Proteins PDF

10/10/2024 1 PROTEINS Primary Structure of Protein Secondary Structure of Protein Tertiary Structure of Protein Quaternary structure of Protein 1 2 Proteins...

10/10/2024 1 PROTEINS Primary Structure of Protein Secondary Structure of Protein Tertiary Structure of Protein Quaternary structure of Protein 1 2 Proteins A large biological molecule made of many amino acids linked together through amide (peptide) bonds. 2 3 Proteins second most abundant substances in nearly all cells (15% of cell’s overall mass) contains element of carbon, hydrogen, oxygen, and nitrogen 3 1  10/10/2024 4 Proteins is a peptide in which at least 40 amino acid residues are present 400-500 amino acid residues are common in protein Small proteins contain 40-100 amino acid residue 4 5 Number of Peptide Chain is a protein in which only one peptide monomeric protein chain is present a protein in which more than one multimeric protein peptide chain is present (insulin) The peptide chains present in multimeric proteins are called protein subunits. 5 6 Based on Chemical Composition is a protein in which only amino acid simple protein residues are present is a protein that has one or more non- conjugated protein amino-acid entities present (Lipoprotein & Glycoprotein) A prosthetic group is a non- amino-acid group present in a conjugated protein. 6 2  10/10/2024 7 7 8 Primary Protein Structure is the sequence in which its amino acids are lined up and connected by peptide bonds 8 9 Primary Protein Structure 9 3  10/10/2024 10 11 12 amino-terminal amino acid (also called N-terminal amino acid, the one with the free -NH3+) on the LEFT carboxyl-terminal amino acid (also called the C-terminal amino acid, the one with the free -COO- group) on the RIGHT 12 4  10/10/2024 13 Residues individual amino acids joined in the chain 13 14 Naming Peptides cite the amino acid residues in order, starting at the N- terminal amino acid and ending with the C-terminal amino acid. All residue names except the C-terminal one have the -yl ending instead of -ine, Example: alanylserine (abbreviated Ala-Ser) or serylalanine (Ser-Ala) 14 15 If its amino acids are not arranged properly, as in hormones for instance, it will not work as it should. 15 5  10/10/2024 16 So crucial is primary structure to function—no matter how big the protein—that the change of only one amino acid can sometimes drastically alter a protein’s biological properties. 16 17 Sickled-cell Anemia is a hereditary disease caused by a genetic difference that replaces one amino acid (glutamate, Glu) with another (valine, Val) in each of two polypeptide chains of the hemoglobin molecule 17 18 SECONDARY PROTEIN STRUCTURE 18 6  10/10/2024 19 Secondary Protein Structure Regular and repeating structural patterns of alpha helix or beta sheet created by hydrogen bonding between backbone atoms in neighboring segments of protein chains. 19 20 alpha-helix (α-helix) Secondary protein structure in which a protein chain forms a right-handed coil stabilized by hydrogen bonds between peptide groups along its backbone. 20 21 21 7  10/10/2024 22 beta-sheet (β-sheet) Secondary protein structure in which adjacent protein chains either in the same molecule or in different molecules are held together by hydrogen bonds along the backbones, forming a flat sheet-like structure. 22 23 23 24 The portions of a protein that have neither alpha helix nor beta pleated sheet structure are called unstructured segments. 24 8  10/10/2024 25 TERTIARY PROTEIN STRUCTURE 25 26 Tertiary protein structure The way in which an entire protein chain is coiled and folded into its specific three- dimensional shape. 26 27 27 9  10/10/2024 28 28 29 Interactions Responsible for Tertiary Structure 1. covalent disulfide bonds, 2. electrostatic attractions (salt bridges), 3. hydrogen bonds, and 4. hydrophobic attractions. 29 30 Disulfide Bonds the strongest of the tertiary-structure interactions, result from the -SH groups of two cysteine residues reacting with each other to form a covalent disulfide bond 30 10  10/10/2024 31 Electrostatic Interactions also called salt bridges, always involve the interaction between an acidic side chain (R group) and a basic side chain (R group) 31 32 Hydrogen Bonds occur between amino acids with polar R groups 32 33 Hydrophobic Interactions result when two nonpolar side chains are close to each other are common between phenyl rings and alkyl side chains 33 11  10/10/2024 34 34 35 QUATERNARY PROTEIN STRUCTURE 35 36 Quaternary protein structure The way in which two or more protein chains aggregate to form large, ordered structures. Examples: Hemoglobin Collagen 36 12  10/10/2024 37 Hemoglobin is a conjugated quaternary protein composed of four polypeptide chains (two each of two different polypeptides called the α-subunits and the β- subunits) And four heme, one in each of the four polypeptides, each contain an iron atom that is essential to their function 37 38 38 39 PROTEIN STRUCTURE BASED ON SHAPE 39 13  10/10/2024 40 40 41 41 42 Collagen 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 42 14  10/10/2024 43 Hemoglobin transports oxygen from the lungs to tissue. It is a tetramer (four peptide subunits) with each subunit also containing a heme group 43 44 Myoglobin functions as an oxygen-storage molecule in muscles is a monomer has a higher affinity for oxygen than does hemoglobin 44 45 PROTEIN CLASSIFICATION BASED ON FUCNTION 45 15  10/10/2024 46 Catalytic proteins Enzymes Immunoglobulins or Defense proteins Antibodies hemoglobin which Transport proteins carries oxygen insulin and glucagon, Messenger proteins human growth hormone actin and myosin, sperm Contractile proteins flagella Structural proteins collagen and a-keratin 46 47 help control the movement of Transmembrane small molecules and ions through proteins the cell membrane Storage proteins ferritin sites at which messenger Regulatory proteins molecules, including messenger proteins such as insulin, can bind Nutrient proteins Casein and ovalbumin part of the system by which the Buffer proteins acid-base balance within body fluids is maintained Fluid-balance albumin and globulin proteins 47 48 GLYCOPROTEINS 48 16  10/10/2024 49 Glycoprotein is a protein that contains carbohydrates or carbohydrate derivatives in addition to amino acids collagen and immunoglobulins blood group markers of the ABO system are also glycoproteins in which the carbohydrate content can reach 85% 49 50 Collagen fibrous protein collagen, whose structure qualifies as a glycoprotein because carbohydrate units are present in its structure glycosidic linkages to collagen at its 5- hydroxylysine residues causes collagen to be classified as a glycoprotein 50 51 Immunoglobulins protective response to the invasion of microorganisms or foreign molecules an antigen is a foreign substance, such as a bacterium or virus that invades the human body antibody is a biochemical molecule that counteracts a specific antigen cyclosporine, the best known "antirejection" drug Human Immunodeficiency Syndrome 51 17  10/10/2024 52 LIPOPROTEINS 52 53 Lipoproteins is a conjugated protein that contains lipids in addition to amino acids. help suspend lipids and transport them through the bloodstream 53 54 Plasma Lipoprotein involved in the transport system for lipids in the bloodstream 54 18  10/10/2024 55 Major Classes of Plasma Lipoproteins Chylomicrons transport dietary triacylglycerols from the intestine to the liver and to adipose tissue. 55 56 Major Classes of Plasma Lipoproteins Very-low-density lipoproteins (VLDLs). transport triacylglycerols synthesized in the liver to adipose tissue. 56 57 Major Classes of Plasma Lipoproteins Low-density lipoproteins (LDLs) transport cholesterol synthesized in the liver to cells throughout the body. 57 19  10/10/2024 58 Major Classes of Plasma Lipoproteins High-density lipoproteins (HDLs) collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids. 58 59 59 20  10/4/2024 1 AMINO ACIDS Structures and Properties Essential Amino Acids Molecular Handedness Peptide Bond Formation and Characteristics Biochemically Important Small Peptides 1 2 Amino acid the building blocks of protein molecule contains both an amino group and a carboxylic acid functional group and a side chain all attached to an ɑ-carbon nature of this side chain distinguishes ɑ-amino acids from each other 2 3 1  10/4/2024 zwitterions: ions in which the amino group is positively charged and the carboxylate group is negatively charged 4 5 Standard Amino Acid is one of the 20 amino acids normally found in proteins building blocks of protein There are four categories: nonpolar amino acids polar neutral amino acids polar acidic amino acids, and polar basic amino acids. 5 6 Nonpolar, Neutral Side Chains is an amino acid that contains one amino group, one carboxyl group, and a nonpolar side chain are hydrophobic 6 2  10/4/2024 7 Nonpolar, Neutral Side Chains 7 8 Nonpolar, Neutral Side Chains 8 9 Nonpolar, Neutral Side Chains 9 3  10/4/2024 10 Polar, Neutral Side Chains is an amino acid that contains one amino group, one carboxyl group and a side chain that is polar but neutral in physiological pH, the side chain of a polar neutral amino acid is neither acidic nor basic 10 11 Polar, Neutral Side Chains 11 12 Polar Acidic 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 physiological pH, the side chain of a polar acidic amino acid bears a negative charge the side-chain carboxyl group 12 4  10/4/2024 13 Polar Acidic Amino Acid 13 14 Polar Basic 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 at physiological pH, the side chain of a polar basic amino acid bears a positive charge, the nitrogen atom of the amino group has accepted a proton 14 15 Polar Basic Amino Acid 15 5  10/4/2024 16 Number of State in Hydrophobic Classification of Carboxyl Physiological or Amino Acids Amino Group pH Hydrophilic Group nonpolar amino acids 1 1 --- Hydrophobic polar neutral amino acids 1 1 Neutral Hydrophilic polar acidic amino acids, 1 2 Acidic Hydrophilic polar basic amino acids. 2 1 Basic Hydrophilic 16 17 Names of the Standard Amino Acids often abbreviated using three-letter codes except in four cases, these abbreviations are the first three letters of the amino acid's name one-letter code for amino acid names 17 18 Names of the Standard Amino Acids 18 6  10/4/2024 19 Names of the Standard Amino Acids 19 20 Three-Letter One-Letter Amino Acid Abbreviation Abbreviation Alanine Ala A Cysteine Cys C Valine Val V Serine Ser S Tryptophan Trp W 20 21 THE ESSENTIAL AMINO ACIDS 21 7  10/4/2024 22 Essential Amino Acid is an amino acid needed by the human body that must be obtained from dietary source because it cannot be synthesized within the body 22 23 * 23 24 Phenylalanine Function/s: precursor for the neurotransmitters tyrosine, dopamine, epinephrine and norepinephrine Sources: milk, cheese, and yogurt 24 8  10/4/2024 25 Valine Function/s: helps stimulate muscle growth and regeneration and is involved in energy production Sources: beef, chicken, pork, fish, tofu, yogurt, beans, podded peas, seeds, nuts, and whole grains like oatmeal 25 26 Threonine Function/s: part of structural proteins such as collagen and elastin, which are important components of the skin and connective tissue Sources: lean beef, soy, pork, chicken, liver, cheese, shellfish, nuts, seeds, and beans 26 27 Tryptophan Function/s: is precursor to serotonin, a neurotransmitter that regulates your appetite, sleep and mood Sources: chicken, eggs, cheese, fish, peanuts, pumpkin and sesame seeds. 27 9  10/4/2024 28 Methionine Function/s: necessary for tissue growth and the absorption of zinc and selenium Sources: beef, fish, pork, tofu, milk, cheese, nuts, beans, and whole grains 28 29 Leucine Function/s: helps regulate blood sugar levels, stimulates wound healing and produces growth hormones Sources: chicken, beef, pork, fish (tuna), tofu, milk, cheese, squash seeds, and eggs 29 30 Isoleucine Function/s: immune function, hemoglobin production and energy regulation Sources: eggs, soy, seaweed, turkey, chicken, cheese, and fish 30 10  10/4/2024 31 Lysine Function/s: protein synthesis, hormone and enzyme production and the absorption of calcium, production of collagen and elastin Meat, specifically red meat, pork, and poultry. Sources: cheese, sardines, eggs, tofu, isolated soy protein, and Spirulina. 31 32 Histidine Function/s: used to produce histamine, a neurotransmitter that is vital to immune response, digestion, sexual function and sleep-wake cycles Sources: meat, eggs, dairy protein (casein), cereal grains, and legumes 32 33 Arginine is an essential amino acid in children required for growth but not an essential amino acid for adults Sources: milk, cheese, and yogurt Functions: wound healing, removing ammonia from the body, immune function 33 11  10/4/2024 34 Complete Dietary Protein contains all of the essential amino acids the same relative amount in which the body needs them animal sources is usually complete dietary protein such as casein from milk and proteins found in meat, fish, and eggs soy is the only common plant protein that is a complete dietary protein 34 35 Incomplete Dietary Protein is a protein that does not contain adequate amounts, relative to the body’s needs of one or more of the essential amino acids Gelatin from animal sources (tryptophan is the limiting amino acid) 35 36 Incomplete Dietary Protein limiting amino acids in plants lysine (wheat, rice, oats, and corn) methionine (beans and peas), and tryptophan (corn and beans). 36 12  10/4/2024 37 Limiting Amino Acid is an essential amino acid that is missing or present but inadequate amounts, in an incomplete dietary protein 37 38 Complementary Dietary Proteins are two or more incomplete dietary proteins that when combined, provide an adequate amount of all essential amino acids Rice and Beans 38 39 CHIRALITY AND MOLECULAR HANDEDNESS 39 13  10/4/2024 40 Alpha (ɑ-) amino acid An amino acid in which the amino group is bonded to the carbon atom next to the -COOH group. 40 41 41 42 Fischer Projection Formulas 1. The -COOH group is put at the top of the projection formula, the R group at the bottom. This positions the carbon chain vertically. 2. The -NH3, group is in a horizontal position. Positioning it on the left denotes the L isomer, and positioning it on the right denotes the D isomer. 42 14  10/4/2024 43 43 44 BIOCHEMICALLY IMPORTANT SMALL PEPTIDES 44 45 Peptide bond is an amide bond that links two amino acids together. 45 15  10/4/2024 46 Polypeptide is a long unbranched chain of amino acids. 46 47 Peptide bond The end with the free H3N+ group is called the N-terminal end and the end with the free COO- group is called the C- terminal end. The individual amino acids within a peptide chain are called amino acid residues. 47 48 Amino Acid Residues residue is the portion of an amino acid structure that remains, after the release of H2O, when an amino acid participates in peptide bond formation becomes part of a peptide chain. 48 16  10/4/2024 49 Peptide Nomenclature 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 (cystenyl), glutamine (glutaminyl), and asparagine (asparaginyl) Rule 3: The amino acid naming sequence begins at the N-terminal amino acid residue 49 50 Peptide Nomenclature Glu-Ser-Ala Glutamyl-seryl-alanine Gly-Tyr-Val Glycyl-tyrosyl-valine 50 51 Isomeric Peptides contain the same amino acids but in different order are different molecules (constitutional isomers) with different properties. 51 17  10/4/2024 52 Small Peptide Hormones produced by the pituitary gland, are oxytocin and vasopressin 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. 52 53 Small Peptide Hormones Oxytocin regulates uterine contractions and lactation. Vasopressin regulates the excretion of water by the kidneys; it also affects blood pressure. Another name for vasopressin is antidiuretic hormone (ADH) 53 54 Small Peptide Neurotransmitters Enkephalins are pentapeptide neurotransmitters produced by the brain itself that bind at receptor sites in the brain to reduce pain 54 18  10/4/2024 55 Small Peptide Neurotransmitters Met-enkephalin is involved in phenomena associated with modulated pain perception, regulation of memory and emotional conditions Leu-enkephalin controls gonadal function. 55 56 Small Peptide Antioxidant Glutathione is a tripeptide (Glu-Cys-Gly) that functions as antioxidant protecting cellular contents from oxidizing agents such as peroxides and superoxides 56 57 Small Peptide Antioxidant an acidic amino acid, is bonded to Cys through the side-chain carboxyl group rather than through its a- carbon carboxyl group 57 19