Basic Science quick facts step1

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BS Hard-to-Remember

BS Hard-to-Remember updated updated 6/96/9

Arrow =

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

with the RER but lacking ribosomes * enzymes involved in biosynthesis of * enzymes involved in biosynthesis of phospholipids, TGs, sterols (e.g.

phospholipids, TGs, sterols (e.g.steroid hormonessteroid hormones)) ABUNDANT IN CORPUS LUTEUM

ABUNDANT IN CORPUS LUTEUM activeactive synthesizers female sex hormones

synthesizers female sex hormones



ADRENALS (steroid hormone synth)ADRENALS (steroid hormone synth) *

*detoxdetoxrxns (rxns (glycogen degredation,glycogen degredation,

gluconeogenesis, lipoprotein particle assembly gluconeogenesis, lipoprotein particle assembly ))



lots inlots in liver liver

MT:

MT:9 doublets + 29 doublets + 2((ciliaryciliaryaxoneme) +axoneme) +2 dynein2 dyneinarms)arms) RER

RER ("parallel arrays of membrane-("parallel arrays of membrane-Bound cisternae populated with Bound cisternae populated with multiple electron-dense dots multiple electron-dense dots

Cell undergoing mitosis Cell undergoing mitosis

((HETEROCHROMATINHETEROCHROMATIN – –condensedcondensed, tightly, tightly wrapped around histones

wrapped around histones vsvs. loosely-packed. loosely-packed transcriptionally active euchromatin) transcriptionally active euchromatin)

1. Gene X is on opposite strand

1. Gene X is on opposite strandsequence will run insequence will run in opposite

oppositedirectiondirection 2.

2.start codonstart codonATP7B is " ATP7B is " near first exon gene X near first exon gene X " "



 5'UTR region ATP7B gene5'UTR region ATP7B geneis thus either is thus either immediately upstream of its translation

immediately upstream of its translationstart codonstart codon or immediately downstream

or immediately downstreamgene X exon 1gene X exon 1 opposite Gene X 1

opposite Gene X 1ststintron (see below)intron (see below)

Different receptor types Different receptor types

ARTERIOLl

ARTERIOLlongitudinal ongitudinal x-sectionx-section A=

A=endothelial cellendothelial cell intima intima B = PMN B = PMNin vesselin vessel C = basal lamina C = basal lamina underlying underlying endothelium endothelium D = D =arteriolararteriolar adventitia adventitia E =

E = smooth musclesmooth muscle cell

cell ininmediamedia(b/c(b/c this section is this section is

longitudinal, the normally "

longitudinal, the normally " fusifor fusiform, spindle-m, spindle-shaped" SM cell

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DO GEL READINGS QUICKLY

DO GEL READINGS QUICKLY –

– if given a gel and asked for the complementary sequence look at

if given a gel and asked for the complementary sequence look at

the

TOP

TOP (which is

(which is negative side + therefore the end

negative side + therefore the end part of the given gene but we want

part of the given gene but we want

complementary so this will be start of that

complementary so this will be start of that ) + then just switch to

) + then just switch to complementary NT (eg A

complementary NT (eg A



T)

T) –

–

only do for as much as needed to find answer in choices

immediately look at the last NT in sequence =

immediately look at the last NT in sequence = G

G

Complementary will start with opposite of this =

C

C so know strand starts C, T (vs. G, A)

so know strand starts C, T (vs. G, A)

MISSENSE mutation = MC MUTATION TYPE

Large segment deletion

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BIOCHEM

Chronic

Chronic arthritis, arthritis, black black urine urine AlkaptonuriaAlkaptonuria

--

TyrosineTyrosine Liver

Liver and and kidney kidney dz dz 2/2 2/2 AA AA issue issue TyrosinosisTyrosinosis Albinism

Albinism Tyrosine Tyrosine def.def.melaninmelanin Pale hair +

Pale hair + ↑↑r/o melanoma/skin car/o melanoma/skin ca Pale

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



 PhenyalaninePhenyalaninetyrisone deficient (phenyl enzyme or TB4tyrisone deficient (phenyl enzyme or TB4 coenzyme)

coenzyme) Branched

Branched AAs AAs IsoleucineIsoleucine

Leucine Leucine Valine Valine

Maple syrup urine dz

Maple syrup urine dz – – CNS, MR, death, sugar-smell diaper)CNS, MR, death, sugar-smell diaper) *"

*"II LLoveoveVVermontermontmaple syrupmaple syrup"" MR,

MR, osteoporosis, osteoporosis, marfinoid-habitus, marfinoid-habitus, lens lens subluxation subluxation HomocysteinuriaHomocysteinuria ↑↑

↑↑methionine/methionine/↓↓↓↓cysteine (cysteine (cysteine becomes essential AAcysteine becomes essential AA)) What RBC changes would you expect in a female who presents with an

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

inherited hemolytic anemia

Inherited

Inherited HEMOLYTIC HEMOLYTIC anemia =anemia =1. G6PD deficiency1. G6PD deficiencyor or 2. PK deficiency2. PK deficiency 

If womanIf woman,, unless information givenunless information given to suggest x-linked (and thento suggest x-linked (and then receiving 2 “bad” x’s),

receiving 2 “bad” x’s), most likelymost likely pyruvate ki pyruvate kinasenasesince this is not sex-since this is not sex-linked (

linked (ARAR))



NONOHeinzHeinz(these are in(these are in G6PDG6PD – – RBC denaturation)RBC denaturation)



RIGHT SHIFT in oxygenation curveRIGHT SHIFT in oxygenation curve – – if if PK, then glycolyticPK, then glycolytic intermediates

intermediates back upback upalternate pathway includesalternate pathway includes 2,32,3 BPGBPG affinity

affinity for O2 (for O2 (more offloading, LESS pickup - (REMEMBER,more offloading, LESS pickup - (REMEMBER, fetal Hgb, HbF has

fetal Hgb, HbF has2,3BPG to allow for2,3BPG to allow foraffinity/more pickupaffinity/more pickup from mom)

from mom) Heritability

Heritability familial familial hypercholesterolemia hypercholesterolemia ADAD

MOLECULAR + CELL BIO

RER

RER  secretory/exported proteinssecretory/exported proteins – –protein folding hereprotein folding here  N-linked oligosacch additionN-linked oligosacch addition

 _Nissl_Nisslbodies inbodies inneuronsneuronsChAT ChAT enzyme that makesenzyme that makesAchAch; peptide; peptideNTsNTs  _↑_↑_{GI goblet cells}_{GI goblet cells}(mucous secretion)(mucous secretion), plasma cells, plasma cells(Ab-secretion)(Ab-secretion) Chaperones

Chaperones Class of specialized proteins that function to Class of specialized proteins that function to assist proper folding newlyassist proper folding newly synthesized proteins (proper

synthesized proteins (properGolgiGolgiplasma mem etc.)plasma mem etc.)



 If they are dysfunctional + poor foldingIf they are dysfunctional + poor folding  protein is polyubiquinated protein is polyubiquinated  

lysosome for degredation lysosome for degredation



 Will detect protein IN RERWill detect protein IN RERBUT BUT WON'T find receptor ( WON'T find receptor ( the proteinthe protein ) on ) on membrane

membrane(e.g. all is good until RER)(e.g. all is good until RER) Ex

Ex – – calnexin, calreticulincalnexin, calreticulin SER

SER  STEROID synthSTEROID synth

 DETOX DETOX rx, poisonrx, poison

 _↑_↑_hepatocytes_hepatocytes(detox)(detox)+ adrenal ctx+ adrenal ctx(produces steroid hormones)(produces steroid hormones)

Golgi

Golgi  _{Proteins/lipids}_{Proteins/lipids ER}_ER___{plasma membrane + vesicles}_{plasma membrane + vesicles}  _{Modifies N-oligos}_{Modifies N-oligos}ononnitrogennitrogenof of asparagineasparagine  Adds O-oligosAdds O-oligosononserine + threonineserine + threonine

 Add MANNOSE-6-phosAdd MANNOSE-6-phosfor traffic tofor traffic tolysosomeslysosomes o

o FYI :FYI : I-CELL DISEASEI-CELL DISEASE – – don't tag with mannosedon't tag with mannosesecretesecrete enzymes OUTSIDE cell instead of

enzymes OUTSIDE cell instead of lysosomelysosome



 Coarse face,Coarse face,clouded corneasclouded corneas,,restricted jtsrestricted jts,, ↑↑

↑↑plasma lysosomal enzymesplasma lysosomal enzymes 

 Fatal in chldhoodFatal in chldhood COPI

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COPII

COPII anterograde, RERanterograde, RERciscis-Golgi-Golgi Endosome

Endosome outside or Golgioutside or Golgilysosome or Golgilysosome or Golgi Clathrin

Clathrin Trans-GolgiTrans-Golgi__lysosomeslysosomes , , Plasma membrane

Plasma membraneendosomesendosomes 

R-mediated endocytosisR-mediated endocytosis(forms coat)(forms coat) Peroxisome

Peroxisome membrane-enclosed organelle for membrane-enclosed organelle for catabolism very LCFAs + AAscatabolism very LCFAs + AAs 

 Proteins destined for peroxisome incorporation synthesized onProteins destined for peroxisome incorporation synthesized on free free polysom

polysomeses(ribosomes?)(ribosomes?) Proteosome

Proteosome = degradation= degradationdamaged/unnecessary damaged/unnecessary proteins tagged byproteins tagged byUBIQUITINUBIQUITIN Microtubule

Microtubule – –general general action, action, processes processes -- Cilia (details below), flagellaCilia (details below), flagella -- Mitotic spindleMitotic spindle

-- Axonal trafficking Axonal trafficking -- CentriolesCentrioles

*arranged with

*arranged withneg ( - ) end neg ( - ) end near near centrosome (MTOC centrosome (MTOC ) + ) + pos (+) pos (+)radiatesradiatesOUT OUT Microtubules

Microtubules -- dyneindynein vs.vs. kinesinkinesin -- Alpha + B-tubulin dimers Alpha + B-tubulin dimers, each with, each with2 GTP2 GTP

-- DYNEIN =DYNEIN = RETROGRADE RETROGRADE (+(+-) e.g. toward -) e.g.toward NNUCLEUS =UCLEUS =NNEGATIVEEGATIVE ((hannahs home-made mnemonicshannahs home-made mnemonics – – "I'm"I'mDYNING INDYNING INtonight"tonight" (coming to the home/nucleus)

(coming to the home/nucleus) **CLINICAL CORRELATE

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

are all exogenous substances that affect neuron cell bodies via RETROGRADE

RETROGRADE axonal transport axonal transport (Im "

(Im "DYDYing over here",ing over here",regressingregressing – –retrograde")retrograde")

-- KINESIN =KINESIN = ANTEROGR ANTEROGRADE ADE ( -( -+) e.g. away from nucleus+) e.g. away from nucleus Tubulin

Tubulin Monomeric unites that compriseMonomeric unites that compriseMTMT((necessary for movement cargo within cell necessary for movement cargo within cell )) Disease caused by defect in microtubule polymerization an

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

fusion of phagosome with lysosome

Chediak-Hagashi

Chediak-Hagashi – – MT polmerization defectMT polmerization defect__{ ↓↓}↓↓fusion phagosomes+lysosomesfusion phagosomes+lysosomes 

 Recurrent pyogenic infectionRecurrent pyogenic infection 

 Partial albinoPartial albino 

 _{Peripheral neuropathy}_{Peripheral neuropathy} Cilia structure

Cilia structure 9+29+2MT arrangementMT arrangement Axonal

Axonal dynein-ATPasedynein-ATPase  links peripheral 9 dbltslinks peripheral 9 dblts cilium bendingcilium bending Disease caused by

Disease caused byimmotile ciliaimmotile cilia((and cause of immotility and cause of immotility )) KARTAGENERSKARTAGENERS – – immotile cilia d/timmotile cilia d/tdynein arm defectdynein arm defect 

 Male/female infertilityMale/female infertility 

 BronchiectasisBronchiectasis 

 Recurrent sinusitisRecurrent sinusitis 

 Situs inversusSitus inversus 

 _{Retrograde axonal transport}_{Retrograde axonal transport}_dysf_dysf Drugs acting on microtubules to treat fungus? To treat

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

worms? To treat cancer (2)? To treat gout?

Mebendazole/thiabendazole

Mebendazole/thiabendazole – – anti-helminthanti-helminth Griseofulvin

Griseofulvin – – anti-fungalanti-fungal Vincristine, Vinblastine

Vincristine, Vinblastine – – anti-CAanti-CA Paclitaxel

Paclitaxel – – anti-breast CAanti-breast CA Colchicine

Colchicine – – anti-goutanti-gout Actin/Myosin

Actin/Myosin – –general actions general actions -- **MicrovilliMicrovilli -- Muscle ctxMuscle ctx -- CytokinesisCytokinesis

-- AdherensAdherensjunctionsjunctions Location where processing "goes wrong" in cystic fi

Location where processing "goes wrong" in cystic fi brosisbrosis CFTR protein isCFTR protein is misfolded in endoplasmic reticulummisfolded in endoplasmic reticulum

--

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

post-translational processing of oligosaccharide side chiains

--

degraded bydegraded byproteosomeproteosomeinstead of instead of membrane translocationmembrane translocation DNA

DNA ligase ligase Catalyzes formationCatalyzes formation phosphodiester bond phosphodiester bond b/w 3' OH of DNA fragment withb/w 3' OH of DNA fragment with adjacent DNA 5'

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DNA Polymerase I

DNA Polymerase I ReadRead 3'3' 5'5'(e.g. start at OH grp and read to(e.g. start at OH grp and read to ward phos grp)ward phos grp) Synth 5'

Synth 5' 3'3'((adding new NT's phospho grp on to the free OH grp of growing strand adding new NT's phospho grp on to the free OH grp of growing strand



""hydroxyl attackhydroxyl attack" + energy from new NTs phos g" + energy from new NTs phos g rp)rp) Both

Both polymerization NTspolymerization NTs and and processing/repair mechsprocessing/repair mechs Polymerase III

Polymerase III Prokaryote only Prokaryote only

Part of multiprotein complex, major replicating enzyme Part of multiprotein complex, major replicating enzyme e. coli e. coli Topoisomerase and Abx

Topoisomerase and Abx

_-

swivel points in DNA to relieve strain at swivel points in DNA to relieve strain at replication (cut+reseal DNA)replication (cut+reseal DNA) Quinolones interfere here

Quinolones interfere here Cytosine deamination

Cytosine deamination ==URACILURACILif intact DNA repair mechanisms, these will if intact DNA repair mechanisms, these will be repaired (be repaired (mismatchmismatch repair genes will eliminate via

repair genes will eliminate viabase excisionbase excision)) Dolichol

Dolichol Substrate for forming branched "Substrate for forming branched "carbohydrate trees" carbohydrate trees" that arethat are transferred totransferred to proteins

proteins inin synthesissynthesisglycoproteinsglycoproteins(mostly protein w/ some attached sugars)(mostly protein w/ some attached sugars)

--

ononRERRER

--

goes to golgi, then either plasma goes to golgi, then either plasma membrane/lysosome/secreted proteinmembrane/lysosome/secreted protein "scientist wants to characterize the carbohydrate chains that

"scientist wants to characterize the carbohydrate chains that will be transferred towill be transferred to protein component of albumin. Which molecule functions for synthesis

protein component of albumin. Which molecule functions for synthesis of theseof these chains?

chains? *

*N-linked carbohydrate chainN-linked carbohydrate chains that s that will be transferred to protein component of will be transferred to protein component of albumin are assembled in RER + attached to colichol phosphate

albumin are assembled in RER + attached to colichol phosphate



transferred totransferred tonitrogen of asparagine to form glycoproeinsnitrogen of asparagine to form glycoproeins

--

secreted = albuminsecreted = albumin

--

retained in membrane = insulin-Rretained in membrane = insulin-R

--

targeted to lysosome = hexosaminidase A (targeted to lysosome = hexosaminidase A (tay-sachstay-sachs))

Arachidonic acid

Arachidonic acid Precursor of:Precursor of:

--

PGsPGs

--

ThromboxanesThromboxanes

--

LeukotrienesLeukotrienes FA in phospholipid membrane

FA in phospholipid membrane released by released by phosp phospholipasholipase A2e A2 Ceramide

Ceramide ParentParent sphingolipid sphingolipid from whichfrom whichsphingomyelin, cerebrosides, gangliosidessphingomyelin, cerebrosides, gangliosides areare derived (think LYSOSOMAL STORAGE DISORDERS e.g. niemann-pick

derived (think LYSOSOMAL STORAGE DISORDERS e.g. niemann-pickgeneticgenetic deficiencies of lysosomal enzymes that should digest these spingolipids cause the deficiencies of lysosomal enzymes that should digest these spingolipids cause the diseases

diseases)) Dermatan sulfate

Dermatan sulfate GAGGAG(glycosaminoglycan)(glycosaminoglycan) -precursor of

-precursor of proteoglycan proteoglycan ((carbs w/ small proteinscarbs w/ small proteinsremember if protein>>carbremember if protein>>carb component =

component = glycoproteinglycoprotein)) - part of

- part of ECMECM Types:

Types:chondroitin sulfate, hyaluronic acid chondroitin sulfate, hyaluronic acid Remember

Remember*dermatan + heparan sulfates*dermatan + heparan sulfatesare substrates to enzymes deficient inare substrates to enzymes deficient in HURLER (Worse, corneal cloud) + HUNTER dz

HURLER (Worse, corneal cloud) + HUNTER dz Tetracycline

Tetracycline Binds ribosomalBinds ribosomal30s subunit30s subunit(( prokaryotic small subunit prokaryotic small subunit – – euk = 40s)euk = 40s)



 prevents aminoacyl-tRNA attachment prevents aminoacyl-tRNA attachment Aminoglycoside

Aminoglycoside Streptomycin, gentamycin, tobramycin, amikacinStreptomycin, gentamycin, tobramycin, amikacin

Inhibits

InhibitseIFseIFs== elongatingelongatinginitiation factorsinitiation factorsthat helpthat helpassemble 30s ribosomal assemble 30s ribosomal subunit with initiatior tRNA

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Ribosome formation, translation

Ribosome formation, translation 30+50s = 70s prok30+50s = 70s prok 40+60=80s euyk 40+60=80s euyk

ATP

ATP activates tRNA (A=activatation)activates tRNA (A=activatation) GTP

GTP = initiation, translocation,= initiation, translocation, holdingholding on toon to tRNA (G=gripping, going places)tRNA (G=gripping, going places)

A site

A site – – incoming aminoacyl-tRNAincoming aminoacyl-tRNA P

P – – growing polypeptide chaingrowing polypeptide chain E =

E =empty tRNAempty tRNAAA has been transferred to growing molecule oAA has been transferred to growing molecule o n P site (n P site (exit exit ))

Ribosome

Ribosome advancesadvances3 NTs3 NTs toward toward 3' end mRNA3' end mRNA(e.g. toward end whose(e.g. toward end whose last NT last NT has free OH

has free OH))

--

This movesThis moves peptidyl RNA peptidyl RNA to P site =to P site =translocationtranslocation

Chloramphenicol

Chloramphenicol 22MOAsMOAsat 50S ribosomeat 50S ribosome 1.

1. InihibitsInihibits50S 50S peptidyltransfepeptidyltransferaserase(this is the "top part" ribosome complex(this is the "top part" ribosome complex 2.

2. BlocksBlockspeptide bond formationpeptide bond formation(so does clinda)(so does clinda) RIBOZYME

RIBOZYME RNA molecule that has catalyst RNA molecule that has catalyst (E.g. enzymatic(E.g. enzymatic – – "yme")"yme")activity activity 

Ribosomal rRNARibosomal rRNAcatalyzescatalyzespeptide bond formationpeptide bond formation,, transfers growingtransfers growing polypeptide to AA in A site

polypeptide to AA in A site (which then moves to P site when ribosome moves 3NTs(which then moves to P site when ribosome moves 3NTs forward)

forward) Hammerhead Ribozyme

Hammerhead Ribozyme CatalyzesCatalyzes sequence-specificsequence-specificcleavage RNA PDE bondscleavage RNA PDE bondsd/t 2° structure they formd/t 2° structure they form ((looks like head of hammer looks like head of hammer ))

- possible use as treatment of "activating"

- possible use as treatment of "activating" mutated genes (e.g. SOD1 in ALS)mutated genes (e.g. SOD1 in ALS)

synthetic hammerhead RNA w/ complementary sequence to

synthetic hammerhead RNA w/ complementary sequence to mutant SOD1 mRNAmutant SOD1 mRNA could potentially bind specifically to mutant + destroy via catalyzing PDE bond could potentially bind specifically to mutant + destroy via catalyzing PDE bond cleavage

cleavage

""removes mRNAremoves mRNAwithout direct inhibition of translation initiation"without direct inhibition of translation initiation" – – it's ait's a destruction rather than inhibition

destruction rather than inhibition Macrolides

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

50S inhibitor

50S inhibitorblocks translocationblocks translocation – – this uses GTP normallythis uses GTP normally *(

*(CHLORAMPHENICOL isCHLORAMPHENICOL is also acting at 50S but blocking PEPTIDYLtransferasealso acting at 50S but blocking PEPTIDYLtransferase))

Clindamycin

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

ribosome ""BuyBuyAT 30, CCELLAT 30, CCELL(sell) at(sell) at5050"" 30S30S

A

Aminoglycosides (Strepto, genta, tobra)minoglycosides (Strepto, genta, tobra) – – bacteriobacteriocidalcidal T

Tetracyclineetracycline – – bacteriobacteriostaticstatic

50S 50S C

Chloramphenicol,hloramphenicol,CClindamycinlindamycin – – staticstatic E

Erythromycin (macrolide)rythromycin (macrolide) – – staticstatic LLincomycinincomycin – – staticstatic

LLinezolid (variable static vs. cidal)inezolid (variable static vs. cidal) **

**Linezolid is for Linezolid is for VREsVREs Mutation in early

Mutation in earlypost-translationpost-translational al modification collagenmodification collagen Ehler-DanlosEhler-Danlos – – skin + msk abnormalitiesskin + msk abnormalities DNA methylation

DNA methylationassociated dzassociated dz Fragile XFragile X

This in addition to TRI-NT repeat EXPANSION This in addition to TRI-NT repeat EXPANSION

CGG triNT

CGG triNTrepeat inrepeat inFMRI FMRI genegene

↑

↑rr

/o /o CHROMOSOMAL BREAK CHROMOSOMAL BREAK -- 22ndnd MCCMCCMRMR(1(1stst= Down’s)= Down’s)

-- MACROCHORDISMMACROCHORDISM(big testes),(big testes),long face,long face,LARGE LARGE + everted ears, autism,+ everted ears, autism, MVP* (

(7)

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

fibroblasts

I-CELL dz I-CELL dz Def.

Def.N-acetylglucosamine-1-phosptransferaseN-acetylglucosamine-1-phosptransferase = defect in addition= defect in additionmannose-6- mannose-6-phosphate

phosphatemoiety tomoiety tolysosomal enzymeslysosomal enzymesreleased to extracellar space soreleased to extracellar space so cculture medium will contain lysosomal enzyme activity ulture medium will contain lysosomal enzyme activity

-

- Coarse facies, Coarse facies, skeletal abnll, psychomotor reskeletal abnll, psychomotor retardationtardation - Type 1

- Type 1 – – complete def., death in childhood complete def., death in childhood - Type 3

- Type 3 – – partial deficiency partial deficiency = milder dz (= milder dz (pseudo-Hurlerpseudo-Hurler))survives to adulthoodsurvives to adulthood Incorrect splicing introns associated with what hematologic

Incorrect splicing introns associated with what hematologic disorder

disorder

B-THALASSEMIA B-THALASSEMIA

--

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

(small function) Hematologic dz caused by

Hematologic dz caused bymissensemissensept mutationpt mutation HbSHbS – – Sickle cellSickle cell

Change A-->T at position 6 allows glutamine

Change A-->T at position 6 allows glutamine  valinevaline

HbC

HbC= modified version this error (= modified version this error (glutamineglutamine  lysinelysine))

--

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

and homozygote HbCC gives hemolytic anemia Transition vs. transversion pt mutation

Transition vs. transversion pt mutation TransitionTransitionis substitutionis substitutionwithin same "class" within same "class" purinepurinepurine / pyrpurine / pyrpyr (samepyr (same ring "type")

ring "type")

Transversion

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

(remember Purine

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

PY = cytosine, thymidine, uracil in proks) Tautomerism switch point mutation

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

Tautomers

Tautomers_are_{are isomers}_isomers_{((structural isomers}_{structural isomers}_{)) of}_{of organic compounds}_{organic compounds}_{that readily}_{that readily}

interconvert by a

interconvert by a chemical reactionchemical reactioncalledcalledtautomerizationtautomerization_..[1][2][1][2]_{This reaction}_{This reaction}

commonly results in the formal migration of a

commonly results in the formal migration of a hydrogenatomhydrogenatomoror protonproton,, accompaniedaccompanied by a switch of a

by a switch of a single bondsingle bondand adjacenand adjacenttdouble bonddouble bond.. The concept ofThe concept of tautomerization

tautomerizations is s is calledcalledtautomerism.tautomerism._{Because of the rapid interconversion,}_{Because of the rapid interconversion,}

tautomers are generally considered to be the same chemical compound. tautomers are generally considered to be the same chemical compound. Tautomerism is a special case of

Tautomerism is a special case of structural isomerismstructural isomerismand can play an important roleand can play an important role in non-canonica

in non-canonicall base pairingbase pairinginin DNADNAand especiallyand especially RNARNAmolecules.molecules. Significance of cytosine deamination

Significance of cytosine deamination C C U U – –this is the only deamination rxn that can be CORRECTED viathis is the only deamination rxn that can be CORRECTED viauracil-DNAuracil-DNA glycosylase

glycosylase((this can be missed inthis can be missed inmismatch repair mismatch repair – – HNPCC, endometrial CA)HNPCC, endometrial CA) *STEPS REPAIR:

*STEPS REPAIR: 1.

1.Uracil-DNA glycosylaseUracil-DNA glycosylasegeneratesgeneratesAbasic site = APAbasic site = AP 2.

2. DNADNA AP endonu AP endonucleasecleasesees newly formed Abasic sitesees newly formed Abasic sitebreaks PDE bondbreaks PDE bond 3.

3. DNADNAPolymerasePolymerasesees break and createssees break and creates nick nick + fills+ fills 4.

4. DNADNALigaseLigasereforms seal with PDE bondreforms seal with PDE bond

--

ALSO CAN RECOGNIZEALSO CAN RECOGNIZErelated deaminase rxnrelated deaminase rxnof of METHYLATED cytosineMETHYLATED cytosine

((methylated in regulation gene transcriptionmethylated in regulation gene transcription – – epigeneticsepigenetics)) o

o 5methylcytosine5methylcytosine thyminethymine+ ammonia (MC single NT+ ammonia (MC single NT mutation)

mutation) – – corrected viacorrected viathymine-DNA glycosylasethymine-DNA glycosylase – fixes –fixes cystine

cystine——thymine pt mutation in daughter cell thymine pt mutation in daughter cell o

o **Remember,**Remember,thymine is a methylated uracil thymine is a methylated uracil so it makesso it makes sense that C

sense that CU would have methyl-CU would have methyl-CTT

--

all others NOTall others NOT recognized recognized

o

o AdenineAdeninehypoxanthine (hypoxanthine (this now prefersthis now preferscytosinecytosineinstead of instead of thymidine

thymidine)) o

o GuanineGuaninexanthine (this nowxanthine (this now prefers prefersthymidinethymidineinstead of instead of cytosine

cytosine)) *recall

*recall – – deamination = removal of amino grp deamination = removal of amino grp from moleculefrom molecule NT base with ketone

NT base with ketone GuanineGuanine

NT base with methyl grp

NT base with methyl grp ThymineThymine

Alkylating

Alkylating agents agents Cross-linkCross-linkguanine NTsguanine NTsin DNA damaging it enough to stop divisionin DNA damaging it enough to stop division Cisplatin

Cisplatin Carboplatin Carboplatin

(8)

Base

Base analog analog agents agents Incorrectly Incorrectly incorporate incorporate the the analog analog into into DNA DNA but but chemically chemically different different enough enough to to notnot make targeted protein, e.g.

make targeted protein, e.g. mismatch at base-pairingmismatch at base-pairing causescausesdaughter DNAdaughter DNA mutated

mutated

BrdU

BrdU – find replicating cells for research –find replicating cells for research Methylating

Methylating agents agents Transfer Transfer methyl methyl grps grps to to DNA DNA NT NT bases bases ((not used for cancer Rx since it doesn't lead not used for cancer Rx since it doesn't lead to cell death

to cell death)) *

*MGMTMGMT= methylguanine methyltransferase repairs= methylguanine methyltransferase repairs

EMS = ethyl methanesulfonate

EMS = ethyl methanesulfonate – – guanine alkylation that can induce high rates of guanine alkylation that can induce high rates of mutations

mutationsused inused ingenetic screens/assaysgenetic screens/assaysto induce mutations to be studiedto induce mutations to be studied Antimetabolite

Antimetabolite 5-FU5-FU(fluorouracil) –(fluorouracil) – pyrimid pyrimidineineanalog;analog; "suicide inhibitor "suicide inhibitor "" – – irreversible inhibitionirreversible inhibition thymidylate synthase

thymidylate synthase

Antipurine

Antipurine – –azathioprineazathioprine((cleaved tocleaved to6-MP6-MP),),thioguaninethioguanine

Antifolate

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

pyrimethamine, pemetrexed DNA

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

Fluorescent dye

Fluorescent dye – – Ethidium BromideEthidium Bromide Cancer Rx

Cancer Rx – –Doxorubicin, DaunorubicinDoxorubicin, Daunorubicin Aflatoxin =

Aflatoxin = Aspergi Aspergillisllis Thalidomide

Thalidomide – – teratogen with strict use policy for last resort teratogen with strict use policy for last resort anti-inflammatory anti-inflammatory (leprosy)

(leprosy)+ salvage chemo in MM+ salvage chemo in MM(With dexamethosone)(With dexamethosone)

 Birth defectBirth defect==PHOCOMELIA (PHOCOMELIA (horrible limb deformitieshorrible limb deformities as well as otheras well as other body regions)

body regions) DNA

DNA cross-linking cross-linking agents agents FormFormcovalent bondcovalent bondb/wb/wDNA NT basesDNA NT bases – –can't replicate/transcribecan't replicate/transcribe

Platinum Platinum Free

Free radicals radicals Highly Highly active active in in presence presence of of unpaired electronsunpaired electrons

--

Age-related cell damage Age-related cell damage

Superoxide Superoxide H2O2 H2O2 Hydroxyl radicals Hydroxyl radicals Ionizing

Ionizing mutagens mutagens + + UV UV UV UV == ↓↓wavelenth/wavelenth/↑↑energy vs. normal lengthenergy vs. normal lengthcovalent adjacent thymine bondcovalent adjacent thymine bond formed

formedTHYMINE DIMERTHYMINE DIMER(r/o skin ca)(r/o skin ca)

Ionizing radiation

Ionizing radiation – – radioactive materials with high energy thatradioactive materials with high energy thatREMOVE electronREMOVE electron from molecule/atom

from molecule/atomdamage/deathdamage/death Mutagens requiring repair via

Mutagens requiring repair viabase excisionbase excision  XraysXrays  O2 radicalsO2 radicals  Alkylating agents Alkylating agents  Spontaneous rxnsSpontaneous rxns



uraciluracilabasicabasicsites created (AP sites) orsites created (AP sites) or single strand break single strand break (MCC = C(MCC = CUU deamination)

deamination)

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

Errors of of replication replication A-G A-G mismatchmismatch T-C mismatch T-C mismatch Insertion Insertion Deletion Deletion Mismatch repair Mismatch repair (hMSH/hMLH)(hMSH/hMLH)

(9)

Recombinational

Recombinational repair repair One One damaged damaged strand strand hashas somesome replicationreplication – – use as templateuse as template Nonhmologous end-joining

Nonhmologous end-joining (ALWAYS MUTAGENIC)(ALWAYS MUTAGENIC) – – DNA ligase complexes joinDNA ligase complexes join separate ends dbl helix

separate ends dbl helix N-terminal hydrophobic signal sequence

N-terminal hydrophobic signal sequenceadded on duringadded on during synthesis via cytoplasmic ribosomes

synthesis via cytoplasmic ribosomes

Sequence =

Sequence ="signal recognition "signal recognition particle" particle" ((SNPSNP)) – – attaches growing peptide +attaches growing peptide + ribosomal complex to RER

ribosomal complex to RERopens up channel allowing peptide to thread into ERopens up channel allowing peptide to thread into ER lumen

lumen



Will be on anyWill be on anyprotein destinedprotein destinedto beto besecreted / membrane-bound / lysosomalsecreted / membrane-bound / lysosomal If absent

If absent protein would be UNABLE TOprotein would be UNABLE TO enter enter RER in first place (RER in first place ( pre pre-folding-folding error)

error) Lysosomes

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

(proteases) Intermediate filament stains

Intermediate filament stains – –vimentinvimentin Connective tissueConnective tissue Intermediate filament stains

Intermediate filament stains – –desmindesmin MuscleMuscle *

*notenote – – connects cytoplasmic bodies to membrane dense plaques in actin filamentconnects cytoplasmic bodies to membrane dense plaques in actin filament structure of smooth muscle;

structure of smooth muscle;cardiac + skeletal myopathies associated w/ cardiac + skeletal myopathies associated w/ mutations in this protein

mutations in this protein Intermediate filament stains

Intermediate filament stains – –cytokeratincytokeratin Epithelial cellsEpithelial cells Intermediate filament stains

Intermediate filament stains – – GFAPGFAP neuroGLIAL cellsneuroGLIAL cells – – astrocytoma,astrocytoma, ependymal cellsependymal cells **

**REMEMBERREMEMBER – – GFAP only marks astrocytomas, for prognosis useGFAP only marks astrocytomas, for prognosis useKi-67Ki-67 Intermediate filament stains

Intermediate filament stains – –neurofilamentsneurofilaments NeuronsNeurons Drugs that act on microtubules

Drugs that act on microtubules Mebendazole/thiabendazoleMebendazole/thiabendazole – – anti-helminthanti-helminth Griseofulvin

Griseofulvin – – anti-fungalanti-fungal Vincristine, Vinblastine

Vincristine, Vinblastine – – anti-CAanti-CA Paclitaxel

Paclitaxel – – anti-breast CAanti-breast CA Colchicine

Colchicine – – anti-goutanti-gout Dynein arm defects

Dynein arm defects KARTAGENERSKARTAGENERS – – immotile cilia d/timmotile cilia d/tdynein arm defectdynein arm defect 

 _{Male/female infertility}_{Male/female infertility} 

 _{Bronchiectasis}_{Bronchiectasis} 

 Recurrent sinusitisRecurrent sinusitis 

 Situs inversusSitus inversus

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

pyogenic infections 2/2 molecular bio issue

Chediak-Hagashi

Chediak-Hagashi – – MT polmerization defectMT polmerization defect↓↓↓↓fusionfusion phago

phagosomes+lysomes+lysosomessosomes 

 Recurrent pyogenic inectionRecurrent pyogenic inection 

 Partial albinoPartial albino 

 Peripheral neuropathyPeripheral neuropathy

Kinesin vs. Dynein

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

KINESIN =

KINESIN = ANTEROGRA ANTEROGRADE DE ( -( -+) e.g. away from nucleus+) e.g. away from nucleus Make-up

Make-up of of microvilli microvilli actin/myosinactin/myosin – – NOT microtubulesNOT microtubules Actin,

Actin, myosin, myosin, MT MT roles roles in in replication replication Actin/myosin Actin/myosin ==cytokinesiscytokinesis Microtubules =

Microtubules = mitotic spindle, centriolesmitotic spindle, centrioles Plasma membrane composition leading to decreased fluidity

Plasma membrane composition leading to decreased fluidity and higher melting temp

and higher melting temp

MORE

MORE cholesteroal cholesteroal and/orand/or MORE MORE long saturated FAslong saturated FAs

RER activity

RER activity + what cells + what cells have morehave more

_-

secretory/exported proteinssecretory/exported proteins

--

N-linked oligosacch additionN-linked oligosacch addition

--

NisslNisslbodies inbodies inneuronsneuronsChAT ChAT enzyme that makesenzyme that makesAchAch; peptide; peptideNTsNTs

--

↑↑GI goblet cellsGI goblet cells(mucous secretion)(mucous secretion), plasma cells, plasma cells(Ab-secretion)(Ab-secretion) SER activity + what cells

SER activity + what cells  STEROID synthSTEROID synth  DETOX DETOX rx, poisonrx, poison

(10)

Mitosis order

Mitosis order InterphaseInterphase

Prophase Prophase Metaphase Metaphase Anaphase Anaphase Telophase Telophase

""PMAT"PMAT"or "or "PPeopleeopleMMeeteetAAndndTTalk"alk"

Hand action mnemonic Hand action mnemonic Prophase

Prophase = fingers linked together in the middle= fingers linked together in the middle Metaphase

Metaphase ==MMIDDLE (flat hands)IDDLE (flat hands) Anaphase

Anaphase = pulled= pulledAAPART (hands apart)PART (hands apart) Telophase

Telophase ==TTWO (close fingers to two fists)WO (close fingers to two fists) Sign and significance of tripolar mitoses

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

 Signifies malignancy in tumor Signifies malignancy in tumor 2 drugs that act on Na/K ATPase channel directly (not neuro)

2 drugs that act on Na/K ATPase channel directly (not neuro) OuabainOuabain – – binds K+ sitebinds K+ site Digoxin/digitoxin

Digoxin/digitoxin (glycosides)(glycosides) – – direct inhibit Na/K =direct inhibit Na/K = indirect indirect inhibinhibNa/CaNa/Ca(true(true target)

target)↑↑[Ca2+]in[Ca2+]in== ↑↑contractcontract Na/K pump activation

Na/K pump activation Phosphorylated = ACTIVE Phosphorylated = ACTIVE ATP

ATP ADPADP(donates phos)(donates phos) Collagen types I

Collagen types I – – IVIV " " BBe ( e ( SSooT T otally)otally)C C ool,ool,RRead ead BBooksooks I =

I =BBone,one,SSkin,kin,ttendonendon  Type ONE = BType ONE = BONE ONE II =

II =ccartilage (with hyaline), vitreous body + artilage (with hyaline), vitreous body + nucleus pulposusnucleus pulposus  Type TWO = car Type TWO = car TWOTWOlagelage

III =

III =RReticulin = skin, vessels, uterus, fetal tissue, granulation tissueeticulin =skin, vessels, uterus, fetal tissue, granulation tissue  TypeTypeIII III = Thre= ThreEE DDdefective indefective inEEhlers-hlers-DDanlosanlos

IV =

IV =BBasement membrane (Easy, think goodpastures)asement membrane (Easy, think goodpastures)  ""Four = Under the Floor Four = Under the Floor ""

Disease a/w

Disease a/w DEFECT inDEFECT in Type 1 collagenType 1 collagen OOsteogenesis imperfectasteogenesis imperfecta("BRITTLE BONE")("BRITTLE BONE") – – COLCOL11 A1/2 A1/2  _{The one that looks like child abuse}_{The one that looks like child abuse}

 Multiple fx w/ minimal traumaMultiple fx w/ minimal trauma

 BLUE SCLERABLUE SCLERA(translucent CT over choroid)(translucent CT over choroid)  _{Hearing loss}_{Hearing loss}(ABNL MIDDLE EAR BONE)(ABNL MIDDLE EAR BONE)  DENTALDENTALlack dentinlack dentin

*remember *remember I =

I =BBone,one,SSkin,kin,ttendonendon  Type ONE = BType ONE = BONE ONE

(11)

Disease a/w

Disease a/w DEFECT inDEFECT in Type 3 collagenType 3 collagen Ehlers-DanlosEhlers-Danlos – – COLCOL33 A1 A1collagen + lysine hydroxylase gene mutationscollagen + lysine hydroxylase gene mutations  Hyperextensible skinHyperextensible skin

 Easy BRUISING/BleedsEasy BRUISING/Bleeds  Hypermobile jtsHypermobile jts **

**6 types6 typesw/ varying inheritance/severity (AD or AR)w/ varying inheritance/severity (AD or AR)



 TYPE 4TYPE 4(rare) =(rare) =MENKE's dzMENKE's dz((x-linkedx-linkeddepigmented, lusterless KINKY hairdepigmented, lusterless KINKY hair with many facial/ocular/vascular/cerebral manigestations, copper with many facial/ocular/vascular/cerebral manigestations, copper transport defect and

transport defect and ↓↓activityactivitycopper-depndent enzymescopper-depndent enzymes LYSYLLYSYL OXIDASE

OXIDASE – –REMEMBER,REMEMBER, THIS IS CU-DEPENDENT ENZYME that THIS IS CU-DEPENDENT ENZYME that crosslinkscrosslinks pre-collagein in ECM

pre-collagein in ECM to form mature collagen)to form mature collagen) +/- associated with:

+/- associated with:  _{Joint disl}_{Joint dislocation}_ocation  _{BERRY ANEURYSM}_{BERRY ANEURYSM}  _{Organ rupture}_{Organ rupture} *

*remember remember III =

III =RReticulin = skin, vessels, uterus, fetal tissue, granulation tissueeticulin =skin, vessels, uterus, fetal tissue, granulation tissue  TypeTypeIII III = Thre= ThreEE DDdefective indefective inEEhlers-hlers-DDanlosanlos

Disease a/w

Disease a/w DEFECT inDEFECT in Type 4 collagenType 4 collagen Alport Sy Alport Syndromendrome(goodpasture = autoimmune not defect)(goodpasture = autoimmune not defect)  hereditaryhereditaryGNGN

 _ESRD_ESRD

 HEARING LOSSHEARING LOSS

 _{+/- ocular disturbances}_{+/- ocular disturbances}

 MC type =MC type = X-LINKED REC X-LINKED RECESSIVE ESSIVE (BOYS)(BOYS)

*

*remember remember IV =

IV =BBasement membrane (Easy, think goodpastures)asement membrane (Easy, think goodpastures) Collagen

Collagen – –4 steps within fibroblasts4 steps within fibroblasts+ location+ location 1.1. SynthesisSynthesis((RERRER)) o

o TranslateTranslatealphaalphachains =chains =PRE-PRO-collagenPRE-PRO-collagen o

o Gly-X-YGly-X-Y

X/YX/Y== PROLINE, hydroxyproline/LYSINE PROLINE, hydroxyproline/LYSINE 2.

2. HydroxylationHydroxylation((ERER)) o

o Of Of Proline + lysine residuesProline + lysine residues VITAMIN CVITAMIN C CRITICALCRITICAL 3.

3. GlycosylationGlycosylation((ERER)) o

o Of Of Pro-alphaPro-alpha-chain-chainhydroxylysinehydroxylysineresidues + formationresidues + formationPROcollagenPROcollagenviavia H + DISULFIDE BONDS

H + DISULFIDE BONDS o

o TRIPLE HELIX of TRIPLE HELIX of 3 alpha chains3 alpha chains 4.

4. ExocytosisExocytosis o

o PROCOLLAGENPROCOLLAGEN  extracell extracell Collagen

Collagen – –2 steps outside fibroblasts2 steps outside fibroblasts 5.5. Proteolytic processingProteolytic processing

-- CLEAVE terminal region = procollagenCLEAVE terminal region = procollagenTROPOcollagen (insoluble)TROPOcollagen (insoluble) 6.

6. Cross-linkCross-link

--reinforcereinforce tropotropocollagen viacollagen viacovalent LYSINE-HYDROZYLYSINE covalent LYSINE-HYDROZYLYSINE CROSS-LINKSCROSS-LINKSbb ((LYSIL OXIDASE)LYSIL OXIDASE)FIBRILSFIBRILS

Implicated genetic defect in osteogenesis imperfecta

Implicated genetic defect in osteogenesis imperfecta Type I collagen disorderType I collagen disorder ColA1, ColA2

ColA1, ColA2unstable collagen triple helix not as strong (phenotypic outcomeunstable collagen triple helix not as strong (phenotypic outcome depends on unique changes in genes)

depends on unique changes in genes) 2 MC AAs in collagen

2 MC AAs in collagen GlycineGlycine

Proline Proline Gly-X-Y

Gly-X-Y where X = proline (or lysin/glycine), Y = hydroxyproline)where X = proline (or lysin/glycine), Y = hydroxyproline) Cartilage with PAS stain

Cartilage with PAS stain Type IIIType III – –ReticulinReticulin (skin,(skin,vesselsvessels, uterus, fetal tissue,, uterus, fetal tissue,granulation tissuegranulation tissue)) Lysyl

Lysyl oxidase oxidase Involved Involved in in formingformingcollagen fibrilscollagen fibrilsfromfrompro-collagen triple helicespro-collagen triple helicesthat have beenthat have been secreted into extracellular space

secreted into extracellular space *Copper-dependent

*Copper-dependent Cross-linkage via

(12)

Cofactor requirement in early collagen synth

Cofactor requirement in early collagen synth VITAMIN C VITAMIN C – – 22ndndstep (HYDROXYLATION)step (HYDROXYLATION) within fibroblast inwithin fibroblast inERER Without =

Without =SCURVYSCURVY 

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

healing, loose teeth, ↓↓bone formationbone formation Elastin

Elastin Stretchy proteinStretchy proteinin in lungs, large arteries, elastic lungs, large arteries, elastic ligaments, vocal cords, ligaments, vocal cords, ligamentaligamenta flava

flava (connect vertebrae for relaxed + stretched conformations)(connect vertebrae for relaxed + stretched conformations)  PROLINE, GLYCINEPROLINE, GLYCINE – – NONglycosylated NONglycosylated formsforms

 TropoelastinTropoelastinw/w/fibrillin scaffoldfibrillin scaffold Disease MC a/w elastin defect

Disease MC a/w elastin defect MarfansMarfans– – fibrillin genefibrillin gene

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

Elastase and and associated associated disease disease Breaks Breaks down down elastaseelastase – – normally balance break down/build up but innormally balance break down/build up but inalpha-1- alpha-1-antitrypsin

antitrypsin excess elastinexcess elastin==EMPHYSEMAEMPHYSEMA((panacinarpanacinar) +) +CIRRHOSIS/liver failureCIRRHOSIS/liver failure (#1 cause liver transplant in newborns!

(#1 cause liver transplant in newborns! Ddx uric acid + gout

Ddx uric acid + gout primary reasons primary reasons Lesch-NyanLesch-Nyan Alcoholism Alcoholism G6PD G6PD

Hereditary fructose

Hereditary fructose intolerancintolerancee Galactose-1

Galactose-1-P uridyle -P uridyle transferase def transferase def . (. (severe galactosemiasevere galactosemia)) **all disoders with

**all disoders with increased accumulation of increased accumulation of phospho phosphorylated srylated sugars =ugars = ↑

↑degradation productsdegradation products(e.g. AMP(e.g. AMP…uric acid)…uric acid) Ddx uric acid + gout

Ddx uric acid + goutsecondary reasonssecondary reasons OVER-PRODUCTIONOVER-PRODUCTION Leukemia Leukemia Myeloproliferative syndromes (MPDs) Myeloproliferative syndromes (MPDs) MM MM Hemolysis Hemolysis Neoplasia Neoplasia Psoriasis Psoriasis Alcoholism Alcoholism UNDER-PRODUCTION UNDER-PRODUCTION Renal failure Renal failure ASA ASA Diuretics Diuretics Alcohol

Alcohol (all 3 categories)(all 3 categories) Direction

Direction DNA DNA synthesis synthesis 5'5'3'3' Direction

Direction RNA RNA synthesis synthesis 5'5'3'3' Direction

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

Protein synth synth NNCC

Actinomycin D

Actinomycin D Binds DNA, preventing RNA polymerase from moving along temBinds DNA, preventing RNA polymerase from moving along tem plateplate Rifampin

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

Interstitial deleting deleting Large Large DNA DNA fragment fragment deleted deleted ononsingle chrsingle chr pairing 2 pairing 2 genesgenesnot not normally innormally in sequence

sequencewith one another (e.g. could bring activation with one another (e.g. could bring activation one gene from another)one gene from another)  _{Fusion oncogene}_{Fusion oncogene}

Chromosomal

Chromosomal inversion inversion Large Large large large segment segment becomesbecomesreversed reversed w/i same chromsomew/i same chromsomerearrangement rearrangement post-bre

post-breakageakagechr chr ==fusion oncogenefusion oncogene Ouabain

Ouabain Binds Binds K+ K+ on on Na/K Na/K pump,pump, inhibitinginhibitingNa/K ATPaseNa/K ATPase Digoxin/digitoxin

Digoxin/digitoxin Cardiac Cardiac glycosidesglycosides Direct

Direct bind/inhibitbind/inhibitNa/K ATPaseNa/K ATPaseindirectly inhibitingindirectly inhibitingNa/Ca exchange =Na/Ca exchange =↑↑Ca inCa in cell =

cell =↑↑contractility contractility Normal amount of an enzyme present yet no enzymatic

Normal amount of an enzyme present yet no enzymatic activity

activity – – where is mutation?where is mutation?

NONSENSE mutation

NONSENSE mutation – – AA change generating 1 of 3 stop codonsAA change generating 1 of 3 stop codons

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

(13)

Test

Test for for carrier carrier genetic genetic disease disease PCRPCR

Amplify sequence of question and compare to Amplify sequence of question and compare to normalnormal Steps in testing Lyme

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

Follow-up with more specificWESTERN BLOT (protein)WESTERN BLOT (protein) Area where splice acceptor mutation occurs

Area where splice acceptor mutation occurs 3' end3' endeukaryotic intron (eukaryotic intron (invariant AG just before end invariant AG just before end intronintron)) – – HIGHLYHIGHLY CONSERVED

CONSERVED 5' end

5' endintron =intron =GT (GU in RNA)GT (GU in RNA)necessary necessary – – splice donor sitesplice donor site snRNP

snRNP SpliceosomeSpliceosome

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

chr11, HBB

chr11, HBBgenegene

additional, contiguous length non-coding mRNA or

discontinuous fragment

discontinuous fragment =

=

SNP

SNP –

– SINGLE NT POLYMORPHISM

SINGLE NT POLYMORPHISM))

Location cleavage propetides collagen

Location cleavage propetides collagen Extracellular Extracellular – – first step; therefore isfirst step; therefore is alwaysalways "pro" type of collagen within cell"pro" type of collagen within cell Cofactor required by

Cofactor required byphenylalanine hydroxylasephenylalanine hydroxylase TetrahydrobiopterinTetrahydrobiopterin *Defect in either

*Defect in eitherPKUPKU (MR, hypopigmentation…)(MR, hypopigmentation…) What "substance" crosses plasma membrane fastest?

What "substance" crosses plasma membrane fastest? CO2, followed by O2CO2, followed by O2 then nitrogen, inhaled anesthetics etc.then nitrogen, inhaled anesthetics etc.  _{diffusion is as}_{diffusion is as rapid for these gases as it}_{rapid for these gases as it is for them in water}_{is for them in water}  _{CO2 has higher solubility vs. water}_{CO2 has higher solubility vs. water}

E-cadherin

E-cadherin Allows formation of Allows formation of junctional com junctional complexesplexes((critical for formation and maintenancecritical for formation and maintenance)) via homotypic

via homotypic interactioninteraction b/w each other (cadherins)b/w each other (cadherins) thatthat initiates formationinitiates formation zona zona adherens

adherens(including signaling paths) which are then(including signaling paths) which are then activated to initiate formationactivated to initiate formation zona occ

zona occludens + ludens + desmosodesmosomesmes

Occludin Transmembrane

Occludin Transmembranecadherincadherinspecific tospecific to zona occl zona occludensudenstight junctionstight junctions

Desmoglein Transmembrane

Desmoglein Transmembranecadherincadherinspecific tospecific todesmosomesdesmosomes e.g. forms

e.g. forms intercellular linkages at desmosomesintercellular linkages at desmosomes which connectwhich connect epithelial epithelial cellscells  _{PEMPHIGOUS VULGARIS}_{PEMPHIGOUS VULGARIS –}_–_{anti-desmoglein Abs}_{anti-desmoglein Abs}

o

o Irregularly shapedIrregularly shapederosions inerosions inGINGIVAL, BUCCAL, palatineGINGIVAL, BUCCAL, palatine mucosae

mucosae o

o POSITIVEPOSITIVENikolsky testNikolsky test – –apply pressure + epidermis appearsapply pressure + epidermis appears to separate

to separatefrom underlying dermisfrom underlying dermis o

o Bx:Bx:acantholysis w subsequent loss of acantholysis w subsequent loss of cohesioncohesion Sites of synthesis

Sites of synthesisproteins destined for lysosomalproteins destined for lysosomal incorporation

incorporation

RER RER

Bullous pemphigous vs. pemphigus vulgaris

Bullous pemphigous vs. pemphigus vulgaris Bullous =Bullous =autoimmuneautoimmuneIgGIgGrxn vs.rxn vs.HEMIDESMOSOMESHEMIDESMOSOMES (collagen type XVII aspect)(collagen type XVII aspect) Pemphigous =

Pemphigous =DESMOGLEIN, tight junctions specific to epithelial cells, blisters,DESMOGLEIN, tight junctions specific to epithelial cells, blisters, positive nikolsky,

positive nikolsky,oraloralulcersulcers Action of alpha-1-adrenergic agonist (e.g.

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

vessels vs. muscarinic

Alpha-1 agonists

Alpha-1 agonists stimulate R on SMstimulate R on SM↑[Ca2+]↑[Ca2+]inin (IP3, DAG(IP3, DAGqqississ – –GqGq))

contraction (constrict vessel contraction (constrict vessel )) Muscarinic

Muscarinic can inducecan induceNO releaseNO release(aka(aka EDRF EDRF – – endo relaxing factor);endo relaxing factor); produced produced from

fromargininearginineby endothelial cellsby endothelial cells Muscle band changes during ctx

Muscle band changes during ctx – –A, I, HA, I, H A = NO CHANGEA = NO CHANGE II= shorten= shorten H

H= shorten= shorten

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

A-A-spansspans widthwidthmyosin thick myosin thick filamentsfilaments ((INCLUDINGINCLUDINGoverlapoverlapactin thin)actin thin)

length set by length of mysoin (thus length set by length of mysoin (thus noΔ

noΔ @ctx)@ctx) H =

H = thick myosinthick myosinWITHOUT overlapWITHOUT overlap actin

actin I =

I = actin filaments ONLY actin filaments ONLY

Z line

(14)

MUST KNOW THIS

MUST KNOW THIS –

– too easy to not

too easy to not

have on tip o tongue

Calculating changing osmolarity

Ex:

Ex: cell with osmolality of

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

MUST KNOW THIS –

– too easy to not have on tip

too easy to not have on tip o

o

tongue

Mass solutes in cell

Mass solutes in cell don’t change

don’t change (while fluid volume

(while fluid volume

does)

Mass intracellular solute

Mass intracellular solute before

before =

=

C

11

V

11

Mass intracellular solute

Mass intracellular solute after

after = C

= C

22

V

22

C

11

V

11

= C

22

V

22

300mosm(1) x(1.5)



X = 200

Diseases caused by DNA mutation/repair defects

KEY

KEY – – NER = NT excision repair, AR = recessive, AD = dominantNER = NT excision repair, AR = recessive, AD = dominant

Dz

Defect

Inheritence

Manifestations

Tx

Xeroderma

Xeroderma pigmentosum pigmentosum NER NER ARAR ↑↑r/o all skin CA (1,000xr/o all skin CA (1,000x↑↑)) ↑

↑incidence Japanincidence Japan

1.

1.retinoidsretinoids-- ↓↓CA butCA but irreversible

irreversiblecalcificationcalcification tendons/ligaments tendons/ligaments

--acitretinacitretin – – treatstreats keratoses,keratoses, also used in psoriasis also used in psoriasis 2.

2. 5-FU5-FU(pyramidine analog(pyramidine analog antimetabolite)

antimetabolite) Cocakyn's syndrome

Cocakyn's syndrome NER NER ARAR Bird-faciesBird-facies (thin nose, small head, large ears)(thin nose, small head, large ears) Retinopathy, dwarf with long limbs,

Retinopathy, dwarf with long limbs, photosensitive

photosensitive

Hyperpigment, erythema, teleangiectasias Hyperpigment, erythema, teleangiectasias Premature aging

Premature aging

No cure

No cure – – supportivesupportive

*CS2

*CS2 worse than 1worse than 1

Trichothiodystrophy

Trichothiodystrophy NER NER ARAR SulfurSulfur

Brittle hair/nails Brittle hair/nails Fish skin

Fish skin – – scalyscaly

Physical/mental retardation Physical/mental retardation

Rare, no cure Rare, no cure

Fanconi's

Fanconi's Anemia Anemia ROSROS

DNA repair DNA repair Cycle ctrl Cycle ctrl AR AR 11 genes 11 genes BM fail

BM failwwDNA repair defectDNA repair defect

-- petechiase, bruise, pallor, petechiase, bruise, pallor,café-au-lait café-au-lait - infection, fatigue

- infection, fatigue - aplastic anemia

- aplastic anemia(pancytopenia),(pancytopenia),leukemia,leukemia, solid tumors (

solid tumors ( CACA – – liver, neck, esophagus,liver, neck, esophagus, vulvar vulvar )) Tx symptoms Tx symptoms (anemia/leukemia/CAs) (anemia/leukemia/CAs) Bloom

Bloom HelicaseHelicase

Chr. Instab. Chr. Instab.

AR

AR ↓growth w/ ↑r/o malignancy↓growth w/ ↑r/o malignancy

Butterfly facial telangiectatic erythema Butterfly facial telangiectatic erythema --resp/GIresp/GIinfectioninfection

Werner's

Werner's HelicaseHelicase ((WS geneWS gene))

AR

AR Aging, thin, tight,Aging, thin, tight, scleroderma-like skinscleroderma-like skin ↓

↓muscle, wrinkle, hyperkeratosismuscle, wrinkle, hyperkeratosis

Cataracts, osteoporosis, arteriosclerosis, CA, Cataracts, osteoporosis, arteriosclerosis, CA, DM

DM

First 10 yrs of life normal First 10 yrs of life normal death 40yo

death 40yo

No tx No tx

(15)

A

TAXIATAXIA

-T

ELANGIECTASIAELANGIECTASIA Chromos +Chromos + chromatid chromatid breaks w breaks w rearrangmt rearrangmt AR AR chr 7 + 14, chr 7 + 14, ATM gene ATM gene **(= TCR + Ig **(= TCR + Ig regulation regulation chr)** chr)**

Heterogenous, but marked by Heterogenous, but marked by

neurodegeneration (ataxia) + telangiectasia neurodegeneration (ataxia) + telangiectasia (2/2 dilation vessels)

(2/2 dilation vessels) --sino-pulmsino-pulminfectionsinfections ↑

↑r/o CA,r/o CA, sensitive to xrays/radiationsensitive to xrays/radiation

Treat Sx Treat Sx Death teens Death teens

HNPCC/

LL

YNCH SYNDROMEYNCH SYNDROME

Mismatch Mismatch repair repair Microsat. Microsat. Instability Instability AD AD MSH2, MSH2, MLH1, MLH1, (PMS2), (PMS2),RasRas genes genes

Change in # of repeats of

Change in # of repeats of germline allelesgermline alleles

accumulation mutations accumulation mutations 80% r/o CRC

80% r/o CRC

Females have 30-50% r/o

Females have 30-50% r/oendometrial endometrial

C'scope q2yr at 25yo, q1yr C'scope q2yr at 25yo, q1yr @40yo (

@40yo (colectomy usual at thiscolectomy usual at this pt)

pt)

**

**L colon>R colonL colon>R colon – – unusual**unusual**

B

REASTREAST

CA

p53p53 DNA repair, DNA repair, cycle cycle AD AD BRCA1 BRCA1 60-80% r/o

60-80% r/oserous adenoCAsserous adenoCAs

BRCA 2 =

BRCA 2 =ovarianovarian , , prostate prostate , , pancre pancreatic atic

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