Chapter 2 Lecture Notes—Essential Chemistry for Biology

Biol 100 – K. Marr – Spring 2007

Topics Discussed in these notes

• Matter, Elements and Compounds

• Periodic Table of the Elements: Metals vs. Nonmetals

• Atomic Structure

• Chemical Bonding: Ionic vs. Covalent Bonding

• Chemical Reactions and Chemical Equations

• The Structure of Water

• Water as a Solvent

• The Importance of Water to Living Things

• Acids, Bases and pH

• Self-test/Review Questions

• Organisms and all other things in the universe consist of matter

Matter: Elements and Compounds

• Matter is anything that occupies space and has mass

– Matter is composed of chemical elements and compounds

– Elements: substances that cannot be broken down into other substances

– There are 92 naturally occurring elements on Earth

– What are compounds? Examples?

BASIC CHEMISTRY

Periodic table of the elements

Location of....• Metals?• Nonmetals?

25 Elements are essential to life

• C, H, O, N: 96% of the weight of the human body

• Elements can combine chemically to form compounds

• Compounds contain two or more elements chemically combined in a fixed ratio

Examples of Compounds:

1. Table salt (sodium chloride): NaCl

2. Water: H2O

3. Glucose: C6H12O6

Some Elements React to Form Compounds

• Each element consists of one kind of atom

Atom: smallest unit of matter that retains the properties of an element

Fig. 2.02

(a) Hydrogen atom (b) Carbon atom (c) Oxygen atom

Proton Neutron Electron

Atomic nucleus

Firstshell

Secondshell

• The subatomic particles of an atom

Atomic Structure

Proton

Positive charge

Determines element

Neutron

No charge

Determines isotope

Electron

Negative charge

• Participates in chemical reactions

• Outer-shell electrons determine chemical behavior

Nucleus

• Consists of neutrons and protons

• Elements

– differ in the number of subatomic particles in their atoms

• Atomic Number: number of protons

– determines which element it is

• Mass number

– sum of the number of protons and neutrons

• Electrons

– Located outside the nucleus of an atom in specific electron shells (energy levels)

• The number of electrons in the outermost shell determines the chemical properties of an atom

Chemical Properties of Atoms

Atoms of the four elements most abundant in life

Electron

Firstelectron shell:can hold2 electrons

Outermostelectron shell:can hold8 electrons

Carbon (C)Atomic number = 6

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Hydrogen (H)Atomic number = 1

Orbital Diagrams of the First 18 Elements

2

8

8

1st Shell

2nd Shell

3rd Shell

• Chemical reactions:

– Atoms give up or acquire electrons in order to complete their outer shells

– Result in atoms staying close together to form molecules

– Chemical bonds hold molecules together

• Ionic Bonds

• Covalent bonds

Chemical Bonding and Molecules

• When an atom loses or gains electrons, it becomes electrically charged

– Charged atoms are called ions

– Ionic bonds are formed between oppositely charged ions

Ionic Bonds: form between metals and nonmetals

Sodium atom (Na) Chlorine atom (Cl)

Completeouter shells

Sodium ion (Na) Chloride ion (Cl)

Sodium chloride (NaCl)

(a) Hydrogen atom (H)

(c) Sodium atom (Na)

(b) Hydrogen ion (H+)

(d) Sodium ion (Na+)

1 electron

1 proton

No net electrical charge

11 electrons

11 protons

No net electrical charge

No electron

1 proton

10 electrons

11 protons

Fig. 2.03

Atoms: electrically neutral Ions: Electrically charged

• A covalent bond forms when two atoms share one or more pairs of outer-shell electrons

Covalent Bonds: form between nonmetallic atoms

Fig. 2.04a

Covalent bonding in water

Full shell with 8 electrons– Slightly negative

Hydrogen atoms with unfilled shells

Full shells with 2 electrons each

+Slightly positive

+

Covalent bond(shared pairof electron)

Oxygen atom with unfilled shell

Water molecule (H2O)

• Cells constantly rearrange molecules by breaking existing chemical bonds and forming new ones

– Such changes in the chemical composition of matter are called chemical reactions

Chemical Reactions

Hydrogen gas Oxygen gas Water

Reactants Products

Reactants: on the left side of the equation – the starting

materials

Chemical Equations: symbolize chemical reactions

Products: on the right side of the equation – the ending materials (the stuff

produces)

Law of Conservation of Mass– Chemical reactions do not create or destroy matter—they only

rearrange it!

• Life on Earth began in water and evolved there for 3 billion years

• The abundance of water is a major reason Earth is habitable

– Modern life still remains tied to water

– Your cells are composed of 70%–95% water

WATER AND LIFE

• The water molecule:

– two hydrogen atoms joined to one oxygen atom by single covalent bonds

The Structure of Water

H

O

H

• The electrons of the covalent bonds are shared unequally between oxygen and hydrogen

– unequal sharing of electrons makes water a polar molecule

– hydrogen atoms: partially positive ( ) Why?

– oxygen atom: partially negative ( -) Why?

()( )

( )

Water: a polar molecule

• The polarity of water results in weak electrical attractions between neighboring water molecules

– These interactions are called hydrogen bonds (b)

()

Hydrogen bond()

()()

()

()

()

()

The Structure of Water

• The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties

1. Versatility of water as a solvent

2. Water’s cohesive nature

3. Water’s ability to moderate temperature

4. Floating ice

Water’s Life-Supporting Properties

• A solution is a liquid consisting of two or more substances evenly mixed

Water as the Solvent of Life

– The dissolving agent is called the solvent

– The dissolved substance is called the solute

Ion in solutionSalt crystal

Dissolving of Sodium Chloride (NaCl) in Water

Salt

Water

Electricalattraction

Watermolecules(H2O)

Hydrogenbonds

Edge of onesalt crystal

Ionic bond

Water molecules dissolve NaCl,breaking ionic bond

• Water molecules stick together as a result of hydrogen bonding

– This is called cohesion

– Cohesion is vital for water transport in plants

The Cohesion of Water

Microscopic tubes

• Surface tension

– is the measure of how difficult it is to stretch or break the surface of a liquid

– Hydrogen bonds give water an unusually high surface tension

Figure 2.13

• Because of hydrogen bonding, water has a strong resistance to temperature change

• Water can absorb and store large amounts of heat while only changing a few degrees in temperature

– Earth’s Oceans cause temperatures to stay within limits that permit life

Water Moderates Temperature

• The density of ice is lower than liquid water

– This is why ice floats

Hydrogen bond

Liquid water

Hydrogen bondsconstantly break and re-form

Ice

Stable hydrogen bonds

• When water molecules get cold, they move apart, forming ice

– A chunk of ice has fewer molecules than an equal volume of liquid water

• Since ice floats, ponds, lakes, and even the oceans do not freeze solid

– Marine life could not survive if bodies of water froze solid

The Biological Significance of Ice Floating

• Acid

– A chemical compound that donates H+ ions to solutions

• Base

– A compound that accepts H+ ions and removes them from solution

Acids, Bases, and pH

Basicsolution

Neutralsolution

Acidicsolution

Oven cleaner

Household bleach

Household ammonia

Milk of magnesia

Seawater

Human bloodPure water

Urine

Tomato juice

Grapefruit juice

Lemon juice;gastric juice

• Acidic: pH < 7

H+ > OH-

• Basic: pH > 7

H+ < OH-

• Neutral: pH = 7

H+ = OH-

pH ScaleThe pH scale is used to describe the acidity of a

solution

Self-test/Review Questions

Use these questions as a self test and then discuss your responses with your study group/classmates—your responses will not be collected.

1. Why is carbon dioxide gas, CO2, classified as a compound but nitrogen gas, N2, is not?

2. Which of the following are compounds? Elements?: C6H12O6, CH4, O2, Cl2, HCl, MgCl2, Fe, Ca, Ne, NaI, I

3. What is the difference between an atom and an ion? Give examples of each to support your response.

4. Which subatomic particle determines the identity of an atom?

5. Which subatomic particle determines the chemical properties of an atom?

Self-test/Review Questions

6. A carbon atom has 6 protons, and the most common isotope of carbon has 6 neutrons. A radioactive isotope of carbon has 8 neutrons. What are the atomic numbers and the mass numbers of the of the stable and radioactive forms of carbon?

7. Explain the difference between an ionic and covalent bond in terms of what happens to the electrons in the outer shell of the participating atoms.

8. Sodium fluoride, NaF, is often added to toothpaste to both kill bacteria that cause cavities. It also helps to harden the enamel of teeth thus helping it resist cavities. Is sodium fluoride an ionic or covalent compound? How do you know? Explain your reasoning.

9. Is carbon dioxide an ionic or covalent compound? How do you know? Explain your reasoning.

Self-test/Review Questions (cont.)

10. Why are the following incorrect structures for the substances below? Rewrite their structures with the correct number of chemical bonds.

a. Carbon dioxide gas: O—C—O

b. Oxygen gas: O—O

c. Nitrogen gas: N—N

11. Explain how water’s versatility as a solvent results from the fact that water is polar molecule.

12. A bottle of Pepsi consists mostly of sugar dissolved in water, with some carbon dioxide gas that makes fizzy and makes the pH less than 7. Describe Pepsi using the following terms: solute, solvent, acidic, aqueous solution

Self-test/Review Questions (cont.)

13. Which of the following are chemical changes? Physical changes? If possible, write the balanced chemical equation for those that are a chemical change.

a. The alcoholic fermentation in Yeast in which yeast produce ethanol, C2H5OH, and carbon dioxide, CO2, from the sugar glucose, C6H12O6

b. Water boils to form steam

c. The healing of a cut finger

d. Cutting a piece of wood with a saw

e. Potassium metal, K, and chlorine gas (Cl2) combine to form potassium chloride.

f. The rusting of iron, Fe, to produce rust, iron (III) oxide (Fe2O3)

Self-test/Review Questions (cont.)

14. Which of these is not a subatomic particle? a) proton; b) ion; c) neutron; d) electron

15. The outermost electron shell of every Noble Gas element (except Helium) has ___ electrons. a) 1; b) 2; c) 4; d) 6; e) 8

16. An organic molecule is likely to contain all of these elements except ___. a) C; b) H; c) O; d) Ne; e) N

17. The chemical bond between water molecules is a ___ bond. a) ionic; b) polar covalent; c) nonpolar covalent; d) hydrogen

18. A solution with a pH of 7 has ___ times more H ions than a solution of pH 9. a) 2; b) 100; c) 1000; d) 9; e) 90

19. The type of chemical bond formed when electrons are shared between atoms is a ___ bond. a) ionic; b) covalent; c) hydrogen

Self-test/Review Questions (cont.)

20. The type of chemical bond formed when oppositely charged particles are attached to each other is a ___ bond. a) ionic; b) covalent; c) hydrogen

21. Carbon has an atomic number of 6. This means it has ___. a) six protons; b) six neutrons; c) six protons plus six neutrons; d) six neutrons and six electrons

22. Each of the isotopes of hydrogen has ___ proton(s). a) 3; b) 1; c) 2; d) 92; e) 1/2

23. A molecule is ___. a) a mixture of various components that can vary; b) a combination of many atoms that will have different ratios; c) a combination of one or more atoms that will have a fixed ratio of its components; d) more important in a chemistry class than in a biology class