1.1 The Fundamental Chemistry of life

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1 1.1 The Fundamental Chemistry of life Matter makes up everything in the universe, including all living organisms. Matter is composed of elements, a pure substance that cannot be broken down into simpler substances by chemical reactions. The smallest particle of an element is an atom. These atoms will often bind to each other chemically in fixed numbers to form molecules. A chemical compound is a stable combination of different elements held together by chemical bonds. Subatomic Particles Neutrons (electrically neutral) and protons (positively charged) are packed together tightly at the centre of the atom in what is called the core. The electrons (negatively charged), moving nearly at the speed of light form a cloud around the nucleus. What are living things made of? For all of their complexity, 96% of the mass of all living things is composed of just four elements. They are carbon, oxygen, hydrogen and nitrogen. The atomic structure of these elements is important for understanding how they form molecules. The valence (outer most) electrons are the most important for bonding. Using a periodic table, let us analyse the composition of these 4 elements.

2 Recall how to use the periodic table: Isotopes and Radioisotopes Isotopes are atoms that have more neutrons that other atoms of the same element and therefore have a greater mass. Although the isotopes of an element have a slightly different mass, they behave identically in chemical reactions The number of protons determines the characteristics of an atom. By changing the number of neutrons present, the chemical properties of the atom remain identical, however the atoms mass and/or stability of the nucleus will be altered. Unstable nuclei decay and produce detectable radiation at a steady rate. This radioisotopes is one in which a nucleus decays spontaneously, giving off particle of energy. When the decay leads to the change in the number of protons, it transforms the atom to an atom of a different element. (Ex: radioactive carbon decays to form nitrogen).

3 Electron Arrangement Orbital: is a region of space that is occupied by electrons located around the nucleus of an atom. The arrangement of electrons determines the chemical properties of an atom. Electrons are directly involved in the forming of breaking of bonds during chemical reactions. Electrons are found moving in specific regions (orbital) around the nucleus of an atom. Only one or two electrons can be found in any one orbital. Electrons can be found in energy levels, with in the orbital. These are also known as energy shells and are numbered 1, 2, 3 as the shells move further away from the nucleus. Energy shell 1, (1s orbital), can hold up to 2 electrons only. Energy shell 2, (2s, 2p orbitals), can hold up to 8 electrons. (2s, 2px, 2py, 2pz). There are also d and f orbitals. The further away an electron is from the nucleus, the greater the energy. Valence Electron : is an electron in the outermost energy level or shell of an atom. Atoms that do not have a complete octet in their outer energy shell, or valence shell, are chemically reactive. Inert atoms, such as; helium and neon have complete octets and are non reactive. Atoms in groups 1, 2 and 17 are more reactive. These have a tendency to lose or gain electrons to complete their valence shells. When metals and non metals combine, they form ionic compounds. When non metals combine, they share electrons to complete their valence shells, and form covalent bonds.

4 Chemical Bonds Atoms often form stable interactions known as chemical bonds by allowing their valence electrons to interact. Electrons may either be transferred from one element to another (ionic bonding), or shared between atoms (covalent / molecular bonding). Ionic Bonding Covalent Bonding Between Metal and non-metal Two or more non-metals Mechanism Metal loses e Non-metal loses e CATION ANION Valence electrons are shared (up to four shared pairs) Example Force of Attraction Electrostatic interaction (attraction between positively and negatively charged ions) Physically shared electron pair(s) Conceptual Diagram Structure Crystal Lattice Individual molecules. Structures vary greatly depending on how individual molecules interact with each other. Depends mostly on: polarity, size and 3D shape

5 Polarity Not all covalent bonds behave the same way. Every element has its own characteristic electronegativity. This is an assigned value used to describe an element s overall pull for electrons. When one element in a covalent bond has a stronger electronegativity than the other, then the electrons will not be shared evenly. If one side of a molecule holds electrons closer, it will gain a slight negative charge. The side with a weaker hold on its electrons will become positively charged. A molecule with an uneven distribution of charge is referred to as a polar molecule! How can we tell an element's electronegativity?

6 Intermolecular Forces If a molecule is polar, or if it is particularly large, forces between different molecules play an important role in their behaviour. The most important intermolecular forces in biology are hydrogen bonds. Hydrogen bonds: Hydrogen often forms strongly polar bonds with electronegative elements like oxygen and nitrogen. The positively charge hydrogen atoms in these bonds will attract any nearby negative charges. These may be charges on a different molecule or a different region of the same molecule. van der Waal Interactions: Intermolecular forces are collectively known as van der Waal forces. Most are extremely weak, however their cumulative effect becomes important for increasingly larger molecules.