1. Proteins

2. The central role of proteins in the chemistry of life Proteins have a variety of functions. Structural proteins make up the physical structure of cells. Enzymes catalyze chemical reactions. Other proteins are involved in transport and storage of chemicals, and yet others, for example hormones, are involved in the regulation of biological processes. Transmembrane proteins are involved in transmission of chemical signals or in the selective transport of chemicals across cellular membranes.

3. A common belief It is generally believed that what happens in a cell at any given time is largely determined by how much of which proteins are present (“expressed”) at that time.

4. The building blocks of proteins As a first approximation, proteins can be thought of as long chains of amino acids, that is, polypeptides. There are 20 different amino acids. Each of them consists of a central carbon atom that is bonded to a carboxyl group, a hydrogen atom, an amino group, and a side chain. Each amino acid has its own characteristic side chain.

5. How proteins differ from each other Proteins differ by their length (typically a few hundred amino acids) and by the sequence of amino acids that make up the polypeptide chain. This sequence is often referred to as the primary structure of a protein. The function of of a protein in the chemistry of the cell is largely determined by the three-dimensional structure of the protein.

6. Abbreviations for amino acids zAlanine A Ala zArginine R Arg zAsparagine N Asn zAspartic acid D Asp zCysteine C Cys zGlutamine Q Gln zGlutamic acid E Glu zGlycin G Gly zHistidine H His zIsoleucine I Ile z Leucine L Leu z Lysine K Lys z Methionine M Met z Phenylalanine F Phe z Proline P Pro z Serine S Ser z Threonine T Thr z Tryptophan W Trp z Tyrosine Y Tyr z Valine V Val

7. Characteristic properties of amino acids Amino acids differ in a number of physical and chemical properties. The most obvious of these properties is size of the side chain, with glycine and tryptophan being on opposite extremes of the spectrum.

8. Characteristic properties of amino acids Another important property is the distinction between hydrophobic and hydrophylic amino acids. Proteins tend to fold in such a way that hydrophylic amino acids will be exposed to aqueous environments, such as the cytoplasm, whereas hydrophobic amino acids tend be located away from water, for example, in the hydrophobic core of a protein, or within the bilipid layer of a cell membrane. Hydrophibicity is strongly correlated with polarity; polar amino acids tend to be hydrophylic, nonpolar ones tend to be hydrophobic.

9. Peptide bonds

10. Three-dimensional structure of proteins The function of a protein is to a large degree determined by its 3D structure which has several levels: zSecondary structure refers to local coils and folds, like alpha-helices and beta-sheets (or pleated sheets). It results from local hydrogen bonds that occur at regular intervals. zTertiary structure of a polypeptide chain is superimposed on the secondary structure. It may result from bonding of side chains or hydrophobic interactions. zQuarternary structure is the overall protein structure that results from the aggregation of polypeptide subunits.