Appendices
Enzyme Endurance
Review of Protein Structure
Great review of Protein Structure and Function:
http://matcmadison.edu/biotech/resources/proteins/labManual/chapter_2.htm
The 20 most common amino acids found in proteins
Amino Acid Basic Structure
Peptide Bond Formation
Enzyme Endurance
Notes on Enzymes
Enzymes are usually proteins that first bind tightly to specific molecules, called
substrates, and then catalyze the making and breaking of covalent bonds in these
molecules.
Background on Enzymes
http://student.biology.arizona.edu
At the active site of an enzyme, the amino acid side chains of the folded protein are
precisely positioned so that they favor the formation of the high-energy transition states
that the substrates must pass through.
Active site of Lysozyme shown with substrate
(green) bound.
http://chemistry.umeche.maine.edu
The three-dimensional structure of many proteins has
evolved so that the binding of a small ligand can induce a
significant change in protein shape.
Most enzymes are allosteric proteins that can exist in two
conformations that differ in catalytic activity, and the
enzyme can be turned on or off by ligands that bind to a
distinct regulatory site to stabilize either the active or the inactive conformation.
The activities of most enzymes within the cell are strictly regulated. One of the most
common forms of regulation is feedback inhibition, in which an enzyme early in a
metabolic pathway is inhibited by it's binding to one of the pathway's end products.
End product inhibition is negative
feedback used to regulate the
production of a given molecule.
The initial substrate is a molecule that
is altered in three steps by enzymes
1,2 and 3. The end product will
combine with enzyme 1 to stop the
reaction.
www.okc.cc.ok.us
Not all enzymes are protein in nature. RNA is also known to have catalytic activity, and
catalytic RNA is termed a ribozyme.
An atomic model of the full-length
hammerhead ribozyme obtained by
UCSC scientists using x-ray
crystallography enabled them to describe
how the structure catalyzes chemical
reactions.
Image: M. Martick and W. G. Scott, Cell
(July 28, 2006)
Enzyme Endurance
Enzyme Types and Naming Conventions
Enzyme
Reaction Catalyzed
Hydrolases
General term for enzymes that catalyze a hydrolytic cleavage
reaction.
Nucleases
Breakdown nucleic acids by hydrolyzing bonds between
nucleotides.
Proteases
Breakdown proteins by hydrolyzing bonds between amino acids.
Synthases
General name used for enzymes that synthesize molecules in
anabolic reactions by condensing two smaller molecules together.
Isomerases
Catalyze the rearrangement of bonds within a single molecule.
Polymerases
Catalyze the polymerization reactions such as the synthesis of
DNA and RNA.
Kinases
Catalyze the addition of phosphate groups to molecules. Protein
kinases are an important group of kinases that attach phosphate
groups to proteins.
Phosphatases
Catalyze the hydrolytic removal of a phosphate group from a
molecule.
Oxido-Reductases
General name for enzymes that catalyze reactions in which one
molecule is oxidized while the other is reduced. Enzymes of this
type are often called oxidases, reductases, and dehydrogenases.
ATPases
Hydrolyze ATP. Many proteins with a wide range of roles have an
energy-harnessing ATPase activity as part of their function, for
example, motor proteins such as myosin and membrane transport
proteins such as the sodium-potassium pump.
Enzyme names typically end in "ase", with the exception of some enzymes, such as
pepsin, trypsin, thrombin, lysosyme, which were discovered before the convention
became generally accepted at the end of the nineteenth century. The common name of an
enzyme usually indicates the substrate and the nature of the reaction catalyzed. For
example, citrate synthase catalyzes the synthesis of citrate by the addition of acetyl CoA
to oxaloacetate.