Figure 724

Metallothionein Is a Metal Binding Protein

This short protein is capable of sequestering four cadmium atoms.

Movement of both muscles and flagella is due to proteins that contract. This consumes energy in the form of ATP.

cases, carrier proteins are found inside specialized cells that themselves travel around the body—such as red blood cells. Classic examples of carrier proteins are hemoglobin and myoglobin, located in the red blood cells and muscle tissue respectively, which are responsible for carrying oxygen in animals.

Storage proteins sequester nutrients or other molecules, but instead of transporting them, they store them. For example, ferritin in animal cells, and the corresponding bacterioferritin in bacteria, store iron. Metallothionein binds assorted heavy metal ions, and its role is largely protective (Fig. 7.24). The metallothionein gene is induced by traces of heavy metals and has a very strong promoter that is widely used in genetic engineering. Protective metal-binding proteins are also found in certain bacteria. They are sometimes exploited in biotechnological processes for extraction of metals such as gold or uranium from ore or industrial waste streams.

The immune systems of higher animals have many highly specialized binding proteins that function in protection against infection by invading bacteria and viruses. These include antibodies and T-cell receptors.

Mechanical proteins are sometimes classified as specialized structural proteins or as enzymes. They perform physical work at the expense of biological energy (usually by hydrolyzing ATP or GTP). Their energy consumption results in a reversible change of conformation. Proteins of the myosin family that contract upon energization are found in muscle fibers and the filaments of eukaryotic flagella. Actins are found in muscle with myosin where the two proteins participate in a contractile function such as shortening of a muscle (Fig. 7.26), but they are also involved in cellular movements such as endocytosis and amoeboid motion.

ferritin An iron storage protein mechanical protein Protein that uses chemical energy to perform physical work metallothionein Protein that protects animal cells by binding toxic metals

FIGURE 7.25 Magnetotactic Bacteria Contain Magnetosomes to Bind Iron

Transmission electron micrograph of Magnetobacterium bavaricum, a rod-shaped magnetotactic bacterium from Lake Chiemsee (Upper Bavaria) with four bundles of chains of magnetosomes. Individual cells containing up to 1000 hook-shaped magnetosomes yield magnetic moments as high as (10-60)x1012 Gauss ccm, which is one to two orders of magnitude more than the values characteristic of other magnetotactic bacteria. The large electron-opaque bodies inside the cell consist of sulfur. The magnetosomes are made of magnetite and measure, on average, 100 nm. Courtesy of Prof. Michael Winklhofer, Institut für Geophysik, Theresienstrasse 41, D-80333 München, Germany.

FIGURE 7.26 Mechanical Proteins

Myosin and actin interact to cause contraction. The participating proteins move relative to one another but do not shorten individually. The movements bring the end attachments of the actin filaments closer together. Numerous units such as those shown here are attached end-to-end, causing skeletal muscle to shorten.

Bacterial flagella do not operate by contraction of filamentous proteins. Instead, the base of the flagellum consists of a protein ring that rotates as it consumes energy. The filament is attached to the rotating ring and makes a helical lashing motion that drives the bacterium along.

Chaperone proteins, or chaperonins, assist other proteins in folding correctly. Some chaperonins are involved in protein export and prevent premature folding of proteins that are to be secreted through membranes (see Ch. 8). Other chaperonins attempt to re-fold proteins that have become denatured due to high temperature or other environmental stresses that damage proteins (see the heat shock response, Ch. 9).

chaperonin Protein that helps other proteins to fold correctly

Enzymes Catalyze Metabolic Reactions 177

Subcellular machines are assemblies of protein and, often, RNA, that carry out complex tasks in the cell.

Beta-galactosidase splits a range of molecules that consist of galactose linked to another component.

Information processing proteins is a rather artificial assemblage of proteins that can all be alternatively classified as enzymes or binding proteins. However, they are sometimes considered together in order to emphasize their role in transmitting biological information. They include cell surface receptors, signal transmission proteins and regulatory proteins that control the expression of genes at various levels. The functions of these proteins are discussed in detail in the appropriate chapters (especially Ch. 9 through Ch. 11). In this chapter the 3-D structural motifs of proteins involved in the binding of proteins to DNA are discussed further below.

Certain proteins emit or absorb light and are sometimes included among the information processing proteins. Luciferases send a signal from one organism to another by emitting light. Luminous bacteria glow to attract deep-sea fish to swallow them so they can take up residence in the intestines of these fish. Fireflies flash as part of their mating strategy. Both bacterial and insect luciferases have been used as reporter enzymes in genetic analysis (see Ch. 25). Green fluorescent protein (GFP) is made by fluorescent jellyfish. GFP is also used as a reporter in genetic analysis. By reporter, it is meant that the green fluorescence can be used to monitor gene expression and/or to localize areas where a particular gene is expressed (see Ch. 25). Rhodopsins are proteins that absorb light. They are used in the eyes of both invertebrate and vertebrate animals to detect light.

Protein Machines

Many cellular processes such as DNA synthesis, RNA splicing or protein degradation are performed by groups of a dozen or more proteins that operate in a coordinated manner. When such groups of proteins stay associated together, consume energy and carry out carefully controlled movements as well as catalyzing chemical reactions, they are sometimes referred to as protein machines.

There is a trend to name these assemblies to rhyme with ribosome. Thus the repli-some moves along the chromosome while synthesizing new DNA (see Ch. 5), the spliceosome is responsible for RNA splicing (see Ch. 12) and the proteasome carries out protein degradation (see below). However, as Chapter 8 will show, ribosomal RNA plays a more critical part in protein synthesis than do the ribosomal proteins. RNA is also involved in spliceosome function. Thus the term "protein machine" is misleading; a better name might be subcellular machine.

Referring to biological components as machines may perhaps be due to influence from the field of nanotechnology. This refers to the ability to manipulate matter by precisely placing atoms and molecules. Nanotechnology relies on molecular-sized nanomachines. These machines would be programmed to reproduce themselves in the millions and then place atoms precisely to build other molecules. These molecules could then be assembled together into whatever components are needed. Perhaps to be truly trendy and take into account the role of RNA as well as proteins, the term bionanomachine should be introduced.

Enzymes Catalyze Metabolic Reactions

Enzymes are proteins that catalyze chemical reactions but are not consumed in the process. Virtually all metabolic reactions depend on enzymes. An enzyme first binds the reacting molecule, known as its substrate, and then performs a chemical operation upon it. Some enzymes bind only a single substrate molecule; others may bind two or more, and react them together to give the final product. Many enzyme-catalyzed reactions are reversible; that is, the enzyme speeds up reaction in either direction.

green fluorescent protein (GFP) A jellyfish protein that emits green fluorescence and is widely used in genetic analysis luciferase Enzyme that consumes energy and generates light reporter gene Gene that is used in genetic analysis because its product is convenient to assay or easy to detect reporter protein A protein that is easy to detect and gives a signal that can be used to reveal its location and/or indicate levels of gene expression substrate Molecule that binds to an enzyme and is the target of enzyme action

FIGURE 7.27 p-Galactosidase Splits Lactose

Lactose is split by the enzymatic action of p-galactosidase into glucose and galactose.

Lactose ch2oh ch2oh

H OH

Galactose oh h

H OH

Glucose

OH OH

H OH

Glucose ch2oh

^ol-poH

H OH

Galactose

FIGURE 7.28 Active Site Consists of Residues Far Apart in the Sequence

Before a polypeptide chain is folded, the amino acid residues that cooperate to carry out the enzymatic reaction are often far apart in the sequence. Upon correct folding, the critical amino acids are brought together and form the active site.

Folding

Folding

Pocket formed by active site residues

Both the substrate and cofactors (if needed) bind to the active site of the enzyme.

The most famous enzyme in molecular biology is b-galactosidase, encoded by the lacZ gene of the bacterium Escherichia coli. This enzyme is so easy to assay that it is widely used in genetic analysis (see Ch. 25 for details). One of the natural substrates of b-galactosidase is the sugar lactose, made by linking together the two simple sugars, glucose and galactose. b-Galactosidase hydrolyses lactose into the two simpler sugars (Fig. 7.27).

Substrates bind to the enzyme at the active site, a pocket or cleft in the protein, where the reaction occurs. The active site is the result of precise folding of the polypep-tide chain so that amino acid residues that may have been far apart in the linear sequence can come together to cooperate in the enzyme reaction (Fig. 7.28 and Fig. 7.29).

Many enzymes rely on cofactors or prosthetic groups to assist in catalysis. These may be organic molecules, such as NAD (nicotinamide adenine dinucleotide), which

ß-galactosidase Enzyme that splits lactose and related compounds

Enzymes Have Varying Specificities 179

FIGURE 7.29 Enzyme Substrate Complex of Aldose Reductase

A three-dimensional computer model of aldose reductase (EC 1.1.1.21) shown binding its substrates, glucose-6-phosphate (orange) and NADP (gray). The image was generated by Dr. Manuel C. Peitsch at the Glaxo Institute for Molecular Biology in Geneva, Switzerland, using coordinates from the Brookhaven Protein Data Bank.

FIGURE 7.29 Enzyme Substrate Complex of Aldose Reductase

A three-dimensional computer model of aldose reductase (EC 1.1.1.21) shown binding its substrates, glucose-6-phosphate (orange) and NADP (gray). The image was generated by Dr. Manuel C. Peitsch at the Glaxo Institute for Molecular Biology in Geneva, Switzerland, using coordinates from the Brookhaven Protein Data Bank.

FIGURE 7.30 Some Enzymes, Such as Aspartase, Can Distinguish Isomers

L-Aspartate is transformed to fumarate plus NH3 by the enzyme aspartase. This enzyme will not transform "look-alike" substrates such as glutamic acid nor structural isomers like maleic acid. Furthermore, aspartase can distinguish optical isomers and only uses the L-form of aspartate.

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