Week 5 - Amino Acid and Proteins PDF

AMINO ACID CHEMISTRY AND PROTEIN ORGANIZATION  Learning Objectives At the end of the session, Student will be able to: 1.Give concrete example of the general functions of proteins 2.Categorize the structural composition of amino acids Explain the acid-base properties of ami...

AMINO ACID CHEMISTRY AND PROTEIN ORGANIZATION  Learning Objectives At the end of the session, Student will be able to: 1.Give concrete example of the general functions of proteins 2.Categorize the structural composition of amino acids Explain the acid-base properties of amino acids and state its importance Differentiate the hierarchy of protein structure Explain the concepts of misfolding Explain the importance of Modification of Amino Acids  Proteins and Amino Acids Amino Acids – “Alphabet” of protein structure – Basic structural units – Amino Acids are the building units of proteins. Proteins are polymers of amino acids linked together by what is called “ Peptide bond” – There are about 700 amino acids occur in nature. Only 20 of them occur in proteins.  Characteristics of Proteins A protein is a naturally- occurring, unbranched polymer in which the monomer units are amino acids Proteins are most abundant molecules in the cells after water – account for about 15% of a cell’s overall mass Importance of Proteins Importance of Proteins Importance of Proteins  General Structure of Amino Acids Each amino acid has 4 different groups attached to α- carbon ( which is C-atom next to COOH). These 4 groups are : amino group, COOH group, Hydrogen atom and side Chain (R)  Zwitterions Under normal cellular conditions amino acids are zwitterions (dipolar ions):  Isoelectric Point The conditions of zwitterions are reliant on pH at which an amino acid solution has no net charge because an equal number of positive and negative charges are present.  Isoelectric Point The structure of an amino acid can change with the pH of the solution: Lowering the pH of the solution causes the zwitterion to pick up a proton  Isoelectric Point The structure of an amino acid can change with the pH of the solution: Increasing the pH of the solution causes the zwitterion to lose a proton  Chirality of Amino Acids 19 of the 20 common amino acids have a chiral α-carbon atom (Gly does not) Chiral carbons –have four different groups attached  General Structure of Amino Acids Threonine and isoleucine have 2 chiral carbons each (4possible stereoisomers each) Stereoisomers-compounds that have the same molecular formula but differ in the arrangement of atoms in space  Stereochemistry of Amino Acids Mirror image pairs of amino acids are designated L (levo) and D (dextro) and are called enantiomers Proteins are assembled from L-amino acids (a few D- amino acids occur in nature) Practice activity Abbreviatons of Amino Acids Classification of Amino Acid Classificati on of Amino Acid R-group Nutrition Catabolism Classification of Amino Acid: Side Chain Classification of Amino Acid: Side Chain Amino Acid with Polar neutral side chain nonpolar side Have side chains with either a net chain positive or a net negative It is hydrophilic and soluble in water Contains uncharged hydrocarbon groups Polar acidic side chain or benzene rings Contains 1 amino group and 2 carboxyl Does not gain or group lose protons or Side chain is negative and is –ic acid participate in Polar basic side chain hydrogen or ionic Contains 2 amino group and 1 carboxyl group bonds Side chain is positive Oily or lipid like -> Hydrophobic PRACTICE EXERCISE PRACTICE EXERCISE CLASSIFICATION OF AMINO ACIDS Based on the Chemical Composition of R Groups  CLASSIFICATION OF AMINO ACIDS Hydrophobicity of Amino Acid Side Hydropathy affects Chains protein folding: Hydrophobic side chains tend to be in the interior Hydrophilic residues tend to be on the surface Free-energy change is for transfer of an amino acid from interior of a lipid bilayer to water) Classification of Amino Acid: Nutrition Essential Amino acid: A standard amino acid needed for protein synthesis that must be obtained from dietary sources – adequate amounts cannot be synthesized in human body. Nonessential Amino acid: Can be synthesized by  Metabolic classification: according to metabolic or degradation products of amino acids they may be: 1- Ketogenic amino acids: which give ketone bodies. Lysine and Leucine are the only pure ketogenic amino acids. Ketogenic amino acids are a subset of amino acids that can be metabolized thru acetyl coa 2- Mixed ketogenic and glucogenic amino acids: which give both ketone bodies and glucose. These are: isoleucine, phenyl alanine, tyrosine and tryptophan. 3- Glucogenic amino acids: Which give glucose. They include the rest of amino acids. These amino acids by catabolism yields products that enter in glycogen and glucose formation.  OTHER AMINO ACIDS AND DERIVATIVES Rare Amino Acids of Proteins 4-Hydroxyproline Found in plant cell wall proteins (extensins) Found in collagen 4-Hydroxylysine Found in collagen  OTHER AMINO ACIDS AND DERIVATIVES Rare Amino Acids of Proteins β-alanine Homocysteine Homoserine Component of Intermediates in amino Intermediates in amino pantothenic acid (vitB5) acid metabolism acid metabolism OTHER AMINO ACIDS AND DERIVATIVES Rare Amino Acids of Proteins OTHER AMINO ACIDS AND DERIVATIVES Rare Amino Acids of Proteins OTHER AMINO ACIDS AND DERIVATIVES Rare Amino Acids of Proteins OTHER AMINO ACIDS AND DERIVATIVES Rare Amino Acids of Proteins  Proteins: Structural Organization What is the Difference between peptides and Protein - The chains containing less than 50 amino acids are called “peptides”, while those containing greater than 50 amino acids are called “proteins”. - Each joined or linked to the next by a peptide bond - 2 amino acid – Dipeptide - 3 amino acid – Tripeptide - 10-20 amino acid – Oligopeptide - Long chain of amino acids - Polypeptide  What is a peptide bond - Peptide bond - linkage between amino acids is a secondary amide bond - Formed by condensation of the α-carboxyl of one amino acid with the α-amino of another amino acid (loss of H2O molecule) Hydrolytic Reaction  Nature of Peptide Bond by convention, the structure of peptides is represented beginning with the amino acid whose amino group is free (N-terminal end). The other end contains a free carboxyl group and is the C-terminal end  ISOMETRIC PEPTIDES Peptides that contain the same amino acids but in different order with different properties Example Glu – Cys – Met –Gly Asp – Val – Ser Gly – His – Lys  BIOCHEMICALLY IMPORTANT SMALL PEPTIDES Hormones Neurotransmitters Antioxidant Artificial sweeteners  BIOCHEMICALLY IMPORTANT SMALL PEPTIDES  BIOCHEMICALLY IMPORTANT SMALL PEPTIDES Enkephalins are pentapeptide neurotransmitters produced by the brain and bind receptors within the brain Help reduce pain Best-known enkephalins: – Met-enkephalin: Tyr–Gly–Gly–Phe–Met – Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu  BIOCHEMICALLY IMPORTANT SMALL PEPTIDES Enkephalins are pentapeptide neurotransmitters produced by the brain and bind receptors within the brain Help reduce pain Best-known enkephalins: – Met-enkephalin: Tyr–Gly–Gly–Phe–Met – Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu  BIOCHEMICALLY IMPORTANT SMALL PEPTIDES Glutathione (Glu–Cys–Gly) – a tripeptide – is present is in high levels in most cells Regulator of oxidation–reduction reactions. Glutathione is an antioxidant and protects 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  BIOCHEMICALLY IMPORTANT SMALL PEPTIDES Aspartame (Asp-Phe) - dipeptide sold under trade names Equal and Nutrasweet; ~180x as sweet as sucrose  Primary structure The primary structure of a protein is its unique sequence of amino acids. differences in the chemical and physiologic properties of peptides result from differences in the amino acid sequence. – Lysozyme, an enzyme that attacks bacteria, consists of a polypeptide chain of 129 amino acids. – The precise primary structure of a protein is determined by inherited genetic information. Importance of Primary structure Importance of Primary structure Enzymatic Hydrolysis  Enzymatic Hydrolysis 1)Exopeptidases – cleaves external peptide bonds a) aminopeptidase – sequentially cleave peptide bonds beginning at the N-terminal end b) carboxypeptidase – sequentially cleave peptide bonds beginning at the C-terminal end  Enzymatic Hydrolysis 2)Endopeptidases – cleaves internal peptide bonds a) trypsin – cleaves peptide bonds at the carboxyl end of two strongly basic aa’s : Arg & Lys b) chymotrypsin – cleaves peptide bonds at the carboxyl end of the three aromatic: Phe, Tyr, & Trp; Leu c) pepsin – cleaves peptide bonds at the amino end of the three aromatic aa’s: Phe, Tyr, & Trp; Ileu  Practice exam Write the peptides generated from chymotrypsin, trypsin, and pepsin digestion of Ala-His-Tyr-Pro-Trp-Arg-Ileu-Phe-Glu-Lys- Cys 2- Secondary structure: Results from hydrogen bond formation between hydrogen of –NH group of peptide bond and the carbonyl oxygen of another peptide bond. According to H-bonding there are two main forms of secondary structure:  Alpha-helix (α-helix) A single protein chain adopts a shape that resembles a coiled spring (helix): H-bonding between amino acids with in the same chain – intramolecular H-bonding Coiled helical spring R-groups stay outside of the helix -- not enough room for them to stay inside The helix is so tightly wound that the space in the center is too small for solvent molecules to enter Beta-Pleated Sheets Completely extended protein chain segments in same or different molecules governed by intermolecular or intramolecular H- bonding H-bonding between different parts of a single chain – intramolecular H-bonding Side chains below or above the axis “U-turn” structure – most frequently encountered Beta-Pleated Sheets Completely extended protein chain segments in same or different molecules H-bonding between different chains – intermolecular H-bonding a) parallel – chains run in the same direction b) antiparallel – chains run in opposite direction; more stable because of fully collinear H- bonds Tertiary structure The overall three-dimensional shape of a protein Results from the interactions between amino acid side chains (R groups) that are widely separated from each other. Defines the biological function of proteins Proteins may have, in general, either of the two forms of tertiary structures: fibrous proteins (insoluble): mechanical strength, structural components, movement globular proteins (soluble): transport, regulatory, enzymes  Tertiary structure is determined by a variety of interactions (bond formation) among R groups and between R groups and the polypeptide backbone. b. Strong covalent bonds include disulfide bridges, that form between the sulfhydryl groups (SH) of cysteine monomers, stabilize the structure. Electrostatic interactions (ionic interaction, salt linkages): Salt Bridge between charged side chains of acidic and basic amino acids –-OH, -NH2, -COOH, -CONH2 H-Bonding between polar, acidic and/or basic R groups –For H-bonding to occur, the H must be attached to O, N or F  Quaternary structure: results from the aggregation (combination) of two or more polypeptide subunits held together by non-covalent interaction like H- bonds, ionic or hydrophobic interactions. Examples on protein having quaternary structure: – Collagen is a fibrous protein of three polypeptides (trimeric) that are supercoiled like a rope. This provides the structural strength for their role in connective tissue. – Hemoglobin is a globular protein with four polypeptide chains (tetrameric) – Insulin : two polypeptide chains (dimeric)  Classification of proteins I- Simple proteins: i.e. on hydrolysis gives only amino acids Examples: 1- Albumin and globulins: present in egg, milk and blood They are proteins of high biological value i.e. contain all essential amino acids and easily digested. Types of globulins: α1 globulin: e.g. antitrypsin: see later α2 globulin: e.g. hepatoglobin: protein that binds hemoglobin to prevent its excretion by the kidney β-globulin: e.g. transferrin: protein that transport iron γ-globulins = Immunoglobulins (antibodies) : responsible for immunity.  Classification of proteins 2- Globins (Histones): They are basic proteins rich in histidine amino acid. They are present in : a - combined with DNA b - combined with heme to form hemoglobin of RBCs. 3- Gliadines are the proteins present in cereals. 4- Scleroproteins: They are structural proteins, not digested. include: keratin, collagen and elastin. a- α-keratin: protein found in hair, nails, enamel of teeth and outer layer of skin. It is α-helical polypeptide chain, rich in cysteine and hydrophobic (non polar) amino acids so it is water insoluble. b- collagens: protein of connective tissues found in bone, teeth, cartilage, tendons, skin and blood vessels.  Collagen may be present as gel e.g. in extracellular matrix Collagens are the most important protein in mammals. They form about 30% of total body proteins. There are more than 20 types of collagens, the most common type is collagen I which constitutes about 90% of cell collagens. Structure of collagen: three helical polypeptide chains (trimeric) twisted around each other forming triplet- helix molecule. Solubility: collagen is insoluble in all solvents and not digested. When collagen is heated with water or dil. HCl it will be converted into gelatin which is soluble , digestible and used as diet ( as jelly). Gelatin is classified as derived protein. Medical Application of the lessons: Collagen 1- Scurvy: disease due to deficiency of vitamin C which is important coenzyme for conversion of proline into hydroxyproline and lysine into hydroxylysine. Thus, synthesis of collagen is decreased leading to abnormal bone development, bleeding, loosing of teeth and swollen gum. 2- Osteogenesis Imperfecta (OI): Inherited disease resulting from genetic deficiency or mutation in gene that synthesizes collagen type I leading to abnormal bone formation in babies and frequent bone fracture in children. It may be lethal.  Medical Application of the lessons: Elastin C- Elastin: present in walls of large blood vessels (such as aorta). It is very important in lungs, elastic ligaments, skin, cartilage,.. It is elastic fiber that can be stretched to several times as its normal length. Structure: composed of 4 polypeptide chains (tetramer), similar to collagen being having 33% glycine and rich in proline but in that it has low hydroxyproline and absence of hydroxy lysine. Emphysema: is a chronic obstructive lung disease (obstruction of air ways) resulting from deficiency of α1-antitrypsin particularly in cigarette smokers. Role of α1-antitrypsin: Elastin is a lung protein. Smoke stimulate enzyme called elastase to be secreted form neutrophils (in lung). Elastase cause destruction of elastin of lung.  Conjugated proteins i.e. On hydrolysis, give protein part and non protein part and subclassified into: 1- Phosphoproteins: These are proteins conjugated with phosphate group. Phosphorus is attached to oh group of serine or threonine. e.g. Casein of milk and vitellin of yolk. 2- Lipoproteins: These are proteins conjugated with lipids. Functions: a- help lipids to transport in blood b- Enter in cell membrane structure helping lipid soluble substances to pass through cell membranes.  Conjugated proteins 3- Glycoproteins: proteins conjugated with sugar (carbohydrate) e.g. – Mucin - Some hormones such as erythropoeitin - present in cell membrane structure - blood groups. 4- Nucleoproteins: These are basic proteins ( e.g. histones) conjugated with nucleic acid (DNA or RNA). e.g. a- chromosomes: are proteins conjugated with DNA b- Ribosomes: are proteins conjugated with RNA  Conjugated proteins 5- Metalloproteins: These are proteins conjugated with metal like iron, copper, zinc, …… a- Iron-containing proteins: Iron may present in heme such as in - hemoglobin (Hb) - myoglobin ( protein of skeletal muscles and cardiacmuscle), - cytochromes, - catalase, peroxidases (destroy H2O2) - tryptophan pyrrolase (desrtroy indole ring of tryptophan). Iron may be present in free state ( not in heme) as in: - Ferritin: Main store of iron in the body. ferritin is present in liver, spleen and bone marrow. - Hemosidrin: another iron store. - Transferrin: is the iron carrier protein in plasma. Protein Classification Based on Shape Protein Globular Fibrous Type Proteins Proteins Spherical or roughly Long, Shape spherical fibrous Enzymes, Structural antibodie support, s, mechanic hormone al Function s strength Hemoglo bin, Collagen, Example insulin, keratin,  Protein Digestion: The process of breaking down proteins into smaller peptides and amino acids. Begins in the Stomach: Pepsin, an enzyme activated by stomach acid, initiates protein digestion. Continues in the Small Intestine: Pancreatic enzymes like trypsin, chymotrypsin, and carboxypeptidase further break down proteins. Absorption: Amino acids are absorbed through the intestinal walls into the bloodstream. Utilization: Amino acids are used by the body for various functions Excess: Excess amino acids are converted to  Protein Misfolding Protein misfolding is a biological phenomenon in which a protein adopts an abnormal three- dimensional structure, deviating from its native conformation. Proteins are essential macromolecules that carry out various functions in living organisms, and their proper function relies heavily on their specific three-dimensional shape. Protein Conformation & the Concept of Misfolding Chaperones prevent proteins from folding incorrectly Proteins that have problems achieving their native configuration are helped by chaperones to fold properly The misfolded proteins can be detected by quality-control mechanisms in the cell that tags them to be sent to the cytoplasm, where they will be degraded  Prions infectious protein responsible for transmissible TSEs spongiform encephalopathies --bovine spongiform encephalopathy (mad cow disease) Creutzfeldt-Jakob and kuru  Misfolded Proteins and Neurodegenerative Diseases Amyloid diseases - accumulation of misfolded proteins Alzheimer's disease: Misfolding of proteins, such as amyloid-beta and tau, leads to the formation of toxic aggregates in the brain, contributing to the development of Alzheimer's disease. Parkinson's disease: Misfolding of the alpha- synuclein protein leads to the formation of Lewy bodies, which are pathological protein aggregates found in the brains of Parkinson's disease patients. Huntington's disease: A genetic mutation causes the huntingtin protein to misfold and form aggregates, which leads to the progressive degeneration of brain cells.  Protein Denaturation Partial or complete disorganization of protein ’s tertiary structure Cooking food denatures the protein but does not change protein nutritional value Coagulation: Precipitation (denaturation of proteins) – Egg white - a concentrated solution of protein albumin - forms a jelly when heated because the albumin is denatured  Protein Denaturation Cooking: – Denatures proteins – Makes it easy for enzymes in our body to hydrolyze/digest protein – Kills microorganisms by denaturation of proteins – Fever: >104 ºF the critical or when your temp rises over 43C it is fatal  Modification of Amino Acids: Protein Denaturation denaturation of a protein means that it loses its natural shape and cannot function properly. Factors that affect protein denaturation: 1. Heat: 2. pH: 3. Organic solvents: 4. Chaotropic agents: 5. Heavy metals: Modification of Amino Acids: Protein Denaturation