Biochemistry
Antioxidants {GCSV}
| Antioxidant | Reaction |
|---|---|
| Glutathione peroxidase | H2O2 + 2GSH → 2H2O + GSSG |
| Catalase | 2H2O2 → 2H2O + O2 |
| Superoxide dismutase | 2O2- + 4H+ → 2H2O + O2 |
| Vitamin A & C & E | - |
Collagen Synthesis
| Steps | Enzyme | Cofactor | Diseases |
|---|---|---|---|
| Hydroxylation | Proline hydroxylase Lysine hydroxylase | Vitamin C | Scurvy |
| Glycosylation | - | - | Osteogenesis imperfecta |
| Exocytosis | - | - | - |
| Cleavage | - | - | - |
| Crosslinking | Lysyl oxidase | Cu | Menkes disease |
Cofactors of Enzymes
Dehydrogenase
| Mnemonic | Cofactor |
|---|---|
| Tender | TPP (B1) |
| Loving | Lipoid acid |
| Care | CoA (B5) |
| For | FAD (B2) |
| Nancy | NAD (B3) |
Carboxylase {ABC}
| Mnemonic | Cofactor |
|---|---|
| A | ATP |
| B | Biotin (B7) |
| C | CO2 |
Vitamin B
| Vitamin | Synonym | Derivatives |
|---|---|---|
| B1 | Thiamin | Thiamine pyrophosphate (TPP) |
| B2 | Riboflavin | Flavin adenine dinucleotide (FAD) Flavin mononucleotide (FMN) |
| B3 | Niacin | Nicotinamide adenine dinucleotide (NAD) Nicotinamide adenine dinucleotide phosphate (NADP) |
| B5 | Pantothenate | CoA |
| B6 | Pyridoxine | Pyridoxal phosphate (PLP) |
| B7 | Biotin | - |
| B9 | Folate | - |
| B12 | Cobalamin | - |
Vitamin D Synthesis
Vitamins as Cofactors
| Vitamin | Enzyme | Deficiency |
|---|---|---|
| B1 & B2 & B3 & B5 | Pyruvate dehydrogenase | Pyruvate dehydrogenase deficiency |
| α-Ketoglutarate dehydrogenase | - | |
| Branched-chain α-ketoacid dehydrogenase | Maple syrup urine disease (MSUD) | |
| B1 | Transketolase | - |
| B2 | Succinate dehydrogenase [ETC complex 2] | - |
| Acyl-CoA dehydrogenase | Acyl-CoA dehydrogenase deficiency | |
| Retinal dehydrogenase | - | |
| B3 | NADH dehydrogenase [ETC complex 1] | - |
| B6 | AST & ALT | - |
| Aminolevulinate (ALA) synthase | Sideroblastic anemia | |
| Cystathionine synthase | Homocystinuria | |
| Dopa decarboxylase | - | |
| Glycogen phosphorylase | McArdle disease Hers disease | |
| B7 | Pyruvate carboxylase | - |
| Acetyl-CoA carboxylase | - | |
| Propionyl-CoA carboxylase | - | |
| B9 & B12 | Methionine synthase | Homocystinuria |
| B12 | Methylmalonyl-CoA mutase | Methylmalonic acidemia |
| C | Proline hydroxylase Lysine hydroxylase | Scurvy |
Summary of Pathways
| Enzyme | Cofactor | Deficiency | Drug Target |
|---|---|---|---|
| Glycogen synthase | - | - | - |
| Glycogen phosphorylase | Vitamin B6 | McArdle disease Hers disease | - |
| Aldose reductase | - | - | - |
| UDP-glucose epimerase | - | - | - |
| Galactose-1-phosphate uridyltransferase | - | Classic galactosemia | - |
| Glucose-1-phosphate uridyltransferase | - | - | - |
| Glucose-6-phosphatase | - | Von Gierke disease | - |
| Hexokinase & Glucokinase | - | - | - |
| Phosphoglucomutase | - | - | - |
| Glucose-6-phosphate dehydrogenase (G6PD) | - | G6PD deficiency | - |
| Galactokinase | - | Galactokinase deficiency | - |
| Galactose-1-phosphatase | - | - | - |
| Phosphoglucose isomerase | - | - | - |
| 6-Phosphogluconate dehydrogenase (6PGD) | - | 6PGD deficiency | - |
| Phosphofructokinase-2 (PFK-2) | - | - | - |
| Fructose bisphosphatase-2 (FBPase-2) | - | - | - |
| Transketolase | Vitamin B1 | - | - |
| Aldose reductase | - | - | - |
| Fructose bisphosphatase-1 (FBPase-1) | - | - | - |
| Phosphofructokinase-2 (PFK-1) | - | - | - |
| Ribose-5-phosphate isomerase (RPI) | - | - | - |
| Carbamoyl phosphate synthetase II | - | - | - |
| Glycerol-3-phosphatase | - | - | - |
| Glycerol kinase | - | - | - |
| Aldolase A & B | - | - | - |
| PRPP synthetase | - | - | - |
| Dihydroorotate dehydrogenase | - | - | Leflunomide |
| Glycerol-3-phosphate dehydrogenase | - | - | - |
| Fructose-1-phosphatase | - | - | - |
| Fructokinase | - | Essential fructosuria | - |
| Aldolase B | - | Fructose intolerance | - |
| Triose phosphate isomerase (TPI) | - | - | - |
| IMP synthesis | - | - | - |
| UMP synthase | - | Orotic aciduria | - |
| Triose kinase | - | - | - |
| Glyceraldehyde-3-phosphate dehydrogenase (G3PDH) | - | - | - |
| PRPP amidotransferase | - | - | Azathioprine 6-MP & 6-TG |
| IMP dehydrogenase | - | - | Ribavirin Mycophenolate |
| Phosphoglycerate kinase (PGK) | - | - | - |
| Ribonucleotide reductase | - | - | Hydroxyurea |
| Thymidylate synthase | - | - | Flucytosine & 5-FU |
| Dihydrofolate reductase | - | - | Trimethoprim Pyrimethamine Methotrexate |
| Phosphoglycerate mutase (PGM) | - | - | - |
| Dihydrofolate synthase | - | - | - |
| Enolase | - | - | - |
| Dihydropteroate synthase | - | - | Sulfonamides |
| Phosphoenolpyruvate carboxykinase | - | - | - |
| Pyruvate kinase | - | Pyruvate kinase deficiency | - |
| Alanine transaminase (ALT) | Vitamin B6 | - | - |
| Lactate dehydrogenase (LDH) | - | - | - |
Carbohydrate Metabolism
Anabolism
| Metabolism | Reaction | Location |
|---|---|---|
| Gluconeogenesis | Pyruvate → Glucose | Both |
| Glycogenesis | Glucose → Glycogen | Cytoplasm |
Catabolism
| Metabolism | Reaction | Location |
|---|---|---|
| Glycogenolysis | Glycogen → Glucose | Cytoplasm |
| Glycolysis | Glucose → Pyruvate | Cytoplasm |
Shuttle
| Metabolism | Reaction | Location |
|---|---|---|
| G3P shuttle | - | Mitochondria |
| Malate-aspartate shuttle | - | Mitochondria |
Cycle
| Metabolism | Reaction | Location |
|---|---|---|
| Citric acid [Krebs] cycle | Acetyl-CoA → Energy | Mitochondria |
| Lactic acid [Cori] cycle | - | - |
Glycolysis
| Enzyme | Product |
|---|---|
| - | Glucose |
| Hexokinase & Glucokinase | Glucose-6-phosphate (G6P) |
| Phosphoglucose isomerase (PGI) | Fructose-6-phosphate (F6P) |
| Phosphofructokinase-1 (PFK-1) | Fructose-1,6-bisphosphate (F1,6BP) |
| Aldolase | Dihydroxyacetone phosphate (DHAP) |
| Triose phosphate isomerase (TPI) | Glyceraldehyde-3-phosphate (G3P) |
| Glyceraldehyde-3-phosphate dehydrogenase (G3PDH) | 1,3-bisphosphoglycerate (1,3BPG) |
| Phosphoglycerate kinase (PGK) | 3-phosphoglycerate (3PG) |
| Phosphoglycerate mutase (PGM) | 2-phosphoglycerate (2PG) |
| Enolase | Phosphoenolpyruvate (PEP) |
| Pyruvate kinase (PK) | Pyruvate |
Citric Acid [Krebs] Cycle
| Enzyme | Mnemonic | Product | #C |
|---|---|---|---|
| - | - | Acetyl-CoA | 2C |
| Citrate synthase | Citrate | Citrate | 6C |
| Aconitase | Is | Isocitrate | 6C |
| Isocitrate dehydrogenase | Krebs' | α-Ketoglutarate | 5C |
| α-Ketoglutarate dehydrogenase | Starting | Succinyl-CoA | 4C |
| Succinate thiokinase | Substrate | Succinate | 4C |
| Succinate dehydrogenase | For | Fumarate | 4C |
| Fumarase | Mitochondrial | Malate | 4C |
| Malate dehydrogenase | Oxidation | Oxaloacetate | 4C |
Gluconeogenesis
| Enzyme | Product |
|---|---|
| - | Pyruvate |
| Pyruvate carboxylase | Oxaloacetate |
| Phosphoenolpyruvate carboxykinase | Phosphoenolpyruvate (PEP) |
| Enolase | 2-Phosphoglycerate (2PG) |
| Phosphoglycerate mutase (PGM) | 3-Phosphoglycerate (3PG) |
| Phosphoglycerate kinase (PGK) | 1,3-Bisphosphoglycerate (1,3BPG) |
| Glyceraldehyde-3-phosphate dehydrogenase (G3PDH) | Glyceraldehyde-3-phosphate (G3P) |
| Triose phosphate isomerase (TPI) | Dihydroxyacetone phosphate (DHAP) |
| Aldolase | Fructose-1,6-bisphosphate (F1,6BP) |
| Fructose bisphosphatase-1 (FBPase-1) | Fructose-6-phosphate (F6P) |
| Phosphoglucose isomerase (PGI) | Glucose-6-phosphate (G6P) |
| Glucose-6-phosphatase (G6Pase) | Glucose |
Glycogenesis
| Enzyme | Product |
|---|---|
| - | Glucose |
| Hexokinase & Glucokinase | Glucose-6-phosphate (G6P) |
| Phosphoglucomutase | Glucose-1-phosphate (G1P) |
| UDP-glucose phosphorylase | UDP-glucose |
| Glycogen synthase | Glycogen |
Glycogenolysis
| Enzyme | Product |
|---|---|
| - | Glycogen |
| Glycogen phosphorylase | Glucose-1-phosphate (G1P) |
| Phosphoglucomutase | Glucose-6-phosphate (G6P) |
| Glucose-6-phosphatase | Glucose |
Glycolysis and Gluconeogenesis Regulation
Glycogenolysis and Glycogenesis Regulation
Electron Transport Chain (ETC)
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Monosaccharide Transporters
| Transporter | Dependency | Monosaccharides | Location |
|---|---|---|---|
| GLUT-1 | Insulin independent | Glc & Gal | Brain RBC Cornea |
| GLUT-2 | Insulin independent | Glc & Gal & Fru | β islet cells Intestine Liver Kidney |
| GLUT-3 | Insulin independent | Glc & Gal | Brain |
| GLUT-4 | Insulin dependent | Glc & Gal | Muscle Fat |
| GLUT-5 | Insulin independent | Fru | Intestine Sperm |
| SGLT-1 | Sodium dependent | Glc & Gal | Intestine |
| SGLT-2 | Sodium dependent | Glc & Gal | Kidney |
Lipid Metabolism
Anabolism
| Metabolism | Reaction | Location |
|---|---|---|
| Fatty acid synthesis | Acetyl-CoA → Fatty acid | Cytoplasm |
| Cholesterol synthesis | Acetyl-CoA → Cholesterol | Cytoplasm |
| Ketogenesis | Acetyl-CoA → Ketone | Mitochondria |
Catabolism
| Metabolism | Reaction | Location |
|---|---|---|
| Fatty acid oxidation | Acyl-CoA → Acetyl-CoA | Mitochondria |
Shuttle
| Metabolism | Reaction | Location |
|---|---|---|
| Citrate shuttle | - | Mitochondria |
| Carnitine shuttle | - | Mitochondria |
Ketone Bodies
- Acetoacetate
- Acetone
- β-hydroxybutyrate
Fatty Acid Metabolism
Fatty Acid Oxidation
Lipoproteins & Apolipoproteins
| Function | Chylomicron | Remnant | VLDL | IDL | LDL | HDL | |
|---|---|---|---|---|---|---|---|
| Triglyceride | - | +++ | ++ | +++ | ++ | + | + |
| Cholesterol | - | + | + | + | + | + | + |
| Cholesterol ester | - | + | ++ | + | ++ | +++ | +++ |
| Apolipoprotein | - | + | ++ | +++ | ++++ | +++++ | ++++++ |
| A1 | Activator of LCAT | + | - | - | - | - | + |
| B48 | Chylomicron synthesis | + | + | - | - | - | - |
| B100 | LDL uptake | - | - | + | + | + | - |
| C2 | Cofactor of LPL | + | - | + | - | - | + |
| E | Remnant uptake | + | + | + | + | - | + |
Amino Acids
Hydrophobic :: Aliphatic {GAVLIP}
| Mnemonic | Abbrevation | Amino acid |
|---|---|---|
| G | G | Glycine |
| A | A | Alanine |
| V | V | Valine |
| L | L | Leucine |
| I | I | Isoleucine |
| P | P | Proline |
Hydrophobic :: Aromatic
| Mnemonic | Abbrevation | Amino acid |
|---|---|---|
| Wait | W | Tryptophan |
| For | F | Phenylalanine |
| You | Y | Tyrosine |
Hydrophilic :: Positive-charged
| Mnemonic | Abbrevation | Amino acid |
|---|---|---|
| Hao | H | Histidine |
| Ren | R | Arginine |
| Ka | K | Lysine |
Hydrophilic :: Negative-charged
| Mnemonic | Abbrevation | Amino acid |
|---|---|---|
| D | D | Aspartate |
| E | E | Glutamate |
Hydrophilic :: Uncharged
| Mnemonic | Abbrevation | Amino acid |
|---|---|---|
| N | N | Asparagine |
| Q | Q | Glutamine |
| Taiwan | T | Threonine |
| Semiconductor | S | Serine |
| Manufacturing | M | Methionine |
| Corporation | C | Cysteine |
Characteristics of Amino Acids
| Characteristic | Amino Acids |
|---|---|
| Essential | VLIWFHKTM |
| Branched-chain | VLI |
| Glucogenic | GAVPHRDENQSMC |
| Glucogenic & Ketogenic | IWFYT & Odd-chain FA |
| Ketogenic | LK & Even-chain FA |
| Degraded to pyruvate | GAWSTC |
| Degraded to α-ketoglutarate | PHREQ |
| Degraded to succinyl-CoA | VIM & Odd-chain FA |
| Degraded to fumarate | FYD |
| Degraded to oxaloacetate | DN |
| Degraded to acetyl-CoA | LIKT & Even-chain FA & Odd-chain FA |
| Degraded to acetoacetate | LWFYK |
Amino Acids & Derivatives
| Amino Acid | Derivatives |
|---|---|
| Glycine | Collagen & Heme & Glutathione & Purine |
| Alanine | Pyruvate |
| Valine | - |
| Leucine | - |
| Isoleucine | - |
| Proline | Collagen |
| Tryptophan | Niacin & Serotonin & Melatonin |
| Phenylalanine | Thyroxine & Catecholamine & Melanin |
| Tyrosine | Thyroxine & Catecholamine & Melanin |
| Histidine | Histamine |
| Arginine | Urea & NO & Creatine |
| Lysine | Collagen |
| Aspartate | Oxaloacetate & Purine & Pyrimidine |
| Glutamate | α-Ketoglutarate & Glutathione & GABA |
| Asparagine | - |
| Glutamine | Purine |
| Threonine | - |
| Serine | - |
| Methionine | S-Adenosyl methionine (SAM) |
| Cysteine | Glutathione |
Amino Acid Metabolism
Anabolism
| Metabolism | Reaction | Location |
|---|---|---|
| Amino acid synthesis | Sugar → Amino acid | Both |
Catabolism
| Metabolism | Reaction | Location |
|---|---|---|
| Amino acid degradation | Amino acid → Sugar | Both |
Cycle
| Metabolism | Reaction | Location |
|---|---|---|
| Urea cycle | Ammonia → Urea | Both |
| Alanine [Cahill] cycle | - | - |
Amino Acid Catabolism
Catecholamine Metabolism
Urea Cycle
| Enzyme | Product |
|---|---|
| - | Carbamoyl phosphate |
| Ornithine transcarbamylase | Citrulline |
| Argininosuccinate synthetase | Argininosuccinate |
| Argininosuccinase | Arginine |
| Arginase | Ornithine |
Cori Cycle & Cahill Cycle
Nucleobases & Nucleosides
| Nucleobases | Ribonucleosides | Deoxyribonucleosides |
|---|---|---|
| Adenine | Adenosine | Deoxyadenosine |
| Cytosine | Cytidine | Deoxycytidine |
| Guanine | Guanosine | Deoxyguanosine |
| Thymine | 5-methyluracil | Deoxythymidine |
| Uracil | Uridine | Deoxyuridine |
| Hypoxanthine | Inosine | Deoxyinosine |
| Xanthine | Xanthosine | Deoxyxanthosine |
Hexose Monophosphate (HMP) Shunt
 Shunt.png)
Compositions of Purine and Pyrimidine
De Novo Pathways for Purines & Pyrimidines
| 1st step | 2nd step | 3rd step |
|---|---|---|
| Inosine (I) | Adenosine (A) | Deoxyadenosine (dA) |
| Guanosine (G) | Deoxyguanosine (dG) | |
| Uridine (U) | Deoxyuridine (dU) | Deoxythymidine (dT) |
| Cytidine (C) | Deoxycytidine (dC) |
De Novo Pathways for Purines and Pyrimidines
Purine Salvage
Cell Cycle Phases
| Cell Type | Examples |
|---|---|
| Permanent | Neurons & Muscles & RBC |
| Stable | Hepatocytes & Lymphocytes & Fibroblasts |
| Labile | Marrow & Gut & Skin & Hair & Germ cells |
DNA Replication
Enzymes for DNA Replication
- DNA polymerase
- Helicase
- Ligase
- Primase
- Reverse transcriptase
- SSBP
- Topoisomerase
- Telomerase
Prokaryote DNA & RNA Polymerases
| Subtype | Functions |
|---|---|
| DNA polymerase I: 5' → 3' exonuclease | DNA replication :: RNA primer removal |
| DNA polymerase II | DNA repair |
| DNA polymerase III: 3' → 5' exonuclease | DNA replication :: proofreading |
| DNA polymerase IV | DNA repair |
| DNA polymerase V | DNA repair |
| RNA polymerase | rRNA & mRNA & tRNA synthesis |
Eukaryote DNA & RNA Polymerases
| Subtype | Functions |
|---|---|
| DNA polymerase α | DNA replication :: initiation |
| DNA polymerase β | DNA repair |
| DNA polymerase γ | DNA replication |
| DNA polymerase δ | DNA replication :: lagging strand |
| DNA polymerase ε | DNA replication :: leading strand |
| RNA polymerase I | rRNA synthesis |
| RNA polymerase II | mRNA synthesis |
| RNA polymerase III | tRNA synthesis |
DNA Repair
| Mechanism | Gene | Damage | Diseases |
|---|---|---|---|
| Base excision repair (BER) | - | Deamination | - |
| - | Single-stranded break | - | |
| Nucleotide excision repair (NER) | ERCC | Pyrimidine dimer | Xeroderma pigmentosum |
| Mismatch repair (MMR) | MLH1 & MSH2 | Mismatch | Lynch syndrome |
| Homologous recombination (HR) Non-homologous end joining (NHEJ) | ATM | Double-stranded break | Ataxia telangiectasia |
| BRCA | Double-stranded break | Breast & Ovarian cancer | |
| FANC | Interstrand crosslinking | Fanconi anemia |
Specific Transcription Factors
| Transcription Factor | Response Element | Protein Class |
|---|---|---|
| cAMP response element binding (CREB) protein | CRE | Leucine zipper |
| Steroid receptor | HRE | Zinc finger |
| Peroxisome proliferator-activated receptor (PPAR) | PPRE | Zinc finger |
| NF-κB | κB element | Rel domain |
| Homeodomain protein | - | Helix-turn-helix |
RNA Types
| RNA | Derivatives |
|---|---|
| Ribosomal RNA (rRNA) | Ribosome |
| Transfer RNA (tRNA) | Aminoacyl-tRNA |
| Messenger RNA (mRNA) | - |
| Heterogeneous nuclear RNA (hnRNA) | mRNA precursor |
| Small nuclear RNA (snRNA) | Spliceosome |
| MicroRNAs (miRNA) | RNA interference (RNAi) |
| Small interfering RNA (siRNA) | RNA interference (RNAi) |
| Ribozymes | RNA enzyme |
Modifications
RNA :: Co-transcription
| Modification | Traget |
|---|---|
| 7-methylguanosine (7-mG) | - |
RNA :: Post-transcription
| Modification | Traget |
|---|---|
| Polyadenylation (Poly-A) | - |
| Splicing | - |
| RNA interference (RNAi) | - |
Protein :: Co-translation
| Modification | Traget |
|---|---|
| N-glycosylation | Asparagine |
| Hydroxylation of collagen | Proline & Lysine |
| γ-carboxylation of prothrombin | Glutamate |
Protein :: Post-translation
| Modification | Traget |
|---|---|
| O-glycosylation | Threonine & Serine |
| ADP-ribosylation | - |
| Ubiquitination | - |
Polymerase Chain Reaction (PCR)
| Step | Temperature |
|---|---|
| Denaturation | 95°C |
| Annealing | 55°C |
| Elongation | 72°C |
Blotting Techniques {SNOW-DROP}
| Mnemonic | Blot | Mnemonic | Target |
|---|---|---|---|
| S | Southern blot | D | DNA |
| N | Northern blot | R | RNA |
| O | - | O | - |
| W | Western blot | P | Protein |
Enzyme-linked Immunosorbent Assay (ELISA)
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