Proteins and Amino Acids PDF

For Your Eyes Only PROTEINS: AMINO ACIDS OVERVIEW A. Proteins - most abundant - every life process depends on this class of molecules 1. Common Structural Feature...

For Your Eyes Only PROTEINS: AMINO ACIDS OVERVIEW A. Proteins - most abundant - every life process depends on this class of molecules 1. Common Structural Feature - linear polymers of amino acids 2. Functions a. Direct and Regulate Metabolism in the Body i. As hormones that carry signals from one group of cells to another - ex. polypeptide hormones ii. As enzymes that increase the rate of biochemical reactions b. Transporters of Hydrophobic Compounds in the Blood - ex. hemoglobin plasma albumin c. Cell Adhesion Molecules - attach cells to each other and to the extracellular matrix d. Ion Channels - through lipid membranes e. Movement - ex. contractile proteins in muscles f. Framework for Deposition of Calcium Phosphate Crystals - collagen in bone g. Protection - ex. immunoglobulins that destroy infectious bacteria and viruses STRUCTURE of AMINO ACIDS - 20 amino acids - at physiologic pH (7.4) in solution - free amino acids exist as zwitterions - carboxyl group is dissociated forming negatively charged carboxylate ion (-COO-) - amino group is protonated (-NH3+) - almost all carboxyl and amino groups are combined in peptide linkage and are not available for chemical reaction (except for hydrogen bond formation) - nature of side chains dictate the role of an amino acid plays in a protein  For Your Eyes Only CLASSIFICATION of AMINO ACID SIDE CHAINS - according to the polarity and structural features - helpful in describing common functional roles or metabolic pathways of the amino acids A. Nonpolar, Aliphatic Amino Acids 1. Glycine - simplest amino acid - really does not fit well into any classification because its side chain is only a hydrogen atom - side chain is so small  causes the least amount of steric hindrance in a protein (i.e., it does not significantly impinge on the space occupied by other atoms or chemical groups)  often found in bends or in the tightly packed chains of fibrous proteins 2. Alanine and the Branched Chain Amino Acids (Valine, Leucine, and Isoleucine) - have bulky, nonpolar, aliphatic side chains - high degree of hydrophobicitiy of the branched chain amino acid side chains  within proteins, these amino acid side chains will cluster together to form hydrophobic cores - oily or lipid like  promote hydrophobic interactions  For Your Eyes Only - electrons are shared equally between the carbon and hydrogen atoms in these side chains  cannot hydrogen bond with water - their association is also promoted by van der Waals forces between the positively charged nucleus of one atom and the electron cloud of another - effective over short distances when many atoms pack closely together 3. Proline - contains a rigid ring involving its -carbon and its -amino group  imino group - causes a kink in the peptide backbone that prevents it from forming its usual configuration - unique geometry of proline contributes to the formation of the fibrous structure of collagen - often interrupts the α-helices found in globular proteins B. Aromatic Amino Acids - side chains contain ring structures with similar properties - polarity differ - side chain aromatic ring is a six-membered carbon-hydrogen ring with three conjugated double bonds (benzene ring or phenyl group) - substituents on the ring determine whether the amino acid side chain engages in polar or hydrophobic interactions 1. Phenylalanine - side chain ring contains no substituents - electrons are shared equally between the carbons in the ring  very nonpolar hydrophobic structure in which the rings can stack on each other  For Your Eyes Only 2. Tyrosine - hydroxyl group on the phenyl ring - engages in hydrogen bonds  the side chain is more polar and more hydrophilic - can participate or serve as a site of attachment (ex: phosphate group) - side chain can lose a proton at alkaline pH 3. Tryptophan - more complex indole ring with a nitrogen that can engage in hydrogen bonds  more polar than phenylalanine C. Aliphatic, Polar, Uncharged Amino Acids 1. Asparagine, Glutamine - side chains contain carbonyl and polar amide group - amides of the amino acids aspartate and glutamate 2. Serine, Threonine - side chains contain a polar hydroxyl group that can participate or serve as a site of attachment (ex: phosphate group)  For Your Eyes Only 3. Hydroxyl and Amide Groups in the Side Chains - allow these amino acids to form hydrogen bonds with - water - each other - peptide backbone - other polar compounds in the binding sites of the proteins - hydrophilic  frequently found on the surface of water-soluble globular proteins 4. Serine - side chain is an important component of the active site of many enzymes 5. Asparagine - amide group as site of attachment of oligosaccharide chains in glycoproteins 6. Threonine - hydroxyl group as site of attachment of oligosaccharide chains in glycoproteins D. Sulfur-Containing Amino Acids 1. Methionine - nonpolar amino acid - with a large bulky side chain that is hydrophobic - does not contain a sulfhydryl group - cannot form disulfide bonds - important and central role in metabolism is related to its ability to transfer the methyl group attached to the sulfur atom to other compounds 2. Cysteine - important component of the active site of many enzymes - side chains can lose a proton at alkaline pH - side chain contains a sulfhydryl group that has a pKa of approximately 8.4 for dissociation of its hydrogen  predominantly undissociated and uncharged at the physiologic pH of 7.4 - free cysteine molecule in solution can form a covalent disulfide bond with another cysteine molecule through spontaneous (nonenzymatic) oxidation of their sulfhydryl groups  cystine (present in blood and tissues, not very water-soluble)  For Your Eyes Only 3. Cystine Disulfide Bond - often plays an important role in holding two polypeptide chains or two different regions of a chain together E. The Acidic and Basic Amino Acids For Your Eyes Only 1. Aspartate and Glutamate - proton donors - fully ionized side chains at neutral pH containing a negatively charged carboxylate group  called aspartate or glutamate at physiologic pH - form ionic (electrostatic) bonds with positively charged molecules, such as the basic amino acids (lysine, arginine, and histidine) 2. Histidine, Lysine, and Arginine - basic amino acids - have side chains containing nitrogen that can be protonated and positively charged at physiologic and lower pH values 3. Histidine - has a nitrogen-containing imidazole ring for a side chain - weakly basic - largely uncharged at physiologic pH - when incorporated into protein, side chain can be either positively charged or neutral depending on the ionic environment provided by the polypeptide chains of the protein (important to the role it plays in the functioning of proteins such as myoglobin) 4. Lysine - has a primary amino group on the 6th or  carbon (from the sequence , , , , ) 5. Arginine - has a guanidinium group 6. Lysine and Arginine - side chains often form ionic bonds with negatively charged compounds bound to the protein binding sites, such as the phosphate groups in ATP - at physiologic pH, side chains are fully ionized and positively charged  For Your Eyes Only 7. Positive Charges on the Basic Amino Acids - enables them to form ionic bonds (electrostatic bonds) with negatively charged groups, such as the side chains of acidic amino acids or the phosphate groups of coenzymes 8. Acidic and Basic Amino Acid Side Chains - also participate in hydrogen bonding and the formation of salt bridges (such as the binding of an inorganic ion such as Na+ between two partially or fully negatively charged groups) - charges on these amino acids at physiologic pH is a function of their pKa for dissociation of protons from the - -carboxylic acid groups - -amino groups - side chains 9. Charge on the Amino Acid at a Particular pH - determined by the pKa of each group that has a dissociable proton CHARACTERISTICS of the SIDE CHAINS that are USEFUL for CLASSIFICATION A. pKa B. Hydropathic Index - scale used to denote the hydrophobicity of the side chain - the more positive the hydropathic index, the greater the tendency to cluster with other nonpolar molecules and exclude water in the hydrophobic effect - the more negative the hydropathic index of an amino acid, the more hydrophilic is its side chain  For Your Eyes Only SUMMARY of the 20 FUNDAMENTAL AMINO ACIDS ACCORDING to their SIDE CHAINS A. Alipathic Nonpolar Side Chains - glycine - alanine - valine - leucine - isoleucine B. Aromatic Side Chains - phenylalanine - tyrosine - tryptophan C. Hydroxyl-Containing Side Chains - serine - threonine D. Acidic Side Chains - aspartate - glutamate  For Your Eyes Only E. Amidic Amino Acids - asparagine - glutamine F. Basic Side Chains - lysine - arginine - histidine G. Sulfur-Containing Side Chains - cysteine - methionine H. Imino Acid - proline NONPROTEIN AMINO ACIDS A. Antibiotics B. Toxins ABBREVIATIONS and SYMBOLS for the COMMONLY OCCURING AMINO ACIDS OPTICAL PROPERTIES of AMINO ACIDS A. -Carbon - attached to 4 different chemical groups  chiral or optically active carbon atom 1. Glycine - is the exception - -carbon has 2 substituents  optically inactive (neither D nor L) B. Mirror Images - amino acids that have asymmetric centre at the -carbon can exist in 2 forms, D and L  For Your Eyes Only - the 2 forms in each pair are termed stereoisomers, optical isomers, enantiomers - all amino acids found in proteins are all in L-configuration - amino group to the left if the carboxyl group is at the top of the structure - D-amino acids are found - some antibiotics - bacterial cell walls MODIFIED AMINO ACIDS - not coded for in the DNA A. Derivation - from one or another of the 20 fundamental amino acids after these have been incorporated into the protein chain B. Result of Modifications - change the structure of one or more specific amino acids on a protein  1. Serve a regulatory function 2. Target or anchor the protein in membranes 3. Enhance a protein’s association with other proteins 4. Target it for degradation C. Modifications - when these reactions are enzyme-catalyzed  referred to as post-translational modifications 1. Glycosylation - oligosaccharides (small carbohydrate chains) are bound to proteins by either N- linkages or O- Linkages a. N-Linked Oligosaccharides - found attached to cell surface proteins - protect the cell from proteolysis or an immune attack b. O-Glycosidic Link - common way of attaching oligosaccharides to the serine or threonine hydroxyl groups in secreted proteins - intracellular polysaccharide glycogen is attached to a protein through an O-glycosidic linkage to a tyrosine For Your Eyes Only 2. Fatty Acylation or Prenylation - many membrane proteins contain a covalently attached lipid group that interacts hydrophobically with lipids in the membrane a. Palmitoyl Groups (C16) - often attached to plasma membrane proteins b. Myristoyl Group (C14) - often attached to proteins in the lipid membranes of intracellular vesicles c. Farnesyl (C15) or Geranyl Group (C20) - synthesized from the five-carbon isoprene unit (isopentenyl pyrophosphate)  called isoprenoids - attached in ether linkage to a specific cysteine residue of certain membrane proteins, particularly proteins involved in regulation 3. Regulatory Modifications - alter bonding by that residue and change the activity of the protein a. Phosphorylation - transfer of a phosphate group (large, bulky, negatively charged group that can alter the activity of a protein) from ATP - phosphorylation of an OH group on - serine - threonine - tyrosine - by protein kinase b. Reversible Acetylation - occurs on lysine residues of histone proteins in the chromosome  changes in their interaction with the negatively charged phosphate groups of DNA c. ADP-Ribosylation - transfer of an ADP-ribose from NAD+ to an arginine, glutamine, or a cysteine residue on a target protein in the membrane (primarily in leukocytes, skeletal muscles, brain, and testes) - may regulate the activity of the proteins For Your Eyes Only 4. Other Amino Acid Posttranslational Modifications a. Carboxylation of the Carbon of Glutamate (Carbon 4) - in certain blood clotting proteins - important for attaching the clot to a surface i. Calcium Ions - mediate the attachment by binding to the two negatively charged carboxyl groups of -glutamate and two additional negatively charged groups provided by phospholipids in the cell membrane b. Hydroxylation/Oxidation i. Collagen - abundant fibrous extracellular protein - contains the oxidized amino acid hydroxyproline - addition of the hydroxyl group to the proline side chain provides an extra polar group that can engage in hydrogen bonding between the polypeptide strands of the fibrous protein For Your Eyes Only 5. Selenocysteine - unusual amino acid - found in a few enzymes and is required for their activity - its synthesis is not a posttranslational modification - modification to serine that occurs while serine is bound to a unique tRNA - inserted into the protein as it is being synthesized  For Your Eyes Only ACID-BASE PROPERTIES of AMINO ACIDS A. Amino Acids are Amphoteric Molecules - have both acidic and basic groups B. Amino Acids in Aqueous Solutions at Physiologic pH (7.4) 1. Amino Group a. pKa - for all of the -amino groups is approximately 9.5 (8.8 - 11.0) b. At pH of 7.4 - most of the amino groups are fully protonated and carry a positive charge 2. Carboxylic Acid Group a. pKa (of the Primary Carboxylic Acid Groups) - approximately 2 (1.8-2.4) b. At pH Values Much Lower Than the pKa - all of the carboxylic acid groups are protonated c. At pKa - 50% of the molecules are dissociated into carboxylate anions and protons d. At pH of 7.4 - more than 99% of the molecules are dissociated  negatively charged C. Amino Acids with Ionisable Groups in Side Chains 1. Acidic- aspartate - glutamate 2. Basic - histidine - lysine - arginine  For Your Eyes Only D. Titration of an Amino Acid 1. Dissociation of the Carboxyl Group (-COOH) - ex: Alanine - contains - -amino group - -carboxyl group - at low pH - both groups are protonated - at pH elevation - -COOH group dissociates losing a proton  carboxylate group (-COO-) formation  the molecule assumes the dipolar (zwitterions or isoelectric) form 2. Application of the Henderson-Hasselbalch Equation K1 = (H+)(II) K1 - dissociation constant (I) I - fully protonated form II - isoelectric form pH = pK1 + log (II) (I) 3. Dissociation of the Amino Group (-NH3+) - much weaker acid than the -COOH group  smaller dissociation constant (K2) 4. pKs of Alanine - each titrable group has a pKa that is numerically equal to the pH at which ½ of the protons have been removed from that group 5. Titration curve of Alanine a. Buffer Pairs - -COOH/-COO- as buffer in the pH region around pK1 - -NH3+/-NH2 as buffer in the region around pK2 b. When pH = pK - pH = pK1  forms I and II are equal in amount in the solution - pH = pK2  forms II and III are equal in amount in the solution c. Isoelectric Point - alanine at neutral pH - exists predominantly as form II - amino and carboxyl groups are ionized - net charge is zero For Your Eyes Only 6. Net Charge of Amino Acids at Physiologic (Nearly Neutral) pH - all amino acids have - -COO- - - NH3+ - amphoteric substances - substances that can act as either an acid or a base - referred as ampholytes (amphoteric electrolytes) 7. Titration Curve of Histidine For Your Eyes Only 8. Titrable Groups in Proteins - only the amino acid side chains and the amino group at the amino terminal and carboxyl group at the carboxyl terminal have dissociable protons  For Your Eyes Only SUMMARY For Your Eyes Only