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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

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chapter 2 lecture notes essential chemistry for biology biol 100 k marr spring 2007

Chapter 2 Lecture Notes—Essential Chemistry for BiologyBiol 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

basic chemistry
  • 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?
periodic table of the elements
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
some elements react to form compounds
Some Elements React to Form Compounds
  • Elements can combine chemically to form compounds
  • Compounds contain two or more elements chemically combined in a fixed ratio

Examples of Compounds:

  • Table salt (sodium chloride): NaCl
  • Water: H2O
  • Glucose: C6H12O6
atom smallest unit of matter that retains the properties of an element
Atom:smallest unit of matter that retains the properties of an element
  • Each element consists of one kind of atom

(a) Hydrogen atom

(b) Carbon atom

(c) Oxygen atom








Atomic nucleus

Fig. 2.02

atomic structure
Atomic Structure
  • The subatomic particles of an atom


 Negative charge


• Participates in chemical


 Positive charge

 Determines element

• Outer-shell electrons

determine chemical



 No charge

 Determines isotope


• Consists of neutrons and protons

    • 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
chemical properties of atoms
Chemical Properties of Atoms
  • 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
Atoms of the four elements most abundant in life


electron shell:

can hold

2 electrons


electron shell:

can hold

8 electrons


Hydrogen (H)

Atomic number = 1

Carbon (C)

Atomic number = 6

Nitrogen (N)

Atomic number = 7

Oxygen (O)

Atomic number = 8


Orbital Diagrams of the First 18 Elements

1st Shell

2nd Shell

3rd Shell




chemical bonding and molecules
Chemical Bonding and Molecules
  • 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
ionic bonds form between metals and nonmetals
Ionic Bonds: form between metals and nonmetals
  • When an atom loses or gains electrons, it becomes electrically charged
    • Charged atoms are called ions
    • Ionic bonds are formed between oppositely charged ions

Sodium atom (Na)

Chlorine atom (Cl)


outer shells

Sodium ion (Na)

Chloride ion (Cl)

Sodium chloride (NaCl)


Atoms: electrically neutral

Ions: Electrically charged

(a) Hydrogen atom (H)

(b) Hydrogen ion (H+)

1 electron

No electron

1 proton

1 proton

No net electrical charge

(c) Sodium atom (Na)

(d) Sodium ion (Na+)

11 electrons

10 electrons

11 protons

11 protons

No net electrical charge

Fig. 2.03

covalent bonds form between nonmetallic atoms
Covalent Bonds: form between nonmetallic atoms
  • A covalent bond forms when two atoms share one or more pairs of outer-shell electrons

Water molecule (H2O)

Covalent bonding in water

Oxygen atom with unfilled shell

Full shell with 8 electrons

Slightly negative

Covalent bond

(shared pair

of electron)



Slightly positive

Full shells with 2 electrons each

Hydrogen atoms with unfilled shells

Fig. 2.04a

chemical reactions
Chemical Reactions
  • 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

Hydrogen gas

Oxygen gas





Chemical Equations: symbolize chemical reactions

Reactants: on the left side of the equation

  • the starting materials

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!
water and life
  • 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
the structure of water
The Structure of Water
  • The water molecule:
    • two hydrogen atoms joined to one oxygen atom by single covalent bonds




water a polar molecule
Water: a polar molecule
  • 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 (d) Why?
    • oxygen atom: partially negative (d-) Why?


(d )


the structure of water22
The Structure of Water
  • The polarity of water results in weak electrical attractions between neighboring water molecules
    • These interactions are called hydrogen bonds


Hydrogen bond









water s life supporting properties
Water’s Life-Supporting Properties
  • The polarity of water molecules and the hydrogen bonding that results explain most of water’s life-supporting properties
    • Versatility of water as a solvent
    • Water’s cohesive nature
    • Water’s ability to moderate temperature
    • Floating ice
water as the solvent of life
Water as the Solvent of Life
  • A solution is a liquid consisting of two or more substances evenly mixed
  • The dissolving agent is called the solvent
  • The dissolved substance is called the solute

Salt crystal

Ion in solution


Dissolving of Sodium Chloride (NaCl) in Water




Water molecules dissolve NaCl,

breaking ionic bond







Ionic bond

Edge of one

salt crystal

the cohesion of water
The Cohesion of Water
  • Water molecules stick together as a result of hydrogen bonding
    • This is called cohesion
    • Cohesion is vital for water transport in plants

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

water moderates temperature
Water Moderates Temperature
  • 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
The density of ice is lower than liquid water
    • This is why ice floats

Hydrogen bond


Liquid water

Stable hydrogen bonds

Hydrogen bonds

constantly break and re-form

the biological significance of ice floating
The Biological Significance of Ice Floating
  • 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
acids bases and ph
Acids, Bases, and pH
  • Acid
    • A chemical compound that donates H+ ions to solutions
  • Base
    • A compound that accepts H+ ions and removes them from solution

The pH scale is used to describe the acidity of a solution

pH Scale

Oven cleaner

  • Acidic: pH < 7

H+ > OH-

  • Basic: pH > 7

H+ < OH-

  • Neutral: pH = 7

H+ = OH-

Household bleach

Household ammonia



Milk of magnesia


Human blood

Pure water




Tomato juice

Grapefruit juice

Lemon juice;

gastric juice



self test review questions
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.

  • Why is carbon dioxide gas, CO2, classified as a compound but nitrogen gas, N2, is not?
  • Which of the following are compounds? Elements?: C6H12O6, CH4, O2, Cl2, HCl, MgCl2, Fe, Ca, Ne, NaI, I
  • What is the difference between an atom and an ion? Give examples of each to support your response.
  • Which subatomic particle determines the identity of an atom?
  • Which subatomic particle determines the chemical properties of an atom?
self test review questions34
Self-test/Review Questions
  • 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?
  • 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.
  • 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.
  • Is carbon dioxide an ionic or covalent compound? How do you know? Explain your reasoning.
self test review questions cont
Self-test/Review Questions (cont.)
  • Why are the following incorrect structures for the substances below? Rewrite their structures with the correct number of chemical bonds.
    • Carbon dioxide gas: O—C—O
    • Oxygen gas: O—O
    • Nitrogen gas: N—N
  • Explain how water’s versatility as a solvent results from the fact that water is polar molecule.
  • 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 cont36
Self-test/Review Questions (cont.)
  • Which of the following are chemical changes? Physical changes? If possible, write the balanced chemical equation for those that are a chemical change.
    • The alcoholic fermentation in Yeast in which yeast produce ethanol, C2H5OH, and carbon dioxide, CO2, from the sugar glucose, C6H12O6
    • Water boils to form steam
    • The healing of a cut finger
    • Cutting a piece of wood with a saw
    • Potassium metal, K, and chlorine gas (Cl2) combine to form potassium chloride.
    • The rusting of iron, Fe, to produce rust, iron (III) oxide (Fe2O3)
self test review questions cont37
Self-test/Review Questions (cont.)
  • Which of these is not a subatomic particle? a) proton; b) ion; c) neutron; d) electron
  • The outermost electron shell of every Noble Gas element (except Helium) has ___ electrons. a) 1; b) 2; c) 4; d) 6; e) 8
  • An organic molecule is likely to contain all of these elements except ___. a) C; b) H; c) O; d) Ne; e) N
  • The chemical bond between water molecules is a ___ bond. a) ionic; b) polar covalent; c) nonpolar covalent; d) hydrogen
  • 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
  • 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 cont38
Self-test/Review Questions (cont.)
  • The type of chemical bond formed when oppositely charged particles are attached to each other is a ___ bond. a) ionic; b) covalent; c) hydrogen
  • 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
  • Each of the isotopes of hydrogen has ___ proton(s). a) 3; b) 1; c) 2; d) 92; e) 1/2
  • 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