Translate alpha chains = PRE-PRO-collageno Gly-X-Y

X/Y = PROLINE, hydroxyproline/LYSINE2. Hydroxylation (ER)

o Of Proline + lysine residues VITAMIN C CRITICAL3. Glycosylation (ER)

o Of Pro-alpha-chain hydroxylysine residues + formation PROcollagen via H + DISULFIDE BONDS

o TRIPLE HELIX of 3 alpha chains 4. Exocytosis

o PROCOLLAGEN extracell

Collagen – 2 steps outside fibroblasts 5. Proteolytic processing- CLEAVE terminal region = procollagenTROPOcollagen (insoluble)

6. Cross-link- reinforce tropocollagen via covalent LYSINE-HYDROZYLYSINE CROSS-LINKSb (LYSIL OXIDASE) FIBRILS

Implicated genetic defect in osteogenesis imperfecta Type I collagen disorderColA1, ColA2 unstable collagen triple helix not as strong (phenotypic outcome depends on unique changes in genes)

2 MC AAs in collagen GlycineProline Gly-X-Y where X = proline (or lysin/glycine), Y = hydroxyproline)

Cartilage with PAS stain Type III – Reticulin (skin, vessels, uterus, fetal tissue, granulation tissue)

Lysyl oxidase Involved in forming collagen fibrils from pro-collagen triple helices that have been secreted into extracellular space *Copper-dependentCross-linkage via covalently binding LYSINE—HYDROXYLISINE Fibrils

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Cofactor requirement in early collagen synth VITAMIN C – 2 nd step (HYDROXYLATION) within fibroblast in ERWithout = SCURVY

Weakened vessels = ulcerated gums, tissue hemorrhage, anemia, ↓wound healing, loose teeth, ↓bone formation

Elastin Stretchy protein in lungs, large arteries, elastic ligaments, vocal cords, ligamenta flava (connect vertebrae for relaxed + stretched conformations)

PROLINE, GLYCINE – NONglycosylated forms Tropoelastin w/ fibrillin scaffold

Disease MC a/w elastin defect Marfans – fibrillin gene**FIBRILLIN = large ECM proteins a/w elastic + non-elastic microfibrils

Elastase and associated disease Breaks down elastase – normally balance break down/build up but in alpha-1-antitrypsin excess elastin = EMPHYSEMA (panacinar) + CIRRHOSIS/liver failure (#1 cause liver transplant in newborns!

Ddx uric acid + gout primary reasons Lesch-NyanAlcoholismG6PDHereditary fructose intoleranceGalactose-1-P uridyle transferase def. (severe galactosemia)**all disoders with increased accumulation of phosphorylated sugars = ↑degradation products (e.g. AMP …uric acid)

Ddx uric acid + gout secondary reasons OVER-PRODUCTIONLeukemiaMyeloproliferative syndromes (MPDs)MMHemolysisNeoplasiaPsoriasis Alcoholism

UNDER-PRODUCTIONRenal failureASADiureticsAlcohol (all 3 categories)

Direction DNA synthesis 5'3'

Direction RNA synthesis 5'3'

Direction DNA/RNA read 5'3' (e.g. mRNA is read 5' 3')

Protein synth NC

Actinomycin D Binds DNA, preventing RNA polymerase from moving along template

Rifampin Binds B-subunit RNA polymerase, inhibits initiation RNA synth

Interstitial deleting Large DNA fragment deleted on single chr pairing 2 genes not normally in sequence with one another (e.g. could bring activation one gene from another)

Fusion oncogene

Chromosomal inversion Large large segment becomes reversed w/i same chromsome rearrangement post-breakage chr = fusion oncogene

Ouabain Binds K+ on Na/K pump, inhibiting Na/K ATPase

Digoxin/digitoxin Cardiac glycosidesDirect bind/inhibit Na/K ATPase indirectly inhibiting Na/Ca exchange = ↑Ca in cell = ↑contractility

Normal amount of an enzyme present yet no enzymatic activity – where is mutation?

NONSENSE mutation – AA change generating 1 of 3 stop codons

mRNA is transcribed correctly but during protein translation, would stop early (truncated, ineffective)

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Three stop codons UGA UAG UAA(U Go Away, U Are Gone, U Are Away)

Test for carrier genetic disease PCRAmplify sequence of question and compare to normal

Steps in testing Lyme ELISA first – screening – sensitive, rapid (can have false+)Follow-up with more specific WESTERN BLOT (protein)

Area where splice acceptor mutation occurs 3' end eukaryotic intron (invariant AG just before end intron) – HIGHLY CONSERVED 5' end intron = GT (GU in RNA) necessary – splice donor site

snRNP Spliceosome

removes introns – recognizing GT at 5' + AG at 3' end = splice sites) mutation here greatly alters protein (B THALASSEMIA = SPLICING DEFECT

chr11, HBB gene additional, contiguous length non-coding mRNA or discontinuous fragment = SNP – SINGLE NT POLYMORPHISM)

Location cleavage propetides collagen Extracellular – first step; therefore is always "pro" type of collagen within cell

Cofactor required by phenylalanine hydroxylase Tetrahydrobiopterin *Defect in either PKU (MR, hypopigmentation…)

What "substance" crosses plasma membrane fastest? CO2, followed by O2 then nitrogen, inhaled anesthetics etc.

diffusion is as rapid for these gases as it is for them in water CO2 has higher solubility vs. water

E-cadherin Allows formation of junctional complexes (critical for formation and maintenance) via homotypic interaction b/w each other (cadherins) that initiates formation zona adherens (including signaling paths) which are then activated to initiate formation zona occludens + desmosomes

Occludin Transmembrane cadherin specific to zona occludens tight junctions

Desmoglein Transmembrane cadherin specific to desmosomes e.g. forms intercellular linkages at desmosomes which connect epithelial cells

PEMPHIGOUS VULGARIS – anti-desmoglein Abso Irregularly shaped erosions in GINGIVAL, BUCCAL, palatine

mucosaeo POSITIVE Nikolsky test – apply pressure + epidermis appears

to separate from underlying dermiso Bx: acantholysis w subsequent loss of cohesion

Sites of synthesis proteins destined for lysosomal incorporation

RER

Bullous pemphigous vs. pemphigus vulgaris Bullous =autoimmune IgG rxn vs. HEMIDESMOSOMES (collagen type XVII aspect)Pemphigous = DESMOGLEIN, tight junctions specific to epithelial cells, blisters, positive nikolsky, oral ulcers

Action of alpha-1-adrenergic agonist (e.g. phenylephrine) on vessels vs. muscarinic

Alpha-1 agonists stimulate R on SM ↑[Ca2+]in (IP3, DAG qiss – Gq) contraction (constrict vessel)Muscarinic can induce NO release (aka EDRF – endo relaxing factor); produced from arginine by endothelial cells

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Muscle band changes during ctx – A, I, H A = NO CHANGEI = shortenH = shorten

(think – A is the best, so no need to improve, no need to Δ)

A-spans width myosin thick filaments (INCLUDING overlap actin thin) length set by length of mysoin (thus noΔ @ctx)

H = thick myosin WITHOUT overlap actin

I = actin filaments ONLY

Z line – where actin filaments attach

MUST KNOW THIS – too easy to not have on tip o tongue

Calculating changing osmolarityEx: cell with osmolality of 300mOsm/kg is placed in salt solution and grows to be 1.5x original size. What is osmolality soln?

MUST KNOW THIS – too easy to not have on tip o tongue

Mass solutes in cell don’t change (while fluid volume does)Mass intracellular solute before = C1V1

Mass intracellular solute after = C2V2

C1V1 = C2V2

300mosm(1) x(1.5) X = 200

Diseases caused by DNA mutation/repair defectsKEY – NER = NT excision repair, AR = recessive, AD = dominant Dz Defect Inheritence Manifestations Tx

Xeroderma pigmentosum NER AR ↑r/o all skin CA (1,000x↑)↑incidence Japan

1. retinoids - ↓CA but irreversible calcification tendons/ligaments- acitretin– treats keratoses, also used in psoriasis2. 5-FU (pyramidine analog antimetabolite)

Cocakyn's syndrome NER AR Bird-facies (thin nose, small head, large ears)Retinopathy, dwarf with long limbs, photosensitiveHyperpigment, erythema, teleangiectasiasPremature aging

No cure – supportive

*CS2 worse than 1

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Trichothiodystrophy NER AR SulfurBrittle hair/nailsFish skin – scalyPhysical/mental retardation

Rare, no cure

Fanconi's Anemia ROS

DNA repair

Cycle ctrl

AR11 genes

BM fail w DNA repair defect- petechiase, bruise, pallor, café-au-lait- infection, fatigue- aplastic anemia (pancytopenia), leukemia, solid tumors (CA – liver, neck, esophagus, vulvar)

Tx symptoms (anemia/leukemia/CAs)

Bloom Helicase

Chr. Instab.

AR ↓growth w/ ↑r/o malignancyButterfly facial telangiectatic erythema-resp/GI infection

Werner's Helicase (WS gene)

AR Aging, thin, tight, scleroderma-like skin↓muscle, wrinkle, hyperkeratosisCataracts, osteoporosis, arteriosclerosis, CA, DMJapan, M=F

First 10 yrs of life normal death 40yo

No tx

ATAXIA-TELANGIECTASIA Chromos + chromatid breaks w rearrangmt

AR chr 7 + 14, ATM gene **(= TCR + Ig regulation chr)**

Heterogenous, but marked by neurodegeneration (ataxia) + telangiectasia (2/2 dilation vessels)- sino-pulm infections↑r/o CA, sensitive to xrays/radiation

Treat SxDeath teens

HNPCC/LYNCH SYNDROME

Mismatch repairMicrosat. Instability

ADMSH2, MLH1, (PMS2), Ras genes

Change in # of repeats of germline alleles accumulation mutations80% r/o CRCFemales have 30-50% r/o endometrial

C'scope q2yr at 25yo, q1yr @40yo (colectomy usual at this pt)

**L colon>R colon – unusual**

BREAST CA p53 DNA repair, cycle

ADBRCA1

60-80% r/o serous adenoCAs

BRCA 2 = ovarian, prostate, pancreatic

CA tx same as regular breast CA but can do ppx mastectomy

GENETICS

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Blotting – which for what SNoW DRoPS = DNAN = RNAW = Protein

Southwest = DNA-binding proteins (TF factors)

This makes sense DNA = South, TF=Protein = West Use labeled oligoNT probes

Blot that allows determination of whether absence of protein is due to failure gene transcribed vs. post-transcriptional defect

Northern blot

Isolate RNA from PMNs gel, blot, 32-P-DNA probe for specific gene

Technique used to separate false positive HIV-ELISA from true positives

Western blot

Uses DNA-DNA hybridization Southern blot

Indirect geenetic testing within families, relatedness of individuals, determination epidemiologic relatedness of bacterial biotypes, e.g. strains S aureus producing TSS

Blot that gives semi-quantitave result for level of gene expression in tissue

Northern blot

Microarray use (for usmle at least) SNP detection (single NT polymorphisms) to study dz/tx

Genotyping Forensics Predisposition to dz Cancer mutations Genetic linkage analysis

*detecting relevant amt complementary nucleic acid sequences to dna/rna probes

Test used to test for antibodies ELISATwo methods:

1. Pts blood + test antigen (coupled to enzyme probe) does pts immune system recognize?

2. Pts blood + test antibody (coupled) is antigen present?

Most sensitive/specific for HIV 100% each

Uses of FISH Microdeletions at molecular level (when deletion too small to see on karyotype

Fluorescent – gene is presentNone = gene has been DELETED

Steps in production recombinant DNA (for cloning)

Isolate eukaryotic mRNA (post-RNA processing) Expose to reverse transcriptase cDNA Insert cDNA into bacterial plasmid containing antibiotic resistance genes surviving bacteria on Ab medium produce cDNA library

Conditional vs. constitutional transgenic mice Conditional = targeted insertion/deletion gene via homologous recombinationConstitutive = random insertion gene into mouse genome

RNAi dsDNA made to separate + degrade target mRNA

Synthesized to complementary mRNA

When in mitosis do you stain for karyotyping? Metaphase

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Microsatellite instability Characteristic with loss-of-function in mismatch repair genes (hMLH, hMSH HNPCC, endometrial CA, ovarian CA, gastric CA)

Areas of diNT repeats a/w "slippage" @replication that Δs number of repeats on new strand (=instability)

o Mismatch repair genes would normally fix

*Normal microsatellites can be 2-4bp totaling <150bp total (↑↑repeats = ↑↑instability)

Lab technique that is best at detecting whether disease is heritable form (E.g. gene deletion) or sproadic

PCR – can see Δ size DNA of amplified bandIf INHERITED – ALL CHROMOSOMES in body will show shorter allele WHEREAS SPORADIC will ONLY have abnormal/short allele IN TUMOR tissue/cell-types

Method of coupling Abs to fluorescent markers to determine cell surface markers of whole cells, e.g. CD34+ stem cells

FACS

Term - Codominance Neither of the 2 alleles are dominantBlood groups (A, B, AB) – O is "no allele"

Term – variable expression Nature + severity phenotype vary 1 personanother2 pts w/ NEUROFIBROMATOSIS may have varying severity

Term – incomplete penetrance Not all individuals with mutant genotype show mutant phenotype

Term – pleiotropy 1 gene > 1 effect on person's phenotype (sort of opposite locus heterogeneity ) PKU causes many seemingly unrelated symptoms (MR hair/skin Δs)OSTEOGENESIS IMPERFECTA (excess atypical fx, scoliosis, basilar skull deformities, blue sclerae, opalescent teeth, skin laxity)

Term - imprinting Diff in phenotype depends on whether mutation is of maternal vs. paternal originPRADER-WILLI – Dad – "happy puppet"ANGELMAN'S – Mom – hyperphagia + obesityChr15*

Term – loss of heterogeneity Patient inherits/develops mutation in tumor suppressor gene then the COMPLEMENTARY allele must be deleted/mutated BEFORE CA developsRETINOBLASTOMA (Rb p100)

Term – Dominant negative mutation Exerts DOMINANT EFFECT heterozygote has non-functional altered protein that prevents normal gene product from functioningMUTATION of TF in its ALLOSTERIC SITE nonfunctioning mutant can still bind DNA thereby PREVENTING wild-type TF from bnding

Term – linkage disequilibrium Tendency for certain alleles to occur together more often than expected by chance

Measured in population NOT family + varies between different pops

Term - Mosaicism Occurs when cells in body have different genetic makeup

- Can be germ-line mosaic – can produce disease not carried in parent's somatic cells

LYONIZATION- random X inactivation in femalesDOWN'S trimsomy w/ mosaicism 47, +21 /46 -2-3% Down's, less severe phenotype (↑IQ etc) – has half normal cells, half not

NON-disjunction chr21 occurs DURING MITOSIS NOT MEIOSIS in an early cell division)

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Term – Locus heterogeneity Mutations at different loci produce same phenotype (Sort of opposite pleiotropy)*MARFAN'S, MEN 2A/B + HOMOCYSTEINURIA all cause MARFINOID HABITUS*ALBINISM (+ acular type – e.g. color-blindnessb)*OSTEOGENESIS IMPERFECTA (type 1 procollagen – chr7 OR chr 17 BOTH lead to imperfect formation trimeric protien)

Term – heteroplasmy Presence both normal + mutated mtDNA = variable expression in mitochondrial inherited dz

LEBER'S HEREDITARY OPTIC NEUROPATHY – degeneration retinal ganglion cells + axon leading to acute loss vision

Term – uniparental disomy Offspring receives 2 copies chr from 1 parent and no copies from other

NONDISJUNCTION – meiosis 1 vs. 2 NONDISJUNCTION = failure of paired chromosomes to separate + go to diff daughter cells leading to one daughter cell getting extra chromosome (n+1) while the other is one chr "short" (n-1)

MEIOSIS I - if NONDISJUNCTION HERE child will get 3 different copies of gene (2 from 1 parent + 1 from other parent) b/c homologues carry SIMILAR but NOT IDENTICAL info

MEIOSIS II – sister chromaatids (2 identical copies SAME chromosome) should separate if NONDISJUNCTION HERE – 2 copies SAME EXACT chrosome passed to progeny (e.g. 1 allele x2 from 1 parent and one from other)

SUM if mom has alleles A+B, dad has C+D if kid gets A, B, C = meiosis I A, A, C = meiosis II

RFLP (restriction fragment length polymorphism) can detect region near centrosome of a chromosome (E.g. chr21) surrounding region exhibits crossover suppression genetic exchange canNOT occur in this area and so probe = reliable marker individual chromosome

Reciprocal vs. Robertsonian translocation Reciprocal: true exchange DNA chrchr (fragments b/w chromosomes) FUSION GENE or CHANGE EXPRESSION existing gene

BCR-ABL 9;22 CML

Robertsonian: large fragment 1 chr another WITHOUT a "return" of DNA (e.g. non-recipricol)

ACROCENTRIC CENTROMERES (o 13, 14, 15, 21, 22

Minority DOWN's has 2114 robertsonian (MCC Downs = trisomy)

3 DIFFERENT types Down's inheritance 1. Trisomy 21 (47, +21) - MCC2. Trisomy MOSAICISM 21 (47, + 21 / 46) – 2-3%

a. 2 "populations" of cell types – normal cell line (46 chrs) AND 2 nd line w/ trisomy 21

i. Less extreme phenotype (e.g. ↑IQ)3. Robertsonian translocation (2114)

Pedigree with horizontal transmission AR – all effected are in same generation, e.g. unaffected parents but affected kids

- 25% offspring 2 carrier parents affected, see in one generation only (usually)

- Commonly more severe than AD disorders shows up in childhood

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Pedigree with vertical transmission AD – 50% offspring affects, across generations

- Often PLEIOTROPIC, presenting after puberty- FH crucial to dx

Pedigree x-linked recessive M > F (female must be homo zygous ), but dad never passes on to his son (e.g. NO malemale transmission)

- 50% sons to MOM CARRIER affected (heterozygoous mom)-

Pedigree x-linked dominant *If DAD is affected ALL DAUGHTERS affected *If MOM is affected Sons and daughters MAY be affected

Example x-linked dominant HYPOPHOSPHATEMIC RICKETS (formerly = vitamin-D-resistant rickets)

- ↑phosphate wasting PROXIMAL TUBULE

rickets-like presentation

Heteroplasmy Normal AND mutant MITOCHONDRIAL DNA (mtDNA)are expressed

Ex of mitochondrial inheritance + genetics inheritance

*transmission via mom only all offspring (M/F) may have signs dz**often d/t failure oxidative phosphorylateion

- Variable exprssion d/t heteroplasmy

MITOCHONDRIAL MYOPATHIES

- LEBER’S HEREDITARY OPTIC NEUROPATHY – acute loss of central vision- MYOCLONIC EPILEPSY

- MITOCHONDRIAL ENCEPHALOPATHY

"RAGGED RED FIBERS" on microscopy

Female who is heterozygous for X-linked recessive gene can sometimes have mild expression of disease phenotype - how?

X inactivation is random event normally, female has enough "normal" phenotype b/c on average, ½ of cells will express normal allele HOWEVER, extrae degrees of X-chr inactivation can lead to predominance one allele can express gene

G6PD – mild anemias Hemophilia – mild bleeding

Female expressing FULL phenoytype of x-linked recessive disease

Possible if concomittant TURNER'S SYNDROME (SHORT stature etc) since only 1 X

WILL SEE ABNORMAL KARYOTYPE – will see a missing sex chr

Hardy-weinberg p2 + 2pq + q2 =1p + q = 1

generally, given disease freq (p2) or allele freq (p)if GIVEN disease freq, than calculate mutant allele freq = √p2 = pUsing, p, find normal allele freq = 1-p = qNow can determine carrier freq = 2pq or if asked to predict FUTURE baby given just one partner, using the calculated p+q AND BE SURE to account for various possible outcomes as you would with ANY baby problem – e.g. if asking about baby carrier status to a heterozygote + normal person, than know it is 50% but if you DON’T know status 2nd partner, use allele freq population as frequency that gene in partner (almost as though treating like variable penetrance) – see below problem

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Given that 1 partner is heterozygous for an autosomal recessive trait (pq) and the frequency of dz (A), AND NO OTHER INFO, how could you predict the chance that the partner will have a diseased baby without knowing the other partner's status?

If frequency of dz = A,, then a = p2

- allelic frequency = √A this will also be EQUAL TO frequency egg carrying the recessive allele (√a, or pA)

- if 1 partner is KNOWN CARRIER, there is 50% of passing on recessive allele- thus, chance that he will have a child with the disease = (0.5)( √A), i.e.

(0.5p)

with numbers: if 1% population has X and 1 partner is carrier, 2nd partner status unknown

0.01= p2 p = 0.1

Change in H-W equation if disease is X-linked Males hemizygous = 1 allele FREQUENCY OF ALLELE will be EXACTLY THE SAME as the GENOTYPE e.g. q2 = q (incidence dz = incidence allele)

MALES: p + q = 1 is equation expressing allele freq AND gen. freqFEMALES: p + q = 1 allele freq ONLY; for gen. freq, need p2 + 2pq + q2 =1

"The incidence of DMD in N. America is 1/3000. Based on this frequency, what is the gene frequency of this trait?" 1/3000!

**ON EXAM, BE CAREFUL – they will not say "THIS IS X-linked" so PAY ATTENTION to the DISEASE BEING MENTIONED – do not go right to equation b/c it changes If x-linked(x-linked = Boys Wish For Hannah's GOLD Hockey Skills – bruton's agammaglobulinemia, wiskot-aldrich, fabry's, hemophilia, G6PD, ocular albimism, lesch-nyhan, duchennes(+beckers), hunters syndrome)

ASSUMPTION MADE IN H-W EQUATIONS P = 1

**DON’T FORGET TO MULTIPLY BY 2 TO GET CARRIER FREQUENCY after calculating q (carrier = 2pq and if p=1, carrier = 2q)

LINKAGE DISEQUILIBRIUM Preferential association of allele at one locus with another allele at nearby locus more frequently than be chance alone

Genetic drift vs. gene flow DRIFT – gene frequency Δ d/t FINATE population size – would ONLY SEE in small/closed communitiesFLOW – gene exchange b/w different populations

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WORKING THROUGH ALPHA-THAL genetics

27yo Asian-American male comes to ED with RUQ abdominal pain + nausea. Studies show mild, microcytic hypochromic anemia + target cells. Has a ____ who died at birth from blood disease and uncle with HbH. Wife has completely normal blood. Chance that patient will have carrier child. We know that BOTH parents must have one completely normal alpha/alpha allele and one completely abnormal - - / - - allele to have had hydrops baby. Because patient is presenting with symptoms, can assume he carries trait, e.g. 2 bad alleles out of 4 AND since he is living must have one full normal + one full abnormal e.g. ( a a / - -) will have 50%

chance passing on (a

a) allele and 50% chance of

passing on bad ( - -) allele. Since wife is clean, 50%

chance child will have trait

*NOTE* the double mutant allele (a a ) is MC in asian population. Otherwise, more frequently have trait with (a - / a - ) or silent carrier (a - / a a )

**REMEMBER** 2 variations "alpha-thal trait" (a a / - -) OR (a - / a - ) 2 allelesHbH = (a a / a - ), Hydrops = (a a / a a) 3 + 4 allelesSilent carrier = ( a - / a a) 1 allele

Disorders by mutated gene/function (see separate "Chromosomal" table too)

ATM gene mutation ATAXIA TELANGIECTASIA

(as name implies…) multiple dilated vessels + progressive ataxiaGene – kinase responsible for recognizing/correcting errors in duplicating DNA during cell division normal = repair ds DNA breakmutant = ↑sensitivity ionizing radiation frequent chromosomal abnormalities↑↑incidence MALIGNANCIES ESPECIALLY lymphoreticular (these cells are dividing most frequently) = HL, NHL, leukemias

Excision endonuclease XERODERMA PIGMENTOSUM

UV light sens freckles, skin CA, corneal ulcerations

Gene thymine dimer repair via nick PDE bond on strand w/ dimer on both sides + removes Defect – dimers persist

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Splice site mutation (5' UTR of ATP7B gene) WILSON'SCopper accumulation (d/t absence ceruloplasmin) in liver, brain, cornea- Asterixis - BG degeneration producing parkinsonian sx-Kayser-Fleisher rings – corneal deposits

DOWN's 1. TRISOMY 21 (47, +21) - MCC2. Trisomy MOSAICISM 21 (47, + 21 / 46) – 2-3%

a. 2 "populations" of cell types – normal cell line (46 chrs) AND 2 nd line w/ trisomy 21 – ½ nl, ½ not

i. Less extreme phenotype (e.g. ↑IQ)

NON-disjunction chr21 occurs DURING MITOSIS NOT MEIOSIS in an early cell division)

3. ROBERTSONIAN TRANSLOCATION (2114)

DOWN'S trimsomy w/ mosaicism 47, +21 /46 -2-3% Down's,

Chromsomal disorders - specific chromosome locations

Disease Chrom-Osome

Gene Manifestations

CYSTIC FIBROSIS 7AR

CFTRΔF508(phenylalanine delete)

Protein misfolded and improper oligosacch additions at endoplasmic reticulumproteasome (degredation) instead of plasma membrane

Pseudomas, S. aureus infections PNA, bronchitis/bronchiectasis Pancreatic insuff, steatorrhea, VitA/D/E/K def Male infertility Biliary cirrhosis, meconium ileus

Dx ↑NaCl on sweat test; PCR + ASO probesTx enzyme + vitamins etcN-acetylcysteine (LOOSENs mucus plugs CLEAVES disulfide bond w/i glycoproteins)

MEN 2A/2B 10AD

RET – RTK that binds neutrophic factors that signal cell to grow+divide (gain of function/activating)

**OTHER RET = hirschsprungs

BOTH 1.medullary thyroid CA 2. pheochromocytoma; plus A=pituitary adenoma B=oral/facial ganlioneuromatosis (e,g, mucosal neuromas- LIPs) +marfinoid

PRADER-WILI VS. ANGELMAN

15q11 (deletion in area affected by imprinting)

M aternal deletion (With silent, methylated father allele) = AngelMans (happy puppet)P aternal deletion (silent/methylated mom allele) = Prader-Willi (MR, hyperphagia+obesity with initial poor feeding)

CRI-DU-CHAT 5q microdeletion High pitched monotonic cry

- Microcephaly, wide-set eyes, MR - Epicanthial folds- CARDIAC ABNORMALITIES , e.g. VSD

LI-FRAUMENI AD p53Loss-of-function mutation/deletion tumor suppress gene

↑r/o breast CA, colon CA, soft-tissue sarcoma, osteosarcoma, brain tumors, leukemia + adrenocortical CA

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MICROSATELLITE INSTABILITY (2+)

AD w/ variable pene-trance

hLMH1 + hMSH2mismatch repair genes

MC association = HNPCC but also in:

- Endometrial CA

- Ovarian CA- Gastric CA

DIGEORGE 22q11 *thymus – structural/functional defect; missing T-cell immunodeficiency*hypoparathyroid = 2° hypercalcemia*craniofacial abnormalities, palate

SICKLE CELL AD Glutaminevaline @position 6 in Beta-globin gene

WILMS TUMOR 11p13 Microdeletion Malignant urinary tract tumor 2/3 dx by 4yo Surgical removal

NEUROFIBROMAT

OSIS TYPE 1 (VON RECKLINGHAUSEN)

17AD

NF1 tumor-suppressor gene 90% NF cases (vs. type 2)

Multiple neurofibromas Café-au-lait Lisch nodules – pigmented iris hamartomas ↑r/o pheochromocytoma + mengingiomas

NEUROFIBROMAT

OSIS TYPE 2

22AD

NF2 tumor suppressor gene BILATERAL acoustic neuromas (schwanomas is tip-off) – otherwise, the rest are both NF1/2:

Neurofibromas Café-au-lait ↑r/o meningioma+pheo

MARFAN 15AD

FBN1 – fibrillin 1

**FIBRILLIN = large ECM proteins a/w elastic + non-elastic microfibrils

Marfinoid habitus – tall, hyperextensible, pectus excavatum + kyphoscoliosis

Subluxation lens Heart defects

o Cystic Medial Necrosis of aortao Dissecting AAo Valvular insufficiency – Mitral regurg = holosystolic murmur

in apexo MVP = midsystolic click)

VON HIPPEL-LINDAU (VHL)

3AD

VHL = tumor suppressor gene Hemangioblastomas CNS + RETINA RENAL CELL CA Cysts internal organs

TUBEROUS SCLEROSIS

AD TS 1/2 Sebaceous adenomas (Angiofibromas of sebaceous glands)o Subependymal nodules = LISCH NODULES

Epilepsy MR dysplastic white matter lesions = Hamartomatous lesions skin, CNS,

viscera Cortical tubers Shahreen patches (see picture -- -- --- --- Ash-leaf spot (hypomelanic, light patches,

Wood's) RENAL ANGIOMYOLIPOMAS

Heart DefectRHABDOMYOMAS

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OSTEOGENESIS IMPERFECTA ("BRITTLE BONE")

7 or 17 - locus hetero-geneityAD

COL1A1/2 – type 1 procollagen **PLEIOTROPY** - blue sclerae seemingly unrelated to fx**LOCUS OF HETEROGENEITY** 2 diff single chromosome mutationssame dz

Looks like child abuse Multiple fx w/ minimal trauma BLUE SCLERA (translucent CT over choroid) Hearing loss (ABNL MIDDLE EAR BONE) DENTAL lack dentin

*rememberI = Bone, Skin, tendonType ONE = BONE

EHLERS-DANLOS AD and AR – many types

COL3AType 3 collagen

Hyperextensible skin Easy BRUISING/Bleeds Hypermobile jts

**6 types w/ varying inheritance/severity (AD or AR)+/- a/w:

Joint dislocation BERRY ANEURYSM Organ rupture

*rememberIII = Reticulin = skin, vessels, uterus, fetal tissue, granulation tissueType III = ThreE D defective in Ehlers-Danlos

ATAXIA-TELANGIECTASIA

Chro-mos + chrom-atid breaks w/ rearrangmt

AR chr 7 + 14, ATM (PI3 kinase) that phosphorylate >700 proteins in DNA repair* inc. p53 + BRCA-1 tumor supp( chrs correspond to = TCR + Ig reg)**

Heterogenous, but marked by neurodegeneration (ataxia) + telangiectasia (2/2 dilation vessels)- sino-pulm infections↑r/o CA, sensitive to xrays/radiation

(WERNERS) AR WS gene helicase error Aging, thin, tight, scleroderma-like skin↓muscle, wrinkle, hyperkeratosisCataracts, osteoporosis, arteriosclerosis, CA, DMJapan, M=F

FANCONI AR 11 genes DNA repair, ROS vulnerability, Cell cycle dysregulation

BM fail w DNA repair defect- petechiase, bruise, pallor, café-au-lait- infection, fatigue- aplastic anemia (pancytopenia), leukemia, solid tumors (CA – liver, neck, esophagus, vulvar)- Tx symptoms (anemia/leukemia, etc)

XERODERMA PIGMENTOSUM

AR Excision endonuclease – thymine dimer repair

UV light sens freckles, skin CA (1,000x↑), corneal ulcerations↑incidence JapanTx: 1. retinoids - ↓CA but irreversible calcification tendons/ligaments- acitretin– treats keratoses, also used in psoriasis2. 5-FU (pyramidine analog antimetabolite)

Normal gene thymine dimer repair via nick PDE bond on strand w/ dimer on both sides + removes Defect – dimers persist

BREAST CA AD BRCA 1 (2 = ovarian/ prostate/ pancreatic)

60-80% r/o serous adenoCAs

ALS AD SOD1 – copper/zinc superoxide dismutase

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MENKE'S (TYPE 4 EHLERS-DANLOS)

X-linked

ATP7A – ATP-dependent copper transport protein

Ehlers-Danlos type 4 – "collagen" connection is due to requirement copper co-factor for lysyl oxidase (final steps collagenin EC space) defective copper transport + abnormally ↓ activity copper-dependent enzymes (one of which is lysyl oxidase) with ↓ ceruloplasmin levels

-depigmented, lusterless hair = "KINKY HAIR"- osteoporosis, anemia- facial/ocular/vascular/cerebral manifestations (think head-up + vessels, which always comes with collagenous dz)

"A 4mth old boy appeared healthy at birth but now has poor growth, ↓feeding and delayed developmental milestones. PE shows listlessness + matted, sparse + very pale hair"

HUNTINGTON 4AD

CAG triNT repeat Depression Progressive dementia Choreiform CAUDATE ATROPHY ↓GABA + ACh in brain 20-50yo

SICKLE CELL AR

FAMILIAL ADENOMATOUS POLYPOSIS

APC - tumor suppressor gene

RETINOBLASTOMA AD w/ variable pene-trance

Rb - tumor suppressor gene**ALSO IN OSTEOSARCOMA**

WILLIAM'S DISEASE

7q Elastin (microdeletion) Elfin facies, HYPER-Ca2+ 2/2 ↑ sensitivity to vitD ), good verbal, very friendly , heart issues

ACHONDROPLASIA 3AD

FGF-R3- cell signaling defect

Dwarf, short limbs, but normal head/trunk size**a/w advanced paternal age

FAP 5AD

APC – deletion - >puberty, colon covered with polyps- CRC always if not resected /(usually ~40yo)

DUCHENNE'S MUSCULAR DYSTRPHY VS. BECKER'S

X-linked

Dystrophin

– LARGE DELETION single gene vs. pt mutation same gene

DUCHENNE = frame-shift = DELETION dystrophin gene accelerated muscle breakdown

- Onset <5yo = pelvic girdle weakness (need UE helpto get out of chair “sign” = COWER’S) progresies superiorly

- PSEUDOHYPERTROPHY CALF muscles 2/2 fibrofatty replacement muscle

- Cardiac Myopathy- Dx = CPK, muscle biopsy- **Dystrophin Gene (DMD) = helps anchor muscle fibers (skeletal +

cardiac)- LONGEST known human gene rate spontaneous mutation

BECKER’S = IN-frame deletion or insertion - less severe, some functional gene made- Onset adolescence early adult

**SUBCLINICAL FEMALES** - heterozygous carriers have degeneration fibers

ADPKD 16AD

APKD1 (90%) *ALWAYS BL, massive ↑ kidneys d/t multiple large cysts*Present flank pain, hematuria,HTN, RF

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FAMILIAL HYPERCHOLESTEROLEMIA (TYPE IIA )

↑↑LDL 2/2 defect/absent LDL-R**Heterozygotes (1/500) = 300**Homozygotes (RARE) = 700+

- Severe atherosclerotic dz early in life- TENDON XANTHOMAS (achilles)- MI <20yo

HEREDITARY HEMORRHAGIC TELANGIECTASIA (OSLER-WEBER-RENDU)

BLOOD VESSELS

- Telandiectasias- Recurrent epistaxis- Skin discoloration- AVMs

HEREDITARY SPHEROCYTOSIS

Spectrin OR Ankyrin Spheroid RBVs d/t hemolytic anemia + SPLENECTOMY CURATIVE↑MCHC

MYOTONIC DYSTROPHY

19AD (can be spont.)

CTG triNT in protein kinase MyoTonic = CTG (vs. CGG = fracile X)Clinically UNIQUE:

- Weakness- Atrophy- Myotonia (tonic ctz) - Head+neck often most weak/atrophic

WONT RELEASE HAND WHEN YOU SHAKE

FRAGILE X X-linked

(xq27)

CGG triNT repeatsFMR-1 gene

↑ r/o CHROMOSOMAL BREAK- 2 nd MCC MR (1st = Down’s)- MACROCHORDISM (big testes), long face, LARGE + everted ears,

autism, MVP* (Fragile X = Xtra larges teses/jaws/ears)IN ADDITION to TRI-nt rpt exp, also role of DNA METHYLATION

Dx = >4% metaphase chromosomes must show specific break-pt on X chr (percentage above 4% does NOT correlate w/ severity MR)

FINAL MIX GENETICS, MOBIO, CELL BIOChild with poor eye contact and HAND FLAPPING Fragile X

CGG repeat

If 1/100 ppl have disease A which is AR, what is carrier population freq?

(1/100)1/2 = 1/10 = p

1 – 1/10 = 9/10 = q2pq = 2(9/10)(1/10) = 18/100

Calculating changes in volume with compartments of different salt concentrations

C1V1 = C2V2 (before and after change in environment)Key is that Mass = C x V and this remains constant

Mediator of lysosomal enzyme delivery to lysosomes

Clathrin-coated vesicles

Given phenotype that is related to inheritable tumor, best lab test to determine if it is due to inherited mutation or sporadic mutation?

PCR

- the cells in an inherited disease will all show the different (mutant) DNA allele size as all cells came from same progeny

- cells in sporadic disease will only have abnormal IF you are testing cells from tumor tissues – all other, non-involved cells will only provide alleles of “normal” size

2 ways that a female can exhibit phenotype of X-linked recessive mutation

1. Concomitant Turner 45X,0 (hints include a short stature, female 2 sex characteristics) – this is similar to being male with only 1 X copy2. 2 copies mutant X gene – must be a disease that does not affect father’s fertility, such as G6PD

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Common sex chromosome aneuploidy that would have fetal tissue expressing Barr bodies

Klinefelters XXY – only ones with two X’s, thereby leading to inactivation of one (Barr) - NOT Turner’s 45XO (even though this is “female” missing 2nd x chr means no Barr)

Type of chromatin in mitotically dividing cell

Heterochromatin (closed/wrapped; euchromatin = open for active transcription)

Part of cell cycle where triNT repeats in number S (synthesis)

Adolescent boy with recent h/o burning + tingling of hands found t have corneal opacities + angiokeratomas (benign cutaneous lesion of capillaries = small marks red/blue color )

Fabry’sBoy = x-linked

Cellular component mitotic spindle Microtubule

Cellular component microvilli ACTIN (+ myosin by extension)

Cellular component cilia Microtubule (9+2 arrangement dynein – think Kartagener’s)

Child diagnosed with an AD disease (e.g. Marfan’s) with no family history – what is most likely cause?

New mutation transmitted by one parent to affected child

What does CREB, SP-1, RNA polymeras, + steroid receptor have in common

All are “TFs” or modulators of transcription on DNA for regulation of protein synthesis

If membrane protein seen in RER but not membrane or cytoplasm…

Misfolding ubiquination + degradation path (proteasome)

Infant with hyperplastic gums, lethargy, misshapen long bones, restricted jt movements, corneal clouding, parents are 1st cousins

I-cell diseaseDefective phosphorylation of mannose moieties lyosomal enzymes not targeted to lysosome = serum levels acid hydrolases + glycosylases

Protein critical in formation + maintenance junctional complexes such as the tight junctions between enterocytes

E-cadherinsOccludins = zona occludeDesmogleins = specific junction protein in epithelial cells (pemphigus vulgaris w mouth ulcerations)

Action of hammerhead ribozymes Degrade mRNA (catalase activity) of which they have homologous sequence (to bind)

Gas that diffuses fastest across lipid membrane CO2, followed by O2, then all others (e.g. nitrogen)

Effect of a mutation AG CG at 3’ end eukaryotic gene intron

Abnormal splicingAG = highly conserved (invariant)) spliceasome acceptor site sequence at 3’ end all introns (matches this with preceding 5’ GT (GU in RNA) seq)

Listless infant with matted, sparse, pale hair, poor growth, developmentald delay

activity LYSYL OXIDASE= MENKE’S X-LINKED (Ehler’s Danlos type 4, ATP7A mutation)- defect copper transport = activity Cu-dependent enzymes with ceruloplasmin levels**DEPIGMENTED LISTLESS/KINKY HAIR is biggest tip off”

Substrate in synthesis of carbohydrate chains that are transferred to protein component of glycoproteins such as albumin

Dolichol

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Hexosaminisae A deficiency TAY-SACHSCherry red macule without hs-megaly (N-P)

Capping of mRNA Occurs immediately after synth 1 st 30 NTs (e.g. before transcription even finishes since read 5’3’ will be “done” earliest)

- GTP condenses w/ available 5’ diphosphate on growing RNA chain forms GUANINE CAP

- Cap recognized during protein synteshsi- Protects RNA from degradation

cytochrome b5 reductase = IRON-dependent enzyme, aka NADH methemoglobin reductase – major pathway that reduces methemoglobin which forms spontaneously with oxidative stress etc.

Deficient METHEMOGLOBINEMIA cyanosis (nl amt <1%)- metHb = OXIDIZED form Hb (Ferrous Fe2= Ferric Fe 3+ ) = affinity O2 (curve shifts LEFT) unloading O2 at tissue (blood has O2-carrying capacity, turns brown)

can arise in pts with PK def d/t impaired NADH production = ESSENTIAL COFACTOR of enzyme or in G6PD def d/t impaired NADPH cofactor

* (Also is recessive genetic defect in chr or can occur with abnl Hb variants, e.g. HbM or HbH)

*remember oxidized = less electrons, reduced = more, so Fe3+ has MORE positive charge/less electrons = oxidized*

CAUSES OF ACQUIRED METHEMOGLOBINEMIA

1. Exogenous oxidizing Rx + metabolites - rate formation metHb overwhelms protective systems = acute metHb levels

o benzocaineo dapsoneo nitrates

2. ABX a. TMPb. Sulfasc. Dapsone

3. Local anesthetics a. Articaineb. prilocaine

4. ANILINE DYES (polyurethane, indigo; normally a/w BLADDER CA)5. Metoclopromide DA-blocking Antiemetic (D2-R antagonist with mild

5HT-3 antagonism + some anti-muscarinic effects)a. ALSO gastric emptying in gastroparesis good antiemetic

for DM pts); stimulates lactation)b. Parkinsonian SEs, contra in SBO

6. Chlorates, bromates7. Nitrate ingestion (bismuth nitrate) “BLUE BABY SYNDROME” in

babies drinking contaminated water from FERTILIZER nitratesa. Babies also get from dehydrration 2/2 diarrheal GE, sepsis,

topical anesthetics w/ benzocaine, prilocaine (benzocaine also often in baby teething gels applied to gum/throat)

*Tx Methylene Blue IV (or flavin) then normal saline flush (= artificial e- acceptor for NADPH methemoglobin reductase (enzyme function at 5x nl) NADPH generated via HMP shunt

RESTORES Fe3+ Fe2+ =normal/reduced O2-carrying state)

Selenium deficiency levels glutathione peroxidase MYOPATHY + CM

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2 congenital diseases with MR + skin hypopigmentation (not neurocutaneous)

MENKE’S (E-D type 4, x-linked Cu-enzyme def., lyosyl oxidase)PKU

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EMBRYO

PATHOLOGY + MISCELLANEOUS

Analine dye association URINARY BLADDER CA – industrial workers (also shistosomal parasites outside of US with general RFs = smoking, exposure to certain chemicals + parasiteic infection)

- Also a/w methomologbloinemia

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Points of exit for Trigeminal nerveStanding Room Only:V1 - Superior orbital fissureV2 - foramen RotundumV3 - foramen Ovale

Extensor Compartment of the Arm

Beer Brachioradialis

Eating CReoLe Extensor Carpi Radialis Longus

Eating CRaB Extensor Carpi Radialis Brevis

Eating Dog Extensor Digitorum

Eating Dog's Mother Extensor Digiti Minimi

Even Cathy's Underwear Extensor Carpi Ulnaris

Great vessels- ABC'S of the aortic arch:Aortic arch, Brachiocephalic trunk, the left common Carotid, and the left Subclavian arteryThoracic ductThe duck is between two gooses:duck = thoracic duct2 gooses = azyGOUS vein and esophaGOUSOrder of structures in groin (from lateral to medial)NAVELNerve, Artery, Vein, Empty space, LymphaticsCarpal bonesSome Lovers Try Positions That They Can't HandleScaphoid, Lunate, Triquetrum, Pisiform, Trapezoid, Trapezium, Capitate, Hamate.Gluteal Muscles Rhmye Time: "Tensor Fasciae Latae, Gluteus Med & Min...first abduct the femur, then rotate it in." All other gluteal muscles are lateral rotators of the femur. BONUS: Tensor Fasciae Latae, Gluteus Minimus, and Gluteus Maximus are all innervated by the Inferior Gluteal Nerve.Radial nerve"BEST"It innervates the Brachioradialis, Extensors, Supinator, Triceps.Median nerve"LOAF"It innervates the Lateral 2 Lumbricals, Opponens pollicis, Abductor pollicis brevis, Flexor pollicis brevis.Brachial Plexus Lesions"DR. CUMA"D - wrist Drop (is caused by...)R - Radial nerve lesion

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C - Claw hand (is caused by...)U - Ulnar nerve lesionM - Median nerve (lesion causes...)A - Ape handMitosisPeople Meet And Talk, orPMATProphase, Metaphase, Anaphase, Telophase.

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