UNIT 1: Biochemistry Chapter 1: The Biochemical Basis of life pg. 6 69 1.1: The Fundamental Chemistry of Life pg. 8 18 The properties of life are based on the hierarchical arrangement of chemical parts. Matter makes up everything, it has mass and volume. Elements are composed of matter. Elements are pure substances and can not be broken down into smaller substances. Elements are composed of atoms. There are different types of elements they differ in their atomic structure. Molecules are created when atoms are arranged in fixed ratios, such as; O 2, and H 2 gas. Compounds are created when different elements are combined together in fixed ratios, held together by chemical bonds (covalent or ionic), such as; H 2 O or CO 2. Living organisms are primarily composed of organic compounds (carbon containing), such as; carbon (C), Oxygen (O), and Hydrogen (H), and can also contain Nitrogen (N), and Phosphate (P). Organizational Hierarchy: Subatomic Particles Organelles Ecosystem Atom Cell Molecule Tissues Compounds Organ Systems Biosphere Organisms
Atomic Structure Elements are made up of atoms, which are the smallest unit that maintains the chemical and physical properties of the element. An atom is made up of three different sub atomic particles; neutrons (no charge), protons (positive charge), and electrons (negative charge). Atomic number is the number of protons found in the nucleus of the atom. It determines the particular atom identity. (Periodic Table) Atomic mass is the sum of the number of protons and neutrons found in the nucleus of an atom. Electrons are not found within the nucleus and do not contribute to the mass of the atom, their mass is negligible in comparison to the proton and neutron. An atom does not have an over all net charge, this is because there is an equal number of protons (positive) and electrons (negative). Table 2: Atomic Number and Mass Number Isotopes Isotope is a form of element that differs in its number of neutrons. All atoms of the same element will have the same number of protons, but may vary in the number of neutrons found within their nucleus. This will
create atoms of the same atomic number but they may have different atomic mass. Radioisotopes and Radioactive Tracers Radioisotope - is a radioactive isotope of an element. Some isotopes have a nucleus that is unstable therefore it may breakdown over time, giving off particles of matter that can be detected as radioactive. As the atoms nucleus breaks down, the atom is transformed into a different element. Examples: Hydrogen and Carbon Figure 3: Comparison of nuclei of different Isotopes Since radioisotopes react in the same way as non - radioactive isotopes of the same elements, they can be used as tracers, because they are easy to detect by the energy they are releasing. Radioactive tracers are used to follow a specific chemical through a chemical reaction. Doctors can trace the path of the chemical as it passes through cells and different locations of the body. Melvin Calvin used the radioactive tracer C 14 to determine the sequence of reactions of photosynthesis. C 14 will decomposes into nitrogen. The extra neutrons decay into a proton. The increases the proton content to seven, which is nitrogen. Beta admissions.
Half- Life Radioactive decay occurs at a steady rate. A constant proportion of radioisotopes atoms break down during a given interval. P = (0.5) t/h x mass 1. 20 g of Iodine 131 has a half life of 8 days. What is its mass after 32 days? P = (0.5) 32/8 x 20 g P = (0.5) 4 x 20 g P = 0.0625 x 20 g P = 1.25 g 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.
Table 3: Type of Electron Orbitals. 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. They form hybridized electron orbitals. Biological molecules are created when covalent bonds form between atoms of C, H, O, and N.
Table 4: Valence Electrons Shells Chemical Bonds Ionic Bonds Ionic Bond - is a bond that results from the attraction between two oppositely charged atoms or molecules. Cation - is an ion that has a positive charge Anion - is an ion that has a negative charge. An ionic bond is form between two elements that have lost or gain electrons, creating charged particles (ions), and oppositely charged particles attract. Alkali and Alkaline Earth metals take on positive charges and Halogens take on a negative charge. (Metals are attracted to non metals) Covalent Bonds Covalent bond - is a bond between two elements that share two or more pairs of electrons. The strength of these bonds is determined by the electronegativity of each atom. Electronegativity - is the measure of an atom s attraction to share electrons. Molecular diagrams use dashes or dots to represent covalent bonds between atoms. The number of covalent bonds formed between atoms depends on the number of valence electrons available to be shared.
Carbon has four valence electrons, therefore carbon can form four single covalent bonds, with hydrogen, or two double covalent bonds with oxygen. Figure 6: Lewis dot diagram showing the structure of methane CH4 Table 5: Orbital and VSEPR models VSEPR valence shell electron pair repulsion is a theory used to predict the arrangement of the bond angles, developed by Ronald L Gillespie. Polar Molecules Polar covalent bond - is a bond between two atoms, make up of unequally shared electrons. Polarity is partial positive or negative charge at the ends of a molecule. Covalent bond deals with the sharing of electrons between atoms, there can be an unequal sharing between these atoms. The greater the electronegativity that atom has, the greater the attraction to an electron from another atom. The unequal sharing of electrons between two atoms, with two different electronegativities, will result in a polar covalent bond. An atom which attracts the valence electron more strongly then the other atom will carry a partial negative charge, while the other will have a partial
positive charge. This will create a molecule with a non-uniform charge distribution. A water molecule is a polar molecule, created by the unequal sharing of electrons. Oxygen takes on a negative charge and the hydrogen is slightly positive. Polar molecules are attracted to other polar molecules. These molecules are also very soluble in water. Intermolecular Forces Intermolecular forces are forces of attraction between two molecules and these forces are known as van der Waals forces. Intermolecular force - is the force of attraction between two molecules. Van der Waals forces - are very weak attractions between two molecules, or parts of molecules, when they are close together. (London force, dipoledipole force, and hydrogen bonds) Hydrogen Bonds Hydrogen bond - is the attractive force between a partially positively charge hydrogen atom and a partially negatively charged atom in another molecule. When a hydrogen atom is covalently bonded to a strong electronegative atom in one molecule, a polar molecule is created. When two polar molecules are attracted to each other because of the positively charged hydrogen of one molecule is attracted to the negatively charge oxygen, nitrogen, or fluorine found in another molecule, a hydrogen bond is created.
Other Van Der Waals Forces London forces is the weakest of all van der Waals forces. It is the attraction between non polar molecules Dipole-dipole occur between polar molecules.
Summary of van der Waals Forces Chemical Reactions Dehydration reaction - is a chemical reaction in which subunits of a larger molecule are joined by the removal of water, also called a condensation reaction. Hydrolysis reaction - is a chemical reaction in which water is used as a reactant to split a larger molecule into smaller subunits.
Neutralization reaction - is a reaction which an acid and a base combine to create a salt and water. Redox reaction - is an electron transfer reaction. Oxidation - is a reaction in which a molecule loses electrons. Reduction - is a reaction in which a molecule gains electrons.