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Chemistry of life Characteristics of life Body Separate self from environment Maintain homeostasis Metabolism Obtaining and using energy and nutrients Inheritable information Pass ability to survive to offspring Method of reproduction Life as we know it Body Cell or...

Chemistry of life Characteristics of life Body Separate self from environment Maintain homeostasis Metabolism Obtaining and using energy and nutrients Inheritable information Pass ability to survive to offspring Method of reproduction Life as we know it Body Cell or cells Metabolism Photo- / Chemo- synthesis & Respiration Inheritable information DNA Carbon based All organic molecules have a carbon “skeleton” Liquid water The most abundant substance in living things Life? J.J. Harrison 2009 J. Soccersmp 2019 Creative Commons CC-BY-SA-2.5 Creative Commons 4.0 Quartz crystal Puppy NASA 2019 C.M. García and J. G. de Lomas, Public domain Universidad de Cádiz, Spain Cyanobacteria Graphite Oxyrrhis Life? M Singla, B Bal. Infectivity Assays For Chlamydia Trachomatis. The Internet Journal of Microbiology. 2005 Volume 2 CDC/D. Loren Ketai, MD Number 2 Chlamydia Hantavirus European Bioinformatics Institute Public domain Diener, T. Discovering viroids — a personal perspective. Nat Rev Microbiol 1, 75–80 (2003). https://doi.org/10.1038/nrmicro736 Potato spindle tuber viroid Major prion protein Life What is alive and what is not alive is not always clear cut Example: viruses Living things are composed of nonliving things Cells are made of molecules, molecules are made of atoms Scales of biological research Elements Element – substance that cannot be broken down to other substances by chemical reactions The periodic table lists all known elements Randall Munroe xkcd.com License Element s of life Atoms Smallest unit of matter that retains the properties of an element Subatomic particles – do not retain the properties of the element Neutrons: no electrical charge Protons: + electrical charge Electrons: - electrical charge Like charges repeal, opposite charges attract Atomic structure Nucleus Composed of neutrons and protons Center of the atom Contains most of the mass of the atom Electron cloud Composed of electrons “Orbits” the nucleus Atom Electron Neutron Proton Atoms Atomic number = number of protons Atomic mass = “average” mass number Mass number = number of protons + number of neutrons 1 H = hydrogen 1 1 12 6C = carbon 12 Electron orbitals Electrons located in electron orbitals The electron orbitals compose the electron cloud Area outside of the nucleus Have distinct shapes and represent where the electrons can be found 90% of the time Atoms usually contain 1 or more electrons located in electron orbitals which are organized into electron shells Represents most of the space of an atom Number of orbitals and number of electrons determine the chemical reactivity of the element Electron orbitals © 2021 Quizlet Inc. Compounds Compound – substance formed by the combination of 2 or more different elements in a fixed ratio Emergent properties 2 H (hydrogen) + O (oxygen) = H2O (water) Molecules 2 or more atoms held together by chemical bonds Smallest unit of a compound that retains the properties of the compound Elements can form molecules without forming compounds MolecularJames bondsBonds Sean Connery George Lazenby Roger Moore Timothy Dalton Pierce Brosnan Daniel Craig Molecular bonds Hold atoms together  form molecules Chemical bond – an attractive force that links atoms together in a molecule Molecular bonds Covalent bond Ionic bond Chemical reactions – occur when molecule bonds are formed or broken Covalent bonds When atoms share 1 or more pairs of electrons Covalent bonds Element Usual number of covalent bonds Carbon 4 Hydrogen 1 Nitrogen 3 Oxygen 2 Phosphorus 5 Sulfur 2 Covalent bonds Covalent bonds 2 atoms can share more than 1 pair of electrons Single bonds – atoms share 1 pair of electrons CH4 (methane), each hydrogen has a single bond with the carbon Double bonds – atoms share 2 pairs of electrons O2 (oxygen), the oxygen atoms share a double bond Triple bonds – atoms share 3 pairs of electrons N2 (nitrogen) , the nitrogen atoms share a triple bond Multiple bonds are stronger and harder to break then single bonds Polar and nonpolar covalent bonds Nonpolar covalent bond – the electrons are shared equally Polar covalent bond – the electrons are not shared equally The electrons are closer to the nucleus of 1 atom than to the nucleus of the other atom Creates a slight negative charge (δ-) near the more electronegative atom and a slight positive charge (δ+) near the less electronegative atom Electronegativity Polar bond Water Ionic bonds Ions form when an atom gains or loses an electron giving it a net electric charge Cations – positive ions – have more protons than electrons Na+, H+ Anions – negative ions – have more electrons than protons Cl-, F- Opposite charges are attracted to one-another Ionic bond – forms as a result of the electrical attraction between ions of opposite charges NaCl – sodium chloride Ions Metals tend to form cations Nonmetals tend to from anions Elements can gain or lose more than 1 electron Ca2+, Mg2+ Some elements can form more than 1 stable ion Fe2+, Fe3+ Cu+, Cu2+ Molecules formed by covalent bonds can be ions = complex ions or polyatomic ions SO42-, PO43-, NH4+ Ions and polar molecules Ions and polar molecules can interact Cations attract the slight negative charge of polar molecules Anions attract the slight positive charge of polar molecules Ions and polar molecules Non-molecular bonds Not true bonds Attractions that cause temporary associations among molecules Weaker than covalent and ionic bonds Hydrogen bonds Hydrophobic interactions van der Waals force Hydrogen bonds Bonding between opposite charges of polar molecules Is not a molecular bond Does not require hydrogen Molecules that interaction with water in this manner are called hydrophillic Hydrogen bonds Hydrogen bonds Polar covalent bonds  C-N  C=O  C-F All of these are polar bonds and all can form hydrogen bonds δ+ signifies a partial positive charge δ- signifies a partial negative charge Hydrophobic interactions Nonpolar molecules do not form hydrogen bonds Nonpolar molecules are called hydrophobic Hydrophobic interactions are far weaker than hydrogen bonds van der Waals force Brief attractions among molecules due to the formation of temporary δ+ and δ- regions in molecules Electrons are in constant motion They may be away from 1 region of the molecule and/or near a different region Polarity can be induced in a molecule Can occur when 1 molecule repulses the electrons in a different molecule Temporary and weak but large number of these attractions can have a strong net force van der Waals force © Shutterstock/Papa Bravo Chemical reactions Making or breaking chemical bonds 2 H2 + O2  2 H2O Reactants  Products 6 CO2 + 6 H20 ↔ C6H12O6 + 6 O2 Rearrangement of matter and energy Molecule shape and function Molecule shape can determine biological function Carbon Forms the skeleton of organic molecules Organisms are composed of organic molecules Organic chemistry = study of carbon containing compounds Most carbon compounds are classified as organic Some carbon compounds are classified as inorganic Organic compounds Created from inorganic components Can be formed outside of organisms Carbon covalent bonds Carbon forms 4 covalent bonds Most C containing compounds also contain H and/or O and/or N Shape of C covalent bonds Diversity of C bonds Functional groups Arrangements of elements that appear frequently in organic compounds 7 functional groups are found in many many organic molecules Amino group (–NH2) & Carboxyl group (–COOH) are part of amino acids Most of the function groups can be part of amino acids Phosphate group (–OPO32-) are part of nucleotides and phospholipids Carbonyl group ( C=O) location determines the identity of monosaccharides Hydroxyl group (–OH) are required for dehydration reactions (formation of polymers) Functional groups Water The most abundant compound in organisms Unique physical and chemical properties Polar molecule Exists as solid, liquid, and gas on Earth © Quora Hydrogen bonds Bonding between opposite charges of polar molecules Are temporary and usually brief Does not require hydrogen Molecules that form hydrogen bonds with water are called hydrophillic Emergent properties of water Emergent property – characteristic not predictable from an examination of the constituents Cohesion Temperature moderation Ice floats Solvent of life All are due to the polar bonds between O and H Directly or indirectly (through hydrogen bonds) Cohesion & temperature Cohesion – mutual Specific heat – amount of heat needed to change the attraction of like temperature of 1g of substance molecules by 1oC Adhesion – clinging of one 1 calorie for water substance to another Heat of fusion – heat needed to “Cohesion” between unlike change a substance from a solid molecules to a liquid Surface tension – Heat released when a substance freezes tendency of the surface of Heat of vaporization – heat a liquid to resist an needed to change a substance external force from a liquid to a vapor Heat released when a substance condenses Ice floats and solvent Solid water forms a crystal Aqueous solution – solution structure held together by with water as the solvent hydrogen bonds Polar and ionic substances will Water molecules in ice are dissolve in water farther apart than in liquid Hydrophilic water Some polar substances will not When a body of water freezes, dissolve in water because they are too big the top layer of water Nonpolar, nonionic substances becomes ice and insulates the bottom layers will not dissolve easily in water Prevents large bodies of water Hydrophobic from completely freezing But some will dissolve to a limited extent (ex. O2)

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