Nitrogen and Phosphorus Containing Compounds

Question 1

Amino Acids are _____ molecules that come together through a _____ reaction where ___ is released with one ___ from the carboxy and two ____ from the amino

Answer 1

dipolar

condensation

water

oxygen

hydrogen

Question 2

Amino Acids

Answer 2

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

Question 3

L-amino acids have ____ configutations, except for ____ which is ____ because of the change in priority caused by the S in its R group.

Answer 3

S

cysteine

R

Question 4

Amphoteric Molecules

Answer 4

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

Question 5

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.

Answer 5

zwitterion

basic

acidic

Question 6

5 Catgories of Amino Acids

Answer 6

Nonpolar non aromatic

aromatic

polar

negatively charged (acidic)

positively charged (basic)

Question 7

Nonpolar Nonaromatic Amino acids

Answer 7

saturated hydrocarbon R chains

glycine, proline, alanine, valine, leucine, isoleucine, methionine (last two contain secondary amine and sulfur respectively)

Question 8

Aromatic Amino Acids

Answer 8

tryptophan, phenyalanine, tyrosine

Question 9

Nonpolar Amino Acids

Answer 9

hydrophobic and in the interior of proteins (aromatic and non aromatic)

Question 10

Polar Amino Acids

Answer 10

terminal groups containing oxygen, nitrogen or sulfur

serine, threonine, asparagine, glutamine, cysteine

Question 11

Negatively Charged Amino Acids

Answer 11

carboxylate anions in their R groups

aspartic acid and glutamic acids

Question 12

Positively Charged Amino Acids

Answer 12

protonated amino group in their R groups

arginine, lysine and histidine

Question 13

Polar, Acidic and Basic Amino Acids are…

Answer 13

all hydrophillic, and form hydrogen bonds with water in aqueous solution

Question 14

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

Answer 14

limits rotation

2

Question 15

Strecker Synthesis

Answer 15

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

Question 16

Aminonitrile

Answer 16

formed as intermediate in strecker synthesis

compound containing both amino group and nitrile group

Question 17

Gabriel Synthesis

Answer 17

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

Question 18

At physiological pH, inorganic phosphate include molecules of both ______ and ______

Answer 18

HPO42-

H2PO4-

Question 19

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.

Answer 19

ATP

DNA

phosphodiester bonds

Question 20

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 ______

Answer 20

pyrophosphate (P2O7 4-)

hydrolytic release

pyrophosphate

inorganic phosphates

Question 21

Phosphotic Acid Properties

Answer 21

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

Question 22

Phosphate Groups on Nucelotide Triphosphates

Answer 22

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!