Biochemistry For Dental Students PDF

8/31/2022 Biochemistry For Dental Students Said El Shamieh, Msc |PhD. Associate Professor of Human Genetics Faculty of Health Sciences, Beirut Arab University...

8/31/2022 Biochemistry For Dental Students Said El Shamieh, Msc |PhD. Associate Professor of Human Genetics Faculty of Health Sciences, Beirut Arab University 1 1  8/31/2022 Beirut Arab University Biochemistry For Dental Students CHAPTER 1 The Foundations of Biochemistry Lectures notes prepared by: Said El Shamieh, PhD | MSc. Dr. Said El Shamieh 3 Introduction About four billion years ago, life arose, simple microorganisms with the ability to extract energy from chemical compounds and, later, from sunlight, which they used to make a vast array of more complex biomolecules from the simple elements and compounds on the Earth’s surface. Biochemistry studies the distinguishing features of living organisms arising from the thousands of different biomolecules. Dr. Said El Shamieh 4 2  8/31/2022 What are these distinguishing features of living organisms? Pancreatic cell section A high degree of chemical complexity and microscopic organization. Systems for extracting, transforming, and using energy from the environment. Mechanisms for sensing and responding to alterations in their surroundings. A capacity for precise self-replication and self-assembly. A capacity to change over time by gradual evolution. 5 Dr. Said El Shamieh Cellular Foundation Dr. Said El Shamieh 6 3  8/31/2022 Three distinct domains of life All living organisms fall into one of three large domains that define three branches. Two large groups of single-celled microorganisms: Bacteria and Archaea. 1. Bacteria : lack a membrane-bounded nucleus and mitochondria, are surrounded by a cell wall, and divide by binary fission. Dr. Said El Shamieh 7 Three distinct domains of life 2. Eukarya: Organisms whose cells contain an elaborate network of internal membranes, a membrane- bounded nucleus, and mitochondria. Their DNA is organized into true chromosomes, and cell division takes place by means of mitosis. 3. Archaea Produce methane gas or that live in extreme environments (hot springs or high salt concentrations). Lack internal membranes. Machinery for DNA replication and transcription resembles that of eukaryans, whereas their metabolism strongly resembles that of bacteria. 8 4  8/31/2022 Structural hierarchy in the molecular organization of cells. The organelles and other relatively large components of cells are composed of supramolecular complexes, which in turn are composed of smaller macromolecules and even smaller molecular subunits. 9 Dr. Said El Shamieh CHEMICAL FOUNDATION Dr. Said El Shamieh 10 5  8/31/2022 Biochemistry aims to explain biological form and function in chemical terms. < 30 of the naturally occurring chemical elements are essential to organisms. The four most abundant elements in living organisms; H, O, N and C which together make up more than 99% of the mass of most cells. Bulk elements are structural components of cells and tissues and are required in the diet in gram quantities daily. For trace elements, the requirements are much Dr. Said Elsmaller: Shamieh for humans, a few milligrams per 11 day of Fe, Cu, and Zn, even less of the others. Proteins Long polymers of amino acids, constitute the largest fraction (besides water) of a cell. Some proteins have catalytic activity and function as enzymes; others serve as structural elements, or transporters that carry specific substances into or out of cells. The most versatile of all biomolecules. Dr. Said El Shamieh 12 6  8/31/2022 Nucleic acids DNA and RNA, are polymers of nucleotides. Store and transmit genetic information, and some RNA molecules Have structural and catalytic roles in supramolecular complexes. Dr. Said El Shamieh 13 Polysaccharides Polymers of simple sugars such as glucose, have three major functions: Energy-rich fuel stores, Rigid structural components of cell walls (in plants and bacteria). Extracellular recognition elements that bind to proteins on other cells. Dr. Said El Shamieh 14 7  8/31/2022 Lipids Water-insoluble hydrocarbon derivatives. Serve as structural components of membranes. Energy-rich fuel stores. Pigments. Intracellular signals. Dr. Said El Shamieh 15 Biomolecules Are Compounds of Carbon with a Variety of Functional Groups Dr. Said El Shamieh 16 8  8/31/2022 Biomolecules Are Compounds of Carbon with a Variety of Functional Groups The chemistry of living organisms is organized around carbon, which accounts for more than half the dry weight of cells. Carbon can form single bonds with hydrogen atoms, and both single and double bonds with oxygen and nitrogen atoms. Most biomolecules can be regarded as derivatives of hydrocarbons, with hydrogen atoms replaced by a variety of functional groups: Alcohols (>=1 hydroxyl groups) Amines, with amino groups Aldehydes and ketones Carboxylic acids Dr. Said El Shamieh 17 Several functional groups in a single biomolecule Many biomolecules are polyfunctional, containing two or more types of functional groups each with its own chemical characteristics and reactions. Dr. Said El Shamieh 18 9  8/31/2022 Interactions between Biomolecules Are Stereospecific (specific in regard to the 3D ) Complementary fit between a macromolecule and a small molecule When biomolecules interact, the “fit” between them must be stereochemically correct. reactant with its enzyme, hormone with its receptor on a cell surface, antigen with its Dr. Said El Shamieh 19 specific antibody. Stereoisomers have different effects in humans Same molecular formula, but a different chemical structure. Why do stereoisomers have different effects in humans ? The ability to distinguish between stereoisomers, is a property of enzymes and other proteins and a characteristic feature of the molecular logic of living cells. If the binding site on a protein is complementary to one isomer of a chiral compound, it will not be complementary to the other isomer, for the Dr.same Said Elreason Shamieh that a left glove does not fit a right 20 hand. 10  8/31/2022 Physical Foundations The first law of thermodynamics describes the principle of the conservation of energy: in any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change. Dr. Said El Shamieh 21 Classification Dr. Said El Shamieh of Organisms 22 11  8/31/2022 Classification of Organisms All organisms can be classified according to their source of energy (sunlight or oxidizable chemical compounds) and their source of carbon for the synthesis of cellular material. Two broad categories based on energy sources: phototrophs trap and use sunlight, and chemotrophs derive their energy from oxidation of a chemical fuel. Phototrophs and chemotrophs may be further divided into those that can synthesize all of their biomolecules directly from CO2 (autotrophs) and those that require some preformed organic nutrients made by other organisms (heterotrophs). Cyanobacteria are photoautotrophs; humans are chemoheterotrophs. Dr. Said El Shamieh 23 The central roles of ATP and NAD(P)H in metabolism. ATP: Shared chemical intermediate linking energy-releasing and energy-consuming cellular processes. Produced in exergonic reactions and consumed in endergonic ones. NAD(P)H: cofactor that collects electrons. Essential to anabolic reactions must be constantly regenerated by catabolic reactions. Dr. Said El Shamieh 24 12  8/31/2022 Enzymes Enzymes are biocatalysts. Proteins can be hydrolyzed with hydrochloric acid by boiling for a very long-time; but inside the body, with the help of enzymes, proteolysis takes place within a short-time at body temperature. The substance upon which an enzyme acts, is called the substrate. The enzyme will convert the substrate into the product or products. Dr. Said El Shamieh 51 I. Characteristics of enzymes 2. Enzymatic reactions are highly specific, both for the substrate and for the reaction type. 3. Enzymatic reactions are carried out in relatively mild conditions (neutral pH, low temperature, etc.). 4. Enzymatic reactions can be modulated. The regulation of enzyme activity can be carried allosterically, by regulatory proteins, by a covalent modification of the enzyme, by a proteolytic activation, by the amount of enzyme produced, etc. Dr. Said El Shamieh 52 26  8/31/2022 Dr. Said El Shamieh 53 II. Nomenclature: The name of the enzymes most often consists of a radical closest to the substrate or product of catalysis followed by the suffix "ase". 1. oxidation - reduction reaction 2. transfers functional groups 3. hydrolytic reactions 4. elimination reaction to form 5. Isomerization 6. forming bonds with ATP hydrolysis Dr. Said El Shamieh 54 27  8/31/2022 The active site Enzyme function is linked to the presence in their structure of a particular site called the active site. Schematically, it has the shape of a cavity or a furrow in which the substrates will bind through several weak chemical bonds. Once attached, the substrates will react and turn into product. The active site is divided into two parts: - Binding site / fixation/ recognition: it recognizes the complementarity of shape with a specific substrate for the enzyme; - Catalytic site: it allows the reaction that converts the substrate to product. Dr. Said El Shamieh 55 Cofactores Enzymes may be simple proteins, or complex enzymes, containing a non-protein part, called Cofactors. Other enzymes have two parts: an inactive protein part called apoenzyme and a cofactor, which together form an holoenzyme. Essential for the biological activity of the enzyme. A coenzyme is a low molecular weight organic substance, without which the enzyme cannot exhibit any reaction. Divided into: (a) Those taking part in reactions catalyzed by oxidoreductases by donating or accepting hydrogen atoms or electrons. (b) Those coenzymes taking part in reactions transferring groups other than hydrogen. Dr. Said El Shamieh 56 28  8/31/2022 First Group of Cofactors Nicotinamide Adenine Dinucleotide (NAD+) The reversible reaction of lactate to pyruvate is catalyzed by the enzyme lactate dehydrogenase, but the actual transfer of hydrogen is taking place on the coenzyme, NAD+. Two hydrogen atoms are removed from lactate, and two electrons are accepted by the NAD+ to form NADH, and the remaining H+ is released into the surrounding medium. The hydrogen is accepted by the nicotinamide group. Lactate Dehydrogenase O O− O O− C NADH + H+ NAD+ C C O HC OH CH3 CH3 pyruvate Dr. Said El Shamieh lactate 57 Second Group of Coenzymes Adenosine Triphosphate (ATP) The energy currency in the body. During the oxidation of food stuffs, energy is released, a part of which is stored as chemical energy in the form of ATP. The second and third phosphate bonds are ‘high energy' bonds. Dr. Said El Shamieh 58 29  8/31/2022 VI. Factors influencing enzyme activity 1. Temperature For temperatures between 10 and 40°C, enzymatic reaction see its rate of reaction increase. Each enzyme is characterized by an optimal temperature at which its activity is maximal. The enzymes are proteins, they are denatured from a certain temperature (around 40-60°C). The loss of the three-dimensional structure results in a loss of function and therefore a drop in enzyme activity. Optimal temperature Activation curve Denaturation curve Dr. Said El Shamieh 59 2. pH Example: digestive enzymes. The enzymes to digest food have different optimal pH to suit the pH conditions in the lumen of the different stages of the digestive tract. Thus the activity of pepsin is maximum for a very acidic environment like the stomach where it is secreted. In contrary, pancreatic enzymes such as amylase and trypsin, have an optimum pH more alkaline action, because the duodenum where they exercise their activity pH is normally close to 8. Example : Trypsin optimum pH range Dr. Said El Shamieh 60 30  8/31/2022 3. Concentrations of enzyme, substrate and product The more the substrate concentration, the higher the reaction speed, until all of the active sites are occupied (saturation). The only way to increase the reaction rate when there is saturation of the enzymes is to increase the enzyme concentration. When the concentration of product is too high, the reaction rate decreases as in any chemical reaction. 4. Presence of cofactors Dr. Said El Shamieh 61 5. Effectors : Presence of activators or inhibitors An effector is a chemical substance that modifies the enzymatic activity, that is to say, the kinetics of an enzyme reaction. Effectors have : - A reversible effect that manifests itself only in the presence of the effector and disappears at its elimination; - An irreversible effect that can increase with the time of contact between the enzyme and the effector and persist after its removal. There are 2 types of effectors: - an activator is an effector which increases the enzymatic activity. - An inhibitor is a substance that decreases the rate of a biochemical reaction. Dr. Said El Shamieh 62 31  8/31/2022 Various types of inhibitors Two types of inhibition: competitive inhibition and non-competitive inhibition. A competitive inhibitor is a molecule with a structural similarity to the substrate, so it can compete with the substrate to occupy the active site of the enzyme. Examples: medication (sulfonamides). An non-competitive inhibitor binds elsewhere of the enzyme active site, causing a conformational change in the enzyme which decreases or stops the enzymatic activity. Inhibitors may be of 2 types: - irreversible inhibitors (covalent). The inhibitor may not dissociate from the enzyme. - reversible inhibitors also called Michaeliens effectors. Dr. Said El Shamieh 63 ENZYMES Dr. Said El Shamieh 64 32  8/31/2022 VIII. Isoenzymes Isoenzymes are enzymes having a different sequence of amino acids but catalyze the same chemical reaction. These enzymes usually have different kinetic parameters or different regulatory properties. The existence of isozymes allows a better adaptation to metabolism to meet the needs of a particular tissue or stage of development. Examples: creatine kinase (CK): composed of 2 subunits: M or B 3 isoenzymes: - CK-MM (muscle); - CK-MB (heart); - CK-BB (brain) In case of myocardial infarction, only CK-MB increases in blood (release of their contents by necrotic heart cells). Dr. Said El Shamieh 65 Clinical Enzymology i. Plasma contains many functional enzymes which are actively secreted into plasma (e.g: enzymes of blood coagulation). ii. On the other hand, there are a few nonfunctional enzymes in plasma, which are coming out from cells of various tissues. Their normal levels in blood are very low; but are drastically increased during cell death (necrosis) or disease. -> Assays of these enzymes are very useful in diagnosis of diseases. Dr. Said El Shamieh 66 33  8/31/2022 Lactate Dehydrogenase (LDH) LDH enzyme is a tetramer with 4 subunits. But the subunit may be either H (heart) or M (muscle) polypeptide chains. M4 form is seen in skeletal muscles; while H4 form is seen in heart. In myocardial infarction, LDH activity is increased. Within a few hours after the heart attack, the enzyme level starts to increase, reaches a peak on the 5th day, and reaches normal levels by 10-12 days. Dr. Said El Shamieh 67 Creatine Kinase (CK) Dimer. The subunits are B for brain and M for muscle. -> 3 isoforms are seen in circulation: MM is originating from skeletal muscles. MB is from heart BB is from brain. Value in serum is increased in myocardial infarction. Level starts to rise within 3 hours of infarction. -> very useful to detect early cases, where ECG changes may be ambiguous. Dr. Said El Shamieh 68 34  8/31/2022 Alanine Amino Transferase (ALT/SGPT) i. Normal serum level of ALT is 10-30 U/L. ii. Very high values (100 to 1000 U/L) are seen in acute hepatitis, either toxic or viral in origin. iii. Both ALT and AST levels are increased in liver disease, but ALT >> AST. Rise in ALT levels may be noticed several days before clinical signs such as jaundice are manifested. iv. Moderate increase (25 to 100 U/L) may be seen in chronic liver diseases such as cirrhosis, and malignancy in liver. Dr. Said El Shamieh 69 Alkaline Phosphatase (ALP) i. ALP is a nonspecific enzyme. optimum pH is between 9 and 10. ii. It is produced by osteoblasts of bone, and is associated with the calcification process. iii. Moderate increase (2-3 times) in ALP level is seen in hepatic diseases such as infective hepatitis, alcoholic hepatitis or hepatocellular carcinoma. iv. Very high levels of ALP (10-12 times of upper limit) may be noticed in bone diseases. Dr. Said El Shamieh 70 35