Chemistry as a

Foundation for Biology

Thursday September 3rd

The Big Ideas• Part 1: Atoms and Elements

– Pruning the periodic table

• Part 2: Basics of bonding– Types of bonds– Implications of different bond types

• Part 3: Application of bonding– The identification of carbon and functional groups– The importance of water

Part 1:Atoms and Elements

The

Ato

mNucleus(6 protons + 6 neutrons)

Electron

Proton

Neutron

Carbon atom

+ ++

+

++ +

Nitrogen (N)8%

Phosphorus (P)3%

Sulfur (S)Potassium (K)Calcium (Ca)Sodium (Na)Chlorine (Cl)Magnesium (Mg)2%

Others1%

Hydrogen (H)9%

Oxygen (O)30%

Carbon (C)47%

Elements of Life

A simplified biology periodic tableAbundance in cells

High Low Trace None

Core Questions

• What do elements in a column of the periodic table have in common?

• What do elements in a row of the periodic table have in common?

Part 2:Basics of Bonding

…this means we are talking about electrons

Core Questions

• How do we define a bond?

• What determines how many bonds an atom can form with other atoms?

• What determines the type of bond that forms between two atoms?

Bond RepresentationsHydrogen gas

H2

Methane

CH4

Ammonia

NH3

Water

H2O

H-H

The number of bonds an atom can form is determined by its valence:

i.e., the number of unpaired electrons.

• We’ll just memorize this for now:• Hydrogen (H) forms 1 bond• Carbon (C) forms 4 bonds• Nitrogen (N) forms 3 bonds• Oxygen (O) forms 2 bonds• Phosphorous (P) forms 5 bonds • Sulfur (S) can form either 2 or 6 bonds

Multiple Bonds

Single bonds

Double bonds

Triple bonds

WaterH2O

AmmoniaNH3

MethaneCH4

Carbon dioxideCO2

Molecular nitrogenN2

(from a different textbook)

The nature of a bond is determined by the relative electronegativities of two atoms:

i.e., a measure of their ability to attract electronsGoing across the table, the number of shells stays the same while the number of protons inside the nucleus increase, thus there is more attraction to electrons; Going down the table, the number of

shells increase thus there is less attraction between the protons in nucleus and electrons. Increasing electronegativity

Incr

easi

ng e

lect

rone

gativ

ity

WHY???

Which is more electronegative?

• Carbon (C) or Nitrogen (N)?• Carbon (C) or Oxygen (O)?• Sodium (Na) or Chloride (Cl)?• Phosphorous (P) or Oxygen (O)?• Carbon (C) or Hydrogen (H)?

Types of Bonds(think electronegativity)

Equal sharing of electrons

Nonpolar covalent bonds(atoms have no charge)

Polar covalent bonds(atoms have partial charge)

Transfer of electrons

Ionic bonds(atoms have full charge)

Hydrogen Methane Ammonia Water Sodium chloride

What type of bond should _____ form with _____?

• Carbon and Carbon• Carbon and Hydrogen• Carbon and Oxygen• Hydrogen and Oxygen• Oxygen and Phosphorous• Sodium and Chloride

Bond choices: nonpolar covalent, polar covalent, ionic

Part 3:Application of Bonding

Core Questions

• What about the chemical property of water allows it to play such a central role in biology?

• How can we use these basic bonding properties to define ‘functional groups’ and predict chemical properties of biomolecules?

Polar covalent bonds within a single water molecule

(leads to partial charges on H and O)

d- d-

Partial charges permit hydrogen bonds between water molecules

Water Questions

• Why don’t oil (a mixture of carbon and hydrogen) and water mix?

• Why does spreading salt (NaCl) on a sidewalk in winter melt the ice?

Functional Groups

(ketones & aldehydes)

Functional Group Question: Describe the chemical properties of this molecule

Valine (an amino acid)

Functional Group Question: Describe the chemical properties of this molecule

Functional Group Question: Describe the chemical properties of this molecule

Fatty acid (a building block of lipids)

And one more functional group

Phosphate in ATP (adenosine triphosphate)

H

OH OH OH