Amino acid chains may form helices as parts of the corresponding protein structure

Certain amino acid sequences form sheets (norwegian «flak»)

Helices and sheets (arrows) can be illustrated in various ways. Note that some parts are neither helices nor sheets.

Proteins can be monomeric, dimeric (as below) or multimeric

An extremely complex multimeric protein

The amino acid sequence of a protein is the same as its primary structure. NB!! The primary structure follows from the corresponding sequence of bases in DNA. A protein may contain many different types of sub-structures covering local parts of the overall structure. These local substructures are called secondary structures and can be reasonably well predicted if the primary structure is known (which is the case in almost all proteins studied). The overall structure of a protein, often containing many different secondary sub-structures, is called the tertiary structure. It is very complicated to predict but may however, be solved by X-ray crystallography in the solid state or by NMR (nuclear magnetic resonance) spectroscopy (small proteins, typically below 20 kDa molecular mass), usually in solution.

A-module R-module Figure 1 a)b) c) An enzyme, C5-mannuronan epimerase acting on alginate (J. Biol. Chem and 2008).

Proteins/enzymes have the following very important properties: One particular enzyme can typically bind only one specific compund (the substrate). This can be a low molecular weight compound (like for example glucose). What it actually binds is determined by the tertiary structure of the protein. This structure is the result of the amino acid sequence of the protein, even though one sequence can give rise to more than one structure (boil an egg and see!). The biggest group of proteins are those that catalyse chemical reactions (they are enzymes), and each enzyme typically catalyses only one reaction by binding a specific substrate. When a particular reaction has taken place the same enzyme molecule can immediately start over again and for example carry out 50 catalytic events in a second. Thus, the enzyme is not ”used up” during catalysis. Enzymes catalyse reactions by lowering the activation energy. Many reactions take place spontaneously by themselves, but often very slowly. Enzymes increase the reaction rates for example thousands of times. Enzymes can also catalyse reactions that will not run by themselves, but then energy needs to be supplied. This is often provided by ATP. One or more phosphate group in ATP is hydrolysed off, and the energy released is used to catalyse the reaction that would otherwise not run. A typical example is in fixation of atmospheric nitrogen, which is very energy-demanding. Some enzymes can bind other (specific) compounds than the substrate, like metals, other low molecular weight organic compounds or other proteins, and this may affect enzyme activity (regulation)

Enzyme catalysis can be formalized in this simple way: ESEP E + P E = Enzyme, S = Substrate, P = Product E + S

For a substrate to be converted to a product it must pass through a transition state, and this makes the reaction run slowly in the absence of an enzyme. To reach the transition state ”Free Energy” (ΔG) must be supplied. The enzyme lowers the energy required to reach the transition state, leading to faster reaction rates. Activation energy

The kinetics of enzyme reactions (all parameters can vary)

The kinetics of most enzyme-catalysed reactions can be described mathematically by the Michaelis–Menten equation: V 0 = V max [S] K m + [S] K m is the substrate concentration that leads to V = ½ x V max V = Reaction velocity at K m under the given conditions

K m varies over a wide range among different enzymes

How ATP makes reactions possible, in this case: Glu + ATP + NH 4 + Gln + ADP + Pi Another way of thinking: You move electrons around, as in ordinary light bulbs

Naming of enzymes: Enzyme names end by ”ase”. The first part of the name reflects what specific type of reaction the enzyme catalyses. Enzymes belong to classes called oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases, depending on what type of reaction they catalyse. Each enzyme has a more specific name, like alginate lyase (it belongs to the lyase class, but specifically acts (cleaves bonds) on the polysaccharide alginate. What is ribonuclease doing?