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8.0: Energy, Matter, and Enzymes - Biology

8.0: Energy, Matter, and Enzymes - Biology


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Learning Objectives

  • Define and describe metabolism
  • Compare and contrast autotrophs and heterotrophs
  • Describe the importance of oxidation-reduction reactions in metabolism
  • Describe why ATP, FAD, NAD+, and NADP+ are important in a cell
  • Identify the structure and structural components of an enzyme
  • Describe the differences between competitive and noncompetitive enzyme inhibitors

part 1

Hannah is a 15-month-old girl from Washington state. She is spending the summer in Gambia, where her parents are working for a nongovernmental organization. About 3 weeks after her arrival in Gambia, Hannah’s appetite began to diminish and her parents noticed that she seemed unusually sluggish, fatigued, and confused. She also seemed very irritable when she was outdoors, especially during the day. When she began vomiting, her parents figured she had caught a 24-hour virus, but when her symptoms persisted, they took her to a clinic. The local physician noticed that Hannah’s reflexes seemed abnormally slow, and when he examined her eyes with a light, she seemed unusually light sensitive. She also seemed to be experiencing a stiff neck.

Exercise (PageIndex{1})

What are some possible causes of Hannah’s symptoms?

The term used to describe all of the chemical reactions inside a cell is metabolism (Figure (PageIndex{1})). Cellular processes such as the building or breaking down of complex molecules occur through series of stepwise, interconnected chemical reactions called metabolic pathways. Reactions that are spontaneous and release energy are exergonic reactions, whereas endergonic reactions require energy to proceed. The term anabolism refers to those endergonic metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules, and fueled by the use of cellular energy. Conversely, the term catabolism refers to exergonic pathways that break down complex molecules into simpler ones. Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce high-energy molecules, which are used to drive anabolic pathways. Thus, in terms of energy and molecules, cells are continually balancing catabolism with anabolism.

Classification by Carbon and Energy Source

Organisms can be identified according to the source of carbon they use for metabolism as well as their energy source. The prefixes auto- (“self”) and hetero- (“other”) refer to the origins of the carbon sources various organisms can use. Organisms that convert inorganic carbon dioxide (CO2) into organic carbon compounds are autotrophs. Plants and cyanobacteria are well-known examples of autotrophs. Conversely, heterotrophs rely on more complex organic carbon compounds as nutrients; these are provided to them initially by autotrophs. Many organisms, ranging from humans to many prokaryotes, including the well-studied Escherichia coli, are heterotrophic.

Organisms can also be identified by the energy source they use. All energy is derived from the transfer of electrons, but the source of electrons differs between various types of organisms. The prefixes photo- (“light”) and chemo- (“chemical”) refer to the energy sources that various organisms use. Those that get their energy for electron transfer from light are phototrophs, whereas chemotrophs obtain energy for electron transfer by breaking chemical bonds. There are two types of chemotrophs: organotrophs and lithotrophs. Organotrophs, including humans, fungi, and many prokaryotes, are chemotrophs that obtain energy from organic compounds. Lithotrophs (“litho” means “rock”) are chemotrophs that get energy from inorganic compounds, including hydrogen sulfide (H2S) and reduced iron. Lithotrophy is unique to the microbial world.

The strategies used to obtain both carbon and energy can be combined for the classification of organisms according to nutritional type. Most organisms are chemoheterotrophs because they use organic molecules as both their electron and carbon sources. Table (PageIndex{1}) summarizes this and the other classifications.

Table (PageIndex{1}): Classifications of Organisms by Energy and Carbon Source
ClassificationsEnergy SourceCarbon SourceExamples
ChemotrophsChemoautotrophsChemicalInorganicHydrogen-, sulfur-, iron-, nitrogen-, and carbon monoxide-oxidizing bacteria
ChemoheterotrophsChemicalOrganic compoundsAll animals, most fungi, protozoa, and bacteria
PhototrophsPhotoautotrophsLightInorganicAll plants, algae, cyanobacteria, and green and purple sulfur bacteria
PhotoheterotrophsLightOrganic compoundsGreen and purple nonsulfur bacteria, heliobacteria

Exercise (PageIndex{2})

  1. Explain the difference between catabolism and anabolism.
  2. Explain the difference between autotrophs and heterotrophs.

Oxidation and Reduction in Metabolism

The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of electrons allows the cell to transfer and use energy incrementally; that is, in small packages rather than a single, destructive burst. Reactions that remove electrons from donor molecules, leaving them oxidized, are oxidation reactions; those that add electrons to acceptor molecules, leaving them reduced, are reduction reactions. Because electrons can move from one molecule to another, oxidation and reduction occur in tandem. These pairs of reactions are called oxidation-reduction reactions, or redox reactions.

Energy Carriers: NAD+, NADP+, FAD, and ATP

The energy released from the breakdown of the chemical bonds within nutrients can be stored either through the reduction of electron carriers or in the bonds of adenosine triphosphate (ATP). In living systems, a small class of compounds functions as mobile electron carriers, molecules that bind to and shuttle high-energy electrons between compounds in pathways. The principal electron carriers we will consider originate from the B vitamin group and are derivatives of nucleotides; they are nicotinamide adenine dinucleotide, nicotine adenine dinucleotide phosphate, and flavin adenine dinucleotide. These compounds can be easily reduced or oxidized. Nicotinamide adenine dinucleotide (NAD+/NADH) is the most common mobile electron carrier used in catabolism. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule. Nicotine adenine dinucleotide phosphate (NADP+), the oxidized form of an NAD+ variant that contains an extra phosphate group, is another important electron carrier; it forms NADPH when reduced. The oxidized form of flavin adenine dinucleotide is FAD, and its reduced form is FADH2. Both NAD+/NADH and FAD/FADH2 are extensively used in energy extraction from sugars during catabolism in chemoheterotrophs, whereas NADP+/NADPH plays an important role in anabolic reactions and photosynthesis. Collectively, FADH2, NADH, and NADPH are often referred to as having reducing power due to their ability to donate electrons to various chemical reactions.

A living cell must be able to handle the energy released during catabolism in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and a single phosphate group. Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms ATP (Figure (PageIndex{2})). Adding a phosphate group to a molecule, a process called phosphorylation, requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. Thus, the bonds between phosphate groups (one in ADP and two in ATP) are called high-energy phosphate bonds. When these high-energy bonds are broken to release one phosphate (called inorganic phosphate [Pi]) or two connected phosphate groups (called pyrophosphate [PPi]) from ATP through a process called dephosphorylation, energy is released to drive endergonic reactions (Figure (PageIndex{3})).

Exercise (PageIndex{3})

What is the function of an electron carrier?

Enzyme Structure and Function

A substance that helps speed up a chemical reaction is a catalyst. Catalysts are not used or changed during chemical reactions and, therefore, are reusable. Whereas inorganic molecules may serve as catalysts for a wide range of chemical reactions, proteins called enzymes serve as catalysts for biochemical reactions inside cells. Enzymes thus play an important role in controlling cellular metabolism.

An enzyme functions by lowering the activation energy of a chemical reaction inside the cell. Activation energy is the energy needed to form or break chemical bonds and convert reactants to products (Figure (PageIndex{4})). Enzymes lower the activation energy by binding to the reactant molecules and holding them in such a way as to speed up the reaction.

The chemical reactants to which an enzyme binds are called substrates, and the location within the enzyme where the substrate binds is called the enzyme’s active site. The characteristics of the amino acids near the active site create a very specific chemical environment within the active site that induces suitability to binding, albeit briefly, to a specific substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates, enzymes are known for their specificity. In fact, as an enzyme binds to its substrate(s), the enzyme structure changes slightly to find the best fit between the transition state (a structural intermediate between the substrate and product) and the active site, just as a rubber glove molds to a hand inserted into it. This active-site modification in the presence of substrate, along with the simultaneous formation of the transition state, is called induced fit (Figure (PageIndex{5})). Overall, there is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, there is some flexibility as well. Some enzymes have the ability to act on several different structurally related substrates.

Enzymes are subject to influences by local environmental conditions such as pH, substrate concentration, and temperature. Although increasing the environmental temperature generally increases reaction rates, enzyme catalyzed or otherwise, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site, making them less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, losing their three-dimensional structure and function. Enzymes are also suited to function best within a certain pH range, and, as with temperature, extreme environmental pH values (acidic or basic) can cause enzymes to denature. Active-site amino-acid side chains have their own acidic or basic properties that are optimal for catalysis and, therefore, are sensitive to changes in pH.

Another factor that influences enzyme activity is substrate concentration: Enzyme activity is increased at higher concentrations of substrate until it reaches a saturation point at which the enzyme can bind no additional substrate. Overall, enzymes are optimized to work best under the environmental conditions in which the organisms that produce them live. For example, while microbes that inhabit hot springs have enzymes that work best at high temperatures, human pathogens have enzymes that work best at 37°C. Similarly, while enzymes produced by most organisms work best at a neutral pH, microbes growing in acidic environments make enzymes optimized to low pH conditions, allowing for their growth at those conditions.

Many enzymes do not work optimally, or even at all, unless bound to other specific nonprotein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Binding to these molecules promotes optimal conformation and function for their respective enzymes. Two types of helper molecules are cofactors and coenzymes. Cofactors are inorganic ions such as iron (Fe2+) and magnesium (Mg2+) that help stabilize enzyme conformation and function. One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires a bound zinc ion (Zn2+) to function.

Coenzymes are organic helper molecules that are required for enzyme action. Like enzymes, they are not consumed and, hence, are reusable. The most common sources of coenzymes are dietary vitamins. Some vitamins are precursors to coenzymes and others act directly as coenzymes.

Some cofactors and coenzymes, like coenzyme A (CoA), often bind to the enzyme’s active site, aiding in the chemistry of the transition of a substrate to a product (Figure (PageIndex{6})). In such cases, an enzyme lacking a necessary cofactor or coenzyme is called an apoenzyme and is inactive. Conversely, an enzyme with the necessary associated cofactor or coenzyme is called a holoenzyme and is active. NADH and ATP are also both examples of commonly used coenzymes that provide high-energy electrons or phosphate groups, respectively, which bind to enzymes, thereby activating them.

Exercise (PageIndex{4})

What role do enzymes play in a chemical reaction?

Enzyme Inhibitors

Enzymes can be regulated in ways that either promote or reduce their activity. There are many different kinds of molecules that inhibit or promote enzyme function, and various mechanisms exist for doing so (Figure (PageIndex{7})). A competitive inhibitor is a molecule similar enough to a substrate that it can compete with the substrate for binding to the active site by simply blocking the substrate from binding. For a competitive inhibitor to be effective, the inhibitor concentration needs to be approximately equal to the substrate concentration. Sulfa drugs provide a good example of competitive competition. They are used to treat bacterial infections because they bind to the active site of an enzyme within the bacterial folic acid synthesis pathway. When present in a sufficient dose, a sulfa drug prevents folic acid synthesis, and bacteria are unable to grow because they cannot synthesize DNA, RNA, and proteins. Humans are unaffected because we obtain folic acid from our diets.

On the other hand, a noncompetitive (allosteric) inhibitor binds to the enzyme at an allosteric site, a location other than the active site, and still manages to block substrate binding to the active site by inducing a conformational change that reduces the affinity of the enzyme for its substrate (Figure (PageIndex{8})). Because only one inhibitor molecule is needed per enzyme for effective inhibition, the concentration of inhibitors needed for noncompetitive inhibition is typically much lower than the substrate concentration.

In addition to allosteric inhibitors, there are allosteric activators that bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s).

Allosteric control is an important mechanism of regulation of metabolic pathways involved in both catabolism and anabolism. In a most efficient and elegant way, cells have evolved also to use the products of their own metabolic reactions for feedback inhibition of enzyme activity. Feedback inhibition involves the use of a pathway product to regulate its own further production. The cell responds to the abundance of specific products by slowing production during anabolic or catabolic reactions (Figure (PageIndex{8})).

Exercise (PageIndex{5})

Explain the difference between a competitive inhibitor and a noncompetitive inhibitor.

Key Concepts and Summary

  • Metabolism includes chemical reactions that break down complex molecules (catabolism) and those that build complex molecules (anabolism).
  • Organisms may be classified according to their source of carbon. Autotrophs convert inorganic carbon dioxide into organic carbon; heterotrophs use fixed organic carbon compounds.
  • Organisms may also be classified according to their energy source. Phototrophs obtain their energy from light. Chemotrophs get their energy from chemical compounds. Organotrophs use organic molecules, and lithotrophs use inorganic chemicals.
  • Cellular electron carriers accept high-energy electrons from foods and later serve as electron donors in subsequent redox reactions. FAD/FADH2, NAD+/NADH, and NADP+/NADPH are important electron carriers.
  • Adenosine triphosphate (ATP) serves as the energy currency of the cell, safely storing chemical energy in its two high-energy phosphate bonds for later use to drive processes requiring energy.
  • Enzymes are biological catalysts that increase the rate of chemical reactions inside cells by lowering the activation energy required for the reaction to proceed.
  • In nature, exergonic reactions do not require energy beyond activation energy to proceed, and they release energy. They may proceed without enzymes, but at a slow rate. Conversely, endergonic reactions require energy beyond activation energy to occur. In cells, endergonic reactions are coupled to exergonic reactions, making the combination energetically favorable.
  • Substrates bind to the enzyme’s active site. This process typically alters the structures of both the active site and the substrate, favoring transition-state formation; this is known as induced fit.
  • Cofactors are inorganic ions that stabilize enzyme conformation and function. Coenzymes are organic molecules required for proper enzyme function and are often derived from vitamins. An enzyme lacking a cofactor or coenzyme is an apoenzyme; an enzyme with a bound cofactor or coenzyme is a holoenzyme.
  • Competitive inhibitors regulate enzymes by binding to an enzyme’s active site, preventing substrate binding. Noncompetitive (allosteric) inhibitors bind to allosteric sites, inducing a conformational change in the enzyme that prevents it from functioning. Feedback inhibition occurs when the product of a metabolic pathway noncompetitively binds to an enzyme early on in the pathway, ultimately preventing the synthesis of the product.

Multiple Choice

Which of the following is an organism that obtains its energy from the transfer of electrons originating from chemical compounds and its carbon from an inorganic source?

A. chemoautotroph
B. chemoheterotroph
C. photoheterotroph
D. photoautotroph

A

Which of the following molecules is reduced?

A. NAD+
B. FAD
C. O2
D. NADPH

D

Enzymes work by which of the following?

A. increasing the activation energy
B. reducing the activation energy
C.making exergonic reactions endergonic
D. making endergonic reactions exergonic

B

To which of the following does a competitive inhibitor most structurally resemble?

A. the active site
B. the allosteric site
C. the substrate
D. a coenzyme

C

Which of the following are organic molecules that help enzymes work correctly?

A. cofactors
B. coenzymes
C. holoenzymes
D. apoenzymes

B

Fill in the Blank

Processes in which cellular energy is used to make complex molecules from simpler ones are described as ________.

anabolic

The loss of an electron from a molecule is called ________.

oxidation

The part of an enzyme to which a substrate binds is called the ________.

active site

True/False

Competitive inhibitors bind to allosteric sites.

False

Short Answer

In cells, can an oxidation reaction happen in the absence of a reduction reaction? Explain.

What is the function of molecules like NAD+/NADH and FAD/FADH2 in cells?


8.0: Energy, Matter, and Enzymes - Biology

PART II. CORNERSTONES: CHEMISTRY, CELLS, AND METABOLISM

5. Enzymes, Coenzymes, and Energy

All living organisms require a constant supply of energy to sustain life. They obtain this energy through enzyme-controlled chemical reactions, which release the internal

potential energy stored in the chemical bonds of molecules (figure 5.10). Burning wood is a chemical reaction that results in the release of energy by breaking chemical bonds. The chemical bonds of cellulose are broken, and smaller end products of carbon dioxide (CO2) and water (H2O) are produced. There is less potential energy in the chemical bonds of carbon dioxide and water than in the complex organic cellulose molecules, and the excess energy is released as light and heat.

FIGURE 5.10. Life's Energy: Chemical Bonds

All living things use the energy contained in chemical bonds. As organisms break down molecules, they can use the energy released for metabolic processes, such as movement, growth, and reproduction. In all cases, there is a certain amount of heat released when chemical bonds are broken.

In living things, energy is also released but it is released in a series of small steps and each is controlled by a specific enzyme. Each step begins with a substrate, which is converted to a product, which in turn becomes the substrate for a different enzyme. Such a series of enzyme-controlled reactions is called a biochemical pathway, or a metabolic pathway. The processes of photosynthesis, respiration, protein synthesis, and many other cellular activities consist of a series of biochemical pathways. Biochemical pathways that result in the breakdown of compounds are generally referred to as catabolism. Biochemical pathways that result in the synthesis of new, larger compounds are known as anabolism. Figure 5.11 illustrates the nature of biochemical pathways.

FIGURE 5.11. Biochemical Pathways

Biochemical pathways are the result of a series of enzyme-controlled reactions. In each step, a substrate is acted upon by an enzyme to produce a product. The product then becomes the substrate for the next enzyme in the chain of reactions. Such pathways can be used to break down molecules, build up molecules, release energy, and perform many other actions.

One of the amazing facts of nature is that most organisms use the same basic biochemical pathways. For example, the bacterium E. coli and human cells have an estimated 1,000 genes that are the same. These two drastically different cell types manufacture many of the same enzymes and, therefore, run many of the same pathways. However, because the kinds of enzymes an organism is able to produce depend on its genes, some variation occurs in the details of the biochemical pathways. The fact that so many kinds of organisms use essentially the same biochemical processes is a strong argument for the idea of evolution from a common ancestor. Once a successful biochemical strategy evolved, the genes and the pathways were retained (conserved) through evolutionary descendents, with slight modifications of the scheme.

Generating Energy in a Useful Form: ATP

The transfer of chemical energy within living things is handled by an RNA nucleotide known as adenosine triphosphate (ATP). Chemical energy is stored when ATP is made and is released when it is broken apart. An ATP molecule is composed of a molecule of adenine (a nitrogenous base), ribose (a sugar), and 3 phosphate groups (figure 5.12). If only 1 phosphate is present, the molecule is known as adenosine monophosphate (AMP).

FIGURE 5.12. Adenosine Triphosphate (ATP)

An ATP molecule is an energy carrier. A molecule of ATP consists of several subunits: a molecule of adenine, a molecule of ribose, and 3 phosphate groups. The 2 end phosphate groups are bonded together by high-energy bonds. These bonds are broken easily, so they release a great amount of energy. Because they are high-energy bonds, they are represented by curved, solid lines.

When a second phosphate group is added to the AMP, a molecule of adenosine diphosphate (ADP) is formed. The ADP, with the addition of even more energy, is able to bond to a third phosphate group and form ATP. (Recall from chapter 3 that the addition of phosphate to a molecule is called a phosphorylation reaction.) The bonds holding the last 2 phosphates to the molecule are easily broken to release energy for cellular processes that require energy. Because the bond between these phosphates is so easy for a cell to use, it is called a high-energy phosphate bond. These bonds are often shown as solid, curved lines (-) in diagrams. Both ADP and ATP, because they contain high-energy bonds, are very unstable molecules and readily lose their phosphates. When this occurs, the energy held in the phosphate’s high-energy bonds can be transferred to a lower-energy molecule or released to the environment. Within a cell, specific enzymes (phosphorylases) speed this release of energy as ATP is broken down to ADP and P (phosphate). When the bond holding the third phosphate of an ATP molecule is broken, energy is released for use in other activities.

When energy is being harvested from a chemical reaction or another energy source, such as sunlight, it is stored when a phosphate is attached to an ADP to form ATP.

An analogy that might be helpful is to think of each ATP molecule used in the cell as a rechargeable battery. When the power has been drained, it can be recharged numerous times before it must be recycled (figure 5.13).

FIGURE 5.13. ATP: The Power Supply for Cells

When rechargeable batteries in a flashlight have been drained of their power, they can be recharged by placing them in a specially designed battery charger. This enables the right amount of power from a power plant to be packed into the batteries for reuse. Cells operate in much the same manner. When the cell’s “batteries,” ATPs are drained while powering a job, such as muscle contraction, the discharged “batteries,” ADPs can be recharged back to full ATP power.

Another important concept that can be applied to many different biochemical pathways is the mechanism of electron transport. Because the electrons of an atom are on its exterior, the electrons in the outer energy level can be lost more easily to the surroundings, particularly if they receive additional energy and move to a higher energy level. When they fall back to their original position, they give up that energy. This activity takes place whenever electrons gain or lose energy. In living things, such energy changes are harnessed by special molecules that capture such “excited” electrons that can be transferred to other chemicals. These electron-transfer reactions are commonly called oxidation-reduction reactions. In oxidation-reduction (redox) reactions, the molecules losing electrons become oxidized and those gaining electrons become reduced. The molecule that loses the electron loses energy the molecule that gains the electron gains energy.

There are many different electron acceptors or carriers in cells. However, the three most important are the coenzymes: nicotinamide adenine dinucleotide (NAD + ), nicotinamide adenine dinucleotide phosphate (NADP + ), and /lavin adenine dinucleotide (FAD). Recall that niacin is needed to make NAD + and NADP + and the riboflavin is needed to make FAD. Because NAD + , NADP + , FAD, and similar molecules accept and release electrons, they are often involved in oxidation-reduction reactions. When NAD + , NADP + , and FAD accept electrons, they become negatively charged. Thus, they readily pick up hydrogen ions (H + ), so when they become reduced they are shown as NADH, NADPH, and FADH2. Therefore, it is also possible to think of these molecules as hydrogen carriers. In many biochemical pathways, there is a series of enzyme controlled oxidation-reduction reactions (electron-transport reactions) in which each step results in the transfer of a small amount of energy from a higher-energy molecule to a lower-energy molecule (figure 5.14). Thus, electron transport is often tied to the formation of ATP.

FIGURE 5.14. Electron Transport and Proton Gradient

The transport of high-energy electrons through a series of electron carriers can allow the energy to be released in discrete, manageable packets. In some cases, the energy given up is used to move or pump protons (H + ) from one side of a membrane to the other and a proton concentration gradient is established. When the protons flow back through the membrane, enzymes in the membrane can capture energy and form ATP.

In many of the oxidation-reduction reactions that take place in cells, the electrons that are transferred come from hydrogen atoms. A hydrogen nucleus (proton) is formed whenever electrons are stripped from hydrogen atoms. When these higher- energy electrons are transferred to lower-energy states, protons are often pumped across membranes. This creates a region with a high concentration of protons on one side of the membrane. Therefore, this process is referred to as a proton pump. The “pressure” created by this high concentration of protons is released when protons flow through pores in the membrane back to the side from which they were pumped. As they pass through the pores, an enzyme, ATP synthetase (a phosphorylase), uses their energy to speed the formation of an ATP molecule by bonding a phosphate to an ADP molecule. Thus, making a proton gradient is an important step in the production of much of the ATP produced in cells (review figure 5.14).

The four concepts of biochemical pathways, ATP production, electron transport, and the proton pump—are all interrelated. We will use these concepts to examine particular aspects of photosynthesis and respiration in chapters 6 and 7.

15. What is a biochemical pathway, and what does it have to do with enzymes?

16. Describe what happens during electron transport and what it has to do with a proton pump.

Enzymes are protein catalysts that speed up the rate of chemical reactions without any significant increase in the temperature. They do this by lowering activation energy. Enzymes have a very specific structure that matches the structure of particular substrate molecules. The substrate molecule comes in contact with only a specific part of the enzyme molecule— the attachment site. The active site of the enzyme is the place where the substrate molecule is changed. The enzyme-substrate complex reacts to form the end product. The protein nature of enzymes makes them sensitive to environmental conditions, such as temperature and pH, that change the structure of proteins. The number and kinds of enzymes are ultimately controlled by the genetic information of the cell. Other kinds of molecules, such as coenzymes, inhibitors, and competing enzymes, can influence specific enzymes. Changing conditions within the cell shift its enzymatic priorities by influencing the turnover number.

Enzymes are also used to speed and link chemical reactions into biochemical pathways. The energy currency of the cell, ATP, is produced by enzymatic pathways known as electron transport and proton pumping. The four concepts of biochemical pathways, ATP production, electron transport, and the proton pump are all interrelated.

1. Something that speeds the rate of a chemical reaction but is not used up in that reaction is called a

2. The amount of energy it takes to get a chemical reaction going is known as

3. A molecule that is acted upon by an enzyme is a

4. Your cells require _____ to manufacture certain coenzymes.

5. When a protein’s three-dimensional structure has been altered to the extent that it no longer functions, it has been

d. competitively inhibited.

6. Whenever there are several different enzymes available to combine with a given substrate, _____ results.

7. In _____, a form of enzyme control, the end product inhibits one step of its formation when its concentration becomes high enough.

8. Which of the following contains the greatest amount of potential chemical-bond energy?

9. Electron-transfer reactions are commonly called _____ reactions.

10. As electrons pass through the pores of cell membranes, an enzyme, _____ (a phosphorylase), uses electron energy to speed the formation of an ATP molecule by bonding a phosphate to an ADP molecule.

11. If a cleaning agent contains an enzyme that will get out stains that are protein in nature, it can also be used to take out stains caused by oil. (T/F)

12. Keeping foods in the refrigerator helps make them last longer because the lower temperature _____ enzyme activity.

13. ATP is generated when hydrogen ions flow from a _____ to a _____ concentration after they have been pumped from one side of the membrane to the other.

14. What are teams competing for in a football game? _____

15. A person who is vitamin deficient will most likely experience a _____ in their metabolism.

1. a 2. c 3. d 4. vitamins 5. a 6. enzymatic competition 7. negative feedback 8. c 9. oxidation-reduction 10. ATP synthetase 11. F 12. slows/inhibits 13. higher, lower 14. the ball 15. Disruption

The following data were obtained by a number of Nobel Prize-winning scientists from Lower Slobovia. As a member of the group, interpret the data with respect to the following:

2. Movement of substrates into and out of the cell

3. Competition among various enzymes for the same substrate

a. A lowering of the atmospheric temperature from 22°C to 18°C causes organisms to form a thick, protective coat.

b. Below 18°C, no additional coat material is produced.

c. If the cell is heated to 35°C and then cooled to 18°C, no coat is produced.

d. The coat consists of a complex carbohydrate.

e. The coat will form even if there is a low concentration of simple sugars in the surroundings.

f. If the cell needs energy for growth, no cell coats are produced at any temperature.

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Enzymes: How they work and what they do

Enzymes help speed up chemical reactions in the human body. They bind to molecules and alter them in specific ways. They are essential for respiration, digesting food, muscle and nerve function, among thousands of other roles.

In this article, we will explain what an enzyme is, how it works, and give some common examples of enzymes in the human body.

Share on Pinterest The enzyme amylase (pictured), breaks down starch into sugars.

Enzymes are built of proteins folded into complicated shapes they are present throughout the body.

The chemical reactions that keep us alive – our metabolism – rely on the work that enzymes carry out.

Enzymes speed up (catalyze) chemical reactions in some cases, enzymes can make a chemical reaction millions of times faster than it would have been without it.

A substrate binds to the active site of an enzyme and is converted into products. Once the products leave the active site, the enzyme is ready to attach to a new substrate and repeat the process.

The digestive system – enzymes help the body break down larger complex molecules into smaller molecules, such as glucose, so that the body can use them as fuel.

DNA replication – each cell in your body contains DNA. Each time a cell divides, that DNA needs to be copied. Enzymes help in this process by unwinding the DNA coils and copying the information.

Liver enzymes – the liver breaks down toxins in the body. To do this, it uses a range of enzymes.

The “lock and key” model was first proposed in 1894. In this model, an enzyme’s active site is a specific shape, and only the substrate will fit into it, like a lock and key.

This model has now been updated and is called the induced-fit model.

In this model, the active site changes shape as it interacts with the substrate. Once the substrate is fully locked in and in the exact position, the catalysis can begin.

Enzymes can only work in certain conditions. Most enzymes in the human body work best at around 37°C – body temperature. At lower temperatures, they will still work but much more slowly.

Similarly, enzymes can only function in a certain pH range (acidic/alkaline). Their preference depends on where they are found in the body. For instance, enzymes in the intestines work best at 7.5 pH, whereas enzymes in the stomach work best at pH 2 because the stomach is much more acidic.

If the temperature is too high or if the environment is too acidic or alkaline, the enzyme changes shape this alters the shape of the active site so that substrates cannot bind to it – the enzyme has become denatured.

Some enzymes cannot function unless they have a specific non-protein molecule attached to them. These are called cofactors. For instance, carbonic anhydrase, an enzyme that helps maintain the pH of the body, cannot function unless it is attached to a zinc ion.

To ensure that the body’s systems work correctly, sometimes enzymes need to be slowed down. For instance, if an enzyme is making too much of a product, there needs to be a way to reduce or stop production.

Enzymes’ activity can be inhibited in a number of ways:

Competitive inhibitors – a molecule blocks the active site so that the substrate has to compete with the inhibitor to attach to the enzyme.

Non-competitive inhibitors – a molecule binds to an enzyme somewhere other than the active site and reduces how effectively it works.

Uncompetitive inhibitors – the inhibitor binds to the enzyme and substrate after they have bound to each other. The products leave the active site less easily, and the reaction is slowed down.

Irreversible inhibitors – an irreversible inhibitor binds to an enzyme and permanently inactivates it.

There are thousands of enzymes in the human body, here are just a few examples:

  • Lipases – a group of enzymes that help digest fats in the gut.
  • Amylase – helps change starches into sugars. Amylase is found in saliva.
  • Maltase – also found in saliva breaks the sugar maltose into glucose. Maltose is found in foods such as potatoes, pasta, and beer.
  • Trypsin – found in the small intestine, breaks proteins down into amino acids.
  • Lactase – also found in the small intestine, breaks lactose, the sugar in milk, into glucose and galactose.
  • Acetylcholinesterase – breaks down the neurotransmitter acetylcholine in nerves and muscles.
  • Helicase – unravels DNA.
  • DNA polymerase – synthesize DNA from deoxyribonucleotides.

Enzymes play a huge part in the day-to-day running of the human body. By binding to and altering compounds, they are vital for the proper functioning of the digestive system, the nervous system, muscles, and much, much more.


How Enzymes Work

Take a look at Figure 2. Note that glucose (C 6 H 12 O 6 ) in the presence of oxygen (6 O 2 ) will generate carbon dioxide (6 CO 2 ) and water (6 H 2 O). The forward reaction from glucose to the top of the energy hill to carbon dioxide and water at the base is energetically favorable, as indicated by the ȭownhill" position of the products. Because energy is released, the forward reaction sequence is called exergonic. Conversely, to synthesize glucose from CO 2 and H 2 O requires energy input to surmount the energy hill and drive the reaction in reverse therefore, glucose synthesis is called endergonic.

Every biochemical reaction involves both bond breaking and bond forming. The reactant molecules or substrates must absorb enough energy from their surroundings to start the reaction by breaking bonds in the reactant molecules. This initial energy investment is called the activation energy. The activation energy is represented by the uphill portion of the graph with the energy content of the reactants increasing. It is the height of this hilltop that is lowered by enzymes. At the top of the energetic hill, the reactants are in an unstable condition known as the transition state. At this fleeting moment, the molecules are energized and poised for the reaction to occur. As the molecules settle into their new bonding arrangements, energy is released to the surroundings (the downhill portion of the curve). At the summit of the energy hill, the reaction can occur in either the forward or the reverse direction.

Look again at Figure 2. The products CO 2 and H 2 O can form spontaneously or through a series of enzyme-catalyzed reactions in the cell. What enzymes do to accelerate reactions is to lower the energy activation barrier (green) to allow the transition state to be reached more rapidly. What is so special about the active site that allows it to accomplish this goal? Several mechanisms are involved.

Proximity Effect. Substrate molecules collide infrequently when their concentrations are low. The active site brings the reactants together for collision. The effective concentration of the reactants is increased significantly at the active site and favors transition state formation.

Orientation Effect. Substrate collisions in solution are random and are less likely to be the specific orientation that promotes the approach to the transition state. The amino acids that form the active site play a significant role in orienting the substrate. Substrate interaction with these specific amino acid side chains promotes strain such that some of the bonds are easier to break and thus the new bonds can form.

Promotion of Acid-Base Reactions. For many enzymes, the amino acids that form the active site have functional side chains that are poised to donate or accept hydrogen ions from the substrate. The loss or the addition of a portion (H ) can destabilize the covalent bonds in the substrate to make it easier for the bonds to break. Hydrolysis and electron transfers also work by this mechanism.

Exclusion of Water. Most active sites are sequestered and somewhat hydrophobic to exclude water. This nonpolar environment can lower the activation energy for certain reactions. In addition, substrate binding to the enzyme is mediated by many weak noncovalent interactions. The presence of water with the substrate can actually disrupt these interactions in many cases.

Enzymes can use one or more of these mechanisms to produce the strain that is required to convert substrates to their transition state. Enzymes speed the rate of a reaction by lowering the amount of activation energy required to reach the transition state, which is always the most difficult step in a reaction.


8.0: Energy, Matter, and Enzymes - Biology

Kinetics, activation energy, activated complex and catalysts.

Biology on Khan Academy: Life is beautiful! From atoms to cells, from genes to proteins, from populations to ecosystems, biology is the study of the fascinating and intricate systems that make life possible. Dive in to learn more about the many branches of biology and why they are exciting and important. Covers topics seen in a high school or first-year college biology course.

Course Index

  1. Introduction to chemistry
  2. Elements and atoms | Atoms, compounds, and ions | Chemistry | Khan Academy
  3. Introduction to the atom | Chemistry of life | Biology | Khan Academy
  4. Orbitals | Electronic structure of atoms | Chemistry | Khan Academy
  5. More on orbitals and electron configuration | Chemistry | Khan Academy
  6. Electron Configurations
  7. Electron configurations 2 | Electronic structure of atoms | Chemistry | Khan Academy
  8. Noble gas configuration (old, low volume)
  9. Noble gas configuration | Electronic structure of atoms | Chemistry | Khan Academy
  10. Valence Electrons
  11. Groups of the Periodic Table
  12. Periodic Table Trends: Ionization Energy
  13. Other Periodic Table Trends
  14. Ionic, covalent, and metallic bonds | Chemical bonds | Chemistry | Khan Academy
  15. Molecular and Empirical Formulas
  16. The mole and Avogadro's number | Atoms, compounds, and ions | Chemistry | Khan Academy
  17. Formula from Mass Composition
  18. Another mass composition problem | Chemistry | Khan Academy
  19. Balancing Chemical Equations
  20. Stoichiometry | Chemical reactions and stoichiometry | Chemistry | Khan Academy
  21. Stoichiometry: Limiting reagent | Chemical reactions and stoichiometry | Chemistry | Khan Academy
  22. Ideal gas equation: PV = nRT | Chemistry | Khan Academy
  23. Ideal gas equation example 1 | Chemistry | Khan Academy
  24. Ideal gas equation example 2 | Chemistry | Khan Academy
  25. Ideal gas equation example 3 | Chemistry | Khan Academy
  26. Ideal gas equation example 4 | Chemistry | Khan Academy
  27. Introduction to partial pressure | Gases and kinetic molecular theory | Chemistry | Khan Academy
  28. Partial pressure example | Chemistry | Khan Academy
  29. States of matter | States of matter and intermolecular forces | Chemistry | Khan Academy
  30. States of matter follow-up | States of matter and intermolecular forces | Chemistry | Khan Academy
  31. Specific heat, heat of fusion and vaporization example | Chemistry | Khan Academy
  32. Chilling water problem | States of matter and intermolecular forces | Chemistry | Khan Academy
  33. Phase diagrams | States of matter and intermolecular forces | Chemistry | Khan Academy
  34. Van der Waals forces | States of matter and intermolecular forces | Chemistry | Khan Academy
  35. Covalent networks, metallic crystals, and ionic crystals | Chemistry | Khan Academy
  36. Vapor pressure | States of matter and intermolecular forces | Chemistry | Khan Academy
  37. Suspensions, colloids and solutions | Chemistry | Khan Academy
  38. Solubility and intermolecular forces | Chemistry | Khan Academy
  39. Boiling point elevation and freezing point depression | Chemistry | Khan Academy
  40. Introduction to kinetics | Energy and enzymes | Biology | Khan Academy
  41. Reactions in equilibrium | Chemical equilibrium | Chemistry | Khan Academy
  42. Group trend for ionization energy | Periodic table | Chemistry | Khan Academy
  43. Keq intuition | Chemical equilibrium | Chemistry | Khan Academy
  44. Keq derivation intuition | Chemical equilibrium | Chemistry | Khan Academy
  45. Heterogeneous equilibrium | Chemical equilibrium | Chemistry | Khan Academy
  46. Le Chatelier's principle | Chemical equilibrium | Chemistry | Khan Academy
  47. Introduction to pH, pOH, and pKw
  48. Acid Base Introduction
  49. pH, pOH of strong acids and bases | Chemistry | Khan Academy
  50. pH of a Weak Acid
  51. pH of a Weak Base
  52. Conjugate acids and bases
  53. pKa and pKb relationship | Acids and bases | Chemistry | Khan Academy
  54. Buffers and Henderson-Hasselbalch | Chemistry | Khan Academy
  55. Strong Acid Titration
  56. Buffer capacity | Buffers, titrations, and solubility equilibria | Chemistry | Khan Academy
  57. Weak Acid Titration
  58. Private video
  59. Titration roundup | Buffers, titrations, and solubility equilibria | Chemistry | Khan Academy
  60. Introduction to Oxidation States
  61. More on Oxidation States
  62. Hydrogen Peroxide Correction
  63. Redox Reactions
  64. Galvanic Cells
  65. Types of decay | Nuclear chemistry | Chemistry | Khan Academy
  66. Half-life and carbon dating | Nuclear chemistry | Chemistry | Khan Academy
  67. Exponential decay formula proof (can skip, involves calculus) | Chemistry | Khan Academy
  68. Introduction to exponential decay | Nuclear chemistry | Chemistry | Khan Academy
  69. More exponential decay examples | Nuclear chemistry | Chemistry | Khan Academy
  70. Macrostates and microstates | Thermodynamics | Physics | Khan Academy
  71. Quasistatic and reversible processes | Thermodynamics | Physics | Khan Academy
  72. First law of thermodynamics / internal energy | Thermodynamics | Physics | Khan Academy
  73. More on internal energy | Thermodynamics | Physics | Khan Academy
  74. Work from expansion | Thermodynamics | Physics | Khan Academy
  75. PV-diagrams and expansion work | Thermodynamics | Physics | Khan Academy
  76. Proof: U = (3/2)PV or U = (3/2)nRT | Thermodynamics | Physics | Khan Academy
  77. Work done by isothermic process | Thermodynamics | Physics | Khan Academy
  78. Carnot cycle and Carnot engine | Thermodynamics | Physics | Khan Academy
  79. Proof: Volume ratios in a carnot cycle | Thermodynamics | Physics | Khan Academy
  80. Proof: S (or entropy) is a valid state variable | Thermodynamics | Physics | Khan Academy
  81. Thermodynamic entropy definition clarification | Physics | Khan Academy
  82. Reconciling thermodynamic and state definitions of entropy | Physics | Khan Academy
  83. Entropy intuition | Thermodynamics | Physics | Khan Academy
  84. Maxwell's demon | Thermodynamics | Physics | Khan Academy
  85. More on entropy | Thermodynamics | Physics | Khan Academy
  86. Efficiency of a Carnot engine | Thermodynamics | Physics | Khan Academy
  87. Carnot efficiency 2: Reversing the cycle | Thermodynamics | Physics | Khan Academy
  88. Carnot efficiency 3: Proving that it is the most efficient | Physics | Khan Academy
  89. Enthalpy | Thermodynamics | Chemistry | Khan Academy
  90. Heat of formation | Thermodynamics | Chemistry | Khan Academy
  91. Hess's law and reaction enthalpy change | Chemistry | Khan Academy
  92. Gibbs free energy and spontaneity | Chemistry | Khan Academy
  93. Gibbs free energy example | Thermodynamics | Chemistry | Khan Academy
  94. More rigorous Gibbs free energy / spontaneity relationship | Chemistry | Khan Academy
  95. A look at a seductive but wrong Gibbs/spontaneity proof | Chemistry | Khan Academy
  96. Stoichiometry example problem 1 | Chemistry | Khan Academy
  97. Stoichiometry example problem 2 | Chemistry | Khan Academy
  98. Limiting reactant example problem 1 | Chemistry | Khan Academy
  99. Empirical and Molecular Formulas from Stoichiometry
  100. Example of Finding Reactant Empirical Formula
  101. Stoichiometry of a Reaction in Solution
  102. Another Stoichiometry Example in a Solution
  103. Molecular and Empirical Forumlas from Percent Composition
  104. Acid base titration example | Chemistry | Khan Academy
  105. Spectrophotometry introduction | Kinetics | Chemistry | Khan Academy
  106. Spectrophotometry example | Kinetics | Chemistry | Khan Academy
  107. Hess's law example | Thermodynamics | Chemistry | Khan Academy
  108. Vapor pressure example | Chemistry | Khan Academy
  109. Change of state example | States of matter and intermolecular forces | Chemistry | Khan Academy
  110. Small x approximation for small Kc | Chemistry | Khan Academy
  111. Small x approximation for large Kc | Chemical equilibrium | Chemistry | Khan Academy
  112. pH and pKa relationship for buffers | Chemistry | Khan Academy
  113. 2015 AP chemistry free response 5a
  114. AP Chemistry multiple choice sample: Boiling points
  115. Rate constant k from half-life example | Knetics | Chemistry | Khan Academy
  116. Ways to get a buffer solution | Chemistry | Khan Academy
  117. Comparing Q vs K example | Chemical equilibrium | Chemistry | Khan Academy
  118. Finding units of rate constant k | Knetics | Chemistry | Khan Academy
  119. Calculating internal energy and work example | Chemistry | Khan Academy
  120. Ionic bonds and Coulombs law
  121. Bond enthalpy and enthalpy of reaction | Chemistry | Khan Academy
  122. Introduction to reaction quotient Qc | Chemical equilibrium | Chemistry | Khan Academy
  123. Le Chatelier's principle: Worked example | Chemical equilibrium | Chemistry | Khan Academy
  124. Conjugate acid-base pairs | Acids and bases | Chemistry | Khan Academy

Course Description

An introductory college-level chemistry course that explores topics such as atoms, compounds, and ions chemical reactions and stoichiometry ideal gases chemical equilibrium acids and bases kinetics thermodynamics redox reactions and electrochemistry and a whole lot more!


Field management effects on soil enzyme activities

There is growing recognition for the need to develop sensitive indicators of soil quality that reflect the effects of land management on soil and assist land managers in promoting long-term sustainability of terrestrial ecosystems. Eleven soil enzymes assays were investigated relative to soil management and soil quality at two study sites. Soils were sampled from the Vegetable Crop Rotation Plots (VRP) (established in 1989 in humid western Oregon) which compared continuous fescue (Festuca arundinacea) and four winter cover crop treatments in annual rotation with a summer vegetable crop. The second site was the Residue Utilization Plots (RUP) (initiated in 1931 in semi-arid Eastern Oregon) which is under a winter wheat–summer fallow and compared inorganic N, green manure and beef manure treatments. Soil also was sampled at the research center from a nearby grass pasture that is on the same soil type. The enzymes were α- and β-glucosidase, α- and β-galactosidase, amidase, arylsulfatase, deaminase, fluorescein diacetate hydrolysis, invertase, cellulase and urease. At both sites there was a significant treatment effect for each enzyme tested (P<0.05). Enzyme activities (except α- and β-glucosidase and α- and β-galactosidase) were generally higher in continuous grass fields than in cultivated fields. In cultivated systems, activity was higher where cover crops or organic residues were added as compared to treatments without organic amendments. It was found that use of air-dried soil samples provided the same ranking of treatments by a number of enzyme assays and would facilitate adoption of these assays for practical or commercial applications. Deaminase was not a good indicator of soil quality, while β-glucosidase was suggested as an assay that reflects soil management effects and has microbial ecological significance because of its role in the C cycle.


Watch the video: Chapter 8 Screencast Energy and Enzymes (May 2022).