Biochemistry For Medical Laboratory Sciences Lecture Notes (PDF)

BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCES School of Medical Technology (Lecture) Donna Selina dG. Bravo, RPh, MD MIDTERMS LESSON 2: Proteins CONTENTS 1. Proteins ❑ Classification 2. Protein Structure ❑ Amino Acids ❑ Levels of Organization ✓ Primary ✓ Secondary...

BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCES School of Medical Technology (Lecture) Donna Selina dG. Bravo, RPh, MD MIDTERMS LESSON 2: Proteins CONTENTS 1. Proteins ❑ Classification 2. Protein Structure ❑ Amino Acids ❑ Levels of Organization ✓ Primary ✓ Secondary ✓ Tertiary ✓ Quaternary 4. Summary Intended Learning Outcomes (ILOs) 1. Describe the structure and function of proteins. 2. Enumerate the biological importance of proteins. 3. Explain the properties and reaction of proteins. PROTEINS PROTEINS o A class of macromolecules that perform a diverse range of functions for the cell. o They help in metabolism, provide structural support and act as enzymes, carriers, or hormones. PROTEINS o Contain carbon, hydrogen, oxygen and nitrogen o Primary source of nitrogen in our diet  PROTEINS Essential component of the body cells, tissues and fluids. Building block of muscle, bone, skin, hair, and virtually every other body part or tissue.  PROTEINS Proteins are constantly needed to replace the wear and tear of the tissue and keep up the protein concentration in the blood serum. The structure of each protein is dictated by the DNA of a gene. CLASSIFICATION OF PROTEINS  Classification of Proteins 1. SIMPLE PROTEINS: They are composed of only amino acid residue. On hydrolysis these proteins yield only constituent amino acids. It is further divided into: Fibrous protein: Keratin, Elastin, Collagen Globular protein: Albumin, Globulin, Glutelin, Histones Classification of Proteins 1. Simple proteins: They are composed of only amino acid residue. On hydrolysis these proteins yield only constituent amino acids. It is further divided into: Fibrous protein: Keratin, Elastin, Collagen Globular protein: Albumin, Globulin, Glutelin, Histones  Classification of Proteins 2. Conjugated proteins: They are combined with non-protein moiety. Eg. Nucleoprotein, Phosphoprotein, Lipoprotein, Metalloprotein etc. 3. Derived proteins: They are derivatives or degraded products of simple and conjugated proteins. They may be primary derived protein: Proteans, Metaproteins, Coagulated proteins. Secondary derived proteins: Proteosesn or albunoses, peptones, peptides. Classification of Proteins PROTEIN STRUCTURE  AMINO ACIDS The building blocks of proteins are amino acids. An amino acid is an organic molecule in which a hydrogen atom, a carboxyl group (–COOH), and an amino group (–NH2) are all bonded to the same carbon atom, the so-called α carbon. AMINO ACIDS The fourth group bonded to the α carbon varies among the different amino acids and is called a residue or a side chain, represented in structural formulas by the letter R. A residue is a monomer that results when two or more amino acids combine and remove water molecules. There are >300 different amino acids in nature. Some common functional groups of biomolecules AMINO ACIDS General structure of an amino acid. This structure is common to all but one of the -amino acids. (Proline, a cyclic amino acid, is the exception.) The R group or side chain attached to the carbon is different in each amino acid. Amino acids General structure of an amino acid. This structure is common to all but one of the -amino acids. (Proline, a cyclic amino acid, is the exception.) The R group or side chain attached to the carbon is different in each amino acid.  Amino acids The unique characteristics of the functional groups and R groups allow these components of the amino acids to form hydrogen, ionic, and disulfide bonds, along with polar/nonpolar interactions needed to form secondary, tertiary, and quaternary protein structures.  20 amino acids that make up proteins Single Single Amino acid Abbreviation Amino acid Abbreviation letter letter Alanine Ala A Leucine Leu L Arginine Arg R Lysine Lys K Asparagine Asn N Methionine Met M Aspartic acid Asp D Phenylalanine Phe F Cysteine Cys C Proline Pro P Glutamine Gln Q Serine Ser S Glutamic acid Glu E Threonine Thr T Glycine Gly G Tryptophan Trp W Histidine His H Tyrosine Tyr Y Isoleucine Ile I Valine Val V Needed to make all the proteins found in the human body and most other forms of life. 20 amino acids that make up proteins  Chemical structures of the 20 amino acids that make up proteins  Amino acids Recommended daily allowances Amino acid (mg/kg body Essential amino acids weight) Cannot be produced or stored Histidine 14 Isoleucine 19 by our bodies Leucine 42 Must be obtained from food Lysine 38 Methionine 19 Nonessential amino acids Phenylalanine 33 Can be made by our bodies Threonine 20 Tryptophan 5 *Arginine Valine 24 Conditional essential amino acid Arginine** Four Levels of Organization  Peptide bonds Amino acids may chemically bond together by reaction of the carboxylic acid group of one molecule with the amine group of another. This reaction forms a peptide bond and a water molecule and is another example of dehydration synthesis. Each amino acid is linked to its neighbors by a peptide bond. A long chain of amino acids is known as a polypeptide. Nomenclature of peptides bonds  Primary structure The primary structure of a protein, a peptide chain, is made of amino acid residues. The unique characteristics of the functional groups and R groups allow these components of the amino acids to form hydrogen, ionic, and disulfide bonds, along with polar/nonpolar interactions needed to form secondary, tertiary, and quaternary protein structures. The size (length) and specific amino acid sequence of a protein are major determinants of its shape, and the shape of a protein is critical to its function. Primary structure  Secondary structure When the chain is sufficiently long, hydrogen bonding may occur between amine and carbonyl functional groups within the peptide backbone resulting in localized folding of the polypeptide chain into helices and sheets.  Secondary structure When the chain is sufficiently long, hydrogen bonding may occur between amine and carbonyl functional groups within the peptide backbone resulting in localized folding of the polypeptide chain into helices and sheets.  Secondary structure When the chain is sufficiently long, hydrogen bonding may occur between amine and carbonyl functional groups within the peptide backbone resulting in localized folding of the polypeptide chain into helices and sheets. Secondary structure Secondary structure α-helix structure - held by hydrogen bonds between the oxygen atom in a carbonyl group of one amino acid and the hydrogen atom of the amino group that is just four amino acid units farther along the chain.  Secondary structure β-pleated sheet - formed by similar hydrogen bonds between continuous sequences of carbonyl and amino groups that are further separated on the backbone of the polypeptide chain.  Tertiary structure Large-scale three-dimensional shape of a single polypeptide chain. Determined by interactions between amino acid residues that are far apart in the chain. A variety of interactions weak and strong, combine to determine the final three-dimensional shape of the protein and its function. Tertiary structure  Tertiary structure PROTEIN FOLDING process by which a polypeptide chain assumes a large-scale, three-dimensional shape.  Tertiary structure Denaturation - the loss of the secondary structure and tertiary structure without the loss of the primary structure.  Quaternary structure Protein subunits - when proteins are assemblies of several separate polypeptides. The interactions that hold these subunits together constitute the quaternary structure of the protein. Hemoglobin - has a quaternary structure of four globular protein subunits: two α and two β polypeptides, each one containing an iron-based heme. Quaternary structure  Conjugated proteins Conjugated proteins - another important class of proteins that have a nonprotein portion: ❑ Glycoprotein - if the conjugated protein has a carbohydrate attached. ❑ Lipoprotein - if it has a lipid attached. These proteins are important components of membranes. Biswas, Sunanda. (2021). CHAPTER-1 PROTEIN. TYPES AND FUNCTIONS OF PROTEINS  Protein Types and Functions Types Examples Functions Digestive Enzymes Amylase, lipase, pepsin, Help in digestion of food by catabolizing trypsin nutrients into monomeric units Transport Hemoglobin, albumin Carry substances in the blood or lymph throughout the body Structural Actin, tubulin, keratin Construct different structures, like the cytoskeleton Hormones Insulin, thyroxine Coordinate the activity of different body systems Defense Immunoglobulins Protect the body from foreign pathogens Contractile Actin, myosin Effect muscle contraction Storage Legume storage proteins, Provide nourishment in early development of egg white (albumin) the embryo and the seedling Some functions of proteins The light produced by fireflies is the result of a reaction involving the protein luciferin and ATP, catalyzed by the enzyme luciferase. Erythrocytes contain large amounts of the oxygen- transporting protein hemoglobin. The protein keratin, formed by all vertebrates, is the chief structural component of hair, scales, horn, wool, nails, and feathers.  Two special and common types of proteins 1. Enzymes Catalysts in biochemical reactions (like digestion) and are usually complex or conjugated proteins. Each enzyme is specific for the substrate (a reactant that binds to an enzyme) it acts on.  Two special and common types of proteins 1. Enzymes The enzyme may help in breakdown, rearrangement, or synthesis reactions: ✓ Catabolic enzymes - break down their substrates ✓ Anabolic enzymes - build more complex molecules from their substrates ✓ Catalytic enzymes - affect the rate of reaction  Two special and common types of proteins 1. Enzymes All enzymes increase the rate of reaction = organic catalysts. An example of an enzyme is salivary amylase, which hydrolyzes its substrate amylose, a component of starch.  Two special and common types of proteins 2. Hormones Chemical-signaling molecules Usually small proteins or steroids, secreted by endocrine cells Act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps to regulate the blood glucose level. BIOLOGICAL IMPORTANCE  Proteins in the Diet Incomplete protein Does not contain all nine essential amino acids Not sufficient for growth and health Considered as “low quality” protein Complete protein Contains sufficient amounts of all 9 essential amino acids Support growth and maintenance of body tissues Considered as “high quality” protein Animal proteins: milk, eggs, cheese, fish, and meat Plant source: brewer's yeast, certain nuts, soybeans/tofu, germ of grains  Proteins in our Diet All protein is not equal. It is important to have a variety of food to make certain the body gets all of the essential amino acids, Ways to make protein complete: By combining plant and animal food. By combining plant protein from a variety of cereals and grains. For example: peanut butter lacks 3 amino acids, but by spreading it on whole wheat bread and serving it with a glass of milk or some yogurt, it becomes a complete protein.  Proteins in our Diet Hazards in eating too much proteins: Converting large amounts of proteins for storage as fat creates products that may place dangerous stress on the liver and kidneys. A very high protein diet may even cause dehydration as extra water is needed to dispose off the products or protein metabolism. Athletes and dancers are already at risk for dehydration and should be especially careful to avoid excess protein.  Proteins in our Diet When do you need protein First meal of the day - to replenish amino acids used for growth and maintenance during the night. Last meal of the day - to build up the protein in the body needed for repair and maintenance during the night. Adults need a minimum of 1g of protein for every kilogram of body weight per day to keep from slowly breaking down their own tissues.  Proteins in our Diet Deficiencies of protein can cause: tiredness loss of weight lack of energy growth can be stunted in children decreased immunity and lower resistance to disease Prolonged lack of protein can result in liver damage, weakening of the heart and respiratory system, and eventually death. SUMMARY  Summary Amino acids are small molecules essential to all life. Each has an α carbon to which a hydrogen atom, carboxyl group, and amine group are bonded. The fourth bonded group, varies in chemical composition, size, polarity, and charge among different amino acids, providing variation in properties. Peptides are polymers formed by the linkage of amino acids via dehydration synthesis. The bonds between the linked amino acids are called peptide bonds.  Summary Proteins are polymers formed by the linkage of a very large number of amino acids. Proteins perform many important functions in a cell, serving as nutrients and enzymes; storage molecules for carbon, nitrogen, and energy; and structural components. The structure of a protein is a critical determinant of its function and is described by a graduated classification: primary, secondary, tertiary, and quaternary.  Summary The native structure of a protein may be disrupted by denaturation, resulting in loss of its higher-order structure and its biological function. Conjugated proteins have a nonpolypeptide portion that can be a carbohydrate (forming a glycoprotein) or a lipid fraction (forming a lipoprotein). These proteins are important components of membranes. You need protein in your diet to help your body repair cells and make new ones. Protein is also important for growth and development in children, teens, and pregnant women. Inborn Errors of Metabolism that respond to dietary therapy Inborn Errors of Metabolism that respond to dietary therapy  Phenylketonuria PKU is one of a class of hyperphenylalaninemia and is the most common IEM requiring nutritional treatment. Insufficient or absent phenylalanine hydroxylase Therapy: Dietary Phe from intact protein sources can be restricted to the amount that allows for normal growth and development while preventing excessive build-up of Phe in the blood. Restriction of all sources of animal protein, legumes and nuts, bread, pasta, rice and some vegetables. Thank you for listening! ☺