Biotech 2:

Atoms and Molecules

OS Text Reading – pp. 36-48

Electron cloud

Protons

2e– Nucleus

Electrons

Mass number = 4

Neutrons

2

2

2

Electron cloud

Protons

6e–

Nucleus

Electrons

Mass number = 12

Neutrons

6

6

6

Helium

Carbon atomic number =

# of protons

mass number =

# of neutrons & protons

Atoms &

Subatomic

Particles

Atoms of the same element having different numbers of

neutrons are referred to as different isotopes, some of

which are unstable and thus radioactive.

Isotopes

• radioactive emissions are of different types

depending on the isotope

*

• each radioactive isotope has a characteristic half-life

Neon, with two filled

Shells (10 electrons)

First shell

Second shell

First shell Second shell

1s orbital 2s orbital Three 2p orbitals

(a) Electron distribution diagram

(b) Separate electron orbitals

(c) Superimposed electron orbitals

1s, 2s, and

2p orbitals

x y

z

Electron

Orbitals

• orbitals are geometrically

arranged regions of

space around an atomic

nucleus in which

electrons are found

• orbitals are arranged

in groups at distinct

energy levels called

electron shells

• each orbital can hold no

more than 2 electrons

(a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons

Third shell (highest energy level)

Second shell (higher energy level)

Energy absorbed

First shell (lowest energy level)

Atomic nucleus

(b)

Energy lost

Energy Shells

First

shell

Second

shell

Third

shell

Hydrogen

1H

Lithium

3Li

Sodium

11Na

Beryllium

4Be

Magnesium

12Mg

Boron

5B

Aluminum

13Al

Carbon

6C

Silicon

14Si

Nitrogen

7N

Phosphorus

15P

Oxygen

8O

Sulfur

16S

Fluorine

9F

Chlorine

17Cl

Neon

10Ne

Argon

18Ar

Helium

2He 2

He

4.00 Mass number

Atomic number

Element symbol

Electron

distribution

diagram

The Periodic Table • elements in the same column have the same number of

valence electrons, and similar chemical properties

Hydrogen atoms (2 H)

Hydrogen molecule (H2)

The Formation of

Molecules

2 or more atoms connected

by a chemical bond(s)

constitute a molecule

• chemical bonds involve

unpaired electrons from each

atom involved in the bond

• covalent bonds involve the

sharing of such electrons

• jonic bonds involve the

donation/acceptance of

such electrons

(a) Hydrogen (H2)

(b) Oxygen (O2)

(c) Water (H2O)

Name and

Molecular

Formula

Electron

Distribution

Diagram

Lewis Dot

Structure and

Structural

Formula

Space-

Filling

Model

(d) Methane (CH4)

Representing

Molecular

Structure

Polarity in Covalent Bonds

–

+ + H H

O

H2O

The sharing of electrons in covalent bonds is not

necessarily equal, depending on the electronegativity

of the atoms involved in the bond:

• non-polar bonds occur between atoms of the same or

similar electronegativities due to equal sharing of e-

• polar bonds occur between

atoms with significantly

different electronegativities

due to unequal sharing of e-

Non-polar Molecules

• electrons are shared equally between identical atoms since

their attraction for electrons (electronegativity) is the same

Polar Molecules

• elements tend to

vary in their

electronegativities

• if atoms sharing

electrons differ

significantly in

electronegativity,

the electrons are

shared unequally

and the bond is

polar

NON-POLAR

POLAR

C & H electronegativies

are ~ the same

O & H electronegativities

are significantly different

+

+

+

+

+

water (H2O)

ammonia (NH3)

Hydrogen bond

Polarity & Hydrogen Bonds Hydrogen bonds are weak interactions that occur

between atoms involved in polar covalent bonds,

one of which is a hydrogen atom:

+ H atom bound

to a more

electronegative

atom (e.g., N or O)

- charge on atom

of another

molecule or

chemical group

+ –

Na

Sodium atom Cl

Chlorine atom

Na+

Sodium ion

(a cation)

Cl–

Chloride ion

(an anion)

Ionic bond

Electronic

transfer

forms ions

Ions and Ionic Bonds

Na+

Cl–

sodium chloride (NaCl)

crystal

opposing ions

form neutral salts

Reactants Reaction Products

2 H2 O2 2 H2O

Chemical Reactions

Covalent bonds in reactant molecules break and

the atoms form new covalent bonds in the products

• all atoms from reactants end up in products

• chemical reactions are reversible, direction depends on

conditions, concentrations of products vs reactants