Metabolism Lecture 1 PDF

Metabolism: An overview Prof. Dr. Gerhard Grüber Nanyang Technological University School of Biological Sciences Singapore 637551 [email protected]  Structure of BS2003 - Biochemistry II 1...

Metabolism: An overview Prof. Dr. Gerhard Grüber Nanyang Technological University School of Biological Sciences Singapore 637551 [email protected]  Structure of BS2003 - Biochemistry II 1. We provided you with the booklet Essentials and Beauty of Biochemistry. Please make yourself familiar with its content, since its contents are the fundamentals for our studies in Biochemistry II. 2. We will provide our prerecorded lectures electronically in time, so that you can decide to study its content with your colleagues at any time. We will announce the uploading of each e-lectures. We recommend to work through the content before each Tuesday, so that you a) can address the tutorial questions, b) formulate queries to the topic for the coffee online session, and to generate a summery of this lecture to prepare yourself for the exam. 5. Coffee-online session via Teams, where you can address additional questions related to BS2003 or your general studies. We will also discuss questions, which we received from you during the week. Like the Tutorials, the Coffee-online sessions will provide you feedback about your learning outcomes. The first coffee online session will be on the 13th of August starting at 8:30 am. You will receive the invitation soon. 3. The Tutorials are organized in small classes, enabling you to be active and to discuss the answers to the tutorial questions or to address even more questions. Please make use of the tutorials as they give you also the feedback, whether you have understood the respective topic. 4. Practical Courses (week 8 + 9): The beauty of principles in carbohydrate catabolism and All I have to know about lipids and fatty acids 6. Mid-term Quiz in the 6th week will give you an orientation and additional feedback. Assessment Components: 1. Laboratories-written report: 30% 2. Mid-term Quiz: 10% 2. Closed-book exam: 60%  BS2003 - Biochemistry II Learning Outcome Identify the classes of organic molecules in our food. Describe the metabolic processes of proteins, carbohydrates, fatty- and nucleic acids. Classify the key catalysts, involved in metabolic processes. Transfer of these enzymatic reactions to related organic reactions Discuss the link of pathways in the digestions and synthesis of amino-, fatty- and nucleic acids as well as carbohydrates. Prof. Dr. G. Grüber Dr. A. Grüber Coordinator [email protected] [email protected]  Recommended textbooks Voet & Voet: Biochemistry – 3rd edition, John Wiley & Sons Mathews, van Holde, Ahern: Biochemistry – 4th edition Berg, Tymoczko & Stryer: Biochemistry – 5th edition, Spectrum Horton, Moran, Scrimgeour, Perry & Rawn: Principles of Biochemistry - 4th edition Essentials and Beauty of Biochemistry  BS2003 - Biochemistry II Metabolism (from Greek: metabolē, "change") is the set of life-sustaining chemical reactions in organisms. The three main purposes of metabolism are: - catabolism break down of complex : a) the conversion of food to energy to run cellular processes; molecules b) the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates; c) and the elimination of metabolic wastes. Metabolism consists of literally hundreds of enzymatic reactions organized into discrete pathways. These pathways proceed in a stepwise fashion, transforming substrates into end products through many specific chemical intermediates. The course will give an understanding about the anabolic and catabolic processes that satisfy the metabolic needs of the biological cell. competesleales This course deals with the basic principles, pathways and regulation of metabolism required to understand modern biological sciences. The lectures will cover introduction to metabolism and regulation and enzyme catalysis, carbohydrate-, lipid-, amino acid- and nucleotide metabolism, citric acid cycle, oxidative phosphorylation and photosynthesis.  Metabolic Fuels and Dietary Components In order to survive, humans must meet two basic metabolic requirements: We must be able to synthesize everything our cells need that is not supplied by our diet, and we must be able to protect our internal environment from toxins and changing conditions in our external environment. In order to meet these requirements, we metabolize our dietary components through four basic types of pathways: fuel oxidative pathways, fuel storage and mobilization pathways, biosynthetic pathways, and detoxification or waste disposal pathways. The foods in our diet are the fuels that supply us with An overview of the general energy in the form of calories. metabolic routes for dietary Our diet also must contain the compounds we cannot components in the body. The types synthesize, as well as all the basic building blocks for of pathways are named in red. compounds we do synthesize in our biosynthetic pathways. For example, we have dietary requirements for some amino allow storage of ~ acids, but we can synthesize other amino acids from our fuels and a dietary nitrogen precursor. The compounds the cell membrane, glucose in required in our diet for biosynthetic pathways include certain 19 rept of DO/ form of glyrogen amino acids, vitamins, and essential fatty acids. RNA Detoxification pathways and waste disposal pathways are metabolic pathways devoted to removing toxins that can be present in our diets or in the air we breathe, introduced into ~ allows us to catabolise our bodies as drugs, or generated internally from the more food into smaller metabolism of dietary components. Dietary components that have no value to the body and must be disposed of are called oxidised molecules giving tro xenobiotics (from the Greek word "xenos" meaning stranger, co2 , & energy guest). C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  Carbohydrates: Monosaccharides ~ aldehyde 7 single Monosaccharides exist in solution mainly as ring structures in which the - ketone carbonyl (aldehyde or ketone) group has reacted with a hydroxyl group in the same molecule to form a five- or six-membered ring (see Fig. right). The oxygen that was on the hydroxyl group is now part of the ring, and the original carbonyl carbon, which now contains an —OH group, has become the anomeric carbon atom. A hydroxyl group on the anomeric carbon drawn down below the ring is in the α position; drawn up above the ring, it is in the β position. In the actual anomeric three-dimensional structure, the ring is not planar but usually takes a chair carbon conformation in which the hydroxyl groups are located at a maximal distance atom from each other. In solution, the hydroxyl group on the anomeric carbon spontaneously changes from the α to the β position through a process called mutarotation. When the ring opens, the straight-chain aldehyde or ketone is formed. When the ring closes, the hydroxyl group may be in either the α or the β position. This process occurs more rapidly in the presence of cellular enzymes called mutarotases. However, if the anomeric carbon forms a bond with another molecule, that bond is fixed in the α or β position, and the sugar cannot mutarotate. Enzymes D-glucose : carbonyl grp in C, rx+F - OH in six-membered are specific for α or β bonds between sugars and other molecules and react with 25 forming , only one type. ring consisting of 52 molecules + O molecule (pyranose) D- fructose : Ketone grp in 22 x+ -OH in C5 , forming fire-membered ring consisting of 42 molecula + 0 Molecula (furnose) Mutarotation of glucose in solution, with percentages of each form at equilibrium. C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  Carbohydrates A disaccharide contains two monosaccharides joined by an O-glycosidic bond. Lactose, which is the sugar in milk, consists of galactose and glucose linked through a β(1→4) bond formed between the β–OH group of the anomeric carbon of galactose and the hydroxyl group on carbon 4 of glucose. Oligosaccharides contain from 3 to roughly 12 monosaccharides linked together. They are often found attached through N- or O-glycosidic bonds to proteins to form glycoproteins. Polysaccharides contain tens to thousands of monosaccharides joined by glycosidic bonds to form linear chains or branched structures. Starch is an example of a branched polymer of glucosyl residues branched linked through α(1→4) and α(1→6) bonds. linens The hydroxyl group on the anomeric carbon of a monosaccharide can react also with an —NH group of another compound to form a N-glycosidic bond. N- glycosidic bonds are found in nucleosides and nucleotides. For example, in the adenosine moiety of adenosine triphosphate (ATP), the nitrogenous base adenine is linked to the sugar ribose through a β-N-glycosidic bond. C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  The three key polysaccharides made from glucose monosaccharides Cellulose is a structural polysaccharide that is found in the cell wall of plants. It is a linear molecule composed of β-glucose subunits (1-4 arrangement). Because it is composed of β-glucose, it is indigestible for most animals (lack the enzyme required to break it down) Starch is an energy storage polysaccharide found in plants. It is composed of α-glucose subunits (1-4 arrangement) and exists in one of two forms – amylose or amylopectin Amylose is a linear (helical) molecule while amylopectin is branched (contains additional 1-6 linkages) Amylose is harder to digest and less soluble, however, as it takes up less Camylopectin allows more space, is the preferred storage form in plants. forage Glycogen is an energy storage polysaccharide formed in the liver in animals. linear branched It is composed of α-glucose subunits linked together by both 1-4 linkages and 1-6 linkages (branching). It is akin to amylopectin in plants, but is more highly branched (1-6 linkages occur every ~10 subunits as opposed to ~20). Packed tyt Molecular images of the polymers Cellulose Amylose Amylopectin Glycogen https://ib.bioninja.com.au/standard-level/topic-2-molecular-biology/23-carbohydrates-and-lipids/sugar-polymers.html  Energy content of food constituents Stored metabolic fuel in a 70-kg person Two important advantages for storing energy in the form of fatty acids: 1. The carbon in fatty acids (mostly –CH2-groups) is almost completely reduced compared to the carbon in sugars or amino acids. Therefore, oxidation of fatty acids will yield more energy in form of ATP than any other form of carbon. 2. Fatty acids are not generally as hydrated as monosaccharides are, and thus they can pack more closely in storage tissues. 1-Palmitoyl-2,3-dioleoyl-glycerol Voet, Voet: BIOCHEMISTRY 3rd edition Garett & Grisham: Biochemistry 4th edition  Saturated fatty acids and unsaturated fatty acids & bonds no double (A) The carbons are either numbered starting with the carboxyl group or given Greek letters starting with the carbon next to the carboxyl group. The methyl (or ω) carbon at the end of the chain is always called the ω-carbon, regardless of the chain length. The symbol 18:0 refers to the number of carbon atoms (18) and the number of double bonds (0). In the unsaturated fatty acids shown, not all of the carbons are numbered, but note that the double bonds are cis and spaced at three-carbon intervals. Both ω3 and ω6 fatty acids are required in the diet. (B) Cis- and trans double bonds in fatty acid side chains. Note unsaturated FA. that the cis double bond causes the chain to bend. The double bonds in most naturally occurring fatty acids are in the cis configuration (Fig. right). The designation cis means that the hydrogens are on the same side of the double bond and the acyl chains are on the other side. In trans-fatty acids, the acyl chains are on opposite sides of the double bond. Margarine and the fat used in preparing French fries are probably the major sources of trans-fatty acids found in humans. Trans-fatty acids are produced by the chemical hydrogenation of polyunsaturated fatty acids in vegetable oils and are not a natural food product. Hi The melting point of a fatty acid increases with chain length 4 H , - H and decreases with the degree of unsaturation. Thus, fatty acids with many double bonds, such as those in vegetable oils, are liquid at room temperature; and saturated fatty acids, such as kink those in butterfat, are solids. Lipids with lower melting points FA I double bond are more fluid at body temperature and contribute to the fluidity of our cellular membranes. have lover melting pf. C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  Amino acids and peptide formation conjugated ~ antage Max. ring system Absorption (nm) nor Trp 280 -branched Tyr 274 Phe 257 branched can form disulfide bridge ↑ protonati projocted/ deprotonate can occur reprforated depending on The planar peptide group. Three bonds separate sequential α-carbons in a polypeptide pu chain. The N-Cα and Cα-C bonds can rotate with bond angles designated Φ and Ψ, respectively. The peptide C-N bond is not free to rotate. Other single bonds in the backbone involved catalytic proces rates in may also be rotationally hindered, depending on the size and charge of the rest (R) groups. In the conformation shown, Φ and Ψ are 180° (or -180°). As one looks out from the α- carbon, the Φ and Ψ angles increase as the carbonyl or amide nitrogens (respectively) rotate clockwise. Aromatic a. a: virgs can be arranged in a way & that be stacked relative toelo they can to certain generate forces befor them leading architecture & dabilisate of peptide/protein protonated/deprotonated depending pll on can be C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition David L. Nelson, Michael M. Cox: Lehninger Principles of Biochemistry, 4th edition  The Acidic and Basic Amino Acids Ihe charged (the charged The charge on amino acids at physiologic pH is a function of their pKa for dissociation of protons from the α-carboxylic acid groups, the α-amino groups, and the side chains. The titration curve of histidine illustrates the changes in amino acid structure that occurs as the pH of the solution is changed from 0 As the pH increases, the charge on the side chain goes from 0 to – or from + to 0. The pKa is the pH at which half the molecules of an amino acid in solution have side chains that are charged. Half are uncharged. C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  pH Scale 0 1 Battery acid Increasingly Acidic 2 Gastric juice, lemon juice + H H+ [H+] [OH ]  H+ 3 Vinegar, wine, − H+ OH + OH− H H+ + cola H H+ Acidic 4 Tomato juice solution Beer 5 Black coffee Rainwater 6 Urine OH− OH− Saliva H+ H+ OH − Neutral  7 Pure water + − OH− OH + H [H+]= [OH ] Human blood, tears H H+ 8 Seawater Neutral Inside of small intestine solution Increasingly Basic 9 [H+] [OH ]  10 OH− Milk of magnesia OH− OH− H+ OH− 11 OH− OH− − + OH Household ammonia H 12 Basic Household solution 13 bleach Oven cleaner 14 © 2017 Pearson Education, Ltd.  Levels of structure in a protein on peptide Protein structure is described in terms of four different levels: primary, secondary, tertiary, and quaternary. The primary structure of a protein is the linear sequence of amino acids in the polypeptide chain. The secondary structure consists of local regions of polypeptide chains formed into structures that are stabilized by a repeating pattern of hydrogen bonds, such as the regular structures called α-helices and β-sheets. The rigidity of the peptide backbone determines the types of secondary structure that can occur. The tertiary structure involves folding of the secondary structural elements into an overall three-dimensional conformation. In globular proteins such as myoglobin, the tertiary structure generally forms a densely packed hydrophobic core with polar amino acid side chains on the outside. Some proteins exhibit quaternary structure, the combination of two or more subunits, each composed of a polypeptide chain. C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  Enzymes as catalysts Reaction in the enzyme active catalytic site (Fig. right). (A) The enzyme contains an active catalytic site, shown in dark red, with a region or domain where the substrate binds. The active site also may contain cofactors, nonprotein components that assist in catalysis. (B) The substrate forms bonds with amino acid residues in the substrate-binding site. Substrate binding induces a conformational change in the active site. (C) Functional groups of amino acid residues and cofactors in the active site participate in forming the transition-state complex, which is stabilized by additional noncovalent bonds with the enzyme, shown in red. (D) Because the products of the reaction dissociate, the enzyme returns to its original conformation. Enzymes are proteins that act as catalysts, compounds that increase the rate of chemical reactions (Fig. right). Enzyme catalysts bind reactants (substrates), convert them to products, and release the products. Many enzymes increase the rate of a chemical reaction by a factor of 1011 or higher. To appreciate an increase in reaction rate by this order of magnitude, consider a room-sized box of golf balls that “react” by releasing energy and turning brown. The 12 ft × 12 ft × 8 ft box contains 380,000 golf balls. If the rate of the reaction in the absence of enzyme were 100 golf balls per year, the presence of 1 molecule of enzyme would turn the entire box of golf balls brown in 1 second (assuming a 1011 increase in reaction rate). C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  Antibiotic penicillin is a transition-state analog The antibiotic penicillin is an example of a transition-state analog that binds very tightly to glycopeptidyl transferase, an enzyme required by bacteria for synthesis of the cell wall (Fig. right). The enzyme normally cleaves the peptide bond between two D-alanine residues in a polypeptide. Penicillin contains a strained peptide bond within the β-lactam ring that resembles the transition state of the normal cleavage reaction, and thus penicillin binds very readily in the enzyme active site. As the bacterial enzyme attempts to cleave this penicillin peptide bond, penicillin becomes irreversibly covalently attached to the enzyme’s active-site serine, thereby inactivating the enzyme. C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  Coenzymes in Catalysis Coenzymes (cofactors) are complex nonprotein organic molecules that participate in catalysis by providing functional groups, much like the amino acid side chains. In the human, they are usually (but not always) synthesized from vitamins. Each coenzyme is involved in catalyzing a specific type of reaction for a class of substrates with certain structural features. Coenzymes can be divided into two general classes: activation-transfer coenzymes and oxidation–reduction coenzymes. 1. Activation-Transfer Coenzymes The activation-transfer coenzymes usually participate directly in catalysis by forming a covalent bond with a portion of the substrate; the tightly held substrate moiety is then activated for transfer, addition of water, or some other reaction. The portion of the coenzyme that forms a covalent bond with the substrate is its functional group. A separate portion of the coenzyme binds tightly to the enzyme. Thiamine pyrophosphate (TPP, see Fig. below), Coenzyme A (CoA), biotin, and pyridoxal phosphate are examples of activation-transfer coenzymes synthesized from vitamins. & bird to in S a a.. active site of enzyme Thiamine pyrophosphate (TPP) & is directly involved in catalytic event by wforming a covalent substrate bord Never forget me! C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  Coenzymes in Catalysis 2. Oxidation–Reduction Coenzymes A large number of coenzymes are involved in oxidation–reduction reactions catalyzed by enzymes categorized as oxidoreductases. When a compound is oxidized, it loses electrons. As a result, the oxidized carbon has fewer H atoms or gains an O atom. The reduction of a compound is the gain of electrons, which shows in its structure as the gain of H or loss of O. Some coenzymes, such as nicotinamide-adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD), can transfer electrons together with hydrogen and have unique roles in the generation of ATP from the oxidation of fuels. To] Y Oxidati lose loge H : e- , , losh H gain o reduct : gain e- , guin H , [H] gain H lose O MND > - NADH Nicotinamide-adenine dinucleotide (NAD+) C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  Regulation Matches Function In the human body, thousands of diverse enzymes are regulated to fulfill their individual functions without waste of dietary components. Changes in the rate of a metabolic pathway occur because at least one enzyme in that pathway, the regulatory enzyme, has been activated or inhibited, or the amount of enzyme has increased or decreased. Regulatory enzymes usually catalyze the rate-limiting, or slowest, step in the pathway, so that increasing or decreasing their rate changes the rate of the entire pathway (Fig. right). The mechanisms used to regulate the rate-limiting enzyme in a pathway reflect the function of the pathway. The flux of substrates down a metabolic pathway is analogous to cars traveling down a highway (Fig. right). The rate-limiting enzyme is the portion of the highway that is narrowed to one lane by a highway barrier. This single portion of the highway limits the rate at which cars can arrive at their final destination miles later. Cars will back up before the barrier (similar to the increase in concentration of a precursor when a rate-limiting enzyme is inhibited). Some cars may exit and take an alternate route (similar to precursors entering another metabolic pathway). Moving the barrier just a little to open an additional lane is like activating a rate-limiting enzyme: It increases flow through the entire length of the pathway. C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  The Michaelis-Menten Equation The velocity of all enzymes is dependent on the concentration of substrate. This dependence is reflected in conditions such as starvation, in which several pathways are deprived of substrate. In contrast, storage pathways (e.g., glucose conversion to glycogen in the liver) and toxic waste disposal pathways (e.g., the urea cycle, which prevents NH4+ toxicity by converting NH4+ to urea) are normally regulated to speed up when more substrate is available. The Michaelis-Menten equation describes the response of an enzyme to changes in substrate concentration (Fig. right). This equation relates the initial velocity (vi) to the concentration of substrate [S] and the two parameters Km and Vmax. The Vmax of the enzyme is the maximal velocity that can be achieved at an infinite concentration of substrate, and the Km of the enzyme for a substrate is the concentration of substrate required to reach ½Vmax. The graph of the Michaelis-Menten equation is a rectangular hyperbola that approaches a finite limit. C. M. Smith, A. D. Marks & M. A. Liebermann, Marks’ Basic Medical Biochemistry: A Clinical Approach, 7th edition  Regulation of enzyme activity 1. Allosteric regulation (Feedback control) 2. Regulation by covalent modification 3. Regulation by proteolytic cleavage ~ 4. Regulation by isoenzymes similar enzymes 5. Regulation by availability 6. Regulation by compartmentation 7. Hormonal regulation  Two types of allosteric interaction ⚫ Heterotropic interaction (heteroallostery): when effector molecules are different from the substrate molecules. ⚫ Homotropic interaction (homoallostery): when binding of one substrate molecule to an active site alters the binding properties of the other (identical) substrate molecules in the same enzyme. ⚫ Hemoglobin, although not an enzyme, is a classic example of homotropic allosteric interaction. bind 4 02  Allosteric interaction Allosteric interaction represents a sigmoid plot between the rate of reaction and the substrate concentration. of first binding I - site is increasing 2 offinity I of following sites toa substrate Alteration in one hemoglobin subunit before O2 binding Alteration in one hemoglobin subunit after O2 binding  Regulation of enzyme activity 1. Allosteric regulation (Feedback control) 2. Regulation by covalent modification 3. Regulation by proteolytic cleavage 4. Regulation by isoenzymes 5. Regulation by availability 6. Regulation by compartmentation 7. Hormonal regulation  Regulation by covalent modification ⚫ Catalytic activities of enzymes are altered by reversible, covalent changes to specific amino acid side chains in the enzyme. Common used modifications are: Phosphorylation of -OH groups of Ser, Thr or Tyr. Attachment of AMP to a similar -OH group. ser The Tyr or , Attachment of ADP-ribosyl group to Arg, Gln or Cys. Methylation of Glu. Reduction of cysteine disulfide bonds. ⚫ Covalent modification itself is an enzymatic reaction. ⚫ In general, by covalent modification, an enzyme is made either completely active or completely inactive.  Regulation of enzyme activity 1. Allosteric regulation (Feedback control) 2. Regulation by covalent modification 3. Regulation by proteolytic cleavage 4. Regulation by isoenzymes 5. Regulation by availability 6. Regulation by compartmentation 7. Hormonal regulation  Enzyme regulation by compartmentation ENDOPLASMIC RETICULUM (ER) Nuclear Smooth ER envelope Nucleolus NUCLEUS Flagellum Rough ER Chromatin Centrosome Plasma membrane CYTOSKELETON: Microfilaments Intermediate Ribosomes filaments (small brown Microtubules dots) Golgi apparatus Microvilli Peroxisome Lysosome © 2017 Pearson Education, Ltd. Mitochondrion  Regulation by compartmentation ⚫ Many enzymes are regulated by localizing them in specific compartments within a cell. everate enve for their compartments 9 pl specific enzymes 2f max : 4 5. may : pH-rate profiles for pepsin and HIV protease Pepsin (pepsis, meaning “digestion”) is produced in the chief cells of the stomach lining. The enzyme uses a catalytic aspartate in its active site.  Regulation of enzyme activity 1. Allosteric regulation (Feedback control) 2. Regulation by covalent modification 3. Regulation by proteolytic cleavage 4. Regulation by isoenzymes 5. Regulation by availability 6. Regulation by compartmentation 7. Hormonal regulation Coffee break  Energy-related organelles S. S. Mader, Inquiry Into Life  Overview of metabolism The metabolic map shown here is the basic road map for this course. It reveals the central pathways and some intermediates. The catabolic pathway (red) proceed downward and anabolic pathways (blue) p r o c e e d u p w a r d. Mathews, van Holde, Ahern: Biochemistry 3rd edition  Integration of metabolism among major organs Each organ has unique metabolic needs, which must be coordinated in a variety of organs to maintain a constant supply of energy while preserving some energy for the future. The body uses the nervous system and hormonal signals to differentially stimulate and inhibit biochemical pathways. The main signals used to regulate metabolism are insulin, glucagon, catecholamine, gluco- corticoids, and growth hormone (in children). The liver actively provides the quick fuel (glucose) the body needs, whereas adipose tissue provides long- term energy storage. Finally, skeletal muscle and the rest of the body constantly demand the energy. L. W. Janson & M. E. Tischler, THE BIG PICTUTE: MEDICAL BIOCHEMISTRY 1st edition  Transport and fate of major carbohydrates and amino acids ~ h testeda t L. W. Janson & M. E. Tischler, THE BIG PICTUTE: MEDICAL BIOCHEMISTRY 1st edition  Energy relationship between the pathways of catabolism and anabolism energy-rich release chemical energy J0] [H) Metabolism serves two fundamentally different purposes: the generation of energy to drive vital functions and the synthesis of biological molecules. To achieve these end, metabolism consists largely of two contrasting processes; catabolism and anabolism. Both processes occur simultaneously in the cell and are controlled (i) by the tight and separate regulation of both catabolism and anabolism, so that metabolic needs are served in an immediate and orderly fashion. (ii) Competing metabolic pathways are often localized within different cellular compartments. Isolating opposing activities within distinct compartments, such as separate organelles, avoids interference between them. Garett & Grisham: Biochemistry 4th edition  NADH and NADPH as sources of free energy helps as cofactor to if lactate to pyruvate as it can take over electrons Never forget me! phosphorylated ~ ribose molecula f adenosine (NAD+) The structures and reaction of nicotinamide-adenine dinucleotide and nicotinamide adenine dinucleotide phosphate (NADP+). Voet, Voet: BIOCHEMISTRY 3rd edition  ATP serves in a cellular energy cycle ATP is the energy currency of the cell. It provides the energy that drives the manifold activities of all living cells-the synthesis of complex biomolecules, the osmotic work involved in transporting substances into cells, the work of cell motility, and the work of muscle contraction. These diverse activities are all powered by energy released in the hydrolysis of ATP to ADP and inorganic phosphate (Pi). There is an energy cycle in cells where ATP serves as the vessel carrying energy from photosynthesis or catabolism to the energy-requiring processes unique to living cells. The structure of ATP indicating its relationship to ADP, AMP, and adenosine. Never forget me! ATP hydrolysis leads to > 30k] mol"energy release Voet, Voet: BIOCHEMISTRY 3rd edition  Corresponding pathways of cata- and anabolism differ in regulation stimulated (a) (b) enzymes involved I in are catabolism diff to those in anabolism & inhibited are enzymes similar - Stimulated & inhibited A second reason for different pathways serving the opposite metabolic directions is that such pathways must be independently regulated. If catabolism and anabolism passed along the same set of metabolic tracks, equilibrium considerations would dictate that slowing the traffic in one direction by inhibiting a particular enzymatic reaction would necessarily slow traffic in the opposite direction. Independent regulation of anabolism and catabolism can be accomplished only if these two contrasting processes move along different routes or, in the case of shared pathways, the rate-limiting steps serving as the points of regulation are catalyzed by enzymes that are unique to each opposing sequence. The figure above shows two possible arrangements of opposing catabolic and anabolic sequences between A and P. (a) The parallel sequences proceed via independent routes. (b) Only one reaction has two different enzymes, a catabolic one (E3) and its anabolic counterpart (E6). These provide sites for regulation. Garett & Grisham: Biochemistry 4th edition  Multienzyme systems carrying out a metabolic pathway The individual metabolic pathways consist of sequential enzymatic steps. Several types of organization are possible. (a) The enzyme of some multienzyme systems may exist as physically separate, soluble entities, with diffusing intermediates. In other instances, (b) the enzymes of a pathway are collected to form a discrete multienzyme complex, and the substrate is sequentially modified as it is passed along from enzyme to enzyme. This type of organization has the advantage that intermediates are not lost or diluted by diffusion. (c) In a third pattern of organization, the enzymes common to a pathway reside together as a membrane-bound system. In this case the enzyme partners (and perhaps the substrates as well) must diffuse in just the two dimensions of the membrane to interact with their neighbors. Garett & Grisham: Biochemistry 4th edition  Metabolic pathways are compartmentalized within cells Each compartment is dedicated to specialized me t a boli c fun ction s, and th e enz yme s appropriate to these specialized functions are confined together within the organellar membrane. Thus, the flow metabolic intermediates in the cell is specially as well as chemically segregated. For example, the 10 enzymes of glycolysis are found in the cytosol, but pyruvate, the product of glycolysis, is fed into the mitochondria. These organelles contain the citric acid cycle enzymes, which oxidize pyruvate to CO2. Compartmentalization of glycolysis, the TCA cycle, and oxidative phosphorylation Garett & Grisham: Biochemistry 4th edition  State of reduction of carbon atoms in biomolecules releasing electrons More reduced state Less reduced state Fats Carbohydrates Carbonyls Carboxyls Carbon dioxide In living systems most of the energy needed to drive biosynthetic reactions is derived from the oxidation of organic substrates. Oxygen, the ultimate electron acceptor for aerobic organisms, is a strong oxidant; it has the tendency to attract electrons, becoming reduced in the process, e.g.: electron acceptor C6H12O6 + 6 O2 → 6 CO2 + 6 H2O ΔGo’ = -2823 KJ/mol The substrates of catabolism - proteins, carbohydrates, and lipids - are good sources of chemical energy, because the carbon atoms in these molecules are in a relatively reduced state. In the oxidative reactions of catabolism, reducing equivalents are released from these substrates, often in the form of hydride ions (a proton coupled with two electrons, H:-). These hydride ions are transferred in enzymatic dehydrogenase reactions from substrates to NAD+ molecules, reducing them to NADH. A second proton accompanies these reactions, appearing in the overall equation as H+. Garett & Grisham: Biochemistry 4th edition  Biochemical reaction types There is no metaphysics in biochemistry - the chemistry of living systems follows the same chemical and physical laws as the rest of nature. The complexity of these biochemical pathways may at first glance seem overwhelming, but only five general types of chemical transformations are commonly used in cells: Nucleophilic substitution Nucleophilic additions Carbonyl condensations Eliminations Oxidations and reductions  Nucleophilic substitution Much of the chemistry in biological molecules is the chemistry of the carbonyl group (C=O) because the vast majority of biological molecules contains them. And most of the chemistry of carbonyl groups involves nucleophiles (Nu:) and electrophiles. Recall that a nucleophile is a “nucleus-loving” substance with a negatively polarized, electron-rich atom that can form a bond by donating a pair of electrons to an electron-poor atom. An electrophile is an “electron- loving” substance with a positively polarized, electron-poor atom that can form a bond by accepting a pair of electrons from an electron-rich atom. Carbonyl groups are polar, with the electron-poor C-atom bearing a partial positive charge and the electron-rich O-atom bearing a partial negative charge. Never forget me! Mathews, van Holde, Ahern: Biochemistry 4th edition  Nucleophilic substitution Carbonyl carbons are very common electrophiles in biochemistry reactions. Other common electrophiles are protonated imines, phosphate groups, and protons. Never forget me! Mathews, van Holde, Ahern: Biochemistry 4th edition  Nucleophilic substitution Oxyanions, carbanions, deprotonated amines, and the imidazole side chain of histidine are common nucleophiles in biochemical reactions. Never forget me! Mathews, van Holde, Ahern: Biochemistry 4th edition  The formation and function of molecules depend on chemical bonding between atoms ⚫ Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms ⚫ This usually results in atoms staying close together, held by attractions called chemical bonds Animation: Covalent Bonds © 2017 Pearson Education, Ltd.  Ionic Bonds ⚫ Atoms sometimes strip electrons from their bonding partners ⚫ An example is the transfer of an electron from sodium to chlorine ⚫ After the transfer of an electron, both atoms have charges and are called ions ⚫ Both atoms also have complete valence shells Animation: Ionic Bonds © 2017 Pearson Education, Ltd.  Quiz 1. Name the three principal modes of enzyme organization in metabolic pathway? (a) The enzyme may exist as physically separate, soluble entities (b) The enzymes of a pathway are collected to form a discrete multienzyme complex (c) The enzymes common to a pathway reside together as a membrane-bound system. 2. What are the advantages of compartmentalizing particular metabolic pathways within specific organelles? 1) Otherwise uncontrolled behaviour is regulated. 2) diffusion is restricted, product of one reaction is released close to the next enzyme in a pathway; 3) selective permeability of the membrane can control the rate of movements of metabolites; 4) ion-gradients formed by certain enzymatic reaction can influence other enzymatic reactions.  Quiz 3. Assign the metabolic functions listed below to the respective eukaryotic organell  Quiz 3. Assign the metabolic functions listed below to the respective eukaryotic organell  Quiz 4. Nucleophiles are electron-rich compounds, are negatively charged or contain unshared electron pairs that easily form covalent bonds with electron-deficient center. hydroxyl …………………. group sulfhydryl …………………. group amino …………………. group imidazole …………………. group  Quiz 4. Nucleophiles are electron-rich compounds, are negatively charged or contain unshared electron pairs that easily form covalent bonds with electron-deficient center.  Quiz 5. Electrophiles are electron-deficient compounds and may be positively charged or contain an unfilled valence electron shell. Add the names to the respective electrophiles below. protons …………………. metalions …………………. carbonyl carbon atom …………………. cationic imine …………………. (Schiff base)  Quiz 5. Electrophiles are electron-deficient compounds and may be positively charged, contain an unfilled valence electron shell, or contain an electronegative atom. Add the names to the respective electrophiles below.  Quiz 6. A protein’s activity is altered when a particular serine side chain is phosphorylated. Which of the following amino acid substitutions at this position could lead to a permanent alteration in normal enzyme activity? 1. S → E 2. S → T subs isglutamine lysine leucine will lead , , to 3. S → Y 4. S → K permanent alterati in eneye activity. 5. S → L ⚫ Catalytic activities of enzymes are altered by reversible, covalent changes to specific amino acid side chains in the enzyme. Common used modifications are: Phosphorylation of -OH groups of Ser, Thr or Tyr. substitute of for : these , nothing sigh will happen Thank you!