Amino Acids PDF

Structure, Function, and Properties of Amino Acids Objectives: 1.To know what are Amino Acids. 2.To classify Amino Acids. 3.To know the functions, structures, and properties of the Amino Acids. Amino acids are the building blocks for the vast assortment of proteins found in all living...

Structure, Function, and Properties of Amino Acids Objectives: 1.To know what are Amino Acids. 2.To classify Amino Acids. 3.To know the functions, structures, and properties of the Amino Acids. Amino acids are the building blocks for the vast assortment of proteins found in all living cells. All of the proteins on earth are made up of the same 20 amino acids. Linked together in long chains called polypeptides. All amino acids have the same basic structure, shown in the figure below. At the center of each amino acid is a carbon called the α carbon and attached to it are four groups – a hydrogen, a carboxylic acid group, an amine group, and an R-group, sometimes referred to as a variable group or side chain. The α carbon, carboxylic acid, and amino groups are common to all amino acids, so the R-group is the only variable feature. With the exception of glycine, which has an R-group consisting of a hydrogen atom, all of the amino acids in proteins have four different groups attached to them and consequently can exist in two mirror isomeric forms. Essential and Non-essential Nutritionists divide amino acids into two groups – essential amino acids and non-essential amino acids. Essential amino acids must be included in our diet because our cells can’t synthesize them. What is essential varies considerably from one organism to another and even differ in humans, depending on whether they are adults or children. Some amino acids that are normally nonessential, may need to be obtained from the diet in certain cases. Individuals who do not synthesize sufficient amounts of arginine, cysteine, glutamine, proline, selenocysteine, serine, and tyrosine, due to illness, for example, may need dietary supplements containing these amino acids. Non-protein amino acids There are also amino acids found in cells that are not incorporated into proteins. Common examples include ornithine and citrulline. Both of these compounds are intermediates in the urea cycle, an important metabolic pathway. Amino acids can be classified based on the chemistry of their R-groups. It is useful to classify amino acids in this way because it is these side chains that give each amino acid its characteristic properties. Thus, amino acids with (chemically) similar side groups can be expected to function in similar ways The names of the standard amino acids are often abbreviated using three letter codes (some four). These abbreviations are the first letter of the AA’s first letter.  The amino acids in this group have Non-polar amino nonpolar, hydrophobic R groups. acids When incorporated into globular proteins they tend to pack inward Alanine (Ala/A) among other hydrophobic groups. In Glycine (Gly/G) proteins that embed themselves Isoleucine (Ile/I) into or through membranes, these Leucine (Leu/L) amino acids can orient themselves Methionine (Met/M) toward hydrophobic portions of the Valine (Val/V) inside of the membrane.  These amino acids each contain a carboxylic acid group as part of the Acidic Amino Acids variable group. At physiological pH, (Carboxylic acid side these groups exist primarily in their chains) deprotonated state. It is easy to be confused if they are drawn in this Aspartic acid (Asp/D) state, because their names include Glutamic acid (Glu/E) “acid” while the structure shows no ionizable proton and the charge on the R group is negative. In addition to its role as a building block in proteins, glutamic acid (with the deprotonated form named “glutamate”) is a neurotransmitter. It also is recognized by a receptor in our mouths, contributing to a taste sensation described as “umami.” Many foods contain appreciable amounts of glutamate that are recognized by our taste receptors, and encourage us to eat these substances. Those foods frequently contain protein that has broken down to some degree: cooked meats, fermented sauces like Worcestershire or soy, tahini, broths, and yeast extracts.  The variable group in each of these Basic amino acids amino acids contains nitrogen, (Nitrogen-containing which imparts to the group the side chains) ability to exist in protonated and deprotonated states. They are Arginine (Arg/R) frequently called basic, but also are Histidine (His/H) often drawn in their protonated Lysine (Lys/K) state which is more prevalent at physiological pH. The variable group in each of these amino acids contains nitrogen, which imparts to the group the ability to exist in protonated and deprotonated states. They are frequently called basic, but also are often drawn in their protonated state which is more prevalent at physiological pH.  These amino acids are included Aromatic amino acids in protein structures but also serve as precursors in some Phenylalanine (Phe/ F) important biochemical Tryptophan (Trp/W) pathways, leading to the Tyrosine (Tyr/Y) production of hormones such as L-Dopa and serotonin.  The amino acids in this group contain alcohol groups, which can engage in Hydroxyl amino hydrogen-bonding interactions. As part acids of protein molecules they are hydrophilic and can be oriented Threonine (Thr/T) outward in watery environments. The Serine (Ser/S) alcohol group is subject to chemical Tyrosine (Tyr/Y) reactions or modifications, for instance when carbohydrate groups are covalently linked to proteins. Other amino acids Asparagine (Asn/N) is a polar amino acid. The amide on the functional group is not basic. Cysteine (Cys/C) Glutamine (Gln/Q) Chirality of Amino Acids Out of the 20 amino acids, 19 possesses a chiral center. The rules for drawing the Fischer projection formula for amino acid structures follow. 1.The –COOH group is put at the top of the projection. 2.The –R group is at the bottom of the projection 3.The –NH2 group is in horizontal position ( positioning it on the left denotes the L-isomer, right is for the D- isomer. With few exceptions, the amino acids found in the nature and in proteins are L-isomers Acid-Base Properties of Amino Acids Amino acids are amphoteric, because they both have an acidic and basic characteristics. Meaning, it can act as an acid or as a base. Zwitterion- a molecule that has a positive charge on one atom and negative charge on another aton on the same molecule. In solution and solid form, alpha- amino acids exists as zwitterion. Activity. Draw the structural structure of amino acids Alanine, Leucine, and Valine at pH 1, 7, and 11. Guidelines for amino acid formulas a function of solution pH follow. Low pH- all acid groups are protonated(-COOH) and all amino groups are protonated (-NH3+). High pH- all acid groups are deprotonated (-COO-) and amino groups are deprotonated (-NH2). Neutral pH- all acids are deprotonated (-COO-) and amino groups are protonated (-NH3). Isoelectric Points and Electrophoresis Isoelectric Point is the pH at which an amino acid solution has no net charge because an equal number of positive and negative charges are present. At this point, almost all amino acid molecules in the solution are present in their zwitterion form. Electrophoresis is the process of separating charged molecules on the bass of their migration towards charged electrodes associated with an electric field.