The Logic of Biological Phenomena

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Pearl Crawford
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1 The Logic of Biological Phenomena molecules are lifeless yet, in appropriate complexity and number, molecules compose living things What makes living things distinct? they can grow they can move they can replicate themselves they can respond to stimuli they can perform metabolism Even though the organisms are alive, they consist of cells. The cells in turn consist of biomolecules that must conform to the chemical and physical principles that govern all matter. Distinctive properties of living systems 1. living organisms are complex and highly organized organisms are large enough to be seen by naked eye the organisms consist of cells (of many types) the cells possess subcellular structures called organelles organelles consist of very large polymeric molecules (also called macromolecules) macromolecules are mainly composed of simple sets of chemical building blocks (e.g. sugars, amino acids) The 3-dimensional structure of a macromolecule is known as its conformation. 2. biological structures serve functional purposes a biological purpose can be given for each component (e.g. limbs, organs, chemical agents) in biology, it is always meaningful to seek the purpose of observed structure (studies of inanimate structures are concerned with properties; e.g. physics, chemistry, geology) 3. living systems are actively engaged in energy transformations living systems are able to extract energy from the environment the ultimate source of energy is the sun organisms capture some of sun s energy (from photosynthesis or metabolism of food) by forming special energized molecules ATP and NADPH are the two most prominent energized molecules; when they react with other molecules in the cell, the energy can be used to drive unfavorable processes A system through which the energy flows is called biosphere. So, the living state is characterized by the flow of energy through the organism. At the expense of this energy flow, the organism can maintain its intricate order and activity. This state of apparent constancy is called steady-state. However, the steady-state is a very dynamic process where the energy is consumed to maintain the organism s stability. 1/7

2 4. living systems can self-replicate simple division by bacteria sexual reproduction in plants and animals It is a high-fidelity reproduction, but it is not perfect!!! In fact this is a requirement for evolution to take place (evolution is a natural selection of organisms that slightly vary in their fitness). Biomolecules Some facts: hydrogen (H), oxygen (O), carbon (C), and nitrogen (N) constitute >99% of human body most of the H and O occur as H 2 O Why are H, O, C, N so suitable to chemistry of life? They can form covalent bonds by electron-pair sharing! Also, H, C, N, and O are among the lightest elements of the periodic table capable of forming covalent bonds. Therefore, they form the strongest bonds. Two other covalent bond-forming elements, phosphorus (P) and sulfur (S), are also important in biomolecules. So, what are biomolecules? all biomolecules contain carbon (a very versatile atom) necessary for the existence of all known forms of life C can share 4 electrons (can form 4 bonds) O has 2 unpaired electrons N has 3 unpaired electrons H has 1 unpaired electron Lewis structures.... Properties of carbon can form bonds with itself can form tetrahedral structures Therefore, there is a potential for linear, branched, and cyclic components of carbon. These structures, by virtue of appropriately included N, O, and H atoms, can display unique chemistries suitable to the living state. 2/7

3 How big/heavy are these atoms/molecules? 1H ~1Da kg H 2 O ~18Da kg typical protein ~300,000Da kg typical cell ~ Da kg How are biomolecules produced? Major precursors for the formation of biomolecules are water, carbon dioxide, and 3 inorganic nitrogen compounds (amonium NH 4 + ; nitrate NO 3 - ; dinitrogen N 2 ). Metabolic processes transform these inorganic precursors into biomolecules. 1. precursors metabolites Metabolites are simple organic compounds that are intermediates in cell energy transformation) 2. metabolites building blocks Building blocks are: amino acids, sugars, nucleotides, fatty acids, glycerols. 3. building blocks macromolecules Macromolecules: proteins, polysaccharides, polynucleotides, lipids (lipids are not polymeric). 4. macromolecules supramolecular complexes Supramolecular complexes: enzyme complexes, ribosomes, chromosomes, cytoskeletal elements. Macromolecules are connected via non-covalent forces (weak forces). Organelles are entities that are within cells (usually have membrane) and have important cellular task exist only in the cells of higher organisms (eukaryotic cells) For example, the most interesting organelles are nucleus, mitochondria, chloroplasts, endoplasmic reticulum, etc. Membranes Membranes define boundaries of cells and organelles Membranes are not supramolecular assemblies nor organelles, but have the properties of both. Membranes are complexes of proteins and lipids maintained by non-covalent forces (hydrophobic interactions interactions where molecules prefer to group together rather than with water). A membrane of each organelle is different and suited to its function. Because of membranes, cells consist of compartments. 3/7

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5 The Cell the unit of life the smallest entity (molecule) displaying life-associated properties: growth, metabolism, stimulus response, replication) Building Blocks Macromolecules in more detail 5/7

6 Weak forces and interactions Examples: Van der Waals forces (result of induced electrical interactions between closely approaching atoms or molecules as their negatively-charged electron clouds fluctuate instantaneously in time; may be attractive between positively charged nuclei and the electrons of nearby atoms- dipole-dipole interactions, dipole induced dipole interactions- or repulsive when two atoms approach to close to one another) hydrogen bonds (form between hydrogen atom covalently bonded to an electronegative atom (O, N) and a second electronegative atom that serves as the hydrogen bond acceptor; stronger than Van der Waals forces; highly directional) ionic interactions (result of attractive forces between oppositely charged polar functions, such as negative carboxyl groups and positive amino groups) hydrophobic interactions (exist due to the strong tendency of water to exclude non-polar groups or molecules; water molecules prefer the stronger interactions that they share with one another, compared with their interaction with non-polar interactions) A commonly-used example of a polar compound is water (H2O). The electrons of water's hydrogen atoms are strongly attracted to the oxygen atom, and are actually closer to oyxgen's nucleus than to the hydrogen nuclei; thus, water has a relatively strong negative charge in the middle (red shade), and a positive charge at the ends (blue shade). weak forces are non-covalent bonds they are 1-3 orders of magnitude weaker than covalent bonds they are several times greater than dissociating tendency due to thermal motion of molecules (at 25 C) Type of bonding Strength (kj/mol) Van der Waals interactions Hydrogen bonds Ionic interactions 20 Hydrophobic interactions <40 The average kinetic energy of molecules at 25 C 2.5 Covalent bond (O 2 ) 402 Covalent bond (N 2 ) 946 6/7

7 Why are these weak forces so important? They are reversible! Rigid molecules would not facilitate cellular activities. Biomolecular recognition is performed via interplay of complementary molecules. So, biological function is achieved through mechanisms based on structural complementarity and weak chemical interactions. If a sufficient number of weak bonds can be formed (as in macromolecules complementary in structure to one another) larger structures assemble spontaneously. A consequence: weak forces restrict organisms to a narrow range of environmental conditions (temperature, ionic strength, relative acidity). The loss of structural order is called denaturation. It is accompanied by loss of function. Metabolism Cells cannot tolerate reactions in which large amounts of energy are released. Nor can they generate a large energy bursts to drive energy requiring processes. Instead, such transformations take place via sequential series of chemical reactions whose overall effect achieves dramatic energy changes. These sequences of reactions are organized to provide for the release of useful energy to the cell from the breakdown of food or to take such energy and use it to drive the synthesis of biomolecules essential to the living state. These reaction sequences constitute metabolism. So, metabolism is the ordered reaction pathways by which cellular chemistry proceeds and biological energy transformations are accomplished Some definitions: Ion: If the number of protons and electrons is not equal, the atom or molecule must be charged and is called an ion (anion negatively charged; cation positively charged). Electron affinity (electronegativity): Electrons can be added to atoms as well as removed. The energy that is released by adding an electron to an atom to form a negatively charged anion is called the atom s electron affinity. The noble gasses have very low electron affinities. Conversely, atoms to which adding an electron would complete a noble gas configuration have high electron affinities. Polarity: In chemistry, a polar molecule is a molecule in which the centers of positive and negative charge distribution do not converge. These molecules are characterized by a dipole moment which measures their polarity. Polar compounds are highly soluble in other polar compounds, and virtually insoluble in nonpolar compounds Sources: Biochemistry by Reginald H. Garrett and Charles M. Grisham Organic Chemistry by Maitland Jones, Jr. Wickipedia ( 7/7

2. Macromolecule - molecules composed of repeating molecular units (biopolymers).

2. Macromolecule - molecules composed of repeating molecular units (biopolymers). Biochemistry I Biological Principles I. FUNDAMENTAL PRINCIPLES UPON WHICH BIOCHEMISTRY IS BASED A. Prerequisite Requirements Technically, you must have completed or earned credit for Organic Chemistry