Amino Acids 1st Semester 2024-2025 PDF

1 Photo by: https://unsplash.com/photos/b9id_N3uI3E  2 Text Source: McMurry, J. (2016). Organic Chemistry (9th ed.). Cengage Learning.  Mass composition data...

1 Photo by: https://unsplash.com/photos/b9id_N3uI3E  2 Text Source: McMurry, J. (2016). Organic Chemistry (9th ed.). Cengage Learning.  Mass composition data for the human body in terms of major types of biochemical substances. Next to water, proteins are the most abundant substances in nearly all cells. They account for ~ 15% of a cell’s overall mass and for almost half of a cell’s dry mass. 3  Proteins A protein is a naturally-occurring, unbranched polymer. The presence of nitrogen in proteins sets them apart from carbohydrates and lipids, which most often do not contain nitrogen. The average nitrogen content of proteins is 15.4% by mass. Other elements, such as phosphorus and iron, are essential constituents of certain specialized proteins. Reading 4 assignment Proteins are major structural and functional polymers in living systems Proteins have a broad range of activities, including catalysis of metabolic reactions and transport of vitamins, minerals, oxygen, and fuels. Some proteins make up the structure of tissues, while others function in nerve transmission, muscle contraction and cell motility, and still others in blood clotting and immunologic defenses, and as hormones and regulatory molecules. 5 TEXT SOURCE: Baynes, J. W., & Dominiczak, M. H. (2014). Medical Biochemistry (4th ed.). Saunders. Photo by Shane Rounce on Unsplash 6  A typical human cell contains about 9000 different kinds of proteins, and the human body contains about 100,000 different proteins. The diversity of functions exhibited by proteins far exceeds the role of other biochemical molecules. The functional versatility of proteins stems from: Ability to bind small molecules specifically and strongly Ability to bind other proteins and form fiber-like structures Ability to be integrated into cell membranes Reading assignment 7 Major Categories of Proteins Based on Function Catalytic proteins: Enzymes serve as biocatalysts. Almost every chemical reaction in the body is driven/catalyzed by an enzyme. Defense proteins: Immunoglobulins or antibodies are central to functioning of the body’s immune system. Transport proteins: Bind small biomolecules, e.g., oxygen and other ligands, and transport them to other locations in the body and release them on demand. (Hemoglobin) Messenger proteins: transmit signals to coordinate biochemical processes between different cells, tissues, and organs. Human growth hormone regulates body growth. Insulin and glucagon regulate carbohydrate metabolism. Reading assignment 8 [VIDEO “HOW DO IMMUNOGLOBULINS/ ANTIBODIES WORK?] 9 10 Major Categories of Proteins Based on Function Contractile proteins: Necessary for all forms of movement. Muscles contain filament-like contractile proteins (actin and myosin). Human reproduction depends on the movement of sperm. Structural proteins: for stiffness and rigidity Collagen is a component of cartilage Keratin gives mechanical strength as well as protective covering to hair, fingernails, feathers, hooves, etc. Transmembrane proteins: Span a cell membrane and help control the movement of small molecules and ions. Serves as channels (help molecules to enter and exit the cell) Transport is very selective (allow passage of one type of molecule or ion). Reading assignment 11 The principles of protein flexibility and proteinprotein interaction through noncovalent interactions are illustrated at an extreme level by the cyclic conformational changes that cause muscles to contract. The proteins myosin and actin are organized into thick and thin filaments, which are themselves arranged in sarcomeres, the repeating units of myofibrils. Many myofibrils make up a muscle fiber; skeletal muscle consists of bundles of muscle fibers. The sliding of the myosin thick filaments along the actin thin filaments, coordinated by nerve impulses, produces the contraction of the muscle. Many other accessory proteins are involved in the structure and temporal control of these assemblies. Trivia 12 [VIDEO “Muscle contraction”] 13 Major Categories of Proteins Based on Function Storage proteins: bind (and store) small molecules. Ferritin (an iron-storage protein) saves iron for use in the biosynthesis of new hemoglobin molecules. Myoglobin - an oxygen-storage protein present in muscle Regulatory proteins: “embedded” in the exterior surface of cell membranes (act as sites for receptor molecules) These proteins bind to enzymes (catalytic proteins), thereby turning them “on” and “off” (controlling enzymatic action). Nutrient proteins: particularly important in the early stages of life - from embryo to infant Milk provide immunological protection for mammalian young. Casein (milk) and ovalalbumin (egg white) are nutrient proteins. Reading assignment 14  A protein is a polypeptide containing at least 40 amino acid residues. The lengths of polypeptide chains in proteins vary considerably. Small proteins contain 40–100 amino acid residues. Common proteins contain 400–500 amino acid residues. The largest known protein is titin (26,926 amino acids), which is a component of vertebrate muscle. Proteins can be: Monomeric- consist of a single polypeptide chain Multimeric (multi subunit) : contains 2 or more associated polypeptide chains - The individual polypeptide chains in a multi-subunit protein can be identical or different. - If at least two subunits are identical, the protein is said to be oligomeric and the identical units (consisting of one or more polypeptide chains) are referred to as protomers. 15 Hemoglobin is a heterotetramer consisting of four subunits (two α and two β), thus, oligomer. Structurally and functionally, hemoglobin is described better as (αβ)2, so we call it a dimer of two αβ-protomers, that is, a diprotomer. 16  Amino Acid Compositions of Proteins The amino acid compositions of proteins differ between proteins and are highly variable. Some amino acids occur only once or not at all in a given protein and other amino acids may occur in large numbers. 17  Proteins Proteins are the most abundant biological macromolecules in cells. Proteins mediate nearly every process that takes place inside a cell. All proteins, regardless of organism, are composed of the same set of these 20 amino acids that are incorporated into them during translation. These 20 amino acids are present in human body and are coded for by DNA, the genetic material in the cell. Reading 18 assignment Proteins are synthesized as a sequence of amino acids linked together in a linear polyamide (polypeptide) structure, but they assume complex three- dimensional shapes in performing their function. https://openstax.org/books/biology-2e/p 19 TEXT SOURCE: Baynes, J. W., & Dominiczak, M. H. (2014). Medical Biochemistry (4th ed.). Saunders. 20 http://clearlyexplained.com/pr 21  There are about 300 amino acids present in various animal, plant and microbial systems, but only 20 amino acids are coded by DNA to appear in proteins. Many proteins also contain modified amino acids and accessory components, termed prosthetic groups. 22 TEXT SOURCE: Baynes, J. W., & Dominiczak, M. H. (2014). Medical Biochemistry (4th ed.). Saunders. Photo source: https://www.genome.gov/genetic  https://aminoco.com/blogs/amino-acids/fun Each amino acid has a central carbon, called the α-carbon, to which four different groups are attached: a basic amino group (–NH ) 2 an acidic carboxyl group (–COOH) a hydrogen atom (–H) a distinctive side chain (–R). 1 R The R group determines the identity of the particular amino acid. 2 The two-dimensional formula shown here can only partially convey the common structure of amino acids because one of the most important properties of these compounds is their three-dimensional shape, or stereochemistry. 2 All amino acids in proteins are of the L-configuration, because proteins are biosynthesized by enzymes that insert only L-amino acids into the peptide chains. 1 TEXT SOURCES: 1. Baynes, J. W., & Dominiczak, M. H. (2014). Medical Biochemistry (4th ed.). Saunders. 23 2. Campbell, M. K., Farrell, S. O., & McDougal, O. M. (2018). Biochemistry. Cengage Learning. What are stereochemistry and isomerism? What is an L-configuration? 24 Let’s review an organic chemistry topic Review 25  STEREOCHEMISTRY the branch of chemistry that deals with the three-dimensional shape of molecules 26 Source: Campbell, M. K., Farrell, S. O., & McDougal, O. M. (2018). Biochemistry. Cengage Learning. ISOMERISM a property between a pair (or more) of molecules, i.e. a molecule is an isomer of another molecule.* 27 *Text Source: https://www.chem.ucalgary.ca/courses/350/Carey5th/useful/isomers.html  The concept of chirality Every object has a mirror image. Many pairs of objects that are mirror images can be superimposed on each other; two identical solid-colored coffee mugs are an example. 28 Source: Campbell, M. K., Farrell, S. O., & McDougal, O. M. (2018). Biochemistry. Cengage Learning.  In other cases, the mirror image objects cannot be superimposed on one another but are related to each other as the right hand is to the left. 29 Source: Campbell, M. K., Farrell, S. O., & McDougal, O. M. (2018). Biochemistry. Cengage Learning. Photo by Shoeib Abolhassani on Unsplash  Such non-superimposable mirror images are said to be chiral (from the Greek cheir, “hand”); many important biomolecules are chiral. The dashed wedges represent bonds directed away from the observer, and the solid triangles represent bonds directed out of the plane of the paper in the direction of the observer. A frequently encountered chiral center in biomolecules is a carbon atom with four different groups bonded to it. Such a center occurs in all amino acids except glycine. Source: Campbell, M. K., Farrell, S. O., & McDougal, O. M. (2018). Biochemistry. Cengage Learning. Reading assignment 30  Glycine has two hydrogen atoms bonded to the α-carbon; in other words, the side chain (R group) of glycine is hydrogen. Glycine is not chiral (or, alternatively, is achiral) because of this symmetry. In all the other commonly occurring amino acids, the α-carbon has four different groups bonded to it, giving rise to two non superimposable mirror- image forms. Source: Campbell, M. K., Farrell, S. O., & McDougal, O. M. (2018). Biochemistry. Cengage Learning. Reading assignment 31  two possibilities of non-superimposable mirror images, or stereoisomers, are shown on the picture. 32 Source: Campbell, M. K., Farrell, S. O., & McDougal, O. M. (2018). Biochemistry. Cengage Learning.  The position of the amino group on the left or right side of the -carbon determines the L or D designation. The amino acids that occur in proteins are all of the L-form. Although D-amino acids occur in nature, most often in bacterial cell walls and in some antibiotics, they are not found in proteins. 33 Source: Campbell, M. K., Farrell, S. O., & McDougal, O. M. (2018). Biochemistry. Cengage Learning.  The point in the molecule that serves as the anchor for the arrangements of other groups of atoms in space, such that interchanging the positions of any two groups, is called a stereocenter. Stereocenter (chiral center): An atom with three or more different attachments, interchanging of two of these attachments leads to another stereoisomer. http://www.chem.ucla.edu/~harding/IGOC/S/stereocenter.html Review 34 35  The terminology comes from the Latin words laevus and dexter, meaning “left” and “right,” respectively, which comes from the ability of optically active compounds to rotate polarized light to the left or the right.* optical activity - ability of these molecules to rotate plane-polarized light by an identical magnitude of opposing directions https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Organic_Chemistry_I_%28Liu%29/05%3A_Stereochemistry/5.04%3A_Optical_Activity 36 *Source: Campbell, M. K., Farrell, S. O., & McDougal, O. M. (2018). Biochemistry. Cengage Learning.  Chirality of Amino Acids Amino acids has a chiral or optically active α carbon atom. The α-carbon of an amino acid is bound to four unique groups, thus, it has a chiral/stereogenic center. A chiral molecule is one that cannot be superimposed with its mirror image. Every amino acid (except glycine) can occur in isomeric forms, L- and D-handed forms, because of the possibility of forming two different enantiomers (stereoisomers) around the central carbon atom. 37 The concept of chirality will be seen many times as we continue our study of biochemistry. Although it may not be obvious, whether a molecule is L- or D- is extremely important to its characteristics and function. A sugar molecule with the D- orientation may be sweet, whereas its L-isomer is bitter. A drug that is helpful in one orientation may be poisonous in the other orientation. We will see more of this in the chapters on proteins and enzymes, where specific orientations about a chiral carbon are critical to a molecule’s function. Reading assignment 38 L and D isomers Only the L isomers are manufactured in the cells and are used to build proteins in human body. All amino acids found in proteins are of the L-configuration. Some D isomers are found in bacterial cell walls and some antibiotics. 39  Glycine Glycine has no enantiomers because it has two hydrogen atoms attached to the central carbon atom. (optically inactive) Since glycine has 2 hydrogen atoms, one each on the parent and side chain, it's the only symmetrical and thus achiral amino acid. Threonine and isoleucine Threonine and isoleucine have two stereogenic centers. 40 41 Practice Exercise Name the following amino acids with correct designation for the enantiomer (chiral carbon is indicated by *). COOH COOH COOH H 2N *C H *C NH2 H 2N *C H CH CH3 CH2 CH2 CH2 SH CH3 OH L-Isoleucine D-Cysteine L-Tyrosine 42 Optically active molecules were discovered in 1843 by Louis Pasteur, who separated crystalline sediments of tartaric acid that accumulated in wine caskets. He discovered that while the crystallized sediments possessed identical shapes and chemical properties, they were mirror images of one another. The active molecules were also found to rotate light by the same magnitude, but in opposing directions. One type rotated polarized light leftwards (laevorotatory) and the other rightwards (dextrorotatory). X-ray crystallographic studies in 1951 confirmed the ‘handedness’ of tartaric acids and established that the absolute configuration of each. Review 43  The side chains determine the properties of amino acids Each functional group of an amino acid exhibits all of its characteristic chemical reactions. For carboxylic acid groups, these reactions include the formation of esters, amides, and acid anhydrides; for amino groups, acylation, amidation, and esterification; and for —OH and —SH groups, oxidation and esterification. 44 SOURCE: Kennely, P. J., Botham, K.M., McGuiness O., Rodwell, V.W., Weil, P.A. (2023) Harper’s Illustrated Biochemistry 32nd ed. McGraw Hill, LLC. The R group present in an α-amino acid is called the amino acid side chain. The nature of this side chain distinguishes α-amino acids from each other. Side chains vary in size, shape, charge, acidity, functional groups present, hydrogen bonding ability, and chemical reactivity. The side chains that ultimately dictates the role an amino acid plays in a protein. Reading 45 assignment One molecular hydrogen molecular atom has molecular mass of 1 Da, so 1 Da = 1 g/mol. Proteins and other molecular macromolecule molecular weights are usually measured in molecular kDa or kD (kilodaltons) - 1000 Da. Based on the frequencies at which the 20 standard amino acids occur in proteins, and their molecular weights, the average molecular weight of an amino acid in a protein is 128 Da. Because a molecule of water (molecular weight = 18 Da) is lost on creation of each peptide bond, the average molecular weight of an amino acid residue in a protein is about 110 Da. 46  Nomenclature of Amino Acid All the amino acids have trivial or common names, in some cases derived from the source from which they were first isolated. Asparagine was first found in asparagus, and glutamate in wheat gluten. Tyrosine (Greek tyros, “cheese”) was first isolated from cheese. Glycine (Greek glykos, “sweet”) was so named because of its sweet taste. 47  Nomenclature of Amino Acid Three letter abbreviations widely used for naming first letter of amino acid name is compulsory and capitalized followed by next two letters not capitalized. One-letter abbreviations commonly used for comparing amino acid sequences of proteins 48  Nomenclature of Amino Acid (Rules for One-letter Code) 1. Unique first letter: If only one amino acid begins with a particular letter, then that letter is used as its symbol. For example, I = isoleucine. 49  Nomenclature of Amino Acid (Rules for One-letter Code) 2. Most commonly occurring amino acids have priority: If more than one amino acid begins with a particular letter, the most common of these amino acids receives this letter as its symbol. For example, glycine is more common than glutamate, so G = glycine. 50  Nomenclature of Amino Acid (Rules for One-letter Code) 3. Similar sounding names: Some one-letter symbols sound like the amino acid they represent. 51  Nomenclature of Amino Acid (Rules for One-letter Code) 4. Letter close to initial letter: For the remaining amino acids, a one letter symbol is assigned that is as close in the alphabet as possible to the initial letter of the amino acid. 52  CLASSIFICATION OF AMINO ACIDS BASED ON R SIDE CHAINS Classification based on the polarity (distribution of electric charge) and presence of acidic or basic group of the R side chain. There are four categories: (1) nonpolar amino acids (2) polar neutral amino acids (3) polar acidic amino acids (4) polar basic amino acids This classification system gives insights into how various types of amino acid side chains help determine the properties of proteins. Reading 53 assignment  Nine (9) Nonpolar Amino Acids A nonpolar amino acid is an amino acid that contains one amino group, one carboxyl groups, and a nonpolar side chain. Hydrophobic (“water-fearing) They are generally found in the interior of proteins, where there is limited contact with water. 54 Reading assignment Nonpolar Amino Acids Aliphatic R groups Aromatic R groups Glycine Smallest or simplest amino acid. Although the hydrogen (H) side- chain of glycine is nonpolar but as a whole molecule, glycine is considered as polar. Tryptophan Phenylalanine Reading 55 assignment Proline Proline is the only cyclic/ secondary amino acid (imino acid). Proline’s side chain and α- amino N form a rigid, five membered ring structure, giving a cyclic side chain. Tryptophan Tryptophan is a borderline member of this group because water can weakly interact through hydrogen bonding with the NH ring location on tryptophan’s side-chain ring structure. Tryptophan is a precursor of serotonin. Reading 56 assignment Six (6) Neutral/Uncharged Polar Amino Acids Aromatic A polar neutral amino acid is an amino acid that contains one amino group, one carboxyl groups, and a side chain that is polar but neutral. In solution at physiological pH, the side chain of a polar neutral amino acid is neither acidic nor basic. These amino acids are more soluble in water. Their R groups can form hydrogen bond with water. Reading assignment 57  Two (2) Acidic Polar Amino Acids An acidic polar amino acid is an amino acid that contains one amino group and two carboxyl groups, the second carboxyl group being part of the side chain. Reading 58 assignment Three (3) Basic Polar Amino Acids A basic polar amino acid is an amino acid that contains two amino groups and one carboxyl group, the second amino group being part of the side chain. Arginine has a 3-carbon aliphatic straight chain ending in a guanidine group. Histidine has an imidazole ring. Reading 59 assignment Non-polar Non-polar Polar Neutral Polar Basic Polar Acidic Reading assignment 60 Derived Amino Acids 61 Acid-Base Properties of Amino Acid Reading 62 assignment  Acid-Base Properties of Amino Acid Amino acids are the best-known examples of zwitterions. A zwitterion is a molecule with functional groups, of which at least one has a positive and one has a negative electrical charge. The net charge of the entire molecule is zero. The zwitterionic form predominates at neutral pH. The nonionic form does not occur in significant amounts in aqueous solution at any pH. A zwitterion can act as either an acid (proton donor) or a base (proton acceptor). Reading 63 assignment  Acid-Base Properties of Amino Acid When an amino acid is in aqueous solution, it exists in various ionic forms, the predominant form depends on the pH of the medium. Equilibrium shifts with change in pH. 64 Reading assignment  e At point(a) predominant form is the cationic fully protonated d [C+] form. At point (e) the predominating c form is the anionic fully deprotonated [A-] form. At point (c) the predominating b form is zwitterion form [Z] which a has a net charge of zero. At point (c) the pH = pI (isoelectric point) of the amino acid. Cationic Zwitterion Anionic [C+] [Z] [A-] 65  At point (b): e 50% of the glycine is in the cationic [C+] form and 50% in the d zwitterions [Z] form [C+]=[Z] c pH = pKa1 Maximum buffer capacity of COOH/– COO– pair At point (d): b 50% of the glycine is in the a zwitterion [Z] form and 50% in the anionic [A-] form. [Z]=[A-] pH = pKa2 Maximum buffer capacity of – NH3+/– NH2 pair Cationic Zwitterion Anionic [C+] [Z] [A-] 66 Buffering Capacity The ability of amino acids to react with both H+ (strong acid) and OH – of Amino Acid (strong base) means that amino acid solutions can function as buffers. An amino acid (glycine) has two regions in which it can act as a buffer. pH 1.34 to pH 3.34 (The COOH/– COO– pair can buffer in the pH region ~ pK1=2.34) pH 8.60 to pH 10.60 (The – NH3+/– NH2 pair can buffer in the region ~ pK2=9.60.) 67  +1 0 -1 Isoelectric Point (pI) The isoelectric point (pI) is the pH at which the concentration of zwitterion is maximum (net charge is zero; electrically neutral). At isoelectric point, amino acids are NOT attracted towards an applied electric field because they carry net zero charge. Different amino acids have different isoelectric points. The isoelectric point, pI, for neutral amino acids is: pKa1+pKa2 pI = 2 68 Reading assignment  +2 +1 0 -1 Based on inspection of the ionic forms in solution (top), it is clear that the zwitterionic form of lysine occurs at a pH midway between that of pKa2 (8.95) and pKa3=R (10.79). Thus, the pI for lysine is 9.87. 69  Classification of Amino Acid (based on Nutritional Value) Essential amino acids - Essential Amino acid: A standard amino acid needed for protein synthesis that must be obtained from dietary sources because it cannot be synthesized or adequate amounts cannot be synthesized in human body. - Their deficiency affects growth, health and protein synthesis. Non-essential amino acids - These are the rest of amino acids that are formed in the body in amount enough for adults and children. Reading assignment 70  Semi-essential amino acids (Arginine and Histidine) - These are synthesized or formed in the body but not in sufficient amount for body requirements especially in children. Reading assignment 71  Essential Amino Acids Villar HM = Ten Thousand Php V= valine i= isoleucine l= lysine l= leucine ar= arginine* H= histidine* M= methionine T= tryptophan Th= threonine Ph= phenylalanine * Arginine and histidine are semi-essential. 72  Complete and Incomplete Protein A complete protein contains all the essential amino acids in the proper amounts. An incomplete protein is low in one or more of the essential amino acids, usually lysine, tryptophan, or methionine. Except for gelatin, proteins from animal sources are complete Except soy protein, proteins from vegetable sources are incomplete. Soy protein is the primary protein found in soy products, such as tofu, soy milk, and other soy-based dairy and meat alternatives. Reading 73 assignment 74 Reading assignment 75  Peptide Bond Under proper conditions, amino acids can bond together to produce an unbranched chain of amino acids. The reactions is between amino group of one amino acid and carboxyl group of another amino acid. Reading 76 assignment  Peptide or Amide bond The covalent bonds between amino acids in a peptide are called peptide bonds (amide). The chain of covalently-linked amino acids is called a peptide. Reading 77 assignment  Peptide Bond The length of the amino acid chain can vary from a few amino acids to hundreds of amino acids. Peptides are further classified by the number of amino acids present in the chain: Dipeptide – contains two amino acids Tripeptide - three amino acids joined together in a chain Oligopeptide - peptides with 10 to 20 amino acid residues Polypeptide - longer peptides There are four (4) peptide bonds present in a pentapeptide. Reading 78 assignment  Nature of Peptide Bond A peptide chain has directionality because its two ends are different. By convention, the direction of the peptide chain is always N-terminal end à C-terminal end The N-terminal end is always on the left, and the C-terminal end is always on the right. Reading 79 assignment  Characteristics of Peptide Bond Peptide bonds have double bond character resulting from resonance stabilization. The C-N bond has a partial double-bond character, 40% double bond character, thus, it is shorter than a single bond (stronger). Reading 80 assignment  Characteristics of Peptide Bond The C – N bond in the peptide linkage has partial double bond character that makes it rigid and prevents free rotation around the bond between the carbonyl carbon and the nitrogen of the peptide bond. Reading 81 assignment  Geometric Characteristics of Peptide Bonds The peptide linkages are essentially planar. This means that for two amino acids linked through a peptide linkage, six atoms lie in the same plane: the α-carbon atom and the C=O group from the first amino acid the N-H group and the α-carbon atom from the second amino acid 82  Geometric Characteristics of Peptide Bonds The planar peptide linkage structure has considerable rigidity, which means that rotation of groups about the C-N bond is hindered, and cis–trans isomerism is possible about this bond. TRANS isomer orientation is the preferred orientation because of steric interference of the R-groups when in the cis position. The net effect of “peptide bond planarity” is the zigzag arrangement. 83 84  Peptide Bonds Peptide bonds are amide linkages that join amino acids in oligopeptides, polypeptides, and proteins. Oligopeptide - polymers with relatively few amino acid residues Polypeptide - polymers of generally less than 10,000 mw Protein - longer polymers 85  Peptide Nomenclature (IUPAC) Rule 1: The C-terminal amino acid residue (located at the far right of the structure) keeps its full amino acid name. Rule 2: All of the other amino acid residues have names that end in -yl. The -yl suffix replaces the -ine or -ic acid ending of the amino acid name, except for tryptophan (tryptophyl), cysteine (cysteinyl), glutamine (glutaminyl), and asparagine (asparaginyl). Rule 3: The amino acid naming sequence begins at the N-terminal amino acid residue. Tyrosine Leucine Serine Glycine Alanine Oligopeptide Serylglycyltyrosylalanylleucine (IUPAC name) Reading 86 assignment Ser–Gly–Tyr–Ala–Leu (SGYAL)  Isomeric Peptides Amino acid sequence in a peptide has biochemical importance. Isomeric peptides give different biochemical responses, that is, they have different biochemical specificities. Peptides that contain the same amino acids but in different order are different molecules (constitutional isomers) with different properties. alanylglycine glycylalanine Reading 87 assignment  Small Peptides with Physiological Activity 1. Aspartame (Asp-Phe) Aspartame (Asp-Phe) - dipeptide sold under trade names Equal and Nutrasweet; ~180x as sweet as sucrose Both amino acids present in the dipeptide must be in the L- form for the sweet taste to occur. The L-D, D-L, and D-D forms have a bitter taste. 88  Small Peptides with Physiological Activity 2. Glutathione, GSH (g-Glu-Cys-Gly) The tripeptide glutathione (gamma-glutamylcysteinylglycine) serves as a regulator of oxidation–reduction reactions. Glutathione functions as an antioxidant, protecting cellular contents from oxidizing agents such as peroxides and superoxides (highly reactive forms of oxygen often generated within the cell in response to bacterial invasion). Structure of glutathione: The glutamic acid is bonded to cysteine through the side-chain carboxyl group rather than through its α-carbon carboxyl group. gamma-glutamylcysteinylglycine Glu 89  Small Peptides with Physiological Activity 3. Enkephalins Enkephalins are pentapeptide neurotransmitters produced by the brain itself that bind at receptor sites in the brain to reduce pain (naturally occurring analgesics/pain relievers). tyrosylglycylglycylphenylalanylleucine tyrosylglycylglycylphenylalanylmethionine 90  Small Peptides with Physiological Activity 4. Oxytocin and Vasopressin The two best-known peptide hormones, both produced by the pituitary gland, are oxytocin and vasopressin. Each hormone is a nonapeptide (nine amino acid residues) with six of the residues held in the form of a loop by a disulfide bond formed from the interaction of two cysteine residues. 91  Oxytocin regulates uterine contractions and lactation (Oxytocin stimulates the flow of milk in a nursing mother.) Vasopressin regulates the excretion of water by the kidneys and affects blood pressure. Another name for vasopressin is antidiuretic hormone (ADH). 92 PROTEINS 93  Protein Structure Primary Assembly STRUCTURE PROCESS Secondary Folding Tertiary Packing Quaternary Interaction 94 Video 4  Primary Structure Protein Assembly Occurs at the ribosome Polymerization (peptide bond formation) of amino acids attached to tRNA which yields the primary structure of protein. The 1o structure of proteins are translations of information contained in genes. Reading 95 assignment  Primary Structure of Proteins Primary structure describes the number, type and sequence of amino acids that make up the polypeptide chain. The backbone of the protein molecule The linear sequence of amino acids within a protein Ordered The polypeptide backbone does not assume a random structure, but instead generally forms regular arrangements of amino acids. Reading 96 assignment  The British biochemist Frederick Sanger determined the primary structure of the protein hormone insulin in 1953. His work is a landmark in biochemistry because it showed for the first time that a protein has a precisely defined amino acid sequence. Sanger was awarded the Nobel Prize in chemistry in 1958 for this work. Later, in 1980, he was awarded a second Nobel Prize in chemistry, this time for work that involved the sequencing of units in nucleic acids 97  Primary Structure Every protein has its own unique amino acid sequence. Differences in the chemical and physiologic properties of peptides result from differences in the amino acid sequence. Bradykinin Boguskinin Partly responsible for triggering pain, Completely inactive, hence, the name movement of smooth muscle, and bogus or false lowering of blood pressure Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe 98 Understanding the primary structure of proteins is important because many genetic diseases result in proteins with abnormal amino acid sequences, which cause improper folding and loss or impairment of normal function If the primary structures of the normal and the mutated proteins are known, this information may be used to diagnose or study the disease. 99 A hydrophobic residue on the outer surface of the β subunit promotes clumping of hemoglobin molecules, producing abnormally shaped erythrocytes with decreased life span. 100  Protein Structure Primary Assembly STRUCTURE PROCESS Secondary Folding Tertiary Packing Quaternary Interaction 101 102  Secondary Structure: Folding and Coiling Secondary structure refers to regular, recurring arrangements in space of adjacent amino acid residues in a polypeptide chain. Three dimensional form of local segments of proteins Stabilized by hydrogen bonds between amide hydrogens (-NH) and carbonyl oxygens (-CO) of the peptide backbone. ▪ The coiling and folding (non- linear) of its polypeptide occur in the cytosol. Polypeptide chains are either: Coiled into a spiral spring (helices) Linked together to form the b-pleated sheet 103 Reading assignment Alpha (α) helix A single protein chain adopts a coiled spring (helix) shape The coil configuration is maintained by intramolecular hydrogen bonds between C=O and N-H entities are orientated parallel to the axis of the helix. The twist of the helix forms a right-handed, or clockwise, spiral. One turn of the spiral includes 3.6 amino acid residues (5.4 A) All of the amino acid R groups extend outward from the spiral Reading 104 assignment Proline: helix breaker Proline disrupts an α-helix because its secondary amino group is not geometrically compatible with the right-handed spiral of the α-helix. Proline interrupts the α-helices found in globular proteins. Reading 105 assignment  β pleated sheet A beta pleated sheet structure is a protein secondary structure in which two fully extended protein chain segments in the same or different molecules are held together by hydrogen bonds. The term pleated sheet arises from the repeated folding (zigzag pattern) due to H-bonding. Hydrogen bonds Reading 106 assignment  β pleated sheet The hydrogen bonds between C=O and N-H entities lie in the plane of the sheet. The hydrogen bonds are perpendicular to the polypeptide backbone. The amino acid R groups are found above and below the plane of the sheet and within a given backbone segment alternating between the top and bottom positions. Reading 107 assignment  β pleated sheet In a β pleated sheet, the hydrogen bonding can be: Intermolecular/interchain (between two different chains) Intramolecular (a single chain folding back on itself) In molecules where the β pleated sheet involves a single molecule (intramolecular), several U-turns in the protein chain arrangement are needed in order to form the structure. “U-turn” structure – most frequently encountered. Reading 108 assignment Parallel structure Antiparallel structure Chains are running in Protein chains alternate the same direction, the Chains are running in opposite –COOH and -NH2 ends directions of the proteins lying all More stable than parallel because at the top or all at the of fully co-linear H-bonds form bottom of the sheet. Reading 109 assignment  Protein Structure Primary Assembly STRUCTURE PROCESS Secondary Folding Tertiary Packing Quaternary Interaction 110 Tertiary Structure Protein Packing Complete Folding occurs in the cytosol 111  Tertiary Structure Ionic interaction The overall three-dimensional shape (globular) that results from the interaction of groups in the side chain (-R) of the amino acids widely separated from each other within the chain. The nature of the R-groups (polar or non-polar) of the constituent amino acids and their interactions plays an important role in determining and maintaining the specific shape of a protein molecule. Reading assignment 112 In tertiary structure, the bending and folding is irregular and it is the result of the formation of different types of bonds between the amino acid residues. 113 Disulfide bonds, electrostatic interactions, hydrogen bonds, and hydrophobic interactions are all stabilizing influences that contribute to the tertiary structure of a protein. Ionic interaction Reading assignment 114 Nonpolar R Side Chains (Hydrophobic interactions) Hydrophobic interactions/ induced dipole-induced dipole The attractive forces are London forces resulting from the momentary uneven distribution of electrons within the side chains. Hydrophobic interactions are common between phenyl rings and alkyl side chains. Reading 115 assignment Polar Side Chains Possess the following functional groups: More hydrophilic Form Hydrogen Bonds Hydrogen bonds are relatively weak and are easily disrupted by changes in pH and temperature. Formation of hydrogen bonds between polar groups on the surface of proteins and the aqueous solvent enhances the solubility of the protein. Reading 116 assignment  Hydrogen Bonds The side chains of asparagine and glutamine each contain a carbonyl group and an amide group, both of which can also participate in hydrogen bonds. Reading 117 assignment  Disulfide bond In proteins, the sulfahydryl group (–SH) of two cysteines can become oxidized to form a dimer, cystine, which contains a covalent cross-link called a disulfide bond (–S–S–). The strongest (the only covalent bond) of the tertiary- structure interactions A disulfide bond contributes to the stability of the three- dimensional shape of the protein molecule, and prevents it from becoming denatured in the extracellular environment. Reading assignment 118  Ionic interactions or Electrostatic attraction or Salt linkages or bridges Positive–negative ion–ion attraction Interaction between an acidic side chain being negatively charged and the basic side chain being positively charged Occur when a - COOH group becomes a – COO- group and when a -NH2 group becomes a - NH3+ group. Acidic R side chain Ionicinteraction Ionic interaction with basic R Ion-ion side chain Reading 119 assignment Problem: Identify the type of noncovalent interaction that occurs between the side chains of the following amino acids, and show the interaction using structural representations for the side chains. Serine and asparagine Glutamic acid and lysine Both serine and asparagine are Glutamic acid and lysine have, polar neutral amino acids. The respectively, acidic and basic side side chains of such amino acids chains. Such side chains carry a interact through hydrogen charge, in solution, as the result of bonding. proton transfer. The interaction between the negatively charged acidic side chain and the positively charged basic side chain is an electrostatic interaction. Reading assignment 120  Hydrophilic Hydrophobic In aqueous solution, many proteins have their polar R groups pointing outward, toward the aqueous solvent (which is also polar), and their nonpolar R groups pointing inward (away from the polar water molecules). This arrangement is more stable (globular proteins). The nonpolar R-groups thus fill up the interior of the folded protein and help give it its three-dimensional shape (stabilizing protein structure). Reading assignment 121  Tertiary structure of a single chain protein: Myoglobin Myoglobin is a single polypeptide chain that consists of 153 amino acid residues. Myoglobin, a protein found mainly in muscle tissue where it serves as an intracellular storage site for oxygen, thus, making the animals to remain submerged for long period of time Particularly abundant in the muscles of diving mammals such as the whale and seal 122  Protein Structure Primary Assembly STRUCTURE PROCESS Secondary Folding Tertiary Packing Quaternary Interaction 123 Quaternary Structure Quaternary structure describes the arrangement of sub-units in a protein consisting of two or more tertiary sub-units (polypeptide chain) with the same R side chain interactions as those of the tertiary structure Highest level of protein organization Occurs in the cytosol Reading 124 assignment  Quaternary Structure Quaternary structure is the highest level of protein organization. ▪ It is found only in multimeric (multiple polypeptide) proteins. Such proteins have structures involving two or more peptide chains that are independent of each other—that is, are not covalently bonded to each other. Proteins with quaternary structure are often referred to as oligomeric Most multimeric proteins contain an even number of subunits Reading 125 assignment  Quaternary Structure Hemoglobin has a quaternary structure. It consists of two pairs of different proteins, designated the α and β chains. There are 141 and 146 amino acids in the α and β chains of hemoglobin, respectively. Each subunit is linked covalently to a molecule of heme. Hemoglobin is a heterotetramer consisting of four subunits (two α and two β), thus, oligomer. Structurally and functionally, hemoglobin is described better as (αβ)2, thus, a diprotomer. 126 Human insulin, a small two-chain protein, has both intrachain and interchain disulfide linkages as part of its tertiary structure. Intrachain for tertiary structure Interchain for quaternary structure 127  Reasons for quaternary structure By combining more than one sub-unit into one functioning protein, enhanced biological activity and control can be achieved. Main points to consider for the reasons of having associated sub-units: Enhanced stability (Reducing surface area vs. protein volume) Genetic economy & efficiency (limited genetic information needed) Coordinated regulation of proteins Defects easily repaired by replacing flawed sub-units 128 Reading assignment Recap: Structure of Protein 129  Recap: Structure of Protein Disulfide bond Reading assignment 130  Protein Classification (Chemical Composition) Simple proteins A protein in which only amino acid residues are present. More than one protein subunit may be present in a simple protein, but all subunits contain only amino acids. - Keratin in skin, hair, nails - Collagen in cartilage - Albumins - egg albumin, serum albumin - Globulins - antibodies - Chromatin in chromosomes - Histones 131 Reading assignment  Protein Classification (Chemical Composition) Complex proteins Conjugated protein A protein that has one or more non-amino acid entities (prosthetic groups) present in its structure Prosthetic group is non– amino acid part (may be organic or inorganic) of a conjugated protein. Conjugated proteins are classified on the basis of the chemical nature of their prosthetic groups. 132 Reading assignment Types of Conjugated Proteins 133 Protein Classification (Shape/Conformation) Fibrous Protein (Secondary Structure) The polypeptide chains are arranged in long strands or sheets. They have long, rod-shaped or string- like molecules that can intertwine with one another and form strong fibers. Fibrous proteins tend to have simple, regular, linear structures. This protein does not have tertiary structure. Secondary structure is important. Water-insoluble. Structural functions Video 5 Reading 134 assignment  Keratin Fibrous Protein (Secondary Structure) Two main forms of keratin: 1. Alpha-keratin is seen in humans and other mammals have alpha-helical coiled coil structure 2. Beta-keratin is present in birds and reptiles. have twisted beta sheet structure. Reading 135 assignment  Hardness of keratin depends upon -S-S- bonds More –S-S– bonds make nail and bones hard and hair brittle. α-Keratin Several α-helices held together by bonds formed between adjacent chains. The bonds (disulfide bridges) form cross-links and the bundles of molecules have strength and the ability to stretch. Provide protective coatings for organs Major proteins constituent of hair, feather, nails, claws, horns, hooves, turtle shells, and much of the outer layer of skin. The α-keratin helix is a right-handed helix, and mainly made of hydrophobic amino acid residues. Reading 136 assignment  Collagen Fibrous Protein (Secondary Structure) Collagen molecules are very long, thin, and rigid. It is left-handed and consists of three polypeptide chains wrapped around each other in a rope-like twist, or triple helix. Rich in proline (up to 20%) -important to maintain structure Collagen, the most abundant of all proteins in humans (30% of total body protein), is a major structural material in tendons, ligaments, blood vessels, and skin. It is also the organic component of bones and teeth. Reading 137 assignment  Fibroin Fibrous Protein (Secondary Structure) Fibroin, the protein of silk, is produced by insects and spiders. Its polypeptide chains are predominantly in the β- conformation. The overall structure is stabilized by extensive hydrogen bonding between all peptide linkages in the polypeptides of each β-sheet and by the optimization of van der Waals interactions between sheets. Cannot be stretched but it is very supple (bent or twisted.) 138  Protein Classification (Shape/Conformation) Globular Proteins (Tertiary or Quaternary Structure) Hydrophilic Folded into spherical or globular shapes Nonpolar amino acids are in Hydrophobic the interior, polar amino acids are on the surface. Water-soluble which allows them to travel through the blood and other body fluids to sites where their activity is needed Dynamic functions. Most enzymes and regulatory proteins (hormones, antibodies) are globular proteins. Reading 139 assignment 140  hemoglobin Myoglobin 141  Myoglobin (Tertiary structure: Single chain protein) A single-chain globular protein (monomer) that consists of 153 amino acids and a heme group (an iron-containing porphyrin) Consists mainly of a- helices linked together by various turns. A relatively small oxygen-binding protein of muscle cells. Binds and stores oxygen in skeletal muscles from blood and supplies the oxygen to active muscle groups during harsh respiration. 142  Hemoglobin (Quaternary structure: Four-chains protein) Globular tetramer (two identical α-chains consisting of 141 amino acid residues and two identical β-chains consisting of 146 amino acid residues) Each subunit is linked covalently to a molecule of heme. Hemoglobin transports oxygen from the lungs to tissue. Binds oxygen in lungs and releases it to metabolically active cells undergoing respiration throughout the body. It is the iron atom at the center of the heme molecule that actually interacts with the O2. 143  Fibrous vs. Globular Fibrous proteins are generally water-insoluble, whereas globular proteins are soluble in water. This enables globular proteins to travel through the blood and other body fluids to sites where their activity is needed. Fibrous proteins usually have a single type of secondary structure, whereas globular proteins often contain several types of secondary structure and have tertiary structure. Reading 144 assignment  Fibrous vs. Globular Fibrous proteins generally have structural functions that provide support and external protection, whereas globular proteins are involved in metabolic chemistry, performing functions such as catalysis, transport, and regulation. Diversity: The number of different kinds of globular protein far exceeds the number of different kinds of fibrous protein. Total mass: most abundant proteins in the human body are fibrous proteins rather than globular proteins, the total mass of fibrous proteins present exceeds the total mass of globular proteins present. Reading 145 assignment Secondary structure 146 PROTEIN DENATURATION Protein denaturation is the partial or complete disorganization or unfolding of a protein’s characteristic three-dimensional shape as a result of disruption of its secondary, tertiary, and quaternary structural interactions, which are not accompanied by hydrolysis of peptide bonds. Protein denaturation does not affect the primary structure of a protein. Reading 147 assignment PROTEIN DENATURATION Because the biochemical function of a protein depends on its three-dimensional shape, the result of denaturation is loss of biochemical activity. Complete loss of such structure produce an “unstructured” protein strand. Denaturation is a phenomenon that involves transformation of a well-defined, folded structure of a protein, formed under physiological conditions, to an unfolded state under non- physiological conditions. Reading assignment 148 Renaturation It is possible to find conditions under which the effects of denaturation can be reversed. This restoration process, in which the protein is “refolded,” is called renaturation. However, for extensive denaturation changes, the process is usually irreversible. Reading 149 assignment  Protein Denaturation For extensive denaturation changes, the process is usually irreversible. Example: Protein Thermal Irreversible Denaturation 150 PROTEIN DENATURATION Loss of water solubility is a frequent physical consequence of protein denaturation. The precipitation out of biochemical solution of denatured protein is called coagulation. Reading 151 assignment Some selected physical and chemical denaturing agents 1. Heat – disrupts H-bonds and hydrophobic attractions by making molecules vibrate too violently; produces coagulation, as in the frying of an egg 2. Microwave radiation – causes violent vibrations of molecules that disrupt H-bonds 3. Ultraviolet radiation – operates very similarly to the action of heat (e.g., sunburn) 4. Violent whipping or shaking – causes molecules in globular shapes to extend to longer lengths, which Reading 152 assignment then entangle Some selected physical and chemical denaturing agents 6. Organic solvents (e.g., ethanol, 2-propanol, acetone) – interfere with H-bonds, because these solvents also can form H-bonds; quickly denatures protein in bacteria, killing them (the disinfectant action of 70% ethanol) 7. Soap/Detergent – affects H-bonds and salt linkages 8. Acids and bases – disrupt H-bonds and salt bridges; prolonged action with strong acids and bases leads to actual hydrolysis of peptide bonds 9. Salts of heavy metals (e.g., salts of Hg2+, Ag+, Pb2+) – metal ions combine with – SH groups and form poisonous salts; precipitates proteins 10. Reducing agents – oxidize disulfide linkages to produce – SH groups Reading 153 assignment Some practical aspects of protein denaturation 1. Heat and UV Cooking foods facilitates digestion. “Cooked” protein is more easily digested because it is easier for digestive enzymes to “work on” denatured (unraveled) protein. Cooking foods kills microorganisms. Ham and bacon can harbor parasites that cause trichinosis. Cooking the ham or bacon denatures parasite protein. Bacteria are destroyed when the heat denatures their protein (Sterilizing surgical instruments and in canning foods) Reading 154 assignment  Some practical aspects of protein denaturation 2. Organic compounds such as soap, detergents, phenol, and aliphatic alcohol Used as disinfectant. Denaturation of bacterial protein takes place when: Swabbing the skin with alcohol before giving an injection Washing of hands with soap and detergent Reading 155 assignment  Role of Alcohol in defense against COVID-19 One of the most commonly used disinfectants, alcohols are known to have antimicrobial properties. Solutions containing alcohols such as ethanol, isopropanol or n- propanol are effective antimicrobial agents that are used as surgical spirits for disinfecting skin surfaces. The ability of alcohols to denature and coagulate proteins makes them effective against a wide range of bacteria and virus. However, pure form of alcohol shows less efficacy as an antimicrobial because in the absence of water, proteins do not denature properly. This is why, an ideal alcohol solution, commonly known as rubbing alcohol, contains 60 to 95 per cent alcohol. Reading assignment 156 Some practical aspects of protein denaturation 3. Salts of heavy metal ions esp. Hg2+, Pb2+, Ag+ ▪ Used as antiseptics in low concentrations, in higher concentrations they act as poisons. ▪ When ingested they precipitate the proteins in cells of body tissues. Effective treatment consists of feeding with egg white, followed by an emetic-vomiting (the egg white forms complex with the poison and taken out of circulation by emetic) Reading 157 assignment Some practical aspects of protein denaturation 4. Permanent hair wave process 80-85% of hair is composed of a protein called keratin (consists of many protein alpha-helices). The α-helices are extensively cross-linked with cysteine disulfide bonds (–S – S – linkages give shape to the hair). Permanent hair wave process Application of reducing agent to break the disulfide linkages in the hair, producing two sulfhydryl (-SH) groups (brings disorderliness of linkages) The reduced hair (whose 3° structure has been disrupted) is then wound on curlers to give it a new configuration (desired pattern). Application of oxidizing agent (neutralizer) to reform the disulfide bonds in their new positions Reading 158 assignment Permanent hair waving Rupture of some of the disulfide cross-links by the reducing agent Reforming the disulfide bonds in their new positions by the oxidizing agent 159 Negative effects of protein denaturation A temperature above (41°C) is extremely dangerous, as the body’s enzymes begin to be inactivated at this level. Inactivation of enzymes through denaturation can have lethal effects on body chemistry. The effect of ultraviolet radiation from the sun, an ionizing radiation, is similar to that of heat. Denatured skin proteins cause most of the problems associated with sunburn. Serious eye damage can result from eye tissue contact with acids or bases, when irreversibly denatured and coagulated protein causes a clouded cornea. This reaction is part of the basis for the rule that students wear protective eyewear in the chemistry laboratory. Reading 160 assignment  Protein Hydrolysis splits the peptide bonds to give smaller peptides and amino acids by acids, alkalis and enzymes affects the primary structure of protein Reading assignment 161 162  -END- Second Long exam next week J 163