Chapter 2 – Chemistry of Life

Basic Chemistry – Atoms to Molecules Matter is anything that takes up space and has mass. Matter can exist as a solid, a liquid, or a gas. An element is one of the basic building blocks of matter and 92 occur naturally. Over 90% of the human body is composed of just four elements. They are: Carbon, Hydrogen, Oxygen, and Nitrogen.

The Elements Every element has a unique name and symbol. The Periodic table contains the complete list of elements. In most tables, besides the symbol used for each element, two numbers can be found within each box.

The Elements The atomic number is always the smaller number and the atomic mass number of an element is always the larger number. Their location does NOT define them.

Portion of the Periodic Table Figure 2.1 – Page 21

What is an Atom? Matter is composed of atoms, which are the smallest unit of an element. Each element is one particular type of atom that retains the physical and chemical properties of that element.

What is an Atom? Most of an atom is empty space, but each atom has a central area called the nucleus and energy levels above called electron shells. Even though an atom is small it contains even smaller parts called subatomic particles.

What is an Atom? The nucleus (central area) of the atom contains protons, which carry a positive charge and neutrons, which have no charge. The shells contain the electrons, which move about quickly and have a negative charge. Electron Proton Neutron Electron Shell Nucleus

Atomic Number and Atomic Mass The atomic number of an atom tells us the number of protons and determines which element it is. In a single atom the atomic number indirectly also tells us the number of electrons. The atomic mass number of an element is the combination of the number of protons and neutrons. The electrons have almost no mass and therefore are not counted.

Energy levels are arranged into groups called shells. An atom is most stable when the innermost shell is filled holding only 2 electrons. After that, the outermost shell of each level only needs to contain 8 electrons for the atom to be completely stable.

Figure 2.2 – Page 22

Isotopes Isotopes are atoms of the same type, so they will have the same number of protons but a different number of neutrons. Most isotopes are stable but some break down over time, release energy as rays, and are called radioisotopes. They have important uses in biology and medicine.

Low Levels of Radiation Radioactive isotopes behave the same chemically as do stable isotopes of the same element. These radioisotopes become a tracer and are used to detect molecular changes or used in obtaining color images of the body organs and tissues.

Medical uses of low-level radiation Medical uses of low-level radiation. Specific tracers such as iodine are used for imaging a body organ like the thyroid gland. Figure 2.3 – Page 22

Positron-Emission Tomography PET scan Reveals which portions of the brain are most active Figure 2.3 – Page 22

High Levels of Radiation High levels of radiation can be harmful to human health by harming cells, damaging DNA, and causing cancer. These harmful effects have also been put to good use for years to: Kill bacteria and viruses Destroy cancer cells Sterilize food Sterilize medical equipment Ensure public safety

Molecules A chemical unit called a molecule is formed when two or more atoms bond together. The atoms can be the same kind or different kinds, if the bonds are covalent. Examples: O2, N2, CO2, H2O are molecules.

NaCl and C6H12O6 are compounds A compound is present only when the combining atoms are different kinds. Examples: NaCl and C6H12O6 are compounds H2O is a molecule of water and a compound

What Joins Atoms Together? Two types of Chemical Bonds join atoms: Ionic and Covalent An important fact to understanding bonding is: Atoms need to be stable. Atoms with more than one shell are most stable when the outer shell contains eight electrons. Most atoms are lacking anywhere from 1 to 7 electrons in their outer shell.

Ionic Bond Ionic Bonding is one type of bonding between atoms that achieves stable outer shells. During an ionic reaction, atoms give up or take on electrons to achieve a stable outer shell. (Give & Take) This causes one atom to become positive (+) due to the loss of its electrons and the other becomes negative (-) due to the gain of electrons. This opposite charge attraction forms the bond. These charged particles are now called ions.

Ionic Example: In its outer shell Sodium with 1 electron is lacking 7, while Chlorine with 7 is lacking 1. A perfect give and take match. Figure 2.5 – Page 23

Ionic Bond

Ionic Bonding Animation

Covalent Bond Covalent Bonding is another type of bonding that achieves stable outer shells between atoms. During covalent bonding there is an overlapping of outermost shells and atoms are sharing electrons. These electrons spend part of their time in the outer shell of each atom; therefore, they are counted as belonging to both atoms. Each atom achieves a stable outer shell. Double and triple bonds can also form sharing pairs of electrons.

Covalent Bond

Figure 2.6 – Page 24

Covalent Bonding Animation

Bonding Activity Why was the first atom positive?

Water and Living Things Life as we know it would be impossible without water which makes up about 60-70% of the cell and body weight.

Hydrogen Bonds Water molecules are polar and bonded to one another by hydrogen bonds. Hydrogen bonds occur whenever slightly positive covalently bonded hydrogen is attracted to a slightly negatively charged atom in the vicinity. Water has + and – ends. Electrons spend more time circling oxygen.

Many characteristics are beneficial to life. Properties of Water Many characteristics are beneficial to life. • Water is a liquid at room temperature • Temperature of liquid water rises and falls slowly • Water has a high heat of evaporation (liquid to gas) • Frozen water is less dense than liquid water (ice a solid floats) • Water is cohesive and adhesive • Water is a solvent for a great number of substances.

Acids and Bases When water molecules dissociate (break up), they release an equal number of: Hydrogen ions (H+) and hydroxide ions (OH-). H2O  H+ + OH-

How Acids Differ from Bases Acidic Solutions (High H+ Concentrations) When acid substances break up in water they release hydrogen ions (H+). HCl  H+ + Cl- Compared to water, acidic solutions have more hydrogen ions (H+) than hydroxide ions (OH-). Examples are: lemon juice, vinegar, coffee.

How Acids Differ from Bases Basic Solutions (Low H+ Concentrations) When basic substances break up: Bases either take up hydrogen ions (H+) or release hydroxide ions (OH-). NaOH  Na+ + OH- Compared to water, basic solutions have more hydroxide ions (OH-) than hydrogen ions (H+). Examples are: ammonia, milk of magnesia, sodium hydroxide.

bases have a pH higher than 7. pH Scale The pH scale is used to indicate the acidity or basicity (alkalinity) of a solution. The pH scale indicates relative amounts of H+ and OH- ions in solution. The pH scales range is from 0 to 14. Acids have a pH lower than 7 and bases have a pH higher than 7. When H+ ions equal OH- ions the pH is 7 or neutral. pH is a very important variable in all chemical reactions.

pH Scale

What are Buffers? Maintaining a pH of body fluids within a narrow range is important to health. Buffers are chemicals that help prevent pH changes by taking up excess H+ and OH- ions. Example: Our blood is maintained around 7.4

Molecules of Life Four categories of organic molecules are unique to cells. The four are: Carbohydrates, Lipids, Proteins, and Nucleic Acids. They are referred to as being organic because they contain carbon and hydrogen . Organic molecules are also usually associated with living things. Each organic molecule is a macromolecule and composed of many subunits called monomers.

Carbohydrates Carbohydrates are molecules composed of three elements: carbon, hydrogen and oxygen. There is a ratio of 2:1 for hydrogen atoms to oxygen atoms. Carbohydrates function for quick and short-term energy sources in cells. Carbohydrates can be simple or complex.

Simple Carbohydrates The subunits (monomers) of carbohydrates are one ring simple sugars or monosaccharide's. Glucose is a common simple sugar and provides an immediate source of energy for cells. Fructose is another simple sugar and found in fruits. Disaccharides are two-sugar molecules made by joining two simple sugars. Examples are: Maltose – (Glucose + Glucose) Sucrose (table sugar) – (Glucose + Fructose)

Complex Carbohydrates Polysaccharides are carbohydrates made up of many glucose units. Starch in plants and Glycogen in animals are examples of polysaccharides and are readily stored forms of glucose. Cellulose is a polysaccharide found in plant cell walls and is commonly called fiber. We can not digest cellulose.

Lipids are composed of three elements: carbon, hydrogen, and oxygen. Lipids are diverse in structure and function, but they have a common characteristic, which is none can dissolve in water. Lipids are composed of three elements: carbon, hydrogen, and oxygen. Lipids contain little oxygen and consist mostly of carbon and hydrogen.

Lipids Lipids function in animal and plants cells as energy storage molecules. In our bodies lipids also insulate against heat loss and form protective cushions for organs. The most familiar lipids are those found in Fats and Oils. Emulsification is a process where chemicals called emulsifiers cause fats or oils to break up into smaller droplets and disperse in water.

Lipids Fats and oils form when the subunits (monomers) of one glycerol molecule reacts with three of the fatty acid molecules. Fats are sometimes called triglycerides because of this structure.

Saturated, Unsaturated and Trans-Fatty Acids In general, saturated fatty acids form a solid at room temperature and unsaturated fatty acids are liquids at room temperature. Trans fats are modified unsaturated fats, making them semi-solid and even more harmful to us than many natural saturated fats.

Lipids - Phospholipids Phospholipids are constructed like fats but have a phosphate group instead of a third fatty acid. They are the primary components of cellular membranes, which will be studied in Chapter 3.

Proteins are Essential to all Life Proteins are of primary importance in the structure and functions of cells. Some examples of their many functions in humans are: Support: Make up hair, nails, ligaments, tendons, skin, and muscle. Motion: Important in contracting muscles. Transport: Hemoglobin in blood transports oxygen. Defense: Antibodies in blood provide immunity. Enzymes: speed up chemical reactions. Hormones: serve as chemical messengers.

Proteins The subunits (monomers) of proteins are amino acids. There are 20 common amino acids. Proteins are composed four elements: carbon, hydrogen, oxygen, and nitrogen. Amino acids join forming a peptide bond and a single chain of amino acids is called a polypeptide.

Primary, secondary, and tertiary structure Proteins Amino acids join in various combinations and make literally thousands of different proteins. Protein molecules cannot function unless they are a specific shape. The main three levels of organization are: Primary, secondary, and tertiary structure This structural organization with be studied further in Chemistry and A&P.

Nucleic Acids Two types of nucleic acids are DNA and RNA. DNA (Deoxyribonucleic Acid) stores genetic information in cells. Each gene is DNA’s information for the sequence of amino acids in proteins. RNA (Ribonucleic Acid) is DNA’s helper in carrying out this process.

Nucleic Acids The subunits (monomers) of nucleic acids are nucleotides. Nucleotides consist of three types of molecules. The five elements found in nucleic acids are: carbon, hydrogen, oxygen, nitrogen, and phosphorus.

ATP ATP (Adenosine Triphosphate) is a modified nucleotide that contains three phosphate groups. ATP serves as the energy carrier in cells. Cells break ATP bonds to get energy when needed.