Ch. 2: Chemistry of Life

1. Ch. 2: Chemistry of Life The Chemical Context of Life

2. Matter • Matter consists of chemical elements in pure form and in combinations called compounds. Matter is anything that takes up space and has mass. • An element is a substance that cannot be broken down to other substances by chemical reactions. • A compound is a substance consisting of 2 or more elements combined in a fixed ratio.

3. Elements • About 25 of the 92 natural elements are known to be essential to life. Trace elements are those required by an organism in only minute quantities [e.g. iron (Fe) and iodine (I)]. • An element’s properties depend on the structure of its atoms. Atoms are the smallest unit of an element that still retains the property of the element. Atoms are made of protons, neutrons, and electrons.

4. Subatomic Particles • p+ and n are close together in the nucleus of the atom, and e- move quickly in a cloud around the nucleus. • The number of protons an element possesses is referred to as its atomic #, and this number is unique to every element. The mass # of an element is the sum of its protons and neutrons.

5. Molecules • The formation and function of molecules depend on chemical bonding between atoms. Chemical bonds are defined as interactions between the valence electrons of different atoms. • Atoms are held together by chemical bonds to form molecules. • A covalent bond occurs when valence electrons are shared by two atoms.

6. Bonding • Nonpolar covalent bonds occur when the electrons beings shared are shared equally between the two atoms. • In polar covalent bonds, one atom has greater electronegativity than the other, resulting in an unequal sharing of the electrons

7. Ionic Bonds • Ionic bonds are ones in which the two bonded atoms attract the shared electrons so unequally that the more electronegative atom steals the electron away from the less electronegative atom. • Ionic bonds form ionic compounds, or salts. • A charged atom or molecule is called an ion.

8. Anions and Cations • If the charge is positive, the atom is called a cation. • If the charge is negative, it is called an anion.

9. Water • In hydrogen bonds, the positively charged hydrogen atom of one molecule is attracted to the negatively charged atom of another molecule. • The polarity of water molecules results in hydrogen bonding. The properties of water are the key to its special properties.

10. Water Water is made up of one atom of oxygen and two atoms of hydrogen, bonded to form a molecule like this:

11. Water • The fact that water molecules are bent means that the opposite ends of the individual molecules have opposite charges. In other words, they are polar.

12. Water • The end bearing the oxygen atom has a partial negative charge, whereas the end bearing the hydrogen atoms has a partial positive charge. This is why water molecules form H bonds- the negatively charged oxygen atom from one water molecule is attracted to the partially positively charged hydrogen end of another water molecule.

13. Hydrogen Bonds • Each water molecule can form 4 hydrogen bonds at a time. • Four emergent properties of water contribute to earth’s fitness for life. Water molecules stay close to each other as a result of hydrogen bonding.

14. Hydrogen Bonds • When water is in its liquid form, its hydrogen bonds are very fragile. They break and re-form with high frequency. • Thus, at any instant, a substantial percentage of all the water molecules are bonded to their neighbors, making water more structured than most other liquids.

15. Hydrogen Bonds • Collectively, the hydrogen bonds hold the substance together, a phenomenon called cohesion. • Cohesion due to hydrogen bonding contributes to the transport of xylem sap form the roots to the stem of plants. • Adhesion is the clinging of one substance to another.

16. Hydrogen Bonds • Water is very adhesive because of its hydrogen bonds. It is this property of adhesion that allows water to travel up the stems of plants. • Adhesion of water to the walls of the cells helps counter the downward pull of gravity.

17. Properties of Water • Specific heat is the amount of heat required to raise or lower the temperature of a substance by 1 degree Celsius. The specific heat of water is 1 cal/gC. • Relative to other materials, the temperature of water changes less when a given amount of heat is lost or absorbed.

18. Properties of water This high specific heat makes the temperature of the earth’s oceans relatively stable and able to support vast quantities of both plant and animal life.

19. Water • Water’s solid state is less dense than its liquid state, whereas the opposite is true of most other substances. • Solid water forms a regular crystal lattice structure, in which each water molecule is hydrogen bonded to four other water molecules. • Because ice is less dense than liquid water, ice floats.

20. Water • Water is also an important solvent. • The substance that something is dissolved in is called the solvent, while the substance being dissolved is called the solute. Together they are called the solution. • Solutions in which water is the solvent are called aqueous solutions.

21. Water • Substances that are water-soluble are hydrophilic substances. These include ionic compounds, polar molecules like sugars and alcohols and some proteins, • Oils, however, are hydrophobic and nonpolar, meaning they do not dissolve in water.

22. pH • Dissociation of water molecules leads to acidic and basic conditions that affect living organisms. • When a hydrogen atom is transferred from one molecule to another, it leaves its electron and is transferred as a hydrogen ion, H+ which is a proton with a charge of +1.

23. pH • This transfer or dissociation makes the water molecule that lost its proton the hydroxide ion (OH-) and the molecule that gains the proton is a hydronium ion (H3O-). • Hydronium and hydroxide ion quantities are about equal in pure water. • But if acids or bases are added to water, this equilibrium shifts.

24. pH • Water has a pH of 7 which means it is neutral. • Buffers are substances that minimize changes in pH. They accept H+ from solution when they are in excess and donate H+ when they are depleted.