Amino Acids & Primary Protein Structure Flashcards
(18 cards)
When does a zwitter ion form?
Under neutral pH
Describe the effect of changes in pH on amino acids
At pH 1 = amino acid is fully protonated
At pH 2.2-2.6 = it is 50% ionised. This is the pKa of the alpha carbonyl group
At pH 7 = both groups are ionised, forms a zwitterion
At pH 9.4 = amino group loses a proton (50% ionised). This is the pKa of the amino group
What are stereoisomers?
Mirror images of each other called enantiomers
Only the L version is incorporated into proteins (group on right)
Aliphatic amino acids
Val
Gly
Ile
Ala
Leu
Aromatic amino acids
His
Tyr
Phe
Trp
Sulfur containing amino acids
Cis
Met
Basic amino acids
Lys
Arg
Acidic amino acids (amides)
Asp
Glu
Asn
Gln
Alcohol amino acids
Ser
Thr
Tyr
What amino acid is not defined by its chemical properties?
Proline
What are aliphatic amino acids?
The side chains are non-aromatic hydrocarbons = no benzene rings
Glycine is achiral
Isoleucine is the most hydrophobic
Describe proline
- contains a heterocycle
- much less hydrophobic
- rotation around the N-C bond is restricted
- so cant be accommodated in some secondary structures
Describe aromatic amino acids
- all have a benzene ring
- have alternating (conjugating) double bonds = delocalised π electrons
- Order of hydrophobicity is Phe, Trp, Tyr then His, with Phe being the most hydrophobic
- Trp and His can engage in hydrogen bonding as they are acidic due to the NH group
Describe hydroxyl amino acids
- polar groups
- hydrogen donors and acceptors
- form phosphate esters with phosphoric acid
- involved in signalling
- Ser and Thr are more polar than Tyr
Describe amino acids containing sulfur
Cysteine
- some similarity with Serine
- weak hydrogen bonds
- ionisable = forms thiolate anion which plays a role in catalytic reactions
- forms disulfide bonds = stabilises extracellular proteins
- strong acid with a pKa of 8.3 in water
Methionine
- fairly hydrophobic
- always the first amino acid in protein biosynthesis = start signal
Describe acidic amino acids
- form salt bridges and polar interactions with water = hydrogen bonding
- side chains have a pKa of 3.9 (Asp) and 4.1 (Glu)
- so surface exposed carbonyl groups are fully ionised as carboxylate ions
Describe amides of amino acids
- Not ionisable (not acidic or basic) but highly polar
- Strong hydrogen donor and acceptors
- found on the surface of proteins
Describe basic amino acids
- N atoms with free electron pairs are basic
- Side chains have a pKa of 10 (Lys) and 12.5 (Arg)
- Arg is the strongest base
