1. Chapter 2 – Atoms, Molecules and Life
2.1 What Are Atoms?
2.2 How Do Atoms Interact to Form Molecules?
2.3 Why Is Water So Important to Life?

2. Figure: 2-CO
Title:
Atoms, Molecules, and Life
Caption:
The basilisk lizard and this child learning to ice skate have something in common: both are "walking on water."

3. 2.1 What Are Atoms?
Atoms are the fundamental structural units of matter
Atoms are composed of a nucleus, protons, neutrons and electrons
We use models to simplify talking about atoms

4. electron shell e- e- p+ p+ p+ n n e- nucleus Hydrogen (H) Helium (He)
Figure :2-1
Title:
Atomic models
Caption:
Structural representations of the two smallest atoms, (a) hydrogen and (b) helium. In these simplified models, the electrons are represented as miniature planets, circling in specific orbits around a nucleus that contains protons and neutrons. e-
nucleus
Hydrogen (H)
Helium (He)

5. Figure :2-T1
Title:
Common Elements Important in Living Organisms
Caption:

6. Radioactivity in Research
Isotope is a form of an element where there is a different number of neutrons than protons
Some isotopes are radioactive which means the nucleus is unstable and will break down releasing radiation

7. PET = positron emission tomography
detector ring
Figure: E2-1
Title:
How positron emission tomography works
PET = positron emission tomography

8. Atoms Positive and negative attract
Electrons are in held around the nucleus in “shells”
The first “shell” holds two electrons
The next “shells” hold eight electrons

9. Copyright © 2005 Pearson Prentice Hall, Inc.
FIGURE 2-2 Electron shells in atoms
Most biologically important atoms have at least two shells of electrons. The first shell, closest to the nucleus, can hold two electrons; the next shell holds a maximum of eight electrons. More-distant shells can hold larger numbers of electrons.
Copyright © 2005 Pearson Prentice Hall, Inc.

10. Energy Capture and Release
Life depends on electrons capturing and releasing energy
Electron shells correspond to energy levels
Energy exciting an atom causes an electron jump from a lower- to higher-energy shell
Later, the electron falls back into its original shell, releasing the energy
Copyright © 2005 Pearson Prentice Hall, Inc.

11. Copyright © 2005 Pearson Prentice Hall, Inc.
FIGURE 2-3 Energy capture and release
Copyright © 2005 Pearson Prentice Hall, Inc.

12. Copyright © 2005 Pearson Prentice Hall, Inc.
FIGURE 2-3 Energy capture and release
Copyright © 2005 Pearson Prentice Hall, Inc.

13. Copyright © 2005 Pearson Prentice Hall, Inc.
FIGURE 2-3 Energy capture and release
Copyright © 2005 Pearson Prentice Hall, Inc.

14. 2.2 How Do Atoms Interact to Form Molecules?
A molecule consists of two or more atoms of the same or different elements
A compound means two different elements
Inert vs. reactive

15. Reactive Inert (Nobel Gases) electron shell e- e- p+ p+ p+ n n e-
Figure :2-1
Title:
Atomic models
Caption:
Structural representations of the two smallest atoms, (a) hydrogen and (b) helium. In these simplified models, the electrons are represented as miniature planets, circling in specific orbits around a nucleus that contains protons and neutrons. e-
nucleus
Hydrogen (H)
Helium (He)
Reactive
Inert (Nobel Gases)

16. 2.2 How Do Atoms Interact to Form Molecules?
Chemical bonds are atoms gaining stability by losing, gaining or sharing electrons
Chemical bonds are attractive forces
Chemical reactions are the making or breaking of chemical bonds

17. Ions interact to form ionic bonds
Sodium atom (neutral) Na
Chlorine atom (neutral) Cl
11p+
11n
17p+
18n
Atoms that have lost or gained 1 or 2 electrons are charged and called ions
Ions interact to form ionic bonds
11p+
11n
17p+
18n
Sodium ion (+)
Chloride ion (–)
Cl–
Na+
Caption:
(a) Sodium has only one electron in its outer electron shell; chlorine has seven. (b) Sodium can become stable by losing an electron, and chlorine can become stable by gaining an electron. Sodium becomes a positively charged ion and chlorine a negatively charged ion. (c) Because oppositely charged particles attract one another, the resulting sodium ions (Na+) and chloride ions (Cl–) nestle closely together in a crystal of salt, NaCl.
An ionic compound: NaCl
Na+
Cl–

18. 2.2 How Do Atoms Interact to Form Molecules?
Uncharged atoms can become stable by sharing electrons, forming covalent bonds
Covalent bonds vary in strength but are always stronger than ionic bonds
Nonpolar vs. polar covalent bonds

19. Nonpolar covalent bonding
Hydrogen (H–H or H2)
Figure :2-4 part a
Title:
Covalent bonds involve shared electrons part a Nonpolar covalent bonding
Caption:
In hydrogen gas (top), an electron from each hydrogen atom is shared, forming a single nonpolar covalent bond. In oxygen gas (bottom), two oxygen atoms share four electrons, forming a double nonpolar covalent bond.
8p+
8p+ 8n 8n
Oxygen (O=O or O2)

20. Polar covalent bonding
(slightly negative)
8p+ 8n
Figure :2-4 part b
Title:
Covalent bonds involve shared electrons part b Polar covalent bonding
Caption:
Oxygen lacks two electrons to fill its outer shell, so oxygen can form polar covalent bonds with two hydrogen atoms, creating water. Oxygen exerts a greater pull on the electrons than does hydrogen, so the “oxygen end” of the molecule has a slight negative charge and the “hydrogen” end has a slight positive charge. Question In water's polar bonds, why is oxygen's pull on electrons greater than hydrogen's?
(slightly positive)
Water (H–O–H or H2O)

21. Figure :2-T2
Title:
Chemical Bonds
Caption:

22. Figure :2-UN3
Title:
Bonding patterns of atoms commonly found in biological molecules
Caption:

23. Figure :2-T3
Title:
Bonding Patterns of Atoms Commonly Found in Biological Molecules
Caption:

24. Free Radicals A molecule with an unpaired electron
Steals electrons from other molecules
Free radicals contribute to cancer and Alzheimer’s disease
Free radicals can be increased by exposure to the sun (radiation) and many chemicals

25. Antioxidants React with free radicals to render them harmless
Vitamin C and Vitamin E
Many can be found in a healthy diet
Your risk of cancer can be lowered 50% simply by eating 5 fruits and veggies a day

26. O (–) H (+) H (+) H (+) O (–) H (+) hydrogen bonds Figure :2-5 Title:
Caption:
The partial charges on different parts of water molecules produce weak attractive forces called hydrogen bonds (dotted lines) between the oxygen and hydrogen atoms in adjacent water molecules. H
(+) H
(+) O
(–) H
(+)
hydrogen
bonds

27. 2.3 Why Is Water So Important to Life?
Water interacts with many other molecules
A solvent is capable of dissolving a wide range of substances
Water is a polar solvent and can dissolve proteins, salts and sugars

28. solutes solution Water as a solvent Na+ H Cl– O– H Cl– H H Na+ O Na+
Figure :2-6
Title:
Water as a solvent
Caption:
When a salt crystal is dropped into water, the water surrounds the sodium and chloride ions with oppositely charged poles of its molecules. Thus insulated from the attractiveness of other molecules of salt, the ions disperse, and the whole crystal gradually dissolves. H H
Na+ O
Na+
solution
Water as a solvent

29. Polar vs. Nonpolar
Ions and polar molecules are hydrophilic (Greek for “water-loving”)
Uncharged and nonpolar molecules are hydrophobic (“water-fearing”)
Think of oil and vinegar

30. Copyright © 2005 Pearson Prentice Hall, Inc.
FIGURE 2-12 Oil and water don't mix
Yellow oil has just been poured into this beaker of water and is rising to the surface. Oil floats because it is lighter than water, and it forms droplets in water because it is a hydrophobic, nonpolar molecule that is not attracted to the water's polar molecules.
Copyright © 2005 Pearson Prentice Hall, Inc.

31. water hydrogen bond glucose hydroxyl group Figure :2-7 Title:
Water dissolves many biological molecules
Caption:
Many biological molecules dissolve in water because they have polar parts—for example, OH– (hydroxyl) groups—that can form hydrogen bonds with water molecules. Here, sugar dissolves because hydrogen bonds form between the hydroxyl groups on a glucose molecule (a simple sugar) and surrounding water molecules. Question Why is it important to human physiology that sugars dissolve easily in water?

32. 2.3 Why Is Water So Important to Life?
Cohesion is the tendency of molecules to stick together
Water’s high cohesion creates surface tension
(Water also has a high specific heat)

33. Figure :2-8
Title:
Cohesion among water molecules
Caption:
(a) Buoyed by surface tension, the fishing spider rushes across the surface of a pond to capture an insect. (b) In giant redwoods, cohesion holds water molecules together in continuous strands from the roots to the topmost leaves as high as 300 feet above the ground.

34. (–) (+) O + H O H H H water (H2O) hydroxide ion (OH–) hydrogen ion
Figure: 2-UN1
Title:
Ionization of Water
Caption:
Although water is generally regarded as a stable compound, a small fraction of water molecules are ionized—that is, broken apart into hydrogen ions (H+) and hydroxide ions (OH–).
hydroxide ion
(OH–)
hydrogen ion
(H+)

35. 2.3 Why Is Water So Important to Life?
Water-Based Solutions Can Be Acidic, Basic, or Neutral
If H+ exceeds OH-, the solution is acidic
If OH- exceeds H+, the solution is basic
If they are equal, the solution is neutral

36. Figure :2-9 Title: The pH scale Caption:
H+ concentration
(moles/liter) pH
value
100
1-molar hydrochloric
acid (HCI)
10–1 1
stomach acid
lime juice
10–2 2
lemon juice
10–3 3
"acid rain" (2.5–5.5)
vinegar, cola, orange juice,
tomatoes
increasingly acidic (H+ > OH–)
10–4 4
beer
10–5 5
black coffee, tea
normal rain (5.6)
urine (5.7)
10–6 – 6 6
neutral
(H+ = OH–)
10–7 – 7 7
pure water (7.0)
saliva
blood, sweat (7.4)
10–8 – 8 8
seawater (7.8 –
8.3)
Figure :2-9
Title:
The pH scale
Caption:
The pH scale expresses the concentration of hydrogen ions in a solution on a scale of 0 (very acidic) to 14 (very basic). Each unit of change on the scale represents a tenfold change in the concentration of hydrogen ions. Lemon juice, for example, is about 10 times more acidic than orange juice, and the most severe acid rains in the northeastern United States are almost 1000 times more acidic than normal rainfall. Except for the inside of your stomach, nearly all the fluids in your body are finely adjusted to a pH of about 7.4. The color-coding shown corresponds to a common pH indicator dye, bromthymol blue.
10–9 – 9 9
baking soda
10–10 – 10 10
phosphate detergents
chlorine bleach
milk of magnesia
increasingly basic (H+ < OH–)
10–11 – 11 11
household ammonia
some detergents
(without phosphates)
10–12 – 12 12
washing soda
10–13 – 13 13
oven cleaner
10–14 – 14 14
1-molar sodium
hydroxide (NaOH)

37. 2.3 Why Is Water So Important to Life?
A buffer helps maintain a solution at a relatively constant pH (homeostatis)
Water moderates the effects of temperature changes (due to high specific heat)
1 calorie of energy will rise the temperature of water 1 ºC (only 0.6 calories are needed for alcohol, 0.2 for salt, 0.02 for granite)

38. Water forms an unusual solid -> ICE
Figure: 2-UN2
Title:
Comparison of liquid and solid phases of water
Water forms an unusual solid -> ICE

39. Figure :E2-2
Title:
Chocolate
Caption:
Cocoa powder is derived from cacao beans (inset), which grow on trees in tropical regions of the Americas.