Life’s Chemical Basis An inorganic look

Fifty-eight elements make up the human body

1.1 Start With Atoms The behavior of elements, which make up all living things, starts with the structure of individual atoms

Characteristics of Atoms Atoms are the building blocks of all substances Made up of electrons, protons and neutrons Electrons (e-) have a negative charge Move around the nucleus Charge is an electrical property Attracts or repels other subatomic particles

Characteristics of Atoms The nucleus contains protons and neutrons Protons (p+) have a positive charge Neutrons have no charge Atoms differ in number of subatomic particles Atomic number (number of protons) determines the element Elements consist only of atoms with the same atomic number

Characteristics of Atoms Isotopes Different forms of the same element, with different numbers of neutrons Mass number Total protons and neutrons in a nucleus Used to identify isotopes

Atoms

The Periodic Table Periodic table of the elements An arrangement of the elements based on their atomic number and chemical properties Created by Dmitry Mendeleev

Periodic Table of the Elements

2.2 Putting Radioisotopes to Use Some radioactive isotopes – radioisotopes – are used in research and medical applications

Radioisotopes Henri Becquerel discovered radioisotopes of uranium in the late 1800s Radioactive decay Radioisotopes emit subatomic particles of energy when their nucleus breaks down, transforming one element into another at a constant rate Example: 14C → 14N

Tracers Tracer Examples: Any molecule with a detectable substance attached Examples: CO2 tagged with 14C used to track carbon through photosynthesis Radioactive tracers used in medical PET scans

A A patient is injected with a radioactive tracer and moved into a scanner like this one. Detectors that intercept radioactive decay of the tracer surround the body part of interest. Figure 2.4 PET scanning. Fig. 2-4a, p. 23

B Radioactive decay detected by the scanner is converted into digital images of the body’s interior. Two tumors (blue) in and near the bowel of a cancer patient are visible in this PET scan. tumors Figure 2.4 PET scanning. Fig. 2-4b, p. 23

2.1-2.2 Key Concepts: Atoms and Elements Atoms are particles that are the building blocks of all matter; they can differ in numbers of protons, electrons, and neutrons Elements are pure substances, each consisting entirely of atoms with the same number of protons

2.3 Why Electrons Matter Atoms acquire, share, and donate electrons Whether an atom will interact with other atoms depends on how many electrons it has

Atoms and Energy Levels Electrons move around nuclei in orbitals Each orbital holds two electrons Each orbital corresponds to an energy level An electron can move in only if there is a vacancy vacancy no vacancy

Why Atoms Interact The shell model of electron orbitals diagrams electron vacancies; filled from inside out First shell: one orbital (2 electrons) Second shell: four orbitals (8 electrons) Third shell: four orbitals (8 electrons) Atoms with vacancies in their outer shell tend to give up, acquire, or share electrons

Shell Models

Figure 2.5 Shell models, which help us check for vacancies in atoms. Each circle, or shell, represents all orbitals at one energy level. Atoms with vacancies in the outermost shell tend to form bonds. Remember, atoms do not look anything like these flat diagrams. Fig. 2-5a, p. 24

argon 18p+, 18e− sodium 11p+, 11e– chlorine 17p+, 17e– carbon 6p+, 6e– C) Third shell. This shell corresponds to the third energy level. It has four orbitals with room for eight electrons. Sodium has one electron in the third shell; chlorine has seven. Both have vacancies, so both form chemical bonds. Argon, with no vacancies, does not. argon 18p+, 18e− sodium 11p+, 11e– chlorine 17p+, 17e– B) Second shell. This shell, which corresponds to the second energy level, has four orbitals—room for a total of eight electrons. Carbon has six electrons: two in the first shell and four in the second. It has four vacancies. Oxygen has two vacancies. Both carbon and oxygen form chemical bonds. Neon, with no vacancies, does not. carbon 6p+, 6e– oxygen 8p+, 8e– neon 10p+, 10e– Figure 2.5 Shell models, which help us check for vacancies in atoms. Each circle, or shell, represents all orbitals at one energy level. Atoms with vacancies in the outermost shell tend to form bonds. Remember, atoms do not look anything like these flat diagrams. A) First shell. A single shell corresponds to the first energy level, which has a single orbital that can hold two electrons. Hydrogen has only one electron in this shell, so it has one vacancy. A helium atom has two electrons (no vacancies), so it does not form bonds. hydrogen 1p+, 1e– helium 2p+, 2e– Stepped Art Fig. 2-5a, p. 24

Atoms and Ions Ion Electronegativity An atom with a positive or negative charge due to loss or gain of electrons in its outer shell Examples: Na+, Cl- Electronegativity A measure of an atom’s ability to pull electrons from another atom

Ion Formation

Sodium ion 11p+ 11e– ______ no net charge Chlorine atom 17p+ 17e– electron loss electron gain Sodium atom 11p+ 10e– ______ net positive charge Chloride ion 17p+ 18e– ______ net negative charge Figure 2.6 Ion formation. Fig. 2-6, p. 25

From Atoms to Molecules Chemical bond An attractive force existing between two atoms when their electrons interact Molecule Two or more atoms joined in chemical bonds

Combining Substances Compounds Mixture Molecules consisting of two or more elements whose proportions do not vary Example: Water (H2O) Mixture Two or more substances that intermingle but do not bond; proportions of each can vary

A Compound: Water

2.3 Key Concepts: Why Electrons Matter Whether one atom will bond with others depends on the element, and the number and arrangement of its electrons

2.4 What Happens When Atoms Interact? The characteristics of a bond arise from the properties of the atoms that participate in it The three most common types of bonds in biological molecules are ionic, covalent, and hydrogen bonds

Different Ways to Represent the Same Molecule

Ionic Bonding Ionic bond A strong mutual attraction between two oppositely charges ions with a large difference in electronegativity (an electron is not transferred) Example: NaCl (table salt)

Figure 2.7 Ionic bonds. Fig. 2-7a, p. 26

A A crystal of table salt is a cubic lattice of many Figure 2.7 Ionic bonds. A A crystal of table salt is a cubic lattice of many sodium and chloride ions. Fig. 2-7a, p. 26

Figure 2.7 Ionic bonds. Fig. 2-7b, p. 26

Covalent Bonding Covalent bond Two atoms with similar electronegativity and unpaired electrons sharing a pair of electrons Can be stronger than ionic bonds Atoms can share one, two, or three pairs of electrons (single, double, or triple covalent bonds)

Characteristics of Covalent Bonds Nonpolar covalent bond Atoms sharing electrons equally; formed between atoms with identical electronegativity Polar covalent bond Atoms with different electronegativity do not share electrons equally; one atom has a more negative charge, the other is more positive

Polarity Polarity Separation of charge into distinct positive and negative regions in a polar covalent molecule Example: Water (H2O)

Molecular oxygen (O=O) Two oxygen atoms, each Molecular hydrogen (H—H) Two hydrogen atoms, each with one proton, share two electrons in a nonpolar covalent bond. Molecular oxygen (O=O) Two oxygen atoms, each with eight protons, share four electrons in a double covalent bond. Water molecule (H—O—H) Two hydrogen atoms share electrons with an oxygen atom in two polar covalent bonds. The oxygen exerts a greater pull on the shared electrons, so it has a slight negative charge. Each hydrogen has a slight positive charge. Figure 2.8 Covalent bonds, in which atoms with unpaired electrons in their outermost shell become more stable by sharing electrons. Two electrons are shared in each covalent bond. When sharing is equal, the bond is nonpolar. When one atom exerts a greater pull on the electrons, the bond is polar. Fig. 2-8, p. 27

Hydrogen Bonding Hydrogen bond A weak attraction between a highly electronegative atom and a hydrogen atom taking part in a separate polar covalent bond Hydrogen bonds do not form molecules and are not chemical bonds Hydrogen bonds stabilize the structures of large biological molecules

Hydrogen Bonds

Figure 2.9 Hydrogen bonds. Hydrogen bonds form at a hydrogen atom taking part in a polar covalent bond. The hydrogen atom’s slight positive charge weakly attracts an electronegative atom. As shown here, hydrogen (H) bonds can form between molecules or between different parts of the same molecule. Fig. 2-9a, p. 27

B Hydrogen bonds are individually weak, but many of them form B Hydrogen bonds are individually weak, but many of them form. Collectively, they are strong enough to stabilize the structures of large biological molecules such as DNA, shown here. Figure 2.9 Hydrogen bonds. Hydrogen bonds form at a hydrogen atom taking part in a polar covalent bond. The hydrogen atom’s slight positive charge weakly attracts an electronegative atom. As shown here, hydrogen (H) bonds can form between molecules or between different parts of the same molecule. Fig. 2-9b, p. 27

2.4 Key Concepts: Atoms Bond Atoms of many elements interact by acquiring, sharing, and giving up electrons Ionic, covalent, and hydrogen bonds are the main interactions between atoms in biological molecules

2.5 Water’s Life-Giving Properties Living organisms are mostly water; all the chemical reactions of life are carried out in water Water is essential to life because of its unique properties The properties of water are a result of extensive hydrogen bonding among water molecules

Polarity of the Water Molecule Overall, water (H2O) has no charge The water molecule is polar Oxygen atom is slightly negative Hydrogen atoms are slightly positive Hydrogen bonds form between water molecules Gives water unique properties

Water: Essential for Life

Figure 2.10 Water, a substance that is essential for life. Fig. 2-10a, p. 28

Figure 2.10 Water, a substance that is essential for life. Fig. 2-10b, p. 28

Figure 2.10 Water, a substance that is essential for life. Fig. 2-10c, p. 28

Figure 2.10 Water, a substance that is essential for life. C Below 0°C (32°F), the hydrogen bonds hold water molecules rigidly in the three-dimensional lattice of ice. The molecules are less densely packed in ice than in liquid water, so ice floats on water. The Arctic ice cap is melting because of global warming. It will probably be gone in fifty years, and so will polar bears. Polar bears must now swim farther between shrinking ice sheets, and they are drowning in alarming numbers. Fig. 2-10c, p. 28

Water’s Solvent Properties A substance (usually liquid) that can dissolve other substances (solutes) Water is a solvent The collective strength of many hydrogen bonds pulls ions apart and keeps them dissolved

Water’s Solvent Properties Water dissolves polar molecules Hydrogen bonds form between water molecules and other polar molecules Polar molecules dissolved by water are hydrophilic (water-loving) Nonpolar (hydrophobic) molecules are not dissolved by water

Water Molecules Surrounding an Ionic Solid

Water’s Temperature-Stabilizing Effects The surface temperature of water decreases during evaporation Evaporation Conversion of a liquid to a gas by heat energy Ice is less dense than liquid water Hydrogen bonds form a lattice during freezing

Water’s Cohesion Hydrogen bonds give water cohesion Cohesion Provides surface tension Draws water up from roots of plants Cohesion Molecules resist separation from one another

Cohesion of Water

2.5 Key Concepts: Water of Life Life originated in water and is adapted to its properties Water has temperature-stabilizing effects, cohesion, and a capacity to act as a solvent for many other substances These properties make life possible on Earth

2.6 Acids and Bases Hydrogen ions have far-reaching effects because they are chemically active, and because there are so many of them Chemical reactions involving acids and bases are important to homeostasis

Biological Reactions Occur In Water Molecules in water (H2O) can separate into hydrogen ions (H+) and hydroxide ions (OH-) H20 ↔ H+ + OH-

The pH Scale pH is a measure of the number of hydrogen ions in a solution The more hydrogen ions, the lower the pH pH 7 is neutral (pure water) Most life chemistry occurs around pH7

A pH Scale

0 — 100 battery acid 1— 10–1 gastric fluid 2 — acid rain 10–2 lemon juice cola more acidic 3 — 10–3 vinegar orange juice tomatoes, wine 4 — 10–4 bananas beer bread 5 — 10–5 coffee urine, tea, typical rain 6 — 10–6 corn butter milk 7 — 10–7 pure water blood, tears 8 — egg white 10–8 seawater baking soda 9 — 10–9 phosphate detergents Tums Figure 2.13 A pH scale. Here, red dots signify hydrogen ions (H+) and blue dots signify hydroxyl ions (OH–). Also shown are approximate pH values for some common solutions. This pH scale ranges from 0 (most acidic) to 14 (most basic). A change of one unit on the scale corresponds to a tenfold change in the amount of H+ ions (blue numbers). toothpaste 10 — 10–10 hand soap milk of magnesia more basic 11— 10–11 household ammonia 12 — 10–12 hair remover bleach 13 — 10–13 oven cleaner 14 — 10–14 drain cleaner Fig. 2-13, p. 30

How Do Acids and Bases Differ? Acids donate hydrogen ions in a water solution pH below 7 Bases accept hydrogen ions in a water solution pH above 7

Acids: Weak or Strong Acids and bases can be weak or strong Gastric fluid, pH 2-3 Acid rain Example: Hydrochloric acid is a strong acid HCl ↔ H+ + Cl-

Acid Rain Sulfur dioxide dissolves in water vapor to form an acidic solution

Salts and Water Salt HCl (acid) + NaOH (base) → NaCl (salt) + H20 A compound that dissolves easily in water and releases ions other than H+ and OH- HCl (acid) + NaOH (base) → NaCl (salt) + H20

Buffers Against Shifts in pH Buffer system A set of chemicals (a weak acid or base and its salt) that can keep the pH of a solution stable OH- + H2CO3 (carbonic acid) → HCO3- (bicarbonate) + H20 H+ + HCO3- (bicarbonate) → H2CO3 (carbonic acid)

Buffering Carbon Dioxide in Blood Carbon dioxide in blood forms carbonic acid, which separates into H+ and bicarbonate H2O + CO2 (carbon dioxide) → H2CO3 (carbonic acid) → H+ + HCO3- (bicarbonate)

2.6 Key Concepts: The Power of Hydrogen Life is responsive to changes in the amounts of hydrogen ions and other substances dissolved in water

Summary: Players in the Chemistry of Life

Animation: Buffer system

Animation: Covalent bonds

Animation: Electron arrangements in atoms

Animation: Isotopes of hydrogen

Animation: Shell models of common elements

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