Active Training Company Dr.

TAMER ELHABIBI

Organic Chemistry and Biochemistry

Organic chemistry
Functional groups affect hydrophilicity, lipophilicity, reactivity, shelf life, stability,
biotransformation, metabolism.

Alkanes
Also called paraffins, saturated hydrocarbons.
General formula: R-CH2-CH3. Lipid soluble.
Chemically inert to air, heat, light, acids, bases. Stable in vivo.

Alkenes
Also called olefins, unsaturated hydrocarbons.
General formula: R-CH=CH2. Lipid soluble.
Common reactions: addition of hydrogen or halogen, hydration (to form glycols), oxidation (to
form peroxides).
Volatile alkenes and peroxides may explode in presence of O2 and spark
Stable in vivo. Hydration, peroxidation, reduction may occur.

Aromatic hydrocarbons
Based on benzene. Exhibit multicenter bonding. Lipid soluble.
Chemically stable.
In vivo: hydroxylation, diol formation.

Alkyl halides
Halogenated hydrocarbons. General formula: R-CH2-X.
Lipid soluble. ↑ degree of halogenation  ↑ Solubility.
Common reactions: dehyro-halogenation, nucleophilic substitution.
Stable on the shelf. Not readily metabolized in vivo.

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Alcohols
Contains OH group. May be primary (R-CH2-OH), secondary (R1/R2-CH-OH), or tertiary
(R1/R2/R3-C-OH).
Alcohols are lipid soluble.
Low molecular weight alcohols are water soluble. ↑ hydrocarbon chain length  ↓ water
solubility.
Common reactions: oxidation, esterification.
Oxidation: primary alcohol  aldehyde  acid. Secondary alcohol  ketone. Tertiary alcohol
 not oxidized.
Stable on shelf. In vivo: oxidation, sulfation, glucuronidation.

Phenols
Aromatic compounds containing OH groups directly connected to aromatic ring. Monophenols
 one OH. Catechols  two OH.
Phenol (carbolic acid): water soluble. ↑ ring substitution  ↓ water solubility. Most phenols
are lipid soluble.
Common reactions: with strong bases to form phenoxide ion, esterification with acids, oxidation
to form colored quinones.
On the shelf: oxidation with air or ferric ions.
In vivo: sulfation, glucuronidation, aromatic hydroxylation, o-methylation.

Ethers
General formula: R-O-R.
Lipid soluble. Partially water soluble. ↑ hydrocarbon chain  ↓ water solubility.
Common reaction: oxidation to form peroxides (may explode).
In vivo: o-dealkylation. Stability ↑ with size of alkyl group.

Aldehydes
General formula: R-CHO (contains a carbonyl group C=O).
Lipid soluble. Low molecular weight aldehytes are also water soluble.
Common reactions: oxidation (to acids, in vivo and in vitro) and acetal formation.

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Ketones
General formula: R-CO-R (contains a carbonyl group C=O).
Lipid soluble. Low molecular weight ketones are also water soluble.
Nonreactive and very stable on the shelf.
In vivo: some oxidation or reduction.

Amines
Contain an amino group (-NH2). Primary (R-NH2), secondary (R1/R2-NH), tertiary
(R1/R2/R3-N), quaternary (R1/R2/R3/R4-N+ X-).
Lipid soluble. Low molecular weight amines  water solubility. ↑ branching  ↓ water
solubility (primary amines and most soluble). Quaternary amines (ionic) and amine salts are
water soluble.
Common reactions: oxidation (air oxidation on shelf), salt formation with acids. Aromatic
amines are ↓ basic  ↓ reactive with acids.
In vivo: glucuronidatin, sulfation, methylation. 1ry oxidative deaminatin. 12y/2ry 
acetylation. 2ry/3ry  dealkylation.

Carboxylic acids
General formula: R-COOH (Carboxyl group –COOH).
Lipid soluble. Low molecular weight acid and Na/K salts  water soluble.
Common reactions: salt formation with bases, esterification, decarboxylation.
Very stable on shelf. In vivo: conjugation (with glucuronic acid, glycine, glutamine), beta
oxidation.

Esters
General formula (R-COOR).
Lipid soluble. Low molecular weight esters are slightly water soluble.
Common reaction: hydrolysis to form carboxylic acid and alcohol (in vivo by esterases / in
vitro).

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Amides
General formula: R-CONH2 or R-CONR1/R2 (lactam form).
Lipid soluble. Low molecular weight amides are slightly water soluble.
No common reactions. Very stable on shelf.
In vivo: enzymatic hydrolysis by amidases in the liver.

Biochemistry

Amino acid and proteins

Monomeric units of protein (peptide bonds). Formula: NH2-CH-R/-COOH. Proteins are made
of 20 AA, differ in R side chain (alpha (C)).
Protein hydrolysis to AAs by acids, bases, enzymes.
AA ionize (depending on pH) to zwitterions structure (NH3+-CH-COO-/R)  ↓ water solubility,
↑ melting point.
Levels of protein structure: primary, secondary (alpha/beta), 3ry, 4ry.

Carbohydrates
Polyhydroxy aldehydes or ketones
Monosaccharides: simple single unit sugars, e.g., glucose, fructose.
Oligosaccharides: short chains of monosaccharides joined covalently, e.g. sucrose (has to
convert into glucose, fructose before GI absorption), maltose (hydrolyzed by maltase into 2x
glucose), lactose (milk sugar, has to convert into galactose, glucose before GI absorption).
Polysaccharides: long chains of monosaccharides, e.g., cellulose, glycogen.

Pyrimidines and purines

Bases  bond with ribose  nucleosides  bond with phosphoric acid  nucleotides 
building blocks of nucleic acid.
Exhibit tautomerism (isomerism): can be keto or enol.
Pyrimidines bases: cytosine, uracil, thymine.
Purine bases: adenine, guanine
DNA bases: thymine, cytosine, adenine, guanine

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RNA bases: uracil, cytosine, adenine, guanine.

Biopolymers

Enzymes
Linked amino acid chains (proteins)  catalysts for biological reactions. They reactions’ ↓
activation energy but do not change reaction equilibrium point, are used up or changed in the
reaction. May require cofactors or coenzymes.
Cofactor: inorganic (metal ion) or nonprotein organic molecule. Prosthetic group: cofactor
firmly bound to apoenzyme (protein portion of a complex enzyme). Coenzymes: organic
cofactor that is not firmly bound but actively involved in catalysis. Holoenzyme: complete
catalytically active enzyme system.
Lyases: removes functional group (deaminase, decarboxylase).
Ligases: bind two molecules (e.g. DNA ligase  2 nucleotides).
Isomerases: change DL, cistrans, vice versa.

Polysaccharides
Also called glycans. Long chain polymers of carbohydrates.
Homopolysaccharides: Contains one type of monomeric units. Starch  plant’s reserve food,
two glucose polymers (linear water soluble amylose, and branched water insoluble
amylopectin), enzymatic hydrolysis  maltose (glucose disaccharide). Glycogen  branched
D-glucose chain, polysaccharide storage in animal cells (liver, muscles). Cellulose  water
soluble, in plant cell wall, linear D-glucose chain, can’t be digested (hydrolyzed) by humans.
Heteropolysaccharides: contains two or more monomeric units. Heparin  acid
mucopolysaccharide with sulfate derivatives, contains glucosamine, in lung tissue, used to
prevent clotting. Hyaluronic acid  in bacterial cell wall, virteous humor, synovial fluid,
contains glucosamine.

Nucleic acids
Linear polymers of nucleotides  pyrimidine and purine bases linked to ribose or deoxyribose
sugars (nucleosides) and bound to phosphate groups.
Phosphodiester bonds: join successive DNA / RNA nucleotides.

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DNA: compared to RNA it lacks an OH group and contains T rather than U. (DT, RU).
DNA: two complementary alpha helical strands coiled to form double helix. Hydrogen bonding
between specific base pairs hold the strands together. Hydrophobic bases are on the inside of
the helix. Hydrophilic deoxyribose phosphate on the outside.
Backbone: alternating phosphate and pentose units with a purine or pyrimidine attached to each.
Strong acids associated with cellular cations and basic proteins (histones, protamines).
rRNA (ribosomal): in ribosomes.
mRNA (messenger): the template for protein synthesis  specifies the polypeptide amino acid
sequence.
tRNA (transfer): carries activated amino acids to ribosomes for incorporation to the growing
polypeptide chain.

Biochemical metabolism
Factors affecting metabolism: substrate concentration, enzymes, allosteric (regulatory)
enzymes, hormones, compartmentation.
Catabolism: degradation reactions that release energy for useful work (e.g. mechanical,
osmotic, biosynthetic).
Anabolism: biosynthetic (build-up) reactions that consumer energy to form new biochemical
compounds (metabolites).
Amphibolic pathways: may be used for anabolic or catabolic purposes. Example: Krebs cycle,
it breaks down metabolites to release 90% of the organism’s energy, but it also uses metabolites
for form compounds such as AA.

Bioenergetics
Substrate level phosphorylation: forms one unit of ATP per unit of metabolite, no oxygen
required.
Oxidative phosphorylation: forms 2 or more ATP per unit of metabolite. Uses oxidoreductase
enzymes (e.g. dehydrogenases) using cofactors NAD (nicotinamide A dinucleotide) or FAD
(flavin). Energy released from the reaction is used to form ATP in the mitochondria.

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Carbohydrate metabolism
Catabolism: releases energy from carbohydrates.
Glycogenolysis: breakdown of glycogen into glucose phosphate in the liver, skeletal muscles 
controlled by glucagon and epinephrine.
Glycolysis: breakdown of sugar phosphates (e.g. glucose, fructose, glycerol) into pyruvate
(aerobically) or lactate (anaerobically) to produce energy (ATP)
Anabolism: consumes energy to build complex from simple molecules
Glycogenesis: formation of glycogen in the liver and muscles from glucose in diet  controlled
by insulin.
Gluconeogenesis: formation of glucose from noncarbohydrate sources (e.g. lactate, pyruvate).

Krebs cycle
Location: in the mitochondria. Absent in RBCs (no mitochondria)
Catabolism: converts pyruvate (glycolysis), acetyl CoA (fatty acid degradation) and amino
acids  into CO2 and water with release of energy. Oxygen dependent (aerobic).
Anabolism: forms amino acids (aspartate, glutamate) and heme ring from metabolites.
Electron transport: accept electrons and hydrogen from oxidation of Krebs cycle metabolites
and couples the energy released to make ATP.

Lipid metabolism

Catabolism
Triglycerides stores in fat cells (adipocytes) are hydrolyzed by hormone-sensitive lipases into
three fatty acids and glycerol
Fatty acids: broken down by beta oxidation to acetyl CoA  to Krebs cycle  breaks down to
CO2, water and energy release.
Ketogenesis: very rapid break down of fatty acids leading to formation of ketone bodies (as in
DM).
Glycerol: enters glycolysis  oxidized to pyruvate  to Krebs cycle  CO2 and water.
Steroids: may be converted to bile acids, vitamin D, hormones.

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Anabolism
Fatty acids: formed in the cytoplasm. Unsaturation occurs I the mitochondria or endoplasmic
reticulum. Essential fatty acids: linoleic acid (can not be synthesized, diet is only sources).
Terpenes: derived from acetyl CoA. Include: cholesterol, steroids, fat soluble vitamins
(ADEK), bile acids.
Sphingolipids: forms a ceramide backbone with fatty acids. Joins with other compounds to
form cerebrosides, sphingomyelin
Phosphatidyl compounds: i.e. phosphatidyl choline (lecithin), ethanolamine.

Nitrogen metabolism

Catabolism
Amino acids: amino group is removed by transaminase. Carbon skeleton is broken down to
acetyl CoA or citric acid derivatives  oxidized to CO2 and water for energy. Glycogenic
amino acids form glucose as needed by guconeogenesis.
Purines: 90% is salvaged, 10% degrade to uric acid using xanthine oxidase.
Pyrimidines: breaks down to B-alanine, ammonia, CO2

Anabolism
Amino acids: from citric acid cycle intermediates. Essential AA: TIM (threonine, isoleucine,
methionine), HALL (histidine, arginine, lysine, leucine), PVT (phenylalanine, valine,
tryptophan)  PVT TIM HALL
Purines / Pyrimidines: from aspartate, carbamoyl phosphate, CO2, other AA.

Nitrogen excretion
Excess nitrogen is toxic  must be eliminated, mainly as urea.
Urea synthesis: in the liver using the Krebs-Henseleit pathway. Amino acid  AA
transferases (transaminases) + pyridoxine (vitamin B6) as coenzyme  Ammonia  +
glutamate  glutamine  + CO2  carbamoyl phosphate  urea cycle  urea.
Uric acid synthesis: most purines are salvages. Remaining purines are excreted as uric acid.

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