Chapter 2 The Chemical Context of Life 02 02 2012 Biology is a multidisciplinary science Organisms are composed of matter Matter is anything that takes up space and has mass Matter is made up of elements An element is a substance that cannot be broken down to other substances by chemical reactions A compound is a substance consisting of two or more elements in a fixed ratio It has characteristics different from those of its elements About 20 25 of the 92 elements are essential to life Carbon Hydrogen Oxygen and Nitrogen make up 96 of living The remaining 4 generally consists of calcium phosphorus matter potassium and sulfur Trace elements are those required by an organism in minute quantities For example iron is a trace element Although it is needed by all elements of life it is not needed in vast amounts Each element consists of unique atoms the smallest unit of matter that still retains the properties of an element They are composed of subatomic particles Proton positive charge Neutron no charge Electron negative charge Protons and neutrons are found in the atomic nucleus while electrons form a cloud around the nucleus The mass of protons and electrons is measured in daltons Atoms of different elements vary in the number of subatomic particles they have Atomic number number of protons in the nucleus Mass number the atom s total mass can be approximated by the atomic number Isotopes are two atoms of an elements that differ in number of neutrons Radioactive Isotopes decay spontaneously giving off particles and energy Applications of radioactive isotopes in biological research o Dating fossils o Tracing atoms through metabolic processes o Diagnosing medical disorders Energy is the capacity to cause change for instance doing work Potential energy is the energy that matter possesses because of its location or structure For example water in a reservoir on a hill has potential energy because of its altitude An electron s energy level is correlated with its average distance from the nucleus Electrons are found in different electron shells each with a characteristic average distance and energy level The chemical behavior of an atom is determined by the distribution of electrons in electron shells Valence electrons are those in the outermost shell or valence shell The chemical behavior of an atom is mostly determined by the valence electrons Elements with a full valence shell are chemically inert For example the noble gases have full valence shells and therefore are largely unreactive An orbital is a three dimensional space where an electron is found 90 of the time Each electron shell consists of a specific number of orbitals Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms held by attractions called chemical bonds Covalent bond very strong bond caused by the sharing of a pair of valence electrons by two atoms which count as part of each atom s valence shell They can occur between atoms of the same element or atoms of different elements o Single bond sharing of one pair of valence electrons o Double bond the sharing of two pairs of valence electrons o Structural formula represents atoms and bonding o Molecule two or more atoms held together by covalent H H bonds for example water molecules H2O A compound is a combination of two or more different elements Bonding capacity is called the atom s valence Electronegativity is an atom s attraction for the electrons in a covalent bond The more electronegative the atom the more strongly it pulls shared electrons toward itself If one atom is more electronegative than the other they do not share the electron s equally and thus create a polar covalent bond o Unequal sharing of the electrons causes partial positive or negative charge for each atom or molecule For example water molecules are polar because oxygen has a much greater electronegativity than hydrogen thus resulting in hydrogen molecules to be positively charged and oxygen molecules to be negatively charged If the atoms share the electron equally it is a nonpolar covalent bond Ionic Bonds weaker than covalent bonds the attraction between an anion and cation an atom that becomes charged as a result of stripping or being stripped of an electron from their bonding partner For example in NaCl there is a transfer of an electron from sodium to chlorine resulting in both atoms to be charged Cation positively charged ion o Na Anion negatively charged ion o Cl o Compounds formed by ionic bonds are called ionic compounds or salts They are often found in nature as crystals Weak chemical bonds such as ionic and hydrogen bonds reinforce shapes of large molecules and help molecules adhere to each other Hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom o In living cells the electronegative partners are usually oxygen or nitrogen atoms Van der Waals Interactions are attractions between molecules that are close together as a result of charges due to electrons distributed asymmetrically that result in hot spots of positive or negative charges For example interactions between molecules of a gecko s toe hairs and a wall surface A molecules shape is very important to its function It is determines by the positions of its atom s valence orbitals Molecules with similar shapes have similar biological functions For example morphine and natural endorphins have very similar molecular shapes In a covalent bond the s and p orbitals hybridize creating specific molecular shapes Chemical Reactions are the making and breaking of chemical bonds The starting molecules of a chemical reaction are the reactants The final molecules of a chemical reaction are the products One important chemical reaction is photosynthesis in which sunlight powers the conversion of carbon dioxide and water to glucose and oxygen 6 CO2 6 H20 C6H12O6 6 O2 All chemical reactions are reversible and the products of the forward reaction become reactants for the reverse reaction Chemical equilibrium is reached when the forward and reverse reaction rates are equal Chapter 3 Water and Life 02 02 2012 Water is the biological medium on earth All living organisms require it more than any other substance Its abundance is the reason the Earth is habitable Cells are 70 95 water The water molecule is a polar molecule the opposite ends have opposite charges This allows water molecules to form hydrogen bonds with eachother Four
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