Nitrogen and Phosphorus Containing Compounds Flashcards
Amino Acids are _____ molecules that come together through a _____ reaction where ___ is released with one ___ from the carboxy and two ____ from the amino
dipolar
condensation
water
oxygen
hydrogen
Amino Acids
amino and carboxyl group attacked to a single alpha carbon with 2 other substituents: H and R group side chain
chiral (except for Glycine) and are L isomers with optical activity
L-amino acids have ____ configutations, except for ____ which is ____ because of the change in priority caused by the S in its R group.
S
cysteine
R
Amphoteric Molecules
act as both acids and bases
amino acids are amphoteric because they take on a positive charge through the amino and negative through deprotonation of the carboxyl group
When an amino acid is put into solution, it takes on both charges forming a _______ where the pH dictates how the amino acts.
Deprotonated in ____ solutions and protonated in ____ solutions.
zwitterion
basic
acidic
5 Catgories of Amino Acids
Nonpolar non aromatic
aromatic
polar
negatively charged (acidic)
positively charged (basic)
Nonpolar Nonaromatic Amino acids
saturated hydrocarbon R chains
glycine, proline, alanine, valine, leucine, isoleucine, methionine (last two contain secondary amine and sulfur respectively)
Aromatic Amino Acids
tryptophan, phenyalanine, tyrosine
Nonpolar Amino Acids
hydrophobic and in the interior of proteins (aromatic and non aromatic)
Polar Amino Acids
terminal groups containing oxygen, nitrogen or sulfur
serine, threonine, asparagine, glutamine, cysteine
Negatively Charged Amino Acids
carboxylate anions in their R groups
aspartic acid and glutamic acids
Positively Charged Amino Acids
protonated amino group in their R groups
arginine, lysine and histidine
Polar, Acidic and Basic Amino Acids are…
all hydrophillic, and form hydrogen bonds with water in aqueous solution
There is partial double bond character between nitrogen atom and the carbonyl carbon, this ______ about the C-N bond which adds to the rigidity and stability of the backbone of proteins.
This means there are __ resonance structures
limits rotation
2
Strecker Synthesis
start with aldehyde, ammonium chloride and potassium cyanide making a racemic mixture as the nucelophiles can attack from either side of the carbonyl so both L and D amino acids are created
1) carbonyl oxygen is protonated to increase electrophicity of the carbonyl carbon
2) ammonia attacks the carbonyl carbon forming an imine which is also susceptible to nucleophilic attack by the CN- and forms an aminonitrile
3) Nitrile nitrogen gets protonated to increase electrophilicty of the nitirle carbon
4) water molecule attacks to create a molecule with both imine and hydroxyl moieties
5) imine is attacked by anoteher water kicking off ammonia and creating a carboxylic acid functionality in aq acid and heat
Aminonitrile
formed as intermediate in strecker synthesis
compound containing both amino group and nitrile group
Gabriel Synthesis
another manner in creating an amino acid
potassium phthalmide is reacted with diethyl bromomalonate
1) diethyl bromalonate has a 2 carbon that is bonded to bromide (a good leaving group) allowing a Sn2 reaction with phtalimide as the nucleophile and the secondary carbon as the electrophile to produce a phthalimidomalonic ester
2) in presence of base, the alpha carbon between the carbonyls is deprotonated and the whole acts as a nucleophile atacking the substrate carbon of a bromoalkane of Sn2 where the electrophile is the alkyl bromide and the leaving group is the bromide
3) molecule is hydrolyzed with strong base and heat as the pthalimide moiety is removed (the bulky 2 Coo-)
4) malonic ester is hydrolyzed to a dicarboxylic acid with an amine on the alpha carbon
5) the 1,3 dicarbonyl is decarboxylated through addition of acid and heat where CO2 leaves
At physiological pH, inorganic phosphate include molecules of both ______ and ______
HPO42-
H2PO4-
In addition to energy carrying nucelotide phosphates such as _____, phosphorus is also found in the backbone of _____ in ____ linking the sugar moieties of the nucleotides.
ATP
DNA
phosphodiester bonds
When a new nucelotide is joined to DNA, an ester dimer of phosphate is released known as ______. The ______ of this molecule provides the energy for the formation of the new phosphodiester bond.
____ is unstable in aq solution so it is hydrozyled to form two ______
pyrophosphate (P2O7 4-)
hydrolytic release
pyrophosphate
inorganic phosphates
Phosphotic Acid Properties
three acidic hydrogens with 3 different pKAs making it an excellent buffer as it can pick up and give up hydrogens based on pH
mildly acidic -> dihydrogen phosphate
weakly basic -> hydrogen phosphate
at physiological pH dihydrogen and hydrogen phosphate dominate
Phosphate Groups on Nucelotide Triphosphates
adjacent phosphates have large repulsion due to negative charge, combined with ability of phosphate to stabilize up to three negative charged by resonance means energy released from phosphate cleavage is high!
