Chapter 02 Lecture Outline*

Chemical Composition of the Body

Eric P. Widmaier
Boston University

Hershel Raff
Medical College of Wisconsin

Kevin T. Strang
University of Wisconsin - Madison

*See PowerPoint Image Slides for all figures and tables pre-inserted into PowerPoint without notes. 1
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Atoms: the Subunits of Elements

Atoms are made of protons, neutrons, and electrons. Each element has an atomic number.
Equal to the number of protons contained in the atom

Each element has an atomic weight. Hydrogen, oxygen, carbon, nitrogen account for >99% of the atoms in the human body.
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Components of Atoms
The chemical properties of atoms can be described in terms of three subatomic particlesprotons, neutrons, and electrons. The protons and neutrons are confined to a very small volume at the center of an atom called the atomic nucleus. The electrons revolve in orbitals at various distances from the nucleus.
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Figure 2-1

Atomic Number
Each chemical element contains a specific number of protons, and it is this number that is known as the atomic number. Example: hydrogen has an atomic number of 1, so it has a single proton.

Because an atom is electrically neutral, the atomic number is also equal to the number of electrons in the atom.
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Atomic Weight
Usually, the number of neutrons in the nucleus of an atom is equal to the number of protons.

However, many chemical elements can exist in multiple forms, called isotopes, which differ in the number of neutrons they contain.
For example, the most abundant form of the carbon atom, 12C, contains 6 protons and 6 neutrons, and has an atomic number of 6 and an atomic weight of 12. The radioactive carbon isotope 14C contains 6 protons and 8 neutrons, giving it an atomic number of 6 but an atomic weight of 14.

Atomic Weight
One gram atomic mass of a chemical element is the amount of the element, in grams, equal to the numerical value of its atomic weight. Thus, 12 g of carbon is 1 gram atomic mass of carbon. One gram atomic mass of any element contains the same number of atoms (6 x1023; Avogadros constant).
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Atomic Weight
The atomic weight scale indicates an atoms mass relative to the mass of other atoms. (comparison done to carbon) Because the atomic weight scale is a ratio of atomic masses, it has no absolute units. The unit of atomic mass is known as a dalton.

Ions
If an atom gains or loses one or more electrons, it acquires a net electric charge and becomes an ion.

Hydrogen atoms and most mineral and trace element atoms readily form ions.
Ions that have a net positive charge are called cations. Examples: Ca2+, Na+ Ions that have a net negative charge are called anions. Example: Cl Because of their charge, ions are able to conduct electricity when dissolved in water; consequently, the ionic forms of mineral elements are collectively referred to as electrolytes.
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Table 2-2

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Molecules
Two or more atoms bonded together form a molecule. Molecules can be represented by their component atoms. Example: C6H12O6

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Chemical Bonds
Chemical bonds between atoms in a molecule form when electrons transfer from the outer energy shell of one atom to that of another, or when two atoms with partially unfilled electron orbitals share electrons.

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Covalent Bonds are the Strongest Chemical Bonds

Fig. 2-2 14

Polar Covalent Bonds

Electrons are not always shared equally between two atoms, but instead reside close to one atom of the pair. This atom thus acquires a slight negative charge, while the other atom becomes slightly positive. Such bonds are known as polar covalent bonds.
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Polar Covalent Bonds

For example, the bond between hydrogen and oxygen in a hydroxyl group (OH) is a polar covalent bond in which the oxygen is slightly negative and the hydrogen slightly positive. Atoms of oxygen, nitrogen and sulfur, which have a relatively strong attraction for electrons, form polar bonds with hydrogen atoms (Table 2-3).

One of the characteristics of polar bonds is that molecules that contain such bonds tend to be more soluble in water than molecules containing the other major type of covalent bond.
Consequently, these polar molecules readily dissolve in the blood, interstitial fluid, and intracellular fluid. Indeed, water itself is the classic example of a polar molecule, with a partially negatively charged oxygen atom and two partially positively charged hydrogen atoms.
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17

Nonpolar Covalent Bonds

In contrast to polar covalent bonds, bonds between atoms with similar electronegativities are said to be nonpolar covalent bonds. In such bonds, the electrons are equally or nearly equally shared by the two atoms. Bonds between carbon and hydrogen atoms and between two carbon atoms are electrically neutral, nonpolar covalent bonds (see Table 23).

Molecules that contain high proportions of nonpolar covalent bonds are called nonpolar molecules; they tend to be less soluble in water than those with polar covalent bonds.
Consequently, such molecules are often found in the lipid bilayers of the membranes of cells and intracellular organelles. When present in body fluids such as the blood, they may associate with a polar molecule that serves as a sort of carrier to prevent the nonpolar molecule from coming out of solution.
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Hydrogen Bonds
When two polar molecules are in close contact, an electrical attraction may form between them. For example, the hydrogen atom in a polar bond in one molecule and an oxygen or nitrogen atom in a polar bond of another molecule attract each other, forming a type of bond called a hydrogen bond. Such bonds may also form between atoms within the same molecule. Hydrogen bonds are very weak, having only about 4 percent of the strength of the polar bonds between the hydrogen and oxygen atoms in a single molecule of water. Although hydrogen bonds are weak individually, when present in large numbers, they play an extremely important role in molecular interactions and in determining the shape of large molecules. Remember that the shape of large molecules often determines their functions and their ability to interact with other molecules. For example, some molecules interact with a lock-and-key arrangement that can only occur if both molecules have the correct shape.
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Hydrogen Bonds Link Adjacent Water Molecules

Fig. 2-3

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Molecular Shape
Rotation around chemical bonds allows different molecular shapes.

Figure 2-5

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Ionic Molecules
The process of ion formation (ionization) occurs in single atoms and atoms that are covalently linked in molecules. Within molecules, two commonly encountered groups of atoms that undergo ionization are the carboxyl group (COOH) and the amino group (NH2). The shorthand formula for only a portion of a molecule can be written as R COOH or RNH2. The carboxyl group ionizes when the oxygen linked to the hydrogen captures the hydrogens only electron to form a carboxyl ion (RCOO), releasing a hydrogen ion (H+): RCOOH 12 R COO + H+. The amino group can bind a hydrogen ion to form an ionized amino group (R NH3+): RNH2 + H+ 12 RNH3+.

The ionization of each of these groups can be reversed.

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Free Radicals
Free radicals are atoms or molecules with unpaired electrons in an outermost orbital. Free radicals are unstable and highly reactive.

Free radicals are formed by the actions of certain enzymes in some cells, such as types of white blood cells that destroy pathogens.
Free radicals are produced in the body following exposure to radiation or toxin ingestion. These free radicals can do considerable harm to the cells of the body. For example, oxidation due to long-term buildup of free radicals has been proposed as one cause of several different human diseases, notably eye, cardiovascular, and neural diseases associated with aging. Examples of biologically important free radicals are superoxide anion, O2 ; hydroxyl radical, OH ; and nitric oxide, NO .
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Solutions
Substances dissolved in a liquid are known as solutes. The liquid in which solutes are dissolved is the solvent. Solutes dissolve in a solvent to form a solution. Water is the most abundant solvent in the body, accounting for approximately 60 percent of total body weight. However, not all molecules dissolve in water.
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NaCl dissolves in water

Fig. 2-6

In this example, Na+ & Cl- are the solutes and water is the solvent.
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Solubility in Water
Molecules with ionic or polar covalent bonds have an electrical attraction to water molecules. These molecules are able to dissolve in water and are called hydrophilic (water loving).

Molecules with nonpolar covalent bonds are not able to dissolve in water and are called hydrophobic (water fearing).
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Amphipathic Molecules
Amphipathic molecules are a special class of molecules that have a polar or ionized region at one end and a nonpolar region at the opposite end.

When mixed with water, amphipathic molecules form clusters, with their polar (hydrophilic) regions at the surface of the cluster where they are attracted to the surrounding water molecules. The nonpolar (hydrophobic) ends are oriented toward the interior of the cluster.
This arrangement provides the maximal interaction between water molecules and the polar ends of the amphipathic molecules. Nonpolar molecules can dissolve in the central nonpolar regions of these clusters and thus exist in aqueous solutions in far higher amounts than would otherwise be possible based on their low solubility in water. The orientation of amphipathic molecules plays an important role in plasma membrane structure.
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Amphipathic Molecules

Fig. 2-7

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Concentration
Concentration is expressed as the amount of solute (based on its molecular weight) dissolved per liter of solution.
The molecular weight in grams = 1 mole 1 M solution = 1 mole/Liter

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Acids and Bases

Acids increase the concentration of H+ in a solution. Bases decrease the concentration of H+ in a solution.

The amount of H+ in a solution is expressed as pH.

pH = -log[H+]
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31

Types of Special Water Reactions

Hydrolysis is the breakdown of a large molecule into a small molecule by using water. Other types of reactions are: Dehydration Condensation

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Osmosis
Water moves between fluid compartments by the process of osmosis (covered more in Chapter 4). In osmosis, water moves from regions of low solute concentrations to regions of high solute concentrations, regardless of the specific type of solute.

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Terminology
Organic chemistry is the study of carboncontaining molecules. Inorganic chemistry is the study of noncarboncontaining molecules. Biochemistry is the chemistry of living organisms. (can be considered part of organic chemistry)
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Classes of Organic Molecules

Carbohydrates
Monosaccharides Disaccharide Polysaccharides

Lipids
Fatty Acids Triglycerides Phospholipids Steroids

Proteins
Amino Acid Subunits Polypeptides

Nucleic Acids
DNA RNA
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Fig. 2-8

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Carbohydrates
Monosaccharides are the simplest carbohydrates.

Fig. 2-9 37

Disaccharide Formation

Fig. 2-10

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Glycogen: a Polysaccharide

Fig. 2-11

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How the Body Uses Sugars

Glycogen exists in the body as a reservoir of available energy that is stored in the chemical bonds within individual glucose monomers. Hydrolysis of glycogen, as occurs during periods of fasting, leads to release of the glucose monomers into the blood, thereby preventing blood glucose from decreasing to dangerously low levels. Glucose is often called blood sugar because it is the major monosaccharide found in the blood.

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Lipids
Lipids are molecules composed predominantly (but not exclusively) of hydrogen and carbon atoms.

These atoms are linked by nonpolar covalent bonds. Thus, lipids are nonpolar and have a very low solubility in water. Lipids can be divided into four subclasses: fatty acids, triglycerides, phospholipids, and steroids.
Lipids are important in physiology partly because some of them provide a valuable source of energy. Other lipids are a major component of all cellular membranes, and still others are important signaling molecules.
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Lipids

Fig. 2-11

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Fatty Acids
Fatty acids consist of a chain of carbon and hydrogen atoms with an acidic carboxyl group at one end.

When all the carbons in a fatty acid are linked by single covalent bonds, the fatty acid is said to be a saturated fatty acid.
Some fatty acids contain one or more double bonds between carbon atoms, and these are known as unsaturated fatty acids.

If one double bond is present, the fatty acid is monounsaturated, and if there is more than one double bond, it is polyunsaturated.
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Triglycerides
Triglycerides (also known as triacylglycerols) constitute the majority of the lipids in the body. Triglycerides form when glycerol, a three-carbon alcohol, bonds to three fatty acids.

Triglycerides are found in all cells and comprise part of cellular membranes, including those of intracellular organelles. They are also stored in great quantities in adipose tissue, where they serve to supply energy to the cells of the body, particularly during times when a person is fasting or requires additional energy (maintained exercise, for example).
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Fig. 2-12A

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Fig. 2-12B

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Fig. 2-12C

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Cholesterol

Fig. 2-13

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Phospholipids
Phospholipids are similar in overall structure to triglycerides, but the third hydroxyl group of glycerol is linked to phosphate.

In addition, a small polar or ionized nitrogen-containing molecule is usually attached to this phosphate. These groups constitute a polar (hydrophilic) region at one end of the phospholipid, whereas the fatty acid chains provide a nonpolar (hydrophobic) region at the opposite end. Therefore, phospholipids are amphipathic. It is this property of phospholipids that permits them to form the lipid bilayers of cellular membranes.
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Steroids
Steroids have a distinctly different structure from those of the other subclasses of lipid molecules. Four interconnected rings of carbon atoms form the skeleton of every steroid.

Steroids are NOT water-soluble.

Examples of steroids are cholesterol, cortisol from the adrenal glands, and female (estrogen) and male (testosterone) sex hormones secreted by the gonads.

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Proteins
Proteins account for about 50 percent of the organic material in the body (17 percent of the body weight), and they play critical roles in almost every physiological process. Proteins are composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulfur. They are macromolecules, often containing thousands of atoms.
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Amino Acids
The subunit monomers of proteins are amino acids. Every amino acid except proline has an amino (NH2) and a carboxyl (COOH) group bound to the terminal carbon atom in the molecule. The proteins of all living organisms are composed of the same set of 20 different amino acids, corresponding to 20 different side chains. The side chains may be nonpolar (8 amino acids), polar (7 amino acids), or ionized (5 amino acids). The human body can synthesize many amino acids, but several must be obtained in the diet; these are known as essential amino acids.
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Proteins are Made of Amino Acids

Fig. 2-14 53

Peptide Bonds

Fig. 2-15 54

Fig. 2-16

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Protein Structures
Primary Protein Structure Secondary Protein Structure Tertiary Protein Structure Quaternary Protein Structure

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Primary Protein Structure

Two variables determine the primary structure of a protein: (1) The number of amino acids in the chain (2) The specific type of amino acid at each position along the chain A polypeptide in the primary protein structure is analogous to a linear string of beads, each bead representing one amino acid.
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Conformation
Proteins do not appear in nature like a linear string of beads on a chain. Interactions between side groups of each amino acid lead to bending, twisting, and folding of the chain into a more compact structure. The final shape of a protein is known as its conformation.
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Secondary Protein Structure

The attractions between various regions along a polypeptide chain creates secondary structure in a protein. Because peptide bonds occur at regular intervals along a polypeptide chain, the hydrogen bonds between them tend to force the chain into a coiled conformation known as an alpha helix. Hydrogen bonds can also form between peptide bonds when extended regions of a polypeptide chain run approximately parallel to each other, forming a relatively straight, extended region known as a beta pleated sheet. The sizes of the side chains and the presence of ionic bonds between side chains with opposite charges can interfere with the repetitive hydrogen bonding required to produce these alpha and beta shapes and result in irregular regions called random coil conformations. These occur in regions linking the more regular helical and beta pleated sheet patterns. Beta pleated sheets and alpha helices tend to impart upon a protein the ability to anchor itself into a lipid bilayer.

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Tertiary Protein Structure

Once secondary structure has been formed, associations between additional amino acid side chains become possible. These interactions fold the polypeptide into its final three-dimensional conformation, making it a functional protein.

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Factors that Determine Tertiary Structure

Five major factors determine the tertiary structure of a polypeptide chain once the amino acid sequence (primary structure) has been formed: 1. Hydrogen bonds between portions of the chain or with surrounding water molecules 2. Ionic bonds between polar and ionized regions along the chain 3. Attraction between nonpolar (hydrophobic) regions 4. Covalent disulfide bonds linking the sulfur-containing side chains of two cysteine amino acids 5. van der Waals forces

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Quaternary Protein Structure

Some proteins are composed of more than one polypeptide chain and are said to have quaternary structure. They are known as multimeric (many parts) proteins. The same factors that influence the conformation of a single polypeptide also determine the interactions between the polypeptides in a multimeric protein.

Therefore, the chains can be held together by interactions between various ionized, polar, and nonpolar side chains, as well as by disulfide covalent bonds between the chains.
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Polypeptides: Conformations

Fig. 2-17 63

Amino acid interactions

Fig. 2-18

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Multimeric example
The polypeptide chains in a multimeric protein may be identical or different. For example, hemoglobin, the protein that transports oxygen in the blood, is a multimeric protein with four polypeptide chains; two of one kind and two of another. Even a single amino acid change resulting from a mutation may have devastating consequences. An example of this is when a molecule of valine replaces a molecule of glutamic acid in the b chains of hemoglobin. The result of this change is a serious disease called sickle cell anemia. When red blood cells in a person with this disease are exposed to low oxygen levels, their hemoglobin precipitates. This contorts the red blood cells into a crescent shape, which makes the cells fragile and unable to function normally.
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Hemoglobin

Fig. 2-19 66

Nucleic Acids
Nucleic acids are extremely important because they are responsible for the storage, expression, and transmission of genetic information. There are two classes of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA molecules store genetic information coded in the sequence of their genes, whereas RNA molecules are involved in decoding this information into instructions for linking together a specific sequence of amino acids to form a specific polypeptide chain.
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Nucleotides

Fig. 2-20 68

Bases

Fig. 2-21 69

DNA
Four different nucleotides are present in DNA, corresponding to the four different bases that can be bound to deoxyribose. These bases are divided into two classes: 1. The purine bases: adenine (A) and guanine (G), which have double rings of nitrogen and carbon atoms 2. The pyrimidine bases, cytosine (C) and thymine (T), which have only a single ring
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DNA
A DNA molecule consists of two chains of nucleotides coiled around each other in the form of a double helix. The two chains are held together by hydrogen bonds between a purine base on one chain and a pyrimidine base on the opposite chain. Specificity is imposed on the base pairings by the location of the hydrogen-bonding groups in the four bases. G is always paired with C, and A with T.
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Deoxyribonucleic acid (DNA)

Fig. 2-22

Fig. 2-23

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RNA
RNA molecules differ in only a few respects from DNA:

1. RNA consists of a single chain of nucleotides. 2. In RNA, the sugar in each nucleotide is ribose rather than deoxyribose. 3. The pyrimidine base thymine in DNA is replaced in RNA by the pyrimidine base uracil (U). (AU pairing)
The other three bases, adenine, guanine, and cytosine, are the same in both DNA and RNA.
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74

ATP
The purine bases are important not only in DNA and RNA synthesis, but also in a molecule that serves as the molecular energy source for all cells. In all cells, from bacterial to human, adenosine triphosphate (ATP) is the primary molecule that receives the transfer of energy from the breakdown of fuel moleculescarbohydrates, fats, and proteins.
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ATP

Fig. 2-24 76