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)

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

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)