1. 2
The Chemical Context of Life

2. Overview: A Chemical Connection to Biology
Biology is a multidisciplinary science
Living organisms are subject to basic laws of physics and chemistry
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3. Figure 2.1 What weapon are these wood ants shooting into the air?
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4. Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compounds
Organisms are composed of matter
Matter is anything that takes up space and has mass
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5. Elements and Compounds
Matter is made up of elements
An element is a substance that cannot be broken down to other substances by chemical reactions
A compound is a substance consisting of two or more elements in a fixed ratio
A compound has emergent properties, characteristics different from those of its elements
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6. Sodium Chlorine Sodium chloride Figure 2.2
Figure 2.2 The emergent properties of a compound
Sodium
Chlorine
Sodium chloride
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7. Figure 2.2-1
Figure The emergent properties of a compound (part 1: sodium)
Sodium
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8. Figure 2.2-2
Figure The emergent properties of a compound (part 2: chloride)
Chlorine
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9. Sodium chloride Figure 2.2-3
Figure The emergent properties of a compound (part 3: sodium chloride)
Sodium chloride
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10. The Elements of Life
Of 92 natural elements, about 20–25% are essential elements, needed by an organism to live a healthy life and reproduce
Trace elements are required in only minute quantities
For example, in vertebrates, iodine (I) is required for normal activity of the thyroid gland
In humans, an iodine deficiency can cause goiter
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11. Table 2.1 Elements in the human body
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12. Evolution of Tolerance to Toxic Elements
Some naturally occurring elements are toxic to organisms
In humans, arsenic is linked to many diseases and can be lethal
Some species have become adapted to environments containing elements that are usually toxic
For example, sunflower plants can take up lead, zinc, and other heavy metals in concentrations lethal to most organisms
Sunflower plants were used to detoxify contaminated soils after Hurricane Katrina
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13. Concept 2.2: An element’s properties depend on the structure of its atoms
Each element consists of a certain type of atom, different from the atoms of any other element
An atom is the smallest unit of matter that still retains the properties of an element
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14. Subatomic Particles
Atoms are composed of smaller parts called subatomic particles
Relevant subatomic particles include
Neutrons (no electrical charge)
Protons (positive charge)
Electrons (negative charge)
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15. Neutrons and protons form the atomic nucleus
Electrons form a “cloud” around the nucleus
Neutron mass and proton mass are almost identical and are measured in daltons
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16. Cloud of negative charge (2 electrons) Electrons Nucleus (a) (b)
Figure 2.3
Cloud of negative
charge (2 electrons)
Electrons
Nucleus
Figure 2.3 Simplified models of a helium (He) atom
(a)
(b)
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17. Atomic Number and Atomic Mass
Atoms of the various elements differ in number of subatomic particles
An element’s atomic number is the number of protons in its nucleus
An element’s mass number is the sum of protons plus neutrons in the nucleus
Atomic mass, the atom’s total mass, can be approximated by the mass number
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18. Mass number = number of protons + neutrons
= 23 for sodium
Because neutrons and protons each have a mass of approximately 1 dalton, we can estimate the atomic mass (total mass of one atom) of sodium as 23 daltons
23Na 11
Atomic number = number of protons
= 11 for sodium
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19. Isotopes
All atoms of an element have the same number of protons but may differ in number of neutrons
Isotopes are two atomic forms of an element that differ in number of neutrons
Radioactive isotopes decay spontaneously, giving off particles and energy
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20. Some applications of radioactive isotopes in biological research are
Dating fossils
Tracing atoms through metabolic processes
Diagnosing medical disorders
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21. Cancerous throat tissue Figure 2.4
Figure 2.4 A PET scan, a medical use for radioactive isotopes
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22. The Energy Levels of Electrons
Energy is the capacity to cause change
Potential energy is the energy that matter has because of its location or structure
The electrons of an atom have potential energy due to their distance from the nucleus
Changes in potential energy occur in steps of fixed amounts
An electron’s energy level is correlated with its average distance from the nucleus
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23. Electrons are found in different electron shells, each with a characteristic average distance from the nucleus
The energy level of each shell increases with distance from the nucleus
Electrons can move to higher or lower shells by absorbing or releasing energy, respectively
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24. Third shell (highest energy level in this model)
Figure 2.5
(a) A ball bouncing down a flight
of stairs can come to rest only
on each step, not between steps.
Third shell (highest energy
level in this model)
Energy
absorbed
Second shell (higher
energy level)
Figure 2.5 Energy levels of an atom’s electrons
First shell (lowest energy
level)
Energy
lost
Atomic
nucleus
(b)
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25. Electron Distribution and Chemical Properties
The chemical behavior of an atom is determined by the distribution of electrons in electron shells
The periodic table of the elements shows the electron distribution for each element
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26. Figure 2.6 Hydrogen 1H 2 He 4.003 Atomic number Helium 2He Atomic mass
First
shell
Element symbol
Electron
distribution
diagram
Lithium
3Li
Beryllium
4Be
Boron 5B
Carbon 6C
Nitrogen 7N
Oxygen 8O
Fluorine 9F
Neon
10Ne
Second
shell
Sodium
11Na
Magnesium
12Mg
Aluminum
13Al
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Figure 2.6 Electron distribution diagrams for the first 18 elements in the periodic table
Third
shell
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27. He 2 4.003 Atomic number Helium 2He Element symbol Electron
Figure 2.6-1 2 He
4.003
Atomic number
Helium
2He
Element symbol
Electron
distribution
diagram
Atomic mass
Figure Electron distribution diagrams for the first 18 elements in the periodic table (part 1)
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28. Helium 2He Hydrogen 1H First shell
Figure 2.6-2
Helium
2He
Hydrogen 1H
First
shell
Figure Electron distribution diagrams for the first 18 elements in the periodic table (part 2)
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29. Lithium 3Li Beryllium 4Be Boron 5B Carbon 6C Second shell Sodium 11Na
Figure 2.6-3
Lithium
3Li
Beryllium
4Be
Boron 5B
Carbon 6C
Second
shell
Sodium
11Na
Magnesium
12Mg
Aluminum
13Al
Silicon
14Si
Figure Electron distribution diagrams for the first 18 elements in the periodic table (part 3)
Third
shell
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30. Nitrogen 7N Oxygen 8O Fluorine 9F Neon 10Ne Second shell Phosphorus
Figure 2.6-4
Nitrogen 7N
Oxygen 8O
Fluorine 9F
Neon
10Ne
Second
shell
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Figure Electron distribution diagrams for the first 18 elements in the periodic table (part 4)
Third
shell
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31. Valence electrons are those that occupy the valence shell
Chemical behavior of an atom depends mostly on the number of electrons in its outermost shell, or valence shell
Valence electrons are those that occupy the valence shell
The reactivity of an atom arises from the presence of one or more unpaired electrons in the valence shell
Atoms with completed valence shells are unreactive, or inert
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32. Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms
Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms
This usually results in atoms staying close together, held by attractions called chemical bonds
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33. Covalent Bonds
A covalent bond is the sharing of a pair of valence electrons by two atoms
In a covalent bond, the shared electrons count as part of each atom’s valence shell
Two or more atoms held together by covalent bonds constitute a molecule
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34. Hydrogen atoms (2 H) Figure 2.7-s1
Figure 2.7-s1 Formation of a covalent bond (step 1)
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35. Hydrogen atoms (2 H) Figure 2.7-s2
Figure 2.7-s2 Formation of a covalent bond (step 2)
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36. Hydrogen atoms (2 H) Hydrogen molecule (H2) Figure 2.7-s3
Figure 2.7 Formation of a covalent bond (step 3)
Hydrogen molecule (H2)
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37. This can be abbreviated further with a molecular formula
The notation used to represent atoms and bonding is called a structural formula
For example, H—H
This can be abbreviated further with a molecular formula
For example, H2
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38. In a structural formula, a single bond, the sharing of one pair of electrons, is indicated by a single line between the atoms
For example, H—H
A double bond, the sharing of two pairs of electrons, is indicated by a double line between atoms
For example,
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39. Electron Distribution
Figure 2.8
Name and Molecular
Formula
Electron Distribution
Diagram
Structural
Formula
Space-Filling
Model
(a) Hydrogen (H2) H H
(b) Oxygen (O2) O O
(c) Water (H2O) O H H
Figure 2.8 Covalent bonding in four molecules
(d) Methane (CH4) H H C H H
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40. Each atom that can share valence electrons has a bonding capacity, the number of bonds that the atom can form
Bonding capacity, or valence, usually corresponds to the number of electrons required to complete the atom
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41. Pure elements are composed of molecules of one type of atom, such as H2 and O2
Molecules composed of a combination of two or more types of atoms, such as H2O or CH4, are called compounds
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42. Atoms in a molecule attract electrons to varying degrees
Electronegativity is an atom’s attraction for the electrons of a covalent bond
The more electronegative an atom, the more strongly it pulls shared electrons toward itself
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43. In a nonpolar covalent bond, the atoms share the electrons equally
In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally
Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule
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44. Animation: Covalent Bonds
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45. Figure 2.9  O H H  
Figure 2.9 Polar covalent bonds in a water molecule
H2O
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46. Ionic Bonds
Atoms sometimes strip electrons from their bonding partners
An example is the transfer of an electron from sodium to chlorine
After the transfer of an electron, both atoms have charges and are called ions
Both atoms also have complete valence shells
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47. Na Cl Na Sodium atom Cl Chlorine atom
Figure 2.10-s1 Na Cl Na
Sodium atom Cl
Chlorine atom
Figure 2.10-s1 Electron transfer and ionic bonding (step 1)
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48. Sodium chloride (NaCl)
Figure 2.10-s2 Na Cl Na Cl Na
Sodium atom Cl
Chlorine atom
Na
Sodium ion
(a cation)
Cl-
Chloride ion
(an anion)
Figure 2.10 Electron transfer and ionic bonding (step 2)
Sodium chloride (NaCl)
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49. A cation is a positively charged ion
An anion is a negatively charged ion
An ionic bond is an attraction between an anion and a cation
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50. Compounds formed by ionic bonds are called ionic compounds, or salts
Salts, such as sodium chloride (table salt), are often found in nature as crystals
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51. Animation: Ionic Bonds
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52. Na Cl- Figure 2.11 Figure 2.11 A sodium chloride (NaCl) crystal
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53. Figure 2.11-1 A sodium chloride (NaCl) crystal (photo)
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54. Weak Chemical Bonds
Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules
Many large biological molecules are held in their functional form by weak bonds
Weak chemical bonds include ionic bonds, hydrogen bonds, and van der Waals interactions
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55. Hydrogen Bonds
A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom
In living cells, the electronegative partners are usually oxygen or nitrogen atoms
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56.   H Water (H2O) O H  Hydrogen bond  Ammonia (NH3) N H H  
Figure 2.12   H
Water (H2O) O H 
Hydrogen bond 
Ammonia (NH3)
Figure 2.12 A hydrogen bond N H H   H 
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