Chapter 2:  The Chemical Level of Organization



In this chapter, you will learn how atoms are bound together to form molecules, the building blocks of cells.


2–1  Atoms, Molecules, and Bonds

 The smallest stable units of matter are called atoms .  Atoms are composed of subatomic particles . Only three are important for understanding the chemical properties of matter: protons, neutrons , and electrons . Protons and neutrons are similar in size and mass, but protons (p+) bear a positive electrical charge, whereas neutrons (n ) are electrically neutral , or uncharged. Electrons are much lighter than protons–only 1/1836th as massive–and bear a negative electrical charge (e-).


Atomic Structure
Atoms normally contain equal numbers of protons and electrons. The number of protons in an atom is known as its atomic number . Hydrogen (H) is the simplest atom, with an atomic number of 1. Thus, an atom of hydrogen contains one proton, and it contains one electron as well.



The electrons occupy a circular electron shell .


The negatively charged electron is attracted to the positively charged proton. The attraction between opposite electrical charges is an example of an electrical force . As you will see in later chapters, electrical forces are involved in many physiological processes.


Atoms are so small that atomic measurements are most conveniently reported in nanometers (nm). One nanometer is one thousandth of a micrometer, or equal to 0.000000001 m, also equal to one billionth of a meter.


Elements and Isotopes
Atoms can be classified on the basis of their atomic number into groups called elements . Only 92 elements exist in nature. Every element has a chemical symbol : (O for oxygen, N for nitrogen, C for carbon, and so on), but a few are abbreviations of their Latin names. For example, the symbol for sodium, Na, comes from the Latin word natrium .




The atoms of a single element can differ in terms of the number of neutrons in the nucleus. Atoms whose nuclei contain the same number of protons, but different numbers of neutrons, are called isotopes . The mass number –the total number of protons plus neutrons in the nucleus–is used to designate a particular isotope. Thus, the three isotopes of hydrogen are hydrogen–1, or with one proton and one electron; hydrogen–2, or also known as deuterium , with one proton, one electron, and one neutron; and hydrogen–3, also known as tritium , with one proton, one electron, and two neutrons.


Atomic Weights
A typical atom of oxygen , which has an atomic number of 8, contains eight protons, but it also contains eight neutrons. The mass number of this isotope is therefore 16. Mass numbers are useful because they tell us the number of subatomic particles in the nuclei of different atoms. However, they do not tell us the actual mass of the atoms. For example, they do not take into account the masses of the electrons or the slight difference between the mass of a proton and that of a neutron. The actual mass of an atom is known as its atomic weight . The unit used to express the atomic weight is the dalton (also known as the atomic mass unit , or amu ).


Electrons and Energy Levels
Atoms are electrically neutral; every positively charged proton is balanced by a negatively charged electron. Within the electron cloud, electrons occupy an orderly series of energy levels . The first energy level can hold at most two electrons, while the next two levels can each hold up to eight electrons. The outermost energy level forms the "surface" of the atom. The number of electrons in this level determines the chemical properties of the element. Atoms with unfilled energy levels are unstable–that is, they will react with other atoms, usually in ways that give them full outer electron shells. In contrast, atoms with a filled outermost energy level are stable and therefore do not readily react with other atoms.


Atoms with filled energy levels are commonly referred to as “inert”. The most righthand column of the periodic table contains the six naturally occurring elemental inert gases, Helium, Neon, Argon, Krypton, Xenon, and Radon. While inert, radon is not “safe” since it is radioactive.




A hydrogen atom has one electron in the first energy level, and the level is thus unfilled. A hydrogen atom readily reacts with other hydrogen atoms or with the atoms of other elements. A helium atom has two electrons in its first energy level. Because its outer energy level is filled, a helium atom is very stable; it will not ordinarily react with other atoms.


These are important- learn them by name and symbol.



Chemical Bonds


Elements with unfilled outermost energy levels, such as hydrogen and lithium, are called reactive.

The interactions often involve the formation of chemical bonds.

When chemical bonding occurs, the result is the creation of new chemical entities that we call molecules and compounds . The term molecule refers to any chemical structure consisting of atoms held together by covalent bonds. A compound is any chemical substance made up of atoms of two or more elements (such as a mixture of powdered sugar and salt). Most biologically important compounds, from water to DNA, are molecular.


 Ionic Bonds form between ions. Ions are atoms or molecules that carry an electric charge, either positive or negative. Ions with a positive charge are called cations; ions with a negative charge are called anions. Ionic bonds are chemical bonds created by the electrical attraction between anions and cations. Atoms become ions by losing or gaining electrons.


In the formation of an ionic bond,

When placed in water most ionic compounds dissolve, and the component anions and cations separate.

Covalent Bonds
Some atoms can complete their outer electron shells not by gaining or losing electrons, but by sharing electrons with other atoms. Such sharing creates covalent bonds between the atoms involved.

Molecular hydrogen consists of a pair of hydrogen atoms. The two hydrogen atoms share their electrons, and each electron whirls around both nuclei. The oxygen atoms in a carbon dioxide molecule form double covalent bonds with the carbon atom.


Covalent bonds usually form molecules that complete the outer energy levels of the atoms involved. An ion or molecule that contains unpaired electrons in its outermost energy level is called a free radical . Free radicals are highly reactive. Almost as fast as it forms, a free radical enters additional reactions that are typically destructive.

It has been suggested that the cumulative damage produced by free radicals inside and outside our cells is a major factor in the aging process.


Nonpolar Covalent Bonds Covalent bonds are very strong, because the shared electrons hold the atoms together. Bonds between two atoms of the same type, are called nonpolar covalent bonds . Nonpolar covalent bonds, especially those between carbon atoms, create the stable framework of the large molecules that make up most of the structural components of the human body.


Polar Covalent Bonds Covalent bonds involving different types of atoms may instead involve an unequal sharing of electrons, because the elements differ in how strongly they attract electrons. An unequal sharing of electrons creates a polar covalent bond.


Polar Covalent Bonds and the Structure of Water.
(a) In forming a water molecule, an oxygen atom completes its outermost energy level by sharing electrons with a pair of hydrogen atoms. The sharing is unequal, because the oxygen atom holds the electrons more tightly than do the hydrogen atoms. (b) Because the oxygen atom has two extra electrons much of the time, it develops a slight negative charge, and the hydrogen atoms become weakly positive. The bonds in a water molecule are polar covalent bonds.


Hydrogen Bonds

There are also comparatively weak forces that act between adjacent molecules and even between atoms within a large molecule. The most important of these weak attractive forces is the hydrogen bond. A hydrogen bond is the attraction between a positve charge  on the hydrogen atom of a polar covalent bond and a negative charge on an oxygen or nitrogen atom of another polar covalent bond.



At the water surface, the attraction between molecules slows the rate of evaporation and creates the phenomenon known as surface tension. Surface tension acts as a barrier that keeps small objects from entering the water.


States of Matter
Matter in our environment exists in one of three states: solid, liquid, or gaseous. Whether a particular substance is a solid, a liquid, or a gas depends on the degree of interaction among its atoms or molecules. For example, hydrogen molecules have little attraction for one another; in our environment, molecular hydrogen exists as a gas. Water is the only substance that occurs as a solid (ice), a liquid (water), and a gas (water vapor) at temperatures compatible with life.


2–2  Chemical Reactions

 Cells remain alive and functional by controlling chemical reactions. In a chemical reaction , new chemical bonds form between atoms, or existing bonds between atoms are broken.


Types of Reactions


Decomposition is a reaction that breaks a molecule into smaller fragments. In hydrolysis, one of the bonds in a complex molecule is broken, and the components of a water molecule (H and OH) are added to the resulting fragments:


Decomposition reactions of complex molecules within the body's cells and tissues are referred to as catabolism.


Synthesis is the opposite of decomposition. A synthesis reaction assembles larger molecules from smaller components. Synthesis always involves the formation of new chemical bonds. Dehydration synthesis , or condensation , is the formation of a complex molecule by the removal of water: Dehydration synthesis is therefore the opposite of hydrolysis.


Synthesis of new compounds within the body's cells and tissues is known as anabolism. Because it takes energy to create a chemical bond, anabolism is usually an "uphill" process.


Reversible Reactions
Chemical reactions are (at least theoretically) reversible. Not all chemical reactions, however, are easily reversed. The requirements for two paired reactions may differ, so at any time and place the overall reaction will proceed chiefly in one direction only. For example, the synthesis reaction may occur only when A and B molecules are heated; the decomposition reaction may occur only when AB molecules are placed in water.


Enzymes, Energy, and Chemical Reactions
Most chemical reactions do not occur spontaneously, or they occur so slowly that they would be of little value to cells. Before a reaction can proceed, enough energy must be provided to activate the reactants. The amount of energy required to start a reaction is called the activation energy .

          Your cells use special proteins called enzymes to perform most of the complex synthesis and decomposition reactions in your body. Enzymes promote chemical reactions by lowering the activation energy requirements.



Enzymes belong to a class of substances called catalysts, compounds that accelerate chemical reactions without themselves being permanently changed or consumed. An enzyme affects only the rate of the reaction, not the direction of the reaction or the products that will be formed. Reactions that release energy (commonly as heat) are said to be exergonic. If more energy is required to begin the reaction than is released as it proceeds, the reaction as a whole will absorb energy. Such reactions are called endergonic (the surrounding environment becomes cooler). Exergonic reactions are relatively common in the body; they are responsible for generating the heat that maintains your body temperature.


2–3  Inorganic Compounds

Nutrients are the essential elements and molecules normally obtained from the diet. Metabolites include all the molecules synthesized or broken down by chemical reactions inside our bodies. Inorganic compounds generally do not contain carbon and hydrogen atoms as their primary structural ingredients, whereas carbon and hydrogen always form the basis for organic compounds . The most important inorganic compounds in the body are (1) carbon dioxide , a by–product of cell metabolism; (2) oxygen , an atmospheric gas required in important metabolic reactions; (3) water , which accounts for most of our body weight; and (4) inorganic acids, bases , and salts (like sodium chloride NaCl) – compounds held together partially or completely by ionic bonds.


Water and Its Properties
Water, is the single most important constituent of the body, accounting for up to two–thirds of total body weight. It has some highly unusual properties. These properties are a direct result of the hydrogen bonding that occurs between adjacent water molecules:

1.     Solubility. A remarkable number of inorganic and organic molecules will dissolve (break up) in water, creating a solution.

2.     Reactivity. In our bodies, chemical reactions occur in water, and water molecules are also participants in some reactions.

3.     High Heat Capacity. Heat capacity is the ability to absorb and retain heat. Water has an unusually high heat capacity, because water molecules in the liquid state are attracted to one another through hydrogen bonding.

The temperature must be quite high before individual molecules have enough energy to break free and become water vapor, a gas. Consequently, water stays in the liquid state over a broad range of environmental temperatures, and the freezing and boiling points of water are far apart.

Water carries a great deal of heat away with it when it finally does change from a liquid to a gas. So when you sweat and the water evaporates the skin is cooled, this cools the blood in the skin, which circulates and cools the interior of the body, etc.

An unusually large amount of heat energy is required to change the temperature of 1 g of water. This property is called thermal inertia. Thermal inertia helps stabilize body temperature, and allows the blood plasma to transport and redistribute large amounts of heat as it circulates within the body.

Lubrication. Water is an effective lubricant. There is little friction between water molecules. Thus, if two opposing surfaces are separated by even a thin layer of water, friction between those surfaces will be greatly reduced.

Aqueous Solutions

The water molecule has positive and negative poles. A water molecule is therefore called a polar molecule, or a dipole.

Many inorganic compounds are held together partially or completely by ionic bonds. In water, these compounds undergo ionization, or dissociation. In this process, ionic bonds are broken as the individual ions interact with the positive or negative ends of polar water molecules.

ELECTROLYTES and Body Fluids Soluble inorganic molecules whose ions will conduct an electrical current in solution are called electrolytes. Sodium chloride is an electrolyte.

 Hydrophilic and Hydrophobic Compounds

Molecules such as glucose , an important soluble sugar, that interact readily with water molecules in this way are called hydrophilic. Molecules that do not readily interact with water are called hydrophobic. Among the most familiar such molecules are fats and oils of all kinds.

Colloids and Suspensions - A solution containing dispersed proteins or other large molecules is called a colloid. A suspension contains even larger particles that will, if undisturbed, settle out of solution due to the force of gravity. Whole blood is another temporary suspension, because the blood cells are suspended in the blood plasma. If clotting is prevented, the cells in a blood sample will gradually settle to the bottom of the container.

Hydrogen Ions in Body Fluids- the pH of blood and other fluids

Hydrogen ions are extremely reactive in solution. The concentration of hydrogen ions in body fluids must be regulated precisely. The dissociation of one water molecule yields a hydrogen ion and a hydroxide ion.

The pH of a solution is defined as the negative logarithm of the hydrogen ion concentration in moles per liter. Thus, instead of using an equation we say that the pH of pure water is 7.0 or 7 (neutral pH). Using pH values saves space, but always remember that the pH number is an exponent and that the pH scale is logarithmic. For instance, a pH of 6 ( or 0.000001) means that the concentration of hydrogen ions is 10 times as great as it is at a pH of 7 ( or 0.0000001).

pH and Hydrogen Ion Concentration.
The scale is logarithmic; an increase or decrease of one unit corresponds to a tenfold change in concentration.

The pH of blood normally ranges from 7.35 to 7.45, a very narrowly controlled range to maintain homeostasis. Acidosis is an abnormal physiological state caused by low blood pH (below 7.35); a pH below 7 can produce coma. Alkalosis results from an abnormally high pH (above 7.45); a blood pH above 7.8 generally causes uncontrollable and sustained skeletal muscle contractions.

Inorganic Acids and Bases
The body contains both inorganic and organic acids and bases that may cause acidosis or alkalosis, respectively. An acid is any solute that dissociates in solution and releases hydrogen ions, thereby lowering the pH. A strong acid dissociates completely in solution. The stomach produces a powerful acid, hydrochloric acid, to assist in the breakdown of food.

A base is a solute that removes hydrogen ions from a solution and thereby acts as a proton acceptor . Sodium hydroxide , NaOH, is a strong base; in solution, it releases sodium ions and hydroxide ions:
Strong bases have a variety of industrial and household uses. Drain openers and lye are two familiar examples. The body produces a weak base, the bicarbonate ion. Weak acids and weak bases fail to dissociate completely. Carbonic acid is a weak acid found in body fluids. In solution, carbonic acid reversibly dissociates into a hydrogen ion and a bicarbonate ion.

A salt is an ionic compound consisting of any cation except a hydrogen ion (H+ ) and any anion except a hydroxide ion (OH¯ ). Sodium chloride (table salt) dissociates immediately in water, releasing and ions. Sodium and chloride are the most abundant ions in body fluids.

 Buffers and pH Control
Buffers are compounds that stabilize the pH of a solution by removing or replacing hydrogen ions. Buffer systems typically involve a weak acid and its related salt, which functions as a weak base. For example, the carbonic acid–bicarbonate buffer consists of carbonic acid and sodium bicarbonate, otherwise known as baking soda. Buffers and buffer systems in body fluids maintain the pH within normal limits.

Antacids such as Tums use sodium bicarbonate to neutralize excess hydrochloric acid in the stomach.

Organic Compounds

 Organic compounds always contain the elements carbon and hydrogen, and generally oxygen as well. Many organic molecules are made up of long chains of carbon atoms linked by covalent bonds. Many organic molecules are soluble in water. For example, lactic acid is an organic acid, generated by active muscle tissues, that must be neutralized by the buffers in body fluids.

 In this discussion, we consider four major classes of organic compounds: carbohydrates, lipids, proteins , and nucleic acids . We also introduce high–energy compounds , which are insignificant in terms of their abundance in the body but vital to the survival of our cells.

Certain groupings of atoms occur again and again, even in very different types of molecules. These functional groups greatly influence the properties of any molecule they are part of.

See Table 2-4

A carbohydrate is an organic molecule that contains carbon, hydrogen, and oxygen in a ratio near 1:2:1. Familiar carbohydrates include the sugars and starches. Carbohydrates are most important as sources of energy that are catabolized rather than stored. We will focus on monosaccharides, disaccharides , and polysaccharides .

A simple sugar , or monosaccharide, is a carbohydrate containing from three to seven carbon atoms. The atoms in a glucose molecule may form a straight chain or a ring.


In the body, the ring form is more common. Some molecules have the same molecular formula–in other words, the same types and numbers of atoms–but different structures. Such molecules are called isomers. Do not confuse isomers with ions and isotopes!! Glucose and fructose are isomers. Fructose is found in many fruits and in secretions of the male reproductive tract.

Disaccharides and Polysaccharides

Two monosaccharides joined together form a disaccharide. Disaccharides such as sucrose (table sugar) have a sweet taste and, like monosaccharides, are quite soluble in water.


The Formation and Breakdown of Complex Sugars.
These reactions are performed by enzymes in the cell.

Polysaccharide chains can be straight or highly branched. Cellulose , a structural component of many plants, is a polysaccharide that our bodies cannot digest. Foods such as celery, which contains cellulose, water, and little else, contribute to the bulk of digestive wastes but are useless as a source of energy. (In fact, you expend more energy when you chew a stalk of celery than you obtain by digesting it.)
Starches are large polysaccharides formed from glucose molecules. Most starches are manufactured by plants. Our digestive tract can break these molecules into monosaccharides. Starches such as those in potatoes and grains are a major dietary energy source.

 The Structure of a Polysaccharide.

Liver and muscle cells store glucose as the polysaccharide glycogen, a long, branching chain of glucose molecules.

Like most other starches, glycogen does not dissolve in water or other body fluids. Liver tissues and muscle tissues make and store glycogen. When these tissues have a high demand for glucose, glycogen molecules are broken down; when the demand is low, liver and muscle tissues absorb glucose from the bloodstream and rebuild glycogen reserves.

Despite their metabolic importance, carbohydrates account for less than 3 percent of our total body weight.

Like carbohydrates, lipids contain carbon, hydrogen, and oxygen, and the carbon–to–hydrogen ratio is commonly 1:2. Familiar lipids include fats, oils , and waxes . Most lipids are insoluble in water. Lipids form essential structural components of all cells. When the supply of lipids exceeds the demand for energy, the excess is stored in fat deposits. We will consider five classes of lipids: fatty acids, eicosanoids, glycerides, steroids , and phospholipids and glycolipids .


Fatty Acids
Fatty acids are long carbon chains with hydrogen atoms attached. One end of the carbon chain always bears a carboxylic acid group , COOH.


When a fatty acid is in solution, only the carboxyl end associates with water molecules, because that is the only hydrophilic portion of the molecule. The hydrocarbon tail is hydrophobic, so fatty acids have a very limited solubility in water. In general, the longer the hydrocarbon tail, the lower the solubility of the molecule.

In a saturated fatty acid, each carbon atom in the hydrocarbon tail has four single covalent bonds. If some of the carbon–to–carbon bonds are double covalent bonds, the fatty acid is said to be unsaturated . A polyunsaturated fatty acid contains multiple unsaturated bonds.

Eskimos have lower rates of heart disease than do other populations, even though the Eskimo diet is high in fats and cholesterol. Interestingly, the fatty acids in the Eskimo diet have an unsaturated bond three carbon's before the last, or omega, carbon, a position known as "omega minus 3," or omega–3 . Fish flesh and fish oils, a substantial portion of the Eskimo diet, contain omega–3 fatty acids. Why does the presence of omega–3 fatty acids (or some other unidentified component of fish) in the diet reduce the risks of heart disease, rheumatoid arthritis, and other inflammatory diseases? The answer is not yet apparent, but as you can imagine, there is a great deal of interest in this area of research.

Eicosanoids are lipids derived from arachidonic acid , a fatty acid that must be absorbed in the diet because it cannot be synthesized by the body. The two major classes of eicosanoids are (1) prostaglandins and (2) leukotrienes .

Prostaglandins are short–chain fatty acids in which five of the carbon atoms are joined in a ring. These compounds are released by cells to coordinate or direct local cellular activities. Almost every tissue in the body produces and responds to prostaglandins, which are extremely powerful and effective even in minute quantities.

1.    Prostaglandins released by damaged tissues stimulate nerve endings and produce the sensation of pain.

2.     Prostaglandins released in the uterus help trigger the start of labor contractions

Prostaglandins are unusual short–chain fatty acids

The body uses several types of chemical messengers. Those that are produced in one part of the body but have effects on distant parts, are called hormones . Hormones are distributed throughout the body in the bloodstream, whereas most prostaglandins affect only the area in which they are produced. As a result, prostaglandins are often called local hormones .

Individual fatty acids cannot be strung together in a chain by dehydration synthesis, as monosaccharides can. But they can be attached to another compound, glycerol, through a similar reaction. The result is a lipid known as a glyceride.

Triglyceride Formation.
The formation of a triglyceride involves the attachment of fatty acids to the carbon's of a glycerol molecule. In this example, a triglyceride is formed by the attachment of one unsaturated and two saturated fatty acids to a glycerol molecule.


Hydrolysis breaks the glycerides into fatty acids and glycerol. Triglycerides have three important functions:

1.    Energy Source. Fatty deposits in specialized sites of the body represent a significant energy reserve. In times of need, the triglycerides are disassembled, yielding fatty acids that can be broken down to provide energy.

2.    Insulation. Fat deposits under the skin serve as insulation, preventing heat loss to the environment. Heat loss across a layer of lipids is only about one–third that through other tissues.

3.    Protection. A fat deposit around a delicate organ such as a kidney provides a cushion that protects against shocks or blows.

Triglycerides are stored in the body as lipid droplets within cells. The droplets absorb and accumulate lipid–soluble vitamins, drugs, or toxins that appear in body fluids. This accumulation has both positive and negative effects. For example, the body's lipid reserves retain both valuable lipid–soluble vitamins (A, D, E, K) and potentially dangerous lipid–soluble pesticides, such as DDT.

Steroids are large lipid molecules that share a distinctive carbon framework.

All steroids share a complex four–ring structure. Individual steroids differ in the side chains attached to the carbon rings. Cholesterol and related steroids are important for the following reasons:

Unfortunately, because the body can synthesize cholesterol as well, blood cholesterol levels can be difficult to control by dietary restriction alone.

Phospholipids and Glycolipids
Phospholipids and glycolipids are structurally related, and our cells can synthesize both types of lipids, primarily from fatty acids.

 Phospholipids and Glycolipids.
(a) The phospholipid lecithin . In a phospholipid, a phosphate group links a nonlipid molecule to a diglyceride. (b) In a glycolipid, a carbohydrate is attached to a diglyceride. (c) In large numbers, phospholipids and glycolipids form micelles, with the hydrophilic heads facing the water molecules and the hydrophobic tails on the inside of each droplet.

Cholesterol, phospholipids, and glycolipids are called structural lipids , because they help form and maintain intracellular structures called membranes. At the cellular level, membranes are sheets or layers composed primarily of hydrophobic lipids. A membrane surrounds each cell and separates the aqueous solution inside the cell from the aqueous solution in the extracellular environment. Because the two solutions are separated by a membrane, their compositions can be very different. A variety of internal membranes subdivide the interior of the cell into specialized compartments, each with a distinctive chemical nature and, as a result, a different function.

Proteins are the most abundant organic components of the human body. All proteins contain carbon, hydrogen, oxygen, and nitrogen; smaller quantities of sulfur may also be present.
Proteins perform a variety of essential functions, which can be classified into seven major categories:

1.    Support. Structural proteins create a three–dimensional framework for the body, providing strength, organization, and support for cells, tissues, and organs.

2.    Movement. Contractile proteins are responsible for muscular contraction; related proteins are responsible for the movement of individual cells.

3.    Transport. Insoluble lipids, respiratory gases, special minerals such as iron, and several hormones cannot be transported in the blood, unless they are first bound to special transport proteins .

4.    Buffering. Proteins provide a considerable buffering action and thereby help prevent dangerous changes in pH in our cells and tissues.

5.    Metabolic Regulation. Enzymes accelerate chemical reactions in cells. The sensitivity of enzymes to environmental factors is extremely important in controlling the pace and direction of metabolic operations.

6.    Coordination and Control. Protein hormones can influence the metabolic activities of every cell in the body or affect the function of specific organs or organ systems.

7.    Defense. The tough, waterproof proteins of the skin, hair, and nails protect the body from environmental hazards. Proteins called antibodies , components of the immune response , help protect us from disease. Special clotting proteins restrict bleeding after an injury to the cardiovascular system.

Structure of Proteins
Proteins consist of long chains of organic molecules called amino acids . Twenty types of amino acids occur in significant quantities in the body. A typical protein contains 1000 amino acids; the largest protein complexes have 100,000 or more. Each amino acid consists of a central carbon atom to which four groups are attached:

It is the different R groups that distinguish one amino acid from another, giving each its own chemical properties. All amino acids are relatively small water–soluble molecules.

As the figure indicates, dehydration synthesis can link two amino acids. The process creates a covalent bond between the carboxylic acid group of one amino acid and the amino group of another. Such a bond is known as a peptide bond . Molecules consisting of amino acids held together by peptide bonds are called peptides .

Peptide Bonds.
The amino acids glycine and alanine, linked to form a dipeptide. Peptides form as dehydration synthesis creates a peptide bond between the carboxylic acid group of one amino acid and the amino group of another.

Attaching a third amino acid produces a tripeptide ; next are tetrapeptides, pentapeptides , and so forth. Tripeptides and larger peptide chains are called polypeptides .

Polypeptides containing more than 100 amino acids are usually called proteins. You may be familiar with the names of several important proteins, including hemoglobin in red blood cells and keratin in fingernails and hair.

Protein Shape- Proteins have four levels of structural complexity:

1.    Primary structure is the sequence of amino acids along the length of a single polypeptide.

2.    Secondary structure results from bonds that develop between atoms at different parts of the polypeptide chain. Hydrogen bonding, for example, may create a simple spiral, known as an alpha–helix , or a flat pleated sheet. The spiral alpha–helix is the most common form, but a single polypeptide chain may have both helical and pleated sections.

3.    Tertiary structure is the complex coiling and folding that gives the protein its final three–dimensional shape.

4.    Quaternary structure is the interaction between individual polypeptide chains to form a protein complex. Each of the polypeptide subunits has its own secondary and tertiary structures. The protein hemoglobin contains four globular subunits. Hemoglobin is found within red blood cells, where it binds and transports oxygen. In keratin and collagen , three alpha–helical polypeptides are wound together like the strands of a rope. Keratin is the tough, water–resistant protein at the surface of the skin and in nails and hair. Collagen is the most abundant structural protein; collagen fibers form the framework that supports cells in most tissues.

Fibrous and Globular Proteins

Shape and Function Proteins are extremely versatile and have a variety of functions. The shape of a protein determines its functional properties, and the ultimate determinant of shape is the sequence of amino acids.

Enzyme Function
Among the most important of all the body's proteins are the enzymes. The reactants in enzymatic reactions are called substrates . Before an enzyme can function as a catalyst–to accelerate a chemical reaction without itself being permanently changed or consumed–the substrates must bind to a special region of the enzyme. This region, called the active site , is typically a groove or pocket into which one or more substrates nestle, like a key fitting into a lock.

 A Simplified View of Enzyme Structure and Function.
Each enzyme contains a specific active site somewhere on its exposed surface.

Enzymes work quickly, cycling rapidly between substrates and products. For example, an enzyme providing energy during a muscular contraction performs its reaction sequence 100 times per second.

Cofactors and Enzyme Function A cofactor is an ion or a molecule that must bind to the enzyme before substrates can also bind. Examples of cofactors include ions such as calcium and magnesium which bind at the enzymes active site. Coenzymes are nonprotein organic molecules that function as cofactors. Our bodies convert many vitamins into essential coenzymes.

Temperature and pH Each enzyme works best at specific temperatures and pH values. Death occurs at very high body temperatures, because proteins undergo denaturation , a change in their tertiary or quaternary structure. Because denatured proteins are nonfunctional, the loss of structural proteins and enzymes soon causes irreparable damage to organs and organ systems.

Enzymes are equally sensitive to changes in pH. Pepsin , an enzyme that breaks down proteins in the contents of your stomach, works best at a pH of 2.0 (strongly acidic). Your small intestine contains trypsin , another enzyme that attacks proteins. Trypsin works only in an alkaline environment, with an optimum pH of 7.7 (weakly basic).

Glycoproteins and Proteoglycans
Glycoproteins and proteoglycans are combinations of protein and carbohydrate molecules.

These molecules may function as enzymes, antibodies, hormones, or protein components of cell membranes. Proteo glycans are large polysaccharide molecules linked by polypeptide chains. The proteoglycans in tissue fluids give them a syrupy consistency.

Nucleic acids are large organic molecules composed of carbon, hydrogen, oxygen, nitrogen, and phosphorus. Nucleic acids store and process information at the molecular level, inside cells. The two classes of nucleic acid molecules are (1) deoxyribonucleic acid , or DNA , and (2) ribonucleic acid , or RNA .

The DNA in our cells determines our inherited characteristics, such as eye color. DNA molecules encode the information needed to build proteins. DNA regulates not only protein synthesis, but all aspects of cellular metabolism, including the creation and destruction of lipids, carbohydrates, and other vital molecules.

Several forms of RNA cooperate to manufacture specific proteins by using the information provided by DNA.

Structure of Nucleic Acids
A nucleic acid consists of nucleotides linked by dehydration synthesis. Each nucleotide has three components: (1) a sugar, (2) a phosphate group, and (3) a nitrogenous (nitrogen–containing) base . The sugar is either ribose (in RNA) or deoxyribose (in DNA). Each pentose is attached to a phosphate group and to a nitrogenous base. Five nitrogenous bases occur in nucleic acids: adenine ( A ), guanine ( G ), cytosine ( C ), thymine ( T ), and uracil ( U )

Both RNA and DNA contain adenine, guanine, and cytosine. Uracil occurs only in RNA and thymine only in DNA.

Purines and Pyrimidines.
(a) Purines and (b) pyrimidines are the nitrogenous bases in nucleic acids.

Nucleic Acids: RNA and DNA.
(a) An RNA molecule has a single nucleotide chain. Its shape is determined by the sequence of nucleotides and by the interactions among them. (b) A DNA molecule has a pair of nucleotide chains linked by hydrogen bonding between complementary base pairs.

Its shape depends on the order of the nucleotides and the interactions among them. Our cells have three types of RNA: (1) messenger RNA ( mRNA ), (2) transfer RNA ( tRNA ), and (3) ribosomal RNA ( rRNA ). These types have different shapes and functions, but all three are required for the synthesis of proteins.

Two strands of DNA twist around one another in a double helix that resembles a spiral staircase.

High–Energy Compounds

Energy transfer involves the creation of high–energy bonds by enzymes within our cells. A high–energy bond is a covalent bond whose breakdown releases energy the cell can harness. In your cells, a high–energy bond generally connects a phosphate group to an organic molecule. The resulting complex is called a high–energy compound .

The attachment of a phosphate group to another molecule is called phosphorylation. The creation of a high–energy compound requires (1) a phosphate group, (2) enzymes capable of catalyzing the reactions involved, and (3) suitable organic substrates to which the phosphate can be added.
The most important such substrate is adenosine , a combination of adenine and ribose, with two phosphate groups attached. This compound, adenosine diphosphate ( ADP ), is created by the phosphorylation of the nucleotide adenosine monophosphate ( AMP ), a building block of nucleic acids. A significant energy input is required to convert AMP to ADP, and the second phosphate is attached by a high–energy bond. Even more energy is required to add a third phosphate and thereby create the high– energy compound adenosine triphosphate ( ATP ).

The Structure of ATP.
A molecule of ATP consists of adenosine (adenine plus ribose) to which three phosphate groups have been joined. Cells most often transfer energy by attaching a third phosphate group to ADP with a high–energy bond and then removing that phosphate group at another site, where the associated release of energy performs cellular work.

The conversion of ADP to ATP and the reversion of ATP to ADP are the most common methods of energy transfer in our cells:
The conversion of ATP to ADP requires an enzyme known as adenosine triphosphatase , or ATPase . Throughout life, our cells continuously generate ATP from ADP and use the energy provided by the ATP to perform vital functions, such as the synthesis of proteins or the contraction of muscles.

Although ATP is the most abundant high–energy compound, there are others–typically, other nucleotides that have undergone phosphorylation. For example, guanosine triphosphate ( GTP ) and uridine triphosphate ( UTP ) are nucleotide–based high–energy compounds that transfer energy in specific enzymatic reactions.

Chemicals and Cells

The human body is more than a collection of chemicals. Biochemical building blocks form functional units called cells . Each cell behaves like a miniature organism, responding to internal and external stimuli. A phospholipid membrane separates the cell from its environment, and internal membranes create compartments with specific functions. Proteins form an internal supporting framework and, as enzymes, accelerate and control the chemical reactions that maintain homeostasis. Nucleic acids direct the synthesis of all cellular proteins, including the enzymes that enable the cell to synthesize a wide variety of other substances. Carbohydrates provide energy (transferred by high–energy compounds) to support vital activities, and they form part of specialized compounds such as proteoglycans and glycolipids.

Their continuous removal and replacement are part of the process of metabolic turnover .