Chap 1 Foundations 2023 PDF

Introduction: The Foundations of Biochemistry Marc A. Ilies, Ph. D. Lehninger - Chapter 1 (p1-44) [email protected]; lab 517, office 517A (Tu, Fr 3-5) For questions, comments please use the discussion tool in Canvas or recitation session 1 Origins of Universe and Earth - Universe was created abo...

Introduction: The Foundations of Biochemistry Marc A. Ilies, Ph. D. Lehninger - Chapter 1 (p1-44) [email protected]; lab 517, office 517A (Tu, Fr 3-5) For questions, comments please use the discussion tool in Canvas or recitation session 1 Origins of Universe and Earth - Universe was created about 14 Bn years ago, and almost immediately after its creation the majority of the chemical elements appeared - Atoms associated into inorganic materials (rocks) and molecules; the organic matter appeared - As the Universe expanded and cooled, stars and planetary systems were formed http://geneticsgroup4.weebly.com/ 2 Earth and life: a timescale - Earth offered unique conditions for development of life, being placed at an optimal position in the Solar System in terms of exposure to the Sun (amount of thermal energy and radiations received); important: revolution around Sun (calendar year); self-rotation (day/night) - Earth Atmosphere and large amounts of water (Oceans) formed soon after Earth formation through complex chemical reactions in the Earth crust; temperature fluctuations and exposure to strong ionizing radiations 3 Biomolecules, living organisms, biochemistry - About 4 Bn years ago life arose under the form of simple microorganisms able to extract energy from chemical compounds and later from solar energy (sunlight), in order to synthesize more complex biomolecules Bios (Greek) = Life Biology = the study of living organisms: ●structure; ●function; ●growth; ●origin; ●evolution; ●distribution Chemistry = the study of matter (atoms and molecules): ●composition; ●structure; ●properties; ●reactions Biochemistry = the study of matter in living organisms = the chemistry of the living matter Biochemistry = Chemistry of Biology = Physiological Chemistry = Biological Chemistry Biomolecules and Biochemical Reactions = all chemical substances and processes occurring in living organisms Objective of Biochemistry: - to describe at the molecular level structures, mechanisms, and chemical processes shared by all organisms and to explain the molecular logic of life 4 Features of living organisms • A high degree of chemical complexity and microscopic organization • Ability to extract/produce, transform and systematically use energy to create and maintain intricate structures and to do mechanical, chemical, osmotic and electric work • Defined functions for each of an organism’s components and regulated interactions among them (dynamic, coordinated) • Ability to sense and respond to alterations in their surroundings • Capacity for precise self-replication and self-assembly • A capacity to change over time by gradual evolution 5 The cell: the universal building block of live • Living organisms are made of cells. • The simplest living organisms are unicellular (single-celled). • Larger organisms are multicellular (many-celled), with different functions for different cells. • Cells have some common features but can contain unique components for different organisms. Cellular (biological) Foundations - Cells of all kinds share certain structural features: - Size of cells: smallest cells defined by minimum number of biomolecules requited to achieve all life features: bacterial mycoplasma (300 nm in diameter); Upper limit of cell size probably set by diffusion of solute molecules in aqueous systems (oxygen, metabolites, etc) - Shape of cells determined by various factors: type of cell, environment in which they live, their function and role in more complex systems of cells (tissues, organs, etc) - Differences in structural and functional features between different types of cells can be exploited to control their growth/selective killing through the use of various chemical, biochemical and biological agents (some them used as drugs) 7 Cellular Foundations - Organisms belong to three distinct domains of life: Cellular Foundations - Organisms differ widely in their source of energy and biosynthetic precursors Cellular Foundations - animal and plant cells contain unique components but are made from the same major components (building blocks of life) (note the structural hierarchy in the molecular organization of the cells) Chemical Foundations • • Other than carbon, elements H, O, N, P, S, etc are also common elements for biological systems; some are required in large amounts (“bulk” elements, gram quantities in everyday diet), others in smaller amounts (“trace” elements) Metal ions (e.g., K+, Na+, Ca2+, Mg2+, Zn2+, Fe2+) play important roles in metabolism g/day mg/day 11 Chemical Foundations - carbon plays a central role in the chemistry of life due to it small size, low electronegativity and propensity to form covalent bonds with itself (C chains) or with other elements: - carbon is hybridized sp3 (simple bonds), sp2 (double bonds) and sp (triple bonds); hybridization dictates geometry and ultimately the shape of the molecules; similarly for other elements (N, P, etc) Chemical Foundations - common functional groups of biological molecules: - can be found simultaneously in different biomolecules, where can be used to induce chemical interactions, chemical recognition, and biochemical function: 13 Chemical Foundations - Besides dependence on the functional groups, the function of biological molecules strongly depends on the three-dimensional structure, which can be represented in different ways: - Stereoisomers are molecules with the same molecular formula and sequence of atoms in the molecule but with different 3D orientation of their atoms in space: • Geometric Isomers (cis vs. trans) • can’t be interconverted without breaking bonds • have different physical and chemical properties mp (oC): 135 SH2O, 20 oC (g/L): 478.8 287 4.9 14 Chemical Foundations - Stereoisomers: • • Enantiomers (chiral objects, object/mirror image relationship, non-superposable) • have identical physical properties (except with regard to polarized light) and react identically with achiral reagents Diastereomers (chiral objects, not in an object/mirror image relationship, nonsuperposable; usually have more than one chiral center) • have different physical and chemical properties 15 Chemical Foundations - Stereoisomers (continued): • Enantiomers vs diastereosiomers, for multiple chiral centers e. g. 2 chiral centers: Number of stereoisomers 2n = 4 (n = # of asymmetric carbons) 16 Chemical Foundations Stereoisomers can elicit different biological effects: - enantiomers: SSRI (Selective Serotonin Reuptake Inhibitor) Antidepressants - diastereoisomers: NutrasweetÒ 17 Chemical Foundations Interactions between molecules are stereospecific: • • • Macromolecules fold into 3D structures with unique binding pockets. Only certain molecules fit in well and can bind. Binding of chiral biomolecules is stereospecific: just one stereoisomer will be accommodated Physical Foundations - living organisms perform energy transductions to accomplish work to stay alive and to maintain its structure and dynamic composition, which is different from the surrounding environment: - molecules are permanently synthesized and broken down; living organisms are in permanent exchange of energy and matter with its surroundings, being open systems - they obey the first law of thermodynamics: “total amount of energy in the Univers remains constant, although the form of energy may change” 19 Physical Foundations - creating and maintaining order in the living systems requires work and energy, therefore living systems perform both catabolic processes, harvesting energy from nutrients, food, sunlight storing it into chemical energy, and anabolic processes, using stored chemical energy to synthesize building blocks and macromolecules - living systems exist in a dynamic steady state, maintaining concentrations of nutrients, ions, building blocks, macromolecules relatively constant and very different from their concentration in the environment - in nature systems tend to evolve to complete randomness (infinite entropy); fighting entropy to maintain the dynamic steady state requires work and energy 20 Physical Foundations - chemical energy is stored into ATP (chemical currency of energy) and in the reduced forms of electron carriers NADH, FADH2 - dynamic transformations used to generate and consume chemical energy to maintain the dynamic steady state can be analyzed from the angle of thermodynamics and kinetics 21 Physical Foundations - Thermodynamics analyzes how stable one state is versus another, analyzing the relationships between all forms of energy (heat, chemical energy) - J. Willard Gibbs developed the theory of energy changes during chemical reactions: ΔG = ΔH -TΔS where ΔG is the variation of the free energy content ΔH is the variation of enthalpy, reflecting the change in the number and type of chemical bonds broken and formed during a chemical reaction T is the absolute temperature (K) ΔS is the variation of entropy – the change in the system’s randomness - Thermodynamics analyzes the difference between two states (initial and final) and does not care about intermediate states, dynamics of the system: if ΔG < 0 the reaction occurs spontaneously (free energy released, exergonic process) ΔG = 0 the reaction is at equilibrium ΔG > 0 the reaction requires free energy (not spontaneous) and can proceed only in 22 the opposite direction (endergonic process) Physical Foundations - Energy coupling links reactions in biology (bioenergetics): chemical coupling of exergonic and endergonic reactions allows otherwise unfavorable reactions if the overall free energy is < 0: e.g. the “high-energy” molecule (ATP) reacts directly with the metabolite that needs “activation” Endergonic cellular reactions are driven by coupling them to exergonic chemical processes through shared chemical intermediates. ATP 23 Physical Foundations Consecutive reactions - biochemical pathways: - DG values in a pathway are additive; if the sum is negative, then the pathway can proceed in the forward direction - the free energy change for ATP hydrolysis is large and negative; phosphorylation is done with ATP instead of phosphate: 24 Physical Foundations - Kinetics analyzes how quickly or slowly species react in living systems - considering the general reaction: kdir aA + bB kinv cC + dD - at equilibrium the rate of the direct reaction equals the rate of the inverse reaction: vdir = kdir [A]a[B]b = vinv = kinv [C]c[D]d kdir [A]a[B]b = kinv [C]c[D]d Keq = kdir kinv = [C]c[D]d [A]a[B]b (a Keq > 0 means reaction tends to proceed till reactants are almost completely converted into products) 25 Physical Foundations - Kinetics and thermodynamics are connected through the relationship between equilibrium constant Keq, DG0 (standard free-energy change), and temperature: DG0 = _ RT ln Keq (the force driving the system towards equilibrium) 26 Physical Foundations - many times although the thermodynamics is favorable (DG < 0), reaction occurs too slowly for biochemical needs ® how to speed reactions up: Higher temperatures Stability of macromolecules is limiting Higher concentration of reactants Costly as more valuable starting material is needed Change the reaction by coupling to a fast one Universally used by living organisms Lower activation barrier by catalysis Universally used by living organisms • • • • A catalyst is a compound that increases the rate of a chemical reaction. ‡ Catalysts lower the activation free energy DG . Catalysts do not alter DG°. Enzymatic catalysis offers: – acceleration under mild conditions – high specificity – possibility for regulation Physical Foundations Biochemical pathways: series of related/consecutive enzymatically catalyzed reactions Metabolic pathway • produces energy or valuable materials Signal transduction pathway • transmits information Biochemical pathways are controlled in order to regulate levels of metabolites Example of a negative regulation: product of enzyme 5 inhibits enzyme 1 to prevent wasteful excess products. Genetic and evolutionary foundations - Life on Earth arose 3.5–3.8 billion years ago. - The most remarkable property of living cells and organisms is their ability to reproduce themselves for countless generations with near perfect fidelity; the formation of self-replicating molecules was a key step towards this ability - Biomolecules first arose through chemical evolution ® the abiotic (non-biological) origin of organic biomolecules proved in 1953 by Stanley Miller/Harold Urey: - proved the formation of 23 aminoacids and 7 organosulfur , plus a large number of simple organic compounds – building blocks for more complex ones - Hydrothermal vents on the bottom of the oceans may have been the sites of early biogenesis Genetic and evolutionary foundations - RNA is believed to be the initial macromolecule used for information storage • RNA can act both as the information carrier and biocatalyst. • Some viruses use RNA as a primary means of genetic information. • A possible RNA scenario of genetic evolution: • DNA (more stable chemically) replaced RNA as the main storage of generic information Genetic and evolutionary foundations Complementarity of bases in DNA allows for replication with near-perfect fidelity: - RNA still occupies a central role in information flow from DNA to proteins encoded (transcription and translation): DNA → RNA → Protein Genetic and evolutionary foundations Natural selection favors some mutations: changes in hereditary instructions allow evolution • • • Mutations occur more or less randomly in DNA and RNA. Mutated polynucleotides may be transcribed and translated into molecular machinery like proteins. Mutations that give organisms an advantage in a given environment are more likely to be propagated ® survival of the fittest (Darwin) - when two genes share readily detectable sequence similarities ® homologous (proteins encoded: homologs) ; if two homologous genes appear in the same organism ® paralogous (protein products: paralogs); paralogous genes believed to have been derived by gene duplication, followed by gradual changes in the sequence through mutations; paralogous proteins are similar in sequence, 3D structure, although may have acquired different functions Genetic and evolutionary foundations - Two homologous genes found in different species are said to be orthologous and their proteins are orthologs; they usually have the same functions in both organisms - molecular anatomy of the genome reveals evolutionary relationships; molecular phylogeny derived from gene sequences is consistent and, in some cases, even more precise than the classical phylogeny based on macroscopic structures Evolution of Eukaryotes Could Also Be Mediated Through Endosymbiosis Goals and Objectives Upon completion of this lecture at minimum you should be able to answer the following: ►Origins of Universe and Earth, timescale of life on Earth, biomolecules and biochemistry, the object of biochemistry ►The cell as universal building block of life and the common features of living organisms ►Cellular foundations of life and biochemistry: types of cells, structural features of cells, main sources of energy used, common and particular organelles ► Chemical foundations of life and biochemistry: What are the bulk and trace elements found in living organisms, central role played by carbon in biochemistry, functional groups in biochemical compounds and their role in chemical interactions, chemical recognition, 3D structure of biomolecules, stereoisomers (types) and their relevance, stereo-specificity of biochemical interactions ►Physical foundations in living organisms: energy transduction in living organisms and the open system concept, first law of thermodynamics, catabolism/anabolism, chemical energy (ATP, NADH, FADH2) and the dynamic steady state of living organisms, thermodynamic aspects (free energy and spontaneity of the reactions, energy coupling of the reactions in pathways), kinetic aspects (rate of chemical reactions and impact of concentration), connection between free energy and equilibrium constant, catalysis in biochemical reactions and pathways, pathway regulation ►Genetic and evolutionary foundations: ability of living organisms to self-reproduce, molecules that store genetic information (RNA, DNA) and the flow of genetic information from DNA into proteins, chemical evolution of biomolecules, mutations and their implications, homologous and orthologous genes, endosymbiosis 34