BIOCHEMISTRY - DR. JAKUBOWSKI
SUMMARY: Biological macromolecule structure and function can be examined and understood by applying principles learned from the study of small molecules to macromolecules. The macromolecules we will discuss in class, (proteins, complex carbohydrates, and nucleic acids) can be understood using principles of organic, physical, analytical, and inorganic chemistry.
The links below will take you to a description of many of the handouts I have distributed in class. This online guide is meant to augment your understanding of what we have discussed in class, and not a replacement for class attendance.
Proteins are polymers of the bifunctional monomer, amino acids. Amino acids form polymers through a nucleophilic attack by the amino group of an amino acid at the electrophilic carbonyl carbon of the carboxyl group of another amino acid. The carboxyl group of the amino acid must first be activated to provide a better leaving group than OH-. (We will discuss this activation by ATP latter in the course.) The resulting link between the amino acids is an amide link which biochemists call a peptide bond. In this reaction, water is released. In a reverse reaction, the peptide bond can hence be cleaved by water (hydrolysis).
COMPLEX CARBOHYDRATES - POLYSACCHARIDES
Monosaccharides are the monomeric units which polymerize to form a polysaccharide. Monosaccharides are simple sugars (polyhydroxyaldehydes or ketones) , which can cyclize by an intramolecular nucleophilic addition of one of the OH groups on the sugar with the aldehyde or ketone, resulting in a hemiacetal or hemiketal. Addition of another alcohol, from an exogenous alcohol under acidic/anhydrous condition results in an acetal. If the added alcohol is from another sugar, a covalent, acetal link between the two sugars results. As with peptides, the process can be reversed under aqueous conditions through hydrolysis of the acetal link, resulting in monomeric sugars. Biochemist name the acetal link between sugars a glycosidic bond. Click to see figures showing these reactions.
The monomeric units of nucleic acids consist of a 5-ring cyclized sugar, ribose (for RNA) and deoxyribose (for DNA), which has been attached at C1 to an organic base (pyrimidine or purine) through an "acetal-like" link. (i.e. Instead of a nucleophilic alcohol reacting with the ribose hemiacetal, a nucleophilic N on the base reacts) The link between the monomers requires the activation of the O on C5 through a triphosphate group. The actual link between the monomers is a phosphodiester link, which likewise can be hydrolyzed. See the figures below.
ROADMAP FOR THE COURSE
Powerpoint: Biochemistry Based on Chemical Logic