Chemical Context of Life

Chapter 2

The Chemical Context of Life

PowerPoint Lectures for Biology, Seventh Edition
Neil Campbell and Jane Reece

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• Overview: Chemical Foundations of Biology

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• The bombardier beetle uses chemistry to defend itself

Figure 2.1
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• Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compounds

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Elements and Compounds
• Organisms are composed of matter, which is anything that takes up space and has mass

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• Matter is made up of elements, substances that cannot be broken down to other substances by chemical reactions

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• A compound
– Is a substance consisting of two or more elements combined in a fixed ratio – Has characteristics different from those of its elements

+

Figure 2.2

Sodium

Chloride

Sodium Chloride

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Essential Elements of Life • Essential elements
– Include carbon, hydrogen, oxygen, and nitrogen – Make up 96% of living matter

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• A few other elements
– Make up the remaining 4% of living matter

Table 2.1
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• The effects of essential element deficiencies

Figure 2.3

(a) Nitrogen deficiency

(b) Iodine deficiency

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• Trace elements
– Are required by an organism in only minute quantities

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• Concept 2.2: An element’s properties depend on the structure of its atoms

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• Each element
– Consists of a certain kind of atom that is different from those of other elements

• An atom
– Is the smallest unit of matter that still retains the properties of an element

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Subatomic Particles • Atoms of each element
– Are composed of even smaller parts called subatomic particles

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• Relevant subatomic particles include
– Neutrons, which have no electrical charge – Protons, which are positively charged – Electrons, which are negatively charged

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• Protons and neutrons
– Are found in the atomic nucleus

• Electrons
– Surround the nucleus in a “cloud”

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• Simplified models of an atom
Cloud of negative charge (2 electrons) Nucleus Electrons

(a) This model represents the electrons as a cloud of negative charge, as if we had taken many snapshots of the 2 electrons over time, with each dot representing an electron‘s position at one point in time.

(b) In this even more simplified model, the electrons are shown as two small blue spheres on a circle around the nucleus.

Figure 2.4

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Atomic Number and Atomic Mass • Atoms of the various elements
– Differ in their number of subatomic particles

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• The atomic number of an element
– Is the number of protons – Is unique to each element

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• The mass number of an element
– Is the sum of protons plus neutrons in the nucleus of an atom – Is an approximation of the atomic mass of an atom

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Isotopes • Atoms of a given element
– May occur in different forms

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• Isotopes of a given element
– Differ in the number of neutrons in the atomic nucleus – Have the same number of protons

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• Radioactive isotopes
– Spontaneously give off particles and energy

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– Can be used in biology
APPLICATION Scientists use radioactive isotopes to label certain chemical substances, creating tracers that can be used to follow a metabolic process or locate the substance within an organism. In this example, radioactive tracers are being used to determine the effect of temperature on the rate at which cells make copies of their DNA. TECHNIQUE Ingredients including Radioactive tracer (bright blue) Human cells 1
Ingredients for making DNA are added to human cells. One ingredient is labeled with 3H, a radioactive isotope of hydrogen. Nine dishes of cells are incubated at different temperatures. The cells make new DNA, incorporating the radioactive tracer with 3H. The cells are placed in test tubes, their DNA is isolated, and unused ingredients are removed.

Incubators
1 2
15°C

10°C 25°C

3
20°C

4

5
30°C

6
35°C

7
40°C

8
45°C

9
50°C

2

DNA (old and new)
1 2 3 4 5 6 7 8 9

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3

A solution called scintillation fluid is added to the test tubes and they are placed in a scintillation counter. As the 3H in the newly made DNA decays, it emits radiation that excites chemicals in the scintillation fluid, causing them to give off light. Flashes of light are recorded by the scintillation counter.

RESULTS The frequency of flashes, which is recorded as counts per minute, is proportional to the amount of the radioactive tracer present, indicating the amount of new DNA. In this experiment, when the counts per minute are plotted against temperature, it is RESULTS clear that temperature affects the rate of DNA synthesis—the most DNA was made at 35°C.
Counts per minute (x 1,000) 30 20 10 0 10 20 30 40 50 Temperature (°C) Optimum temperature for DNA synthesis

Figure 2.5

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– Can be used in biology

Cancerous throat tissue
Figure 2.6
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The Energy Levels of Electrons • An atom’s electrons
– Vary in the amount of energy they possess

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• Energy
– Is defined as the capacity to cause change

• Potential energy
– Is the energy that matter possesses because of its location or structure

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• The electrons of an atom
– Differ in the amounts of potential energy they possess

Figure 2.7A

(a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons, because the ball can only rest on each step, not between steps.

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• Energy levels
– Are represented by electron shells
Third energy level (shell)

Second energy level (shell)

Energy absorbed

First energy level (shell) Energy lost Atomic nucleus (b) An electron can move from one level to another only if the energy it gains or loses is exactly equal to the difference in energy between the two levels. Arrows indicate some of the step-wise changes in potential energy that are possible.

Figure 2.7B

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Electron Configuration and Chemical Properties • The chemical behavior of an atom
– Is defined by its electron configuration and distribution

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• The periodic table of the elements
– Shows the electron distribution for all the elements
Hydrogen 1H First shell Lithium 3Li Second shell Sodium Magnesium Aluminum Silicon Phosphorus Sulfur 13Al 16S 11Na 12Mg 14Si 15P Third shell Figure 2.8
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Atomic mass

2 He 4.00

Atomic number Helium 2He
Element symbol

Electron-shell diagram Beryllium 4Be Boron 3B Carbon 6C Nitrogen 7N Oxygen Fluorine 8O 9F Neon 10Ne

Chlorine 17Cl

Argon 18Ar

• Valence electrons
– Are those in the outermost, or valence shell – Determine the chemical behavior of an atom

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Electron Orbitals • An orbital
– Is the three-dimensional space where an electron is found 90% of the time

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• Each electron shell
– Consists of a specific number of orbitals

Electron orbitals. Each orbital holds up to two electrons.
1s orbital 2s orbital

x
Z

Y

Three 2p orbitals

1s, 2s, and 2p orbitals

Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. (a) First shell (maximum 2 electrons) (b) Second shell (maximum 8 electrons) (c) Neon, with two filled shells (10 electrons)

Figure 2.9

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• Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms

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Covalent Bonds • A covalent bond
– Is the sharing of a pair of valence electrons

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• Formation of a covalent bond
Hydrogen atoms (2 H) 1
In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus.

+

+

2

When two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus.

+

+

3

The two electrons become shared in a covalent bond, forming an H2 molecule.

+

+

Hydrogen molecule (H2)

Figure 2.10
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• A molecule
– Consists of two or more atoms held together by covalent bonds

• A single bond
– Is the sharing of one pair of valence electrons

• A double bond
– Is the sharing of two pairs of valence electrons

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• Single and double covalent bonds
Name (molecular formula) Electronshell diagram Structural formula Spacefilling model

(a) Hydrogen (H2). Two hydrogen atoms can form a single bond.

H

H

(b) Oxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.

O

O

Figure 2.11 A, B

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• Covalent bonding in compounds
Name (molecular formula) Electronshell diagram Structural formula Spacefilling model

(c) Water (H2O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water.

O H

H

(d) Methane (CH4). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane.

H H C H H

Figure 2.11 C, D
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• Electronegativity
– Is the attraction of a particular kind of atom for the electrons in a covalent bond

• The more electronegative an atom
– The more strongly it pulls shared electrons toward itself

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• In a nonpolar covalent bond
– The atoms have similar electronegativities – Share the electron equally

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• In a polar covalent bond
– The atoms have differing electronegativities – Share the electrons unequally
Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

–

O

This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens.

Figure 2.12

+

H H2O

H

+

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Ionic Bonds • In some cases, atoms strip electrons away from their bonding partners

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• Electron transfer between two atoms creates ions • Ions
– Are atoms with more or fewer electrons than usual – Are charged atoms

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• An anion
– Is negatively charged ions

• A cation
– Is positively charged

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• An ionic bond
– Is an attraction between anions and cations
1

The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom.

2 Each resulting ion has a completed

valence shell. An ionic bond can form between the oppositely charged ions.

+

–

Na

Cl

Na

Cl

Na Figure 2.13
Sodium atom (an uncharged atom)

Cl Chlorine atom (an uncharged atom)

Na+ Sodium on (a cation)

Cl– Chloride ion (an anion)

Sodium chloride (NaCl)

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• Ionic compounds
– Are often called salts, which may form crystals

Na+ Cl– Figure 2.14

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Weak Chemical Bonds • Several types of weak chemical bonds are important in living systems

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Hydrogen Bonds • A hydrogen bond
– Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom
– Water (H2O) +

H O H + –
A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.

Ammonia (NH3)

N H + H H + +

Figure 2.15

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Van der Waals Interactions • Van der Waals interactions
– Occur when transiently positive and negative regions of molecules attract each other

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• Weak chemical bonds
– Reinforce the shapes of large molecules – Help molecules adhere to each other

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Molecular Shape and Function • The precise shape of a molecule
– Is usually very important to its function in the living cell – Is determined by the positions of its atoms’ valence orbitals

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• In a covalent bond
– The s and p orbitals may hybridize, creating specific molecular shapes
Z s orbital Three p orbitals Four hybrid orbitals

X

Y Tetrahedron (a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron Figure 2.16 (a) (outlined in pink).
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Space-filling model

Ball-and-stick model

Hybrid-orbital model (with ball-and-stick model superimposed)
Unbonded Electron pair

O

O H H H

H Water (H2O)

104.5°

H C H Methane (CH4) H H H

H

C H H

(b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the Figure 2.16 (b) shapes of the molecules
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• Molecular shape
– Determines how biological molecules recognize and respond to one another with specificity

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Carbon Hydrogen Natural endorphin

Nitrogen Sulfur Oxygen Morphine

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match.

Natural endorphin

Morphine

Brain cell

Endorphin receptors

Figure 2.17

(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine.

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Concept 2.4: Chemical reactions make and break chemical bonds

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• A Chemical reaction
– Is the making and breaking of chemical bonds – Leads to changes in the composition of matter

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• Chemical reactions
– Convert reactants to products

+

2 H2

+

O2

2 H2O

Reactants

Reaction

Product

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• Photosynthesis
– Is an example of a chemical reaction

Figure 2.18
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• Chemical equilibrium
– Is reached when the forward and reverse reaction rates are equal

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