General Biochemistry: Part II (CHEM 3420) Chapter 17 - Introduction to Metabolism PDF

GENERAL BIOCHEMISTRY: PART II (CHEM 3420) CHAPTER 17: INTRODUCTION TO METABOLISM Developed by Dr. Koen Vercruysse Associate Professor Chemistry Department Tennessee State University 1 ...

GENERAL BIOCHEMISTRY: PART II (CHEM 3420) CHAPTER 17: INTRODUCTION TO METABOLISM Developed by Dr. Koen Vercruysse Associate Professor Chemistry Department Tennessee State University 1  Introduction to metabolism Studying the metabolic pathways is like studying the interstate system of freeways. The movement of biochemical molecules through different sequences of biochemical pathways is like the movement of cars on the interstates. There may be different pathways (“interstates”) available for the carbohydrates, lipids or amino acids, but these pathways do intersect with each other and “traffic” (= biomolecules) may well be redirected from one biochemical pathway (“interstate”) to another depending on the needs of the cell. The next slide presents a very rudimentary scheme of the pathways that will be discussed in this course. The student should be aware that behind each and every arrow in this scheme, sits a biochemical pathway; a sequence of biochemical reactions that transforms one biomolecule into another. 2 3  Introduction to metabolism (continued)  From the previous slide, a few observations can be made about our metabolism in general: The endpoint of our metabolism is the synthesis of ATP. ATP is the “universal” carrier of chemical energy. All organisms will convert their energy input (organic nutrients, sunlight, energy from the interior of the Earth, …) into ATP and use this ATP as a source of chemical energy to build the organism’s own biomolecules, cells, tissues, etc., and to replicate itself. At the endpoint of our metabolism, oxygen is reduced to water and this makes humans an example of the aerobic life forms. Anaerobic life forms do exist; they use a different type of reduction reaction (e.g., SO42- to S2-) as the endpoint of their metabolic pathways. The so-called citric acid or Krebs cycle is the “central roundabout” of our metabolism. The breakdown of all our nutrients leads to biomolecules that feed into the Krebs cycle. At the Krebs cycle stage all the carbons are completely oxidized to CO2 and important cofactors like NADH and FADH2 are generated. The cofactors NADH and FADH2 are electron “collectors” that will be used to initiate the ATP synthesis in the so-called electron transport process. All living creatures, one way or another, “collect electrons” from some source and use those electrons to drive their ATP synthesis. The electron transport / ATP synthesis is one of those fundamental aspects of Life; at the same level as the “DNA-to-mRNA-to-protein” aspect of Life or the use of enzymes to drive all chemical reactions. 4  Introduction to metabolism (continued) From the previous slide, a few observations can be made about our metabolism in general: The main storage form of excess calories are the lipids. From the diagram shown on the earlier slide it can be observed that all classes of nutrients (carbohydrates, lipids, proteins, nucleic acids) can be broken down to acetyl-Coenzyme A (AcCoA). AcCoA can either go into the Krebs cycle for further breakdown or be built into fatty acids to be stored as triglycerides in the lipid or fatty tissues. (thus, low-fat or fat-free does not mean low-calorie or calorie-free if the fats in the dietary items have been replaced with carbohydrates; excess carbohydrates will be converted into fats in our physiology!!) What will not be discussed in this course, but is included in the diagram on the previous slide:  The making of proteins from amino acids; this was discussed in General Biochemistry Part I and is the translation process.  The making of DNA or RNA from the individual nucleotides; this was discussed in General Biochemistry Part I and is the replication or transcription process. 5  Metabolic strategies When studying prokaryotic organisms, one encounters different metabolic strategies: Aerobes: have an absolute requirement for oxygen Anaerobes: can not tolerate the presence of oxygen Facultative anaerobes: they can switch between an aerobic or anaerobic “lifestyle” depending on the conditions Amongst all living organisms, different approaches to obtain energy are used and different sources for the necessary biomolecules are used: Autotrophs: use CO2 as their main source of carbons to build up their biomolecules. Heterotrophs: use complex organic molecules (e.g., carbohydrates) as their main source of carbons. Phototrophs: use sunlight as their main source of energy. Chemotrophs: use redox reactions as the source of energy.  Thus humans, and all other animals, are chemoheterotrophs; while all photosynthetic plants are photoautotrophs. 6 Metabolic pathways: general features Metabolic pathways are a sequence of biochemical reactions catalyzed by specific enzymes: A first enzyme will use one molecule as its substrate and produce a first product. This first product is then substrate for a second enzyme, leading to a second product. This second product is the substrate for a third enzyme, and so on … All the substrates/products featured in the metabolic pathways are referred to as metabolites.  The enzymes in a metabolic pathways can be: Loosely organized, i.e., the enzymes work together, but are essentially stand-alone entities and the products they generate can “leave” the pathway and go a “different direction” depending on the needs of the cell. Complexed together into a multi-enzyme, quaternary structure. Once the initial substrate enters the complex, there is “no escape”; it will be passed on from one enzyme to another until the final product is generated. Present in specific locations inside a cell, e.g., in cytosol, in mitochondria, or can be found embedded inside a membrane.  The figure on the next slide tries to illustrate some of these possibilities. 7  Metabolic pathway organized Metabolic pathway with as a multi-enzyme complex “loosely” organized set of enzymes Membrane-embedded metabolic pathway 8  Metabolic pathways: general features (continued) Many enzymes require cofactors (aka coenzymes) in order for them to function as chemical catalysts. Some small organic molecules serve as such cofactors, many of which the human biochemistry can not generate on its own. Thus, these necessary cofactors or the building blocks for these cofactors need to be obtained from dietary resources and are often classified as “vitamins”. Many cations like Fe2+ or Cu2+ serve essential roles as cofactors for many enzymes involved in redox reactions. Some biochemical reactions or pathways release chemical energy; these are termed exothermic, while other biochemical reactions or pathways require the input of energy; these are termed endothermic. An organism’s metabolism typically has two main branches: Anabolic reactions = building up of biomolecules or cellular components. Catabolic reactions = breakdown of existing complex biomolecules. 9 General discussion of some important cofactors: ATP, ADP and AMP  As mentioned before, ATP is the universal carrier of chemical energy.  ATP stands for adenosine triphosphate.  Its chemical structure is shown in the figure on the side.  It consists of adenine (one of the building blocks for DNA and RNA) bound to b-D- ribose with its 5’ alcohol group in an ester bond with three phosphate groups in a row.  Each phosphate group contains a negative charge and it is the close proximity of these repulsive, negative charges that gives the ATP molecule, and particularly its cluster of phosphate groups, its high energy; its high chemical potential.  The “high energy” in the chemical bonds between the phosphate groups is indicated by using “ ~ ” as an indicator for a “high-energy chemical bond”.  When the phosphate groups (Pi) are hydrolyzed off, energy is released and ATP (adenosine triphosphate) turns into ADP (adenosine diphosphate) and ultimately into AMP (adenosine monophosphate).  In a similar fashion, the other nucleotide bases can be used as carriers of chemical energy, e.g., GTP, CTP, etc., but ATP is by far the most commonly used high-energy cofactor.  Exothermic reactions may lead to the generation of ATP, while endothermic reactions may require the hydrolysis of ATP to provide the necessary energy. 10  General discussion of some important cofactors: ATP, ADP and AMP (continued)  In the previous slide, the hydrolysis of ATP towards AMP was shown in a stepwise fashion; whereby one phosphate (Pi) group at a time was removed.  However, ATP can be hydrolyzed such that a cluster of two phosphate groups, known as pyrophosphate or PPi, is removed and ATP is directly converted into AMP.  The pyrophosphate combination is still a high- energy entity and can be hydrolyzed into the two individual phosphates with release of the energy stored in the pyrophosphate group. 11  General discussion of some important cofactors: NAD+ - NADP+ / NADH - NADPH  NAD+ stands for nicotinamide dinucleotide; NADP+ is a phosphorylated version of NAD+.  The functions of NAD+ and NADP+ are identical, however the enzymes that use any of these two cofactors will have a preference for binding either NAD+ or NADP+.  The portion of the structure shown in red is the fragment known as nicotinamide and is the essential portion of the cofactor. This portion can not be synthesized by human biochemistry and is a member of the vitamin B complex.  The function of these cofactors is to capture a pair of electrons, given off by some metabolite during catabolic reactions and turn these electrons into ATP or make them available for anabolic reactions.  The nicotinamide portion of NAD+ or NADP+ can capture a hydride anion, i.e., a hydrogen with two electrons: H:-  Thus, NAD+ or NADP+ are reduced to NADH or NADPH. Remark: the student should always remember that chemical bonds are not “bars” between atoms, but are made through the sharing of a pair of electrons. The energy of a chemical bond resides in this pair of electrons. Thus, NADH and NADPH, as carriers of electrons carry chemical energy in their own way. 12 General discussion of some important cofactors: FAD – FADH2  FAD is a second type of electron carrier found in our metabolic pathways.  FAD stands for flavin adenine dinucleotide and its structure is shown.  It consists of adenine, attached to ribose, attached to pyrophosphate, attached to (open-chain) ribose, attached to riboflavin (the portion in red).  Riboflavin is a molecule the human biochemistry can not produce and is one of the components of the vitamin B complex.  FAD captures a pair of electrons, but in a two-step way; one electron at a time in a radical mechanism.  An intermediate with an unpaired electron is generated, but quickly reduced to the final form; FADH2.  As for NADH or NADPH, FADH2 carries chemical energy that can be converted into ATP by carrying a pair of electrons. 13  Metabolic pathways: redox reactions Oxidation-reduction or redox reactions are extremely important in biochemistry. Redox reactions involve the exchange of electrons between two chemicals; oxidation typically involves the loss of electrons (and is often exothermic) and reduction involves the gain of electrons (and is often endothermic). For inorganic ions, oxidation is recognized by an increase in oxidation number of the ion; reduction by the decrease in oxidation number. For organic compounds, oxidation is recognized as an increase in oxygen atoms in the structure OR as a decrease in hydrogen atoms in the structure. For organic compounds, reduction is recognized as an increase in hydrogen atoms in the structure OR as a decrease in oxygen atoms in the structure. The next slide shows some typical examples of oxidation or reduction reactions. 14 Metabolic pathways: some examples of oxidations or reductions 15