nucleobases, amino acids, and biological functional groups

nucleobases

nitrogen-containing heterocyclic bases found in dna and rna

pyrimidine

six-membered aromatic ring containing two nitrogen atoms

purine

fused bicyclic system containing six-membered and five-membered nitrogen-containing ring

which nucleobases are pyrimidines

cytosine, thymine, and uracil

which nucleobases are purines

adenine and guanine

heterocycle

ring containing at least one atom other than carbon

why are nitrogen-containing heterocycles important in medicinal chemistry

provide sites for molecular recognition, hydrogen bonding, and electronic interactions

why can nucleobases form hydrogen bonds

contain suitable donor and acceptor groups, including N-H, amino, and carbonyl groups

nucleoside

nucleobase attached to a sugar

nucleotide

nucleoside with one or more phosphate groups

amino acid structure

central α-carbon bonded to an amino group, carboxyl group, hydrogen, and side chain

what determines chemical properties of different amino acids

side chains (R groups)

hydrophobic amino side chain

mostly nonpolar side chain that interacts poorly with water

which amino acids have hydrophobic side chains

alanine, valine, isoleucine, leucine, phenylalanine, and tryptophan

which amino acids have acidic side chains

aspartic acid and glutamic acid

functional group found in acidic amino side chains

carboxylic acid/carboxylate group

approximate side-chain pKa of aspartic acid and glutamic acid

around 4-5

which amino acids have amide-containing side chains

asparagine and glutamine

how do amide side chains interact with water

through hydrogen bonding

which amino acids have basic side chains

lysine, arginine, and histidine

functional group found in lysine’s side chain

primary amine

functional group found in arginine’s side chain

guanidine group

functional group found in histidine’s side chain

imidazole ring

approximate side-chain pKa of lysine, arginine, and histidine

10.5, 12.5, and 7

functional group is found in cysteine’s side chain

thiol (-SH)

why is cysteine important for protein structure

two cysteine thiols can oxidize to form disulfide bond

functional group found in tyrosine’s side chain

phenol

why is proline structurally distinctive

side chain forms ring with backbone nitrogen, restricting flexibility

peptide bond

amide linkage between amino acid residues

why do amino acid side chains influence protein folding

hydrophobic, polar, ionic, and hydrogen-bonding interactions affect protein structure

how do nonpolar amino acid side chains commonly behave in water

tend to associate away from water through hydrophobic effect

how can charged amino acid side chains interact with other molecules

through electorstatic and ion-dipole interactions

why is histidine useful in biological acid-base chemistry

side chain pKa is near physiological pH, allowing protonation changes

why are aromatic amino side chains important in molecular recognition

aromatic rings can contribute hydrophobic and pi-related interactions