Elements and Atoms: The Building Blocks of Matter

Elements and Compounds

• All matter in the natural world is composed of one or more of the 92 fundamental substances called elements.

• An element is a pure substance that is distinguished from all other matter by the fact that it cannot be created or broken down by ordinary chemical means.

• A compound is a substance composed of two or more elements joined by chemical bonds.

  • For example, the compound glucose is an important body fuel.

    • It is always composed of the same three elements: carbon, hydrogen, and oxygen.

Atoms and Subatomic Particles

• An atom is the smallest quantity of an element that retains the unique properties of that element.

• Atoms are made up of even smaller subatomic particles, three types of which are important: the proton, neutron, and electron.

Atomic Number and Mass Number

• Atomic number, which is the number of protons in the nucleus of the atom, identifies the element.

  • Because an atom usually has the same number of electrons as protons, the atomic number identifies the usual number of electrons as well.

• Mass number is the sum of the number of protons and neutrons in its nucleus.

• Periodic table of the elements, is a chart identifying the 92 elements found in nature, as well as several larger, unstable elements discovered experimentally.

Isotopes

• An isotope is one of the different forms of an element, distinguished from one another by different numbers of neutrons.

  • An isotope that contains more than the usual number of neutrons is referred to as a heavy isotope.

• A radioactive isotope is an isotope whose nucleus readily decays, giving off subatomic particles and electromagnetic energy.

  • Different radioactive isotopes (also called radioisotopes) differ in their half-life, the time it takes for half of any size sample of an isotope to decay.

The Behavior of Electrons

• An electron shell is a layer of electrons that encircle the nucleus at a distinct energy level.

  • The atoms of the elements found in the human body have from one to five electron shells, and all electron shells hold eight electrons except the first shell, which can only hold two.

• A valence shell is an atom’s outermost electron shell. If the valence shell is full, the atom is stable; meaning its electrons are unlikely to be pulled away from the nucleus by the electrical charge of other atoms.

  • If the valence shell is not full, the atom is reactive; meaning it will tend to react with other atoms in ways that make the valence shell full.

Chemical Bonds

• A bond is a weak or strong electrical attraction that holds atoms in the same vicinity.

• A more or less stable grouping of two or more atoms held together by chemical bonds is called a molecule.

• When a molecule is made up of two or more atoms of different elements, it is called a chemical compound.

Ions and Ionic Bonds

• An atom that has an electrical charge—whether positive or negative—is an ion.

• A positively charged ion is known as a cation.

• A negatively charged ion is known as an anion.

• An ionic bond is an ongoing, close association between ions of opposite charge.

Covalent Bonds

• Unlike ionic bonds formed by the attraction between a cation’s positive charge and an anion’s negative charge, molecules formed by a covalent bond share electrons in a mutually stabilizing relationship.

Nonpolar Covalent Bonds

• Nonpolar covalent bonds are a type of chemical bond where two atoms share electrons equally.

  • This type of bond does not create a net charge, and is usually found in molecules with similar electronegativities.

Polar Covalent Bonds

• A polar molecule is a molecule that contains regions that have opposite electrical charges.

• Polar molecules occur when atoms share electrons unequally, in polar covalent bonds.

Hydrogen Bonds

• A hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another molecule.

• In other words, hydrogen bonds always include hydrogen that is already part of a polar molecule.

Chemical Reactions

The Role of Energy in Chemical Reactions

• Chemical reactions require a sufficient amount of energy to cause the matter to collide with enough precision and force that old chemical bonds can be broken and new ones formed.

• In general, kinetic energy is the form of energy powering any type of matter in motion. Imagine you are building a brick wall.

• Potential energy is the energy of position, or the energy matter possesses because of the positioning or structure of its components.

• Chemical energy is the form of potential energy in which energy is stored in chemical bonds.

Characteristics of Chemical Reactions

• All chemical reactions begin with a reactant, the general term for the one or more substances that enter into the reaction.

• Sodium and chloride ions, for example, are the reactants in the production of table salt.

  • The one or more substances produced by a chemical reaction are called the product.

• A synthesis reaction is a chemical reaction that results in the synthesis (joining) of components that were formerly separate.

• A decomposition reaction is a chemical reaction that breaks down or “de-composes” something larger into its constituent parts.

• An exchange reaction is a chemical reaction in which both synthesis and decomposition occur, chemical bonds are both formed and broken, and chemical energy is absorbed, stored, and released.

Factors Influencing the Rate of Chemical Reactions

• Properties of the Reactants

  • The properties of reactants in chemical reactions include their physical and chemical properties, such as their reactivity, solubility, and boiling point.

  • Reactants also have different amounts of energy, which can affect the rate and outcome of a reaction.

• Temperature

  • Increasing the temperature of a reaction can increase the rate of reaction, while increasing the concentration of reactants can also increase the rate of reaction.

  • Increasing the surface area of reactants can also increase the rate of reaction, as more molecules can come into contact with each other.

• Concentration and Pressure

  • Increasing the concentration of particles—the number of particles in the space—but also by decreasing the volume of the space, which would correspondingly increase the pressure.

• Enzymes and Other Catalysts

  • A catalyst is a substance that increases the rate of a chemical reaction without itself undergoing any change.

  • An enzyme is a catalyst composed of protein or ribonucleic acid (RNA).

  • A chemical reaction’s activation energy is the “threshold” level of energy needed to break the bonds in the reactants.

Inorganic Compounds Essential to Human Functioning

• An inorganic compound is a substance that does not contain both carbon and hydrogen.

• An organic compound, then, is a substance that contains both carbon and hydrogen.

Water

• Adults are 70% water.

• Water is inside and between tissues and organ cells.

• Water is essential to human life.

Water as a Lubricant and Cushion

• Many body lubricants contain water.

• Water in synovial fluid lubricates joints and pleural fluid helps the lungs expand and contract.

• Watery fluids keep food flowing through the digestive tract and stomach organs from rubbing.

• Water protects the brain and ocular nerve tissue.

  • Water shields fetuses.

Water as a Heat Sink

• Heat sinks transfer heat without raising temperature.

• Water cools chemical reactions without elevating body temperature.

• Water cools the body.

• Warm core blood cools the surroundings in skin blood vessels.

• Sweat glands heat water.

• Water evaporates into the air, cooling the blood, which returns to the center.

Water as a Component of Liquid Mixtures

• A mixture is a combination of two or more substances, each of which maintains its own chemical identity.

• A liquid solution consists of a solvent that dissolves a substance called a solute.

  • An important characteristic of solutions is that they are homogeneous; that is, the solute molecules are distributed evenly throughout the solution.

• Water is considered the “universal solvent” and it is believed that life cannot exist without water because of this.

• Nonpolar molecules, which do not readily dissolve in water, are called hydrophobic, or “water-fearing.”

Concentrations of Solutes

• A colloid is a mixture that is somewhat like a heavy solution.

• A suspension is a liquid mixture in which a heavier substance is suspended temporarily in a liquid, but over time, settles out.

The Role of Water in Chemical Reactions

• Two types of chemical reactions involve the creation or the consumption of water: dehydration synthesis and hydrolysis.

• Dehydration synthesis is a type of chemical reaction in which two molecules are joined together by the removal of a water molecule.

  • This reaction is also known as a condensation reaction.

• Hydrolysis is a chemical reaction in which a molecule is broken down into two parts by the addition of a molecule of water.

  • It is a type of chemical reaction that is used to break down complex molecules into simpler ones.

Acids and Bases

Acids

• An acid is a substance that releases hydrogen ions (H+) in solution.

• Weak acids do not ionize completely; that is, some of their hydrogen ions remain bonded within a compound in solution.

• Bases: A base is a substance that releases hydroxyl ions (OH–) in solution, or one that accepts H+ already present in solution.

Buffers

• A buffer is a solution of a weak acid and its conjugate base.

• A buffer can neutralize small amounts of acids or bases in body fluids.

Organic Compounds Essential to Human Functioning

The Chemistry of Carbon

• A functional group is a group of atoms linked by strong covalent bonds and tending to function in chemical reactions as a single unit.

Functional Groups Important in Human Physiology

Carbohydrates

• The term carbohydrate means “hydrated carbon.”

• A carbohydrate is a molecule composed of carbon, hydrogen, and oxygen; in most carbohydrates, hydrogen and oxygen are found in the same two-to-one relative proportions they have in water.

• Carbohydrates are referred to as saccharides, a word meaning “sugars.”

• Monosaccharides are the monomers of carbohydrates.

  • Five monosaccharides are important in the body: Glucose, Fructose, Galactose, Deoxyribose, Ribose.

• Disaccharides (di- = “two”) are made up of two monomers.

  • Sucrose, Lactose, Maltose

• Polysaccharides are the polymers, and can consist of hundreds to thousands of monomers.

  • Starches are polymers of glucose.

  • Glycogen is also a polymer of glucose, but it is stored in the tissues of animals, especially in the muscles and liver.

  • Cellulose, a polysaccharide that is the primary component of the cell wall of green plants, is the component of plant food referred to as “fiber”.
    

Functions of Carbohydrates

• Adenosine triphosphate (ATP) is composed of a ribose sugar, an adenine base, and three phosphate groups.

• Lipids: A lipid is one of a highly diverse group of compounds made up mostly of hydrocarbons.

• Triglycerides: A triglyceride is one of the most common dietary lipid groups, and the type found most abundantly in body tissues.

• Phospholipids: A phospholipid is a bond between the glycerol component of a lipid and a phosphorus molecule.

• Steroids: A steroid compound (referred to as a sterol) has as its foundation a set of four hydrocarbon rings bonded to a variety of other atoms and molecules.

• Prostaglandins: A prostaglandin is one of a group of signaling molecules, but prostaglandins are derived from unsaturated fatty acids.

• Proteins: A protein is an organic molecule composed of amino acids linked by peptide bonds.

Microstructure of Proteins

• Proteins are polymers made up of nitrogen-containing monomers called amino acids.

• An amino acid is a molecule composed of an amino group and a carboxyl group, together with a variable side chain.

• A peptide bond is a covalent bond between two amino acids that forms by dehydration synthesis.

• A disulfide bond is a covalent bond between sulfur atoms in a polypeptide.

• Denaturation is a change in the structure of a molecule through physical or chemical means.

Proteins Function as Enzymes

• A substrate is a reactant in an enzymatic reaction.

  • This occurs on regions of the enzyme known as active sites.

Nucleotides

A nucleotide is one of a class of organic compounds composed of three subunits:

• One or more phosphate groups

• A pentose sugar: either deoxyribose or ribose

• A nitrogen-containing base: adenine, cytosine, guanine, thymine, or uracil

Nucleic Acids

• Deoxyribonucleic acid (DNA) is a nucleotide that stores genetic information.

• Ribonucleic acid (RNA) is a ribose-containing nucleotide that helps manifest the genetic code as protein.

• A purine is a nitrogen-containing molecule with a double ring structure, which accommodates several nitrogen atoms.

• A pyramidine is a nitrogen-containing base with a single ring structure.

• Adenosine Triphosphate: Phosphorylation is the addition of a phosphate group to an organic compound, in this case, resulting in ATP.