BIOCHEMISTRY REFERENCE MANUAL

BIOCHEMISTRY REFERENCE MANUALIntroduction -------------------------------------------------------------------------------- 1Amino acids ------------------------------------------------------------------------------- 2Citric acid cycle--------------------------------------------------------------------------- 3Glycolysis ---------------------------------------------------------------------------------- 4Pentose phosphate pathway---------------------------------------------------------- 5Urea cycle---------------------------------------------------------------------------------- 6Fatty acid catabolism ------------------------------------------------------------------- 7Fatty acid synthesis --------------------------------------------------------------------- 8Triacylglycerol and phospholipids synthesis -------------------------------------- 9Cholesterol and ketone body synthesis -------------------------------------------- 10Porphyrin synthesis---------------------------------------------------------------------- 11Purine synthesis-------------------------------------------------------------------------- 12Pyrimidine synthesis -------------------------------------------------------------------- 13Purine catabolism------------------------------------------------------------------------ 14Pyrimidine catabolism ------------------------------------------------------------------ 15The standard genetic code ------------------------------------------------------------ 16

IntroductionNUS policy is to reduce excessive memorisation on the part of students andsubstitute for this the development of thinking skills. To this end theBiochemistry Department offers a compendium of basic metabolic pathwayswhich will no longer need to be memorised as such but which may berequired to answer problem or concept based questions, and thus will bemade available during tests and examinations.The metabolic pathways herein are presented in a unidirectional manner, thatis the products shown are those which are thought of as the normal results ofthose pathways. Reversibility of individual reactions, compartmentalisation,the names of enzymes, cofactors, and the participation of phosphate, carbondioxide, water and all the low molecular weight participants incidental to thesubstantive carbon flow have been omitted. It follows that some knowledge ofthese aspects is still required.The book must not be written on, marked or defaced in any way. As for allexaminations and tests, you must write only on the blank scripts provided.August 2002

Amino acidsCOO-COO-COO-COO-COO-COO-H 3 + NCHH 3 + NCHH 3 + NCHH 3 + NCHH 3 + NCHH 3 + NCHHGlycineCH 3AlanineCHCH 3 CH 3ValineCH 2CH 2CH 2C CHNHH 2 + NCOO-3COO-CH 3H + 3 N C H H + 3 N C HCH 2 H C CH 3CHCHCH 2CH 3LeucineIsoleucineCOO-HCCH 2H 2 C CH 2ProlinePhenylalanineOHTyrosineTryptophanCOO-COO-COO-H 3 + NCHH 3 + NCHH 3 + NCHCH 2CH 2CH 2CH 2CH 2CNHCH 2CH 2CHCOO-H + 3 N C HCH 2 OHSerineCOO-H + 3 N C HH C OHCH 3ThreonineCOO-H + 3 N C HCH 2SHCysteineCH 2+ NH 3LysineNHC N + H 2NH 2ArginineC NHHistidineCOO-COO-COO-H 3 + NCHH 3 + NCHH 3 + NCHCOO-COO-CH 2CH 2CH 2H 3 + NCHH 3 + NCHCH 2SCH 3MethionineCH 2 N OAsparagineCH 2CH 2 N OGlutamineCH 2COO-AspartateCH 2CH 2COO-Glutamate

AcetylCoAOCH 3 C SCoACoASHCoenzyme ACOO-COCH 2Cis-aconitateCOO-HO C HCH 2COO-L-malateCOO-Citric acid cycleCOO-CH 2HO C COO-COO-CH 2OxaloacetateCOO-CitrateCOO-CH 2C COO-CHCOO-COO-HCCH 2CHCOO-COO-COO-HCCOO-COO-CH 2CH 2CH 2HOCHFumarateCH 2CH 2COO-CH 2S CoACOO-COCOIsocitrateSuccinateCOO-SuccinylCoAα-ketoglutarate

CHOHCOHHOCHHCOHHCOHCH 2 OHGlucoseCHOHCOHHOCHHCOHHCOHCH 2 OPO 3=Glucose6-phosphateCH 2 OHCHOCHOHCOHHCOHCH 2 OPO 3=CH 2 OPO 3=CHOCHOHCOHFructose6-phosphateFructose 1, 6-bisphosphateGlycolysisHCOHCH 2 OPO 3=CH 2 OPO 3=CHOC OCH 2 OHHCOHCH 2 OPO 3=Glyceraldehyde3-phosphateDihydroxyacetone phosphateO=COPO 3HCOH1,3 BisphosphoglycerateCH 2 OPO 3=COO-HCOHCH 2 OPO 3=3-PhosphoglycerateCOO-COO-C OCH 3COO-C OPO 3=CH 2HCOPO 3=CH 2 OH2-PhosphoglyceratePyruvatePhosphoenolpyruvate

CHOHCOHHOCHGlucose6-phosphateHCOHHCOHPentose phosphate pathwayCH 2 OPO 3=OCOO-CH 2 OHCHCOHHCOHHOCHCOHCOHRibulose5-phosphateHOCHOHCOHHCOHHCOHHCOHCH 2 OPO 3=HCCH 2 OPO 3=CH 2 OPO 3=6-Phosphoglucono--lactone δ6-PhosphogluconateXylulose5-phosphateCH 2 OHCOHOCHHCOHCHOHCOHHCOHHCOHRibose5-phosphateCH 2 OPO 3=CH 2 OPO 3=Glyceraldehyde3-phosphateCHOHCOHCH 2 OHCOGlyceraldehyde3-phosphateCHOHCOHCH 2 OPO 3=CH 2 OHCO=CH 2 OPO 3CHOHCOHHOCHHCOHHCOHHCOHCH 2 OPO 3=CH 2 OHSedoheptulose7-phosphateHOCHHCOHCOFructose6-phosphateHCOHHCOH=CH 2 OPO 3CH 2 OPO 3=Erythrose4-phosphateHOCHHCOHHCOHFructose6-phosphateCH 2 OPO 3=

Urea cycleO--O P O CONH 2ONH 2C ONHH 3 + NCOO-CH 2AspartateCH COO-CarbamoylphosphateH 3 + N(CH 2 ) 3CHCOO-CitrullineNH 2+COO-CH 2NH 3+C NH CH(CH 2 ) 3OrnithineArgininosuccinateNHCOO-H 3 + NCHCOO-(CH 2 ) 3H 3 + NCHCOO-NH 2+UreaNH 2C ONH 2H 3 + NCOO-CHCHCOO-FumarateC NH 2NH(CH 2 ) 3CH COO-Arginine

Fatty acid catabolismFatty acidFatty acyl-CoAAcyl-carnitineR.CH 2 CH 2 COO-R.CH 2 CH 2 COR.CH 2 CH 2 CO.OS CoACH 2 COO-CHCH + 2 N(CHOH3 (CH 3 )+ NCH 2 CH.CH 2 COO-Carnitine3 ) 3- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -COO-CH 2Acyl-carnitineR.CH 2 CH 2 CO.OCHCH 2 + N(CH 3 ) 3Fatty acyl-CoAR.CH 2 CH 2 CO S CoAtrans-! 2 -Enoyl-CoAR.CH CH.CO S CoAOH3-L-Hydroxyacyl-CoAR.CH.CH 2 CO S CoAβ-Ketoacyl-CoAR.CO.CH 2 CO S CoAFatty acyl-CoAR.CO S CoA + CH 3 CO S CoAAcetyl-CoA

Fatty acid synthesisCH 3 CO S CoAAcetyl-CoAAcetyl-CoACH 3 CO S CoA-OOCCH 2 CO S CoAMalonyl-CoACH 3 CO S EnAcetyl-En-OOCCH 2 CO S ACPMalonyl-ACPCH 3 COCH 2 CO S ACPAcetoacetyl-ACPCH 3 CHOH.CH 2 CO S ACPD- β-Hydroxybutyryl-ACPCH 3 CH CHCO S ACPα , β-trans-Butenoyl-ACPCH 3 CH 2 CH 2 CO S ACPButyryl-ACP

Triacylglycerol and phospholipid synthesisCH 2 OHCHOHCH 2 OHCHOHGlycerol-3-phosphateCH 2 OHGlycerolLysophosphatidicacidR'CO S CoAFatty acyl-CoAPhosphatidicacidR''CO S CoA=CH 2 OPO 3CH 2 OCORCHOH=CH 2 OPO 3CH 2 OCORCHOCOR'=CH 2 OPO 3R.CO S CoAFatty acyl-CoA3 (CH 3 )+ NCH 2 CH 2 OHCholineCTP3 (CH 3 )+ NCH 2 CH 2 OCDPCDP-cholineFatty acyl-CoACH 2 OCORCHOCOR'CH 2 OCOR''CH 2 OCORCHOCOR'O-TriacylglycerolCH 2 .OPOCH 2 CH 2 N + (CH 3 ) 3OPhosphatidylcholine

CH 3 CO S CoAAcetyl-CoACH 3 CO.CH 2 CO S CoACholesterol and ketonebody synthesisAcetoacetyl-CoACH 3-OOC.CH 2 C .CH 2 CO S CoACH 3 COCH 2 COO-AcetoacetateOHHMG-CoACH 3-OOC.CH 2 C .CH 2 CH 2 OHCH 3 COCH 3AcetoneCH 3 CHOHCH 2 COO-D- β-HydroxybutyrateOHMevalonateCH 3OC CHCH 2CH 22 O P O=PO 3IsopentenylpyrophosphateO-SqualeneIanosterolHOCholesterolHO

Porphyrin synthesisSuccinyl CoACOO-COO-COO-COO-CH 2CH 2CH 2CH 2CH 2CH 2COO-CH 2CH 2CH 2Porphobilinogen(PBG)COCOCOCCS CoA++CH 2 NH 3COO-HC NH 3+COO-(intermediate)COO-2 HC NH 3 + C CHCH N2Hδ -aminolevulinicacid+NH 3(ALA)GlycineCOO-COO-CH 2CH 2CCCH 2CH 2 CH 2Protoporphyrin IX-OOCCH 2 CCNHCNHCH 2CH 2CCHNCHCH 2 COO-MPCHNCHMNHHNVCHNCHMV-OOCCH 2 CH 2 CCCH 2CN HCCH 2CC CH CH 2 CH 2 COO-C CH 2COO-Uroporphyrinogen IIIPM

=CH 2 OPO 3O HH HH OHPurine synthesis=CH 2 OPO 3O HOH HH O POGlutaminePO 3=CH 2 OPO 3=HHO NH 2HHGlycineONH 3+CH 2CO-NH 3+CH 2O C=3 OPOC H 2 NHOH HH HFormylglycinamideribonucleotideO2 HC CHNNHCHOOHOHRibose-5-phosphateOHOHO-5-PhosphoribosylpyrophosphateCOO-CHNH 3+OHOHPhosphoribosyl-amineOHOHGlycinamideribonucleotideR5PCOO-COO-CH-OOCHC2 HC-OOCNHOC2 HNCCSAICARNNCHR5PCH 2-OO2 HN CNNRCH5P2 HNHCCNNCHR5PHN2 HC CN HNHRCHO5PCHCOO-FumarateOC2 HN 2 HNCCAICARNCHNR 5POC2 HN OHCNHCCNCHNR 5PHNHCOCNCCNNCHR5PInosine monophosphate(IMP)

Pyrimidine synthesisOO2 HNCO=O PO 3CarbamoylphosphateO+AspartateCarbamoylaspartateOHNCOCNHOCH 2COO--O CCH2 HN CH 222 HN C CHCH COO- O N COO-HCHCOO-Dihydroorotate(DHO)HNHNHNONRUMP5PCOO-O N COO-R 5POrotidine-5-monophosphate(OMP)ONHOrotate

NH 2NNNN=3 OPO 2 HCOC CHH HHOH OHAMPPurine catabolismOHNONGMPHNNNNNN=3 OPO 2 HCOC CHH HHIMP2 HN C=3 OPO 2 HCOC CHH HHCOH OHOH OHXanthineHNONHNONHNONNNHONHNH2 HN NNHHypoxanthineGuanineHNOHNOONHNHUrate

NH 2Pyrimidine catabolismNONHOCytosineHNOONHCH 3ThymineHNONHUracilHNOONHCH 3OCOO-OHNNHO2HNCNHCH 2CH 2O2HNCCOO- CH 3CHCH 2NH+3 HN CH 2 CH 2 COO-β -Alanine+3 HN CH 2 CH.COO-CH 3β -Aminoisobutyric acid

The standard genetic codeUUU Phe UCU Ser UAU Tyr UGU CysUUC Phe UCC Ser UAC Tyr UGC CysUUA Leu UCA Ser UAA Stop UGA StopUUG Leu UCG Ser UAG Stop UGG TrpCUU Leu CCU Pro CAU His CGU ArgCUC Leu CCC Pro CAC His CGC ArgCUA Leu CCA Pro CAA Gln CGA ArgCUG Leu CCG Pro CAG Gln CGG ArgAUU Ile ACU Thr AAU Asn AGU SerAUC Ile ACC Thr AAC Asn AGC SerAUA Ile ACA Thr AAA Lys AGA ArgAUG Met ACG Thr AAG Lys AGG ArgGUU Val GCU Ala GAU Asp GGU GlyGUC Val GCC Ala GAC Asp GGC GlyGUA Val GCA Ala GAA Glu GGA GlyGUG Val GCG Ala GAG Glu GGG Gly