1. 2.1 What Are Atoms?
Elements: An element is a substance that cannot be broken down or converted into another substance by ordinary chemical means. For example, carbon is an element, and a “perfect” diamond is made of pure carbon. If you cut the diamond into pieces, each one is still a diamond, made of carbon. If you kept cutting into the smallest pieces that still looked and felt like shiny diamonds you could theoretically get to individual carbon atoms.
Atoms are the basic structural units of matter.

2. 2.1 What Are Atoms?
Atoms: The subatomic particles called protons, neutrons and electrons are the ones we shall consider in this course.
Protons – Located in the center of the atom (the nucleus), have a mass of 1 amu and are positively charged (+1)
Neutrons – Located in the nucleus, have a mass of 1 amu and are neutral (have no charge)
Electrons – Orbit the nucleus, have essentially no mass and are negatively charged (-1).

3. 2.1 What Are Atoms?
Atomic number: Each particular type of atom has a specific number of protons. Hydrogen has 1 proton, helium has 2 protons and so on. The atomic number of an element is its number of protons. So, the atomic number of hydrogen is 1, the atomic number of helium is 2, etc. Also, atoms are electrically neutral. Therefore, the number of electrons in an atom must equal the number of protons.
Isotopes are atoms with an “unusual” number of neutrons. Some isotopes, but not all, are radioactive. They are unstable and release energy for a certain amount of time. The amount of energy and the time that the energy is emitted tends to be specific to the isotope. Think about cancer and medical testing.

5. Hydrogen and helium have the simplest atomic structure.
2.1 What Are Atoms?
Hydrogen and helium have the simplest atomic structure.
Hydrogen has one proton and one electron.
Helium has two protons, two neutrons, and two electrons. e- e- p+ p+ p+ n n e-
atomic nucleus
(a) Hydrogen (H)
(b) Helium (He)
Fig. 2-1

6. Different atoms have different electron shells:
2.1 What Are Atoms?
Electron shells: electrons orbit around atomic nuclei at specific distances, called electron shells.
Different atoms have different electron shells:
The inner shell only has two electrons.
The second shell holds up to eight electrons.
Additional shells hold up to eight electrons.

7. The first four atomic electron shells
2.1 What Are Atoms?
The first four atomic electron shells
Carbon (C)
Oxygen (O)
Phosphorus (P)
Calcium (Ca)
2e-
5e-
8e-
4e-
6e-
8e-
8e-
2e-
2e-
2e-
2e-
6p+
8p+
15p+
20p+ 6n 8n
16n
20n
Carbon (C)
Oxygen (O)
Phosphorus (P)
Calcium (Ca) C O P Ca
Fig. 2-2

8. 2.2 How Do Atoms Form Molecules?
Molecules: two or more atoms of one or more elements held together by interactions among their outermost electron shells
Atoms interact with one another according to two basic principles:
An inert atom will not react with other atoms when its outermost electron shell is completely full or empty.
A reactive atom will react with other atoms when its outermost electron shell is only partially full.

9. 2.2 How Do Atoms Form Molecules?
If an atom’s outermost shell is only partially full it can gain stability in one of three ways:
1. It can lose electrons,
2. It can gain electrons,
3. It can share electrons.
Losing, gaining and sharing electrons results in chemical bonds. See table 2-1. Chemical reactions make and break chemical bonds.

10. 2.2 How Do Atoms Form Molecules?
A molecule may be depicted in different ways. (You are not required to reproduce these.) H C C C C O H H H H H
(a) All bonds shown
CH3
CH2
CH2
CH2 OH
(b) Bonds within common groups omitted OH
(c) Carbons and their attached hydrogens omitted
(d) Overall shape depicted
Fig. 2-4

11. 2.2 How Do Atoms Form Molecules?
Types of bonds
Ionic bonds: formed by passing an electron from one atom to another
One partner becomes positive, the other negative, and they attract one another.
Na+ + Cl– becomes NaCl (sodium chloride)
Positively or negatively charged atoms are called ions.

12. 2.2 How Do Atoms Form Molecules?
Sodium atom (neutral)
Chlorine atom (neutral) – – –
Charged atoms interact to form ionic bonds.
Positively charged atoms
Negatively charged atoms – – – – – – – – – – – – – – –
11p+
17p+ –
11n – –
18n – – – – – – –
Electron transferred
(a)
Neutral atoms
Sodium ion (+)
Chloride ion (–) – – – – – – – – – – – – – – – – – –
11p+
17p+ –
11n – –
18n – – – – – – –
Attraction between opposite charges
(b)
Ions
Cl-
Na+
Cl-
Na+
Cl-
Na+
Cl-
Na+
Cl-
Fig. 2-5
(c)
An ionic compound: NaCl

13. 2.2 How Do Atoms Form Molecules?
Types of bonds (continued)
Covalent bonds: bond between two atoms that share electrons in their outer electron shell
For example, an H atom can become stable by sharing its electron with another H atom, forming H2 gas.

14. 2.2 How Do Atoms Form Molecules?
Covalent bonds produce either nonpolar or polar molecules.
Nonpolar molecule: atoms in a molecule equally share electrons that spend equal time around each atom, producing a nonpolar covalent bond

15. 2.2 How Do Atoms Form Molecules?
Nonpolar covalent bonding in hydrogen
Same charge on both nuclei – + + –
Electrons spend equal time near each nucleus
(uncharged)
(a)
Nonpolar covalent bonding in hydrogen
Fig. 2-6a

16. 2.2 How Do Atoms Form Molecules?
Covalent bonds produce either nonpolar or polar molecules (continued).
Polar molecules: atoms in a bond unequally share electrons, producing a polar covalent bond
One atom in the bond has a more positive charge in the nucleus, and so attracts electrons more strongly, becoming the negative pole of the molecule.
The atom in the bond that has a less positive charge in the nucleus gives up electrons, becoming the positive pole of the molecule.

17. 2.2 How Do Atoms Form Molecules?
Polar covalent bonding in water
(oxygen: slightly negative)
(–)
Larger positive charge – – – – –
Electrons spend more time near the larger nucleus – – –
8p+ – 8n – + +
Smaller positive charge
(hydrogens: slightly positive)
(+)
(+)
(b)
Polar covalent bonding in water
Fig. 2-6b

18. 2.2 How Do Atoms Form Molecules?
Types of bonds (continued)
Hydrogen bonds: weak electrical attraction between positive and negative parts of polar molecules
Example: the negative charge of oxygen atoms in water molecules attract the positive charge of hydrogen atoms in other water molecules

19. 2.2 How Do Atoms Form Molecules?
Hydrogen bonds
O (–)
H (+)
H (+)
H (+)
O (–)
H (+)
hydrogen bonds
Fig. 2-7

20. 2.2 How Do Atoms Form Molecules?

21. 2.3 Why Is Water So Important To Life?
Water interacts with many other molecules.
Oxygen released by plants during photosynthesis comes from water.
Water is used by animals to digest food and thus breakdown large biomolecules – hydrolysis reactions.
Water is produced in chemical reactions that combine small biomolecules forming larger, more complex ones – dehydration synthesis reactions.

22. 2.3 Why Is Water So Important To Life?
Many molecules dissolve easily in water.
Water is an excellent solvent, capable of dissolving a wide range of substances because of its positive and negative poles.
NaCl dropped into H2O
The positive end of H2O is attracted to Cl–.
The negative end of H2O is attracted to Na+.
These attractions tend to push apart the components of the original salt.

23. 2.3 Why Is Water So Important To Life?
Water as a solvent
Cl–
Na+ H
Na+
Cl– O H
Cl–
Na+
Fig. 2-8

24. 2.3 Why Is Water So Important To Life?
Water molecules tend to stick together.
Surface tension: water tends to resist being broken
Cohesion: water molecules stick together
Fig. 2-9

25. 2.3 Why Is Water So Important To Life?
Water can form ions.
Water spontaneously becomes H+ and OH–.
Acid solutions have a lot of H+ (protons).
Alkaline solutions have a lot of OH– (hydroxyl ions).
A base is a substance that combines with H+, reducing their numbers.
pH measures the relative amount of H+ and OH– in a solution.

26. 2.3 Why Is Water So Important To Life?
A water molecule is ionized.
(–)
(+) O O + H H H H
water
(H2O)
hydroxide ion (OH–)
hydrogen ion (H+)
Fig. 2-10

27. 2.3 Why Is Water So Important To Life?
pH measures acidity.
Acids have a pH below 7.
Bases have a pH above 7.
Neutral solutions have a pH of 7.
Buffers are substances that maintain a constant pH in a solution.

28. 2.3 Why Is Water So Important To Life?
The pH scale
stomach acid (2) lemon juice (2.3)
vinegar, cola (3.0)
1 molar hydrochloric acid (HCl)
black coffee (5.0)
normal rain (5.6) urine (5.7)
orange (3.5) tomatoes beer (4.1)
water from faucet milk (6.4) pure water (7.0)
household ammonia (11.9) washing soda (12)
drain cleaner (14.0) 1 molar sodium hydroxide (NaOH)
blood, sweat (7.4)
phosphate detergents chlorine bleach (12.6)
seawater (7.8–8.3)
baking soda (8.4)
oven cleaner (13.0)
toothpaste (9.9) 1 2 3 4
pH value 5 6 7 8 9 10 11 12 13 14
(H+ > OH–)
(H+ < OH–)
neutral (H+ = OH–)
100
10–1
10–2
10–3
10–4
10–5
10–6
10–7
10–8
10–9
10–10
10–11
10–12
10–13
10–14
increasingly acidic
increasingly basic
H+ concentration in moles/liter
Fig. 2-11

29. 3.1 Why Is Carbon So Important To Life?
An organic molecule is one that contains carbon.
This is possible because carbon has four electrons in its outermost shell, leaving room for four more electrons from other atoms.
Therefore, carbon can form many bonds with other atoms.

30. 3.2 How Are Biological Molecules Joined Together Or Broken Apart?
Dehydration synthesis
The construction of large molecules yields water.
Small molecules are joined together to form large molecules.
During the joining of small molecules, water is released.
This water-releasing reaction is called dehydration synthesis.

31. 3.2 How Are Biological Molecules Joined Together Or Broken Apart?
Dehydration synthesis
dehydration synthesis + O HO O H HO OH HO OH O H H
(a)
Dehydration synthesis
Fig. 2-12a

32. 3.2 How Are Biological Molecules Joined Together Or Broken Apart?
Hydrolysis reactions
During the breakdown of large molecules, covalent bonds are broken, separating the subunits

33. 3.2 How Are Biological Molecules Joined Together Or Broken Apart?
Hydrolysis
hydrolysis + O HO OH HO O H HO OH O H H
(b)
Hydrolysis
Fig. 2-12b