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: 14C → 14N

Tracers

• Tracer• 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

PET Scanning

Animation: PET scan

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

novacancy

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 (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)

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

• Polarity• Separation of charge into distinct positive and

negative regions in a polar covalent molecule

• Example: Water (H2O)

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 (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

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 (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

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) + 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: Shell models of common elements

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