Proteins PDF

PROTEINS DR. ROMEO T. CRUZ, JR. DMD, MACT, EdD  PROTEINS  Proteinsare the most abundant of all organic substances in the cell. They are generally large, complex molecules that are required in different aspects of cell structure and function. Composition Proteins are made up of a...

PROTEINS DR. ROMEO T. CRUZ, JR. DMD, MACT, EdD  PROTEINS  Proteinsare the most abundant of all organic substances in the cell. They are generally large, complex molecules that are required in different aspects of cell structure and function. Composition Proteins are made up of amino acids. Each amino acid has an asymmetrical alpha carbon to which are attached 1. a hydrogen, H 2. an amino group NH2 3. a carboxyl group, COOH 4. a radical, R which vary in different amino acids. Amino acids may be classified into different types based on the R group present. 1.Acidic Amino Acids (abbreviated as Asp or D). Non essential Aspartic Acid amino acid, which means that it can be synthesized from central metabolic pathway intermediates in humans. ☻ Aspartic acid is found in: Animal sources: luncheon meats, sausage meat. Vegetable sources: sprouting seeds, oat flakes, avocado, asparagus, young sugarcane, and molasses from sugar beets. Dietary supplements: either as aspartic acid itself or salts (such as magnesium aspartate) The sweetener aspartame (NutraSweet, Equal, Canderel, etc.) 1.Acidic Amino Acids Glutamic Acid Glutamic acid (abbreviated as Glu or E) It is a non-essential amino acid. The carboxylate anions and salts of glutamic acid are known as glutamates. 2. Basic Amino Acids Arginine plays an important role in cell Arginine division, the healing of wounds, removing ammonia from the body, immune function, and the release of hormones. The benefits and functions attributed to oral supplementation of L-arginine include: Reduces healing time of injuries (particularly bone) Quickens repair time of damaged tissue Helps decrease blood pressure 2. Basic Amino Acids Histidine Histidine (abbreviated as His or H) is one of the 22 proteinogenic amino acids. In terms of nutrition, histidine is considered an essential amino acid in human infants. 2. Basic Amino Acids Lysine (abbreviated as Lys or K) is an essential Lysine amino acid, which means that humans cannot synthesize it. 3. Branched-Chain AminoAcids Leucine Leucine (abbreviated as Leu or L) is an essential α-amino acid, classified as a hydrophobic amino acid. Leucine is a major component of the sub units in ferritin, astacin and other 'buffer' proteins. 3. Branched-Chain Amino Acids Isoleucine Isoleucine (abbreviated as Ile or I) is an essential α-amino acid. With a hydrocarbon side chain, isoleucine is classified as a hydrophobic amino acid. Together with threonine, isoleucine is one of two common amino acids that have a chiral side chain. 3. Branched-Chain Amino Acids Valine Valine (abbreviated as Val or V) This essential amino acid is classified as nonpolar. Human dietary sources include cottage cheese, fish, poultry, peanuts, sesame seeds, and lentils. 4. Aromatic Amino Acids Phenylalanine Phenylalanine (abbreviated as Phe or F) is an α-amino acid. This essential amino acid and classified as nonpolar because of the hydrophobic nature of the benzyl side chain. Phenylalanine is found naturally in the breast milk of mammals. It is used in the manufacture of food and drink products and sold as a nutritional supplement for its reputed analgesic and antidepressant effects. 4. Aromatic Amino Acids Histidine (abbreviated as Histidine His or H) is considered an essential amino acid in human infants. Histidine was first isolated by German physician Albrecht Kossel in 1896. 4. Aromatic Amino Acids Tryptophan (Trp or W) An essential amino acid in the Tryptophan human diet. The distinguishing structural characteristic of tryptophan is that it contains an indole functional group. 5. Sulfur Containing Amino Acids Cystine is a dimeric Cystine amino acid formed by the oxidation of two cysteine residues which covalently link to make a disulfide bond. It is a colorless solid, and melts at 247-249 °C. Human hair contains approximately 5% cystine by mass. 5. Sulfur Containing Amino Acids Methionine Together with cysteine, methionine is one of two sulfur-containing proteinogenic amino acids. Improper conversion of methionine can lead to atherosclerosis. Methionine is encoded by a single codon (AUG) in the standard genetic code. 6. Hydroxy Amino Acids Serine Serine is important in metabolism in that it participates in the biosynthesis of purines and pyrimidines. It is the precursor to several amino acids including glycine, cysteine, and tryptophan in bacteria. It is also the precursor to numerous of other metabolites, including sphingolipids and folate. 6. Hydroxy Amino Acids Threonine (abbreviated Threonine as Thr or T) This essential amino acid is classified as polar. Together with serine and tyrosine, threonine is one of three proteinogenic amino acids bearing an alcohol group. 7. Neutral Amino Acids Glycine (abbreviated as Gly or G) is an organic Glycine compound with only a hydrogen atom as its side chain, glycine is the smallest of the 20 amino acids commonly found in proteins. Glycine is a colourless, sweet-tasting crystalline solid. 7. Neutral Amino Acids Alanine Alanine (abbreviated as Ala or A) is an α-amino acid that helps the body convert the simple sugar glucose into energy and eliminate excess toxins from the liver. Alanine has been shown to help protect cells from being damaged during intense aerobic activity, when the body cannibalizes muscle protein to help produce energy. 8. Acid Amide Amino Acids Asparagine (abbreviated Asparagine as Asn or N) is one of the 20 most common natural amino acids on Earth. It has carboxamide as the side chain's functional group. It is not an essential amino acid. 8. Acid Amide Amino Acids Glutamine (abbreviated as Gln or Q). In human blood, glutamine is the most abundant free amino acid Glutamine and it plays a role in a variety of biochemical functions including: Protein synthesis Regulation of acid-base balance in the kidney by producing ammonium Cellular energy, as a source, next to glucose Nitrogen donation for many anabolic processes Carbon donation, as a source, refilling the Citric acid cycle. 9. Imino Acid Proline (abbreviated as Pro or P) is an non- Proline essential α-amino acid. Proline and its derivatives are often used as asymmetric catalysts in organic reactions. L-Proline is an osmoprotectant and therefore is used in many pharmaceutical, biotechnological applications. These amino acids are further classified into 1. Non-essential amino acids - are those amino acids which the body can synthesize. 2. Essential amino acids - are those which the body cannot synthesize and thus must be supplied to the body from the diet. Of the 20 amino acids needed in the synthesis of body proteins, the following are classified as essential: histidine, leucine, isoleucine, lysine, methionine, arginine, threonine, phenylalanine, valine, and tryptophan. Under appropriate isoelectric pH for a given amino acid, the molecule may appear as a dipolar ion or Zwitterion. The molecule is also amphoteric since it can behave both as an acid or proton donor and a base or proton acceptor. Peptide Bond Formation Polypeptides or proteins are formed by the chemical reaction between the amino group of one amino acid and the carboxyl group of another amino acid forming amide linkages called peptide bonds. These bonds arise from the elimination of water from the carboxyl group of one amino acid and the amino group of the next amino acid. Structural Levels of Proteins These levels are manifested in the shape of the molecule which is the result of the type of bonding that the R group can form. 1. The primary structure refers to the sequence of amino acids in the polypeptide chain. These amino acids are covalently linked by peptide bonds resulting in a long unbranched molecule.  2. The secondary structure refers to the regular recurring arrangement of the polypeptide chain along one dimension. It is the result of H bonds formed between oxygen of C=O and the hydrogen of –N-H. the molecule may be helical like in myosin or in the form of a pleated sheet as in stretched chain keratin.  3. The protein’s tertiary structure is formed by folding, refolding, and supercoiling of the polypeptide chain. The type of bonds present are hydrophobic, ionic, covalent, disulfide, and H bonds. It results in either a compact globular structure as in ovalbumin or a fibrous or rod-like structure as in fibrinogen and collagen.  4. The quaternary structure of proteins refers to how individual polypeptide chains of protein having 2 or more chains are arranged in relation to each other. Each component chain is called a protomer. The chains may be held by –S-S- bonds or by covalent bonds of the R groups. This type is exemplified by insulin with 2, thrombin with 3 and hemoglobin with 4 protomers respectively. Characteristics Proteins are easily denatured or destroyed upon exposure to high temperature or extremes of pH. Due to their large size, all are undialyzable or they cannot pass through plant or animal membranes. Gives specific color reactions to certain reagents that can be used to detect their specific chemical composition. Can behave both as an acid and as a base and above all have the property of specificity. Chemical Properties Proteins are hydrolyzed by dilute acids, alkalis and enzymes and are precipitated by acids, salts of heavy metals and alcohol. They may form complexes with nucleic acids, carbohydrates, lipids, enzymes, and pigments. Regardless of its amount, it has a constant solubility Classification Proteins may be classified on the basis of the following: A. Composition 1. Simple protein – contain only amino acids 2. Complex or Conjugated proteins – contain additional non-amino acid materials a. chromoproteins – with a pigment like hemoglobin, cytochromes, flavoproteins b. nucleoproteins – with nucleic acids like histones nad protamines c. glycoproteins – with carbohydrates like mucin in saliva d. Phosphoproteins – with phosphoric acid like the enzyme phosphodiesterase e. Lipoprotein – with fatty substances found in brain tissue  B. Conformation of three-dimensional shape of molecule 1. Fibrous protein where the polypeptide chains are arranged in parallel chains along a single axis to form long sheets or fibers. Elastin, collagen, and keratin are examples of this type. 2. Globular protein where the polypeptide chains are tightly folded into spherical or globular shapes as exemplified by enzymes, serum albumin, antibodies, and hormones.  C. Solubility 1. Albumins – soluble in water and salt solution; with no distinctive amino acid 2. Globulins – sparingly soluble in water but insoluble in salt solution; with no distinctive amino acid 3. Pro amines – soluble in 70-80% ethanol but insoluble in water and absolute ethanol; arginine-rich 4. Histones – soluble in salt solution 5. Scleroproteins – insoluble in water or salt solution; rich in glycine, alanine, proline Biological Functions of Proteins Proteins have varied functions. they act as organic catalysts in different kinds of chemical reactions. the regulatory function of proteins may be exercised by acting as hormones such as insulin, necessary for the proper cellular absorption of glucose. Some proteins serve as food reserves especially for the growing embryo. Examples are ovalbumin of egg white, casein of milk, gliadin of wheat seeds and zein, the seed protein of corn. has the ability to bind and transport specific molecules via the blood have protective or defensive function as in the case of immunoglobulins or antibodies it serve as structural materials of cells and tissues.