Chapter 6: Metabolism AP Biology Fall 2012

Metabolism and Metabolic Pathways Metabolism is the totality of an organism’s chemical reactions. Molecules are altered in a step-by-step way called a metabolic pathway. There are 2 kinds of metabolic pathways: Catabolic Anabolic

Metabolic Pathways Pictured here (Fig. 6.1 on page 88) is only a few hundred of the thousands of metabolic reactions occurring in all cells. Memorize this diagram. Kidding!

Catabolic vs. Anabolic Degradative They release energy Molecules are broken down. Pathways are “downhill” meaning they go from high potential energy in the reactant to products with less energy. Also called exergonic Consummative They absorb energy Molecules are built up Pathways are “uphill” meaning that the pathway goes from reactants that have less energy to the products that have more Also called endergonic

Page 93 Fig. 6.6 Catabolic reactions can be illustrated as downhill just as anabolic can be illustrated as uphill. The reaction on the left has a loss of free energy as the reaction on the right has a gain in free energy

Energy Coupling Living things will often have metabolic pathways that intersect in such a way that energy from the downhill (catabolic) reaction will drive (provide energy for) the uphill (anabolic) reaction. This is called energy coupling. ATP will be the molecule responsible for the energy coupling in living things

Three main kinds of work done by cells Chemical – synthesis of polymers Transport – pumping of materials across a cell membrane Mechanical – muscle cells contract, cilia beat, movement of chromosomes during mitosis The immediate source of energy that gives the cell the ability to do these things is ATP

ATP – adenosine triphosphate Three components: adenine (purine), a ribose sugar, 3 phosphates.

ATP

ATP ADP + P + energy The three phosphate are all negatively charged and thus have a high degree of instability. When hydrolyzed ATP will lose a phosphate and move to a more stable state. This will release energy and the resulting molecule is ADP (adenosine diphosphate)

How ATP performs work The extra phosphate group is transferred to a molecule that is, as a result, phosphorylated. The phosphorylated molecule is more reactive. Thus ATP is broken down to provide energy to drive an anabolic reaction. Catabolic reactions will release energy that can be used to phosphorylate ADP (regenerate ATP)

Page 95 figure 6.9 An example: ATP drives the reaction that makes glutamic acid (Glu) into glutamine (Gln). It is an anabolic reaction (takes energy)

Page 95 figure 6.9 Now consider that ADP and P are left after the formation of Gln. The ATP can be regenerated from this reaction using energy from another catabolic pathway

Enzymes Enzymes are biological catalysts and they speed up the rate in which a reaction occurs. The reason that enzymes speed up a reaction is that they lower the activation energy (EA) EA is the energy required to get a reaction started.

Page 97, Fig 6.12

Page 97, Fig 6.12 A B C D A B C D A B C D

Page 97, Figure 6.13

How Enzymes Work How enzymes work Enzyme bind to the reactant which is called the substrate. Enzyme Substrate(s) Product(s) EX: Lactase Lactose glucose + galactase

Very Specific Enzymes are very specific based on their shape. There is only a small part of the enzyme that binds to the substrate. This is called the active site

Induced Fit When an enzyme finds a substrate: The substrate enters the active site. The substrate induces the enzyme to slightly change shape so that the active site fits even more tightly around the substrate. This is called induced fit and results in the enzyme-substrate complex. The enzyme catalyzes the reaction and then will float away unchanged.

Lock and Key Enzymatic action is called a lock-and-key mechanism. The lock is the substrate and is changed (locked or unlocked) and the key represents the enzyme with the grooves on the key being the active site. Notice that like the enzyme, the key remains unchanged and can be used over and over.

Recycling Enzymes Enzymes, because they are unchanged, can be used over and over again. So a few enzymes can have a tremendous effect because they can work on one substrate after another at a rate of thousands per second

Reversible reactions If the reaction is reversible, the enzyme can catalyze it in both directions and enzymes will catalyze in the direction of equilibrium.

How they lower the activation energy Enzymes may bring together substrates, and may stress molecules, stretching and bending chemical bonds They also create microenvironments around the active site such as a small pocket of low pH in an otherwise neutral cell.

Saturation When the concentration of substrate is so high that all the active sites are full it is called saturation. In order to increase productivity past saturation, the cell has to make more enzymes.

Optimal Conditions: pH Each enzyme has an optimal pH at which it works. Pepsin works in our stomach and has an optimal pH about 2, however, trypsin, which works in the small intestine has an optimal pH of about 8.

Optimal Conditions Each enzyme has an optimal temperature at which it works. Human enzymes work at a temperature of about 38oC. Thermophilic bacteria have an optimal termperature closer to 80oC.

Control of Enzymes Enzyme activity is controlled, in part, by inhibitors Two kinds of inhibitors: Competitive Noncompetitive Mimics substrate binds somewhere Takes up space on else on enzyme & active site blocking changes shape of substrate access active site

Inhibitors Inhibitors can be reversible or irreversible Competitive Noncompetitive Not inhibited

Control of Metabolism Metabolism in living things is controlled by a special set of inhibitors and activators and is called allosteric regulation. An allosteric site is a specific receptor site on some part of an enzyme molecule remote from the active site.

Feedback inhibition Many times the product of a reaction works as an allosteric inhibitor. This is called feedback inhibition.