basic principles of science summaries

8/12/2019 Basic Principles of Science Summaries

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BP Summaries


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Microscopy SummaryLight (.2 m)

Condenser: focuses lightObjective: resolutionOcular: magnifiesNo screen (only in EM)

SEM (2 nm)Light source = elec. beamSurface onlyNo obj lens (doesnt penetrate)

TEM (.2 nm)PenetratesExpensive

Methods (TEM & light)Fixation (glutraldehyde), dehydration

(EtOH), Infiltration/embedding (Epon812 resin), section (diamond knife),staining (heavy metals for TEM)Freeze-fracture: fixation (optional),freezing, fracturing/etch,coating/replication (mold) avoidsartifacts of chemical

Common dyes: Hematoxylin (basic dye-stains acids blue); eosin (stains basesred); PAS (carbs); Sudan Black (lipids)Common metals: uranyl acetate, thelead citrate for TEM

Markers Antibodies

polyclonal: many bands, quick;monoclonal: need 1 specificantibody

Direct method: 1 antibody, shortlife, $$$. Indirect method: 2antibody marked.

Flourecence FITC: green . Rhodamine: red

Heavy metal Gold colloid

Enzyme Catalse: DAB method- turns black

with osmium


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DNA SummaryProkary. Genome

Circular, DS, no membraneMitochondria similar, but import hostsenzymes

VirusesRetroviruses: use rev transcriptase tomake DS DNA from RNA, insert into host.Orthomyxovirus: make only RNA , notDNA

DNA StructureNucleotides: base, sugar, phosphate. ( Sides: no P)Chargaffs Rule: A -T (2 H-bonds) G-C (3bonds)DS helix: antiparallel; B-form common(major/minor groves); phosphodiester

bonds.Chromosome structure

Nucleosome: DNA around histone (H1,H2ab, H3, H4 subunits) Heterochromatin: tightly woundEuchromatin: exposed, cleaved byDNAse.P arm small. Q arm long. Centromere center.

DNA replication (Eukary)Semiconservative: 1 strand original,1 strand built anew

Enzymes: Gyrase/topioisomerase: stop

supercoiling DNAses: cleave phosphod bonds Helicase: unzip DNA (form

replication fork).Lagging strand: Okazaki

Primase: put down RNA primer DNA pol: read in 3 -5 direction

(strand built in 5 -3) . Use dNTPas NRG.

Pol III: Prokary . Has only 3 to 5exonuclease activity during repair.Pol : Eukary.

Exonuclease (part of DNA Pol):5 -remove primer. 3 -removesingle-base errors

Ligase: close gaps btw Okazakifragments

Final steps Eukary genomes arent circular,

have telomeres. Telomeraseextends 5 ends of original strand(rev. transcribes RNA primer) .Long telomere folds over to cap3 end of new short strand

Review anti-caner drugs!


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Acid/Base Summary Acid: proton donorpH = -log[H +]HH equation: pH = pK + log [A -/HA]Buffer: mixture of weak acid and its salt. Adding some acid pushes rxn to make moresalt.Buffering zone: pH changes very little. Narrow! (+/- 1 pk unit)

Best buffering: pK = pKaPhysiological Buffers:

Bicarbonate: metabolic component.CO2: Respiratory componentEg: Resp. acidosis: increase in CO 2, body compensates by inc. bicarb.Note: Alkalosis is rare.


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Carb/Lipid SummaryChirality: image cant be superimposed

Enantiomers: mirror imagesDiasteromers: not mirror images

CarbsD-isomer: -OH is right of highest numberchiral carbon5 & 6 chain carbs can form cyclic

hemiacetals in solutionHawethorne: : -OH is downGlucose ring: pyranose. Fructose ring:furanoseSee notes for illustrationStraight chains are reducing sugarsGlycosidic linkage: forms disaccharides

LipidsCH3 (CH2)n COOHCarbon 1: COOHCarbon 2 (): ( CH2)COOHUnsaturated: at least 1 cis doublebond (Hs on same side) CH3(CH2)4CH = CH CH 2 CH =

CH(CH 2)7COOH

9, 12 octadecadienoic acid

Polyunsaturated: numberedfrom the CH3 end.Triglyceride: glycerol esterified

with 3 fatty acid chainsOthers: Phospholipids (cellmembrane), steroids


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Amino Acid Summary AA properties:

Most are L (-NH 3 to left)Zwitterion: + and charge. Makes aamore soluble, compatible w/ life(melting pts, etc)Isoelectric pt: where aa has nochargePeptide bonds form chains (N-terminus to C-terminus). Stable &planar.1 structure: aa sequence2: sheets, helices, random coils3: how prot folds (hydrophobic,electrostatic, disulfide interactions)4: subunits

Some names: Asparginine-N; Aspartic acid-D;Glutamine-Q; Lysine-K

Cleavage (Enzyme/chemical)Trypsin: cleaves C-end of Arg andLys GLY ARG SER -- GLY ARG + SER

Chymotrypsin: cleaves aromaticsPhe, Tyr, TryPepsin: same as above, also Metand LeuCNBr: cleaves Met

Protein CharacterizationGel electro: separates proteins bycharge (neg. ones move towardspos. anode)SDS-page: molecular weightIsoelectric: pH (stops migrating when

it hits pI)Ion-exchange chromatography CM-cellulose: neg. ligand,

pushes - prot out column, +remain ( cation exchanger )

DEAE-cellulose: anion exchangerGel-filtration (smaller prot caught ingel, bigger ones elute out 1 st)

Affinity chromatography: antibodiesare stationary phase ($$$!)Spectroscopy methods(fluorescence, mass, etc)


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Cell Membrane SummaryCell membrane structure

Fluid mosaic : integral prot(amphopathic); peripheral(hydrophillic); glycoproteins (cell-cell recognition, neg. charge)Membrane lipids: phosholipids,cholesterol. Turn black fromosmium dye

Has tri-laminar appearanceMembrane proteins: transporters,enzymes, receptors, linkers (holdcytoskeleton)

Cell membrane fxnsSelectively permeable Passive transport (down conc.

grad): simple diffusion = smallmlx. Facilitated transport(through protein channels) =large or polar

Active transport: Up conc.Gradient, use NRG (Na/K

ATPase: Na pumped out)

Signal transduction Transmitter-gated ion channel (ligand

bind, lets ions through); enzyme-linedreceptor (binding opens up active site); G-protein-linked receptor (amplies signalsw/ GTP)

Endocytosis Phagocytosis (large things) Pinocytosis (small dissolved solutes) Receptor-mediated = receptor proteins w/

target on inside of vesicle, clathrin coatoutside.

Exocytosis From Golgi Secretion can be Mediated (by

hormone/neurotransmitter) or Constitutive (unregulated)Membrane Flow Btw. Membrane-bound organelles After de-coating, V-snare binds to T-snare

on target destination. Vesicle needs to be 1.5 nm away to fuse.


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Cell OrganellesRough ER

Parallel cisternae, covered w/ribosomes (hematoxylin dye turnsacid [RNA in ribosomes] dark)Makes proteins for secretion,insertion in membrane, fusion tolysosomeFree ribosome reads signal onmRNA, signal recognition particlestops translation until ribosomedocked to ER (by receptorribophorin ), continues trans.protein into ER lumen. N-terminustranslated 1 st. Ribosome detachesfrom mRNA strand at completion.Ribosome also glycosylatesproteins AND insertstransmembrane proteins w/ help oftranslocon.Plasma cells, liver, pancreas,fibroblasts, osteo/chrondocytes &prot storing cells rich in RER

Smooth ERTubular cisternae, no ribosomes. Notdyed dark.Makes steroids and glycogen,metabolises lipids, stores ANDrelaeases Ca ions, drug detox

Steroid-secreting cells (adrenals,gonads), active metabolic cells(liver/pancreas) and muscle rich in SER

GolgiCis face (Convex): where proteinsenter. Vesicles leave from transVesicle coat proteins: COP II (ER to

Golgi), Clathrin (Golgi to cell memb),COP I (Golgi to organelles)Packages proteins, adds prostheticgroups, glycolysation/sulfation.Transfer vesicles: btw ER & Golgi.Secretory: about to leave cell.Present in cells with a lot of RER.


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Cell Organelles 2Mitochondia

Outer membrane (porins), inner membrane (ETC) cristae (folds), matrix (Krebs,own DNA, calcium granules)Steroid-secreting cells have tubular cristae

LysosomesDigest macromolecules, pathogens, old organelles1 (pre-ingestion, uniform appearance), 2 (post, mottled) and residual bodies(products not expelled from cell)Cytosol is basic in case of leaks

Peroxisomes (microbodies)Lighter than lysosomes, contain crystalsPeroxide & lipid metab.

Inclusions (no membranes)Lipid droplets: In adipocytes (signet rings).

Oil Red O dyes lipids, but are usually washed out Stores lipids and fat-soluble vitamins Adrenals, gonads, sebaceous, liver

Melanocytes Melanocytes in upper layer of dermis, deposit melanin there. Block UV, reduce visual noise Reduced amounts in substantia nigra of Parkinsons brains

Glycogen granules Liver cells, muscles, neutrophils


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Cytoskeleton SummaryHelps cell change shape, moves organelles

Microfilaments (5 nm) Actin: broken down by profilin/thymosin , repolymerized by formin/ARPMyosin : pulls actinSits on terminal web (stability)Movement; cell adhesion ( viniculin links actin w/ integrin receptors); shape changes (cytokinesis)Found in motile cells

Toxin: cytochalasin (stops repolymerization)Intermidiate filaments (10 nm)

ScaffoldingFormed like rope (alpha helix monomers form sheets of tetramers, which coil around each other)Keratin in epithelial, vimentin in connective, desmin muscle,

Microtubules (25 nm) Alpha and beta monomers. Form protofilaments (13 protofilaments per microtubule)Centriole/basal bodies: 9 + 0 triplets Centriole surrounded by satellite bodies (gamma monomers), bind to microtubules (form organizing center )

- ends of microtubules face centriole 2 centrioles make up mitotic spindle , attached to kinetochore of chromosomes w/ aster microtubulesCilia/flagella: 9 + 2 doublets (axoneme in center) subunit has 13 subunits, 10. Doublets joined by nexin. Cilia: anchored in basal bodies, flagella in centriole.Kinesin : vesicles out. Dynein : vesicles in, moves flagella


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Enzyme KinematicsSummary

EnzymesClass I: Oxidoreductases Oxidases, oxygenases, catalases,

dehydrogenases (move 2 H or e-)

Class II: Transferases Kinases

Class III: Hydrolases (hydrolysis ofC-O, C-N, C-S, O-P bonds) Peptidases

Class IV: Lyases (add/removewater, ammonia, CO2 to doublebonds)Class V: Ligases

Class Vi: Isomerases (mutases)Specific activity : number of enzymaticsites per mg protein. Reaches equil. inpure samples.MM assumptions: E + S ES E + P.

Under high [S], all of enzyme

becomes ES

MM equationV = Vmax[S]/Km+[S]Km = Vmax/2

InhibitionCompetitive: Vmax unchanged(can be overcome w/ a lot of

substrate)Noncompetitive: Km unchanged(binds near binding site, destroysenzyme activity)Uncompetitive: Km and Vmdecrease

Remember: Enzymes lower the

activation NRGStabilize transition state viasubstrate strainEntropic NRG: doesnt do work,but rather sets up the rxn.


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Glycolysis SummaryOverview:

In cytosolGlucose 2 pyruvate

Net 4 ATP & 2 NADHKey steps:

Hexokinase, PFK, and pyruvate kinase have free NRG, drive rxns forward.PFK is committed step

Fates of PyruvateKrebs CycleLactose & NADH (anaerobic & RBCs) lactosedehydrogenase

Alanine (-CH3 becomes NH3)2-3 BPG shunt

1,3 BPG -- ( 2,3 BPG mutase ) 2,3 BPG.Bypasses ATP-producing stepLower heme affinity for O2 in low oxygenenvirons

Hormonal regulationInsulin stimulates glycolysis (increases F 2,6 biP) AND lowers blood sugar (cells take it in)GLUT 2: liver/pancreas; GLUT4: fat, muscles;GLUT5: small intestines/liver. All go to cellmembraneGlucagon inhibits glycolysis, incgluconeogenesis

InhibitionG3P dehydro inhibited by arsenate andiodoacetate

Steps (w/ enzymes )Glucose -- ( Hex) -- Glucose 6P-- ( p-glucoisomerase ) -- Fructose 6P -- ( PFK ) --Fructose 1,6 bi-P -- ( F bi-P aldolase ) --dihydoxyacetone P & glyceraldehyde 3-P [interconvert due to triose isomerase ] -- (G 3Pdehydrogenase ) -- NADH & 1,3 BPG --(phosphoglycerate kinase ) -- ATP & 3phosphoglycerate -- ( PG mutase ) -- 2 PG --(Enolase ) -- phosphoenolpyruvate -- ( PyruvateKinase ) -- ATP & PyruvatePyruvate kinase / PG kinase are misnomers!!!1 ATP used at Hex. Step and 1 at PFK

Regulation of enzymesHex inhibited by its product; Glucokinase (isomer of hex) has a high Km for glucose, notinhibited by product. Works best at high gluconc. (such as liver portal vein)PFK : inhibited by ATP, citrate, and low pH(from lactic acid). Activated by AMP andfructose 2,6 bi-P PFK2 makes this F 2,6 bi-P from FGP. More ATP,

PFK2 is phophpho, less active

Pyruvate Kinase : inhibited by ATP,phosphorylation, and alanine; activated byFructose 1,6 bi-P

Read clinical correlations!


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RNA SummarySingle-stranded, has ribose.Replication and transcription in nucleus,translation in cytosolrRNA: Large & small subunit, 80% of allRNA. Proteins + rRNA = ribosometRNA: clover leaf. Anticodon, CCA- 3acceptor region for a.a. Made by RNA polIII.mRNA: codons identical to the sense(coding) DNA strand, but have U insteadof T.

Prokaryoytes- mRNA polycistronic (1strand = many genes), have Shine-Delg Sequence for ribosome binding.Eukaryotes- 5 cap: protects from RNAexonucleases, binds to ribosome tostart translation

RNA pol/transcription3 to 5, error -prone (RNA temporary),no primer needed, eukary has 3 RNApolsOn DNA: +1 = start of transcription,not translation.Promoters: need to be by start site.Enhancers: not position-dep, maketransxn faster (Eukary only)

Post-trans processingrRNA: split in two, always = amounts due totandem repeated arrays , methylated,becomes ribosome. Happens in nucleolus.tRNA: introns removed, methylated,glycolatedmRNA: Cap & 3 poly(A) tail added, intronsremoved, exons spliced when spliceosome [snRNA + proteins] recognizes 5 GU, 3

AG, A branch site in middle to removeslariat. Splicing inc. protein diversity

InhibitorsRifampicin (some TB resistant): inhibitsbeta subunit of prokary RNA pol

Amanitin : Blocks RNA pol II Acintomyocin : stops DNA from unwindingEthidium Br : intercalcates btw bases, stopsunwinding

OtherPro-opiomelanocortin is eukaryoticpoltycistronic geneMature onset diabetes of young:glucokinase gene spliced incorrectly inpancreas, not insulin dependent


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Krebs Summary Basics

Pyruvate loses CO 2 to become acetyl CoA.(pyruvate dehydro ). NADH also made.PDH has 3 enzymes (PDH, dihydrolipyltransferase, dihydrolipyl dehydro), 5cofactors (thiamine pyrophosphate, FAD,Lipoic acid, NAD, CoA)Pyruvate

RegulationPDH: Acetyl CoA, NADH inhibit. ATPfavors phospho (inactive) form. Insulinfavors dephospho (active).

ATP inhibits citrate synthase ; ATP/NADHinhibits isocitrate dehydro ; all above + GTPinhibits ketoglu dehydro ; malonic acidinhibits succinate dehydro ; fluoroacetateinhibits aconitase

Also limited by availability of acetyl-CoA,activity of ETC.PDH irreversibly damaged by arsenite

DeficienciesOften cause brain/developmental defects

Steps (w/ enzymes ) Acetyl CoA + oxaloacetate --( citrate synthase )--citrate-- ( aconitase ) -- isocitrate -- ( isocitratedehydo ) --NADH + CO2 + ketoglutarate --( ketoglu dehydro + CoA) -- NADH + CO 2 +succinyl CoA -- ( succinyl CoA synthetase ) --GTP +succinate -- ( succinate dehydro ) -- FADH2 +fumerate --( fumerase ) -- maltate-- ( maltatedehydro ) -- NADH + oxaloacetate

TCA intermediates in biosynthesisCitrate: fatty acid, sterols

keto: glutamine, glutarateSuccinyl CoA: heme

Oxalo: carbs, nucleotide, asp/arg Anaplerosis

Balance. Puts more acetyl-CoA in TCA bybreaking down stored fats/sugars (like btw meals),pulls intermediates away from biosynth rxns.


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Electron Chain SummaryOverview

Inner mitochondrial membraneElectrons pump H+ into mitosol , form pHgradientO2: final e- acceptor, makes water

ATP synthase: powered by H+ fallingdown gradient. 3 binding sites for

ATP/ADP + Pi (chemiosmotichypothesis)

ShuttlesBecause inner memb sel perm, needshuttles to oxidize NADH and bring itinto matrix to be reduced againMalate-Asp : Brings NAD+ inside More of this in LIVER and HEART: more

NRG

glycerol-phos : FADH2 donates e-directly to UbiQ pool, but bypassesproton pumpTricarboxylate : Brings acetyl-CoA insideby turning it to citrate (only when Krebscycle is slow ) for lipid biosynthesisNADH pumps 3 H+; FADH2 only pumps2 H+

Steps (w/ complexes )NADH to UbiQ ox-redase ( Complex I ):pumps H+[FADH2 to UbiQ ( Complex II )]UbiQ to CytochromeC ox-redase ( ComplexIII): pumps H+CytC oxidase to O2 ( Complex IV ): pumpsH+UbiQ: long/non-polar, found in membrane

Complexes have Fe-S clusters orcytochromes (like heme w/ Fe or Cu)Inhibitors

Uncouplers: allow H+ to diffuse throughmembrane instead of ATP synthase, makesheat 2,4 dintrophenol, pentachlorol phenol,

thermogenin (good for babies)

Valinomycin: transport K+ instead of H+,disrupts pH gradientOligomycin: inhibits ATPaseRotenone/Amytal: Complex I

Antmycin A: Complex IIICN & Azide: Complex IV (enters cell

rapidly)


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Nucleus/NucleolusSummaryBringing proteins inside:

Importins (alpha and beta): recognize NLS(Nuc. Local. Signal) on protein of interest,bind it. This complex is recognized by thenupe, passes through pore.RanGDP (in pore) helps NLS passthrough. Releases INSIDE of nucleuswhen it is replaced by GTP. Process doneby G-exchange factor , called RCC1 .

Importins recycled: pass back throughpore w/ help of RanGTP (alpha importinneeds CAS also). GTPase activatingproteins help re-form RanGDP, andimportins are released OUTSIDE ofnucleus into cytoplasm.CAS re-enters nucleus through diffusion.

Cytoplasm: GDP -(pore) GTP : Nuc.Protein released inside.Nuc: GTP (pore) GDP : CytoplasmProcess can begin again

Nuclear LaminaMaintain integrity of cytoskeleton and bindchromatin (intermediate filaments)Lamin binding proteins : Nurim, Emerim, & MAN1.Lamin A and B are made from same gene, spliceddifferently.Lamin C: Spliced differently, has no CaaX box (forbinding). Uses its N-terminus to bind to Lamins Aand B to form a scaffold.LAP: Lamin binding site (to chromatin)

Dystrophies and cancer : caused in part by nucleiw/out laminar supportCajal : make snRNP and snoRNP (small nucleolarribosomal nuc prot). Found near nucleus.

Nucleolus:Pars Fibrosa: where RNA is being transcribedfrom DNAPars Granulosa: proteins associated w/ modifyingRNArRNA subunits are split and spliced, except 5S.


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Transport Across MembranesNernst Eqn

E ion (mV) = 60/z *log C out /C in

Na is high on outside of cell (E ~ 60), K is low on outside of cell (E ~ -90)Total of solutes on inside of cell is ~300mM. Always assume this.Cholesterol: too much = rigid membrane. Too little = fluidCarbs: sialic acid residues (on membrane). Neg charge. Flu virus binds to it.Ficks Law: if you have a thin membrane w/ a lot of surface area, your solutes willdiffuse through at fast rate.

Diffusion coefficient when temp and viscosity and molecular size .Osmosis: net diffusion of waterOsmolarity (Osm):

60 mM of glucose = 60 mOsm while 60mM NaCl =120 mOsm (salt dissociates)Hyperosmotic soln: cell shrinks as water leaves (more solute/less water outside) (greater osmotic pressureoutside). Opposite for hypoosmotic soln

Tonicity: concerned w/ NaCl ONLY.Hypertonic: water leaves, cell shrinks. Hypotonic soln: little or no salt (


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Mitosis/Cell Proliferation5 phases:

Go (senescence)

G1 (GAP1) make proteins for DNAreplication Checkpoint 1: excision DNA repairS phase - DNA synthesisG2 (GAP2) make proteins for cell divisionCheckpoint 2: mismatch DNA repairM (mitosis) - division of the nuclear material

Cell cycle controlled by 6 proteins:Cyclins: regulate CDK activity D (G1 phase) , E (Chkpt 1), A (S phase),

B (G2/M).Cyclin dependent kinases (CDKs): proteinkinases ( 4 in G1, 2 in middle phases, 1 in G2)Cyclin dependent kinase inhibitors (CDKIs): inhibit CDK (INKs)

Wee kinase: inhibits CDKs by phospho Thr14 /Tyr 15. Expressed at Checkpoint 2 so anyerrors in DNA replication are fixed before cellcontinues. Cdc25c phosphatase: activates CDKs bydephospho . Thr 14 /Tyr 15CDK-activating kinase (CAK): activates CDKsby phospho . Thr 172 /Thr 161

***Cyclins/CDK complex provide specificity forwhich proteins need to be made in each phase.

Before Mitosis:

E2F (regulated/sequestered by Rb):transcription factor needed. W/out Rb, E2Ftoo active, proliferation goes unchecked.Causes retinoblastoma. CDK4

phopsphorylates Rb, which activates E2F,which in turn makes Cylcin E & CDK2.INK4 (p16) : inhibit Cyclin D only. Cip/K inhibits all cyclins. Expressed at checkpointsONLY if there is a problem duringtranscription. p53 makes these inhibitors.

Phosphoryltation causes lamins to dissasmbleduring prophase, reappear in telophaseCancer Correlations

ATM (ataxia-teleng gene): Stops cellproliferation to check for errors at Chkpt 1Tumor supressing genes: p53, p21, p27 .Checks for DNA errors. If too many, p53levels stay high, tells cell to undergoapoptosis. Cyclins/CDK can act as oncogenes


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Protein-Mediated Transport & Ion DistributionImportant Factors

Rxn rate: The more solutes that bind, thefaster the transport rate.Saturation: Transport maximum = TmSpecificity: if it transports an L-isomer, itwont transport the d -isomerComp. inhib.: many monosaccharidescompete w/ glucose transport.***Low Km = high affinity = hightransport rate.

Channels (most common!) Aquaporins = water. Pore diameter toosmall for solute mlx. Mainly in RBC andepithelia lining kidney, lung, intestines.Gap jxns : smooth & cardiac muscles,epithelia/endothelia. Non-selective

pores.Ion channels : Voltage-gated (Na+ gate),ligand-binding (conformational changeopens it), and mechanical distortion(pressure)

CarriersOnly open at one end

Binding site hidden on the side ofmembrane where cargo is released.

PumpsPrimary : uses ATP to pump against

conc/elec gradient. Na/K ATPase: Most common pump! and

subunits. 3 Na out, 2 K in. Controls cellvolume and resting potential.

Inhibited by ouabain (thus Na cant leave cell. Affects Na/Ca exchanger, and more Caavailable inside heart muscle to restart heartcontractions).

Ca2+

ATPase: in muscle. Sends Ca outSecondary : using NRG from ion fallingdown its conc/elec gradient to pushanother ion up its gradient. Na is usuallythe driver solute. Include cotransporters and

countertransporters (like Na/glucose cotransor Na/Ca countertrans.)

Ions Movement (in/out of cell) Youll get a + Nernst potential if conc. grad.

for a cation (like Na) is high outside cell (dueto their movement into cell).

Gibbs-Donnan: Cell interior hasimpermeable, mainly neg proteins. Couldattract outside cations and cause swelling if itwerent for pumps.


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Translation SummaryRibosomes

Prokaryotic ribosomal subunits: 50S + 30SMitochondria: 12S + 16SEukary: 60S + 40SE, P, A sites: tRNA binds to A site, peptide bond forms atP, released at E.

tRNAMade in nucleusNeeds amino acyl in order to bind codons.iMet tRNA (fMet in prokary) can only recognize startcodon (AUG), and not internal AUG. It binds initiationfactor. Mmet binds elongation factors.

Always read codons and anticodons in 5 to 3 direction. Stop codons: UGA, UAG, UAA

ProkaryotesShine-Delgarno sequence (AGGAGGU) is always in frontof a start codon (Eukaryotes have a Kozak region)

MitochondriaImport most translation proteins from hostStop codons for mitochondria ( AGG and AGA)

InhibitionProkary: Buy AT 30 (subunit) , CE LL at 50 A = Aminoglycosides (Streptomycin, Neomycin) T = Tetracycline C = Chloramphenical E = Erythromycin

Eukary Diptheria toxin : inhibits elongation factor 2 Cyclohexamide: 80S

Initiation (Eukaryotes)eIF4E binds 5 cap , eIF4B phosphorylates it so it canrelease cap. eI4G is scaffold .5 UTR stop sign always in front of AUG, needs to

be unwound w/ elF4A helicase. Initiation factor 4F . iMet tRNA needs eIF2-GTP for activation/recognitionof start codon AUG. eIF2-GDP needs a GEF(guanine exchange factor) to become GTP. THISSTEP CAN BE REGULATED!met tRNA/eIF2 combines w/ 40 S subunit to become43S Preinit Complex .eIF4 + 43S Preinit Complex = 48S Preinit Complex .

Goes to AUG start codon, but needs 60S subunit tostart translation!When 60S binds (w/ eIF5 ), 80S subunit completeOVERVIEW: [eIF4(E, G, A) ] + [eIF2 + tRNA + 40S ] + 60S

Termination of translationEukary: eIF6 (dissociation factor) makes 80S leavemRNA

Prokaryotes: 3 release factors. 1 is a GTPaseEukaryotes: 2 release factors. 1 is a GTPase

IronFe levels in cell low: need more transferrin receptors.Transferrin RNA is not degraded. If too high: ferritinRNA is not degraded, more toxic Fe can be bound bynewly-made ferritin.


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Embryology (Week 1 and 2)Week 1 - Fertilization

Sperm passes corona radiata , binds to ZP3

receptors on zona pellucida . Acrosome enzyme on sperm head released(digests ZP)Fast block : ion channels on egg open up(depolarization)Slow block : cortical granules on eggmembrane ( oolemna ) release enzymes that

cause the ZP to harden ( cortical rxn )Primary oocyte: caught in prophase II ofmeiosis until sperm entersPronuclei from parents meet, complete meioticdivisions. Sperm centrioles used here.Cleavages form morulla .Morulla becomes blastocyst : outer trophoblast surround inner cell mass . Uterine fluid fillsblastocoel .Blasto leaves Fallopian tube for uterus (takes5 days). Safe from toxins.ZP degrades, blasto hatches and is sticky. Blasto attaches to uterus w/ integrin.Trophoblast cells invade uterine wall(syncytiotrophoblast ). Begins to differntiate!Trophoblast secretes HCG hormone

Week 2 BlastocystTrophoblast Differentiation:

Cytotrophoblast : forms chorionic villi.Syncytio .: becomes placenta. Dissolvenearby capillaries in uterus to nourishblasto.Inner Cell Mass (2 Layers):Epiblast (upper layer; forms amnionic cavity).

Hypoblast (lower layer; forms primitiveyolk sac ). AKA exocoelomic membraneMesoderm: Forms btw hypo & epiblast. Extraembryonic coelem (used to be

the blastocoel ) forms in mesoderm,splitting it into sphlanchnic (onlyaround yolk sac) & somatic (aroundembryo and coelem) layers.

Primary yolk sac pinches off of largersecondary yolk, stays beneath embryo.

Prechordal Plate: AKA buccopharyngeal membrane Thickening of the hypoblast. Becomes

mouth.Primitive streak formed in e i la er.


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Embryology (Week 3)Week 3- Gastrula (3 layers)

Primitive pit : in front of primitive

streak. Cells of epiblast enter the pit,form a neural groove ( notochord ).Remember tissue demo in class!The 1 st cells displace the hypoblastand become the endoderm . The nextcells to enter become the mesoderm .The cells on top become theectoderm .Gut tube forms in the endodermabove the yolk sac.Neural crest (on side of neural tube)forms in the ectoderm, induced bynotochord.Mesoderm forms paraxial,intermediate, and lateral plates.

2nd Week

3rd Week
http://nba.uth.tmc.edu/courses/devo2004/lectures/block_1/gibson/early%20development/images/3_5A.jpg


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Cell Signaling SummaryOverview

Endocrine: signal goes through bloodParacrine: acts on nearby cells

Autocrine: acts on selfSignaling by cell-membrane proteins

Lipid Ligands (hydrophobic)Have a long-lasting effect.Bind to transcription factors (either in

nucleus or cytosol) which then bind toDNA. Their binding removes inhibitoryproteins.

All lipid receptors have similar DNA-binding domains (hormone responseelements)Need carrier proteins to transport them

through the cytosol to nucleus.Ex: Steroids, thyroid hormones

Protein Ligands (hydrophilic)Bind to surface receptors, activatesecondary messengers, have a quickphysiological response.Stored in vesicles for later use.Ex: Insulin

2 messengerscAMP

Ligands bind to surface G-proteins ( subunitinactive w/ GDP, becomes active w/ GTP).Ligand-receptor complex causes this change.

w/ GTP activates effector (adenylatecyclase), which makes cAMP.

Adenylate cyclase inhibited/stimulated byGi/Gs proteins.

Deactivated by phosphodiesterase.cGMP Made by guanylyl cyclase. Nitrous Oxide also stimulates cytosolic

guanylyl cyclase.Protein kinase activity

Activated by cAMP Goes on to phospho other proteinsCalcium & phosphoinositides Gq proteins stimulate phosphoino. Makes IP3 (releases Ca ions) and DAG

(activates Protein Kinase C).2 messengers are always present in the cell


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Epithelial SummaryBackground

Forms liningsCells very tightly packed

LayersSimple: one layerStratified: 2+ layers Look at top layer to determine cell type or see if

theres keratin Pseudostratified: Different heights. All cells touch basement memb. Often have cilia

ShapeSquamous: flatCuboidalColumnarTransitional Is stratified, but change shape. Found in bladder,

ureter.

Glands (lined by epithelial cells)Exocrine : Connected to ductEndocrine : No duct, relies on nearby capillariesMerocrine : release only product (sweat)

Apocrine : some cell parts released (mammary)Holocrine : entire cell destroyed in release (sebaceous)Mucous secretions : contain glycoproteins

Serous secretions : proteins in waterSeromucous : in btw.

Regions Apical

Cilia (motile, have microtubules, sit onbasal bodies, have a raggedyappearance).

Microvilli (increase surface area, sit onterminal web, have actin, have stickyglycocalyx, have uniform/brush-likeappearance).

Lateral Zona occulada: forms seal, keeps

material from seeping btw cells Zona adherens: Made of actin. Used in

adhesion & to withstand mechanicalstress.

Gap Jxns: used in communication, havepores (connexons).

Desmosome: Button shaped, havekeratin, dont encircle cell.Hemidesmosomes sit on cell bottom.

Basal Basal lamina: secreted by epithelial

cells. Contain collagen & laminin.

Basement memb: Basal lamina +reticular lamina (made by connectivecells


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Differentiation in EmbryoBackground

Embryonic stem cells transcribe our entire genome at a very low rate.Terminally- differentiated cells arent replaced after they die (neurons and muscle) Muscles only grow in size: hypertophy. Cancer = hyperplasia.Induction : occurs in gastrulation when different cell types come in contact.Notochord induces neural crest formation. frog neural fold transplantation experiment

Ectoderm derivativesMakes neural crest, epidermis, gut liningNeural crest makes connective tissue of the face, peripheral nerves, APUD cells(make bioactive amines), and melanocytes

Mesoderm derivativesParaxial (somites) 1 somite per body segment. Sclerotome = vertebrae. Dermatome = dermis.

Myotome = skeletal muscles.Intermediate (urogenital)

Lateral (axial skeleton)Endoderm derivativesPinching of aminion helps form gut tube. Part of yolk sac gets drawn up into it.Endoderm forms lining of digestive and respiratory system.


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Birth DefectsStages

GametogenesisFertilizationGerm disk formsImplantationEmbryonic period (1 st 8 weeks). Very vulnerable to birth defects. Any problems here will cause death of fetusFetal period Any problems here may not result in death, but may affect how well fetus grows (intrauterine growth retardation)

Causes of birth defectsGenetics (main cause)InfectionsDrugsSample from amniotic fluid (or chorionic villi) is grown on culture & made into karyotype to find chromosomalabnormalities.

Autosomal Chromosome Problems

Trisomy 21: Down's SyndromeTrisomy 18: Edward's SyndromeTrisomy 13: Patu Rocking-chair foot

Sex Chromosomes ProblemsResult from incorrect meiotic divisions (causes monosomy and trisomy)Turner's: mentally normal (XO)Kleinfelter's: XXY, XXXY


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End of Exam 1


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Connective TissueBackground

Maintains form and structureStores fatDefense against pathogensCome from mesenchyme cellsMade of cells, ground substance, and fibers.

FibersCollagenMost abundant proteinProvides strength/flexibility1/3 glycine. Also has hydroxyproline andhydroxylysineMade of polypeptide chains ( -chains) whichform triple helix (done w/ help of registrationpeptides )Leaves cell, removal of reg peptides =tropcollogen (type I common). Forms fiberbundles.Banding pattern on fibers: 64 nm

Elastic fibersStretches and relaxes easily. Very resistant todegradation.Made of elastin (desmosine and isodesmosine)and microbrils (fibrillin protein) Microfibrilssurround elastin.Branches (UNLIKE collagen)Reticular fibersHeavily glycosylated Type-III collagen.Forms a hammock for cells

Ground Substance Clear gel Fills spaces Lubricant Barrier- very viscous Glycosaminoglycan (GAG) Made from repeating Uronic acid + Hexosamine sugars. Most sulfated, attracts water. Proteoglycan GAG w/ protein core attached (resembles pipe cleaner)

Glycoprotein Protein is main component, has branched carbs. Helps in adhesion Found in basal laminaCells

Fixed : Makes the fibers and ground substsance. Fibroblasts, adipocytes, chrondocytes, osteocytes,

reticular cells.Wandering : Made elsewhere, transported by blood tothe matrix. Macrophage : contain lysosomes Plasma cell : has clock face nuclei, makes

antibodies Mast cell : histamine/heparin granules


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Connective, contd Connective Tissue Proper:

Dense Regular : resists one-directional pulling forces.Collagen fibers run in samedirection. In tendons.Dense Irregular: Collagen w/outdirection. Can resist pullingforces in multiple directions.

Surrounds organs.Loose (areolar): Mostly groundsubstance. Open to infection:has macrophages. Not asstrong as regular, but moreflexible. Dermis, gland/cavitylinings.

Specialized CTElastic CT: has elastic fibers,yellowish. Rare.Reticular CT: very little groundsubstance, looks like a giant net.Mucous CT: mostly groundsubstance (hyaluronic acid). Fewfibers, some fibroblasts

Adipose CT: has reticular fibers.Mostly cells (unilocular andmultilocular). Highly vascularized.

Also cartilage, bone, blood.

Diseases

Marfans : fibrilin gene mutation.Tall, disproportionate skeleton.Ehlers-Danlos : hyper-stretchy skin.Collagen fibrils uneven in diameter,uneven spacing btw them.


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CartilageBackground

AvascularBears stress w/out being deformed.Shock absorber

StructureCells Come from progenitor (mesenchyme) cells Chrondoblasts: active. Found in per ichondr ium . Chrondocytes: surrounded by matrix. Live in

lacunae.

Isogenous group: cluster of recently dividedcells.

Ground substance Proteoglycan (aggrecan) & glycoprotein

(chrondronectin & fibronectin) Territorial matrix: immediately around cell. More

GAG, fewer collagen. Interterritorial matrix: farther from cell, lighter staining.

Fibers

Mainly type II collagenHyaline CartilageMost commonType-II collagenFetal skeleton

Articular cartilage = joints. No perichondriumTrachea, larynx, plates of growing bones

FibrocartilageLots of Type I and II collagenBtw. dense CT and hyaline cartilage.No perichondriumVertebral discs (annulus fibrosous)

Elastic CartilageYellowishMore elastic fibers.Type-II collagenEar, epiglottis

Joints

Synarthroses : limited/no movement Synostosis : bone to bone (skull) Synchondrosis : bone to hyaline cartilage

(ephyseal plates in bones) Syndesmosis : bone to dense CT (fibula-tibia)Diarthrosis : free movement, most common Capsule: fibrous layer (dense CT) and synovial

membrane (lines articular cavity) Ends of bones surrounded by capsule Synovial membrane A cells: phagocytic, clear

debris . B cells: make fluid.Problems

Osteoarthritis : loss of articular cartilageRheumatoid arthritis : inflammation of synovialmembrane, cavity calcifies.

B


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BoneSTRUCTURECells

Osteoblasts : secrete osteoid Cuboidal, lots of RER, found on bone surface.

NOT epithelial tissue!Osteocytes : surrounded by matrix Dont make new matrix. Cant divide. Have filopodial process: extension of cell. Joined by canaliculi: extension of lacuna.Osteoclast : macrophage that breaks down matrix. Contains acids. sits in Howship capsule. Has

ruffled edge to increase surface area. Manynuclei.

Periosteum: Surrounds bone Blood supply & source of osteoblasts Fibrous layer: Dense CT (collagen/fibrovlasts) Osteogenic layer: cellular, bound to bone by

Sharpeys Fibers. Endosteum: Lines interior of bone Thin, reticular fibers Also has osteoprogenitor cells

Matrix (fiber, ground substance, minerals)Osteoid: Type I collagen, ground substance, nomineral. Helps give it shape, resistance to tension.Mineral: rigid, but not flexible. Calcium, phosphate(make hydroxyapatite).Calcification: need osteocalcin, osteonectin,

phosphotase enzymes.

Calcium mobilizationParathyroid Hormone Acts on osteoblasts. Blasts stimulate osteoclasts,

which activity. Bone breaks down, frees Ca(resorption)

Calcitonin Acts on osteoclasts. activity. Bone formation.

Spongy BonePrimary or secondary boneLocation: epiphyses (long bone ends), interior, center offlat skull bonesForms trabeculae (bone spicules) projecting intocavities for marrowOsteocytes in spicules dont form neat lameallae.

Compact BoneSecondary bone only!Location: right beneath periosteom and in diaphyses(long bone middle).Forms osteons (Haversian sysytems) Haversian canal : center. Holds nerve, blood vesses, lymph.

Runs along length of bone. Volkmanns canal: Connects Haversian canal Collagen fibers in same lamellae are parallel, but crisscross

fibers in adjacent layers. Osteon surrounded by cement (minearls w/ few fibers).

Lamallae farthest from canal formed 1 st Outer circum. lamallae : Beneath periosteum. Noosteons.Inner circum. lamallae : Surround marrow. No osteons. Intersitial lamallae : Remains of old osteons

Bone contd


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Bone, contdTIME OF SYNTHESISPrimary Bone

Always spongyCollagen fibers more unorganized, lessminerals.Temporary, except in tooth sockets & flatbone sutures.

Secondary BoneSpongy or compactCollagen fibers more organized

Mature boneOsteons continuously remodeled

As bone grows, marrow cavity expands.Compact bone thickness stays same.Hormones

Growth Hormone: stimulates chrondocytesVitamin A: stimulates osteoblastsVitamin D: Calcium absorptionEstrogen: stimulates bone formation

METHODS OF FORMATIONIntramembraneous Ossification:

Formation of skull bones (derived fromneural crest)

No cartilage model formed. Mesenchymegoes straight to osteoblasts

Endochrondal Ossification:Formation of long bones.Mesenchyme forms chrondocytes, which formepiphyseal plates (responsible for growth)ZONES:

Proliferation : isogenous groups stacked one on top ofthe other as they divide.Hypertrophy/Calcification : chrondocytes startmineralizing, blood vessels can enter.Ossification : cartilage is now bone.Cartilage begins in long bone center. Pushes outwardsto both ends during growth.Ossification Centers:

1: Middle of long bones2: In epiphysis. Form after primary.3: Form tubercles and ridges.

Fracture RepairBlood vessels break. Clot forms around fractured ends.Progenitor cells enter, become osteoblasts,chronodocytes, fibroblasts.Callus formed (CT and cartilage model). Replaced by 1bone, then 2 bone.

DISORDERSDwarfism : epiphyeal plates understimulatedChrondodysplasia : Type II cartilage mutation = shortdeformed limbsOsteogenesis Imperfecta : Type II cartilage mutation = short,fragile limbsRickets : Ca deficiencyOsteomalacia : osteoid doesnt mineralize = soft bones

Gluconeogenesis & Glycogen


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Gluconeogenesis & GlycogenBackground

Glycolysis in reverse. 6 ADP equiv, 2 NAD+ made.Diff enzymes used for irreversible rxnsPrimary location: liver. Makes glucose for brain, RBCNRG ( ATP ) comes from fatty acid oxidation!

ATP, citrate, and acetyl CoA stimulate gluconeo Key Steps (w/ enzymes )

Pyruvate - ( pyruvate carboxylase ) oxaloacetate (PEP carboxykinase ) PEP Reverse of Pyruvate Kinase Pyruvate carb uses ATP, biotin, K, Mg to add CO 2

to pyruvate.

Oxaloacetate leaves mitocho via mal-asp shuttle .PEPCK is in cytosol. PEPCK uses GTP, K, Mn to remove CO 2, add Pi If ATP low, oxalo goes to Krebs.Fructose 1,6 BP (Fructose 1,6 phosphatase ) Fructose 6P Reverse of PFK1 RATE-LIMITING STEP!

Glucose 6P (Glucose 6 phosphatase ) Glucose Reverse of hexokinase Membrane-bound in ER

No net flow of carbons from acetyl CoA to glucose.Most sugars, most aa (not lys & leu), succinyl-CoA and -keto are glucogenicGlucagon stimulates gluconeo, but slows glycogensynthesis. Phosphorylates synthase & phosphorylase.Insulin inhibits gluconeo & stimulates glycogen synthesis

Non-pyruvate sourcesRBC and muscles make lactate from pyruvate when O 2 low.Liver removes extra lactate by using it for gluconeo ( CoriCycle )NADH made from breaking down EtOH. Too much NADHinhibits rxns that need NAD+. Also, fatty acid oxidation in liverand gluconeo from lactate is inhibited.

Alanine (pyruvate + NH 2) also fed into gluconeo. Makes urea.Glycogen Synthesis

Glucose (hex ) Glu 6P (phosoglucose mutase )Glu 1P(G1P uridyl transferase )- UDP -glu

Add UDP-glucose to protein glycogenin (done by transferase for 1 st 2 residues). Glycogenin primes itself up to 8 glucoseresidues.

Additional glucoses added by glycogen synthase . Forms 1,4glycosidic linkage on non-reducing ends. Stimulated by glu-6Once chain has ~11 residues, branching enzyme removes 6residues, forms 1-6 linkage w/ nearby chain.

RegulationDe phospho form of glycogen synthase ( a ) is active and isNOT sensitive to stimulation by glucose 6PPhospho form ( b) is inactive and sensitive to stimulation byglucose 6PSeveral kinases and 2 messengers aid in regulation

GlycogenolysisGlycogen phosphorylase breaks 1-4 linkage in glycogen,makes glucose 1P. Regulated by phophorylase kinase.Phospho form = a = active.Debranching enzyme when you hit last 4 glucoses of each

chain, it puts 3 on the C4 of next branch (last hydrolyzed bywater).

Connective Tissue Fibers


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Connective Tissue FibersCollagen

Background: Abundant (~30% of all proteins)Gly every 3 rd aa. Forms tighter turns than helix. chainsform triple helix.

Type I : Ligaments, tendons, skinType II : CartilageType III : Skin vessels, tendonsType IV : Basement membraneType V : Fetal membranes

Collagen Synthesis (w/ enzymes )In RER lumen : some pro & lys get hydroxylated by prolyl& lsyl hydroxylases . Cofactor: ascorbic acid (vitamin C).Lys later glycosylated ( glycosyl tranferase ). Helps formpreprocollagen left-handed triple helix. Signal peptidecleaved in RER, becomes procollagen. Helix secreted. Peptidases cleave registration peptides onends. Procollagen becomes tropocollagen . Formsmicrofibrlis, then fibers.Lysyl oxidase : deaminases chain and turns it to analdehyde so it can undergo crosslink rxn . w/ other

microfibrils. Cofactor: copper .Lysinonorleucine : main collagen crosslink.If not properly made, fibrers gets degraded.

ElastinBackground:Not a triple helix. Gly not every 3 rd residue.Mostly nonpolar aa. No carbs!Only one type.Desmosine : main crosslink . 4 aa join together, formsheteroc clic crosslink.

ProteoglycansLubricates, supports. Antithrombic (heparin)GAGs: long chains of repeating disaccharides.Proteoglycans = Mucopolysaccharides = GAGs

bound to core proteinGAG Structures:Heparin : GlcUA or IdUA ( Sulf ) + GlcNAc ( Sulf )Heparine sulfate : same as above, but fewer Sresidues.Dermatan sulfate : GlcUA or IdUA + GalNAc ( S )Chrondroitin sulfate : GlcUA + GalNAc( S)Keratan sulfate : GlcNAc ( S) + Gal

Hyaluronic acid : GlcUA + GlcNAcAdhesive Fibers

Help in cell movement, adhesion, wound healing.Fibronectin : fibroblast, endothelial cells, monocytes,neutophils Has binding domains that bind proteoglycans,

collagen, fibrin, integrin (in cell membrane).Helps cells detect changes in extracellularmatrix.

Chrondonectin : cartilageLamin : epithelial cells Also has different binding domains.


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CT Fibers, contd Disorders:

Scurvy : w/out vitamin C, collagen not hydroxylated. Get weak chains.

Crosslink rxn inhibited by sulfhydryl groups (found in homocystine )Lathyrism : -aminoproprionitrile (from sweet peas) inactivates lysyl oxidase.Decreased crosslinking of collagen. Also caused by Penicillamine (used in copperchelation therapy).Collagenase : In tissue- reshapes collagen. In Clostridium histolyticum (bacteria)-causes gangrene (bacteria breaks down fibers to spread).

Elastase : Breaks down elastin. Antiproteases : -antitrypsin normally in balance w/ elastase, except in

emphysema (too moch elastase).Hurler : No a-L- iduronidase. Cant make dermantan, heparin S. Hunter : No a-L-iduronidase-2-sulftase. Same as above.Sanfillippo A-D : No heparin made. See clinical correlations for enzymes affected.

Rheumatoid arthritis : Hyaluronic acid depolymerized.

Pentose Phosphate Pathway & Other Sugars


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Pentose Phosphate Pathway & Other SugarsPent Phos Path (2 Phases)

Makes NADPH for biosynth (H+ donor, not carrier)Makes nucleotides from Rib 5PNot very active in brain/muscle tissue

Oxidative Phase (non-reversible)

Glu-6P (Glu-6P Dehydro ) NADPH + 6P glucono- lactone (Lactonase ) 6P-gluconate (6P-GlucoDehydro ) NADPH + CO 2 + Ribulose 5P

Non-Ox Phase (reversible)Rib 5P + Xyl 5P (transketolase ) G 3P +Sedoheptulose 7P - ( transaldolase ) Fru 6P +Erythrose 4PEry 4P + Xyl 5P (transketolase ) Fru 6P + G 3P

Phosphopentose isomerase & epimerase turn Rib 5P toXyl 5PTransketolase needs thiamine!Net: 3 5C sugars turned to 2 6C & 1 3C sugars

RegulationFru 6P & G 3P can be diverted from glycolysis if Rib 5P(but not NADPH) needed.Can become Glu-6P ( gluconeo ) if more NADPH needed,

Glutathione and AnemiaOx. Glutathione + NADPH (Glut Reductase ) Red.Glut + NADP+ -SH on glutathione helps RBC scavenge free radicals inlungs. Otherwise, oxidative damage causes hemolyticanemia.Glu-6P Dehydro deficiency : Cant make red. glut w/outNADPH. ox stress, sensitivity to drugs that cause cellprotein ox, sensitivity to fava beans (have pro -oxidants).

Very common inborn metabolic defect. Helps combat P.falciparum malaria, which needs lots of reduced glut inRBC.

Metabolizing Non-Glucose SugarsMaltose, sucrose, lactose dissachs broken down to

glucose, fructose, galactose.Fructose MetabolismEnters cells through GLUT-5. Sperm fuel.Fruc-( Fructokinase )-Fruc-1P-( Aldolase B )- DHAP+ Dglyceraldehyde (triose kinase ) G 3PG3P enters glycolysis. Bypasses insulin and PFK1regulation. Kinase uses ATP.Fruc not metabolized as well as glu.Fruc Intolerance : W/out Aldolase B, Fruc-1Paccumulates. Traps available Pi, inhibits ATP synthesisGalactose MetabolismGal (Lactokinase )- Gal 1P + UDP-glu (Uridyltransferase )- UDP-gal + Glu 1PGalactosemia : W/out lactokinase or UD transferase, Ga1P can become galacticol, accumulates in eye. Pi also Sugar AlcoholsGlu- (aldolase reductase )-sorbitol-( sorbitol dehydro )-FruDiabetics have more glu, more aldolase reductase isinduced. Sorbitol forms crystals which build up in eyes,kidneys.

Glucuronic PathwayUses glucoronic acid to make GAG (proteoglycans),glycoproteins, glycolipids

UDP-glu (UDP-glu dehydro ) UDP glucoronic acid.Most animals can make Vitamin C from glucoronic acid.

R i M b P i l


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Resting Membrane PotentialBackground

Cells resting membrane potential is overall negative.

Goldman-Hodgson Eqn.Vm = 61 log P K[K+]o + P Na[Na+]o

P K[K+]i + P Na[Na+]I Nernst for more than 1 ion.Cl- already near cell resting potential, ignore its contribution to eqn. P = permeability constantsThe more permeable a membrane is to an ion, the closer the resting membrane potential will be to

that ions Nernst equilibrium Ohms Law

Iion = g ion(Emembrane potential ENernst )Current =I, conductance = gIf the membrane potential equals the Nernst potential for an ion, youll get 0! Therell be no current!

TermsHyperpolarized : membrane potential is MORE negative relative to outside. Less excitable. RMP.

Depolarized : membrane potential is LESS negative relative to outside. More excitable. RMP . Approaches threshold!

It always takes the cell awhile to respond to a stimulus. Not instantaneous!Cell is 100x MORE permeable to K than to Na, so Na will always slightly hyper/depolarize cell.

Action Potentials & Propagation


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Action Potentials & PropagationElectrotonic Potentials:

No threshold (soft & hard touches detected); passiveconductance; size-graded; not self- generating; doesntpropagate; no refractory period; spatial/temporalsummationMechanoreceptors (skin), chemoreceptors (taste buds)

Action Potentials:Threshold potential; all-or-nothing conductance; stimuli allproduce same amplitude; self generating; can propagate;refractory period needs to end before channel can re-open; potentials arent summed. Nerve and muscle cells

Phases of Action Potential

During threshold and rising phase, membrane becomesmore permeable to Na. Voltage-gated Na channels open.Cell interior becomes more positive.Peak : 1 st Na channels to open start to close theirinactivation gates (right before peak). Activation gatesstay open until voltage falls. K channels begin opening, Kleaves cell.During repolarization phase and at rest, membrane ismost permeable to K. Na channels closed.

Afterhyperpolarization : K channels start to close. Restingmembrane potential restored.

Voltage-Gated Channel DetailsNa channel: 2 gates. Active state (both gates open),inactive state (inactivation gate closed, cant conduct) andresting (active gate closed, ready to be opened bystimulus)K channel: Only one gate that opens at threshold.

Absolute Refractory Period : From start to point of highest Kconductance. Na channels in inactive state cant be o ened.

Relative Refractory Period : After Peak. Na channels at rest andready to open again, but some K channels still open. Stimulusneeds to be much higher than threshold voltage to open them(accomodation). Toxins

Tetrodotoxin (TTX ): Blocks voltage-gated Na channels.Tetraethylammonium (TEA): Blocks voltage gated Kchannels

Propagating Action PotentialsTime Constant : = R membrane Cmembrane

Capacitance = membrane ability to store chage (rate ofcharging up). Low capacitance means faster propagation.Resistance: higer in small diameter nerves (ions hit eachother rather than flow through cytosol).Refers to time it takes nerve to reach 63% of threshold.R = 1 / g (conductance)

Length (Space) Constant : = (Rmemb d / R interior 4)Non-myleinated nerve diameter would need to be 4X aslarge to have same propagation speed as myleinated ones.Rmemb needs to be high to keep ions from leaking out.

Space constant is distance it takes for nerve A.P. to lose63% of its original voltage.Non-Myleinated Nerves

Na influx leaves net charge outside membrane, whichattracts neighboring Na ions, and they leave a net behindand so on.

Myleinated NervesSaltatory propagation: action potentials travel to Nodes

Schwann cells: insulation, increase memb resistance, lowecapacitance. Cell charges up faster, ions travel down axon

Blood Clotting


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Blood ClottingBackground

Involves: 1) Constriction of injured vessel 2) Clumping ofplatelets to plug hole 3) Clot formation on top of plug

PlateletsNo nuclei, disc-shaped, contain granules.

Activated by collagen: become spiky, release granules. Adhere to each other and collagen w/ von WillebrandFactor.Platelet Granules Thromboxane A 2: : stimulates ADP release ADP : promotes platelet aggregation Vasoactive amines ( norepinephrine , serotonin ):

constrict inured vessel.Fibrinogen

Has 2 , 2 , 2 subunits. Joined by disulfide linkages(knots).Thrombin cleaves off part of and chains, leaves mostof fibrinogen intact.Cleaved chains on top of fibrinogen are electostaticallyrepulsive, but once removed fibrin fibers (monomers)can aggregate.Fibrin covalently joined, but flowing blood could disrupt it.Needs to be stabilized by transglutamase (Factor 13 ).

Activated by thrombin.Thrombin

Inactive form in blood = prothrombin.Factor 10 a (w/ 5a and Ca++) cleaves 2 places btw

Arg/Thr and Arg/Ile . Forms 2 chain enzyme joined bydisulfide bond. B-chain is trypsin-like (cleaves Arg-Gly)Thrombin makes fibrin monomers, and activates factors5, 7, 8, 13.

Clotting Factors10a : activated 2 ways:Extrinsic = Tissue Factor (Factor 3) from woundforms complex w/ 7a and Ca. Complex activates 10.7 activated by wounded tissue or thrombin.

Contact w/ glass & kallikrein activates 7.Intrinsic: Factor 12 in blood activated by woundedtissue. 12a 11a -9a -8a 10a . Cascade!Redundancy: if no 12, Tissue Factor activates 11. 7acan also enter intrinsic by activating 9.

Modification of factorsBefore activation, they are proproteins . Before that,they are pre-proproteins (still have signal sequence).Carboxylation: allows Ca to bind. Factors 2, 7, 9, 10 .Glu aa becomes carboxylglutamyl (gla) at N-terminus.Vitamin K dependent carboxylase makes gla.Vitamin K1: comes from plants.Gut flora: make MK-n (menonquinone). Has moredouble bonds.

Factor 9 has Gla residue. 11a cleaves it twice, but 9is still docked to membrane.B/c of gla, thrombin (w/ Ca) can bind to phospholipidmembrane of platelets rapidly. Increase cascade by10,000x!Prothrombin has NO gla residues (needs to movearound in blood).W/out K, you cant clot quickly!

Blood Clotting (Part II)


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Blood Clotting (Part II)Clotting Regulation

Coumarins (anticoagulants): Vitamin K epoxide is reduced to its quinone form by

Vit-K reductase. This enzyme is inhibited by thecoumarin Warfarin .Thus, clotting factors arent

carboxylated! Overdose of coumarin can be fixed w/ dose of Vit-K.

Antithrombin III : forms irreversible complexes w/ thrombin& activated factors, inhibiting them.Heparin : helps antithrombin III bind to factors quickly.Used as a fast anticoagulant during surgery.Protein C : inactivates 8a and 5a. Activated bythrombomodulin -bound thrombin, which is found on lining

of healed blood vessels.Protein Z : binds w/ protease inhibitor to inactivate 10.

Antitrypsin : inhibits proteases, including many of theclotting factorsLipoprotein associated coagulation inhibitor : inhibitsTissue Factor-10a complex.

Clot DissolvingPlasmin : Protease made in kidneys. Breaks up fibrin.TPA: tissue plasminogen activator (cleaves plasminogeninto plasmin). In wounded tissue.PAI: plasminogen activator inhibitor.Urokinase : removes clots in kidney.Streptokinase : used mainly in European hospitals.Complexes w/ plasminogen to activate it.

Treatments

Asprin : inhibits formaation of thromboxane A2Plavix : inhibits ADP and platelet aggregation

Diseases / Disorders Abnormal Clotting (genetic) : Antithrombin 3 deficiencyProtein C deficiency: causes venous thrombosisProtein S deficiency: C cofactorFactor 5 lieden: 5 cant bind Protein C = excessclotting.Factor 20210a: makes prothrombin mRNA verystable, and more prothrombin made than can bebroken down.Excess fibrinogenClots can travel through blood, cause stroke,heart attack, pulmonary embolism. Oral contraceptives increase this risk by decreasing

antithrombin 3)

Dietary :Christmas Dinner: Factor 7a increased by highlipid meals, can cause clots.

Abnormal Bleeding (genetic) :VKCFD: not carboxylating enough of your clottingfactors.Von Willebrand Disease: poor platelet adhesionHemophilia: mostly factor 8 mutations. Some hemophiliacs received blood transfusions from

people w/ HIV in the early days.

Post-clottingBradykinin dilates healed blood vessel, increasesits permeability. Cleaved from kininogen bykallikrein. Must be remade constantly: 10% lost inlungs.

Blood


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BloodComposition

55% Plasma, 40-50% RBS, ~1% WBCPlasma

90% water. Albumin protein maintains osmotic pressure.Carries metabolic waste. Yellow from iron

RBCHave no nuclei! But do have mitochondria (make heme),cytoplasmic enzymes.Membranes have carb compobebts that determine bloodtype.

Amount regulated by hypoxia, erythropoietin (fromkidneys), filtration by spleen.Reticulocytes: Young RBC which still have RNA. Slightlymore purple. Presence indicates patient trying to producemore RBC.PROBLEMS:Microcytosis: too small thassalemia, Fe deficiencyMacrocytosis: too big Vitamin B12/Folic acid deficiency.Hyperchromia: too dark more Hb b/c cell is smallHypochromia: too pale Fe deficiency

Spur cells: spiny shape - renal problemsBasophilic stippling: Pb binding to heme indtead of iron,cell trying to make more Hb.Howell Jolly Body: nucleated RBC not removed by spleen

PlateletsCome from megakaryocytes in marrow.Form plugs by binding to basement membrane of woundedepithelial cells.

No nuclei, but have mitochondria & glycogenOverproliferation: means body is stressed.

LeukocytesGranulocytesNeutrophils: neutral colored granules. Poly-lobed nuclei. Younger forms have U- shaped band nuclei

Engulf and digest bacteria using activated O 2 35-62% of all WBC. Granulocytosis= large amount

present (during infection). Neutropenia = low amounts(during leukemia treatments)

Eosinophils: Red granules Bi-lobed. Large granules w/ histamine, peroxidases, crystals.

Crystals have bar-shaped major basic proteins.

Combat worms, but can be over stimulated duringallergic rxns. 1-4% of WBCBasophils: Blue granules. Grabules have heparin, histamine . Granule contents

released after IgE binding.


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HematopoeisisIn fetus

Yolk sac (makes angioblasts and vessles); liver(platelets, granulocytes); spleen (RBC); T-cells (thymus)

Bone MarrowMarrow in axial skeleton makes blood throughoutadulthood. Long bones stop after adolesence.Biggest cells: adipocytes & megakaryocytes.Blood made on hematopoietic cords. Stroma:connecctive tissue. Sinusoids: capillary system thatallows cells to enter main circulation.3 developing WBC to every 1 developing RBC b/c RBClive much longer, dont need to make as many of them. Marrow is also where Fe recycled from heme.

Early CellsColony-forming cells: young cells that can form a colonyof hematopoietic cells. Come from multipotent stem cellsStimulated by cytokines (growth factors). G-CSF =makes granulocytes . M-CSF = monocytes . Interleukin-5= eosinophils . GM-CSF / thrombopoietin = megakary. GM-CSF / IL5 = RBCCytokines used in clinical settings. However, early onestend to cause leaky capillaries.

RBC FormationProerthroblast: dark blue cytoplasm, large nucleusBasophil erythroblast: blue cyroplasm, smaller nucleusPolychroamtic erythriblast: checkerboard nucleusOrthochromic normoblast: small nucleus, pinkishcytoplasmReticulocyte: no nucleusRBC

Granulocyte FormationMyleoblast: large nucleus, medium blue cytoplasmPromyelocyte: 1 granules overlie nucleusMyelocyte: named for type of granules it has.Smaller nucleus, pink cytoplasmMetamylocyte: Mardi-gras mask nulceusBand form: U-shaped nucleusMature granulocyte.

Monocyte FormationMonoblastPromonocyte: may have folded nucleusMonocyte / macrophage

Other CellsLymphoblast lymphocyteMegakaryoblast megakaryocyte-platelets

DiseasesDeficient synthesis too little marrow, cytopenia (too few of a cell

type), aplastic / Fanconis anemia (too few cellsin general)

Disordered hematopoeisis Granulocytes may have too many nuclear lobes Macrophages may not break down ingested material

(Gauchers Disease)

Overproliferation Leukemia

Gene Regulation


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Gene RegulationDiff. btw Prokary & Eukary

Eukary DNA wound up tightly in chromatin, while bacterialDNA quickly accessedBacteria: 1 RNA Pol. Eukary: 3 RNA Pols.Eukary RNA undergoes modifications after transcriptionEukary RNA must pass through nucleus to be translated.In prokary transcxn & translxn are coupled.

Prokaryotic RegulationDepends on initiation, termination, and stability of mRNA(which is rapidly degraded)Operon: has control sequences that are associated w/structural gene sequences.

Catabolic operon : when a certain nutrient is present(inducer ), operon begins transcxn of genes to metabolizeit. Ex: Lac operon (breaks lactose to glu)

Anabolic operon : w/out an essential nutrient, operonremains on in order to synthesize it. Ex: Trp operon (trp isco-repressor, turns operon off if too much Trp made)

Features of OperonPromoter : where RNAPol binds. Upstream of init site.

Operator : where repressor protein bindsRegulator: codes for repressor protein. Always transcribed.Not always in same operon.cAMP receptor/catabolite activator protein ( CRP/CAP ):helps RNApol bind to DNA w/out falling off. By promoter.

Attenuator: terminates transcxn if an RNApol accidentallyslips by repressor.

Lac Operon Regulation

Codes for 3 genes, most important is Lac Y (permease :brings things into cell)

W/out lactose, transcription continues at verylow level (that way, some permease is alwayspresent to bring in lac if it appears).Repressor: coded by Lac I gene. Tetramer:together the subunits bind strongly to DNA.Inducer is a negative allosteric modifer, andwhen it binds to repressor it causes it to releaseDNARepressor recognizes palindrome sequence ofoperator (RNApol does not, since itsunidirectional)Catabolite repression : if glucose present(preferred food), Lac operon turned off (Caplevels drop b/c less cAMP made)

Eukaryotic RegulationCis-acting : gene sequences that regulate thesame gene. Need to work w/ trans-acting.Trans-acting : other elements that act on thegene (like repressor or RNApol). Bind to cisCTCF can enhance or inhibit transcxn (canblock RNApol, keep chromatin from unwinding,etc). Its zinc fingers can bind to DNA in diff waysdepend on what fxn is needed. It can bindinsulators.Silencer: binds repressor (eukary version ofoperator)

Gene Regulation II


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Gene Regulation IIEukaryotic Regulation, contd DNA-binding Proteins

Protein surface complementary to surface of double helix.Subunits each have weak hold, but together bind verystrongly. Subunits can be joined by: Homeobox: have helix-turn-helix domain that holds

DNA (ex: CAP) Zinc Finger Leucine Zipper

Antisense RNAInsulin-like growth factor receptor 2: Both alleles have 2promoters.

From mom , downstream one is methylated. Can make asense RNA that makes Igf2. Always transcribed. From dad ,upstream one is methylated. Antisense RNA is made, whichhelps to down-regulate this gene.If you inherit 2 copies from one parent it can be fatal. Thisis one reason why humans arent parthenogenic.

SiRNA/microRNAsiRNA becomes double-stranded so that dicer protein can

recognize / cut it. Becomes single strand again, binds toantisense mRNA (w/ RISC protein ). RISC degrades targetmRNA by slicing. Humans use it to attack HIV RNA.miRNA down-regulates mRNA by forming UTR-stem loops

Riboswitch RNARiboswitch RNA folds up gene-coding sequence into aninactive form.When a certain protein or chemical binds, RNA unfolds into

an active form and translation of gene sequence occursfaster.

Alternate PromotersDystrophin gene: longest human gene. Has 8promoters w/ their own exons. Each one makes atissue-specific product. More variety in mRNAsproduced by alternative splicing, adding poly-Atails, etc.

CancerOverall, cells very good at removing spontaneousmutations. Most cancers caused by 3-7independent changes in cell regulatory genes(unless youre already born w/ one)Oncogenes: need only one mutant allele (loss ofheterogeneity) to cause uncontrolled proliferationTumor-suppressor genes: need both alleles to bemutated to cause loss of normal fxn. Rarer. Loss of p53 fxn found in ~50% of all Stage IV

carcinomas.Mdm2 overproliferation binds too much p53, keepsit from initiating transcription of regulatory genes.(Ex: it may not be able to make apoptotic proteinsto destroy faulty cells)Li Fraumeni syndrome: inherited mutant p53.

Cell Junctions


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Cell JunctionsBasic Info

Tight Jxns (zonula occludens) Forms blood-brain barrier in brain capillary linings.

Zonula AdherensDesmisomes (Macula Adherens)Gap Jxns

ProteinsTight Jxn: transmembrane proteins (occludin & claudin); actin Na/K pumps in retina have reversed polarity: found in apical membrane instead of

basolateralZonula Adherens Calcium-dependent adherin jxn (cadherins); Actin E-cadherin: found in epithelail N-cadherin: found in neurons.Desmosome Desmosomal cadherins, keratin Hemidesmosomes have integrin. KeratinGap Jxn Connexin proteins (~20 types): 6 per connexon Close to prevent toxic amounts of Ca or H+ from spreading to neighboring cells.

DiseasePemi hi us: autoimmune desmosomal disease of skin roteins

Myoglobin & Hemoglobin


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Myoglobin & HemoglobinHemoglobin

4 chains, each w/ O 2 binding siteChains cooperatively bind O 2 : 1 st doesnt bind easily, but makes it easier for successive O 2 to bind

Readily releases in low oxygen environments (tissues). Binding sites only fully saturated in lungs. and chains prevalent post-birth. chain in fetus, releases O 2 from placenta.OxyHb looks red. DeoxyHb looks more blue. Hb bound to CO looks bright red.R-form: relaxed (high affinity for O 2). T-form: tight (deoxy Hb).

Myoglobin1 chain w/ single O 2 binding site

Accepts O2

from Hb in muscleHeme

Porphyrin: attached to F chain (by proximal histidine) and E chain (distal histidine)Fe needs to be +2 state, or else it will bind but not release O 2

CO & CO 2 80% flows in blood as bicarbonate. 20% bound to Hb ( carbamate ), but not at O 2 binding sites.CO does bind to O 2 binding sites. Hb reverts to R state, and holds on to remaining O 2 rather thanrelease them.

Bohr EffectHb readily releases O 2 in low pH environments (tissue w/ more lactic acid)

2,3 BPG- charges on BPG stabilize the + charged cavity on T-form Hb (deoxy). Causes Hb to release O 2 morereadily.

Sensory Receptors & Transduction


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Sensory Receptors & TransductionBackground

Sensory cells convert physical stimuli (mechanical,chemical, light, heat) to electrical signals.***Nerve cells are influenced by neurotransmittersacross a synapse!

Adequate stimulus : lowest stimulus picked up by areceptor.Receptor (generator) potential : caused by stimulus,sets off action potential if it reaches threshold. Nadoesnt influx through voltage gated channel. Made up of 1st order (receptor) neuron , which synapsesw/ at least 2 other neuronsMore action potentials can be generated based on the

intensity and duration of stimulus.Classes of Sensory Receptors

Exteroceptors : stimuli come from our sensesInteroceptors: concerned w/ internal environment ofbodies.Proprioceptors: relay info about our bodies in space.

MechanoreceptorsMeissners Corpuscles: fingertips Hair Follicle Receptors: detect movement on skin.Merkels Disks: non -hairy skinTactile Disks: similar to aboveRuffinis Corpuscles : detect stretching in joints Pacinian Corpuscles : Sub Q layers of non-hairy skin,muscles:

- Contain nerve ending wrapped around gel & conn tissue

- Initial pressure causes nerve fiber to deform. Gel allowsreturn to shape. When pressure removed, nerve deformsa ain intensit chan e

Other Somatic Sensory ReceptorsThermoreceptors: 36-45 C = warmNociceptors: respond to anything that will cause tissuedamagePhotoreceptors: Na gate open in the dark, closes in

light (activated by hyperpolarization)Chemoreceptors

Sensory AttributesModality: specific tissue receptors and neuronpathways for each stimulus: light only detected by eyepathway (labled line).Intensity : Frequency code: More a.p. for more intense

stimuli Population code: More a.p. for more receptors in

the regionDuration : nerves can adapt rapidly ( phasic ) or slowly(tonic ) to a continuous stimulusLocation: 2 point threshold: ability to discern this depends

on amount of nerves in region getting poked by 2needles.

Lateral inhibitory region: surrounds excitatoryregion so that we can localize where a stimulus is.

Somatosensory PathwaysDorsal column: 1st order neuron on left side of body;2nd order neuron crosses over to right side of the bodyin brain stem. Pressure, proprioception .

Anteriolateral: 2nd order neuron crosses over to right

side in spinal cord. Temperature, pain .

Gene Technology


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Gene TechnologyCloning

Making exact copy of DNA sequence of interestMaking Vectors

Vectors: allow you to insert & copy any DNA sequence ofinterest. Plasmid: bacterial. Usually have antibiotic resistance

genes. Cosmid: viral (bacteriophage) Yeast Artificial Chromosome: Can hold thousands of

base pairs.Restriction endonucleases : cleave palindromicsequences, make sticky ends. Allow unrelated DNA to beput together w/ ligase.

TechniquesPlasmid: Insert gene of interest into antibiotic resistancegene. Bacteria now sensitive to that drug (screens).Expression plasmid: gene of interest is expressed, fusedto bacterias normal protein products from its ownoperons.CaCl2 : makes it easier for bacteria to import recombinantplasmids. Neutralizes DNA charge so it can entermembrane.

cDNAcDNA: made from mRNA using reverse transcriptase.cDNA now only contains exon sequences for yourplasmid (bacteria cant remove introns) cDNA collection = cDNA library . When placed into vectors= expression library .Genomic library = entire genome (exons & introns).

Probes & HybridizationProbe: finds a specific DNA sequence in cDNA library(antibodies find expressed proteins in expressionlibrary)Hybridization: when probe binds to its complimentaryDNA strand. Can bind strongly to one sequence(stringent), and less strongly to others.Southern Blot : seeing which sequence probe binds too.Run DNA through gel (smallest pieces move farther).Blot it from gel onto filter paper so its more durable.Probe will hybridize to target sequence on filter paper.Western Blot : Proteins. Northern Blot : mRNAYou can use probes to see if a patient has a mutantallele for a given DNA sequence. Mutations will giveyou a different length RFLP from normal.Removal of tandem repeats in a mutant allele isanother way to see what disease a patient has.

Sequencing (Building Probe)Use deoxynucleotides to build a chain. Usedideoxynucleotides to stop elongation

PCRRapidly amplifies DNA sequence.

Use taq polymerase (from thermophilic bacteria): canwithstand heat.Practical Uses

Transgenic animals: mixture of self genes and genesfrom other stem cells inserted into them.

PharmingMaking an ovum express the DNA of sequence. Theadult will produce in large quantities a protein productthat it normally wouldnt make (like a drug in its milk)

Synaptic Transmission


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Synaptic TransmissionElectrical Synapses

Ions move through hemichannels (connexons in gap jxns)Bidirectional flow of ionsConnexons only 5nm apart

In smooth & cardiac muscleChemical Synapses

Most common type of synapseSynaptic cleft = 30-50 nmUnidirectional flow of transmitter

A.p. in pre-synaptic cell opens Ca gates, which enterspresyn nerve, promotes release of neurotrans vesicles.Release neurotrans, which bind to ligand-gated non-specific channels (both Na & K move through). Thisbinding acts as generator potential, which sets off actionpotential (opens fast Na channels, and later K channels).Channel closes when neurotrans unbinds.Excitatory (open Na channels) & inhibitory (open K or Cl)post-synaptic potentials affect the action potential. SLOWER than electrical synapses.

Neurotransmitter DetailsQuanta: the release of products from a vesicle. Vesicleshold same number of neurotrans molecules (quantum).Need to release a lot b/c some neurotrans diffuse away orget degraded (Ach degraded by Acetylcholinesterase)

Synaptic Contacts Axosomatic : axon synapses to soma. Strong signal,greater influence on trigger zone

Axodendritic : synapses to shaft/spine. Signal decays if itstoo far from soma, so you need a lot on dendrites

Axo-axonic : synapses to axon. Inhibitory or excitatory forneurotrans release (affects Ca influx). Doesnt affectsignal.

Input/Output RelationshipsOne-on-One : single a.p. in presynaptic cell to 1 a.p. in possynaptic cell. Neuromuscular jxnOne-to-Many (Divergence): 1 a.p. to many a.p. in manypost synaptic cells. Renshaw cells in spinal cordMany-to-One (Convergence): many a.p. to 1 a.p. Mostcommon one. Motor neurons

Summation & Other OccurencesSpatial : when 2 separate presynaptic signals reach post-syn nerve at same timeTemporal : when same pre-syn nerve sends 2 consecutivesignals to post-syn nervePre-syn Inhibition : Block Ca channels, lessens Ca influxinto presynaptic axon, fewer transmitters released to bindpost-syn. No a.p. made. Done at axo-axonic synapse.Post-syn Facilitation : More Ca flows in. TEA can also dothis.

Potentiation (rapid firing of pre-syn) : Some residual Ca remainin pre-syn before it can diffuse out. Several effects:

Facilitation : More neurotrans released, then falls off quickl(short-term memory)Posttotonic : Neurotrans falls off slowly (long-term memoryDepression : depletes all neurotrans vesicles (why seizureend)

DrugsNifedipine, nisoldipine (dihydropyridines): Ca antagonists.Block Ca channels. Decrease blood pressure!

Neurotransmitters


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NeurotransmittersNeurotransmitter Criteria

Has to be made in neuronReleased by pre-syn neuron to affect post-synneuronExogenous application of substance mimicsendogenous release

A mechanism exists for removing it from cleft.Types

Small molecule (fast acting). Sensory signals to brain, motor signals to

musclesLarge molecule (slow acting): cause more prolonged

response Long term opening or closing of channels

Classical Neurotransmitters (small mlx) Acetylcholine

Released by cholinergic nerves. Made inmitochondria from acetyl CoA & choline.

Used in neuromuscular jxns. Inhibitory forcardiac muscle.

2 molecules bind to -chains of receptorCatecholamines (Biogenic amines) Epinepherine, Norepinepherine, Dopamine Deficiencies = bipolar disorder, depression Made from tyrosine. Dopa hydroxylase turns

DA into norepi. Broken down by monoamine oxidase. Pargyline (antidepressant) blocks MAO (norepi

breakdown), more stays in cleft. Imipramine(better antidepressant) blocks norepi reuptake.

Reserpine blocks storage in vesicles so it cant bereleased (tranquilizer)

Dengeration of dopaminergic neurons associated w/Parkinsons. Treated w/ L-Dopa .

Seritonin (5-HT)

Eating, sleeping, arousal. Inhibitory effects. Prozac blocks 5-HT reuptake only.Glutamate Memory, learning ExcitatoryGABA (a and b receptors) Inhibitory. Stabilizes neuron electrical activity.

A: increases Cl influx. Benzodiazepine : facilitateGABAs fxn by further calming down neron activity. B: increases K conductance.Glycine : inhibitory

Neuropeptides (large mlx)Usually affect metabolism, gene acitvation in nucleus.Include opiates (regulate pain)

Neuromuscular Junctions


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Neuromuscular JunctionsStructure

1-to-1 synapsePost-syn muscle has muscle has folds to increase surface area for ACh binding.

ACh located near top of fold. ACherase ready to break it down.Signal Transmission

EPP (end plate potential): very large generator potential. Always large enough to trigger a.p. inmuscle fiber to contract it.MEPP (miniature EPP): Small depolarizations occur after EPP (.4 mV). Happens when a lone vesiclein synaptic happens to release its neurotransmitters.

DrugsCurare (tubocurarune): nicotinic receptor antagonist. Competes w/ ACh. Inhibits EPP, keeps it fromgenerating a.p.

Atropine (muscarininc antagonist): has no effect, b/c no muscarinic receptors at neuromuscular jxnMyasthenia Gravis

Autoimmune: Antibodies attack folds and ACh receptors. Synaptic cleft also grows wider, so more of ACh diffuses away. Need anti-ACherases (to preserve ACh). Immunotherapy needed (removethymus in adults).

DenervationNerve is severed. TTX-insensitve-Na channels and more ACh receptors appear to make musclehyper-sensitive.Unless muscle is re-innervated, it atrophies and is replaced by CT, fat.

Heme Synthesis & Breakdown


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Heme Synthesis & BreakdownBACKGROUND

Heme: type of porphyrin (4 pyrole rings)15% heme synthesis occurs in liver. Rest is made by RBCprecursors (mature RBC have no mitochon)

HEME SYNTHESISGlycine + Succinyl CoA -- ( Aminolevulinic acid synthase )

ALA ( ALA dehydratase ) porphobilinogen [ 4 needed ] (PBdeaminase )- Bilane - ( uroporphyinogen I synthase / UP IIIcosynthase ) UP III (UP decarboxy ) coproporphyrinogenIII (CP oxidase ) protoporphyrinogen IX (PP oxidase ) protoporphyrin IX (ferricholase ) heme ALA synthase: In mitochondria. Cofactors: Mg and

pyridoxal 5-phos. Rate-limiting step ! Inhibited by excessheme, glucose. Stimulated by barbiturates (removeshemes by making other porphyrins). Half life ~ 1 hr.

ALA dehydratase : has its own 2 rings. Acts as a primerin putting 4 ALA together in porphyrin ring.

CP oxidase: back in mitochondria.-inogen rings have acetate & propionate substituents. All Aand most P later decarboxylated to methyl & vinyl.UP III rings : AP-AP-AP-PA. UP I : last ring is AP. Non-functioning. UP I made when UP III cosynth defecient.

HEME BREAKDOWNHappens mainly in spleen, also liver & bone marrowHb globin, which break down to a.a. Heme now exposed, oxidized to heminNADPH reduces hemin 2x to make hydroxyheme-oxogenasecomplex.Complex loses Fe & CO (ring opens) BiliverdinBiliverdin Reductase Bilirubin Travels from spleen through blood bound to albumin .Unconjugated bilrubin (indirect)

In liver: becomes conjugated bilirubin (water-soluble). Getsbound to 2 glucoronate. Leaves as bile.

Direct bilirubin = water soluble. Van den Bergh rxn tests for it.Z-protein & liagndin bind bilirubin in liver cytosol.Hemopexin : in liver. Picks up hemin from albumin

Removal From BodyGlucoronate removed in bowel. Bilirubin duced by

microorganisms to urobilin. Excreted by kidneys (makes urineyellow).Further reduced to stercobilin (makes feces brown).

Glutathione and MethemoglobinUsed to remove reactive oxygen compounds in RBCMethemeglobin (Hb Fe 3+) reduced by NADH to Hb Fe 2+.Methemeglobin has no carrying capacity for oxygen, need toremove it!

Fe InfoFerritin : binds Fe for storage in liver. Regulated by Iron ResponElements on gene.Transferrin : carries Fe 3+ into liver cell. Also has IREHemosiderin : another way to bind Fe. Amorphous.Ferroportin : sends Fe from cells into plasma.Hepcidin : MAJOR regulator of Fe absorption. Made in liver, butalso used by macrophages & enterocytes (intestines). Binds &destroys ferroportin, stops them from sending excess Fe to

plasma. Enterocvytes sloughed off after ~week, their Fe gets picke

up by ferroportin. Macrophages keep Fe, use it to kill pathogens during

infections. Hepcidin synthesis inhibitied by EtOH.Hemin is most easily-absorbed source of Fe. Vitamin C alsomakes Fe more easily absorbed (same as methemoglobin, butw/out globin chain)

Hb in RBC has most of our bodies Fe. Ferritin is next largest.


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,Contd DISORDERS

Jaundice : Body contains excess bilirubin. Symptom, not a disease.Deposited in skin, eyes.Pre- hepatic: heme breakdown (from hemolysis), indirect bilirubin in blood.

Intra-hepatic: many liver cells not working (from hepatitis), slightly more indirect bilirubin.Post- hepatic: bilirubin excretion (bile duct obstruction), direct bilirubin. Lab tests can detect elevated levels of LDH enzyme (from lysed RBC)Infant-mother Rh incompatibility : infants RBC lyse. Cause jaundice. Babies put under blue light to turn skinbilirubin into more-soluble photobilirubin.Crieger-Najar : too much unconjugated bilirubin accumulates in liver, damaging it. Can also move to brain (causeskernicturus ).

Anemia : Fe deficiencyCan cause koilonychia (spoon nails), pallor, beefy tongue.Sickle Cell Anemia : point mutation in -globin side chain. SS = disease, SA = carrier. SC: 2 nd most common, another side-chain mutation. S = Thallasemia

Hemachromatosis : too much FeHeriditary form: caused by mutations in HFE (hepcidin not made in high amounts, Fe from intestines picked up inlarge amounts by liver).Need to remove blood (phlebotomy)

Hb is saturated, Fe carrying capacity shrinks. Bronze Diabetes : Causes pigmentation in skin, Fe deposited in pancreatic & muscle cells, damaging them.Secondary Hemachromatosis: ingesting too much Fe when Fe storage is already high. Can be caused by blood transfusions for thallasemia (get good globin, but too much Fe. Need Fe chelating).Porphyrias : accumulation of intermediates that can only be used for heme synthesis. Porphyrins in skin causephotosensitvity. Use hemin or glucose to stop heme synthesis (basically, induce anemia). Accute Intermittent Porphyria : Porphobilinogen accumulates, causes red urine in light. Porphyria cutanea tarda : UP III accumulates. Causes chest hair in womenPb inhibits many points of heme synthesis. Pb binds ALA dehydratase, but can be treated w/ Zn (its cofactor).Binds Ferrochelatase, needs to be removed by Pb chelating agent.

Nerve Tissue Summary


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Nerve Tissue SummaryFunctional Divisions

CNS: Brain, spinal cordPNS: All other nervesSomatic: Conscious control

Autonomic: No conscious controlClassification

Motor, Sensory, Interneuron (lie btw sensory & motor)Structure

BipolarMultipolarPseudopolar (soma lies off of axon, but signal stillpasses through it). Structure of sensory nerves.

Nerve AnatomySoma: has pigmented inclusions Lipofuscin- build up w/ age Neuromelanin- found in substantia nigra neurons.

Loss associated w/ Parkinsons. Cytokeleton Microtubule association proteins: MAP2 in

dendrites, MAP3 in axons.

Mylein Schwann cells (in PNS) : myleinate only one

section of one axon (w/out mylein, it can surroundseveral nerve fibers)

Gives white matter its color (soma = gray) Axon Hillock: has Nissl Bodies (RER & ribosomes), butdont extend into axon.

Vesicles Anterograde: Moves from soma to synapse. Kinesin.

Motor neuronsNeuromuscular jxn: axon to fiberMotor unit: single motor neuron synapsing toseveral muscle fibers. The smaller the motor unit

(the fewer muscle fibers a nerve connects to), themore accurate and controlled the movement wecan make.

Neuroglial CellsOligochrondocytes: myleination in CNS (noSchwann cells)

Astrocytes: supports nerves & blood vessels.Fibrous = white matter. Protoplasmic = gray matter

Microglial: small nuclei. Rare. Dormant until aninjury occurs; then act as macrophages to removedamaged cellsEpendymal cells: ciliated. Line fluid filled ventricles.Forms a barrier.

Peripheral Nerve OrganizationEndoneurium: CT bundles myleinated & non-myleinated nerves

Perineurium: Bunle of many endos.Epineuria: Bundle of many peris. Autonomic Nerves

Innervate glands, smooth muscleDorsal root ganglion: input from sensory nerves.Satellite cells: support root ganglion nerves.Sympathetic nerves found in paravertebral gangliarunning along spinal cord

Enteric nerves: Line smooth muscles of gut.Control peristalsis


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End of Exam 2

Skeletal Muscle & Contraction


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Skeletal Muscle & ContractionLOCATION

Evenly distributed through body Attaches to bones except for facial muscles and intrinsictongue muscles (connects to CT)

STRUCTURE

Arise from myotomes (somites). Grow by hypertrophy(size increase), not hyperplasia (proliferation)Cells: multinucleated, unbranched, striated. Haveabundant mitochondria. Sarcolemma = cell membraneOrganiztion: myofilaments (actin / myosin) insarcomeres. Muscle fibers organized into fascicles. Eachcell surrounded by endomysium (CT w/ fibroblasts) andsmooth sarcoplasmic reticulum .Proteins

Actin: made up of G-actin monomers.Tropomyosin : sits on actin.Troponin : small protein on tropomyocin. 3 units: TnT=attachment. TnI = blocks myosin-binding site on actin.TnC = where Ca binds, causing tropomyocin to move somyosin can bind actin.Myosin : 2 heavy chains in middle, flanked on each end by

2 light chains w/ heads. Has myosin & ATP binding sites.Tropomodulin : caps actin, prevents depolymerazation.Titin: maintains structure of sarcomere. Connected tomyosin by

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