Organic Chemistry

Carbon: the Chemical Foundation of All Living Organisms

• The chemistry of carbon is called organic chemistry.
  • Organic chemistry derives its name from the word “organism,” since the chemistry of all living organisms is based on carbon.
• There are literally millions of different compounds found in living organisms that are based on carbon.
  • Making sense of all these different compounds and their chemistry can be rather daunting.
  • We will take a look at some of the essential things a biology student should know about organic chemistry; hopefully you will see that the basics are fairly straightforward and understandable…

The Key to Carbon Chemistry

• The key to understanding carbon chemistry is simple: carbon has four valence electrons, so it can form four bonds.
• It can form four single bonds as shown here.
• It can form double or triple bonds as well.

Part of Figure 2.9, page 28; figure 2.10(d), page 29, Campbell's Biology, 5th Edition

Carbon Diversity

• Biodiversity refers to the diversity of life on Earth.
  • Earth originated 3.8 billion years ago with an original prokaryote.
  • This prokaryote evolved into the 1.7 million different species we have so far identified on earth.
• Since all living things are based on the element carbon, we can think of “carbon diversity” as the diversity of carbon compounds among all living organisms.

Two Reasons for Carbon-Compound Diversity

1. Diversity of carbon chains
   • Carbon can form chains—sometimes called carbon skeletons—in a variety of ways:
     • Straight chains, single bonded
     • Straight chains, double bonded
     • Branched chains
     • Ringed structures
2. Diversity of functional groups
   • Functional groups are the parts of the carbon compound responsible for chemical reactions.
   • There are six important functional groups:
     1. Hydroxyl
     2. Carbonyl
     3. Carboxyl
     4. Amino
     5. Sulfhydryl
     6. Phosphate

Carbon Chains

• Carbon can form long chains.
• These chains can be extremely long; they vary in length. In some cases 20 to 30 carbons can be bonded together!
• They can be arranged in straight chains with single bonds (as shown immediately below) or…

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Carbon Chains Can Have Double Bonds

• Double bonds are not uncommon in carbon compounds.
• The location of these double bonds within the chain can vary.
• Note that each carbon still has four bonds; this will always be true.

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Carbon Chains Can Branch

• Carbons chains do not have to always be in straight lines; they can branch.
• Here we see both unbranched (straight) and branched carbon skeletons.
• Note each carbon still only has four bonds.

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Carbon Chains Can Form Rings

• Carbon can also form ringed structures.
• The ringed structures can have single or double bonds.
• Note how the abbreviated structural formulas omit the corner carbons and the hydrogens attached to them.
• Again, each carbon has only four bonds.

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Functional Groups

• Why are they important?
  • Functional groups are generally found at the end of the carbon chain and are responsible for the way the carbon compound reacts chemically with other compounds.
  • Since chemistry is all about reactions, functional groups, in a large measure, determine the chemical nature of carbon-based compounds.
• We need to be familiar with six different functional groups:
  1. Hydroxyl
  2. Carbonyl
  3. Carboxyl
  4. Amino
  5. Sulfhydryl
  6. Phosphate

1. Hydroxyl Group

• This is an —OH group which replaces what would otherwise be a hydrogen.
• This is the group that makes a molecule an alcohol.

Functional Group	Formula	Name of Compounds	Example
Hydroxyl		Alcohols

2. Carbonyl Group

• This is a carbon atom joined to an oxygen atom by a double bond.
• When at the end, the molecule is called an aldehyde.
• When in the middle, the molecule is called a ketone.

Functional Group	Formula	Name of Compounds	Example
Carbonyl		Aldehydes
		Ketones

3. Carboxyl Group

• The carboxyl group has an oxygen atom bonded to a carbon atom that is also bonded to a hydroxyl group.
• The carboxyl group makes the compound acidic, so these substances are often called carboxylic acids, or organic acids.
• Reason they are acidic:
  • Oxygen is very electronegative and therefore loves electrons more than the carbon or hydrogen do.
  • The oxygen atoms pull the electrons away from the hydrogen, causing the hydrogen to dissociate (i.e., fall away from the compound).
  • This increase in H⁺ ions makes the solution acidic.

Functional Group	Formula	Name of Compounds	Example
Carboxyl		Carboxylic acids

4. Amino Group

• The amino group consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton.
• Compounds with this functional group are called amines.
• This functional group is where the “amino” part of “amino acid” comes from.

Functional Group	Formula	Name of Compounds	Example
Amino		Amines

5. Sulfhydryl Group

• In the sulfhydryl group, a sulfur atom is bonded to an atom of hydrogen.
• Compounds with this group are called thiols.
• It looks similar to a hydroxyl group, but with a sulfur rather than an oxygen atom.
• They can be important in the formation of protein structure (see the lecture on proteins).

Functional Group	Formula	Name of Compounds	Example
Sulfhydryl		Thiols

6. Phosphate Group

• A phosphate group is a phosphate atom surrounded by four oxygen atoms.
  • One of the four oxygen atoms connects the functional group to a carbon atom in a carbon chain.
• Compounds with this group are called organic phosphates.
• It has a negative charge (is an anion)

Functional Group	Formula	Name of Compounds	Example
Phosphate		Organic phosphates