BCC Amino Acid Lecture Handouts PDF

Amino Acids Nükhet Aykın-Burns, PhD Division of Radiation Health Pharmaceutical Sciences Biomed II, Room 441A-2 [email protected] LEARNING OBJECTIV...

Amino Acids Nükhet Aykın-Burns, PhD Division of Radiation Health Pharmaceutical Sciences Biomed II, Room 441A-2 [email protected] LEARNING OBJECTIVES: At the end of this lecture, students should be able to: 1. List the main roles of proteins. 2. Define basic levels of protein structure. 3. Recognize and describe the general structure of an amino acid. 4. Associate the structure and side chain properties of amino acids found in mammalians with their ionization properties. 5. Describe the terms zwitterion and isoelectric point. 6. Describe how amino acid side chains can affect protein structure and function. 7. List the 3 letter abbreviations of amino acids correctly. 8. List the names of common posttranslational modifications in proteins. 9. Describe which amino acids are biosynthesized (non-essential) and and which ones must be obtained from the diet (essential). 10.Give examples of uncommon amino acids.  Proteins are large biomolecules, consisting of long chains of amino acid molecules. ² Proteins have many functions in the body. ² Proteins differ in their sequence of amino acids, determined by the nucleotide sequence of their genes, which usually results in folding of the protein into a specific three-dimensional structure that determines its activity. ² Few examples of protein function: catalysts transport and store other molecules such as oxygen provide mechanical support and immune protection generate movement transmit nerve impulse control growth and differentiation.  Levels of structure in proteins Proteins are linear polymers consist of monomer units called amino acids, which are linked by peptide bonds. § Primary structure – determined by the sequence of linked amino acids. § Secondary structure – determined by 3D structure formed by H-bonds between amino acids in close proximity. § Tertiary structure - is formed by folding of secondary structural elements into three-dimensional conformation due to long-range interactions between amino acids. § Quaternary structure - the three-dimensional structure of proteins with more than one subunit and how the subunits fit together.  General structure of an amino acid Proline is an exception due to its cyclic structure § This structure is common to all but one of the α-amino acids. (Proline, a cyclic amino acid, is the exception.) § Amino acids have three common functional groups attached to the α-carbon (Proline is the exception). an acidic carboxyl group connected to the α carbon a basic amino group connected to the α carbon an α hydrogen connected to the α carbon § The fourth substituent (R) is unique in glycine, the simplest amino acid. The fourth substituent is also hydrogen.  All amino acids are chiral (except Glycine) § Every amino acid (except glycine) can occur in two isomeric forms, because of the possibility of forming two different enantiomers (stereoisomers) around the central carbon atom. § By convention, these are called L- and D- forms, analogous to left-handed and right-handed configurations. § Only L-amino acids are incorporated into proteins. Some D- amino acids are found in the cell walls of bacteria, but not in bacterial proteins and antibiotics. Evolution??? § Recent studies suggest D-amino acids may play roles in human diseases.  Important functional groups in biology § Hydroxyl Group: In biology the important role of hydroxyl groups mostly has to do with their ability to form hydrogen bonds. The polarity of the functional group and the ability to form two simultaneous H-bonds increase the water solubility of any molecule that has a hydroxyl group attached to it. § Phosphate Group Phosphate groups are vital structural units for nucleic acids, and biological membranes; they have a perfectly balanced reduction potential to make them excellent intermediaries in redox reactions; Their large size, and electronegativity can cause deformations in the 3D structure of proteins which make them the primary way to control enzymatic function, and cell signaling. § Carboxyl Group (Carboxylic Acid): Carboxylic acids are ubiquitous in biology and include amino acids, fatty acids, acetic acid, and many others. Carboxyl groups are also susceptible to nucleophilic attack, especially when modified in an enzymatic pocket. This is what allows amino acids to chain together into proteins. § Amino Group: Amines function as bases by accepting protons and important for maintaining the structure of many macromolecules through electrostatic interactions and H-bonding. § Thiol Group: The thiol group is nucleophilic and readily undergo redox reactions, giving it a variety of biological functions. The most common place students will see thiols is in the amino acid cysteine. Two cysteines can form a sulfur-sulfur bonds which give additional 3D structure to the protein. § Carbonyl Group: Carbonyl groups have a large partial positive charge on the carbon attached to the oxygen which makes it susceptible to nucleophilic attack.  Amino acids polymerize to form peptides n tio sa en nd Co Carnosine PEPTIDE BOND (beta-alanyl-L-histidine) § Peptides are small condensation products of amino acids. § They are “small” compared with proteins § Numerous peptide based drugs are already in the market.  Amino acids : Classification Over 300 amino acids are present in the nature but mammalian proteins are composed of only 20 amino acids. Common amino acids can be placed in five basic groups depending on their R substituents: vnonpolar, aliphatic (7) Their chemical varomatic (3) properties determine the vpolar, uncharged (5) types of bonds they make and their vpositively charged (3) interactions with vnegatively charged (2) other molecules. § The chemical properties of the side chain determine the types of bonds and interactions each amino acid in a polypeptide chain can make with other molecules. § These groupings are helpful in describing common functional roles or metabolic pathways of the amino acids. MEMORIZE ONLY “3 LETTERS” ABBREVIATIONS Memorize ONLY 3-letters abbreviations  Ionization of amino acids § All free amino acids, plus charged amino acids in peptide chains, can serve as buffers. § Amino acids contain at least two ionizable protons, each with its own pKa. § The carboxylic acid has an acidic pKa and will be protonated at an acidic (low) pH: COOH ↔ COO− + H+ § The amino group has a basic pKa and will be protonated until basic pH (high) is achieved: NH4+ ↔ NH3 + H+  Ionization state of amino acids as a function of pH Under the physiological pH range (6.8-7.4), amino acids are zwitterions § Zwitterion is a neutral molecule with both positive and negative electrical charges. § Under the physiological pH range (6.8-7.4), amino acids are zwitterions, or dipolar ions. § Ionization state of an amino acid varies with pH § In acid solution, amino acid’s amino group protonated (-NH3+) & carboxyl group is not dissociated (-COOH), predominantly positively charged. § pH raised: carboxylic acid group give out a proton. (Zwitterionic form – both charges) § Until pH ~9: protonated amino group loses a proton , predominantly negatively charged. § Predicting amino acids’ electrical charges at a particular pH is important since it affects structure and function.  Isoelectric point (pI) Achieving sufficient solubility in the formulation and maintaining chemical and physical stability are highly dependent on the pH. Thus isoelectric point is an important concept in development of peptide based drugs. § The isoelectric point (pI) - the pH at which a molecule carries no net electrical charge. § The net charge on the molecule is affected by pH and can become more positively or negatively charged due to the gain or loss, respectively, of protons (H+). § The pI value can affect the solubility of a molecule at a given pH. They have minimum solubility in water or salt solutions at the pH that corresponds to their pI and often precipitate out of solution.  Nonpolar (hydrophobic) amino acids § In proteins found in aqueous solutions––a polar environment––the side chains of the nonpolar amino acids tend to cluster together in the interior of the protein. § This phenomenon is called the hydrophobic effect § The hydrophobic effect is the result of the hydrophobicity of the nonpolar R-groups. § The nonpolar R-groups fill up the interior of the folded protein and help give it its 3 dimensional shape. § Proteins that are located in a hydrophobic environment, such as a membrane, the nonpolar R-groups are found on the outside surface of the protein, interacting with the lipid environment. § Proline differs from other amino acids in that proline’s side chain and α- amino N form a rigid, five-membered ring structure. § Proline has a secondary amino group. The unique geometry of proline contributes to the formation of the fibrous structure of collagen, and often interrupts the α-helices found in globular proteins.  Amino acids in humans ** § Essential amino acid - an amino acid that cannot be synthesized de novo (from scratch) by the organism being considered, and therefore must be supplied in its diet. If they are not taken through diet, they will not be available for protein synthesis. § Some amino acids are considered conditionally essential. Under certain conditions like illness or stress the body might not be able, or might be limited in the ability, to synthesize them. § PVT : Phe, Val, Thr § TIM : Trp, Ile, Met § HALL : His, Arg**, Leu, Lys § Pro and Tyr are not essential amino acids – do not confuse them with Phe, Thr and Trp § Arginine may or may not considered as essential, depending on certain conditions.  Uncommon / Modified Amino Acids Found in Proteins § Some uncommon amino acids found in proteins, are derived from common amino acids. § Extra functional groups added by modification reactions are shown in red. § Desmosine is formed from four Lys residues (the carbon backbones are shaded in light red). § Selecysteine is sometimes called as the 21st amino acid, which is commonly involved in many proteins with antioxidant properties. Selenocysteine has both a lower pKa and a lower reduction potential than cysteine.  Reversible modifications of amino acids Cys Reversible amino acid modifications involved in regulation of protein activity. Phosphorylation is the most common type of regulatory modification. Lys Ser, Thr POST TRANSLATIONAL MODIFICATIONS OF PROTEINS Nitration – Tyr Deamination – Gln Hydroxylation – Pro Glycosylation - Asn