The way atoms come together in biological molecules is dependent on the nature of the carbon atom.

Compounds made by cells and containing carbon are called organic compounds.

Hydrocarbons - contain hydrogen and carbon but may also have many functional groups.

Hydrocarbon chains: methane, ethane, propane, butane, isobutane, etc.

Functional groups

Hydroxyl (-OH) makes an alcohol

Carbonyl (C=O) makes an aldehyde or a ketone

Carboxyl (HO-C=O) carboxylic acids

Amino (NH₂)

Phosphate (H₂PO₄)

In general, functional groups can make a non-polar hydrocarbon more polar and may give the molecule very different chemical properties.

Macromolecules – large polymers (molecules with many units) made by joining smaller units together. We will study four types of macromolecules, or ‘biomolecules’.

Monomers (single subunits) are linked together into polymers by a process called dehydration synthesis (because a water molecule is removed in the process). When a polymer is broken down into its monomers, water is used in the process and it is called hydrolysis.

Carbohydrates are made of carbon, hydrogen and oxygen and have the generic formula (CH₂O)_n so if n=6, the formula is C₆H₁₂O₆. The monomers of carbohydrates are sugars. Simple sugars are monosaccharides. Two simple sugars linked by dehydration synthesis are disaccharides. Generally, monosaccharides have between 3 and 7 carbons, with 6 being the most familiar. Glucose, fructose and galactose are 6-carbon monosaccharide isomers (same formula, different structure).

Glucose + glucose = maltose

Glucose + fructose = sucrose

Glucose + galactose = lactose

When monosaccharides are continuously linked together through dehydration synthesis, the result is a macromolecule called a polysaccharide. There are three important classes of polysaccharides.

Starches primarily come from plants and consist of chains of glucose monomers

Glycogen is called animal starch. It’s a way of storing excess sugar and the process is performed in the liver. The polymers are actually branching chains of glucose.

Cellulose is also a glucose polymer that is chemically linked in a different way. Most animals do not have the ability to digest those chemical bonds. (Those that can have specific microorganisms in their digestive tracts.)

Lipids (fats and oils) are generally hydrophobic. They are made by linking three fatty acids to a glycerol backbone by dehydration synthesis. Since they occupy less space than starches, animals store excess energy as lipids.

Lipids may be saturated or unsaturated.

Phospholipids contain 2 fatty acid chains and phosphorus. They are important components of cell membranes.

Waxes consist of 1 fatty acid linked to an alcohol. They are more hydrophobic than other lipids.

Steroids are lipids with a twisted carbon skeleton which gives them a ‘ring’ structure. Steroids play important roles in cell membranes and are also precursor molecules in hormone synthesis.

Cholesterol

Anabolic Steroids

Monomers are amino acids

Proteins are a diverse group of macromolecules and can be classified into 7 groups

Structural

Contractile

Storage

Defense

Transport proteins

Signal proteins

Enzymes

Enzymes are chemical catalysts which regulate the rate of a chemical reaction, without being changed into something else. Enzymes are very efficient and since they aren’t changed during a chemical reaction, they are ‘recyclable’ and the same molecule used repeatedly.

Amino acid structure – Amino acids have a carboxylic acid group (that’s why they’re acids!) as well as an amino group. Those two features are common to all amino acids. The only part that differs from one amino acid to another is the R group. There are 20 possible R groups, and each R group has an effect on the amino acid—so some are acidic, some are basic, some are hydrophilic and some hydrophobic.

To make a protein, amino acids must be linked together through dehydration synthesis. The resulting chemical bond between adjacent amino acids is then called a peptide bond. The resulting molecule then grows from a single amino acid to a dipeptide, tripeptide……polypeptide.

In a protein, the polypeptide sequence plays an important role in what the protein ‘looks’ like and also determines its function. The specific shape of the protein is critical. If environmental conditions become unfavorable, then the protein will likely become non-functional. (Those environmental factors might include temperature, pH or salt concentration.)

There are four levels of organization to protein structure; primary, secondary, tertiary and quaternary.

Primary – precise sequence of amino acids

Secondary – polypeptide folds or coils; due to hydrogen bonds between amino and carboxyl groups.

a-helix

b-pleated sheet

Tertiary – overall shape of the polypeptide (eg. globular or fibrous), resulting from secondary structure and chemical interactions between R-groups.

Quaternary – some proteins have more than one polypeptide chain and protein function depends on all the subunits getting together in the right conformation.

Monomers are nucleotides. Nucleotides have 3 components:

1. Phosphate
2. 5-carbon sugar (ribose or deoxyribose)
3. Nitrogen base

Adenine (A)

Thymine (T)

Guanine (G)

Cytosine (C)

Uracil (U)

Nucleotides are linked together by dehydration synthesis to form polynucleotides. (The chemical bond is called a phosphodiester bond.) The sequence of the polynucleotide chain carries the genetic blueprint for making proteins in a cell.