CHAPTER 2

Part 1: ATOMS & MOLECULES

Chemistry- an integral aspect of biology

Living organisms are made of natural elements

Roadmap 2

In this chapter you will learn that

Chemistry is intimately linked to the evolution of life by reviewing and How are atoms asking bonded together in molecules? and The structure of asking atoms, ions, and molecules 2.1 How do chemical reactions occur?

2.3
then examining Carbon: The most versatile atom on Earth 2.5

then examining

The unique properties of water

2.2

Current models for chemical evolution 2.4

Key Concepts
Chemical Evolution Theory Molecules formed from atoms, via chemical bonds Water is the most important small molecules for life Chemical reactions depend on potential energy and entropy Functional groups are important in reactions

Matter, Elements, Compounds, Molecules

Organisms are composed of matter Matter: anything that takes up space and has mass Element: A substance that cannot be broken down to other substances by chemical reactions Compound: A substance contains two or more elements Molecules: Two or more atoms combined

Chemical Evolution
Chemical Evolution Theory proposes that simple chemical compounds in the atmosphere and ocean combined to form larger, more complex substances One of these compounds was able toself-replicate

Atoms consist of protons, neutrons, and electrons

An atom: the smallest unit of matter that still retains the properties of an element Subatomic particles:
Protons positively charged Neutrons neutral Electrons negatively charged

Protons and neutrons are in the nucleus Electrons are found in orbitals

Atomic Structure

Key terms
Nucleus Atomic # Mass # - the central core of an atom - the number of protons - The total number of protons and neutrons Atomic weight - whole number; approx. equal to mass number Neutral atoms have equal numbers of protons & electrons (+ and charges)

Periodic Table
Element symbol

Atomic number is unique to each element, basis for arrangement on the periodic table

Isotopes
The same element, different number of neutrons May be radioactive: spontaneously giving off particles and energy May be used to date fossils or as medical tracers
Example:
12C, 13C, 14C

Cancerous throat tissue

Radioactive Decay
14C 12C

Half-life time it takes for one half of the atoms in a sample to decay

The importance of Electrons

The configuration of electrons determines how an atom behaves chemically Orbitals: Regions where electrons move
Each orbital holds 2 electrons

Shells: Levels of orbitals

each has different energy levels

Why shells? Electron Energy Levels

Third energy level (shell)

Second energy level (shell)

Energy absorbed

First energy level (shell) Energy lost Atomic nucleus

14

Atoms combine to form molecules

Atom +Atom + (n)

Molecule

What holds atoms together?

Chemical bonds (ionic and covalent bonds)

Chemical bonds
Possible when there is unfilled electron orbitals When shells are filled, atoms are more stable Valence shell is most important

Atoms of 4 elements important for life

Valence shell: the outermost shell of an atom. The number of electrons in this shell (= valence electrons), determines the number of bonds an atom can make

Electron shells

Atomic Energy Levels

Octet Rule atoms tend to establish full outer shells

1st shell filled with 2 e2nd shell filled with 8 e3rd shell filled with 18 e4th shell filled with 32 e-

How does Covalent Bond form?

Covalent Bonds

BLAST Animation: Covalent Bonds

How Many Bonds Can an Atom Have?

The number of unpaired electrons determines the number of bonds an atom can make.
Atoms with more than one unpaired electron can form multiple single bonds or double or triple bonds

Single, double and triple covalent bonds

Electrons are not always equally shared

Electronegativity: an atoms affinity (pull) for electrons An atom with a high electronegativity will hold the electrons more tightly and have a partial negative charge (), whereas the other atom will have a partial positive charge (+) Level of electronegativity: O>>N>C~H

Types of covalent bonds

How Does Ionic Bonding Hold Molecules Together?

Ionic bonds form as a result of electrons completely transferred from one atom to another, forming ions Ions of opposite charges attract

Ionic bond formation

Neutral atoms have equal numbers of protons & electrons Ions atom with a net charge

Cations Positively charged ion (Na+)

Anions Negatively charged ion (Cl-) Remember the Octet Rule!

Emergent Properties of a Compound

Sodium

Chloride

Sodium Chloride

Electron sharing in chemical bonds

Molecules found in cells often have the much stronger covalent bonds

Weak Bonds are Important too!

Weak bond between slightly positive Hydrogen bond - hydrogen and neighboring slightly negative atom; strength in numbers
+

Van der Waals interactions weak areas of positive and negative charge that help atoms and molecules to stick together when they are very close

Water (H2O) Hydrogen bond

+ +

Ammonia (NH3)

Representing Molecules