Proteins (Bioorganic) PDF

Protection BIOCHEM LEC  When a protein from the outside (antigen) PROTEINS (bioorganic) the body make its own protein for...

Protection BIOCHEM LEC  When a protein from the outside (antigen) PROTEINS (bioorganic) the body make its own protein for protection (antibodies). o Is a naturally occurring, unbranched polymer in which the monomer units are Storage amino acids. o Derived from the greek word proteios “of  Some proteins store materials in the way the first importance/rank” starch and glycogen store energy. Like Ferritin (Iron) FUNCTIONS OF PROTEINS Regulation Structure  Some proteins not only control the  Structural proteins are the chief expression of genes thereby regulating the constituents of skin, bones, hair, and nails kinds of proteins.  Two important structural proteins: Collagen and Keratin AMINO ACIDS (Building Block) Catalysis  An organic compound that contains both an amino (-NH2) group and a carboxyl (-  Usually all reactions that take place in the COOH) group. living organism are catalyzed by proteins called enzymes a-amino acids Movement  An amino acid in which the amino group and the carbonyl group are attached to  Muscles are made up of protein molecules the a-carbon atom. called: Myosin and Actin Transport  Number of proteins performs transportation duties like hemoglobin, other transport molecules across the cell membrane. STANDARD AMINO ACID Hormones One of the 20-a-amino acids normally found in protein, usually grouped into:  Many hormones are protein including insulin, EPO (erythropoietin), human 1. Non Polar Amino Acid growth hormone. o An amino acid that contains one (1) amine group, one (1) carboxyl group, and a non-polar side chain. JHMR SMRLD  o And when incorporated to a protein, such amino acids are hydrophobic (water-fearing). 3. Polar Acidic Amino Acid o An amino acid that contains one (1) amino group, two (2) carboxyl groups, the second carboxyl group being part of the side chain. o At physiological pH, the side chain of a polar acidic amino acid bears a negative charge; the side chain carboxyl group has lost its acidic hydrogen atom. o There are two polar acidic amino acids: aspartic acid and glutamic acid. 4. Polar Basic Amino Acid 2. Polar Neutral Amino Acid o An amino acid that contains two (2) o An amino acid that contains one (1) amino groups, one (1) carboxyl group. amino group, one (1) carboxyl group, The second amino acid group being part and a polar but neutral side chain. of the side chain. o At physiological pH, the side chains are o At physiological pH, the side chain of a neither basic nor acidic. polar basic amino acid bears a positive o There are six polar neutral amino acids. charge; the nitrogen atom of the amino These amino acids are more soluble in group has accepted a proton. water than the nonpolar amino acids as, o There are three polar basic amino acids: in each case, the R group present can lysine, arginine, and histidine. hydrogen bond to water. JHMR SMRLD  Incomplete Dietary Protein  A protein that does not contain adequate amounts, relative to the body’s needs, of one or more of the essential amino acids. Limiting Amino Acids  Is an essential amino acid that is missing, Note: In naming protons we remember the first or present in inadequate amounts, in an three letters. incomplete dietary protein. ESSENTIAL AMINO ACIDS Complementary Dietary Proteins  Are two or more incomplete dietary o a-amino acids that must extract in our diet. proteins that, when combined, provide an o Is a standard amino acid needed for protein adequate amount of all essential amino synthesis that must be obtained from acids relative to the body’s needs. dietary source because the human body cannot synthesize. CHIRALITY o It is adequate amounts from other substances. o Four different groups are attached to the a- carbon atom in all of the standard amino acids except glycine, where the R group is a hydrogen atom. o Glycine, the simplest of the standard amino PROTEIN DIET acids, is achiral. All of the other standard amino acids are chiral. Complete Dietary Protein Note: The amino acids found in nature and in  A protein that contains all the essential proteins are L – isomers and D – isomers. amino acid in the same relative amount in which the body needs them.  Most animal proteins, including casein from milk and pro teins found in meat, fi sh, and eggs, are complete proteins. JHMR SMRLD The rules for drawing Fischer projection In Acidic: Zwitterion accepts a proton (H+) to formulas for amino acid structures follow: form a positively charged ion. 1. The —COOH group is put at the top of the In Basic: The –NH3 of the Zwitterion loses a projection, the R group at the bottom. proton, and a negatively charged particle is This positions the carbon chain vertically. formed. 2. The —NH2 group is in a horizontal position. Positioning it on the left denotes ISOELECTRIC POINTS the L isomer, and positioning it on the o The pH at which an amino acids exists right denotes the D isomer. primarily in its zwitterion form. o At this point, almost all amino acid molecules in a solution are present in the zwitterion form. CYSTEINE o The only standard amino acid that has a side chain that contains a sulfhydryl group. o Cysteine in the presence of mild oxidizing agents readily dimerizes or reacts with another cysteine molecule to form cysteine molecule. ACID-BASE PROPERTIES OF AMINO ACID  Amino acids are white crystalline solids with relatively high decomposition points. o In cysteine, the two (2) cysteine residues And most are not very soluble in water. are linked via covalent disulfide bond. o The disulfide bonds are readily broken to ZWITTERION produce two (2) cysteine molecules. o Is a molecule that has a positive charge on PEPTIDE one atom and a negative charge on another atom, but which has no net charge. o An unbranched chains of amino acid and o Note that the net charge on a zwitterion is can further be classifies according to the zero. number of amino acid present in the chain. o Structure changes when the pH of a solution containing an amino acid is changed from neutral either to acidic (low pH) by adding an acid such as HCl or to basic (high pH) by adding a base such as NaOH. JHMR SMRLD NATURE OF PEPTIDE BOND  Is a peptide in which at least 40 amino acid residues are present. Monomeric Protein o A covalent bond between the carboxyl  Is a protein in which only one peptide group of one (1) amino acid and the amino chain is present. group of another amino acid.  N-terminal: end w/ free H3N Multimeric Protein  C-terminal: end w/ free COO  In convention, amino acids are written  Is a protein in which more than one with N-terminal at the left peptide chain is present (insulin).  Amino Acid Residue: Portion of amino BASIS OF CHEMICAL COMPOSITION acid structure that remains after the release of H2O. Simple Protein  Backbone: Repeating sequence of  Is a protein in which only amino acid peptide bonds and a-carbon group residues are present. PEPTIDE NOMENCLATURE  More than one protein subunit may be present in a simple protein, but all IUPAC rules for naming small peptides are as subunits contain only amino acids. follows: Conjugated Protein  Rule 1: The C-terminal amino acid residue (located at the far right of the structure)  Is a protein that has one or more non keeps its full amino acid name. amino acid entities present in its structure  Rule 2: All of the other amino acid residues in addition to one or more peptide chains. have names that end in -yl. The -yl suffi x Types of Conjugated Proteins replaces the -ine or -ic acid ending of the amino acid name, except for tryptophan Class Prosthetic Example (tryptophyl), cysteine (cysteinyl), glutamine Group (glutaminyl), and asparagine (asparaginyl). Hemoproteins Heme UnitHemoglobin &  Rule 3: The amino acid naming sequence Myoglobin begins at the N-terminal amino acid Lipoproteins Lipid LDL & HDL residue. Glycoproteins Carbohydrate Gamma globulin, Mucin, & Example: Glu-Ser-Ala = glutamylserylalanine, Interferon Gly-Tyr-Leu-Val = glycyltyrosilleucylvaline Phosphoproteins Phosphate Glycogen group Phosphorylase GENERAL STRUCTURAL CHARACTERISTICS OF Nucleoproteins Nucleic Acid Ribosomes PROTEINS Metalloproteins Metal Ion Ferritin & alcohol dehydrogenase PROTEIN JHMR SMRLD Prosthetic Group Interactions Responsible for Tertiary Structure  Is a non-amino acid group present in a Covalent Disulfide Bonds conjugated protein.  The strongest of the tertiary-structure  Non-amino acid components, which may interactions, result from the (-SH) groups be organic or inorganic. of two cysteine residues reacting with PRIMARY STRUCTURE each other to form a covalent disulfide bond. o The order in which amino acids are linked together in a protein Electrostatic Attractions (Salt Bridges) o Primary structure of a specific protein is always the same regardless of where the  Involve interaction of acidic-basic protein is found in the organism. sidechain o Linked together by peptide linkages. Hydrogen Bonds SECONDARY STRUCTURE  Can occur between amino acids with polar o The arrangement in space adopted by the R groups. backbone portion of the protein. Hydrophobic Attractions. o Hydrogen bond is responsible for this interaction.  Result when two nonpolar side chains are close to each other. Alpha Helix QUATERNARY STRUCTURE  A protein secondary structure in which a single protein chain adopts a shape that o Is the organization among the various resembles a coiled spring (helix), with the peptide chains in a multimeric protein. coil configuration maintained by hydrogen o Two (2) or more peptide that are bonds. independent of each other. o Subunits held together by hydrophobic Beta Pleated Sheet interactions between amino acid R groups.  Is a protein secondary structure in which o Multiple combinations of tertiary structure. two fully extended protein chain segments in the same or different molecules are held together by Hydrogen bonds. TERTIARY STRUCTURE o Is the overall three-dimensional shape of a protein that results from the interactions between amino acid side chains (R groups). JHMR SMRLD