Chapter 2 Life ’ s Chemical Basis

Albia Dugger • Miami Dade College

Chapter 2Life’s Chemical

Basis

2.1 Mercury Rising

• Mercury is released into the atmosphere by volcanic activity, and by human activities such as burning coal

• Once airborne, mercury can drift long distances before settling to Earth’s surface, where microbes convert it to a toxic substance called methylmercury

• Once mercury enters the body, it damages the nervous system, brain, kidneys, and other organs

• All human bodies now have detectable amounts of mercury

Atmospheric Fallout from Coal-Fired Power Plant Emissions

2.2 Start With Atoms

• The behavior of elements, which make up all living things, starts with the structure of individual atoms

• The number of protons in the atomic nucleus defines the element, and the number of neutrons defines the isotope

Structure of Atoms

• Atoms are the building blocks of all substances• Made up of electrons, protons and neutrons

• Charge is an electrical property• Attracts or repels other subatomic particles

Characteristics of Atoms

• Electrons (e-) have a negative charge• Move around the nucleus

• The nucleus contains protons and neutrons• Protons (p+) have a positive charge• Neutrons (n) have no charge

Characteristics of Atoms

• 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

• Mass number• Total protons and neutrons in a nucleus• Used to identify isotopes

Atoms

proton

neutron

electron

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

ANIMATED FIGURE: Atomic number, mass number

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Isotopes and Radioisotopes

• Isotopes • Different forms of the same element, with different

numbers of neutrons

• 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

Radioactive Decay

• Example: 14C → 14N

nucleus of 14C, with 6 protons, 8 neutrons

nucleus of 14N, with 7 protons, 7 neutrons

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

Figure 2-4 p25

brain

lungs

heart

liver

kidneys

Non-smoker Smoker

ANIMATED FIGURE: PET scan



Take Home Message:

The basic building blocks of all matter

• All matter consists of atoms, tiny particles that in turn consist of electrons moving around a nucleus of protons and neutrons

• An element is a pure substance that consists only of atoms with the same number of protons. Isotopes are forms of an element that have different numbers of neutrons

• Unstable nuclei of radioisotopes disintegrate spontaneously (decay) at a predictable rate to form predictable products

ANIMATION: Subatomic particles



ANIMATION: Isotopes of hydrogen

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

About Vacancies

• 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

• free radical • Atom with an unpaired electron

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

6

B The second shell corresponds to the second energy level, and it can hold up to 8 electrons. Carbon has 6 protons, so its first shell is full. Its second shell has 4 electrons, and four vacancies. Oxygen has 8 protons and two vacancies. Neon has 10 protons and no vacancies.

neon (Ne)second shell carbon (C) oxygen (O)

8 10

C The third shell, which corresponds to the third energy level, can hold up to 8 electrons. A sodium atom has 11 protons, so its first two shells are full; the third shell has one electron. Thus, sodium has seven vacancies. Chlorine has 17 pro tons and one vacancy. Argon has 18 protons and no vacancies.

third shell argon (Ar)chlorine (Cl)sodium (Na)

181711

A The first shell corresponds to the first energy level, and it can hold up to 2 electrons. Hydrogen has one proton, so it has 1 electron and 1 vacancy. A helium atom has 2 protons, 2 electrons, and no vacancies. The number of protons in each model is shown.

first shell hydrogen (H) helium (He)

11 proton1 electron

2

Stepped Art

Figure 2-5 p26

ANIMATED FIGURE: 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

Figure 2-6 p27

electron loss electron gain

Sodium atom

Chlorine atom

charge: 0 charge: 0

Sodium ion

Chloride ion

11p+ 10e–

17p+ 18e–

charge: +1 charge: –1

11p+ 11e–

17p+ 17e–

ANIMATED FIGURE: Ionic bonding



Take-Home Message:Why do atoms interact?

• An atom’s electrons are the basis of its chemical behavior

• Shells represent all electron orbitals at one energy level in an atom; when the outermost shell is not full of electrons, the atom has a vacancy

• Atoms with vacancies tend to interact with other atoms

2.4 Chemical Bonds:From Atoms to Molecules

• Chemical bonds link atoms into molecules

• The characteristics of a chemical bond arise from the properties of the atoms taking part in it

Chemical Bonds

• 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

The Water Molecule

one oxygen atom

two hydrogen atoms

Bonds and Electrons

• Whether one atom will bond with others depends on the element, and the number and arrangement of its electrons

• electronegativity • Measure of the ability of an atom to pull electrons away

from other atoms

Three Types of Bonds

• 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

Ionic Bonds

• Ionic bond• A strong mutual attraction between two oppositely charges

ions with a large difference in electronegativity (no electron transferred)

• Example: NaCl (table salt)

Ionic Bond: Sodium Chloride

ionic bond

Sodium ion 11p+, 10e–

Chloride ion 17p+, 18e–

11 17


Cl– Na+


positive charge

negative charge

ANIMATED FIGURE: How atoms bond



Covalent Bonds

• 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)

Figure 2-9 p29

molecular hydrogen (H2)

molecular oxygen (O2)

water (H2O)

ANIMATED FIGURE: Covalent bonds

Table 2-1 p29

Take-Home Message:How do atoms interact in chemical bonds?

• A chemical bond forms between atoms when their electrons interact

• A chemical bond may be ionic or covalent depending on the atoms taking part in it

• An ionic bond is a strong mutual attraction between two ions of opposite charge

• Atoms share a pair of electrons in a covalent bond; when the atoms share electrons unequally, the bond is polar

2.5 Hydrogen Bonds and Water

• The unique properties of liquid water arise because of the water molecule's polarity

• Extensive hydrogen bonds form 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

Polarity of the Water Molecule

negative charge

positive charge

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

Figure 2-11a p31

a hydrogen bond

Figure 2-11b p31

Figure 2-11c p31

ANIMATED FIGURE: Structure of water



Water’s Special 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

Water Has Cohesion

• Hydrogen bonds give water cohesion• Provides surface tension• Draws water up from roots of plants

• Cohesion• Molecules resist separation from one another

Water Cohesion and Surface Tension

Water Stabilizes Temperature

• 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 Stabilizes Temperature

• 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 is a Solvent

• 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 is a Solvent

• 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

Take-Home Message: What gives water the special properties that make life possible?

• The polarity of a water molecule gives rise to extensive hydrogen bonding among water molecules

• Hydrogen bonding among water molecules imparts cohesion to liquid water, and the ability to stabilize temperature and dissolve many substances

2.6 Acids and Bases

• 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 biological processes occur within a narrow range of

pH, typically around pH 7

• Concentration refers to the amount of a particular solute that is dissolved in a given volume of fluid

Figure 2-12 p32

battery acid— 0

— 1 gastric fluid

— 2 lemon juice

— 3

tomatoes, winebananas

orange juice

vinegarcola

acid rain

— 4beerbread

— 5black coffeeurine, tea, typical rain

— 6 butter

corn

milk

— 7

blood, tearsegg white

pure water

— 8 seawater

baking soda

— 9 Tums

toothpaste— 10 hand soap

milk of magnesia

detergents

— 11

— 12 hair remover

household ammonia

bleach

— 13 oven cleaner

— 14 drain cleaner

mo

re b

asic

mo

re a

cid

ic

Biological Reactions Occur In Water

• Molecules in water (H2O) can separate into hydrogen ions (H+) and hydroxide ions (OH-)

H20 ↔ H+ + OH-

Acids and Bases

• 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-

Salts

• 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• 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)

Take Home Message: Why is hydrogen important in biological systems?

• pH reflects the number of hydrogen ions in a fluid. Most biological systems function properly only within a narrow range of pH

• Acids release hydrogen ions in water; bases accept them

• Salts release ions other than H+ and OH–

• Buffers help keep pH stable. Inside organisms, they are part of homeostasis

Table 2-1 p34

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Chapter 2 Life ’ s Chemical Basis