Chapter 3 - Amino Acids
Histidine (additional info)
Because its pKa is very close to physiological pH, its ionization state can easily change with changes in its surrounding. This makes it a good residue to catalyze dynamic reactions. When charged, the charges can be shared by both nitrogens, making it more stable.
Charges of amino acids
Charges at pH 7.4 -NH2, pKa=9.0 -COOH, pKa=3.1 At pH 7.4, both are in ionized states. Most amino acids are zwitterions at pH 7.4 Note: in peptides both groups are changed to amides, which is neutral.
Cysteine
Cys C Polar
Histidine
His H Positively charged
Alanine
Ala A Hydrophobic
Amino Acid Classification
Amino acids are classified according to the properties of their side chains: -Hydrophobic -Polar -Positively charged (basic) -Negatively charged (acidic)
Basic frame work of amino acids
Amino acids are consisted of a sp3 carbon attached to: -Amine group, -NH2. -Carboxyl group, -COOH -Proton -Functional group R (aka side chain), whose identity is determined by amino acid type.
Arginine
Arg R Positively charged
Asparagine
Asn N Polar
Aspatic acid
Asp D Negatively charged
Glutamate
Gln Q Polar
Glutamic Acid
Glu E Negatively charged
Glycine
Gly G Hydrophobic
Shikimate & Glyphosate
Human's inability to synthesize certain amino acids can work to our advantage. 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase catalyzes an important step in aromatic amino acid synthesis. Only plants and bacteria have this enzyme. The potent herbicide glyphosate ("roundup") is an inhibitor of the enzyme EPSP synthase. It is structurally similar to phosphoenolpyruvate, the native substrate of EPSP synthase. Because humans do not have EPSP synthase, glyphosate is almost inert to humans.
Isoleucine
Ile I Hydrophobic
The concept of isoelectric point
Isoelectric point of the molecule is the pH at which the molecule has no net charge. No net charge means: -The molecule may contain no charged group at all. -The molecule may contain equal amounts of negatively and positively charged groups.
Leucine
Leu L Hydrophobic
Lysine
Lys K Positively charged
Methionine
Met M Hydrophobic
Essential Amino Acids
Most bacteria and plants can synthesize all 20 amino acids using basic compounds such as glucose and ammonia. But higher organisms lack the ability to make all 20 and must acquire certain amino acids through diet. Nonessential: Alanine Arginine Asparagine Aspartate Cysteine Glutamate Glutamine Glycine Proline Serine Tyrosine Essential: Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine
Phenylalanine
Phe F Hydrophobic
Proline
Pro P Hydrophobic
Serine
Ser S Polar
Know Fisher Projections
Seriously
Amino Acids
The building block of proteins. 20 different amino acids are found in most organisms. Their properties give proteins their diverse functionalities.
Chirality of amino acids
The sp3 carbon in the center of an amino acid has 4 different substitutions. This makes it a chiral center. Only L-isomer is found in normal proteins. L=S D=R (L=life D=death)
Threonine
Thr T Polar
Tryptophan
Trp W Hydrophobic
Tyrosine
Tyr Y Polar
Valine
Val V Hydrophobic
How side chain charges are determined
by side chain pKa pKas of individual amino acids can be greatly influenced by protein microenvironments. At pH 7.4: -Lys, Arg are always positively charged. -Asp, Glu are always negatively charged. -His can be either neutral or positively charged depending on pKa. -Cys and Tyr are usually neutral.
Properties of amnio acid side chain determine properties of proteins
α-amine and carboxyl groups are converted to amides, thus their charge does not influence protein property. Side chains of amino acids have a much higher influence on the behavior of proteins.
