CHEMISTRY

The Building Blocks of Biology

Matter• Anything that has mass and occupies

space.

• Solid, Liquid, Gas

Elements

Biological Elements

• Nitrogen• Carbon• Hydrogen• Oxygen• Phosphorous• Sulfur• Calcium• Potassium (K)

96%

Elements

• Atom = smallest unit of matter unique to a particular element.– (smallest “piece” of an element)

• Molecule = union of 2 or more atoms.

• Compound = union of 2 or more different atoms.

Atomic Structure

• Determines how atoms act.

• Various hypotheses exist about how atoms are actually structured…– Bohr – circular orbits– Summerfield – elliptical orbits– Pauli – wave theory/quantum

mechanics:

“Clouds of Probability”

Atomic Structure• Protons (+)• Neutrons (no charge)

• Electrons (-)

• Atomic # • Atomic Mass (Mass #) – an approximation.

– Each Proton is approx. 1 x 10-24g= 1 Dalton

Nucleus

Orbiting

Models of Atomic Structure…

Nucleus

(a) (b) In this even more simplifiedmodel, the electrons areshown as two small bluespheres on a circle around thenucleus.

Cloud of negativecharge (2 electrons)

Electrons

This model represents theelectrons as a cloud ofnegative charge, as if we hadtaken many snapshots of the 2electrons over time, with eachdot representing an electron‘sposition at one point in time.

“Normally”

• # Protons = # Neutrons = # Electrons

• BUT, not always…

• Isotopes – Atoms with variable #’s of Neutrons– Stable & Unstable

• Ions – Atoms with variable #’s of Electrons

Electron Shells

• 1st Shell holds up to 2e-

• 2nd Shell holds up to 8e-

• 3rd Shell holds up to 8e-

Electrons• Have different amounts of energy.

• The amount of energy depends on location…Which “shell” it occupies.

Third energy level (shell)

Second energy level (shell)

First energy level (shell)

(b)

Atomic nucleus

“Shell” Models

Secondshell

Helium

2He

Firstshell

Thirdshell

Hydrogen

1H

2He

4.00Atomic mass

Atomic number

Element symbol

Electron-shelldiagram

Lithium

3LiBeryllium

4BeBoron

3BCarbon

6CNitrogen

7NOxygen

8OFluorine

9FNeon

10Ne

Sodium

11NaMagnesium

12MgAluminum

13AlSilicon

14SiPhosphorus

15PSulfur

16SChlorine

17ClArgon

18Ar

Figure 2.8

Which element is this?

Electron Orbitals• The three-dimensional space where an

electron is found 90% of the time.

Electron orbitals.Each orbital holds

up to two electrons.

1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals

(a) First shell (maximum 2 electrons)

(b) Second shell (maximum 8 electrons)

(c) Neon, with two filled shells (10 electrons)

Electron-shell diagrams.Each shell is shown withits maximum number of

electrons, grouped in pairs.

x

Z

Y

Figure 2.9

Atoms “like” to do 2 things:1. Be Balanced.

2. Fill their outer-most shells.

Formation of Ions

• Oxidation – Departure of an e-

• Reduction – Gaining of an e-

e-

Valence Electrons

• Those electrons occupying an atom’s outer-most shell (its “Valence Shell”)

Bonding• Linking together atoms to form

molecules…1. Covalent Bonding2. Ionic Bonding3. Hydrogen Bonding4. (Peptide Bonding)

• Electronegativity– The attraction of a particular kind of atom for

the electrons in another.– The more electronegative an atom, the more

strongly it pulls shared electrons toward itself.

Covalent Bonding• Strong

• Sharing of valence electronsA. Non-Polar Covalent Bonds

EQUAL SHARING

H2 O2

• The “Electronegativity” of the component atoms is equal.

H HO O

Covalent Bonding• Strong• Sharing of valence electrons

B. Polar Covalent BondsUNEQUAL SHARING

H2O

• The “Electronegativity” of the component atoms is not the same.

O H

H

Polar Covalent Bonds

• Water…

This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.

H2O

–

O

H H+ +

Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

Ionic Bonding

• Huge differences in Electronegativity.

• Electrons are transferred (not shared)– Oxidation forms a Cation (+ charged).– Reduction forms an Anion (- charged).

• Bond results from the attraction between ions of different charge…

Ionic Bonding

• Attraction between a Cation & an Anion.

Cl–

Chloride ion(an anion)

–

The lone valence electron of a sodiumatom is transferred to join the 7 valenceelectrons of a chlorine atom.

1 Each resulting ion has a completedvalence shell. An ionic bond can formbetween the oppositely charged ions.

2

Na NaCl Cl

+

NaSodium atom

(an unchargedatom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium on(a cation)

Sodium chloride (NaCl)

Hydrogen Bonding

• Weak

• A hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom.

+—

Hydrogen Bonding

Water(H2O)

Ammonia(NH3)

OH

H

+

–

N

HH H

A hydrogenbond results from the attraction between thepartial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.

+ +

Van der Waals Interactions

• Transient weak attractions between molecules

• (not really “bonds”)

• Due to inherent vibrational state of electrons…at any given time.

• Help reinforce molecular shape.

Next…Water