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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