Amino acids are dipolar molecules that come together through a condensation reaction to form peptides.
Larger, folded peptides are called proteins
Amino Acid: contains an amino group a carboxyl group attached to a single carbon atom
Alpha carbon in this chain is considered a chiral center since it has four different groups.
Glycine is the simplest amino acid, and its R group is an H atom.
All natural amino acids except for glycine are optically active and are L-isomers
Fischer projections are always drawn with the amino group on the left
Amino acids have (S) configurations
Except for cysteine which has (R) configuration since there is a Sulfur involved.
Amphoteric molecules since they have an acidic carboxyl group and a basic amino group.
Dipolar Ion or Zwitterion: when an amino acid is put into solution, it takes on both charges from the carboxyl group being deprotonated and the amino group being protonated.
All amino acids have zwitterion state properties that are common, but their distinction is defined by the R group.
20 eukaryotic proteogenic amino acids can be grouped into five categories:
Nonpolar nonaromatic: tend to have side chains that are saturated hydrocarbons
E.g. – alanine, valine, leucine, isoleucine, glycine, proline, and methionine
Both aromatic and non-aromatic nonpolar are hydrophobic and tend to be found within the interior of proteins.
Aromatic: tryptophan, phenylalanine, tyrosine
Polar: tend to have terminal groups containing oxygen, nitrogen, or sulfur
E.g.- serine, threonine, asparagine, glutamine and cysteine
Negatively charged (Acidic): Terminal carboxylate anions in their R groups
E.g. – aspartic acid and glutamic acid
Positively charged (Basic): protonated amino group in their R groups
E.g. – arginine, lysine, and histidine
Amino acids undergo condensation reaction to form peptide bonds.
Polypeptides are molecule that are formed from peptide bonds
Amides have two resonance structures for its amide bond, and the true structure is a hybrid between these two.
One resonance structure has a double bond between the nitrogen atom and the carbonyl carbon. The other has a double bond is between the oxygen and carbonyl carbon
Double bond between the carbon and nitrogen limits the rotation of this bond and thus increases the rigidity and stability of the backbone for proteins.
Synthesis of a-Amino Acid
Step 1: Start with aldehyde, ammonium chloride (NH4Cl), and potassium cyanide (KCN).
Carbonyl oxygen is protonated which increases the electrophilicity of the carbonyl carbon.
Ammonia then attacks the carbonyl carbon to from an imine
Imine carbon is susceptible to nucleophilic addition reaction and is thus attacked by the CN– anion to form a nitrile group (carbon triple bonded to nitrogen).
Final molecule at end of step one is aminonitrile (contains an amino group and a nitrile group).
Step 2: nitrile nitrogen is protonated which increases the electrophilicity of the nitrile carbon
Water molecule attacks the carbon which leads to both imine and hydroxyl groups on the same molecule
Imine is attacked by another water and a carbonyl is formed
Overall step is performed in aqueous acid and can be accelerated by using heat.
Both L & D amino acids are generated through this process. Produces a racemix mixture.
Starts with acidic potassium phthalimide is reacted with diethyl bromomalonate (secondary carbon bonded to a bromine)
Set up is similar to an SN2 mechanism with the phthalimide as the nucleophile, the secondary substrate carbon as the electrophile and bromine as the leaving group.
Produces a phthalimidomalonic ester
Potassium phthalimide is a large nucleophile which prevents the substrate carbon from undergoing multiple substitutions since it creates steric hindrance.
Alpha carbon is then easily deprotonated in a basic solution. This deprotonated molecule can then act as a nucleophile and attack the substrate carbon of a bromoalkane.
SN2 mechanism: leaving group is the bromide anion.
Molecule is then hydrolyzed with a strong base and heat.
Phthalimide moiety is removed as phthalic acid
Final product is a dicarboxylic acid with an amine on the alpha carbon
Dicarboxylic acid is decarboxylated through the addition of acid and heat.
Carbon dioxide molecule is lost and this results in the formation of the complete amino acid.
Phosphoric Acid forms the high-energy bonds that carry ATP
Phosphoric acid is sometimes referred to as a phosphate group or inorganic phosphate, denoted by Pi.
Inorganic phosphate is found in either HPO42- or H2PO4–
Phosphorus is also found in the backbone of DNA: phosphodiester bonds link the sugar moieties of the nucleotides.
Pyrophosphate: ester dimer that is released when a new nucleotide joins a growing strand of DNA
Denoted PPi (P2O74-)
This molecule provides the energy for the formation of the new phosphodiester bond.
Nucleotides such as ATP, GTP are referred to as organic phosphates
Phosphoric acid has three acidic hydrogens.
Most strongly acidic environment is with H3PO4. If conditions change to mildly acidic, then it will lose proton relatively easily (pKa of 2.15).
In weakly basic solutions H2PO4– will lose a second proton to become HPO32- (pKa of 7.20)
Phosphate exists in strongly basic solutions. (pKa of 12.32)
For a pH of seven, dihydrogen phosphate and hydrogen phosphate predominate in equal proportions.
Since adjacent groups on a nucleotide triphosphate experience large repulsion, and the fact that the phosphate can stabilize up to three negative charges by resonance, the energy released when a phosphate is cleaved is high.