Biochem Prelims - Baby E Coenzymes UDP-Glucose/UDP-Galactose COP -acylalycerol ADP cAMP / eGMP TP GDP Heterocycles Clockwise Ccouterclockwise then Clockwis Planar Character ‘Ammino-mine and Keto-Ena! ‘Amino and Oxo Nucleoside Derbose 2-deoxy-D-ibose BeNsglycosidic bond Ne Na Mononueleotid Hydroxyl group 7 ‘Acid Anydri Ant Otigenucteotide recognition and RNA Halfife regulation Hypoxanthine, Xanthine and Urie Acid ‘Trimethybeanthine ‘Theobromine ‘Theophylline 1.0 and 62 Negative 260 nm bonds S.adenosylmethionine cre cGMP UDP-Glucoronie acid om ‘Y¥-phosphory| group Enzyme inhibition and Incorporation into Nucelleacid+Base Pair Disruption {Allopurino! Xanthine oxidase cytarabine ‘Azathioprine Phosphodlester bonds 30H of pentose Water Phosphodiostorases carbon-carbon bond Ribose ro8 Left ‘men purnelpyimidines are linked to Vitamin and Vitamin Derivatives they form Participate in augar interconversion ike in formation of starch and glycogen Intermediate in Ip Biosynthesis contol ate of exidatve phosphoryation secondary messengers inracalully play key role in signal transduction pathways Cyete structures that contain nt onty carbon but alse nzogen or eter elements nthe ring Diocton of pyrimidine numeoring Drecton of purine numering ‘Allows slacking of rueleoides ths forming the backbone of DNA ‘wo types of tautomerism exhibited by purines and pyrimidines most favored typeof tautomerism PunnelPyimicine + Sugar ‘sugar in ribonucleosieos sugar in deoxytbonuceoside bond formed between sugar and putinelpyrimidne in nuctoside inwhat Ntrogen i the lycoseic bond usual found in purines in what Ntrogon is the glycosidic bond usualy found in pyrimidines these are nucleotides with a single phosphey group nen menonuceotdes are formed, the phosphor group attaches to what group inthe sugar substrate inwhat carbon rumber af the sugar are most phosphor groups attached to in menanucleotdes the typeof bond between the phosphory groups in dit nucoosidos ‘most common conformer that predominates in N-Glycosides ive two functions of modtied polmucteties hate are intermediates i the catabolam of adavine and guanine and a motatedhetorocyete found in cofooeataine metlate heterocycle found in cocoa metlated heterocyete found in tea \What ar the respective pH values ofthe primary ané secondary phosphory| groups of ruclecties in physologie pH whats the cnarge of nelooises ‘tpi 7.0, what wavelength does the conjugated double bond absorb UV Hight 's the principal biologie transduce of fee energy and is the most abundant fee nucleotide in mammaban cols free heterocyclic bases nucleode that serves as methyl group dono: in various reactions ‘serves as allosterte regulator and soure of energy in poten synthesis serves a8 second messanger in response to NO (nite oxide) in smooth muscle relaxation forms the urinary slucoronide conjugate of bilrubin and aspitin rucleolde tat patipate inthe biosynthesis of phosphoplycerdes,sphingonwyeln and sphingosines ‘ofthe tw terminal phosphoryl groups in nucslatid tiphagphates, which is commonly assecated wh high-energy group transfer potertil ‘wo mechanisms by which synthetic analogs of purnesipyriidesinuclsosida!nucectide workin clnical medicine isa purine analog thats given for hyperuricemia and gout Enzyme tats nhibites by alpine! synthetic analog used in chemotherapy ‘synthoic analog used in organ transplants to supross immune function bonds formed when nuclecties ae inked the common ste ofthe second nucleotide where the 5:phosphoryl group ofthe fst nucleotide attaches the ie released or limnated inthe formation of dinuceloaelphosphodiester bonds the absonce ofthis enzyme prevents hyerolsis of phosphodiester bonds despite being thermodynamvealy favored bond formad between the C-5 of uracl and D-ribese in pseucourdine wat sugar doos TMP contain what cretion does the phosphodiester follow when t inks monomers of polynucleotides the 5" basis wil on what sie in representations of polmucelolde sequences Chapter 32Biochem Prelims - Baby E ‘Synthesis de nove Une Aol Parasite proozoe Aspartate, Glycine and Amide nitrogen of lutmine Respiratory C02 and Tetrahydrofolt Foe Acld IMP or Inasine Monophosphate Riboss-5-Phosphate Ribose-5-Phosphate » ATP-+ PRPP Synthetase Stops [3.461 178), [10,111 Tetranyérfoiate ‘Azaserne, Dazanortoucine, 6-mereaptopurine, Mycophenolic Acid * Pu (Free purine), PRLPP(Phosphorbosy|Pyrophosphate) “Pu (Purine Rbonuceosise) ‘Availabilty of ribose-5PO6 and PR-PP synthetase AMPIADP and GMPIGDP P82 (cytosli)-Carbameoyl Phosphate Synthase II-Cyoselle. ‘rotate Phosphoriboxy Tansferase Uracil and Cystine (UriainlCytcine) Methotrexate Dinyaydrotetate reductase ‘Allopurine| and Stuorourac Gout Gouty Artis Leschyhan Syndrome Von Girt Disease Hypoureem Purine Nucleoside Phosphorylase Deficiency 602, NH, Alanine and AminolsoButyrat Reye's Syndrome ‘Type 1 -Orotie Acldura ‘Alopurinel and @azauraine 02, Ghtamine, ATP yong cia “Pyrimidine dsordars ro rare sinc is ond post ar water slue MP or CMP IMP biosythesproduts) Creator of purnapwinisine Hom seat Process in bosytreis of prhepyrimie using eng prnelpyindhe of he carespondngnuseoside nd product of puns catabolism in mammals Cnty orm that doesnot ythesiae purine and pyridine What ae te 3 sourees of Nirogen nthe production of purines vis de novo eyriesis Putnedafieney als rales deen inthis vitamin (component of starycrfolaa) End product of de novo purine antral Ira sunsrae f de ravo pune syne ated upon by PR-PP syetase + ATP Ir maneals,mulfurctonal ezyras catalyse what spec steps in purine bioeyrthos= ant-cancer drugs wok n blocking purine synths ying the is sstance Cv 4 ergs that lock pune nuosatie synasie Theft purine salage resco involves what subsites Ste Oman ofthe boy for purine bosyiness wat orgenstissuestats require purne/puine ucaloides What cetorinnos rae of PR-PP concentration Wat aot reguetors of purine syrihoss Enzyme complox hat fctate the rascton. Catal NaP > Deoxyrbonvcalotde above complex only activin scvly diving elo esha equi DNA, Ine Bosyntnes of pyrimidines, what the ita att? Enzyme requires n converting Ort Acd o OMP (Crate Monophosphit) Tris anticancer drugs bot he reduction of dnyoflats in pyri Bosyiveis Essential onzymo nthe eduction of aystfoats Drugs tat compate arin wh oot acid / ore phosgharboaytanstrane ‘sorer of purine metaslsn, slovate Vax, gon cisorde of PRLPP syinetase, ads to ovrprosucton of pure Elevated sodium urate cya i sot issu0s, ints, igh rc aid nefornse Glucose Phophstaso Osficency (G8PD),inesass pure production, hyperurcemia olvatd body uals etsency lo xannne exes, creased secteono hypoxantine and xahne only sever col decency, duo cep his ONA precursors End products of prise catabolism all ao waar sll) ‘Asscited wih Orote Aci acura, eds 0 oveproducton af erote act (2 pes) Detelentn BOTH rotate phosphorbosytarstarase and orate decaboxsase Drags hat acto oral acura aw mates in pyrimidine bosyshoss prince sor cu lo efient dhysopyinidine dehysrogenase, may alo be an amino ac biosynthesis DIO, alo cal thyinuriaaracaia Chapter 33Biochem Prelims - Baby E Ma a a ac os wow Major Concepts DNA (Deoxyribonucieic ac) Ge Avery, MacLeod, MeCarty Deoxyadenylate ‘Thymidylate Deoxyeytidyate Deoxyguanylato 315 - phospodt ‘hydroxy! terminus and 3-phosphate terminus Chargaft Watson, Crick, Wikins Hydrogen bonds (horlzont van der Waals and hydrophobic interactions (vrtical) 2 single hydrogen bonds 3 single hydrogen bonds Watson-Crick Base pales Clockwise direction 1. Rotation about the the phosphodiester bond 2 antheonfiguration of glycosidic bond 3 predominant tautomers of ATCG bases 5-3, others 35 (antiparallel) “Template Strand Noncoding strand Coding Strand Double helix 6 forms (A.B.C.D.E2) Bform 10 base pairs 3.4mm or 34 Angstroms (A) 2 nm oF 20 Angstroms (A) Nitrogen and Oxygen Base-Stacking forces 6-6 base pair Increased Temperature & Decreased Salt concentratio, Hyperchromicty Mottin Temperature or Tm Formamide Hybridization Renaturation DNA or cognate complementary RNA Souther blotting Northern blotting Major ana minor grooves: Relaxed and Supercoit Nogative Supercoils, Supercoiled ONA Topolsomerases Semiconservative nature of DNA Template ONA strand mRNA (messenger) FRNA (ribosomal) ter bonds forme Chapter 34 Minor ino seiyere molec, and base of hredy, recs shes of RNA, bac nformatonpallway es are convoled by gone products wong wth various gone ranaducton pathways expat of DNA. darrian of gene nfermaion “ranserming factor-a tm for DNA ft to demonstrat that NA contained genet nfo 1944 using capsule of reuracocs boca mole cloned DNA’ use as donor ena information 4 Deorynclottespresentin DNA ema code -itratonal content of ONA Franklin -ganeraia ray eiacton da of ONS NA ome dite eo it- an eran erctons (XE, 2) paral charges in base ir frm vr der Weal and lactic neacons olds monomeric uit of NA no pohmei orm Meting - term used fr NA denaturation or stand sparton Port DNA (eves ok oo yon and Sphoshae teins) hing donation, bose pais pull apa AND unstack BUT st connected to backbone ele hat concerratons of A=T, G=C Fado that fence Tn -buse pa conposion ard al concataio/ckfea proposed dubi-svaned DNA mance tends betwen rucietde bates Fonaide eects betwen ache pars 1. sapmios ONa or ONA-RNA hybrid bond a ver om send between Aan 1 2. Mnze phospodase bond beskage tend between Card S 4 Minivizas cericaldarnage to moscide Ac and 6-6 base paving common fom o! ON rentatonsecbon ster DNA os, rae valent resend, polr BUT na and yen ane peporl arse basepair restctons Strand separation -prerqusetanciion fr DNA tensiponeplcation note: supercols mostly occur in eculrclsed fom buy may accurn near DNA, Direction exited by DNA cue to polarity “Two purposes of stored info in DNA strand of DNA, thats copied oF Vansribed during RNA synthesis 1. Souree of inf for protein synthesis (ia RNA) same as femplaa sand 2 Provides information thrid by daughter calsospring (via. DNA repcaton) strand that mates the RNA transcrip form exhib by ONA, RNA vs DNA (5) Number of forms that DNA can exhib 1. Ribose as suger [ONA form thats usualy founa under physiotoge conditions 2. Urn instead of Thymine humor of base pis per single tum of B form DNA. 3, RNAi single stranded (most ofthe time ‘stance spannes by one tum of DNA, 4 In RNA A not lays equal fo U, of G not equal to (content) slements where hydrogen bonding occurs van der Wasls and electrostatic interactions (base prs) “4 main lasses of RNA (page 344) which Watson-Crek base pair has higher melting pent and is more sable/sronger. more resistant to denaturatlen/separal 1. mRNA 2 facors that causa DNA denaturation 2.1RNA Increase n opal absorbance of DNA when itis denatured 3. RNA, midpoint of temperature range where DNA strand soparato 4, small RNA ‘oxgan slvent that destolizesnydrogen bonds between hase pars thus lowering Tm reassociaton of soparated DNA strands that's dependent on complemantary strand concentration ‘mRNA cap -trarsationrecogniton, str of tanstaton two examples of strands that DNA can palr with DNAVDNA hybridizations! electrophoresis radioactvaluorescent complementary prob same as above but with ONARNA labeling, allows high-sensivtyidenteaton of specic nucleic acas 2 grooves found in DNA ofA 4arms of INA DATE Closed crete ONA form may extn two forme what ar they mRNA-259% ‘Acceptor am ‘ecurs when stand wisng' opposite from the clockwise tums of right handed double helix (B-ONA) IRNA- 20% o ferred DNA form in biological system (igh amounts of stared energy) FRNA TO% Tye ‘enzymes that catalyze topological changes in DNA (laxatiovinserton, uses ATP as orergy) small RNA <5% coxa ams when DNA is replicated or passed to daughter cal, its identical but RNA molecule ean bind with what DNA strand {jlelasmic RNA meloculs that sorve as lemplates for proton syntosis Intron Removal snRNA, RNA that have structural o ‘and contribute ta formation and siture of nbosomes usBiochem Prelims - Baby E cca {RNA (transfer) Ribozymes Peptiy| ansterases RNA splicing snRNA (Small nuc Reverse Tansctstase MRNA (messenger) ‘T-methylguanosine triphosphate S-exonbonucleases 5-9 terminus t terminus poly (A) tail promRNA {RNA (ranstr) ccpopavon) ucleatidy wansteras Potysome 20s 60s 0s small RNA snRNA (Small nuclear) Uren RNA ncRNA siRNA ‘MIRNA and siRNA fe RNA RNA Deoxytbonuceases Ribonuceases Endonuclesses CCRISPR-Cas Exonucleases genetic code adapter molecules fortanslaon of RNA ino into Amino acs we RNA that exhibit catalytic actly Ike nutoic acié cleavage us bezyme that catalyzes peptide bond formation us Aanoter ribozyme i invoved inthis process us nal invalved in rosin synthesis but important in RNA processing, sp mRNA processing ized by HIV ftherrevovruses to produce a DNA copy of ther RNA genome, also called RNA-dependent ONA polymerase most heterogenous RNAin size, abundance ané stably, uncon as massengers or prolen-sytheize machinery forms the cap of eukartarie mRNA at 5 terminus ‘enzyme that prevented by mRNA cap polaty exit by mRNA polanty ecribited by pretin found at hydroxyl terminus, provents 3-oxoribonucleatealiack, manlains it MRNA precursor molecules around 74-95 NT in ong, at east 20 spaces oxst fr each aminoacid, secondary structure Is “clover” shaped termination of acceptor arm of RNA, enzyme that adds acceptor arm base sequence post ransciptionally assembly omed by bosomes #m RNA sedimentation vloctycosfitcent of RNA “lager subunit of RNA, contrbutes fo peptdyl transferase activity, is a nbozyme eral subunit of INA, 20.1000 NT. highly conserved subset of small RNA involved in Ra and mRNA processing involved in prdouction of correct 3 en of histone mRNA (lacks poly(A at regulatory nonprtsin casing RNA rmicro-RNI, inhibit gene expression silencing RNA, also inibts gene expression two types of small néRNA that nhs gene expression and are potential agants for therapeutic drug development rarger noncoding RNA, ivolved in RNA-spleng ype reactions, abundant in nervous system, gene raguation via RNA polymrace found in bacteria, may repressor acvais proton syrhesis when bound to mRNA. grades nuctele acids spect for ONA, same as above but for RNA, ‘tacks interal phosphodiester sonds, proaucsing hydroxy and phosphnoy terminals aso termed estrictlon enzymes, claves DNA by bindhng at BP 4,56, or 8 family of enzymes which are ribrucleoprolsin complaxas thal uses a guide RNA for ONAIRNA sequence cleavage hydrolyzes nudeotde at terminal partion. Only acts in one dection 3-5 or 5-3 the soquence th monomers are ordered car sabi, around 20-260 adenylate residues Chapter 34Biochem Prelims - Baby E MAP-SAM Chapter 35 Vertical transmission Horizontal transmission 80x chromosome mutation, passable to offsprings, hereditary -mutations in autosomes, limited to individual, germ/somatic cells Cancersicisease occur due to combination of horizontal and vertical transmission [Composition of Chromatin [Very long dsDNA (2x stranded DNA) Histones (small basic proteins, nearly equal mass) [Non-histone proteins (larger and aciaic) [small ay of RNA Histones Nucteosomes Hit histone proteins that condense DNA, regulate gene, DNA.dlrected molecular transactions ~10nm in diameter, connected by ONA filaments, DNA wound in histone ectamers. organizational unt of soluble chromatin loosely bound, located outside, removed easly by sat solution [4 Major Histone Types / CORE histones 2A, Hae 3. Ha Methylation [Acetylation Phosporylation [Sumoyfation [ADP-rbosylation Monoubiquitiaton [Octamer Composition (He-Ha)2-(HaA-H28)2 DNA linker Higher Order Structure (from low to high) naked double-helical DNA 10-nm chromatin FIBRIL [30-nm chromatin FIBER Loops/Domains [Chromosome (Metaphase) [chromatin Types [Heterochromatin a. Constitute dimer with H2B, stabilizes histone and adds hal-tuns dimer with H2A, stabilizes hisone and adds halt-turns tetramer with H4, central rle in nucleasome formation tetamer with H3, central role in nucleosome formation [6 types of Covalent Modification / Postiranslational Modifications of Histones gene transcription (+) H3IH4 (gene transcription +) Core histone (Chromosomal assembly) H1- codensation of chromosomes during replication transcription repression DNA Repair ]gene activation, repression and heterochromatic gene sliencing -30 base pairs that join adjacent nucleosomes - interphase chromosomes anchored to scaffoldinuclear matrix -inactive, densely packed (interphase), sains densely -essentially inactive, always condensed DNAs transmitted by exact replication DNA exchange occurs via crossing over, recombination, transposition and gene conversion “Mutations - changes in DNA base sequences, due to faulty replication, transposition or repair ‘Mutations occur in one / 1M cal dvsions ‘Mutations can occur in transcribed protein coding DNA, non protein coding DNA or nontranscribed regulatory region DNA Factors that increase rate of mutation Viruses [chemicals [Uv tight Tonizing Radiation [Non-histone proteins include [DNA replication and repair enzymes RNA synthesis, processing and transport Histones are the mast abundant chromatin proteins Core histones (4) have been highly conserved bet, species but may vary Carboxy 2/3 -> hysrophabie ‘Amino 1/3-> rich in basic Amino acids PTM - have important rles in chromatin structure and function Ht histone is not always present, fit iit interacts with DNA during is exit and entrance to nucleosome Histone octamer has around 145-160 bp and 1.75 superhelical turns ‘SUMO - small ubiqutin-related modifor ‘Metaphase chromosomes are likely almost totally inert (inactive). transcriptonally INACTIVE. Neither H1 or noncore histones are needed for nucleosome reconstituion DNA in nucleosome is supercoiled in a left-handed helix [Majority of histone-DNA interactions occur inside the supercoil Histone chaperones - releases histone after assembly Phasing - non random clstibution of histones in DNA Ht histones stabilzes the 30nm chromatin fiver From fiber to Loops - 100x increase in length All cells have same genetic information, but ctf in expression resulting to differences in cell ypes hypersensitive sites - Highly active DNA (transcribing) have regions that are sensitive to nuclease digestion (e.g. DNase |)Biochem Prelims - Baby E MRS [b. Facuitative [Euchromatin Sister Chromatids Centromere Telomere inetochore Telomerase primary transcriptsimRNA precursors Introns RNA splicing 1. LINEs (Long interspersed Nuclear Elements) 2. SINEs (Shor interspersed Nuclear Elements] relatively active during gametogenesis and early embryogenesis -opposite of heterochromatin -duplicated chromosomes that are symmetrical .chment point of sister chromatids, A-T rich region. ends of chromosomes, T-G rich region centromeres + CENP-A + bindng proteins, site of attachment for mi spindle Chapter 35 Humans have 5-TTAGGG-<" in telomere area ‘Telomere shortening = aging enzyme that maintains telomere length and synthesis, decreased activity assoc w/ aging -previously called hnRNA, with introns and exons, spliced to bcome mRNA noncoding intervening sequences, to be removed -coding regions, retained or spiced, then ligated -femaval of introns from mRNA precursor [Categorias of Moderataly-repetitive sequences >1000bps (70-300bps) -both of above are retrospons, arise from transposition(moving from one location to another) Microsatellite Repeat Sequences 6G sequence Mitochondrial DNA Chromosomal Recombination Deletion Insertion or Duplication = 246 bp X 50, dinucleotide repeats of ACITG, useful in genetic linkage mapping associated with fragile X syndrome -composes 1% of cellular DNA, transmitted via nonmendelian maternal inheritance has 13 proteins that play key role in respiratory chain (Complexes 1,3,4) -creular and double stranded -5-10x higher mutation Insertion or deletion, may afect gene product or gene expression (noncoding DNA) exchange bet, similarihomologous, occurs in meiosis primary, METAPHASE -one chromosomes recieves less genetic material one chromsome receives more genetic material ‘The further apart two genes are in an individual chromosome the greater Is crossover recambination 1) Homologous [2)Nonhomologous via protein site speciic Reverse Transcriptase [Baceriophage Chromosomal Integration can oceur via enzyme used by viruses to create DNA genome from RNA, -also called RNA-dependent DNA polymerase human haploid = 8 trilion (3x10°9 bp) ‘each chromosome = 1.3 x 10°8 nucleotides Lamins - proteins that attaches loopsidomains to nuclear matrix Introns - seperate functional domains (exons), permit recombination, allow rapid evolution of biologic function 1% of human genome is axonic Rest (99% - non protein cading, serve lo regulate gene expression, binding sites for regulatory proteins or encode ncRNA) [Eukaryotic genome Sequence classes (2) 1, Uniqu sequence (Tor proteins), compromises >50% of eukarotic genome. 2. Repetitive - sequence, at east 30% in human genome highly repetitive sequences (HRS) are found in the centromeres and telomeres -HRS are transcriptonally inactive and play a structural role in chromosome ‘Alu Family (‘arly of SINEs) - 10% of human genome, mRNA precursors, or discrete RNA molecules, mobile elements mutations of ALU family causes neurofibromatosis “Trinucleotide sequence - whan increased can cause disease [Other trinucleotide sequences disorders Huntington Chorea (CAG) Myotonie Dystrophy (CTS) Kennedy Disease (GAG) Spinobulbar Muscular Atrophy (AG) [Difference bet mtDNA and standard code [UGA (stop) becomes Trp [AGAIAGG (for Arg) becomes STOP “some forms of Diabetis mellitus can be inherited via mtONA LLepore/AntiLeopre - unequal crossing over in hurman hemaglobinpathy Jumping DNA - small mobile DNA Pseudogenes - contain nonsense codonsicannot encode functional protein sents capable of ranspasiionBiochem Prelims - Baby E oF unwind prime, fork synthesis bubble close [3 Mechanisms of Rapid changes in Genetic Material 1) Unequal Gross Over 2) Transposition 3) Accidantal Fixation! Gene Conversion * Sister Chromatid exange (only in ciploid eukaryote) [6 Stops in DNA replication (Eukaryotes) (Origin of replication "or - leads to denaturation of adjacent AT rich region Removal of Nucleosomes and Uwinding of DNA Replication fork formation, RNA primer synthesh Replication bubble formation and DNA segment ligation 1 2 3. 4, DNA synthesis and elongation B 6. Reconsitution of chromatin [Proteins involved in Replication (6) DNA Polymerases 1 2. Heleases [ATP driven DNA unwinding 3, Topoisomerases -relieves torsional strain cue to unwinding, nicking-resealing, no ATP Needed 4. DNA primase -intates RNA primer synthesis, 5. SSB (single strand binding protein) -pravents reannealing of ssDNA to dsDNA 6. DNA igas 1660 ATP, seals nascent chain (leading) and Okazak’ fragments (lagging) [a Components needed in Replication fork 1, DNA helicase 2. SSB 3, Primase 4. DNA polymerase Direction of DNA polymerization is ALWAYS 5'-3" Leading Strand Continuous, also called forward strand Lagging strand fragmented (Okazaki fragments, opposite of leading strand, reverse strand 3 properties of DNA polymerases: 1. Chain elongation (nus) 2, Chain processivity (lenght before releas) 3. Proofreading (correction of errors) * Initiation of DNA synthesis requires priming by short length of RNA. Okazaki fragments, segments of DNA attached to RNA primer ‘Semidiscontinous DNA synthesis polarity in replication, opposite directions, non continous in lagging strand [2 strategies to speed up replication 1. Bidirectional 2, Multiple Origin of replication LLight-chain Variable and Constant portions of IgG can rearrange association of sequence-specic dsDNA-binding proteins with direct repeat ONA sequences + review ARS, ORE, ORC, DUE = Ori defines short region of ssDNA for DNA synthesis initiaton Primasome - mobile complex of hoicase and primase Eukaryotes use DNA Pol Alpha priming invalves nucleophilic attack by 3-OH Group on phosphate Pyrophosphate - released during dNTP attack [stops in lagging strand 1, Removal of RNA primers 2. Filing of gaps 3. Sealing of rioks by DNA ligase Chapter 35Biochem Prelims - Baby E ‘Seperation of DNA strands is promoted by SSBs(RPA in eukaryotes - Replication Protein A) DNA toposimoerases 'S Phase of Call cycle cyelin Cyclin-dependent Protein Kinase (CDKs) Cyclin EA, and CDK2 Restriction point DSB (Double strand break repair) nicking -resealing enzymes capable of unwinding supercoiled ONA, Where DNA synthesis occurs, Synthetic phase -DNA syntnesis only occurs ONCE per cell cycle - proteins that regulate cell cycle 'S phase, DNA synthesis between G1 and $ phase Homologous recombination (HR) and Non homologous End-joining ‘most DBS repair occur via NHEJ al GOIG1 phase for SIG2IM via HR ‘There are 4 checkpoint controls for each phase of the cell cycle, most understood are at G1 and G2 ps3, p2t -tumor supressor, stablized in response to DNA damage potent CDK-Cycin Inhibitor (CK!) ‘Mammalian genome takes 9 hours to replicate Unwinding must occur every 10 base pairs hexameric MCM complex unwinds DNA in eukaryotes Okazaki in Eukeryotes (100-250 8P) Cancer (oncogenes/oncoviruses) attack the transition from Gt into $ phase Replication licensing - marking of newly copied chromatin Origins only fire once per cycle Single base alteration (Cytosine to Uracil / Deamination) ‘Single base alteration (Adenine to Hypoxanthine / Deamination) [4 outcomes of DNA damage 1. calhcycle delay 2. cell-cycle arrest 3. apoptosis 4. senescence 80% of human cancer Is due to p53 dysfunction Chapter 35Biochem Prelims - Baby E Genetic Engineering ‘manipulate oa ONA Sequnce ard const of time molecules, proves means stung cau uncon contol of DNA [portance ofmoiec ogy F.Undertanrg alec basis fear (aesoma, sla al isat,abnatar,) fz Treresy nln GH, pararapen aren) s vaccines (60) ane senoste esting (aM Disease paconnsdual espns shumucolye etapa (Personalized medicine) 5. Foverscwescie (Ora arabs even for ede cl 5 Crtve gene teapy (essed by le ol defensin) Via RWAnducble syste [NA rapnats cen Be sted sgl elchoghorei cn agarose of plyaryamide gue RISPR-coed NA Poly ez (Cee must ba taker nt weap coer unten of va ug DNAnsecion parsze "YAC wea anbath bactril ar yas cle himare Mecus lees corning Sth human an baal DNA squencs ina Soqenes:nopandent shen, eonce of NA recombi seach Recombindant DNA ech Isdaton,manpustono ONA nutes eno-e ng of severe make rere Mee Endonucenses erzyes tat cu DNA aspect equences WITHIN be mokcul 4 als RecoinnnlONA esearch Exonulentes anzyeshal ct DNA pec equeces al dios romans of DNA, sequeren INDEPENDENT eatin Ensen bathe an erdonukssa,etrcereverted baceal vis growh, cat ONA at SEQUENCE.SPECIFIG manner, nt RANDOM nl ears enzymes hat prea: Pst ase ONA Rom DNA genome of fron organs inettes retin pogo ONA by agin * Rosieon Eraymes ALWAYS cure wih Sequence Spec DNA methylaes al ge exc sae se [Romane Ras ames] fare Et sat eter irr” Gane ceeneoia fz. Nest Two irs om Species cot ce [Mov crmayratuetaiowedby sain despration Stn “Rositon enzymes clave DNA hat eke +-¢o lng esting te BLUNT o STICKY (overpercbodve) ENDS ‘Sto end are uettncontrzng yards or chmare NA Mees Formub or DNA ceavge hequoney a RE Aaa to NN ecagnilon capac fen) seal RE win sp sequence can clave every 256 tp, (aed 4 abet tet ened ton Thermus equaus, heat esstn RE used PCR Restiction Map neat ery son DNA whee nays soo ‘when ONAs sted yan RE, of sagen itv he arse of NA zoguncss| [Pr esac wih ape cy es x Sty ends may reconneet wi erie edig W NO NET GAIN of NA, [ars st ony oe rosters uso of Du ends seas crusPR-card [zSicy ends ao ANNEAL Toringhteapenaus oti [rpse of Goning Vator iz Proges aceal ae] [x SN Gaara ial Cronesones) 5 VAG (eset til Crerosores. [s.P1or PAC. Gat vaderomnege Pre Faeroe curs of beceropnage T4 anya ONA et rach a gto) ctustared rout narspese sor paloml reas asco gone 9 Jor of ects mmm, previ reniecton of ecteium Bybeceeogos cn be uote gee delet. eding, euzaon and gore vaneaipton mdulton ‘ave Inear DNA ian tin DNA cree DA culled rey pads of rae infetve phage pride), ONA net see 10-200 Iyer af isis and tages. we lari with ONA sequences calc COS SITES can cary ONA rst of 5.5049 Jona neon 80.250 Jona nee 500 20008 Jona ner £02500 Chapter 39 wohl foe past RNA vases in mara [Ganone et anzyra, Nests gon “ean gerne ln ne or ky ene “ara CRISPR-Casd, ste-speate RNA dosage “hs rotlanca obo aeycie an anitinBiochem Prelims - Baby E Chapter 39 fpasronrawsonot wel AAV) “cura tates we val repre sng RE that us equ (etal digestion of ONA) he Tal GOAL st goreae aye amen 0 goes alt nat xpraion actor vectra cally steals a poten the wae nodes bygone may ao Nave anos Dt code for PROTEASE INMIBITORS, Dus nteashg ney osu Probes places of DNA ot RNA bel wit cP of aotcais, used in aching lr spec gore or ONA rlesdos in quarying DNA or RNAi eleckophrases I mustrecopniz a conplomeriy sequence or ta be acre DNAs gonna cRNA ar unl ted in Sone oF Narar Bs an cece or alertons in gone fesloonrcrions of earners) (opener er Taras Sous or Gray BT poten nucle AceBiochem - Midterms ‘uisot s the main way for deals to be quenched ‘Oxygen radials (most damaging) reais refered toa Gwe ROS Oxidative camage ta AA tyrosine forme what? now slp paroxide measured in the body now ar caldshydes measure inthe body Perondation of 6 polyunsaturated FA forms? Peroxdaion of 8 palyunaturated FA forms? DNA ¢amageto somatic cls may result to ANProtens tat ae drectyvinroctyintractodateciod by Free rads inate Kile Lipid-engorged macrophages under damaged endotrelum leads to Invemaslat o nike oxide before becoming re radial ‘hi the resplatory burst enzymes on Is bound to what hee poting Cuppar i bound to hie poten ‘thar metals are bound oprtein as ‘Super onde + S00 (Superoxide Dismutase) = what organale contains most enzymes producingrequiing superoe a ‘Selonium-depandont enzyme that reduces hydraxyfaty acids ‘Oxkizod glutathione fe reduced by whtat enzyme Radical formed trom vt E Tocopherol radical +vtC = back to tocapherel this isan aulocatalyicpro-vidant ‘am that protects agains athorosleas and cardiovascular ‘ype of vi E used by tals Answor wo aces react togeter Reactive Oxygen Species (ROS) superoxide, hydroxyl and pernyeroxl Ahyeroxyprenyllenine FOX assay (Ferrous Oxsistion in xylan orange) via thiobaroitre ace (TBARS) TBARS: total thiobariire acd reactive substances Pentanes Ethane Cancer fitiation) Autoimmune ease ‘Auhorostorosis Transfer, Fertn, nemosiderin Ceruloplasmin Netaatonein oxygen and hydrogen peroxide Peronisomes Glutathione peroxidase NADPH dapendant glutathione Tocopherol radial Beearotene vie Need to Know 6 protective lox nutionts ave 4. peartone 5. carotenoids 6 plant polyenes free racials cause t.cancer 2, atheroselerosis 5. AID (autoimmune esas) Fre rade rary stabiize due to 1. vary sort at ie Free Radicals ‘Nice to know {ree radels damage 2 proteins pis ungat FA > pis peroxides > Dialdehydes @ cell mamrane and fnoprotens chromophores are frmedin acide contin Fe2 > Fo -pentanes and ehanes can be measured in exhaled ir aldehydes can macy bases in DNA -tigh conten of unesteced cholsteral kis Hpd-engorged macrophages -LDL Free rad = abnormal LDL (ngested by macrophages) -catalasos and poroidases remove N202 -NADPH- dependent gbtatione 2 very low tssue adel concenatons ‘Fes rads are sat perpetuating chain nn Sowrees of Organ radicals 1. onizing radiation Xray/UV > hycroxyl) 2, Transition metal + 020202 wero) 4. Nive oxide + superoxiso = poroxyntile > hyn 5.5% of 1.5 mol of ROS aro formed inthe body naturally 2 ee ack 2 plant potyanencs 2 tpi soluble anoxidants 1. Uiauinone 2, CarotonesBiochem - Midterms ‘pat pe rhon Gna une cae a ae Pea ac weet pre) tore tpl et nen rs A Pg i oe Sami) inp sean been nurs cay A) earcmrant cue tn, Paha pt rma ce cote 485% "mt te NutritionBiochem - Midterms ‘une ‘camgounes frgn to bdy 9. drugs. plans hat we he 2 erzyesnledin phase 1 ‘rou fons a nam p50 rzy ecto lecron Yarra NADPH in CPS Wo ts of xan ate reducoytonyaten in ohase 1 vate hs me most CP4EO Intraoral lure hare aretha CP found rata p50 reduc compound fonin gape lane) ‘hs epln pt80 ong erpone aration ‘sth most quai conan eaten Enyanes tet cetayze UDPducroe ae croton ‘metabo ef hol nd many toi nornones 6s ‘lle donor aby sre eo, peck ae anes “sole ingotant congo a decvopieconoounds aie ently neler afer aarage ‘saves act onoin acon reason o ences “sires ttyl nara metiaon eactons| ‘ne err pois poecton ayant carcnogansin Be ER products of CP4SD son on procarcnagensuneates ‘newer phase t-nytsaton, ress 2 coioaton ‘moraosygntees and cpetome ASD vatersobl gle carpaide llr) ronan esos NADPANADPHofotrome p80 redura ‘hyo gou of subsets 2 war yo peotally ER warren} an enrages Pobmarshan of 480 ‘Ghearondson| ‘vernosraetrses (17) ‘ohearndes PAS adenosine hosp Satoepesuae tone ‘testa (067) ‘cyan a ation nny S-eno64motono (SAW) pov Neato Know Mesaneem ofxorbots i 2 (atvstonescovatennert—act) Compounds ta conupate guarone (oacas) 1. pednes 2 ocarnogens ergata eo couse seston or nactatn 1 serodhemense| 2eatenogene 4 physologca compounds (vt > Cae) Nomenchure of pzeomes reo CYP dete ptS0 2) foiy- navbar 45) stam capil e: “natal -ramber ea.cvrras ‘arous CP#s0 have oeraping mtscae spaces sf. sutseaos ok Indl eanetou -c80-> BLE Soltar eles of ssione 1. pro ett fer hyeogen pero water 2 miacolr eet ard arcosiar (raaine SH guns rene) 2. arin sc raneprt sccytonsereses sry a tase octane: elon and at oars many 460 are NDUCILE tons of ona 1. calquyltaape- acted DNA par machas via ADP-bosyaon 2 Aturedarigeneiy > aulemrune disease Xenobiotics Neto know etaotam of xooscics gnarl consdored a ettaton pects ‘er 1088 in pase 1 ss tom hytonyaon 4 epoxition Thy steal 57 cfstrome ps0 genes 2 huane ‘oral dove roman (ER grt ‘ssomtn peak at 450rm att gs ee mtabtized by CPS e950 8aHENE enzyme 5 fay “have 0% AA sagonce ny pS aly - hve 55% A sguenc ery jr on dua metabo ‘ever Motonal acon ram ER rambranes, sujet to subaclubr faconaton warn: arabia (2¥P209) tobacco sre: tana (C¥PZE) rate > coin C¥P2AB) ottstons oraktanyystenyene yo GTS (stones vases 6 UPREGULATED by ure retest accreted In uti oe N-callon of eae Scots) 3 ach chara cerchopen (nec crsncoun) vi chan carageraBiochem - Midterms @ 1. Exracelular uid is distbsted to 2 compartments, What are those? 2. Give 4lonslsubstances thal are higher intracellularly 2. Major phasphosiycerida by mass in human cells 4, Type of ekage between eloments of a phosphoglyeerde 5. This replaces the glycrol backbone is sphingolipid 6. Glucosy and Galactosy-ceramides are generally called as. 7. This contributes or increases cell membrane fui 8. Give 3 substances hal readly pass tru cell membranes 9. Tis protein structure allows proteins lo span the entire membrane 10. This is used to compute where an Amino aid sequence is consistent wih a vansmembrane location 11. The enzyme ATP synthase is an enaymatc marker of what membrane? 12, Give two lypos of movements exhibited by membrane lipids 13. Type of phospholipid hat are usually located inthe inner leat of membranes 14, SubstancelEnzyme tha allow phosphalipts to lip lp (nner<>outer leaf transfer) 15. Proteins that exchanges lipids (no net gairloss) 18. Tue False - Sugar moietos (og. alycosphingalipids and glycoproteins) are prosontin both leaflets 17. Type of membrane protein that do not require detergents for ther solublization 18. These lipids can be used as carriers of drugs. enzymes or proteins 19. Most accepted model of plasma membrane, proposed by Nicholson and Singer 20, This typeof conviguation in unsaturated bonds exhibit lower Traniton temperature (Tm) 21. Lipid that both promotes membrane fidly and limits membrane Nusty 22, Areas inthe exoplasmicleaie thats involved in signal ransduction and other processes 23, Most common protein thats present In caveolae A Inertia id an pasa I. Ma, POs, Protns phosphatslehotne Estrlinkapes Sphingosine corebosies Protconce of unsaturated fat aso: Ks ‘Carbon ccsde, Ntrogen ana Oxygen ‘Alpha eli strture (usualy ~20A) Hydropaty plot Irnermitochondial merrane Lateral and Trenaversa movement ipsop) Aminophosphaiss(PhosphataysernePhospnatylethanolming) “ranslocases (or Flopsses) PP Phosphotps Exchange Proeins) opi TranserPoteine FALSE- only inovter Petoheral proteins Liposomes Fid Mossie Mode Cis Contguation Cholesterol parts caveolin 24, Aside fom lipid rafts, caveolae and tight junctions give 3 othe specialized structures found in surface membrar desmosomes, adherens Jncns and mice 25, Simple dtusion is movement down a concentration gradient due to___? 25, Give twa mediators of Facitated diusion 27. Tiss the sololity ofa solute or ably ta pass thru membranes 28, Give 4 hormones that facilitate ar enhance Amino acid transport 28, Give the 3 types of gating mechanisms exhibited by lon channels 30, Transporters are also called as carriers and 531. Between ion channels and transporters which has a faster transport ate? 422, Trangpor eystem that fs dependent on stoichiometric simuitaneous or sequental transfer af another solute 238, Give 4 simiartes between ranspor systems and enzyme-substrate interactons, 34. Important example ofa primary transport system 36, Valinomyein and Gramictin are examples of? Random Thermal movement Permeatilycooticont Ineuln, Geaooraids, Growth Hormone and Estrogen Ligand, Votage ane Mechanical lon chamele cotransport system ining st, maximum rate oftranspon (Vax) ining constant kr) canbe blocked by compaitwe inhibitors lenophores 36, Give 2 examples of bacterial substances that disturb cellular membrane itegity (allows leakage, uncontrolled Dither toxin (Conabscterum epheriae) and Alphe.temolysin (Steplocoeess) 37. Mutation inthis tetrameric protein caves nephrogenic dabetes insipidus 38, ATP is usualy the enerey source for Active transport, give two other altemais sources of e “Aquapotns (special AP-2) ry fortis tronspc Ligh an electron movement 939, The body spends how many percent ofits energy to preserve the electrochemical gradient in the Body 20% 40. Among the 4 types of ATP-Driven transporters, which is associated with cystic fibrosis and mulicrug resistance ABC wansporer (CFTR and MOR.) 41. How many Na and pumped out and how many K are pumped in bythe Na-K-ATPase pump? 42. Give two drugs that are capable of inhibitng the Ne-K-ATPase, 48, Segment of myelinated nourons where there is re fn ow 4, Two pathological states where demystinaton and impairment of nerve conduction occurs 3 Sedum Out, 2Potassom in Ousbain and Digits Nodes of Ranvier Multiple Slooss and Guian- Bar syntrome 45, Transport system found in adipose cals and skeletal muscles tha allows anspor of glucose, promoted by isi GLUTA 46, What type of cantransport system is found inthe smal intestine 47. Typo of glucose transport prosent inte basolateral membranes 48, What are the 3 requirements fr endocytosis to occur 49, TrviF alse - Granulocytes are oly capable of phagocytosis 50, Give an example ofa protein that is commonly used to fectats endocytosis 51, Main on or element that trggersexacyaie? 52. Gap Junctions are formed when 12 units of his protein are joined to form a channel 58, Give an example ofa disease duo lo mutations in connexins '54, Size ime that oan pass thru connexon channels Na-Ghicone Sympor (dependent on Ne-XATPase fr Na gradionl maintenance) LUT2 (Unipan) Energy, Calum, and Contacte elements (Mierofisment system) FALSE- al all an undergo pceyoels but only macroshagas and granulocytes can perfor phagocjose latin Clem Connaxins (Not: nvidia connexn, henichannal 8 connesi ul 12connexis = connexon) Chart Mare Tooth disease (demyeinatng csease) 120008 MembranesBiochem - Midterms 56, Type of extracel vesicle formed by MVB (Multvsiculr body) ‘56, Mutations in LDL-gene encoding 7. Mutations in copper-dependent ATPase genes '58. Mutations that result to deticient GP anchor attachment 659, Protein affected in Hereditary spherocytosis 60, 2 Example of eiseases affecting mutatons in other membrane bound compartments BONUS: Key conto stp in Facitates afin Exosomes(Oter ane is Mizoveil rom membrane budding ony) Familial Myperchotesterolomia Wilson Dias Paroxsymal Noctural Hemeplobinuria Specuin 6 “Amount ofcarser avaiable MembranesBiochem - Midterms Vitamins/MineralsBiochem - Midterms ‘Breakdown 60 Easy 10Net so Eaoy ‘5 Noor nos Tose. Easy 1 Any callin when he hormone or gan binds ot acepar,ahaher ono 2 bochenicalphysilegel reponse has eon delrmined 2 Proximity ofthe eget cal tothe hormone source 5 Tavgel cal iferentate beeen diferent harmones and ener nolecues tn proline lad 4 Provides the rt sie in amplicon of the hormonal response er coping of home birding sgl arsducion 5 Ara prolins that re bound o ahormene but dows no generate a gal or cause a Solopea eek plans hale 65 Recesor wth NO Know tganss 7 Wat mito ie weed by Group Ihormanes, ls al the instar massanger 8 Refers to hormanes that ae bolgealy cine and can readily cross he plsma mentane 9 Give the cssieaton ot hormones based on chemical eamgoston 10 clyeosatains ao composed af ipa and beta subuats, which among the wo Inparthemional unquenass 11 Tha colestln th adnate ee eset ane tren wnat fo? 12 Al mammalan str homanes are formed rom enolesea va ths ntamadiate nthe ER or Mochondia 13 Ths orzye is essonsible fr convaring cheestrl to preqnencane int mtochonsia 14 pés05cc ness this prot when * wanssers cholesterol he Ine moshonai menbrars (AGTH dependent) 18 Ths hormone soves as an itamediat inthe loses of ead and OHT 18 Ths hormone saves as a precursorin he formation of Glucscerods, mnaralocoricats, estostrone and esrogan 17 Serves as te staring pit the synthe of ntechaamines,eaidotyrnine ad isohyonne 18 The Bosyihess of mineralbcrtcis the aldostarne oars what area ofthe adrenal atx 19 Hydonation of what aton i xsantal othe syrthese of bath gluce and mineaocotads 20 The enzyme 16hyonae i alo calles. 21 i the mos pote! naira glucocorticoid homaren hunans 22 What ae tn wo pari of he adrenal eorex whee ghcoenead antes occurs 23 lth major arragono” androgen precursor produced bythe areal corto 26 an crease aden androgen paducton duet a lek of ueacatondBosynthesi ue awack of hyeranlase 25 ls cualtuncion enzyme Ral has ase and hyroylse actly end works on BOP aden ana gonads 25 iar call ound inthe ess where etsterane is aynasized 2 Wit are tho wo tastostarone syrtoss patways 28 Is the most sgnfcant metab prosuct of testosarone 23 Testosterone is converie o anycroastoserone using wht enzyme 30 the primary estrogen of varan origin 831 Durngprograncy, hs ‘rm of estogans moe abundent ands poducodby the placenta 22 Testosterone + Aromatase 23 Andeslnesone + Aromaaee {3 Myenaonoactons requires are {85 This he maor sours of esvogon in postmanopaveal women 38 125(0H2.03 when sre atv for of Vs lo eile = 37 Wat ayer af hes contnins os! he precursors for clei ythass a holla ancon wih UV {38 Ths protsin serves as the Yarspe of revit Drom sk ovr ano drys 39 ops Ep’ end Nowpi are sytheized in wa eal fhe adrenal medula 40 I he rte Emiing op in calecolanine Bosyrihose 41 CNS dase duet dicen epamine, uted with L-dopa 42 Th enzyme ealayzos be conversion of doparine 1 norepinsting| 43 Enzyme oxporab fr conveting novesineprine a einepsine ‘4 Procusor molecule of Tore ae) ard T thyroxine) 145 Neal 74:73 rai? 146 Saves a rensportr ct edine against grader ito Tyld ot 41 Normal raton in humans? (Thy ied: Serum od), relects he vansportar acy 48 atatamere protan wth a malecle mass of 60 KDa, equres hydrogen paronse as an oxsng ager. 49 compounds thet ii xii /Ionaton ‘5 Removes: naive DIT andr 51 Holts tne A and 8 chain forinelin anawor “Target (ea) Dilan eet Recepios recepio-electereouging Plasma Carer Prot Psa Transport rte rohan resptos Recepior-tamone comple o Lganaeceplr complex Free hoemanes 1PG (crates, yrosine, ppt, gheopotein) Beta subun, apa is common Oyeplasmestpé copes Pragneslene _ejochvome Pac (side cain cleavage) erayre SAR (Strodogeic aout equator prtsn Progesterone Zona Glmerlosa (va @-hytonlae and 19ysronyterold detvirogonase) cat kostorene syihsse Cotist DHEA (denycopandrostaron) Aarenogenial sacra 72080 Leys cls Progesterone and DHEA patway (nest used aot) snyarotststrone Sevaducias (wNADPH) ‘rpesvedot Esto! ‘rp-esvedol stone ‘oxygen ard NADPH stone Caleta! Malpion oyr ‘vitamin D bineng ten Chromatin cos (60% Epinephe -Mso) “Tyrosine Hydroxyl (sot erahydroptriine 9 cole) BH (dopamine Baryoxylese) wit ascorbate as locvon done, umarae as Module, copper st active ste PNMT (Phenylethanclamine-N-Mathy transferase) Tyroptbutn Nav -Ke ATPase dependent yrold!|~vanspotr 24 Thyroperoedase Toure dogs ‘sodinase cystine Deu rpes (2) EndocrineBiochem - Midterms 52 Sucre desved fom proinsulin 153 Biosys of PTH regulate oy ‘54 Enzyme For jcaglemeuer oa, released due to BP, Na and Cl changes, ua, lod vos ss 55, Ocapeptde tom angiotensinogen, rpuates BP, point vasoconstctr, srulaos ldsterane production ‘56. Gv hee tesues where ACE can be founa 57 prs of homoneactngpepies ike ACTH, LPH, MSH and neuromodulators (endorphins) 58. Mutations in ths rceporis inte owar-onse best 159 Thyrishonranes are ranspored vs {80 whathormone is ost hy bound to SHBG? 1 Give 3 eaures of homane receptor ineracon 2 Give wo ways on how Coualng of Sita randcton cere 9 Gi thet nto doin feces 4 Give he 2hormonas at use cGMP a8 Ur secondary messengers '5 What arene 3 ganerl enzymes needed during te synthesis ofharmones tom cholesteto! 15 Wat ae te 2 enzymes needed forthe conversa o preganlone to progesterone 1 An etemdiate in maneraocoricod syne that has 20h luc and maetalcoricald aco Endocrine peste (Connecting) lenzed Calum Renin “Argjtonsin lung, enaotolum, sma POMC (Preopiomelanocartin) (2S! rceptr| “T8G (Tyridsining but) bar Sing should be SPECIFIC, SATURABLE, occur win CONCENTRATION RANGE of expected BIOLOGICAL RESPONSE 1. Bindg vi receptor in Pasa Mebane b,neacton wih inal receptors 5 Recogniton drain b. CousinSignalwarsaucon domaet ANE (ava avila) and NO (Nie ox) _.yaroylasesb cehyarogenass ¢ yases Sp-yéronstaroid denystogerase (92-OHSD) and As somorese Comeasieene 8 ACTH susuay used ne conversion of sales preprenobne saad of ACTH, the sis and ovaries use what homo rte LH 8 Wat are ho # stops inthe conversion of yosino‘2 epnephene 10 Pyrdoxal phosphate is ao known as |. Ring Hyromlaton 8, decaroxyaton e Se chan hydroxaton > Norep o,Nenaty ton ‘VtBS (use by dopa cocaroniase) 1 Ths isthe ony Cae Il homane(hyerophie) tht is ranspoed bound to pen 2 ive ho 4 secondary messongers vz by Group I hormones 8 Precursor of Tyrosine 4 TRH Thyrtopielasng hormone) is a pepe hormone cmposed of what ino acids 5 Degrade PT int native pent 16F 2: AMP b CGMP c.Caorland phospatdy-nositld Knase/Phosphatass Cascade Phenyaarne Gb.HiePro Cahepins 8 and 9Biochem - Midterms Trevonded tape panes ny Virdee nar ir tr al oe enroute ns eatin och cogs ‘pimin acres wha ta oe Nontonman sare oA DS maw anams (chonds) Fre ndcalcranng meee al eae eanes ne natn ‘enemy te nea cain porry t ntbnde Gre omeprne he poison rere Gane nen ged oy ROS mana pat (One tate emt Pot rns pega belay 89 crwth 8 wood ey ng ‘Treen EE enone onl oer mee ‘ty opine sae al ge ae a po kur Wola ancvoman ‘moi cost es ccd alee pee hen Sreeegertl pin ine atin ‘Ore wslng te pers nw src yan hten cysnnecmiong rte tear ROS ‘Sows a carsan oon (Gr ny meer ts pr ing hgh a ‘Seep eaks sours pete sere ‘nv ase ar ona chars Ferme ta ee eof er ‘ocean tar htt ee sane tsa Esepinte pepenmure edn roe ua ar yy prt ion ae ‘ui Pe poo eee tle “ne to nt esas cnonon Stee pteain ween anon ato ‘Rbonchoronin tad coc ha or hes ore une tard aun ermine expan ON ye LUsessoane organ ean sh ncn) adoro an Cte. src vey nd een nas ret Longe ‘eran Twat pr = tage one tcc tl ntl you of tlre ‘ur 0, i 04) Varney wea rodent onan age a: dad agus DEVOID of omra pea mang ei PRECAANCY sess tty Canmeneont emt) (hope alpsndoy meeps aloha haope cara thea ran ue ans wpa cnet a. om aed Faden Hasan» atv Be orton 1 Hotton lg Pome Stone {taro ret Con eng mare 2 ema Sane eons ‘feminine oa sytame ateashohee Prins wertepeatia NA et mfg anor Peace Ange Lie an 2498 ye syoorore ofc wots rg tri wr pata Tay Wn eng 6 yun Fon amon Fh) incense ls bebo ro elon rts ers 22 ‘tan ton pane aa rn +0 > aie eso) boone ype Irn enone can Geneon ee nstdebne nssenibne mony RONA a ness Exons mise dan OWA mac aan int = a ces ROS (OA dere» poh ron OS i rece pn, r i aus arse pansy PEO) re “tr intge fA oe) napa mabe = Mt ‘mee Dre 2. Pepodatr bons Pcs Ing Ppa Lipton gra aaice Soars antares ct) etn ‘cmt antigen ha ATP aan 08 auger, bape 2 bets une CPS ‘peti hangin nse sh Dean open cs Sevan pate mente tone tunere |. Reausnor ol aoeete gouge infovncotating eres ei cononin ae) Faplon O48) 6 Gowran heigl in tuna ia ETC Oval DNA rep nya ry aye jon rare a ‘comntione onpoe te rch ‘howe ve tne Siesuntne ne Stovoente =< 2 ornate paren mi tes eerste 2royeemm ya Cound eee rarest un ape rome me ROS pris tn pene > oer tion, Np eyed ka. iio soma of OS) man miacerta west eon {Two a(125 wa 15) 2 pepsin tangas, ans Weir srg snes erate neue cones end nig ie conen Aging :pBiochem - Midterms ge Pa omin BV, Cann we 5 Trew Sprsomnepndopmy SE) “ant dab ogo Aging :pBiochem - Midterms 4 toca of generated amplified intracellular signal eect ctv af poten (nzymes, anspor a heme) eects general processes ike ptsin syria, ol owt ad relation va gone expresso) [Aside fom hoxmonas these serve a signaling molecule (they use same hormonal mechanisms and signal transduction patways) ntlos -retbotas “General eteps in stimulus response lini rcoriton> pm alae > signal raion > Bolg Recognition voles etganism etl nerves sytem ap spec sensos € otan, sue, ct-physlcochmcal actor (ph, 2 trp, osreb.) ‘ther nor-tormone sgnaling molecules are hormones na sense snc hey posses in spect cee “4 Coordinated repeponsosietets to stimlus * Group homones param 142 only, Group harmanes pet a Signals used by hormones (Group: Ligane-Recear complex Group cAMP, cGMP. CaProsphaeylnostisas, proniphosshstae nat escaso (a re SECONDARY MESSENGERS) ‘2mechanlems for activation reaction (Group) 8 Glucozatcis enter eyoplasm, br ormonesitectrs that ure Direct repeats of DNA sequences (AGGTCA) Retro Aes RARE * above tee ube RAR rtd X Recep) Hormones/etectr that ue invert indore of halsitesha binding sites ofthe SAME ONA sequences Information Patsy Gene (ransenpton > Primary Transcript (MosisatonProcesing) > mRNA (ranaaton ar Trangpon)> Potala +e tw oc in les, el be cca n epi ormones that iii Adenyh cyclase (M1) ‘eayieine Hormone Action cognate recap unin bing protsine (7 laa hele nyekophbi), et 8 INTERMEDIATES fo goip 2 Cproacoute acpi, oy eolargas family of ot suse recess hurans (RE-NnEne pete Phosponosde-desendent ra ‘Sonal baredicers md chs of Fanci ‘ORs assooatad wit HBP wich sa chaperone protein receplor-corepressor complex serves ab lonc repressor af gore tantrpion hsmonae dec afets LESS than 1% of genes. mRNA a prota ithe are call PC (Popes, Citeonines)- GROUP thernanas VER groups use vot epi a ater de to SPACING ‘ANP: edanyl cyte, cOMP-quanyy cans (GPCRS. tay ate hres fam fal etc acpi nhnans wh cognate receptor (onal cargo) eso lassosation of ap80 (alo nuclear ranslcaton) and activation of receptor, bids to HRE, ile coaetvatr pon, gene transrption Sti, Tyr and linac acienter nucous drecy, binds wth HRE bound receptor tally corepresed tinting casos corforatral charge), igssoclton of corepressor coactivator Bnd ne tranceription (va RNAPI ard GIT)Biochem - Midterms ‘Alpha Adrneraie ‘pagaten Sommscsin| tes stmt, A ie no Important concepts in cAMP pathway sb ssi sci, ana Bound o GOP ~ epha shas GTPase aeity CTP oversee ne eactates th G poten “station azurs when GDP bocomes GTP ADP tosyaon (ue ocala and russ ons) of bhi subuns rat GTPase acy causing eves aban, pravering subunit efematon “ sunts have actor indapancent of ad sla con an von - Protayotes use CAP (AMP actuator paains) and ds actly 0 ONA far ne expression eukaryotes ese Protein Kinases ( PKA with R202 eae uns, ro dee DNA Badag 4 eANPS we neased acta R2C2 + snino 248 equate nphoschotator- epnospnoryson prays (SERINE and THREONINE) <-prosphonated alarm met phosporylon rescon = Magheslum “AKAPs serves a8 eto, ales PRAosubetates and enhanoas PKA acy ~ elie Pah prorporys sole > phoeshopain parang physlope eect AVP» CRED > CRE (nenphospharyated = wk) ' CREB « phosphonate, ns win coactntr CPIfI00 = mare patent proestrus reves cAMP pay, cAMP-> SAMP Ceono(netfsod xine deviate) inns pogpkadtaes, ts erosing AMD and acy ‘ANF bin to membrane fr Guy cycle Nir rus ad oum anos and sosum ti i Ye Seuble fom of amy case stonat = visa cGMP phosprosestarase INHIBITOR) CMP putwayutee-PKG (Peat Ksse G) NaICA pump Mh spay. tay {iproon sump - bw apacy, high n'y Swayeta change CA etal levee ‘.Inrease memrane CA parmeabity 2. mele om ER or Miochondra alour- tacts GLYCOLYSISIGLYCEGENOL ya armas ipa + Phospoliase PKC and CA-Clmodlin complex produces phosphoprotans pas Ps ses tose ase -2oth evenly bro ONA element lo avaleFarseroton (29 REtnterrn reponse elorert) EKG - p60 ane p-value in iarminiey rapens oes ek complex phospho and ecivetes KB fo NEKS (Ach) _cucooreas nis NF-KB by 2. compola wt NFB anchor 2 ps ining Hormone ActionBiochem - Midterms NES coentents (5) buthes 6 cama AF 1 AF-1 = prove dan! physlopefrcions 2, DBD- nds to ONR ingest ar rast | LB0- bias ramnesmstaoltes — species loge reoones 800200) -INNTRINSIT HAT eciviy 160 -BHLH mot oss hlcloce nes ‘wea cry tng N tinal elitr suns - Inc cea rocsp-nacvaor cmos o RNAPI ad basal ansipion appartis Hormone ActionBiochem - Midterms GlycoProteins *NOTE: GPS = GlycoProteins Concepts I Glycosylation - onzymatc attachment of sugars VS Glycation - nonenzymatic allachment of sugars Reversible glycosylation with Reversible phosphorylation is possible with single sugar (N-AcetylGlucosamine) + Serine/Threonine ‘Almost ALL human proteins are GPs wih notable exception of ALBUMIN Carb content in GPS range trom 1-85%. * GPs MICROHETEROGENECITY (diversity in structure/en) are due to GLYCOSYLTRANSFERASE activiy/oxprossion dependent on notmal physiclogy, cll ferentiation or metastasieineoplasm. Biological information inthe Oligosaccharide chains of GPs are only secondary and NOT dependent on amino acid sequence but on GLUCSYLTRANSFERASES, Conventional protein purfying methods ALSO work on glycoprotein. 3 methods used to identty glycan chain structures: Mass spectrometry, High-Res NMR spectroscopy and Glycan Microarrays Neuraminidases ang Galaclosidases are EXOGLYCOSIDASES and affect the terminal N-acelyineuraminic acid and galactose ENDOGLYCOSIDASES cleave inte)mal N-acetylglucosamine residues. : SUGAR NUCLEOTIDES are the sugar DONORS nat free or phosphorylated sugars. In the Golg’ apparatus, ANTIPORTER systems are used to exhange Nucleotide sugars with corresponding nucleotide. GLYCOPROTEIN + NEURAMINIDASE = ASIALOGLYCOPROTEIN ( have exposed galactose residues ar moletes) = ASIALOGLYCOPROTEIN RECEPTORS In hepatocytes clear GPS from plasma by recognizing galactose moieties, which are then cataboized Lectins must contain AT LEAST 2 SUGAR BINDING SITES to function (preciptaton/agglutination} Asialoglycoprotein is @ C-type lectin * ‘Among the 4 types of Ouinks MOST COMMON is GalNAe-Ser(The) linkage - can be found in mucins 2 important characteristics of MUGINS: a) high content of O-inked oligosaccharides and b) VNTRs (variable numbers of tandem repeats of Serine, Threonine and Proline) {60% of dietary Threonine are used to produce mucins Giycan chains are built by sequential donations of sugar nucleo catalyzed by glycoprotsin glycosyltransterases “The first sugar moiety n O-linked is usvally N-acellygalactosamine (GalNAc) [Linked GPS are distinguished by presence of ASPARAGINE-N-AcotyIGlucosamine Linkage and have same BRANCHED PENTASACHARRIDE (3 Mannose + 2 N-acotylglucosamine/ GleNAc) linked GPS have 3 classes: Complex, High-Mannose and Hybrid, (see table below) ‘ INdinked GPS biosynthes require Dolichol-P-P-Oligosacharride (from dolichol pyrophosphate) and Glucosidases and Mannosidases . Calnexin (Chaperone protein) + GPS = ensure proper protein folding i ot foes properly they ae catabolized in the cytoplasm Glycosylransterases also assist in proper protein folding Glycophosphatidyl-inositol (GPI) linkage isthe commonest way fr proteins to anchor in cell membraneslliid bilayer ‘functions of GPIinkages: a) Enhanced mobility vs transmembrane proteins b) Connects wth signal transduction pattwrays c) Can target prateins to apical or basolateral cll domains Consensus sequence that allow reversibie glycosylation and phosporylation is PRO-VAL-SER Maillard Reaction (Glycation process): glucose > Schif base > Amadori rearrangement > keloamine > AGE (advanced glycated end products) Bowing of foods/Flavoring is due to Mallard reaction AGE can cause tissue damage in DM and increases LDL and may lead to Atherosclerosis transcription factor NF-KB when actvaled by glycated proteins lead to generation of cytokines and proinlammalory molecules HbAtc = formed due to glycation of hemoglobin, best way to measure DM mangement, stays in body for 3 months GPS - ZP3 (Induces acrosomal reacton) and PH-30 (allows sperm to bind with oocyte) are needed in fertiiztion : Neutrophilsieukocytes and Endothellal calls use SELECTINS to bind wit one nother, INTEGRINS cause change in neutrophil to allow it to pseudopose (squeeze into blood vessels) Mannose binding protein - plays @ rle In Innate immunity (presents pathogens when bound to thelr sugars) Lysosomal hydrolases -catabolize oligosaccharide chains for turnover of GPS Influenza viruses use Hemagglutinin (H) and Aminidase (N) for binding and reproduction to host cells, numbered according to type used (e.g. HN) HIV-1 uses GP120 to attach to host calls, and use GP4t to fuse with cell membrane, antibodies are produced against GP120 Diseases LAD It (Leukocyte adhesion Deficiency) - mutaton of GDP-fucose tansparter. causes repeated bacterial infections and retardation, veated with gral fucose HEMPAS - abnormality in biosynthesis of Nglycans in RBC (Mannosidase I}Biochem - Midterms GlycoProteins Paroxsymal Nocturnal Hemeglobinuria (PNH) - hemolysis of RBC during sleep, deficient in Decay Accolarating factor (DAF) and CD59 Congenital muscular dystrophy (CMD) - defect protein alpha-dystroglycan, Rheumatoid Arthritis - lack galactose in Fc region, altered IgG molecules glycosylation Cell disas lack almast al normal lysosomal enzymes, lack GluNAc Phosphotransferase, leads lo psychomotor retardation Terms Glycoforms - proteins with identical amino acid sequences but show micro-neterogenecity of glycan chains Lectins - carbohydrate binding proteins that agglutinate glycoconjugates including GPS Glycophorin- Important RBC GPS with BOTH 0-ané Nirked oligosaccharides Antennae - the oligosaccharides branches of complex olgosacharrdes (usually 2-5 in number) Calnexin - chaperone protein, in ER, that prevents protein aggregation ERpST - facilitates proper protein fading along with calnexn and GPS: Catretculln- found in ER, has similar function with Calnexin HEMPAS - Herctary Erythroblasic Multinucleaty with postive acidified serum lysis test (mild anemia) Tables [s Principal Sugars in GPS. aminie acid (NeuAc) [Giucose Mannose Fucose N-acetyiglucosamine yiose First 3 are usualy Terminal, remaning 5 are infemal 5 Major Classes of Glycoproteins (GON) [important Feature 1, 0-Giycosialc linkage (O-tinked) [(OH) Hydroxyl side chain of SERINE/THREONINE/TYROSINE + Sugar (og. N-acotylgslactosamine) 2. N-Giycosiaic linkage (N-inked) Jamide Nitrogen (N) of ASPARAGINE (Asn) + N-acetylglucosamine (GlcNAc) [3 GPIanchored [carboxyl terminal of Protein + Phasphory| Ethanolamine + Glyean + Glucosamine? Phosphatidyinositol [a Subclasses of Oinkages: 1, GalNAe-Ser(Th) most predominant [2 Link Trisaccharida - (Gal-GabxytSer) [seen in proteoglycans 3. Hy Linkage (Gal-Nyaroxyysine) [seen i collagens [. Single GleNAe-SertThe] [seen in many nucloar and eystosalis proteins [2types of Mucins [Characteristics 1, Secretory (Mucus) | secreted by Gastrointestinal, respratory and reproductive tract (for hbriclion and provides physical bari) [high viscosity and forms a gel High content of NeUAG and Sulfate gives fe negative charge | Resistant to PROTEASES [2: Membrane baund | particinate in cal to call interactions, mask surface antigens, protect canoer calls 5 Classes of N-Linkages [characteristics 1. High Mannose lbase pentasaccharide > 2-6 additional mannose (neade glucosidases)Biochem - Midterms [Shortout [Other differentiating factors [GalliAc-SerThviTyr| No DolicokP-P-Oligosaocharide and Glucosidases, NOT inhibited by TUNICAMYCIN [GleNAc-Asn Neades Dolichal Pyrophosphate and Glucosidases, INHIBITED by TUNICAMYCIN WALEY GlycoProteinsBiochem - Midterms GlycoProteins [2s Complex [base pontasaccharido + 2-5 branches or antennae of GleNAc, Galactose and terminal N-acotyIneuraminic acid (NeuAc) 3, Hybrid [combinaton of above (one side just mannose, one side complex) formed by paral processingBIOCHEM FINAL END TERMS! BBG Cancer Main cancers that account for mortality lung stomach colon rectum liver breast -cervical, esophageal, prostate (may also lead to death) Incidence of cancer increases with AGE Neoplasm - any abnormal new growth of tissue, maybe benign or malignant 8 Key properties of Cancer cells 1. Proliferate rapidly 2. Display diminished growth control 3. Display increased genomic mutations at nucleotide level (indets, duplicates, loss and rearrangements) 4. Loss of contact inhibition 5. Invade local tissues and metastasize 6. Self-sufficient in growth signals and INSENSITIVE to ANTIGROWTH signals 7. Stimulate local ANGIOGENESIS 8. Evade Apoptosis Metastasis - is generally responsible for death of cancer patients Benign tumors - show diminished growth control but NOT tissue invasion and spread (metastasis) 2 factors also involved in carcinogenesis a. Organismal immunologic status b. tissue microenvironment NON-LETHAL genetic damage - thought to be initiating event in carcinogenesis, 6 major genes involved in cancerimutation POG 1. Proto-oncogenes TSG 2. Tumor Supressor genes 3. DNA synthesis genes 4. DNA repair genes 5. Genes regulating apoptosis, 6. Genes causing evasion of immune surveillanceBIOCHEM FINAL END TERMS! BBG Cancer Cancer is of CLONAL ORIGIN (from one abnormal cell) * Review Figure 56-2 for complete biochemical and genetic changes - Increased telomerase activity - alterations in transcription of mRNA and ncRNA - appearance of fetal antigens - appearance of abnormal sugar chains (CAM) - decreased adhesion (CAM) - release of exosomes, biomarkers, angiogenic factors, ECM altering anzymes - increased aerobic glycolysis (altered metabolism) EXOSOMES - vesicles released from cancer cells that contain various molecules Hers Causes /Types of Mutations Hereary mutation -inhered mutations from one or both parents Environmental mutations -rom relation, chemicals or viruses Replication mutations -erors in DNA repicaton/repair [I seontancous mutation -low trequency 10-7 to 10-6, geaerin tissue with high proliferation rate Oxidative Stress - enhanced ROS production, may also play a factor in increasing mutation rates Rev 3 classes of environmental carcinogens/tumors 1. Radiation - DNA mutation 2. Chemicals - DNA mutation (HUI 5 Wises -insoduce novel genes ino normal cls 4 types of damage due to Radiation 41. Pyrimidine dimer (Ex. Thymine-Thymine dimers) 2. apurinic or apyrimidinic site via base elimination 3. single-double strand breaks 4 cross-linking of DNA strands UV, Xray and Gamma rays - BOTH mutagenic and carcinogenic, IF NOT CORRECTED Xray and Gamma rays - increase ROS Carcinogenic Chemicals (see table 56-2 for more) PAH Palycylic aromatic hydrocarbons AA Aromatic AminesBIOCHEM FINAL END TERMS! BBG Cancer NS Nitrosamines cpp Alkylating agents (cyclophosphamide) DES Diethyistilbesterol AB Aflatoxin 8 Chemical carcinogens - covalently modify DNA to form NUCLEOTIDE ADDUCTS Chemicals that directly interact with DNA - mechlorethamine and beta-propriolactone PROCARCINOGENS - chemicals that need enzyme conversion before becoming ULTIMATE CARCINOGENS ~ most ult. carcniogens are ELECTROPHILES and attack DNA Nucleophilic groups - this is due to actions of CYTOCHROME P450 (CP450) in ER 2 stages in chemical carcinogenesis 1. Initiation - exposure to chemical causes genomic DNA damage 2. Promotion - growth and abnormal proliferation of initiated cell 1 and 2 = NEOPLASM AMES assay - used to identify if chemical carcinogens can induce mutations - uses Salmonella typhimurium - animal testing is used to show unambiguity of results, - epigenetic factors DO NOT test postive in this test ‘Tumor viruses - can be both DNA and RNA viruses [HII screray genetic material ofviuses are incorporated ino genome of host cll RNA viruses - occurs ae reverse transcription ofthe viral RNA to vial DNA (integration fs called a PROVIRUS) Effects of virus integration or provirus a. cell cycle deregulation b. inhibition of apoptosis ©. cell-signaling pathway abnormalities DNA viruses - often act by downregulation of expression/function of tumor supressor genes P53 and RB and their protein products Hepatitis C and Human t-cell Leukemia virus type 1 - are RNA viruses Viruses Genome Cancer caused Epstein barr virus. DNA burkitt lymphoma Hep B DNA Hepatocellular carcinomaBIOCHEM FINAL END TERMS! BBG PEGMC GP-RD Hep C RNA Hepatocellular carcinoma HHV-8 (Human herp DNA Kaposi sarcoma HPV 16 and 18 DNA Cervix HTLVT1 RNA ‘Adult T-cell leukemia Oncogene = * altered gene", accelerates cell growth or cell division, derived from proto-oncogenes (normal in body - encode growth stimulating proteins) 5 mechanisms by which Oncogenes are ACTIVATED ‘a. Mutation - point mutation of RAS oncogene, lost intrinsic GTPase activity, active MAP (mitogen activated protein) kinase pathway b. Promoter insertion - causes increased transcription c. Enhancer insertion- causes increased transcription d. Chromosomal translocation - chromosome is split off and joined with another - activating oncogene at point of insertion, also causes MYC activation e. Gene amplification - abnormal muttiplication of oncogene, increased production of growth-promoting protein RSV or Rous Sarcoma Virus when activated via (promoter/enhancer) - activates MYC stimulating unregulated cell proliferation 4 ways how oncogene protein products affect CELL SIGNALING PATHWAYS, a. act as growth factor b. act as receptor for growth factor ©. G- protein 4. downstream signaling molecule ‘Tumor viruses contain oncogenes (e.g. RSV) - first revealed thru viral studies TSG / Tumor Suppressor Gene - produces protein that suppresses cell growthidivision (I etvpes oF 15 functions 1. Gatekeeper - control call proliferation, cell cycle regulation and apoptosis, 2. Caretaker - genome integrity preservation, DNA damage recognition and repair, maintenance of chromosomal integrity [II oncogene vs Tumor Suppressor Gene Oncogene Ts -one allele needed for mutation to occur - needs both alleles for mutation - gain of function of protein for cell growth -loss of funetion (inhibition of cell growth) - in somatic only, NOT INHERITIED -both somatic and germ (can be INHERITED) - no tissue preference - strong tissue preference Important Oncogenes CancerBIOCHEM FINAL END TERMS! BBG Myc alters transcription of key regulator genes, stimulates cell growth, cell cycle progression and DNA replication, seen in a variety of tumors RAS encodes small G-proteins, GTPases Important TSG a>. induces call clearest, apoptosis, senescence and DNA repair, fund in 50% of tuners RB represses transcription of various genes from G1 phase to S phase, mutation in this gene causes RETINOBLASTOMA Early studies of cancer where in the development of COLORECTAL CANCER Dysplastic epithelium - preneoplastic condition, with abn. development of epithelium ‘Tumor progression - phenomenon whereby clones of tumor cells are selected for fast growth rate and ability to metastasize “a tumor may contain different cells with different genotypes - makes treatment difficult” MAGS 4 Conclusions derived from colorectal studies 1. Cancer is truly a genetic disease - due to somatic mutation 2. CAis a multistep process - needs a minimum of 5-6 genes for it to occur 3. Selective advantages are passed to clones like ability to Metastasize 4. CA involves alterations in cell signaling Growth factors - can act in endocrine, autocrine and paracrine manners to produce a mitogenic response, act thru various signaling events Growth inhibitory factors - like TGF- B (tumor growth factor B - both +/-) Polypeptide Growth Factors (Table 56-8) Growth Factor Function Epidermal Growth Factor (EGF) - growth of epidermal and epithelial cells, Exythropoeitin (EPO) - development of early erythropoetic cells, Fibroblast Growth Factor (FGF) - growth of many cells Interleukins - effect on immune system cells Nerve Growth Factor (NGF) - trophic effect on certain neurons Platelet-derived Growth factor (PDGF) - glial and mesenchymal cells, TGF-Alpha -similar to EGF TGF- Beta -both stimulatory and inhibitory on certain cells Growth factors with Tyrosine kinase activity (EGF, insulin and PDGF) [III tyrosine kinaee- ound in cytoplasm domain, causes autophospheryletion of receptor proteins end eer proline PDGF - has activity similar to Phospholipase C (PIP-> IP3+DAG) -see slides for table (old topic) CancerBIOCHEM FINAL ENI ID TERMS! BBG Micro-RNA (miRNA) - 22 NT long, decreases mRNA translation or mRNA stability, dysregulated in many cancers oncomiRs - oncogenic miRNA, overexpressed in cancerous tissues - tumor supressive miRNA are underexpressed in cancer - miRNA can be used as CA biomarkers (diagnosis, prognosis and classification) - can also be used for therapy - able to potentiate therapeutic responses during anti-CA chemotherapy and radiotherapy Extracelullar vesicles (EV, Exosomes and microvesicles) - lipid bilayer, released from both normal and diseased cells -are loaded with ncRNA which exert paracrine effects on surrounding cells -modulate expression of crucial genes involved in tumorigenesis (cell proliferation, angiogenesis, TME, tumor immunity) - can act on distant organs affecting metasis = neRNA are highly stable, found in blood, urine and saliva, can serve as NONINVASIVE BIOMARKERS -can also be used as delivery molecules to transfer (miRNA or anti-RNA) for treatment Epigenetic Mechanisms - involved in cancer causation, produce nonmutational changes that regulate gene expression - usually inolves methlation/demethylation of CYTOSINE bases -> alteration of this pattern have been detected in cancer cells -altered Histone posttransiational modifications also found in CA cells -nucleotide remodeling complexes (SWI/SWF complex- for chromatin remodeling - may act as TSG) - actions are potentially REVERSIBLE - 5-azadeoxycytidine and decitabine (ONMT inhibitor - DNA methyltransferases) - valproic acid and vorinostat (HDAC inhibitors - histone deacetylases), <- used in treatment of leukemia and lymphoma CANCER is HEREDITARY -discovered oncogenes and TSG was used as basis for this phenomenon -breast cancer (due to BRCA1 and BRCA2) are due to DNA repair errors Li-Fraumeni syndrome - rare syndrome with cancers at different sites, early age development Neurofibromatosis - presence of cafe au lait spots(brown spots), neurofibromas Cyclins and Cyclin-dependent kinases - regulate cell cycle -RB gene binds to transcription factor EF, blocking transcription ( G1-S phase) * review table in slides Genomic Instability ~ also termed as errors in genome replicative functions = due fo mutator phenotypes Cancer ncRNA miRNA Antigens Plasma lons (e.9. Ca)BIOCHEM FINAL ENI cc ens mb jes ID TERMS! BBG 2CA cell genomic instability 1) Microsatellite instability (MIN) - involves expansion or contraction of microsatellite DNA sequences due to abnormal DNA repairireplication 2) Chromosomal instability (CIN)- occurs more often than MIN, GAIN or LOSS of chromosomes due to abnormal chromosomal segragation during mitosis - above two are often mutually exclusive (one only can occur, not both) 2.a) CNV - copy number variation - alteration in gene copies (indels) 2.b.) Aneuploidy - not a mutiple of haploid number, degree correlates with poor prognosis, fundamental aspect of cancer Factors involved in chromosomal segregation ‘a. centrosome number b. CIN syndromes ©. cell cycle regulation 4. chromosomal cohesion e. spindle assembly checkpoint kinetochore-microtubule attachment TELOMERASE, - short felomeres when CA cells divide (predicts predictive value of inflmmatory diseases and cancer) - elevated telomerase activity is exhibited by most cancer cells APOPTOSIS and CASPASES - caspases (main proteins/proteolytic involved in apoptosis), inactive form as procaspases - derived from cysteine and aspartic residues - includes caspases (2,3,6,7,8,9,10) upstream caspases are called initiators (2,8,10) -downstream are effectors or executioners (3,6,7) -DNA fragmentation is due to CAD (Caspase-activated DNase) Microscopic features of apoptosis 1) chromatin condensation 2) changes in nuclear shape 3) membrane blebbing -NO INFLAMMATION in apoptosis (cells are disposed of by phagocytes) 2 Pathways of Apoptosis ic or Death Receptor - via TNF-alpha and FAS ligand, caspase 8 -> caspase 3 (DNA digestion) I pathway - via cytochrome C -> caspase 9 -> caspase 3 (affects lamins) 2) Intrinsic or chondl * caspase 3 - common in both pathways CancerBIOCHEM FINAL END TERMS! BBG Cancer NECROSIS - pathologic cell death (not genetically programmed) ~ causes INFLAMMATION, release of intraceulluar contents into surrounding microenvironment - inflammatory cells have active tumor-producting effects (eg. angiogenesis) upregulation of p53 gene, upgregulates BAX (pro-apoptosis- initiates mitochondrial pathway) CA cells evade apoptosis by /oss of function of p53, or BAX or favoring anti-apoptotic proteins EXTENSIVE CELL DEATH - abnormal apoptosis (seen in Alzheimers and Parkinsons disease) TME (Tumor Mleroenvironment) CA calls pus nor-cancer cells and ECM components ~ major non-CA cells are rom immune system (F and B hmphocytes, NK cls and macrophages), and mesenchymal cells (Adipocytes, endothelial cel.) [I nec (nuclear Factor Kappa B)-> reprogrammes T lymphocytes to promote tumor growth and sunval,eseaping immune survellance “mesenchymal cals stom cl riches [ve (rom endothe cel / Vascular endothelial GF promote tumor anglogenests and metastasis [7 warsune EFFECT- CA col perform Glycolss (aerobic) but produce LACTIC acd fam GLUCOSE PKM2 (Protein Kinase M2)- highly expressed in CA cel, has low activ and dimeric orm, accumulates glycolic inlermediates Metabolic reprogramming leads to less ATP production and more cellar biomass (CHON, NA, FATS) Soll umors have poor blood suply, produce lactic acid, leading to ACIDOSIS, allowing CA calls to invade mare easly low oxygen and bod supply releases HIF-t(nyposia inducible fctor-t)- upregulates atleast 8 glycolysis enzymes pH and Oxygen tension > 2 important actor affecing ancancer drugs STEM cells, ~ cancer chemo is unsuccessful due to POOL of CANCER STEM cells - they are relatively dormant, but can expel anti-CA drugs, resistant to apoptosis ANGIOGENESIS - angiogenic factors are released by BOTH tumor cells and surrounding tissues (TME) - HIF-1 -> causes release of VEGF -> Tyrosine kinase receptors -> upregulation of NF-KB pathway > blood vessel formation - BV from CA are not normal, often disorganized, lower integrity, leaky - can be inhibited by ANGIOGENIN and ENDOSTATIN -MABS (Monoclonal antibodies) (eg. Avastatin) - used in treatment of some cancers -combined mABS + other cancer therapy = more effective METASTASIS - 85% of CA mortality is due to metastasis - starts with DETACHMENT of tumor cells from primary tumorBIOCHEM FINAL END TERMS! BBG Cancer (gains access to circulation or lymphatics (process of INTRAVASATION) - arrestin nearest small capillary bed - extravasate and migrate to neighboring ECM, then eventually setles CAM Cell adhesion Molecules - allow CA cells to detach from parent tumor = CAM E-cadherin -> found in normal cells, accounts for decreased adhesiveness of CA cells, - due to changes in glycosylation (eg. GlcNAc transferase- forms elongated chains) - CA cells release proteinases into ECM (eg. serine, cysteine, aspartate and metalloproteinases) - Matrix Metalloproteinases (MMP - zinc-dependent enzyme, degrades collagen, invades basement membrane and ECM - EMT or epithelial-to- mesenchymal transition - Mesenychymal cells have MORE ACTIN filaments -> more mobile, can metastasize Chemokines - released by immune cells, attracting leukocytes, causes inflammatory response to tumor cells - only 1 in 10,000 CA cells can fully colonize - CA have predilection to specific organs (eg. prostate cells TO bone) - there are genes that enhance andor suppress metastasis, - aging = decline immune responsiveness = more prone to CA. [7 immuNoTHERAPY- used in CA treatment due to speci, can be tagged as 4th major weapon versus CA (surgery, chemo, rad) Chronic inflammation -predisose to cancer, hgh ROS and can cause DNA damage Inflammation (via NF-kB and STAT 3/ signal transducer and activator of transcription 3) INFLAMMASOME - multiprotein complex that act as sensor of cellular damage, mediates inflammation OBESITY = low-grade inflammation, adipose -> important source of proinflammatory cytokines -Caloric restriction - shown to inhibit tumorigenesis, TUMOR BIOMARKERS - eg. elevated Calcium levels, - can occur in other conditions (PSA in prostitis, BPH) - CEA (carcinoembryonic antigen) - high in smokers, colitis and cirrhosis [not use0 as PRIMARY clgancsis of Cancer -driver mutations -> can cause cancer “passenger mulations -> accelerates cancer IMATINIB - inhibits Tyrosine Kinase, decreasing certain growth factors MABS - used in treatment of some neoplastic cell (IIIT TAMOXIFEN - used in breast CA ins estogenactiyBIOCHEM FINAL END TERMS! BBG Cancer CHEMOPREVENTION - use of drugs to prevent CA development FINASTERIDE - inhibits 5A reductase, no DHT is fromed from Testosterone ASPIRIN - reduces colon cancer 10BIOCHEM FINAL END TERMS! BBG FAG FATCC 10 major functions of blood }. Hormone Transport/ Regulation of Metabolism 9. Transport of Metabolites (0. Coagulation 3 Groups of proteins in plasma (based on relative solubilities o.g. ethano/AISo4) a. Fibrinogen b. Albumin . Globulins 5 salt-soluble proteins soparated by cellulose acetate and y-globulins 3 characteristices of plasma proteins a. Rich in disulfide bonds b. contain bound carbohydrates (glycoproteins) 6. lipid containing (lipoproteins) Starling Forces a. Osmotic pressure (oncotic pressure) - 25mmHg b. Interstitialissue pressure - ImmHg ©. Arterial Hydrostatic pressure - 37mmHg d. Venous Hydrostatic pressure - 17mmHg Total Arterial Pressure = 37-1-25 = 11mmHg Towards tissue (+) Total Venous Pressure = 17-1-25 mmhg Toward circulation (-) - if ow plasma proteins in blood, fluid stays in tissues and accumulates in extravascular space: Plasma Protein Synthesis + roughly 70-80% of PP synthesized in the liver + includes albumin, fibrinogen, transferrin, complement and coagulation cascades, 1. Respiration Oxygen/Co2 exchange bet. lungs and tissues 2. Nutrition 3. Excretion metabolic waste to kidneys, lungs, skin and intestines 4. Acid-Base balance 6. Water balance exchanges bel. circulating fluid and tissue fluid 6. Body Temp regulation distribution of body heat 7. Defense against infection Via WBC and antibodies 8. 9. 1 EDEMA, Nice to knows ~ human plasma protein range (7-7.5g/dL) -foritn is not classified as a PP - PP (transcortin, tansthyretin (binds with t4 and retinol)) PP IGGBIOCHEM FINAL END TERMS! BBG CHAT! 2 Plasma Proteins NOT Produced in the liver 1. von Willebrand Factor - made in vascular endothelium, 2. y-globulins - made by lymphocytes - most PP are N- or O- linked covalently modified EXCEPT albumin = loss of terminal sialic acid residue: clearance accelerates plasma glycoprot ‘SECRETORY PROTEINS Pathway: RER> SER> GA> Secretory vesicles Needs: Signal sequence, Signal recognition particle (SRP), and Signal Peptidase (cleaves of the leader sequence) - proteins are subjected to various post translational modifications Protein Polymorphism Polymorphism - a MENDELIAN or MONOGENIC trait with at /east 2 phenotypes, neither are rare example: ABO blood group substances PP with polymorphisms: a-antitrypsin, haptoglobin, transferrin, ceruloplasmin and immunoglobulin PP and Half Lif Half life = time for 50% of molecule to be degraded or cleared from blood Albumin = 20 days, Haptoglobin = 5 days Tum over - replace old proteins with new ones, should remain constant Steady State - constant process of synthesis and clearance = some diseases reduce PP half life, ex. Crohn disease/regional ieitis - PP lost in bowel via inflammed intestinal mucosa Protein-losing gastroenteropathy - condition where albumin halt life is as little as 1 day only Albumin = liver makes 12g per day = 25% of total hepatic protein synthesis - 50% of its secreted protein + about 40% of albumin is in plasma, accounting for 3/5 of total plasma protein by weight - remaining plasma is in extracellular space - contributes 75-80% of osmotic pressure due to low molecular mass and high concentration + secreted as a preprotein = mature albumin is a SINGLE polypeptide chain with 585 amino acids, with 3 functional domains - has ellipsoidal conformation stabilized by 17 intrachain disulfide bonds Major role of albumin - binding and transport of ligands including Free fatty acids (FFA), Calcium, Steroid hormones, Bilirubin, Copper and Tryptophan also binds drugs incuding PP IGGBIOCHEM FINAL END TERMS! BBG CHA-FA m cccs sulfonamides, Pen G, dicumarol and aspirin - also used in treatment of burns and hemmorhagie shock * Analbuminemia - plasma completely devoid of albumin, displays only moderate edema Liver disease causes a) decreased albumin synthesis b) decreased albumin-globulin ratio Acute Phase proteins/Inflammation ‘Acute phase proteins - plays role in inflammation includes: a. CRP (C-reactive protein’ reacts with C polysaccharide of pneumococci) - stimulates the complement pathway b. at-antiproteinase/ at-antitrypsin > neutralizes proteases released during acute inflammation ©. haptoglobin d. fibrinogen e. at-acid glycoprotein - APP increases 50% to 1000x during CHRONIC inflammatory states and in CANCER, Interleukin-t (IL-1) > principal stimulator of APP synthesis by liver IL-6, also plays a role in APP synthesis CRP - used as biomarker of tissue injury, infection and inflammation Cytokines - small proteins that facilitate cell to cell communication, includes inteferons, interleukins and TNFs (tumor necrosis factors) NFkB (Nuclear Factor kappa 8) - primary target of IL1 and IL6 NFkB regulates transcription of the following a. cytokines: b. chemokines . growth factors d_ coll adhesion molecules NFKE is normally inactive (IkBa), phosphorylated when active, translocates to NUCLEUS and stimulates transcription Haptoglobin/RBC normal RBC lifespan is 120 days - damaged R&C phagocytosed by RES (reticuloendothelial system) macrophages in spleen and liver = 200 billion catabolized daily Hemoglobin -> Biliverdi (via Heme oxygenase) + Iron and CO NRAMP!1 (Natural resistance-Associated protein 1) - exports iron out from phagocytotic vessels, similar to DMT1 (divalent metal transporter) Ferroportin - transmembrane protein that secretes iron into circulation, central role in iron absorption in intestine and secretion from macrophages Ferrous Iron (Fe2) —> Ferric Iron (Fe3) via ferroxidase ceruloplasmin, [Fenton Reaction] Ceruloplasmin - Copper containing plasma enzyme, from liver Fe3 is then bound to Ferritin in blood + dally iron absorption needed via intestine = 1-2mg/d PP IGGBIOCHEM FINAL END TERMS! BBG PP IGG 10% of Hgb escapes into circulation-> very small @ 64kDA > passes thru tubles> can damage kidneys Haptogtobin - plasma glycoprotein that binds with extracorpuscular Hgb, forming a tight noncovalent complex (Hb-Hp) Heme only binding PP a. B1-globulin b. hemopexin c. albumin (binds ferric hemelmetheme) -> hemopexin (transfered to) In hemolytic anemia, haptoglobin is low haptoglobin-related protein (HRP) is high in cancer ron - majority of Iron is in ferritin Hemoglobin (2500mg) + ron is found in many human proteins including Hgb, myoglobin, cp450 enzymes, ETC enzymes, ribonucleotide reductase + ton is highly conserved in the body normal loss per day is 1-1.5mg/day -fotal iron in body is 3-4g + females have higher iron losses due to menstruation Iron is absorbed in its free, ferrous (fe2+) or as heme by enterocytes non heme is also absorbed in proximal duodenum Steps in Iron absorption ( see p 632) 1. Ferric iron -> Ferrous iron via Deytb (duodenal cytochrome b) 2. Ferrous iron enters apical enterocyte via OMT 1 (divalent metal transporter 1) 3. Some Ferrous iron is stored in Ferritin (post conversion to Ferric by ceruloplasmin) 4. some Ferrous iron passes basolateral membrane via ferroportin 5. Hephaestin converts Ferrous iron to ferric iron 6. Ferric ron is bount to transferrin DMT - is non specific divalent transporter, transports Mn, Co, Zn, Cu and Pb Reducing agents like Vitamin C, converts ferric iron to ferrous Ferroportin- iron exporter protein Hephaestin - copper contaning ferroxidase, converts ferrous to ferric iron human body can store up to 1g of iron, most of it bound to ferritin, Forritin has 2 subunits a. Hssubunit > posseses ferroxidase activity, needed for iron loading