Lecture 1 - Metabolism Introduction PDF

Bioc 211 Chapter 1 Introduction to Metabolism Understanding Biochemical Terminology The School of Athens by Raphael (1509-1511)  Let’s Practice! Phytohormone Hematolysis Why do we eat?  What kind of food can provide us with energy? There are three macronutrients require...

Bioc 211 Chapter 1 Introduction to Metabolism Understanding Biochemical Terminology The School of Athens by Raphael (1509-1511)  Let’s Practice! Phytohormone Hematolysis Why do we eat?  What kind of food can provide us with energy? There are three macronutrients required by humans: carbohydrates (sugar), lipids (fats), and proteins. Each of these macronutrients provides energy in the form of calories.  Major purpose Living things require energy for: 1- Mechanical work in muscle contraction and other cellular movement 2- Synthesis of biomolecules and simple precursors 3- Active transport of molecules and ions  What carries this energy?????? The major energy currency molecule of the cell, ATP. ATP is an abbreviation for adenosine triphosphate, a complex molecule that contains the nucleoside adenosine and a tail consisting of three phosphates. The 2 phosphate bonds (phosphoanhydride bond) is where the energy is stored in ATP  The energy (ATP) Energy is usually liberated from the ATP molecule to do work in the cell by a reaction that removes one of the phosphate-oxygen groups, leaving adenosine diphosphate (ADP) – ATP → ADP + Pi (orthophosphate) – ATP → AMP + PPi (pyrophosphate) The free energy liberated with the hydrolysis of ATP is used to drive reactions that require input of free energy ATP ADP + Pi  The energy (ATP) ATP is continuously formed and consumed It’s the principal immediate donor and not long term storage of energy Rate of turnover of ATP is high. A molecule of ATP is consumed within a minute of it is formation Resting person consumes 40 kg of ATP / 24hr  How do cells make ATP? By phosphorylation: adding a phosphate to ADP ADP + P → ATP 3 mechanisms of phosphorylation: 1. Substrate level phosphorylation: where a substrate molecule (X-P) donates its high energy P to ADP making ATP.  How do cells make ATP? 3 mechanisms of phosphorylation: 2. Photophosphorylation: occurs during photosynthesis- light energy used to make ATP.  How do cells make ATP? 3 mechanisms of phosphorylation: 3. Oxidative phosphorylation: electron (e-) transferred from organic molecules and passed through a series of acceptors to O2  Electron carriers When food molecules are oxidized – electrons are removed These electrons are carried to oxygen e- How does the e- get to oxygen?? O2 Answers: electron carriers NAD+/ FAD Reduced form with electrons bound is NADH/ FADH2 NADH/ FADH2 transfer e- to O2 in the mitochondria by means of ETC ( ATP generated in this process) We are going to look at two major questions in biochemistry: How do cells extract energy from their environment? How do cells synthesize the building blocks of their macromolecules? This leads to the study of …….. METABOLISM  What is Metabolism? Metabolism: is a term that is used to describe all chemical reactions involved in maintaining the living state of the cells and the organism. It is the biochemical basis of life processes.  The nature of Metabolism Complex substances are broken down for: energy, required metabolites, structural components, etc. Cells must synthesize new complex substances. Thousands of such reactions are occurring simultaneously in a single cell. These reactions occur with a minimum of side products, energy loss or undesired interferences and at reasonable temperatures, pH and pressure. All of these reactions must be controlled or regulated for optimum efficiency.  The nature of Metabolism Metabolic pathways are irreversible (because they must be regulated) The pathway to synthesize a complex substance is not simply the reverse of the degradative pathway. Anabolism and catabolism are not usually balanced - one or the other may predominate in certain cells or at different times depending on cell needs Metabolic reactions are often reversible Metabolic pathways have (first) committed step Metabolic pathways are regulated  The nature of Metabolism Metabolic pathways are compartmentalized ✓Cytosol (glycolysis, fatty acid biosynthesis, pentose phosphate cycle) ✓Mitochondria (TCA cycle, OxPhos, fatty acid oxidation, amino acid breakdown) ✓Nucleus (DNA replication, transcription, RNA processing) ✓ER ▪ Rough ER: synthesis of membrane and secretory proteins ▪ smooth ER: lipid and steroid biosynthesis ✓Golgi (posttranslational processing of proteins)  Main Characters of metabolism Catalyzed by a specific enzyme Natural proteins produced in tiny quantities by all living organisms (bacteria, plants, and animals) and functioning as highly selective biochemical catalysts in converting one molecule into another  Main Characters of metabolism It occurs in what we call metabolic pathway series of chemical reactions whereby the product of one reaction are the substrate for the next reaction and so on until the end product is generated. Each reaction require a specific enzyme.  Main Characters of metabolism Two major groups 1- Catabolism: the breakdown of complex substances-- Usually energy-yielding!. 2- Anabolism: the synthesis of complex substances needed by cells from simpler ones such as DNA-- Usually energy-requiring!.  Free Energy Changes in Metabolism Overall G is negative (-) for catabolic processes CATABOLISM For an anabolic process, the G Large Small molecule ought to be positive (+) molecule Energy So generally catabolic processes generate energy for anabolic processes ANABOLISM * ΔG a measure of the amount of usable energy Small Large (energy that can do work) in that system molecule molecules * ΔG=G final–G initial  I- Catabolism Catabolism: is the breakdown of larger molecules into smaller ones (monomers): “an oxidative process that releases energy” → Cells use the monomers released from breaking down polymers to either: or degrade the monomers further to simple waste products like CO2, releasing energy through different a central oxidative pathways: ✓The Citric Acid Cycle or TCA or the Krebs Cycle. ✓Electron transport chain ETC ✓finally, the production of ATP by a process called oxidative phosphorylation. construct new polymer molecules (anabolism),  Catabolism polysaccharides Proteins lipids Glucose/other Amino acids sugars Glycerol/fatty acids Pyruvate NH4+ Acetyl CoA ETC Co2  II- Anabolism Anabolism: the synthesis of larger molecules from smaller ones; a reductive process that requires energy –utilization of critical Common intermediates including pyruvate, acetyl CoA and components of TCA cycle to make building blocks Making building block requires energy = ATP Synthesis of macromolecules requires energy = ATP note CO2 not generally reused  polysaccharides Proteins lipids Glucose/other sugars Glycerol/fatty Amino acids acids Pyruvate NH4+ Acetyl CoA Citric acid cycle Anabolism Summary In catabolism, large molecules are broken down to smaller products, releasing energy and transferring electrons to acceptor molecules of various sorts. The overall process is one of oxidation. In anabolism, small molecules react to give rise to larger ones; this process requires energy and involves acceptance of electrons from a variety of donors. The overall process is one of reduction  Catabolism vs Anabolism Breakdown of macromolecules to building blocks generally hydrolytic Large units of the cell Building blocks of the cell Metabolism I polysaccharides Glucose, other sugars Fatty Acids/ Glycerol Lipid membranes Metabolism II proteins Amino Acids Nucleic acids Nucleotides  Anabolic vs catabolic reactions Anabolism Catabolism Synthesis reactions Degradation reactions Descriptive terms Building, constructive, anabolic Breakdown, digestive, decomposition, catabolic General Building of a large molecule Breakdown of polymer into description (polymer) from smaller building individual monomers: blocks (monomer): C—D → C + D A + B → A—B Bond formed broken Energy Energy is required (= Endergonic) Energy is released (= Exergonic) Water Water is released (= Dehydration) Water is required (= Hydrolysis) Example Building a protein from individual Breaking a protein into individual amino acids; amino acids; Building a triglyceride from Breaking starch down into glycerol and 3 fatty acids, etc monosaccharides, etc.  General Pathways of Metabolism Metabolism is the sum total of the chemical reactions of biomolecules in an organism By the end of this chapter you should be able to: Define metabolism (CLO K1). Distinguish between anabolism and catabolism (CLO K1).