Biochem 3rd Edition

Jd 3rd edition 94 By 95 2006.6 / 2006.7 / 2006.12 USMLEmade ridiculously simple

I. A. 20 -- (G)AV-LI -- five FYW -- EQ DN-EQ -- LAH (OH) --STY --MC

( 108.7)

* * * * * * * * * *

Glycine Alanine Valine Leucine Isoleucine Phenylalanine Tyrosine Tryptophan Aspartic acid [Asparagine] Glutamic acid [Glutamine] Histidine Lysine Arginine Serine Threonine Methionine Cysteine Proline

Gly Ala Val Leu Ile Phe Tyr Trp Asp Asn Glu Gln His Lys Arg Ser Thr Met Cys Pro

G A V L I F Y W D N E Q H K R S T M C P

R= -H () -CH3 -C(C)-C -C-C(C)-C -C(C)-C-C -C-[C6H5] -C-[C6H4]-OH -C-[indole] -C-COOH -C-CONH2 -C-C-COOH -C-C-CONH2 -C-[imidazole] -C-C-C-C-NH2 -C-C-C-[guanidine] -C-OH -C(OH)-C -C-C-S-C -C-SH (imino acid)

P/N N N* N* N* N* P N* P P P P P* P* P* P P* N* P N

*

1. 8 R ()S (Met)7 OHSHHC=O(Asn, Gln) 3 (+1)LAH ( Lys, Arg, His) * pH 7 2 (-1)DE ( Asp, Glu) 2. Trp (indole)Arg (guanidine)His (imidazole) 3. Alanine(+H3N-CH(CH3)-COO-) HFWYHigh Frequency Wave Y 240nm UV Try pKa 7 HispKa=6RBC LAH (KRH)AsnGlnTrp Cysteine=Cys+Cys ()Hydroxy-Proline Proline

B. ((FT VW MILK(fetal VW))) Phe(F), Thr(T), Val(V), Trp(W), Met(M), Ile(I), Leu(L), Lys(K) C. (LAH )Arg, His ((ArgH)) D. Glutathione = Glu + Cys +Gly [Gluta-thi-one, Gluta Glu, Thi S Cys, One aa=Gly]

E. Cysteine MethionineSerine F. Creatinine GlyArgMet

G. N-glycosidic linkAsp O-glycosidic linkSerineThreonine H. peptide 1. Fully cleavage6N HCL ( Val-ValVal-IleIle-Ile ) 2. Partial cleavage!! Trypsin Chymotrypsin Pepsin CNBr Carboxylpeptidase Aminopeptidase Arg, Lys(C) Tyr, Phe, Tyr (C) Tyr, Phe, Tyr (N) Met(C) C N KR(C) FYW(C) FYW(N) M(C)

3. SDS-PAGE: 4. 5. DIPF(Di-isopropylfluophosphate) Chymotrypsin Ser-OH I. Bohr effectH+, T, CO2, 2,3 DPG 1. (H+, T, CO2) Hb O2 () J. 1. Glycogenic aa 14 TCA cycle 2. Ketogenic aa LeuLys WK-L P.727 acetylCoA/acetoacetate 3. Mixed aa FYW+IKIF-Y P.727 1. pH7.0 pentapeptideAla-Asp-Leu-Glu-Lys (netdischarge) a.-1 b.0 c.-2 d.1 (94 192 1 so) 2. Indole-3-aceticacid a.Arginie b.Histine c.Tryptophan d.Phenylalanine (95 1)

K. Amino acid () Tyrosine Tryptophan Methionine DOPAdopamineEpiNE VMA 5-HTNiacin ( 3D ) 5-HIAA (1) SAM (2) HomocysteineCysteine ( Serine) (3) Creatinine ( GlyArg) (4) polypeptide (AUG) Histamine GABA Gly + Succinyl-CoA ALA Porphobilinogen (2 ALA ) Uroporphyrinogen (4 Porphobilinogen) UroporphyrinCoproporphyrin Protoporphyrinogen Protoporphyrin Heme (1) Glycine conjugates

Histidine Glutamine Prophyrin

Glycine

(2) (3) (4) (5)

Creatinine (GlyArgMet) Glutathione (GlyCysGlu) Heme (Succinyl-CoAGly) Purine (GlyAsnGlnCO2-FH4)

II. A. Glutamine 1. NH4+ Alanine Glutamine Valine Serine 2. -KG + NH4+ GlutamateGlutamate + NH4+ Glutamine + 3. Pyruvate + NH4 (GPT = ALT) Alanine Alanine 4. Oxaloacetate + NH4+ (GOP = AST) AspartateAspartate + NH4+ Asparagine B. Urea 1. CO2 + NH4+ + Asp + 2H2O + 3ATP CO(NH2)2 + Fumarate a. TCA cycle : OAA + NH4+ + Asp Arginino-succinate b. Urea cycle: 1. Arginino-succinate (Arginino-succinatelyse)Arginine + Fumarate [TCA/urea cycle]

2. Arginine (Arginase)Urea + Ornithine [ urea ] 3. Ornithine (Ornithine transcarbamylase)Citrulline [] 2. Urea cycle 6 aa5 4 3 ATP 3. 6 aa GlutamateOrnithineCitrullineAspartateArginineArginosuccinate

C. N Carbamonyl phosphate synthase (CPS) CPS1 CPS2 1. Transamination (1) - -KG Urea cycle Thymidine De novo (2) ASTALT N NH Glutamine amide (3) Pyridoxal phosphate Biotin () () 2. Oxidative deamination (1) D-amino acid oxidase (2) Glutamate dehydrogenation (FAD) (NAD+NADP+)3

III. A. Michaelis- Menten 1. Vmax/V = Km/[s] +1, Km = K-1+K2/K1 2. V = 1/2Vmax Km = [s] B. Lineweaver-Burk ---Michaelis- Menten C. KTV (K/V ) 1.K Kmm = (Km/Vmax) 2.Vmaxm 3.VK under m Vmax (non-) (un-) X = X Km X m X

m = (Km/Vmax)

( X )

IV. A. Thiamine, Vit B1Thiamin pyrophosphate(TPP)= , 1. (Decarboxylation) (Transketolase) a. -KG Succinyl-CoA -KG dehydrogenase complex b. Pyruvate Acetyl-CoA pyruvate dehydrogenase complex (5 B B B B lipoid1 2 3 5

acid)

c. Pentose Phosphate Pathway Transketplase 2. a. b. Wernickes encephalopathy () / Korsakoff () B. Riboflavin, Vit B2FMN, FAD+H2FADH2 1. 2. FAD NAD ribose CoA

C. Niacin & Nicotinamide, Vit B3NADP, NAD++H-NADH (60mg Trp 1mg Niacin) 1. 2. Pellagra: 3D (dermatitis, dementia, diarrhea) D. Panthothenic acid, VitB5 CoA

1. (Acetylation) TCA cycle-oxidation E. Pyridoxine, Vit B6Pridoxal phosphate 1. glycogen phosphorylation 2. TB INH Vit B6 F. Cobalamine, Vit B12 Homocysteine (Methionine synthase) Methionine G. Folic acid Histidine, PheTyr H. Biotin 1. Carboxylation() 2. [: B1, Biotin] 3. Biotin Gluconeogenesis Urea cycle Fatty acid F.A. Pyruvate OAA (Pyruvate carboxylase) ATPCO2NH3 Carbomyl phosphate (CPS-1) Acetyl-CoA Malonyl-CoA (Acetyl-CoA carboxylase) Propionyl-CoA Methylmalonyl-CoA Succinyl-CoA biotin Vit. B12

I. Retinol, Vit A 1. 2. 3. all-trans retinoid ---APL 4. () 5. J. Vit C, Ascorbic acid, Ascorbate 1. collagen proline (hydroxylation) 2. dehydroascorbic acid K. Vit D 1, 25-Dihydroxycholecalciferol ((1, 25-(OH)2-D3)) 1. rickets and osteomalcia ( rickets osteomalacia ) L. Vit E, Topopherol free radical M. Succinate 1. (ribose)? a.CoA Choline b.NAD c.FAD V. FAD (94- 1) d.thiamine pyrophosphate

A. NADH PyruvateLipoateFpNADFMNQ Cyt bCyt C1CytCCyt aa3O2H2O 1. G3P shuttle (,)2ATP (FAD FADH2) -KG 2. Malate shuttle() 3ATP (NAD NADH) complex 1 complex 2 complex 3 complex 4 ( Cu) FMN-FeS FAD-FeS Cyt b-Cyt C1-FeS Cyt aa3-Cu

(-)malonateCarboxinTTFA

Rotenone Piericidine A Amobarbital

Antimycin A Dimercaprol

CO,CN- H2S

B. mole H+ 3 mole ATP 1. FMN-FeS NADH DeH ( FMN) 2. Cyt b-Cyt C1 Cyt DeH 3. Cyt aa3 Cyt oxidase C. H2SCOCN Dinitrophenol (DNP, Uncoupling agent) [phen=] Oligomycin ( H+) D. Ex. Glucose 6CO2 1*Glucose (6C) 2*Pyruvate (3C) 2*Acetyl-CoA (2C) +2*CO2 (1C) 4*CO2 (1C) +2*CO2 (1C) All 2ATP, 2NADH 2*1 NADH 2*3 NADH1FADH21GTP 8 ATP 2*3 or 2*2 ATP 2*12ATP 38 or 36ATP

VI. A. 1. Maltose (1, 4) Sucrose (1, 2) Lactose (1, 4)Cellulose (1, 4) Glu + Glu Glu + Fru Glu + Gal 2. (1, 4) (1, 4) (1, 6)Glycogen (1, 4) (1, 6) Inulin(1, 2)ChitinN-acetyl-D-glycosamine (1, 4) B. Glycolysis(GlcPyruvate) 1. 2ATP+2NADH 2+2*3=8ATPATP ATP Aldolase A (PGAL=G3P)

G(HK/GK)G6PF6P(PFK-I, )F1,6BPPGAL /DHAP2 PGAL ( *2) PGAL1,3BPG(PGK)3PG2PGPEP(PK, )Pyruvate

NADH ATP ATP Ps. Dihydroacetone phosphate(DHAP),Glyceraldehyde-3-P(PGAL),1,3bisphosphoglycerate(1,3BPG),3phosphoglycerate(3PG),Phosphoenopyruvte(PEP)

2. kinase 4 ATP 3 ? GG6P F6PF1,6BP 1,3BPG3PG PEPPyruvate 4 Kinase (HK/GK) (PFK-I,) (PGK,) (PK) ATP 1ATP ATP 1ATP 2ATP 2ATP G6P-HK ATP;Citrate +

AMPF2,6BP

F1,6BP ATPAla

F1,6BPPGAL /DHAP (Aldolase) PGAL1,3BPG (GAPDeH) G3P 2NADH a. Hexokinase vs Glucokinase 1. HK G6P 2. GK Km ( Glucose) Capacity(Vmax) b. Glycerol (Glycerol kinase)Glyerol-3-P + ATPDHAP+ADP+Pi Hexokinase () G-6-P Glucokinase Liver-cell insulin

Km Vm

C. Pyruvate oxidative decarboxylasePyruvate (PDeH)acetyl-CoA 1. 1NADH=3ATP Pyruvate + CoA + NAD+(PDeH)Acetyl-CoA + CO2 + NADH + H+ 2. Pyruvate Dehydrogenase (PDeH) =E1Pyruvate decarboxylase E2Dihydrolipoyl transacetylase E3Dihydrolipoyl dehydrogenase a. ATP ( E1 Ser-OH ), Acetly-CoA, NADH, Glucogan b. () NAD+,ADP, CA++ 3. Coenzyme: TPP (B1 E1 ), FAD(B2), NAD(B3), CoA(B5), Lipoid acid

a. B1Pyruvate Neurologic defect

D. TCA cycle1. Citrate

(1) TCA cycle (2) Acetyl-CoA (3) (4) Glycolysis keyenzyme PFK-1 keyenzyme Acetyl-CoACarboxylase

TCA cycle keyenzyme (1) Citrate synthase (2) Isocitrate dehydrogenase (3) -KG dehydrogenase complex

2. a. I K SSM( K ) 1. SS==1 GTP1 FADH NADH 2. K CO2 (OAA Biotin ) Isocitrate (6C)-KG (5C) -KG Succinyl-CoA (4C) b. Isocitrate DeH -KG DeH Succinyl thiokinase Succinate DeH Malate DeH Mg++,Mn+++ CoA GDP NADH (3ATP) NADH (3ATP) GTP

FeS; OAA, Melonate- FAD (2ATP) NADH (3ATP)

()CitrateIsocitrate (IDeH)-KG (-KGDeH)Succinyl-CoA (STK) ()Succinate (SDeH)FumarateMalate (MDeH)OAA c. glucose CO2 H2O, 38 ATP[8+2*(3+12)] d. CitrateFatty acid, Ketone body, Cholesterol e. OAAPEPGlucose OAAAspartate f. Succinyl-CoA + GlyPorphyrinsHeme g. -KGGlutamate ++ Mg Mn++ a. Enolase 2-phosphoglycerate phosphenolpyruvate 1. Acetyl-CoA 12 ATP 2. Pyruvate 15 ATP 3. Glucose 38 ATP 4. Palmitate 129ATP

b. Pyruvate kinase PEP pyruvate c. Isocitrate dehydrogenase Isocitrate -KG E. (Glycogen) & Glycogen (Phosphorylase)G1PG6PGlc/Pyr GlcG6PG1P ( 1ATPADP) G1P+UTPUDP-Glc+Pi ( 1ADPAMP) UDP-Glc (Glycogen synthase)(Glycogen)n+1 2ATP 1-4 UDP-Glucose cAMP() Synthase Insulin cAMP

G1P ()cAMP Phosphorylase Epinephrine cAMP Glycogen Fatty acid UDP UDP-Glucose

Muscle Gluconeogenesis G-6-Pase Adipose Glycerol-3-P glycerol kinase

Malonyl-CoA ACP

( DHAP Glycerol)

F. (Gluconeogenesis) 1. LactatePyruvateGlycerol-keto acid ( Acetyl-CoA ) 2. 90% liver10% kidney ( muscle G6Pase) 3. Glycolysis 4 Glycolysis 3 () Glycolysis GG6P Hexokinase (HK) F6PF1,6BP () Phosphofructose-1 (PFK1) PEPPyruvate Pyruvate kinase (PK) Gluconeogenesis G6Pase F1,6BPase PEPCK (Cytosol ) Pyr carboxylase (Mito )

Ps.

Phospoenolpyruvate carboxykinase(PEPCK), Glucose/Fructose-6-phosphatase(G6Pase/ F6Pase)

4. 5. 6. 7. 8.

(2PyruvateGlucose) 6ATP G3P Glycolysis 1*2ATPGluconeogenesis G3P Glycolysis 2*2ATPGluconeogenesis 2*3ATP PyrOAA Malate mitochondria OAAPEP 2 Pyruvate + 4 ATP + 2 GTP + 2 NADH Glucose + 4 ADP + 2 GDP + 2 NAD+ + 6 Pi

G. (Pentose phosphate pathway, PPP) 1. NADPH

ribose 2. a. G6P + 2 NADP (G6P DeH)Ribose-5-P + CO2 + 2 NADPH b. Ribose-5-P F6P + G3P c. (Transketolase) C2 unit(Transaldolase) C3 unit 3. ATP NADPH ( G6P dehydrogenase) 4. NADPH : a. 60% G6P DeH(PPP)30% Malic enzyme10% Isocitrate DeH

H. Pyruvate & Cori cycleCori CycleLiver Glucose 2 NAD+ 2 NADH 6 ~P 2 Pyruvate 2 NADH + 2 NAD 2 Lactate Blood Muscle Glucose 2 NAD+ 2 NADH 2 ~P 2 Pyruvate 2 NADH + 2 NAD 2 Lactate

I. 1. Urea cycle Carbomoyl phosphate Ornithine Citrulline 2. TCA cycle Pyruvate 3. Fatty acid -oxidation (1) Carnitine (Acyl-CoA) (2) Acetyl-CoA + OAA citrate 4. NADH (1) Malate shuttleNADH (3ATP) (2) G-3-P shuttleFADH2 (2ATP) J. 1. Citric acid cycle porphyrin (95 2) a.oxaloacetate b.alpha-ketoglutarate c.citrate d.succinyl-CoA 2. cytosol mitochondria matrix (94 1) a.pentose phosphate pathway b.fatty acid synthesis c.gluconeogenesis d.citric acid cycle

VII. A. , Lenoleic acid, 18:2(9,12)

, Lenolenic acid, 18:3(9,12.15)B. () 1. a. Acetyl-CoA Pyruvate, -oxidation, Ketogenic aa (Leu, Lys) Acetyl-CoA + OAA Citrate b. Acetyl-CoA Citrate(Citrate lyase,1ATP)Acetyl-CoA c. 2 NADPH PPP 2. Cytosol a. 1ATPBiotin Carboxylation 1. Acetyl CoA + CO2 (Acetyl-CoA carboxylase, ACC) Malonyl-CoA 2. Acetyl-CoA carboxylase citrateinsulin palmitoyl-CoAmalonyl-CoAglucagonepinephrine b. Acyl carrier protein (ACP) 1. Malonyl-CoA + ACP Malonyl-ACP + CoA

c. b oxidation () 1. Malonyl-CoA + Acetyl-CoA + 2 NADPH 7 16:0 (Palmitic acid) C. () 2 Cmalonyl-CoA 1. Mitochondria NADPH a. 1ATP ER 1. Fatty acid + CoA Acyl-CoA b. FA Carnitine 1. Carnitine + Acyl-CoA (Carnitine palmitoly transerase, CPT-1) CarnitineAcyl-CoA 2. malonyl CoA c. -oxidation ( ) 1. Acyl-CoA (Acyl-CoA DeH)Enacyl-CoA+FADH2 Hydroxyenacyl CoA (HECoA DeH)(n-2) Acyl-CoA + Acetly CoA+ NADH 2. Acetly CoA + Propionyl CoA Propionyl CoA +CO2Succinyl CoA VitB12 2. 2n (N-1) b oxidation N Acetyl-CoA a. -oxidation 1 NADH1 FADH2 5ATP Acetyl-CoA TCA cycle 12 ATP b. -oxidation FADH2 -oxidation 3ATP 3. Palmitate() a. 16 C 8 Acetyl-CoA 7 (-oxidation) b. 7 NADPH7 FADH8 Acetyl-CoA 7*3 + 7*2 + 8*12 2=129 c. 2 FFA acyl-CoA 2 P palmitate 16C 129 ATP D. () = & 1. a. DM OAA Acetyl-CoA TCA cycle (ketone body) Acetyl-CoA b. ketone body BBB CoA transferase c. Hgb O2 () Kussmaul breathing ( ^_^)

2. Mitochondria (Ketone body: 3-hydroxybutyrate, acetoacetate, acetate) a. 3Acetyl-CoA (Thiolase, HMG-CoA synthase)HMG-CoA b. Hydroxy-methly-glutaryl-CoA (HMG-CoA lyase)Acetly CoA + Acetoacetate c. Acetoacetate + NADHD-3-hydroxybutyrate + NAD+ d. Acetoacetate / D-3-hydroxybutyrate Acetone + CO2 3. Mitochondria a. Acetoacetate + Succinyl-CoA (CoA transferase)Acetoacetate-CoA + Succinate HMG-CoA b. Acetoacetate-CoA (Thiolase)2 Acetyl-CoA Acetone c. ATP cholesterol

E. 1. Cytosol a. 3 Acetyl-CoAHMG-CoA b. HMG-CoA + 2NAPDH(HMG-CoA reductase)Mevalonate + 2NADP+ c. Mevalonate + 3ATPIsopentenyl pyrophosphate(IPP)+CO2 d. IPPGeranyl pyrophosphate(10C)Farnesyl pyrophosphate(15C)Squalene(30C)Cholesterol 2. HMG-CoA reductase Insulin Glucogan, Starvation F. ( Glycerol-3-phosphate Fatty acyl-CoA ) 1. Glycerol-3-phosphate (G-3-P) Glycerol phosphate dehydrogenase => DHAP + NADH+ + H+ L-G-3-P + NAD+ LiverGlycerol kinase => Glycerol + ATP L-G-3-P + NAD+ 2. G-3-P PA (Phosphatic acid = Diacylglycerol-3-phosphate) Glycerol-3-P + Fatty Acyl-S-CoA Monoacylglycerol-3-P + CoA-SH Monoacylglycerol-3-P + Fatty Acyl-S-CoA Diacylglycerol-3-P + CoA-SH 3.

G. 1. EICOSANOIDS 20C a. 1 PGE1, PGF1, TXA1 ()=Linoleic acid 3 b. 2 PGE2, PGF2, TXA2 =Arachidoic acid 4 c. 3 PGE3, PGF3, TXA3 =Eisocapentanoic 5 2. elongationdesaturation C 3. insulin lipogenesis hormone lipogenesis 4. Lipid a. Chylmicron (1) Chylomicron TG RemanantVLDL TG IDL b. VLDL (2) VLDL IDL TG LDL c. HDL (3) HDL LCAT d. TG ChylmicronVLDL e. Cholesterol esterfree cholesterol LDL f. formTG 5. Apoprotein A-I Lipoprotein HDL, Chylomicron + LCAT Apoprotei n C-I + LCAT

B-100 (E) B-48

IDL, LDL, VLDL Chylomicron

LDL receptor Chylomicron

C-II C-III

+ LPL(Liproprotein lipase) - LPL(Liproprotein lipase)

6. ACATcholesterol + fatty Acyl-CoA cholesterol ester LCAT HDL cholesterol liver 7. Lipase a. lipaseGI tract b. Lipoprotein lipase insulin TG TG Fibrate heparin c. Hormone sensitive lipase cAMP dependent protein kinase insulin TG H. 1. acetyl CoA carboxylase (committed step) (allosteric activator) a. palmitoyl CoA b. AMP c. NADPH d. citrate (95 2 ) 2. Fructose 1,6-biphosphatase (allosteric control) a. citrate b. F-2,6-BP c. AMP d. acetyl CoA (94 1 )

VIII. A. Nucleotide = Nucleoside( C1-N9 ) + 3 1. PPPRibose-5-P (PRPP synthase, -1ATP) PRPP (5phosphoribosyl1pyrophosphate)

2. (De novo)(salvage) a. de novo , PRPP b. salvage , PRPP

B. 1. (De novo) PRPP synthase key enzyme a. Ribose-5-P (PRPP synthase) PRPP (5phosphoribosyl-1pyrophosphate) b. PRPP+ AA IMP 1. Gly+Asp+Gln+CO2+Methenyl-FH4+Formyl-FH4+6PiIMP c. IMPGMP, AMP 1. IMP(, IMP DeH)XMP+GlnGMP; 2. IMP+Asp(, Adenylsuccinate synthase)AMPS(Adenylsuccinase)AMP d. GMP, AMPGTP, ATPRNA e. GDP, ADP (Ribonucleotide reductase)dGDP, dADPDNA f. 1. PRPP de novo pathway PRPP synthase

AMP, GMP, IMP 2. AMP,GMP,6MP IMPAMP, GMP ATP,GTP IMPAMP, GMP 2. a. AMP, IMP Inosine 1. AMP (,Pi,) Adenosine ( Adenosine deaminase) Inosine 2. GMP (,Pi) Guanosine b. Inosine, Guanosine Hypoxanthine, Guanine 1. Purine nucleoside phosphorylase c. Hypoxanthine, Guanine 1. Xanthine (Xanthine oxidase)Uric acid 2. d. 1. SCID (Severe combined immunodeficiency) RAG ADA Adenosine deaminase defiency i. Adenosine immature T-cell, B-cell apoptosis. (Harrison p 1942) 2. Allopurinol Xanthine oxidase 3. (salvage) HGPRT key enzyme a. Hypoxanthine/Guanine + PRPP(HGPRT)IMP/GMP (PRT=phoribosyltransferast) b. Adenine+PRPP(APRT)AMP c. 1. Lesch-Nyhan syndromeHGPRT Hypoxanthine, Guanine (3.a.)(2.c.1.)X-linked

C. 1. (De novo) a. Asp + Carbamoxyl phosphate (Gln+CO2)Ototic acid b. Ototic acid+ PRPPUMP RNA UMPUTP UTP+Gln(CTP synthase)CTP DNA UDP(1)dUDPdUMP(2)dTMP CDP(1)dCDP

1. dATP, dGTP, dCDP Ribonucleotide reductase 2. dTMP Thymidylate synthase i. Folate conenzyme Methylene THFH2 folate MTX HGPRT APRT TK ii. 5FUFdUMP 2. (salvage) a. Thymidine + PRPP(TK)TMP D. 1. SalvageGuanine HypoxanthineGMP IMPAdenineAMPThymidineTMP 2. De novoRNA MP (CTP )DNA DP (dTMP ) Purine AMP, GMP, IMP dADP, dGDP Pyrimidine UMP, CTP (dCDP), dTMP

RNA DNA E. 1. salvage pathway (95 2) a. b. de nono pathway c. adenosine kinase salvage pathway d. salvage pathway Inosine 5monophosphate hypoxanthine

IX. DNA, RNA

A. DNADNA (DNA )1. a. Leading strand: 5`3` b. Lagging strand: 5`3` (okazaki fragment) (1) Helicase ( Helicase + Primase = Primosome) (2) RNA polymerase (3) DNA polymerase III (4) Single strand binding (SSB) protein (5) DNA polymerase I ( gap) (6) DNA ligase ( nick) c. d. e. f. g. h. i. DNA polymerase I : 5`3` 5`3` DNA polymerase II : DNA polymerase III : 5`3`() Helicase : Primase : primer (RNA) Ligase : okazaki fragment Topoisomerase I and II : superhelix (formation of the replication fork) DNA polymerase I Lagging strand gap RNA primer Editingproof-reading DNA polymerase III leading strand () Proof-reading

5-3 polymerase 5-3 exonuclease 3-5 exonuclease

2. a. Telemerase, DNA Polymerase, Histone, Cell cycle b. (primer), (leading), (lagging), (mitochondria), (DNA repair)

B. DNARNA (Transcription ) RNA polymerase RNA polymerase :RooMaTe(r ,m ,t ) RNA polymerase I (Nucleolus) rRNA 5`3` RNA polymerase II (Nucleo plasma) mRNAsnRNA RNA polymerase III(Cytoplasma) tRNA5S rRNAsnRNA m RNA 5Capping Clipping 3poly-A tailsplicing Pribnow box(-25-30) Stem and loop, factor notecapping 7-methyl-guanosine triphosphate TATA box(-10,TATAAT), CAAT box (-75) enhancer CTD elongation Amatin RNA polymerase II( ), III( )

RNA polymerase (1) Core enzyme 4 5-3 RNA polymerase DNA promotor (2) Holoenzyme-factor + core enzyme-factor RNA polymerase DNA promotor

1.

a. (Operon): Regulatory gene(I) + Contol site(P,O) + Structural gene 1. (Promotor)Polymerase II, foot printing 2. (Operator) i. Repressor( Regulatory gene ) ii. Inducer( Ex. Allolactate, IPTG) Repressor Repressor 3. i. Trp operon ( =Attenuator )

C. 3. a. Transition AG TC (ex.AGTC...) b. Transversion 4. a. RifampicinStreptovaricin RNA polymerase initiation b. Actinomycin D DNA double helix DNA Guanine c. Tetracycline Aminoacyl-tRNA ribosome d. -Amantin RNA polymerase II ( II III) e. Puromycin Aminoacyl-tRNA elongation f. Nitrous acid adenineHypoxanthineCytosineUracilGuanineXanthine 5. Thymidine dimer a. Direct repairDNA photolyase b. NER (Nucleotide excision repair) excinuclease UvrABC complex c. BER (Base excision repair) DNA-N-glycosylase AP endonuclease 6. 53 NC 7. (codon) (anti-codon) tRNA 3UAC5 anti-codon = CAU!! mRNA5AUG3 codon = AUG 8. a. codonAUG (Metf-Met) (: August ) b. codonUAA, UAG, UGA 9. mRNA 3 codon (tRNA)wobble 10. 60S E(empty)P(peptyl)-A(amino)site mRNA 5AUG------------------------------------UAA 3 40S 11. a. DNA (:) b. RNA (: R) c. Protein (:CPR) d. PCRdenaturation95 C -annealing55 C -extension72 C DNA template, primer, Tag DNA polymerase( 72 C ), nucleotides B. 1. A site aminoacyl-tRNA amino group P site peptidyl-tRNA

a.carbonyl oxygen 1)

b.amide oxygen

c.amide nitrogen

d.carboynyl carbon (94

2. 5TGATCAAGC3 a. 5TCCGACTGC3 b. 5ACTAGTTCG3 c. 5GTTGATCAC3 d. 5ACATTCGCC3 (94 1)

X. () A. GSD (glycogen storage disease) 1. Type I von Gierkes dz () G6-PhosphataseG6Pglucose (X) Type II Pompes dz () lysosomal-glucosidase glucose (X) Type III Coris dz () debranching enzyme /G1P (X) Type IV Andersons dz branching enzymeamylose (or ) (X) Type VMcArdles dz () muscle phosphorylase Type VI Hers dz liver phosphorylase Type VII phosphofrutokinase(PFK) Type VIII liver phosphorylase kinase 2. 1-2-7 3-4 5-6-8 B. LSD (lysosomal storage disease) 1. a. Gauchers disease glucosyl ceramidaseglucosyl cerebroside() Niemann-Pick disease(sphingomyelinase)phosphoro-choline Tay-Sachs disease hexosaminidiase A (ganglioside) Fabrys disease lysosomal galactosidase AX-linked Karbbs disease b. Gau () -NP-TS () -Fa () 2. type I Hurlers dz(DS/HS)II Hunters dz(DS/HS)III Sanfilippo dz(HS)IV Morquio(KS)VI Maroteaux-Lamy(DS)VII Sly(DS/HS)DS=dermatin sulfateHS=heparin sulfateKS=keratin sulfate 3. Pompes disease C.

1. (FWY)PKU pheylalanine hydroylase Alkaptonuria homogenisate oxidase Albinism tyrosinase 2. (VLI)maple syrup urine syndrome -keto acid dehydrogenase VLI VLI 3. (MC)homocysteinuriaXcystathionine cystathionine synthasevit B6 homocysteinuria variantXMet vit B12 folate D. Purine and pyrimidine metabolism 1. purineLesch-Nyhan syndrom ADA deficiency 2. pyrimidine a. Xeroderma pigmentosum DNA b. Ataxia telangiectasia & Faconis anemia E. () Disorder Familial hypercholesterolemia(FH) Comments Defective LDL receptor

CAD risk

type IIa Familial combinded hyperlipidemia DMtype (FCH) IIb Familial dysbetaplipoproteinemia Apo E2, ARtype III No risk of CAD Familial hyperchylomicronemia Familial hypertriglyceridemia Type V hyperlipidemia LDL type I VLDL type IV

F. ornithine transcarbamoylaseX-linked G. Vitamin () 1. vit B6Trp niacin Xanthurenate() 2. vit B12 methylmalonate 3. folate FIGlu (formiminoglutamate) H. 1. Tay-Sachs (lysosomal storage disease) a.beta-N-acetylhexosaminidiase b.HMG-CoA reductase c.alpha-1,4-glucosidase d.amylo-1,6-glucosidase (95 2)