Life’s Chemical Basis Chapter 2 Hsueh-Fen Juan ( 阮雪芬 ) Sep. 18, 2012

Video: What are you worth?

Impacts, Issues: What Are You Worth? 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: 14 C → 14 N

Tracers Tracer Any molecule with a detectable substance attached Examples: CO 2 tagged with 14 C used to track carbon through photosynthesis Radioactive tracers used in medical PET scans

PET Scanning

Animation: PET scan

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

Animation: The shell model of electron distribution

Atoms and Ions Ion 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

Animation: How atoms bond

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 Molecules consisting of two or more elements whose proportions do not vary Example: Water (H 2 O) 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)

Ionic Bonds

Animation: Ionic bonding

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 Separation of charge into distinct positive and negative regions in a polar covalent molecule Example: Water (H 2 O)

Covalent Bonds

Animation: Covalent bonds

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

Animation: Examples of hydrogen bonds

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 (H 2 O) 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

Fig. 2-10a, p. 28 Water: Essential for Life

Fig. 2-10b, p. 28 Water: Essential for Life

Fig. 2-10c, p. 28 Water: Essential for Life

Animation: Structure of water

Water’s Solvent Properties Solvent 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

Animation: Spheres of hydration

Water’s Temperature-Stabilizing Effects Compared with other molecules, water absorbs more heat before it becomes measurably hotter Temperature A way to measure the energy of molecular motion Molecules move faster as they absorb heat

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 Provides surface tension Draws water up from roots of plants Cohesion ( 內聚力 ) 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 (H 2 O) can separate into hydrogen ions (H + ) and hydroxide ions (OH - ) H 2 0 ↔ 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

Animation: The pH scale

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 A compound that dissolves easily in water and releases ions other than H + and OH - HCl (acid) + NaOH (base) → NaCl (salt) + H 2 0

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 - + H 2 CO 3 (carbonic acid) → HCO 3 - (bicarbonate) + H 2 0 H + + HCO 3 - (bicarbonate) → H 2 CO 3 (carbonic acid)

Buffering Carbon Dioxide in Blood Carbon dioxide in blood forms carbonic acid, which separates into H + and bicarbonate H 2 O + CO 2 (carbon dioxide) → H 2 CO 3 (carbonic acid) → H + + HCO 3 - (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: Shell models of common elements

ABC video: The Wine of Life