Chapter 2

The Chemistry of Life

Basic Chemistry
Chemistry is the science of matter, its properties and its interactions. Matter is anything that occupies space and mass. Three states of matter: solid, liquid, and gas. These states occur because of difference in thermal energy.

Elements and Atoms

Matter is composed of 109 known elements. Elements are pure substances that cannot be further broken down. Atom is the smallest unit of an element that still exhibits the characteristics of that element. No one has clearly seen the structure of an individual atom. We only have workable models.

Periodic Table
The periodic table is an arrangement of the elements according to the structure of their atoms. The table display the element symbols.

Atoms
The nucleus of an atom is composed of Protons (positively charged particles) and Neutrons (particles that have no charge). Electrons (negatively charged particles) constantly circle the nucleus in orbits or shells at different distances from the nucleus. Atoms from different elements vary in their subatomic particles. In an atom the number of proton and the number of electron are equal making the net charge of the atom zero.

Atoms
The number of neutrons is not always equal to the number of protons and electrons. The mass number is the sum of the protons and neutrons in the nucleus.

Chemical Bonding
The arrangement of electrons in the shells is known as the electron configuration. Most atoms are unstable and will normally bond with other atoms to become more stable. An atom is most stable when its outermost electron shells is full.

Chemical Bonding
Atoms with naturally full shells are quite stable (noble gases). Other atoms may lack one or two electrons or have one or two electrons in their outermost shells. Therefore they have to give, take or share electrons in order to have a full outermost shell. They are chemically active.

Ionic Bond
The attraction between the oppositely charged ions. Sodium Chloride Bonding.

Covalent Bond
This type of bonding involves sharing of electrons. The bonding of a water molecule is a good example.

Comparison Between Ionic and Covalent Bonds

Covalent Bonds Ionic Bonds

What is it?

Chemical bond caused by the sharing of electrons.

Chemical bond caused by the attraction between oppositely charged ions.

No definite shape One metal and one nonmetal Solid Weak

Shape Occurs between

Definite shape Two non-metals

State at room temperature Strength

Liquid or gaseous Strong

Compounds
Compound- is a substance that is made of two or more elements. Molecule- is the smallest unit of a compound that is still that compound in a natural state. Most molecules are compounds composed of different elements. Molecular Formula- expresses the number and type of atoms in a compound. (C6H12O6) Structural Formula- shows where the atoms are actually located and the arrangement of the chemical bonds.

Chemical Changes
Chemical Change
A change in which a substance loses its characteristics and changes into one or more new substances. Na is highly reactive in water and produces flammable Hydrogen. Cl is poisonous gas that is used to kill bacteria in swimming pools. Bonded together they form salt crystals essential to living things. Characteristics of all chemical changes:
Takes place in definite proportions New compounds are formed Energy is involved

Physical Change
Alteration of a substance in its state of matter and appearance without its being changed into a new substance. There is no sharing or giving of electrons. A mixture is formed when two substances are combined without chemical bonding. They can be separated by heating or by mechanical methods. Mixtures maintain the individual properties of the components of which they are made.

Physical or Chemical change??

Energy
The ability to do work or to cause change. Two types: Kinetic energyenergy of motion Potential energystored energy Potential energy can be converted into Kinetic energy.

Kinetic Molecular Energy

Each molecule has kinetic energy. Example: the molecules of your textbooks are in constant motion. The amount of thermal energy in a substance determines how fast its molecules move. We can also determine its physical state (solid, liquid or gas).

Potential Molecular Energy

Potential energy of a molecule is stored in the chemical bonds between its atoms. There are two types of chemical reactions:
Endothermic- it absorbs heat (like baking a cake) Exothermic- it gives off heat (like a burning piece of wood). A+B C+D Reactants Yield Products Ex: 12H2O + 6CO2 C6H12O6 + 6O2 If the energy is on the reactants side the chemical reaction is endothermic. If it is on the product side the chemical reaction is exothermic.

Catalysts
Many reactions are spontaneous; that is, whenever the proper substances come into contact with one another, the reaction immediately takes place. Some reaction need energy to start them.
Activation energy is the energy necessary to start a reaction. Catalysts are substances that affect the rate of a reaction but are not themselves changed in the reaction. They reduce the amount of activation energy.

Catalysts

Solutions
A solution is a homogenous mixture of one or more substances within another substance. The kinetic energy of the molecules in the solution keeps it uniformly mixed. The substance dissolved is called the solute. They are usually made of ions or small molecules. The substance in which it is dissolved is called the solvent. Water is the best solvent. The concentration of a solution is the ratio of the solute in the solvent. The more solute in the solution the greater the concentration.

Diffusion and Osmosis

They are the most important physical processes that affect organisms. They regulate the proper concentration of solutes inside and outside the cell. Diffusion is the net movement of molecule from an area of higher concentration of a substance to an are of lower concentration of that substance. When there are no longer places of higher and lower concentrations, a state of equilibrium has been reached and diffusion stops.

Diffusion and Osmosis

Osmosis is the diffusion of water molecule through a semipermeable membrane. There is no equilibrium that is reached. The water will eventually cease from passing through the membrane when there is no net gain or loss of water between the two compartments. Figures 2A.13 to 2A.18

Diffusion and Osmosis

http://youtu.be/AYNwynwaALo http://youtu.be/9QCxTf0QfTo

Organic Chemistry
Next to water organic compounds are the most common substances in living organisms. They are the result of biosynthesis which is the putting together of substances by living things. It is the process by which assimilation is accomplished.

Organic Compound
The elements C, H, O and N are the major constituents of most organic compounds. Organic compounds are based on the carbon atom and its unusual bonding characteristics. Carbon atom has four electrons in its outer shell that will readily form covalent bonds.

Carbon bonding

Organic Compound
Carbon backbone-The chain or ring upon which the remainder of the molecule is built. A carbon atom can share more than one electron with other atoms:
If a carbon shares one electron, it forms a single bond. If a carbon shares two electrons, it forms a double bond. If a carbon shares three electrons, it forms a triple bond.

Functions of Organic Compounds

Structural- used as building blocks of a cellular or extracellular structure. Enzymatic- compounds that are enzymes. Storage- compounds that store energy. Organic Compounds are often classified into four groups: carbohydrates, lipids, proteins and nucleic acids.

Enzymes
Enzymes are proteins that serve as organic catalysts that speed up chemical reactions. Enzymes lower the activation energy of the reaction. The active site on the enzyme fits the shape of the substrate. The shape of the active site of the enzyme is specific for the substrate. When the enzyme and the substrate are combined, its called the enzyme-substrate complex. This causes the chemical bonds to weaken. Enzymes are the essential keys to life. They catalyze every reaction within a living organism.

Enzymes

Carbohydrates and Lipids

Carbohydrates and lipids have the same chemical structures whether they are found in plants, animals or humans. Both are organic compound Both store energy; lipids store more energy.

Carbohydrates
Organic compounds that contain carbon, hydrogen and oxygen. Monosaccharide - are the basic units of carbohydrates; they are the simple sugars. They may contain as few as 3 carbon atoms. The important monosaccharide to biology are 6 carbon atoms: glucose, galactose and fructose.

Carbohydrates
Dissaccharides two monosaccharide joined together by an enzyme. The reaction is called dehydration synthesis because a water molecule is produced in the process.

Carbohydrates
When the cell needs the monosaccharide from a disaccharide, enzymes will combine the disaccharide and a water molecule to separate them. This is known as hydrolysis.

Carbohydrates
Polysaccharides a large molecule that has three or more monosaccharide. Four polysaccharides are significant to biology:
Starch one of the primary substances that plants store as food. Also, its in our diets as the major energy source. Glycogen is a branching chain of glucose molecule that is stored temporary in the liver. Cellulose are molecules much larger than starch that are made of long chains of glucose bonded in an alternating arrangement. They are important for the strength and structure of plant cell walls.

Carbohydrates
Chitin one of the most abundant polysaccharides in nature and makes up the shells of crustaceans such as shrimp, crabs and lobsters. Chitin is strong, insoluble yet extremely flexible.

Lipids
Lipids are a group of organic substances that are only soluble in organic solvents such as alcohol and acetone.
Fatty Acids the most abundant lipids which are unbranched chains of 14 to 28 carbon atoms that have a carboxyl group added to one end. The carboxyl end of the molecule is polar and attracted to water (hydrophilic). The other end is repelled by water (hydrophobic).

Fatty Acids

Lipids
Triglyceride they are formed by combining three fatty acid molecules to a molecule of glycerol (a molecule of alcohol). Phospholipids is composed of two fatty acid molecules attached to a glycerol molecule. The third carbon atom of the glycerol molecule has a phosphate group attached to it. They have a hydrophilic and a hydrophobic end. Our cells membranes are made up of them.

Phospholipids

Proteins and Nucleic Acids

Proteins are what make a person unique. Amino acids are what make proteins unique. Proteins and amino acids depend on each others, they are codependent.

Proteins
Proteins consist primarily of C, H, O and N; but they sometimes include phosphorus, sulfur and a few other elements. The basic building blocks of protein are amino acids.
There are 20 amino acids They are linked together by a peptide bond A protein is a polypeptide chain

When the proper sequence of aa is arranged, the chain twists then folds back upon itself. It forms a 3D arrangement.

Nucleic Acids
They are the hereditary material that make up our DNA and RNA. They direct the activities of a cell by guiding the formation of both structural and enzymatic proteins.