ATOMS AND BONDS. Bonds

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1 ATOMS AND BONDS Atoms of elements are the simplest units of organization in the natural world. Atoms consist of protons (positive charge), neutrons (neutral charge) and electrons (negative charge). The simplest element is hydrogen which consists only of a proton and an electron. Protons and neutrons have mass and exist in the nucleus of an atom. Electrons have no mass and orbit the nucleus in defined orbits (valence shells). An element s atomic number is the number of protons it has. The number of electrons will equal the number of protons. An element s atomic weight is the sum of the number of protons and neutrons. Carbon has an atomic number of N equal to 6 so it has six protons, six neutrons and six electrons in its most common version. Other versions of an element are termed isotopes. Isotopes differ in the number of neutrons and thus different isotopes have different weights. At the time the earth was formed from a molten mass elements like uranium were formed in the starting ratio of different isotopes. Isotopes degrade into other forms at predictable rates so the ratios of the different isotopes of an element in a sample can be used to determine the age of the sample. The halflife of an isotope is the time that is required for half of an isotope to degrade into the degradation form. Carbon occurs as the common C 12 but also as an isotope called C 14. C 14 differs from say U 238 in that it is rejuvenated in the atmosphere. When plants die they stop acquiring C 14 so dead plant materials and artifacts derived from plant materials can be dated by examining the ratio of C 14 to C 12. The isotope C 14 has 6 protons but 8 neutrons (68=14). It degrades into N 14 or Nitrogen which has 7 protons and 7 neutrons. In the process of degrading C 14 converts one neutron to a proton and releases some energy. The half life of C 14 is about 6000 years so the utility of using C 14 :C 12 ratios in a sample in order to age the sample is useful for relatively modern artifacts (e.g., 10,000 year old pottery, etc). For samples which might be millions of years old isotopes with really long halflives are used (e.g., U 238, 4.5 billion years). Radioactive isotopes have many uses in the biomedical fields. Different isotopes of any element behave chemically identically so they can be used as tracers to study the fate of chemicals. Isotopes can be used diagnostically to identify tumors. Radioactive isotopes can also be used to treat tumors. Isotopes of uranium and plutonium are used in the nuclear power industry. Living things are composed of about 25 elements out of 92 naturally occurring elements. Four of these (C,H, O, N) make up 96% of the human body and are called the major elements. Minor elements comprise 0.1 to about 1% of the human body and include Calcium, Phosphorus, Potassium, Sulphur, Sodium, Chloride and Magnesium. Trace elements are present in even smaller percentages but that does not mean they are less important. Many trace elements serve as cofactors in vital chemical reactions. Bonds Molecules form when two or more atoms bond by sharing or borrowing electrons. Electrons are the basis of chemical bonds between atoms. An ionic bond involves the donation of one or more electrons from one atom to another. The space between an atom s nucleus and its electrons is so large relative to a nucleus s size that if you could compress or minimize this space the entire human race could fit in a sugar cube (about 1 cm 3 ). Covalent bonds involve sharing of electrons. Electrons orbit the nucleus of an atom in valence or energy shells. Shared electrons spend time orbiting two different atom s nucleus. The first or inner most shell can only hold two electrons. The second shell can hold eight electrons and the third can hold eighteen. Bonds form because physical laws drive atoms to fill these valence shells by means of donation or sharing of electrons.

2 Ionic Bonding Sodium has an atomic number of 11 so its electrons are arranged 2, 8 and the 11 th or just one electron in the outer shell. Chlorine has an atomic number of 17 so its electrons are arranged 2, 8 and 7 in the third shell. The third shell does have a capacity for 18 electrons but since the third shell has subshells of 2, 6 and 10, chlorine s 7 outer electrons are just 1 electron shy of filling the first two subshells (2 and 6). Thus the addition of just one electron would fill the inner two subshells of chlorine s 3 rd shell. Sodium donates its 11 th electron to chlorine. Sodium becomes 1 and chlorine becomes 1 and an ionic bond is formed. The product is NaCl or common salt. Sodium is a highly reactive metal and chlorine is a very toxic liquid and gas. But bonded as the crystal we know as salt they are quite harmless. This is an example of emergent properties. Sodium (Na) Chlorine (Cl) 11th e 7 electrons arranged 2/2, 5/6 and 0/10 (after bond will be 2/2, 6/6 and 0/10) Covalent Bonding Nonpolar Covalent Bonding Covalent bonds involve atoms sharing electrons. Shared electrons orbit both atom's nuclei. Some elements exert greater pull on the electrons so their orbits are not shared equally. This is termed a polar covalent bond and the polar molecule has positive and negative poles. Molecules where the atoms share the electrons equally are nonpolar covalent bonds. Methane is a good example of a simple molecule with four nonpolar covalent bonds. Carbon has an atomic number of six so two electrons are in the inner orbit (valence shell) and four electrons are in the next shell (which has capacity for eight electrons and thus needs four electrons to fill the shell). Hydrogen has a single electron which of course resides in the first shell leaving space for one additional electron. When four hydrogens bond to a single carbon sharing of electrons results in all four hydrogen's first electron shell filled and carbon's second shell filled. The electrons are shared equally so it is a nonpolar bonding.

3 Carbon N=6 Polar Covalent Bonds Our watery world begins with the polar covalent bonds that exist between oxygen and hydrogens in the water molecule. All the properties of water that exist are the result of the fact that two hydrogen atoms are polarcovalently bonded to a single oxygen atom. Oxygen has an atomic number of 8. Two electrons orbit in the inner valence shell leaving 6 to orbit in the second shell which always has a capacity of 8. So oxygen needs 2 electrons to fill the outermost shell. Each hydrogen atom has only a single electron and of course it orbits in the innermost shell which has a capacity of 2. Hydrogen would like to add a single electron. By bonding and sharing electrons both oxygen and each of two hydrogen atoms fill their outermost valence shells. But oxygen is very strong electronegatively speaking. It does not share the electrons equally, but it does share. The unequal sharing results in the water molecule being polar. Since oxygen is not letting the negatively charged electrons find their way to hydrogen as much as orbiting oxygen the oxygen side of the molecule becomes negative and the two sides of molecule with hydrogen atoms become positive. These three poles are responsible for all the properties of water which will be covered.

4 Oxygen N=8 Hydrogen bonds are weak very temporary bonds between adjacent polar covalent molecules. Water is a good example. Electrons are briefly shared between adjacent molecules. This brief sharing occurs between positive side of one molecule and the negative side of the other. This sharing created partial bonding or cohesion so to speak. It s what holds the adjacent molecules together. If water were not a polar covalently bonded molecule the hydrogen bonds would never occur. Kinetic energy or heat greatly influences these hydrogen bonds. Coldness results in the hydrogen bonds being a little less temporary or more permanent. In contrast, heat makes the hydrogen bonds more fleeting or more temporary. Heating water to 100 C weakens the bonds greatly and water molecules separate and vaporize into a gas (boils). Cool water to 0 C and the bonds will become permanent and water will solidify into ice. As a solid or ice, the structure is very organized with relatively large spaces between molecules making ice less dense (weight per unit volume) than water. The hydrogen bonds which result because of water's inherent polar covalent bonds are responsible for all of water's unique properties. Hydrogen bonds give water its cohesion properties where water molecules want to stick together. This is what creates the socalled surface tension. Surface tension is why a drop of water on a table top does not just spread out until it is a thin film of water rather than the beaded drop you see. Water adheres to other structures (adhesion) and as it does it will pull other water molecules with it by means of cohesion. Without adhesion and cohesion water could not climb the vascular tissues of trees. Water has a high specific heat meaning it can absorb a lot of heat or kinetic energy and not change its temperature that much. Water has a high heat of vaporization. When it does change to a gas it takes a lot of heat with it. Water is considered the universal solvent because it dissolves more substances than any other liquid. The proportion of free hydrogen ions in a solution of water is termed ph. Since ph is calculated as log10 of the

5 hydrogen ion concentration each change of a single ph unit is a 10 fold change. If ph changes by 2 units a 100 fold change occurs. Most animals maintain internal ph in a narrow range (6.87.2) so a change of ph from 7 to say 6 or 8 is a huge change which probably cannot be tolerated. hydrogen bond hydrogen bond hydrogen bond CHNOPS The elements carbon, hydrogen, oxygen, nitrogen, phosphorus and sulphur are very important in the living world. We will touch on the details of these importances later. Hydrogen and oxygen being constituents of water have already demonstrated their importance but much is to follow. Carbon is the earth's fuel for the living world. The fuel is stored in CH bonds in biomolecules. Ancient biomolecules become hydrocarbons or "fossil fuels" over millions or even billions of years. Nitrogen is the element of information. Nitrogen is part of nucleic acids (DNA and RNA) and amino acids which are the building blocks of proteins. Thousands of proteins serve as enzymes or catalysts for thousands of chemical reactions for virtually every biological process needed for life. Proteins are also important structural molecules in cells. All proteins are the result of a sequence of nucleotide bases (adenine, thymine, guanine and cytosine). By the way, the two strands of DNA s double helix are held together by millions of hydrogen bonds.

6 One possible explanation why nitrogenous compounds are so prevalent in the biological world is the versatile bonding ability of nitrogen. Its atomic number is 7 so it has 7 electrons. Two of these are in the inner shell and 5 are in the outer shell. This means it needs three electrons in order to fill the outer shell to that shell s capacity of 8. It can form three single bonds, a double bond and a single bond or a triple bond. Phosphorus is stored energy waiting to be put to work. Stored energy in the form of ATP is the universal energy currency of life. Notice how even ATP contains nitrogen. The energy stored in ATP (adenosine triphosphate) lies in the bonding of the third Phosphorus group (left side of diagram below).