structure of amino acids

what is the general structure of an amino acid

what is a chiral carbon?

a carbon bonded to four different groups (means that stereoisomers can exist)

what is an R group/sidechain?

• each amino acid has unique R group

• gives amino acid unique chemical and physical properties

• can have various properties

how many common amino acids are there?

20

what are the two different states that the amino group/carboxyl group can exist in?

can exist in protonated or deprotonated form

depends on environmental pH

when do the amino group and carboxyl group exist in their protonated form?

when the pH is smaller than their respective pKa

when do the amino group and carboxyl group exist in their deprotonated form?

when the pH is greater than their respective pKa

what is the approximate pKa of the amino group?

9.5

what is the approximate pKa of the carboxyl group?

2

how many possible stereoisomers can amino acids have and what are they called?

2 possible stereoisomers

L stereoisomer and D stereoisomer

what properties do these stereoisomers have?

they are enantiomers (non-superimposable)

they are optically active

how to determine if an amino acid is L/D stereoisomer?

1. Draw molecule as Fischer projection (carboxyl group on top and side chain on bottom)

2. If amino group is located on left side of carbon chain, molecule is L

If amino group is located on right side of carbon chain, molecule is D

what types of stereoisomers are usually found in proteins?

L-stereoisomers

where do D stereoisomers exist?

found in plants and animals

they are signalling molecules in organs in mammals

thought to be early biomarkers of disease

where do D amino acid containing peptides come from?

1. Spontaneous isomerisation - can convert into D-form during aging

2. Enzyme catalysed post-translational modifications (PTMs)

3. Non-ribosomal peptide synthesis

what are essential amino acids

amino acids that the body cannot synthesise so must be obtained through diet

what are non-essential amino acids

amino acids that the body can synthesise

what are conditionally essential amino acids?

amino acids that are non-essential but become essential under certain conditions (e.g. phenylketonuria)

what are non-proteogenic amino acids?

amino acids that are not incorporated into proteins but have important biological roles e.g. neurotransmission or sociochemical communication

what are examples of non-proteogenic amino acids

L-DOPA (neurotransmission) and Felinine (sociochemical communication)

what are some properties of amino acids that can arise due to their unique side chains?

• hydrophobic

• aliphatic

• polar

• positive/negative charge

• small

• beta carbon branching

• amphipathic (polar and non-polar character)

what are the general characteristics of hydrophobic amino acids?

• found in protein cores

• stabilise protein structure through hydrophobic interactions

what are the general characteristics of polar/uncharged amino acids (hydrophilic)?

• side chains are soluble in water because of hydroxyl and amide functional groups

• these functional groups can form hydrogen bonds with water

• found on the surface of proteins

what are the general characteristics of polar/charged amino acids

• found on surface of protein

• involved in salt bridges in protein core (positively and negatively charged residues)

• acids (D,E) — proton donors, R groups have net negative charge

• bases (KR) — proton acceptors, R groups have net positive charge

• histidine can act as proton acceptor/donor

general characteristics of aromatic amino acids

• aromatic ring in side chain

• relatively non-polar

• participate in hydrophobic interactions

• aromatic ring absorbs UV light (~280nm)

general characteristics of proline

• ring structure

• rigid conformation (reduced flexibility)

• found in protein turns

• found on protein surface

general characteristics of cysteine

• can form disulfide bridges (very hydrophobic)

• can form covalent links between different parts of protein molecule