Unit 2 – The Chemical Basis of Life

I. Life requires about 25 Chemical Elements A. Elements 1. Matter – anything that occupies space and has mass 2. The various forms of matter are composed of one or more chemical elements a) Element- a pure substance that cannot be broken down into other substances by chemical means

3. About 25 elements are essential to life.

a) Oxygen (O), Carbon (C), Hydrogen (H), and Nitrogen (N) make up about 96% of the living matter in your body. b) Calcium (Ca), Phosphorus (P), Potassium (K), Sulfur (S), and a few other elements account for most of the remaining 4%.

c) Trace elements are elements that make up less than 0.01% of your body mass, but are critical to your health 1) Example: Iron (Fe); essential for carrying oxygen in your blood

B. Compounds 1. A compound is a substance containing two or more elements that are chemically combined in a fixed ratio.

a) Example: water (H 2 O) 2. A compound’s properties may differ greatly from those of its component elements.

a) Example: Salt (NaCl)

II. Chemical properties are based on the structure of atoms A. Atoms 1. An atom is the smallest possible particle of an element a) comes from the Greek word atomos meaning “indivisible”

2. Structure of the atom a) Proton- a subatomic particle with a positive charge (+); found in the nucleus b) Electron- a subatomic particle with a negative charge (-); found outside the nucleus in energy levels c) Neutron- a subatomic particle that is neutral (no charge); found in the nucleus d) Nucleus- the center of the atom containing protons and neutrons

Neutrons Color Purple Protons + Color Green E E E Electrons (E-) E Color Red N P+ P+ N N P+ N P+ N P+ N Nucleus E Energy Level – Color Blue

3. Atomic Number- the number of protons in an atom’s nucleus; also the number of electrons a) Left alone, an atom tends to hold as many electrons as protons b) The number of electrons is NOT constant like the number of protons 1) The number of electrons determines how the atom interacts with other atoms 2) The number of protons determines the atom’s properties 4. Atomic Mass- the number of protons plus the number of neutrons

B. Isotopes 1. Isotopes of an element have the same number of protons in their atoms but different numbers of neutrons.

a) Example:

C. Electrons and Reactivity 1. An atom’s electrons determine how it reacts with other atoms.

a) Electrons differ in the amount of energy they have and how tightly they are held by the protons in the nucleus.

b) Electrons in the highest energy level of an atom determine how that atom reacts.

1) The first or lowest energy level (nearest the nucleus) can hold two electrons.

2) Every energy level after the first can hold up to 8 electrons.

III. Chemical bonds join atoms to one another A. Ionic Bonds 1. An ionic bond occurs when an atom transfers an electron to another atom a) Example:

2. Ions- atoms (or groups of atoms) that have become electrically charged as a result of gaining or losing electrons

B. Covalent Bonds 1. A covalent bond forms when two atoms share electrons 2. The number of bonds an atom can form usually equals the number of additional electrons that will fill its highest energy level a) Example:

3. Molecules- two or more atoms held together by covalent bonds a) chemical formula- tells you the number and types of atoms in a molecule b) structural formula- indicates how atoms in a molecule are linked by bonds c) space-filling model- a drawing that depicts a 3-D model of a molecule

C. Chemical Reactions 1. A chemical reaction is the breaking of old bonds and the formation of new bonds that result in new substances a) Example:

b) Reactants- the starting materials for a chemical reaction c) Products- the ending materials in a chemical reaction FYI… 2. Exothermic reactions- chemical reactions that release energy 3. Endothermic reactions- chemical reactions that absorb energy

IV. Life depends on the unique properties of water A. The structure of water 1. Water is made up of 2 hydrogen atoms and one oxygen atom a) Oxygen pulls electrons much more strongly than does hydrogen. This unequal pull results in the shared electrons spending more of their time with the oxygen atom (creates a V shape).

b) The oxygen end has a slight negative charge, while the hydrogen atoms are slightly positive. This is called a polar molecule.

2. Hydrogen bond- a bond created by the weak attraction of a slightly positive hydrogen atom to a slightly negative portion of another molecule.

B. Water’s Life-Supporting Properties 1. Cohesion and Adhesion a) Cohesion – the tendency of molecules of the same kind to stick to one another 1) Example: beads of water on the outside of a glass

b) Adhesion- the attraction between unlike molecules 1) Example: Figure 4-13 Cohesion and adhesion contribute to the rise of water molecules within a tree's water transport system. The dotted lines in the diagram indicate hydrogen bonds.

3. Low Density of Ice a) Density is the amount of matter in a given volume.

b) The solid state is more dense than the liquid state.

c) This is important to living things because if ice didn’t float, bodies of water would freeze from bottom to top, trapping the fish and other organisms in a shrinking layer of water without access to nutrients.

Figure 4-15 Ice floats because its molecules are less densely packed than those in liquid water.

C. Water’s ability to Dissolve other substances a) Solution- a uniform mixture of two or more substances 1) Solvent- the substance that dissolves the other substance 2) Solute- the substance that is dissolved

b) Aqueous solution- a solution in which water is the solvent 1) Water is the main solvent in all cells, blood, and plant sap Figure 4-16 Sodium chloride dissolves as Na+ and Cl- ions become attracted to water molecules and break away from the surface of the solid.

D. Acids, Bases, and pH 1. Acid- A compound that donates H+ ions to a solution 2. Base- A compound that removes H+ ions from an aqueous solution 3. pH scale-describes how acidic or basic a solution is

a) pH scale ranges from 0 to 14, with 0 being the most acidic and 14 being the most basic.

b) Pure water and aqueous solutions that have equal amounts of H+ and OH- ions are said to be neutral (pH of 7).

4. Buffers- substances that cause a solution to resist changes in pH; works by accepting H+ ions when their levels rise and donating H+ ions when their levels fall

V. Carbon is the main ingredient of Organic molecules A. Carbon Skeletons and Functional Groups 1. Carbon has 4 electrons in its highest energy level, which means they can form up to 4 bonds with other atoms.

2. Most carbon-based molecules are organic molecules; non carbon-based molecules are classified as inorganic molecules.

3. Carbon can also bond with atoms of other elements a) Hydrocarbons- organic molecules that are composed of only carbon and hydrogen

4. Functional group- a group of atoms within a molecule that interacts in predictable ways with other molecules a) Hydrophilic- molecules that attract water molecules (hydroxyl groups)

B. Monomers and Polymers 1. Monomers – small molecular unit that is the building block of a larger molecule 2. Polymers- long chains of small molecular units (monomers) a) Every living cell has thousands of different kinds of polymers and yet all of these polymers are built from a collection of fewer than 50 kinds of monomers.

C. Building and Breaking Polymers 1. Each time a monomer is added to a chain, a water molecule is released; this is called dehydration synthesis.

2. Cells break bonds between monomers by adding water to them; this is called hydrolysis reaction.

Figure 5-4 In the dehydration reaction, two monomers bond to each other, making a polymer chain longer. The hydroxyl group of one monomer reacts with a hydrogen atom from the other monomer. The reactions involved ultimately release a water molecule.

Figure 5-5 In the hydrolysis reaction, the addition of a water molecule breaks the polymer chain.

VI. Carbohydrates provide fuel and building material A. Sugars 1. Carbohydrate- an organic compound made up of sugar molecules a) contains the elements carbon, hydrogen, and oxygen in the ratio of 1 carbon: 2 hydrogen: 1 oxygen b) the carbon skeletons of carbohydrates have a ring shape

2. Monosaccharides- simple sugars that contain just one sugar unit a) Examples: glucose, fructose, and galactose b) Sugar molecules, particularly glucose, are the main fuel supply for cellular work

Figure 5-6 The complete structural diagram of the monosaccharide glucose (left) shows all its atoms. The simplified representation (right) shows just the core ring formed by some of the carbon and oxygen atoms. Ring shapes are common in sugar molecules found in nature.

3. Disaccharides- consists of 2 monosaccharides (double sugar) a) the most common disaccharide is sucrose; consists of a glucose molecule linked to a fructose molecule 1) major carbohydrate in plant sap

Figure 5-7 Sucrose is a disaccharide (double sugar) consisting of two monosaccharides linked together.

B. Polysaccharides 1. Polysaccharides are long polymer chains made up of simple sugar monomers a) Starch is a polysaccharide found in plant cells 1) Examples: potatoes, rice, and corn are all rich in starch

b) Animal cells store excess sugar in the form of glycogen; this is stored as granules in liver and muscle cells.

c) Cellulose serves as a building material in plants; they protect cells and stiffen the plant.

1) Most animals cannot digest cellulose because they lack the molecule necessary to break the bonds between the glucose monomers in cellulose.

2) Cellulose is referred to as fiber and serves to keep the digestive system healthy.

d) Almost all carbohydrates are hydrophilic; this is due to the many hydroxyl groups in their sugar units. Therefore, monosaccharides and disaccharides dissolve readily in water.

Figure 5-8 Glycogen, cellulose, and starch are three types of polysaccharides found in food. Though all three polymers are composed of the same monomer, glucose, the way the glucose monomers link together is different for each.

VII. Lipids include Fats and Steroids A. Characteristics of Lipids 1. One of a class of water-avoiding compounds a) Water-avoiding molecules are said to be hydrophobic B. Fats 1. Consists of a three-carbon backbone called glycerol attached to three fatty acids

a) Saturated fat- a fat in which all 3 fatty acid chains contain the maximum possible number of hydrogen atoms 1) Diets rich in this type of fat are said to be unhealthy because they promote the buildup of lipid-containing deposits called plaques, within the walls of blood vessels. 2) They are solid at room temperature 3) Examples: lard, butter

b) Unsaturated fat- a fat that contains less than the maximum number of hydrogen atoms in one or more of its fatty acid chains because some of its carbon atoms are double-bonded to each other 1) Examples: Vegetable oil, corn oil, olive oil; fats in fruits, vegetables, and fish

C. Steroids 1. Classified as lipids because they are hydrophobic, but they are different from fats in structure and function.

a) Example: estrogen, testosterone, cholesterol 2. The best-known steroid is cholesterol. This is an essential molecule found in the membranes that surround your cells.

Figure 5-10 The only difference in these two steroid hormones is the location of their functional groups. Yet, these two molecules contribute to major differences in the appearance and behavior of male and female mammals.

VIII. Proteins perform most functions in cells A. The Functions of Proteins 1. A protein is a polymer constructed from a set of just 20 kinds of monomers called amino acids.

a) responsible for almost all of the day-to-day functioning of organisms 1) example: hair, fur, make up muscles, and provide long-term nutrient storage

B. Amino Acids 1. An amino acid monomer consists of central carbon atom bonded to four partners. One partner is a hydrogen atom. Two others are a carboxyl group and an amino group.

2. What is different about each amino acid is the “side group” called the R group.

Figure 5-12 All amino acids consist of a central carbon bonded to an amino group, a carboxyl group, and a hydrogen atom. The fourth bond is with a unique side group. The differences in side groups convey different properties to each amino acid.

C. Building a Protein 1. Polypeptide- a chain of linked amino acids 2. Each link is created by a dehydration reaction between the amino group of one amino acid and the carboxyl group of another amino acid.

3. The protein “alphabet” consists of 20 “letters” or amino acids.

a) each protein has its own unique sentence of amino acids

Figure 5-13 The order of amino acids makes each polypeptide unique. There are 129 amino acids in this protein, called lysozyme. The three-letter symbols are abbreviations for the amino acid names.

D. Protein Shape 1. The shape of a protein is influenced by the following: a) temperature b) pH c) other qualities of its environment 1) denaturation- loss of normal shape of a protein due to heat or other factor

IX. Enzymes are proteins that speed up specific reactions in cells A. Enzymes and Activation Energy that 1. To start a chemical reaction, it is first necessary to weaken chemical bonds in the reactant molecules. This activation process requires the molecules absorb energy.

a) activation energy- the minimum amount of energy required to trigger a chemical reaction

2. Catalysts- compounds that speed up chemical reactions a) The main catalysts of chemical reactions in organisms are specialized proteins called enzymes.

1) An enzyme doesn’t supply activation energy, but instead lowers the energy requirement barrier so that the reaction can proceed at normal cell temperatures 2) Each enzyme catalyzes a a specific kind of chemical reaction

Figure 5-15 The activation energy barrier is like a wall between two parts of a pond. If an enzyme lowers the wall, more frogs have enough energy to reach the other side.

B. How enzymes work 1. The substrate of each enzyme fits the active site (like a key in a lock) a) substrate- specific reactant acted on by an enzyme b) active site- region of an enzyme into which a particular substrate fits

Figure 5-16 A substrate binds to an enzyme at an active site. The enzyme substrate interaction lowers the activation energy required for the reaction to proceed. In this example, water is added to the weakened bond in sucrose, breaking sucrose into glucose and fructose.