Lectures 2 & 3: Chemistry and the Building Blocks of Life

The organization of Matter - Atoms

The organization of Matter - Chemical Bonds

Molecular bonds depend upon the arrangement of electrons. There are two types of molecular bonds that we will be looking at, covalent bonds and ionic bonds

Covalent Bonds

  • Atoms are most stable when they have a full electron shell. 
  • In order to accomplish this, they must share electrons 

Ionic Bonds

  • Some atoms have a very strong or very weak attraction to electrons 
  • The atoms with a very strong attraction to electrons can "steal" an electron from the atom with a very weak attraction to electrons 
  • Compounds formed in this way are called salts.

Hydrogen Bonds

  • Often when atoms share electrons in a covalent bond, the sharing is not equal. The electrons tend to aggregate nearer to one atom than to the other atom. 
  • This creates what is known as a dipole. In a molecule with a dipole, one end has a higher concentration of electrons than the other end. The end with more electrons has a partial negative charge while the other end has a partial positive charge. Water, as will be discussed below, has a strong dipole. 
  • A hydrogen bond is formed when the negative end of one molecule becomes oriented to and semi-attached to the positive end of another. Hydrogen bonds are fairly weak, but many of them in series, as seen in DNA, can be quite strong. 
  • Molecules with a dipole are known as polar or hydrophilic molecules, those without a dipole are known as non-polar or hydrophobic molecules. 
Hydrophilic Interactions Hydrophobic Interactions


Some properties of water

More fun facts about water

Acids and Bases

Redox Reactions in Biology

In summary, redox reactions primarily involve the transfer of electrons between two chemical species. The compound that loses an electron is said to be oxidized, the one that gains an electron is said to be reduced. There are also specific terms that describe the specific chemical species. A compound that is oxidized is referred to as a reducing agent, while a compound that is reduced is referred to as the oxidizing agent. Confusing, ain't it?


The Molecules of Life

Most biologically important molecules are polymers - long chains of similar repeating sub units There are four classes of important and common molecules: carbohydrates, lipids, proteins, and nucleic acids





Alpha Helix Beta Pleated Sheet
Hemoglobin - an example of a four-subunit protein

Nucleic Acids


Note: the carbons of the ribose sugar of DNA and RNA are numbered as illustrated below:

When a DNA or RNA polymer is created, the bond is formed between the 3' -OH group and the 5' phosphate group. Hold onto this - you'll need it later when we talk about DNA and RNA in more detail

The image of the periodic table was taken from http://mwanal.lanl.gov./C ST/imagemap/periodic/periodic.html
The images of many of the molecules were taken from http://esg-www.mit.edu:8001/esg bio/chem/review.html