Carbon and Molecular Diversity

Based on Chapter 4

Major Elements of life

Compounds and Molecules

Structure and Function

• Carbon molecule and ring structure– Polysaccharides

Importance of Carbon• Most molecules from which living organisms are

derived are based on C.• C has the ability to form large, complex and

diverse molecules.– Cells and tissues are made up of these basic molecules:

carbohydrates, lipids, proteins and nucleic acids.

• The study that deals with C and and C-H molecules (hydrocarbons) is called organic chemistry.

• In order to get familiar with macromolecules, we need to examine C, hydrocarbons and the functional groups which bond to hydrocarbons.

Properties of Carbon• Chemical characteristics and bonds formed by an

atom are determined by the atom’s electrons. – Carbon has 6 electrons (2 first shell, 4 second shell)– With 4 valence electrons, it has little tendency to gain or

loose electrons and form ionic bonds. • It forms covalent bonds to become stable. Most commonly

with H, O and N• These bonds are in 4 different directions and C is known as

having tetravalence because of this.– Carbon will form double and triple bonds with other C

atoms. Even though you will see molecules written in their structural formula as flat, they are 3d structures and their molecular shape often determine their function.

Hydrocarbons• When C is not bonding to itself, it covalently

bonds to other atoms (H, O and N)• The basic C compound is called a hydrocarbon,

formed from C and H.

Hydrocarbons• Hydrocarbons vary in:

– The number of C on the chain– Straight, branching, or ring structures– Where and how many H atoms are attached to the

carbon chain.

• Most hydrocarbons have similar properties (the C-H bond is energy rich) so hydrocarbons are capable of storing vast amounts of energy (fats and petroleum)

• Carbon variations that differ only in the arrangements of atoms are called isomers.

Isomers• Compounds that have the same

molecular formula, but different structures and thus different functions.

• There are 3 types of isomers:1. Structural2. Geometric3. Enantiomers

Structural Isomers• Vary in their covalent bonding

arrangement.• Also may vary in the placement of double

C bonds.

Geometric Isomers• Have the same covalent partnerships but differ in their spatial

arrangements.• Geometric isomers share common covalent bonding, but because

double bonds are inflexible (prevent rotation) compared to single bonds which rotate freely around the bonds axis.

• The differing shape of geometric isomers can dramatically affect their biological function (sometimes called the cis-trans difference).

Enantiomers (stereoisomers)• Molecules that are mirror images

of each other and have the same molecular formula.

• Enantiomers are formed when 4 different molecular groups are bonded to a central (asymmetric) carbon so that they can be arranged in 2 different ways.

• The different shapes of enantiomers can dramatically alter function.

• One example is Vitamin E which has a L and D form. One is more active and found naturally, the other is frequent in vitamin pills but lacks the same biologic activity.

• L-dopa example

Functional Groups• These are molecular fragments which, when

substituted for one or more H atoms in a hydrocarbon, confer particular chemical properties to the new compound.1

• The functional group determines the “behavior” of the molecule and is consistent in different organic molecules.

• There are 6 main functional groups we will consider.

1Richardson, Rosemary, 2003 http://www.scidiv.bcc.ctc.edu/rkr/

Hydroxyl Group

1Richardson, Rosemary, 2003 http://www.scidiv.bcc.ctc.edu/rkr/

• The hydroxyl function group is formed by an oxygen bonded to a hydrogen, with the second bond of the oxygen free to attach to the carbon chain (-OH).

• Hydroxyl functional groups confer properties of an alcohol to hydrocarbons.

• Hydroxyl functional groups are polar (the oxygen end's electronegativity), and attract water. This helps dissolve in water those macromolecules, such as sugars, which have hydroxyl functional groups in their structure.

• The naming convention for alcohols is to have the alcohol end in "ol" and the prefix be determined by the number of carbons (based on the alkane or pure hydrocarbon naming convention). For example, the two-carbon alcohol is ethanol.1

Carbonyl Group• The carbonyl functional group is a double bonded oxygen (=O).

• Carbonyl functional groups confer properties of aldehydes or ketones to hydrocarbons.

• Because double bonds restrict flexibility and rotation on the carbon skeleton, the location of the carbonyl functional group affects structure, and function.

• Carbonyl functional groups attached to an "end" carbon form aldehydes. Carbonyl functional groups attached to a non-end carbon form ketones. The naming convention for ketones uses the suffix “-one" and aldehydes the suffix “-al". The prefix may be determined by the number of carbons. It is not always so. For example, propanal is the 3-carbon aldehyde, but the 3-carbon ketone, by convention, is called acetone.

Carboxyl Group• The carboxyl function group combines the hydroxyl and

the carbonyl functional groups attached to a common carbon atom. The carboxyl functional group will always be at the end of a carbon chain.

• Carboxyl functional groups form organic (or carboxylic) acids. The -OH portion of the functional group dissociates in solution, donating a H+. This dissociation is aided by the electronegativity of the =O of the carbonyl portion of the functional group.

Amino Group• The amino function group is - NH2 . The amino functional group

added to organic compounds forms amines. Most amines in living organisms are found in molecules which also have carboxyl function groups and form the important class of molecules called amino acids.

• The amino functional group is a base. The nitrogen region of the amino functional group can attract a proton (generally attached to a hydrogen, thereby removing hydrogen ions from solution) resulting in a positive charge (+1).

Sulfhydryl Group• Sulfur, like oxygen, forms two covalent bonds. The

sulfhydryl functional group (-SH) is similar to the hydroxyl functional group.

• Sulfhydryl functional groups are important in the structure of proteins, where the sulfur bonds help stabilize the protein's functional structure.

• Compounds containing sulfhydryl groups are called -thiols.

Phosphate Group• Phosphate is a negative ion composed of

phosphate bonded to 4 oxygen atoms. (PO4), formed by the dissociation of phosphoric acid.

• The loss of two hydrogen ions from the acid results in the negative charge. One of the oxygen molecules of the phosphate functional group bonds to the carbon chain.

• Phosphate functional groups are important in energy transfer.