Amino Acids - Structure to full name

Name, 3 letter abbreviation and Classification

special features?

Glycine. Gly. Polar (up for debate)

Achiral and very small

Which amino acid may be found at tight turns in a protein due to its flexibility?

Glycine

Name, 3 letter abbreviation and Classification

special features?

Alanine. Ala. Non-polar/hydrophobic

Would alanine or valine be more hydrophobic?

valine since it has a larger non-polar side chain 

Name, 3 letter abbreviation and Classification

special features?

Proline. Pro. Non-polar/Hydrophobic.

Cyclic but not aromatic.

Is the amino group primary, secondary or tertiary in proline?

secondary

Name, 3 letter abbreviation and Classification

special features?

Valine. Val, Non-polar/hydrophobic

What are aliphatic amino side chains?

Aliphatic amino acids are non-polar and hydrophobic. contain only carbon and hydrogen.

Name, 3 letter abbreviation and Classification

special features?

Leucine. Leu. Hydrophobic/Non-polar

Name, 3 letter abbreviation and Classification

special features?

Isoleucine. Ile. Hydrophobic/Non-polar

2 chiral carbons!

What are all the aromatic aminos?

Tryptophan, Histidine, Tyrosine, Phenylaline

Which 2 aminos have >1 chiral carbon

isoleucine and threonine

Name, 3 letter abbreviation and Classification

special features?

Methionine. Met. Hydrophobic

even though sulfur is present (thioether), it is a non-polar side chain.

Unlikely to form H bonds.

Name, 3 letter abbreviation and Classification

special features?

Phenylalanine. Phe. Hydrophobic

Aromatic R group: absorbs UV very weakly at 280nm

Name, 3 letter abbreviation and Classification

special features?

Tyrosine. Tyr. Polar.

Can form H-bonds but also participate in hydrophobic interactions!!

Absorbs UV at 280nm

due to OH group, it can be phosphorylated

pKa = 10.5 therefore has H under biological conditions (negative charge at pH 14)

Which 7 aminos have ionizable R groups?

Glutamate, Aspartate, Lysine, Arginine, Tyrosine, Histidine, Cytsteine

Name, 3 letter abbreviation and Classification

special features?

Tryptophan. Trp. Hydrophobic.

Biggest and bulkiest side chain. Hydrophobic but can form an H bond.

Heterocyclic and Absorbs UV Strongly at 280nm

Name, 3 letter abbreviation and Classification

special features?

Serine. Ser. Polar

Can be phosphorylated due to OH group.

Participates in H bonding.

Name, 3 letter abbreviation and Classification

special features?

Threonine. Thr. Polar

2 chiral carbons!

Can be phosphorylated

H-bonds as donor and acceptor

Name, 3 letter abbreviation and Classification

special features?

Cysteine. Cys. Polar.

Can form disulphide bridges/bonds with other Cys.

Can form H-bonds but doesn't act as an acceptor

pKa = 8.5 can give up H at pH 14

What are the necessary conditions to form a disulphide bridge and where can this occur?

1. Two Cys residues must be close enough to form a bond

2. Oxidizing environment such as the mitochondria or the extracellular fluid

If S-S bonds are formed in an oxidizing environment, what breaks a disulphide bond?

A reducing env.

What is Cystine? Is it polar or hydrophobic?

Two cysteine side chains interacting in a disulphide bond. 

Relatively hydrophobic (S-S bond not S-H)

Name, 3 letter abbreviation and Classification

special features?

Asparagine. Asn. Polar.

Amide group and forms hydrogen bonds (O acceptor, N donor)

Name, 3 letter abbreviation and Classification

special features?

Glutamine. Gln. Polar

Amide group, forms H-bonds

Name, 3 letter abbreviation and Classification

special features?

Lysine. Lys. Charged.

Positive charge from NH3 at pH 7

pKa = 10.5 therefore neutral/loses H at pH 14. Basic amino acid

Long CH chain is hydrophobic?

Name, 3 letter abbreviation and Classification

special features?

Arginine

Basic, but never deprotonated under biological conditions

pKa = 12.5

H bond donor only!

Name, 3 letter abbreviation and Classification

special features?

Histidine. His. Polar

Aromatic - abs weakly at 280nm

pKa = 6 therefore neutral at 7 but becomes protonated at pH 1 with a positive charge!

Histidine can act as an acid or a base in reactions and also participates in H-bonding. 

At pH 10 and 1 is histidine protonated or not? what is its pKa

pKa = 6 therefore;

10 = no

1 = yes

Name, 3 letter abbreviation and Classification

special features?

Aspartate. Asp. Charged

acidic amino acid. pKa = 4.0

Negative charge at pH = 7 but called aspartic acid at pH 1 since it becomes protonated

Negatively Name, 3 letter abbreviation and Classification

special features?

Glutamate. Glu. Charged. 

pKa = 4: Negative at pH 7 

acidic amino acid

called glutamic acid at pH 1 since becomes protonated