splash contents chapter introduction general chemistry 1.1atoms, molecules, and compounds 1.2the...

Chapter IntroductionGeneral Chemistry

1.1 Atoms, Molecules, and Compounds1.2 The Structure of Atoms

Reactions in Living Cells1.3 Chemical Reactions1.4 Chemical Bonds1.5 Ions and Living Cells

Biochemistry1.6 Organic Compounds and Life1.7 Carbohydrates1.8 Lipids1.9 Proteins1.10 Nucleic Acids

Genetic Coding in Cells1.11 The Double Helix1.12 The Functions of DNA

Chapter HighlightsChapter Animations

ChapterMenu

A Explain the relationships among atoms, molecules, elements, and compounds.

Learning Outcomes

By the end of this chapter you will be able to:

B Describe the types of chemical bonds.

C Explain the pH scale and its use.

D Relate the characteristics and functions of the four classes of macromolecules.

E Recognize the importance of nucleic acids in inheritance.

What evidence do you see of chemicals in this hot spring?

The Chemistry of Life What roles do chemicals

play in life?

The Champagne Pool, a mineral rich hot spring at Waiotapu Thermal Park in New Zealand

The Chemistry of Life• A scientist named Lavoisier founded modern

chemistry by using physical laws and measurement to understand how chemicals react.

• Biochemistry—the chemistry of living organisms—plays a central role in our understanding of today’s biological questions.

The Champagne Pool, a mineral rich hot spring at Waiotapu Thermal Park in New Zealand

• 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.

General Chemistry

1.1 Atoms, Molecules, and Compounds

• 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.

1.1 Atoms, Molecules, and Compounds (cont.)

General Chemistry

• Under certain conditions, water molecules can break down into two different substances (which are also molecules), hydrogen and oxygen.

• Hydrogen and oxygen are elements—substances that cannot be broken down chemically into simpler substances.

• Atoms are the smallest unit of an element that still has the chemical properties of that element.

1.1 Atoms, Molecules, and Compounds (cont.)

General Chemistry

• 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.

• Elements can combine chemically in many ways to form the millions of compounds that give Earth its variety of materials.

Molecules of water, hydrogen, and oxygen are made from combinations of atoms, as shown in these models.

1.1 Atoms, Molecules, and Compounds (cont.)

General Chemistry

• 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).

1.1 Atoms, Molecules, and Compounds (cont.)

General Chemistry

• 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).

• The remaining 3% contain small amounts of other elements.

1.1 Atoms, Molecules, and Compounds (cont.)

General Chemistry

• Atoms themselves are built of many smaller subatomic particles.

1.2 The Structure of Atoms

• The subatomic particles of atoms that are basic to an understanding of biology are electrons, protons, and neutrons.

General Chemistry

– an electron carries a negative electric charge

– a proton has a positive charge

– a neutron has no charge (it is neutral)

• 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.

1.2 The Structure of Atoms (cont.)

General Chemistry

• 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.

• An atom of carbon has six protons and six neutrons in its nucleus and six electrons orbiting the nucleus.

1.2 The Structure of Atoms (cont.)

General Chemistry

• Nitrogen has seven protons and seven electrons (two in the innermost shell, five in an outer shell which can hold eight).

• Oxygen has eight protons and eight electrons (two in the innermost shell, six in an outer shell which can hold eight).

1.2 The Structure of Atoms (cont.)

General Chemistry

• 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.

1.2 The Structure of Atoms (cont.)

General Chemistry

• 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 isotopes.

1.2 The Structure of Atoms (cont.)

General Chemistry

• Some isotopes, called radioisotopes, have unstable atomic nuclei that break down, releasing radiation energy.

• Chemical bonds are the attraction, sharing, or transfer of outer shell electrons from one atom to another.

Reactions in Living Cells

1.3 Chemical Reactions

• 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.

Reactions in Living Cells

1.3 Chemical Reactions (cont.)

• 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

Reactions in Living Cells

1.3 Chemical Reactions (cont.)

• 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):

Reactions in Living Cells

1.3 Chemical Reactions (cont.)

Models of chemical reactions

• 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.

Reactions in Living Cells

1.3 Chemical Reactions (cont.)

• One type of chemical bond forms when electrons move from one atom to another atom.

1.4 Chemical Bonds

• This type of chemical bond occurs in many substances, including sodium chloride (NaCl).

Reactions in Living Cells

• 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.

1.4 Chemical Bonds (cont.)

Reactions in Living Cells

Reactions in Living Cells

(a) Sodium and (b) chlorine can react to form (c) the salt sodium chloride (NaCl). By losing one electron, sodium achieves two filled shells (2 + 8) and becomes a stable positive ion. By gaining one electron, chlorine achieves three filled shells (2 + 8 + 8) and becomes a stable negative ion, chloride.

• 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.

• In a molecule of water, each of the two hydrogen atoms shares a pair of electrons with the same oxygen atom.

1.4 Chemical Bonds (cont.)

Reactions in Living Cells

• 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.

1.4 Chemical Bonds (cont.)

Reactions in Living Cells

• 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.

1.4 Chemical Bonds (cont.)

Reactions in Living Cells

• 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).

• A large number of hydrogen bonds can be quite strong, but single hydrogen bonds are much weaker than covalent bonds.

1.4 Chemical Bonds (cont.)

Reactions in 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.

1.5 Ions and Living Cells

• 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.

Reactions in Living Cells

• The level of H+ and OH- ions in solution is described on a scale from 0 to 14 known as the pH scale.

1.5 Ions and Living Cells (cont.)

• A solution (a mixture in water) that has the same number of H+ and OH- ions is neutral and has a pH of 7.

Reactions in Living Cells

• A solution having more H+ than OH- is acidic and has a pH less than 7 (low pH).

1.5 Ions and Living Cells (cont.)

• A solution that has more OH- than H+ ions is basic (or alkaline) and has a pH greater than 7 (high pH).

Reactions in Living Cells

• 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.

1.5 Ions and Living Cells (cont.)

Reactions in Living Cells

The pH of some common substances. Note that most biological substances are slightly acidic (pH 6–7). The greater acidity of soft drinks (pH 3) is partly responsible for contributing to tooth decay.

• The pH of a cell’s interior helps regulate the cell’s chemical reactions.

1.5 Ions and Living Cells (cont.)

Reactions in Living Cells

• Organisms have ways to control pH and to respond to changes in the pH of their environment.

• Organic compounds, in which carbon atoms are combined with hydrogen and usually oxygen, are needed for life to exist.

Biochemistry

1.6 Organic Compounds and Life

• 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.

Biochemistry

1.6 Organic Compounds and Life (cont.)

Biochemistry

1.6 Organic Compounds and Life (cont.)

Carbon atoms (black) make up a carbon skeleton and link with other atoms, such as hydrogen (white). In each formula, a short line indicates a covalent bond: (a), a molecule of methane; (b), part of the carbon skeleton of a larger molecule; (c), a view of (b) that indicates the three-dimensional structure of the molecule.

• 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.

1.7 Carbohydrates

• The simplest carbohydrates are single sugars, such as glucose, called monosaccharides, which may contain three to seven carbon atoms in their carbon skeletons.

Biochemistry

• Biologically important sugars often have a phosphate group composed of an atom of phosphorus and four atoms of oxygen attached to the carbon skeleton and are called sugar-phosphates.

1.7 Carbohydrates (cont.)

Biochemistry

• Two simple sugar molecules, or monosaccharides, may bond to form a double sugar, or disaccharide, such as sucrose.

1.7 Carbohydrates (cont.)

Biochemistry

• Several glucose molecules may bond to form complex carbohydrates called polysaccharides, such as starch and cellulose.

1.7 Carbohydrates (cont.)

Biochemistry

• Lipids, or fats and oils, are macromolecules that have two primary functions:

1.8 Lipids

– long-term storage of energy

– carbon and building of structural parts of cell membranes

Biochemistry

• Lipids:

1.8 Lipids (cont.)

Biochemistry

– are nonpolar and generally do not dissolve in water

– 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.

1.8 Lipids (cont.)

Biochemistry

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.

• The biologically important properties of simple fats depend on their fatty acids.

– Fatty acids in which single bonds join the carbon atoms are saturated fatty acids.

– Unsaturated fatty acids are fatty acids in which double bonds join some of the carbon atoms.

1.8 Lipids (cont.)

Biochemistry

• 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.

1.8 Lipids (cont.)

Biochemistry

• Phospholipids form when a molecule of glycerol combines with two fatty acids and a phosphate group.

• Together with proteins, phospholipids form cellular membranes.

1.8 Lipids (cont.)

Biochemistry

Glycerol joins with two fatty acids and a polar phosphate group to form a phospholipid (a) and (b). When phospholipids form membranes (c), the polar head associates with water on the membrane surface, and the nonpolar tail faces the interior of the membrane, away from water. Membranes prevent the cell contents from mixing with the external environment.

• Cholesterol is part of the membrane structure of animal cells and is important in nutrition.

1.8 Lipids (cont.)

Biochemistry

Cholesterol has a fused four-ring structure with additional side groups. Cholesterol is important in membrane structure, and the sex hormones are derived from it.

• Every living cell contains from several hundred to several thousand different macromolecules known as proteins.

1.9 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.

Biochemistry

• Cells make proteins by linking building blocks called amino acids which are small molecules that contain carbon, hydrogen, oxygen, and nitrogen atoms; two also contain sulfur atoms.

1.9 Proteins (cont.)

Biochemistry

Amino acids (except for proline) have a central carbon atom bonded to a hydrogen atom, an amino group, an acid group, and an R-group. The R-group is any of 20 arrangements of C, H, O, N, and S atoms, depending on, and giving unique structure to, each amino acid.

• 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.

1.9 Proteins (cont.)

Biochemistry

Formation of a polypeptide

• The sequence of amino acids in a polypeptide chain forms the primary structure of a protein.

• In most proteins, the chain folds or twists to form local structures known as secondary structures.

1.9 Proteins (cont.)

Biochemistry

• More complex folding creates a tertiary structure, which usually is globular, or spherical.

• One of the major forces controlling how a protein folds is hydrophobicity, or the tendency for nonpolar amino acids to avoid water.

1.9 Proteins (cont.)

Biochemistry

• 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.

1.9 Proteins (cont.)

Biochemistry

• Nucleic acids are macromolecules that dictate the amino-acid sequence of proteins, which in turn control the basic life processes.

1.10 Nucleic Acids

• Nucleic acids also are the source of genetic information in chromosomes, which are passedfrom parent to offspring during reproduction.

Biochemistry

• Nucleic acids are made of relatively simple units called nucleotides connected to form long chains.

• Each nucleotide consists of three parts:

1.10 Nucleic Acids (cont.)

Biochemistry

– a 5-carbon sugar (a pentose), which may be either ribose or deoxyribose

– a nitrogen-containing base, which is a single or double ringlike structure of carbon, hydrogen, and nitrogen

– a phosphate group

1.10 Nucleic Acids (cont.)

Biochemistry

Two sugars found in nucleotides. Ribose and deoxyribose form ring structures with four of their carbon atoms joined by an oxygen atom. The blue boxes highlight the difference between the two sugars. Ribose has a hydroxyl group (—OH), whereas deoxyribose has only a hydrogen atom at the same carbon. Compared to ribose, deoxyribose is missing one oxygen atom.

1.10 Nucleic Acids (cont.)

Biochemistry

Four nitrogen bases that occur in nucleotides. Symbols are used to represent the nucleotides adenine, guanine, cytosine, and thymine. Note that cytosine and thymine have a single-ring structure; adenine and guanine have a double ring.

• Nucleic acids that contain ribose in their nucleotides are called ribonucleic acids, or RNA.

• Nucleotides containing deoxyribose form deoxyribonucleic acids, or DNA.

1.10 Nucleic Acids (cont.)

Biochemistry

• 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.

The components of DNA. Each nucleotide contains one of the bases, one sugar, and one phosphate group. The sugar is deoxyribose, making these the four nucleotides of DNA.

1.10 Nucleic Acids (cont.)

Biochemistry

• RNA is a nucleic acid much like DNA, except:

1.10 Nucleic Acids (cont.)

Biochemistry

– it contains the sugar ribose instead of deoxyribose

– the nitrogen base uracil replaces the base thymine

– it is single stranded, although it can fold into complex shapes

• 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).

Genetic Coding in Cells

1.11 The Double Helix

• 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).

Genetic Coding in Cells

A diagram showing the pairing of two nitrogen bases. Hydrogen bonds connect cytosine to guanine and thymine to adenine.

• Experiments done by Rosalind Franklin in the laboratory of Maurice Wilkins suggested to Watson and Crick that DNA molecules have a double-helix structure.

1.11 The Double Helix (cont.)

Genetic Coding in Cells

Maurice Wilkins Rosalind Franklin

• 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.

1.11 The Double Helix (cont.)

Genetic Coding in Cells

The structure of DNA

• The folds in RNA are held together by the same type of base pairing as in DNA.

1.11 The Double Helix (cont.)

Genetic Coding in Cells

Most of the RNA molecule is single stranded, but the shaded region shows hydrogen bonding between base pairs, which forms a double-stranded region. Note the four bases in RNA.

• DNA forms the genes, units of genetic information, that pass from parent to offspring.

1.12 The Functions of DNA

• 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.

Genetic Coding in Cells

• 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 protein.

• 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.

1.12 The Functions of DNA (cont.)

Genetic Coding in Cells

This concept map summarizes the major cellular processes that involve DNA. Note that both the information stored in the structure of DNA and the copying of that information during DNA synthesis have important effects on the life of a cell.

Summary

• 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 bonds involving a partially positive hydrogen atom are called hydrogen bonds.

• Cells, the basic units of life, carry out their biological functions through chemical reactions which occur continuously.

Summary (cont.)

• 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.

• In chemical reactions, molecules interact and form different substances.

Reviewing Key TermsMatch the term on the left with the correct description.

___ lipids

___ proteins

___ elements

___ carbohydrate

___ basic

a. an organic compound that contains hydrogen and oxygen atoms in a 2:1 ratio

b. an organic compound composed of one or more polypeptide chains of amino acids

c. pH value reflecting more dissolved hydroxide ions than hydrogen ions

d. a fatlike compound that usually has fatty acids in its molecular structure

e. a substance composed of atoms that are chemically identical

d

b

e

a

c

Reviewing Ideas1. Why is the polar nature of water biologically

significant?

Most cells and tissues contain large amounts of water. Molecules must dissolve in water in order to move easily in and between living cells. Polar molecules, such as sugar, and ions, such as Na+, dissolve in water because of the electric attraction between them and the water molecules. Nonpolar molecules, such as fats and oils, do not dissolve in water.

Reviewing Ideas2. Describe the differences in composition and

structure between RNA and DNA.

RNA is a nucleic acid much like DNA, except that it contains the sugar ribose instead of deoxyribose. Also, in RNA the nitrogen base uracil replaces the base thymine. Structurally, DNA always occurs in cells as a double-stranded helix; RNA is single stranded, although it can fold into complex shapes.

Using Concepts3. What properties of phospholipids makes them

useful in cellular membranes?

The polar phosphate group of a phospholipid allows one end of the lipid molecule to associate with water while the nonpolar end is hydrophobic.

Using Concepts4. Why is the complimentary structure of a DNA

molecule important in passing genetic information from parent to offspring?

Complementarity is the basis for copying DNA.

Synthesize5. What effect could rainfall with a pH of 3.5 have

on a lake ecosystem?

Normal rainwater has a pH of 5.5–6.0. Highly acidic rainfall could cause the pH level in the lake to fall causing the decline of organisms that are adapted to the previous pH level. Organisms that thrive in lower pH levels could become the dominant life forms in the ecosystem.

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Chapter Animations

Models of chemical reactions

Formation of a polypeptide

The structure of DNA

Models of chemical reactions

Formation of a polypeptide

The structure of DNA

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