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Chapter 8.4 Notes EQ
What are three mechanisms of enzyme catalysis?
How Do Enzymes Work? Enzymes can orient substrates -When free in solution, substrates are moving from place to place randomly while at the same time vibrating, rotating, and tumbling around. -Part of activation energy needed to start a reaction is used to bring together specific atoms so bonds can form Enzymes can induce strain in the substrate -Once a substrate has bound to its active site, an enzyme can cause bonds in the substrate to stretch, putting it in an unstable transition state. Enzymes can temporarily add chemical groups to substrates -The side chains (R groups) of an enzyme’s amino acids may be direct participants in making its substrates more chemically reactive. • In acid–base catalysis, the acidic or basic side chains of the amino acids in the active site transfer H+ to or from the substrate, destabilizing a covalent bond in the substrate, and permitting it to break. • In c ovalent catalysis, a functional group in a side chain forms a temporary covalent bond with a portion of the substrate. • In metal ion catalysis, metal ions such as copper, iron, and manganese, which are firmly bound to side chains of enzymes, can lose or gain electrons without detaching from the enzymes. ability makes them important participants in oxidation–reduction reactions, which involve loss/gain of electrons.
Figure 8.11 Molecular structure determines enzyme function -Most enzymes are much larger than their substrates. -typically a protein containing hundreds of amino acids and may consist of a single folded polypeptide chain or of several subunits -Its substrate is generally a small molecule or a small part of a large molecule. The active site of the enzyme is usually quite small, not more than 6–12 amino acids. THE ACTIVE SITE IS SPECIFIC TO THE SUBSTRATE
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-The binding of the substrate to the active site depends on the same kinds of forces that maintain the tertiary structure of the enzyme: hydrogen bonds, the attraction and repulsion of electrically charged groups, and hydrophobic interactions. AN ENZYME CHANGES SHAPE WHEN IT BINDS A SUBSTRATE -Just as a membrane receptor protein may undergo precise changes in conformation upon binding to its ligand some enzymes change their shapes when they bind their substrate. -Induced fit: (Changed shape of enzyme): expose the active site (or sites) of the enzyme. -Induced fit brings reactive side chains from the hexokinase active site into alignment with the substrates, facilitating its catalytic mechanisms. -Ex: glucose + ATP → glucose 6-phosphate + ADP -Induced fit at least partly explains why enzymes are so large. -The rest of the macromolecule may have three roles: • It provides a framework so that the amino acids of the active site are properly positioned in relation to the substrate(s). • It participates in significant changes in protein shape and structure that result in induced fit. • It provides binding sites for regulatory molecules
Figure 8.12 What are the chemical roles of coenzymes in enzymatic reactions?
Some enzymes require other molecules in order to function -As large and complex as enzymes are, many of them require the presence of non protein chemical “partners” in order to function. • Prosthetic groups are distinctive, non-amino acid atoms or molecular groupings that are permanently bound to their enzymes. An example is a flavin nucleotide, which binds to succinate dehydrogenase, an important enzyme in cellular respiration • Cofactors are inorganic ions such as copper, zinc, and iron that bind to certain enzymes. For example, the cofactor zinc binds to the enzyme alcohol dehydrogenase. • A coenzyme is a carbon-containing molecule that is required for the action of one or more enzymes. It is usually relatively small compared with the enzyme to which it temporarily binds. Conezymes: - move from enzyme to enzyme, adding or removing chemical groups from the substrate. - like a substrate in that it does not permanently bind to the enzyme; it binds to the active site, changes chemically during the reaction, and then separates from the enzyme to participate in other reactions. ATP and ADP, as energy carriers, can be considered coenzymes, even though they are really substrates
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Table 8.1 The substrate concentration affects the reaction rate -Addition of the appropriate enzyme speeds up the reaction, of course, but it also changes the shape of a plot of rate versus substrate concentration -Since the concentration of an enzyme is usually much lower than that of its substrate and does not change as substrate concentration changes, what we see is a saturation phenomenon like the one that occurs in facilitated diffusion.
Figure 8.13 Summary:
Enzymes orient their substrates to bring together specific atoms so that bonds can form. An enzyme can participate in the reaction it catalyzes. It does this by temporarily changing shape or destabilizing the enzyme substrate complex. Some enzymes require cofactors, coenzymes, or prosthetic groups in order to function. Enzymes have a great deal of functions in the world. Some enzymes require other substances, known as cofactors, to carry out catalysis. Prosthetic groups are permanently bound to enzymes; coenzymes are not. A coenzyme can be considered a substrate, as it is changed by the reaction and then released from the enzyme.