Chapter 1: The Chemistry of Life

Chapter 1 The Chemistry of Life

1.1 Atoms, Molecules and Compounds

1.2 The Structure of Atoms

1.3 Chemical Reactions

1.4 Chemical Bonds

1.5 Ions and Living Cells

1.6 Organic Compounds and Life

1.7 Carbohydrates

1.8 Lipids

1.9 Proteins

1.10 Nucleic Acids

1.11 The Double Helix

1.12 The functions of DNA

Chapter Summary

Review Questions

1.1 Atoms, Molecules and Compounds

Water is abundant on Earth today, and it exists in three physical states depending on temperature – as a gas, as a liquid and as a solid.
Although the forms of water may vary, its chemical composition remains the same.
Molecules of water are the smallest units into which water can be subdivided and still have the essential chemical properties of water.
Under certain conditions, water molecules can break down in to two different substances (which are also molecules), hydrogen and oxygen.
Hydrogen and oxygen are elements – substances that cannot be broken down chemically in to simpler substances.
Atoms are the smallest unit of an element that still has the chemical properties of that element.
Molecules are made of atoms that have combined chemically.
Molecules may be made from more than one type of atom or from atoms of the same type. (Fig. 1.2)
Elements can combine chemically in many ways to form the millions of compounds that give Earth its variety of materials.
Chemists have given each element a symbol of letters from the element’s name.
The number of atoms of each element in a molecule is shown by the number, called a subscript, following the symbol for the element (the number 1 is always understood and not written).
About 97% of the compounds present in organisms contain only six elements which are essential to every organism – carbon (C), hydrogen (H), oxygen (O), nitrogen (N), phosphorus (P) and sulfur (S). (Fig. 1.3)
The remaining 3% contain small amounts of other elements.

1.2 The Structure of Atoms

Atoms themselves are built of many smaller subatomic particles.
The subatomic particles of atoms that are basic to an understanding of biology are electrons, protons and neutrons.
Protons and neutrons remain in the center, or nucleus, of the atom.
The rapidly moving electrons form a negatively charged “cloud” around the nucleus.
Electrons are distributed throughout the cloud based on differing levels of energy (or attraction) called electron shells.
Electrons in shells near the nucleus are held more tightly than those in shells farther from the nucleus.
With a single proton, no neutron, and a single electron that orbits in the energy shell closest to the nucleus, hydrogen is the simplest of all atoms. (Fig. 1.4)
An atom of carbon has six protons and six neutrons in its nucleus and six electrons orbiting the nucleus. (Fig. 1.4)
Nitrogen has seven protons and seven electrons (two in the innermost shell, five in an outer shell which can hold eight). (Fig. 1.4)
Oxygen has eight protons and eight electrons (two in the innermost shell, six in an outer shell which can h old eight). (Fig. 1.4)
Every atom has an equal number of protons and electrons.
The atoms of most elements can undergo chemical change by gaining, losing, or sharing one or more electrons with other atoms.
Atoms with unfilled shells have a strong tendency to lose or gain electrons to complete their outer shells.
Atoms of the same element always have the same number of protons and electrons, but they may differ in their number of neutrons.
Atoms of the same element that differ in their number of neutrons are called isotope.
Some isotopes, called radioisotopes, have unstable atomic nuclei that break down, releasing radiation energy.

1.3 Chemical Reactions

Chemical bonds are the attraction, sharing, or transfer of outer shell electrons from one atom to another.
A chemical reaction involves the making and breaking of chemical bonds which produces new substances.
For atoms with electrons in more than one energy shell, only the outermost electrons normally interact during chemical changes.
Chemical reactions occur in the cells – the basic units of life – of all living organisms. (Fig. 1.5)
Chemical reactions are important to a cell for two reasons:
1. They are the only way to form new molecules that the cell requires for such things as growth and maintenance.
2. The making and breaking of bonds involves changes in energy which allow it to be stored, used to do work or released.
Chemical reactions can be represented as short statements called chemical equations.
The breakdown of water can be represented by the following equation (note that the arrow points from the reactants to products): (p.28)

Balancing chemical equations illustrates the law of conservation of matter, which states that matter is neither created nor destroyed in chemical reactions.
When molecules collide, they may or may not react, depending on the energy and orientation of the molecules.
Activation energy is the energy needed to get a chemical reaction started.

1.4 Chemical Bonds

One type of chemical bond forms when electrons move from one atom to another atom.
This type of chemical bond occurs in many substances, including sodium chloride (NaCl).
An ion is an atom or a molecule that has acquired a positive or negative charge as a result of gaining or losing electrons.
An ionic bond is the attraction between oppositely charged ions, such as the sodium chloride bond. (Fig. 1.7)
In a covalent bond, two atoms share one or more pairs of electrons.
Two atoms of hydrogen join to form a molecule of hydrogen gas (H2) by sharing a pair of electrons. (Fig. 1.8)
In a molecule of water, each of the two hydrogen atoms shares a pair of electrons with the same oxygen atom.
If the electrons of a bond are not shared equally, such as in water, the bond is called a polar covalent bond.
When the electrons in a molecule are shared equally, such as in hydrogen gas, the resulting covalent bond is said to be nonpolar.
The unequal sharing of electrons in a water molecule gives the oxygen atom a slight negative charge and each hydrogen atom a slight positive charge creating a polar molecule.
The polar nature of water is biologically significant as molecules must dissolve in water in order to move easily in and between living cells. (Fig. 1.9)
A hydrogen bond, or weak attraction, can occur between a slightly positive hydrogen atom in a molecule and a nearby slightly negative atom of another molecule (or of the same molecule if it is large enough). Fig. 1.10)
A large number of hydrogen bonds can be quite strong, but single hydrogen bonds are much weaker than covalent bonds.

1.5 Ions and Living Cells

When table salt dissolves in water, the ionic bonds are broken and Na+ and Cl- ions separate, or dissociate, but remain as ions in solution.
Sodium ions are important in regulating water balance in organisms.
When a nonionic compound, such as water, is converted to ions, the process is called ionization.
Only about one in every 500 million water molecules ionizes in living cells, yet all life processes depend on this tiny amount of ionization.
The level of H+ and OH- ions in solution is described on a scale from 0 to 14 known as the pH scale. (Fig. 1.12)
A solution (a mixture in water) that has the same number of H+ and OH- ions is neutral and has a pH of 7.
A solution having more H+ than OH- is acidic and has a pH less than 7 (low pH).
A solution that has more OH- than H+ ions is basic (or alkaline) and has a pH greater than 7 (high pH).
The pH scale is a logarithmic scale meaning that a change of one pH unit is equal to a tenfold change in the level of H+ ions. (Fig. 1.13)
The pH of a cell’s interior helps regulate the cell’s chemical reactions.
Organisms have ways to control pH and to respond to changes in the pH of their environment.

1.6 Organic Compounds and Life

Organic compounds, in which carbon atoms are combined with hydrogen and usually oxygen, are needed for life to exist.
Carbon atoms can combine in long chains that form the backbone of large complex molecules, or macromolecules.
The backbone of carbon atoms, to which other atoms and molecules can attach, is called the carbon skeleton.
The four most important classes of molecules in living cells are carbohydrates, lipids, proteins, and nucleic acids. (Fig. 1.15 and Fig. 1.16)

1.7 Carbohydrates

All known types of living cells contain carbohydrates which contain carbon atoms and hydrogen and oxygen atoms in the same two-to-one ratio as water.
The simplest carbohydrates are single sugars, such as glucose, called monosaccharides, which may contain three to seven carbon atoms in their carbon skeletons. (Fig. 1.17)
Biologically important sugars often have a phosphate group composed of an atom of phosphorus and four atoms of oxygen attached to the carbon skeleton are called sugar-phosphates. (Fig. 1.17)
Two simple sugar molecules, or monosaccharides, may bond to form a double sugar, or disaccharide, such as sucrose. (Fig. 1.18)
Several glucose molecules may bond to form complex carbohydrates called polysaccharides, such as starch and cellulose. (Fig. 1.18)

1.8 Lipids

Lipids, or fats and oils, are macromolecules that have two primary functions:
1. Long-term storage of energy
2. Carbon and building of structural parts of cell membranes
Lipids:
1. Are nonpolar and generally do not dissolve in water
2. Contain carbon, hydrogen, and oxygen, but not in a fixed ratio
Building blocks of lipids, called fatty acids and glycerol, make up the simple fats.
To form a fat, one molecule of glycerol combines with three molecules of fatty acids. The fatty acids in one fat may be alike or different. (Fig. 1.19)
The biologically important properties of simple fats depend on their fatty acids.
1. Fatty acids in which single bonds join the carbon atoms are saturated fatty acids.
2. Unsaturated fatty acids are fatty acids in which double bonds join some of the carbon atoms.
Fats are a more efficient form of energy storage than are carbohydrates because fats contain a larger number of hydrogen atoms and less oxygen.
Two other types of lipids important in cells are phospholipids and cholesterol.
Phospholipids form when a molecule of glycerol combines with two fatty acids and a phosphate group.
Together with proteins, phospholipids form cellular membranes. (Fig. 1.20)
Cholesterol is part of the membrane structure of animal cells and is important in nutrition. (Fig. 1.20)

1.9 Proteins

Every living cell contains from several hundred to several thousand different macromolecules known as proteins.
Proteins are structural components of cells as well as messengers and receivers of messages (also called receptors) between cells.
The most essential role of proteins is as enzymes, specialized molecules that assist the many reactions occurring in cells.
Cells make proteins by linking building clocks called amino acids which are small molecules that contain carbon, hydrogen, oxygen, and nitrogen atoms; two also contain sulfur atoms. (Fig. 1.21)
Covalent bonds between the acid group of one amino acid molecule and the amino group of another are called peptide bonds.
Additional peptide bonds may form, resulting in a long chain of amino acids, or polypeptide. (Fig. 1.22)
The sequence of amino acids in a polypeptide chain forms the primary structure of proteins. (Fig. 1.23a)
In most proteins, the chain folds or twists to form local structures known as secondary structures. (Fig. 1.23b)
More complex folding creates a tertiary structure, which usually is globular, or spherical. (Fig. 1.23c)
One of the major forces controlling how a protein folds is hydrophobicity, or the tendency for nonpolar amino acids to avoid water.
Each individual protein has a unique shape and, therefore, a specific function.
A few proteins become active only when two or more tertiary forms combine to form a complex quaternary structure. (Fig. 1.23d)

1.10 Nucleic Acids

Nucleic acids are macromolecules that dictate the amino-acid sequence of proteins, which in turn control the basic life processes.
Nucleic acids also are the source of genetic information in chromosomes, which are passed from parent to offspring during reproduction.
Nucleic acids are made of relatively simple units called nucleotides connected to form long chains.
Each nucleotide consists of three parts:
1. A 5-carbon sugar (a pentose), which may be either ribose or deoxyribose (Fig. 1.24)
2. A nitrogen-containing base, which is a single or double ringlike structure of carbon, hydrogen and nitrogen. (Fig. 1.25)
3. A phosphate group
Nucleic acids that contain ribose in their nucleotides are called ribonucleic acids, or RNA.
Nucleotides containing deoxyribose form deoxyribonucleic acids, or DNA.
In DNA, each of the four different nucleotides contains a deoxyribose, a phosphate group and one of the four bases – adenine, thymine, guanine, or cytosine – in a double-stranded helix. (Fig. 1.26)
RNA is a nucleic acid mush like DNA, except:
- It contains the sugar ribose instead of deoxyribose
- The nitrogen base uracil replaces the base thymine (Fig. 1.28)
- It is single stranded, although it can fold into complex shapes

1.11 The Double Helix

In 1953, James Watson and Francis Crick proposed a model for the structure of the DNA molecule that is still accepted today (with some modification). (Fig. 1.29a,b)
Their model was based on the principle that hydrogen bonds form only between the nucleotide bases of adenine (A) and thymine (T) or cytosine (C) and guanine(G). (Fig. 1.30)
Experiments done by Rosalind Franklin in the laboratory of Maurice Wilkins suggested to Watson and Crick that DNA molecules have a double-helix structure. (Fig. 1.29c,d)
The DNA double helix is composed of two long chains of nucleotides connected between their deoxyribose sugars by phosphate groups.
The two chains are connected by hydrogen bonding between nitrogen bases to form a long double-stranded molecule.
Because of the specific pairing between bases, each strand is the complement of the other.
The two strands intertwine, forming a double helix that winds around a central axis. (Fig. 1.31)
The folds in RNA are held together by the same type of base pairing as in DNA. (Fig. 1.32)

1.12 The functions of DNA

DNA forms the genes, units of genetic information, that pass from parent to offspring.
The structure of DNA explains how DNA functions as the molecule of genetic information.
DNA stores information in a code consisting of units that are three nucleotides long called triplet codons.
Certain codons are translated by the cell to mean certain amino acids allowing the sequence of nucleotides in DNA to indicate a sequence of amino acids in proteins.
The sequence of amino acids in a protein determines its shape, which then determines function.
The structure of DNA also accounts for its ability to be copied and passed through inheritance from one generation to the next.
Note the concept map that summarized the major cellular processes that involve DNA – Fig. 1.35.

Chapter 1 Summary –

Cells, the basic units of life, carry out their biological functions through chemical reactions which occur continuously.
Elements are the basic chemical form of matter and cannot break down into substances with new or different properties.
Atoms contain a characteristic number of positively charged protons, negatively charged electrons and neutral neutrons.
Ions are atoms or molecules that have gained or lost electrons; ions have a positive or negative charge.
Chemical bonds hold atoms together to form molecules. There are two types of chemical bonds, ionic and covalent.
Weak bond involving a partially positive hydrogen atom are called hydrogen bonds.
In chemical reactions, molecules interact and form different substances.
The membranes that surround cells enclose the chemical reactions of the cells and isolate them from the outside environment.
Organisms contain four major types of macromolecules: Carbohydrates, Lipids, Proteins and Nucleic Acids.
Chemical compounds have biological activity because of their specific chemical structures. Chemical structure dictates biological function.

Reviewing Ideas –

Why is the polar nature of water biologically significant?
Describe the differences in composition and structure between RNA and DNA.
What properties of phospholipids makes them useful in cellular membranes?
Why is the complimentary structure of a DNA molecule important in passing genetic information from parent to offspring?
What effect could rainfall with a pH of 3.5 have on a lake ecosystem?