ch 10 - Nitrogen- and Phosphorous-Containing Compound

Question 1

amino acids

Answer 1

contain an amino group and a carboxyl group attached to a single carbon atom (and the alpha-carbon). The other substituents attached to alpha-carbon are hydrogen and an R group

Question 2

Glycine

Answer 2

only achiral amino acid with R group of just H

Question 3

cysteine

Answer 3

only R configured amino acid because the sulfur in its R group takes priority

Question 4

amphoteric

Answer 4

molecular property in which molecules can act as both acids and bases. This applies to amino acids because of their acidic carboxyl group and basic amino group

Question 5

carboxyl

Answer 5

-C(double bond O)OH

Question 6

zwitterion

Answer 6

molecule that has both positive and negative charges

Question 7

nonpolar nonaromatic amino acid R groups

Answer 7

tend to have side chains that are saturated hydrocarbons: alanine, valine, leucine, isoleucine but also include glycine, proline (cyclic with a secondary amine), and methionine (which contains sulfur)

Question 8

aromatic amino acid side chains

Answer 8

tryptophan, phenylalanine, tyrosine

Question 9

polar amino acid side chains

Answer 9

tend to have terminal groups containing oxygen, nitrogen, or sulfur: serine, threonine, asparagine, glutamine, cysteine

Question 10

negatively charged (acidic) amino acid side chains

Answer 10

aspartic acid, glutamic acid (have terminal carboxylate anions in their R groups)

Question 11

positively charged (basic) amino acid side chains

Answer 11

arginine, lysine, histidine (have protonated amino group in R groups)

Question 12

peptide bonds

Answer 12

bonds formed by amino acids through condensation reactions

Question 13

polypeptides

Answer 13

molecules formed by peptide bonds; comprise proteins

Question 14

Strecker synthesis

Answer 14

step 1: aldehyde, ammonium chloride (NH4Cl), and potassium cyanide (KCN): carbonyl oxygen is protonated, increasing electrophilicity of carbonyl carbon; then ammonia can attacked carbonyl carbon, forming imine; then CN- from KCN attacks, forming a nitrile group (–C(triple bond)N); final molecule at end of step is aminonitrile (containing an amino group (–NH2) and nitrile group. Step 2: nitrile nitrogen is protonated increasing electrophilicity of nitrile carbon; water attacks, creating molecule with imine and hydroxyl moieties at same C; this imine is attacked by another equivalent of water forming carbonyl and kicking off ammonia; creates carboxylic acid functionality which is performed in aqueous acid and sped up with heat; racemic mixture pathway and can produce L- or D-amino acids; pg 231, 232

Question 15

Gabriel Synthesis

Answer 15

also called malonic-ester synthesis, another way of synthesizing amino acids; potassium phthalimide reacted with diethyl bromomalonate via SN2 (leaving group is bromo); then add base, leaving group H, C is negative; then add Br-R through SN2, R group attaches to C; then add NaOH with water and heat (delta) to get a dicarboxylic acid and an NH2 connected to the C where that used to be. Finally add H3O+ and heat (and a CO2 is released) forming the amino acid. pg 233

Question 16

Phosphoric acid

Answer 16

sometimes referred to as phosphate group or inorganic phosphate, denoted P sub I. extremely important molecule biochemically; forms high-energy bonds that carry energy in adenosine triphosphate

Question 17

inorganic phosphate at physiological pH

Answer 17

contains molecules of hydrogen phosphate (HPO4)2-, and phosphate (H2PO4)-.

Question 18

phosphorous in DNA

Answer 18

found in backbone of DNA forming phosphodiester bonds linking sugar moieties of nucleotides

Question 19

pyrophsophate

Answer 19

denoted as PP sub i. (P2O7)4- when a new nucleotide is joined to a growing strand of DNA by a DNA polymerase, it releases this ester dimer of phosphate; its hydrolytic release provides energy for formation of new phosphodiester bond

Question 20

organic phosphates

Answer 20

nucleotides (like ATP, GTP, and those in DNA) with presence of phosphate group bonded to a carbon-containing molecule

Question 21

properties of phosphoric acid

Answer 21

three acidic hydrogens each with their own pKa which makes it a good buffer because these hydrogens span so widely; the term refers to the form that predominates in strongly acidic conditions: H3PO4 which can lose proton (pKa is then 2.15) in mildly acidic conditions to become dihydrogen phosphate (H2PO4)- and will lose a second proton (pKa then of 7.20) to become hydrogen phosphate (HPO4)2- in weakly basic solutions; strongly basic solution it turns to phosphate (PO4)3- (pKa then of 12.32)