PHAR 202 Amino Acids

this only has the basics of the 20 standard α-amino acids (no optical activity, fischer conventions, CIP system, or prochirality yet because i need to watch the lecture again cause i don't understand it yet ;-; )

What are proteins made up of?

20 standard amino acids called α-amino acids

• they are called this because the nitrogen atom is attached to the alpha carbon

Standard α-amino acid general structure

• contains 20 different R groups that yield distinct physicochemical characteristics

• amphoteric/can act as either an acid or a base

  • this is because the carboxylic acid and the amino group of the amino acid are completely ionized in the physiological pH range

• zwitterions (bear charged groups of opposite polarity)

  • COOH → COO- which acts as the base component

  • H2N → H3N+ which acts as the acid component

How do peptide bonds form?

• two α-amino acids undergo a condensation reaction to form a dipeptide

How to calculate the chemical sequence space for polypeptides?

• general formula when considering all 20 distinct α-amino acids: 20^n, where n is the number of building blocks

• formula for considering x number of α-amino acids: x^n, where x is the number of total possible amino acids and n is the total possible positions for a building block to go

How are the standard α-amino acids categorized?

They are distinguished by their R groups and the characteristic interactions of their R groups

What are the nonpolar amino acids?

• Glycine

• Alanine

• Valine

• Leucine

• Isoleucine

• Methionine

• Proline

• Phenylalanine

• Tryptophan

What are the uncharged polar amino acids?

• Serine

• Threonine

• Asparagine

• Glutamine

• Tyrosine

• Cysteine

What are the negatively-charged polar amino acids?

• Aspartic acid

• Glutamic acid

What are the positively-charged polar amino acids?

• Histidine

• Lysine

• Arginine

Glycine

• abbreviations: Gly, G

• smallest amino acid as its R group is a hydrogen atom

Alanine

• abbreviations: Ala, A

• R group for alanine is a methyl group

Valine

• abbreviations: Val, V

Leucine

• abbreviations: Leu, L

• same number of carbons as isoleucine, but different atom arrangement

Isoleucine

• abbreviations: Ile, I

• same number of carbons as isoleucine, but different atom arrangement

Methionine

• abbreviations: Met, M

• thiol ether side chain resembles an n-butyl group in physical resemblance and chemical properties

  • C and S have nearly equal electronegativities and S is about the size of a methylene group

Proline

• abbreviations: Pro, P

• only amino acid that makes a tertiary amide linkage due to the single hydrogen on linkage point

• cyclic secondary amino acid, which is unique among the 20 standard amino acids

• cyclic nature of pyrrolidine side chain provides conformational constraints in 3D space

Phenylalanine

• abbreviations: Phe, F

• alanine with a phenyl group attached, hence the name

Tryptophan

• abbreviations: Trp, W

• lone pair of electrons on Trp are in a pi orbital so within the aromatic ring, it means it will be flat

Serine

• abbreviations: Ser, S

• R group can have favourable interactions with water

Threonine

• abbreviations: Thr, T

• R group can have favourable interactions with water

Asparagine

• abbreviations: Asn, N

• R group can have favourable interactions with water

Glutamine

• abbreviations: Gln, Q

• R group can have favourable interactions with water

Tyrosine

• abbreviations: Tyr, Y

• R group can have favourable interactions with water

Cysteine

• abbreviations: Cys, C

• R group can have favourable interactions with water

• SH is an ionizable group but due to its pKa being higher than the physiological pH, the entire molecule is considered an uncharged polar amino acid

• two cysteine residues can link via a condensation reaction to form a disulfide bond

Aspartic acid

• abbreviations: Asp, D

• similar structure to aspargine, but on the gamma carbon, the attached NH2 is swapped for OH to become its current COOH

Glutamic acid

• abbreviations: Glu, E

• similar structure to glutamine, but on the delta carbon, the attached NH2 is swapped for OH to become its current COOH

Histidine

• abbreviations: His, H

• indol ring appended to the beta carbon

• indol component of the molecule can act as a base

Lysine

• abbreviations: Lys, K

Arginine

• abbreviations: Arg, R

Which amino acids have charged polar amino sidechains?

• Asp and Glu

• His

• Arg