Basic Chemistry and Biological Molecules

Chapter 2

Atoms and Ions

Atoms are the smallest unit of matter with definitive properties.

Even atoms have substructure.

Hydrogen

ProtonMass = 1 amuCharge = +1

NeutronMass = 1 amuCharge = 0

ElectronMass = O*Charge = -1

* Not quite zero, but close enough for government work

Atomic Number = Number of protons

Atomic Mass = Protons + Neutrons

Hydrogen

Also Hydrogen

Isotopes

Number of Electrons = Number of Protons, if the atom is neutral.

Neutrons removed for clarity

Lithium+1Ions

Bonding

Bonding is governed by Electronegativity*

*Among other things, but we don’t need to go there right now.

Ionic Bonds = Large Differences in Electronegativity.

Covalent Bonds = No to Moderate differences in Electronegativity

Polar vs. Nonpolar

Hydrogen Bonds

Polymers

Biological Molecules

are Organic

Functional Groups, subunits of structure

Hydroxyl (-OH)

Carboxyl (-COOH)

Amino (-NH2)

Sulfhydryl (-SH)

Phosphate (PO4)

Methyl (-CH3)

Together these groups give organic molecules their functions

How do we go from small molecules to large polymers?

Dehydration Reaction

HHO HO H

How do we break them back apart?

Hydrolysis

HO H

HHO

Carbohydrates, the Sugars

Carbohydrates are polymers of Simple Sugars

Carbohydrates have two functions

Structural

Energy Storage

Function comes from Structure

Structure comes from the arrangement of monomers

New Arrangement = New Function

Nucleic Acids, Information

Nucleic Acids are polymers of nucleotides

Nucleic Acids have two functions

Heredity

Energy Transfer

Function is determined bythe order of nucleotides

Proteins, Diverse Functions

Proteins are linear polymers of amino acids

Amino Acids have an amino and a carboxylic acid functional group

There are twenty natural amino acids.

In essence, they are a chemistry tool kit.

Amino Acids bind together by peptide bonds

Proteins are extremely varied in Function

Function is derived from Structure

Structure is an emergent property.

There are four levels of structure.

Now pull them together…

Evolution likes to reuse what works.

A protein’s function is destroyed if the structure is destroyed (denatured).

Lipids, Diverse Structures

Lipids are polymers composed of the monomer acetyl-CoA

Very diverse structures can be formed.

Trigylceride

Phospholipid

Sterols/Steroids

Lipids have three functions

Structural

Long-Term Energy Storage

Signaling