Biochemistry - Advanced

Douglas Wilkin, Ph.D.Jean Brainard, Ph.D.

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Printed: March 15, 2016

AUTHORSDouglas Wilkin, Ph.D.Jean Brainard, Ph.D.

EDITORDouglas Wilkin, Ph.D.

www.ck12.org Chapter 1. Biochemistry - Advanced

CHAPTER 1 Biochemistry - AdvancedCHAPTER OUTLINE

1.1 Biochemical Energy - Advanced

1.2 States of Matter in Biological Systems - Advanced

1.3 Chemical Reactions - Advanced

1.4 Chemical Reactions and Energy - Advanced

1.5 Enzymes and Activation Energy - Advanced

1.6 Enzymes and Biochemical Reactions - Advanced

1.7 References

Introduction

What do you get when you cross biology and chemistry?

Hummingbirds, with their tiny bodies and high levels of activity, have the highest metabolic rates of any animals—roughly a dozen times that of a pigeon and a hundred times that of an elephant. The metabolic rate, or rate ofmetabolism, has to do with the amount of energy the organism uses. And that energy is used to drive the chemicalreactions in cells —or the biochemical reactions. And, of course, it is all the biochemical reactions that allow thecells function properly, and maintain life.

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1.1. Biochemical Energy - Advanced www.ck12.org

1.1 Biochemical Energy - Advanced

• Define energy, and describe how energy can be changed from one form to another.

What is energy? Where does your energy come from? Can energy be recycled?

This team of ants is breaking down a dead tree. A classic example of teamwork. And all that work takes energy. Infact, each chemical reaction - the chemical reactions that allow the cells in those ants to do the work - needs energyto get started. And all that energy comes from the food the ants eat. Whatever eats the ants gets their energy fromthe ants. Energy passes through an ecosystem in one direction only.

Matter and Energy

All living things are made of matter. In fact, matter is the “stuff” of which all organisms are made. Anythingthat occupies space and has mass is known as matter. Matter, in turn, consists of chemical substances. It is thecarbons, hydrogens, oxygens and other elements that combine to form molecules, compounds, organelles, cells andeventually tissues, organs and organisms. In addition to being made of matter, all living organisms also need energyto survive.

Energy is a property of matter that is defined as the ability to do work. The concept of energy is useful for explainingand predicting most natural phenomena, and it is the foundation for an understanding of biology. All living organismsneed energy to grow and reproduce. However, energy can never be created nor destroyed. Energy can only betransformed. That is, energy is always conserved. This is called the law of conservation of energy. Therefore,organisms cannot create the energy they need. Instead, they must obtain energy from the environment. Organismsalso cannot destroy or use up the energy they obtain. They can only change it from one form to another. Organismswill either use their energy (for metabolism) or release it to the environment as heat.

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In biology, energy is required for ecosystems to survive, as all living organisms need energy. Within an organism,energy is needed for growth and development of a biological cell or an organelle within that cell. Energy is alsoneeded for all biochemical reactions within that cell. Therefore, energy is stored within cells in the chemical bondsof substances such as carbohydrates (including sugars), lipids, and proteins. This energy is released during aerobicrespiration.

The energy for most living organisms initially originates from the sun. This energy is absorbed by producers,usually photosynthetic organisms such as plants. Plants convert this energy into chemical energy, in the form ofcarbohydrates, such as glucose. Energy can be stored in this state, or converted into a usable form of energy,adenosine triphosphate (ATP). This occurs in both the plant, as well as the organisms that eat the plant, or eat theorganism that ate the plant.

Forms of Energy

Energy can take several different forms. Common forms of energy include light, chemical, and heat energy. Othercommon forms are kinetic and potential energy.

How Organisms Change Energy

In organisms, energy is always changing from one form to another. For example, plants obtain light energy fromsunlight and change it to chemical energy in food molecules, such as glucose. Chemical energy is energy stored inbonds between atoms within food molecules. When other organisms eat and digest the food, they break the chemicalbonds and release the chemical energy. Organisms do not use energy very efficiently. About 90 percent of the energythey obtain from food is converted to heat energy that is given off to the environment.

Kinetic and Potential Energy

Energy also constantly changes back and forth between kinetic and potential energy. Kinetic energy is the energyof movement. For example, a ball falling through the air has kinetic energy because it is moving (Figure 1.1). Therandom motion of molecules is due to kinetic energy, and the driving force behind diffusion.

Potential energy is the energy stored in an object due to its position. A bouncing ball at the top of a bounce, justbefore it starts to fall, has potential energy. For that instant, the ball is not moving, but it has the potential to movebecause gravity is pulling on it. Once the ball starts to fall, the potential energy changes to kinetic energy. When theball hits the ground, it gains potential energy from the impact. The potential energy changes to kinetic energy whenthe ball bounces back up into the air. As the ball gains height, it regains potential energy because of gravity.

Like the ball, every time you move you have kinetic energy —whether you jump or run or just blink your eyes.Can you think of situations in which you have potential energy? Obvious examples might include when you arestanding on a diving board or at the top of a ski slope or bungee jump. What gives you potential energy in all ofthese situations? The answer is gravity.

Vocabulary

• adenosine triphosphate (ATP): Energy-carrying molecule that cells use to power their metabolic processes;energy-currency of the cell.

• energy: Property of matter that is defined as the ability to do work.

• kinetic energy: Form of energy that an object has when it is moving.

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1.1. Biochemical Energy - Advanced www.ck12.org

FIGURE 1.1Energy in a bouncing ball is transformedfrom potential energy to kinetic energyand then back to potential energy. Thiscycle of energy changes keeps repeatingas long as the ball continues to bounce.The ball rises less on each successivebounce because some energy is used toresist air molecules.

• law of conservation of energy: Law of physics that states that energy may neither be created nor destroyed;the sum of all the energies in a system remains constant over time.

• matter: All the substances of which things are made.

• potential energy: Form of energy that is stored in an object due to its position.

Summary

• Energy is a property of matter. It cannot be created or destroyed. Organisms obtain light energy from sunlightor chemical energy from food and change the energy into different forms, including heat energy.

Explore More

Use this resource to answer the questions that follow.

• http://www.hippocampus.org/Biology → Non-Majors Biology → Search: Energy

1. What is energy?2. Why do living organisms need energy?3. What is the main difference between potential and kinetic energy?4. What is the original source of most energy used by living organisms on Earth?

Explore More Answers

1. Energy is the ability to do work.2. All living organisms need energy to survive and reproduce. Energy drives their metabolism, movement and

growth.3. Potential energy is the energy stored in an object-energy that is there but not in use. Kinetic energy is the

energy of motion- energy that is in the process of being used.4. All living organisms on Earth take in energy from outside sources, the most original source is the sun (light

energy).

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Review

1. What is energy?2. Describe two ways that energy changes form in the following sequence of events: A plant grows in the sun.

→ A rabbit eats the plant.3. Describe a real-life situation in which the energy of an object or person changes back and forth between kinetic

energy and potential energy. Identify each time energy changes form.

Review Answers

1. Energy is the property of matter that is defined as the ability to do work.2. The plant obtains light energy from sunlight and changes it to chemical energy in food molecules, such as

glucose. The rabbit eats the food molecules to produce chemical energy.3. A roller coaster demonstrates how energy is constantly changing between potential and kinetic energy. At the

top of the first lift hill there is maximum potential energy because the train is as high as it gets. As the trainstarts down the hill, this potential energy is converted into kinetic energy. At the bottom of the hill, there ismaximum kinetic energy and little potential energy. The kinetic energy propels the train up the second hill,building up the potential energy level. As the train enters the loop-the-loop, it has a lot of kinetic energy andnot much potential energy. The potential energy level builds as the train speeds to the top of the loop, but it issoon converted back to kinetic energy as the train leaves the loop.

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1.2. States of Matter in Biological Systems - Advanced www.ck12.org

1.2 States of Matter in Biological Systems -Advanced

• Identify three states of matter and explain how they differ.

Solid, liquid or gas?

The state of matter is a physical property of that matter. H2O can exist in three different states of matter. This glacieris obviously a solid state of H2O, floating in the liquid state. Why does the ice float on water? Which has a greaterdensity, solid H2O or liquid H2O?

States of Matter

The amount of energy in molecules of matter determines the state of matter. Matter can exist in one of severaldifferent states, including a gas, liquid, or solid state. These different states of matter have different properties,which are illustrated in Figure 1.2. Gasses have the most energy, and solids have the least energy.

• A gas is a state of matter in which atoms or molecules have enough energy to move freely. The moleculescome into contact with one another only when they randomly collide. Forces between atoms or molecules arenot strong enough to hold them together, allowing the molecules to move independently of one another.

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• A liquid is a state of matter in which atoms or molecules are constantly in contact but have enough energyto keep changing positions relative to one another. Forces between atoms or molecules are strong enough tokeep the molecules together but not strong enough to prevent them from moving. The particles of a liquidhave enough energy to allow them to slide past one another, but not enough energy to allow them to movefreely.

• A solid is a state of matter in which atoms or molecules do not have enough energy to move. They areconstantly in contact and in fixed positions relative to one another. Forces between atoms or molecules arestrong enough to keep the molecules together and to prevent them from moving. The particles of a solid onlyhave enough energy to vibrate in place.

FIGURE 1.2States of Matter.

All three containers contain a substance with the same mass, but the substances are in different states. In the left-hand container, the substance is a gas, which has spread to fill its container. It takes both the shape and volume of thecontainer. In the middle container, the substance is a liquid, which has spread to take the shape of its container butnot the volume. In the right-hand container, the substance is a solid, which takes neither the shape nor the volumeof its container.

What Determines a Substance’s State?

A substance’s state depends partly on temperature and air pressure. For example, at the air pressure found at sealevel, water exists as a liquid at temperatures between 0°C and 100°C. Above 100°C, water exists as a gas (watervapor). Below 0°C, water exists as a solid (ice). Different substances have a different range of temperatures at whichthey exist in each state. For example, oxygen is gas above -183°C, but iron is a gas only above 2861°C. Thesedifferences explain why some substances are always solids at normal Earth temperatures, whereas others are alwaysgases or liquids.

Changing States

Matter constantly goes through cycles that involve changing states. Water and all the elements important to organ-isms, including carbon and nitrogen, are constantly recycled on Earth (see Principles of Ecology). As matter movesthrough its cycles, it changes state repeatedly. For example, in the water cycle, water repeatedly changes from a gasto a liquid or solid and back to a gas again. How does this happen?

Adding energy to matter gives its atoms or molecules the ability to resist some of the forces holding them together.For example, heating ice to its melting point (0°C) gives its molecules enough energy to move. The ice melts andbecomes liquid water. Similarly, heating liquid water to its boiling point (100°C) gives its molecules enough energyto pull apart from one another so they no longer have contact. The liquid water vaporizes and becomes water vapor.

In biological systems, matter is continuously changing states as well. For example, carbon in the form of the gascarbon dioxide is changed into glucose, a solid. This change, of course, occurs during photosynthesis. Duringcellular respiration, carbons from the glucose molecule are changed back into the carbon dioxide gas.

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1.2. States of Matter in Biological Systems - Advanced www.ck12.org

Conservation of Matter

Though matter can change states, and it often does, matter cannot be created or destroyed. Similar to the law ofthe conservation of energy, the law of conservation of mass states that the mass (or matter) of an isolated systemwill remain constant over time. This means that mass or matter cannot be created or destroyed, although it maybe rearranged and changed into different types of substances. Hence, matter is continuously recycled, resulting inthe so called "circle of life." The carbon and other elements of organisms are recycled to be used by other livingorganisms. This law also states that in a chemical reaction, or a biochemical reaction, as mass cannot be created ordestroyed, the mass of the reactants must equal the mass of the products. In other words, the atoms in the startingmaterials must be equivalent to the atoms in the ending materials.

Vocabulary

• biochemical reaction: Chemical reaction within a cell or organism; usually controlled by an enzyme.

• boiling point: The temperature at which a liquid changes state into a gas.

• gas: State of matter in which atoms or molecules have enough energy to move freely.

• law of conservation of mass: Law that states that the mass of an isolated system will remain constant overtime.

• liquid: State of matter in which atoms or molecules are constantly in contact but have enough energy to keepchanging positions relative to one another.

• melting point: The temperature at which a solid changes state into a liquid.

• solid: State of matter in which atoms or molecules do not have enough energy to move.

• state of matter: Condition that matter is in, depending on how much energy its atoms or molecules have.

Summary

• Matter can exist in one of several different states, including a gas, liquid, or solid state. States of matter differin the amount of energy their molecules have. When matter recycles, it changes state by gaining or losingenergy.

Explore More

Use this resource to answer the questions that follow.

• States of Matter at http://www.youtube.com/watch?v=HAPc6JH85pM

MEDIAClick image to the left or use the URL below.URL: http://www.ck12.org/flx/render/embeddedobject/139422

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1. What state of matter is glass?2. How and why does the glass in the video change states?

Explore More Answers

1. Glass can be both in a liquid and a solid state.2. Glass changes states because of the change in temperature. To melt glass the temperature needs to be around

2000 degrees Fahrenheit. During cooling temperatures, the glass becomes solid.

Review

1. Compare and contrast the three common states of matter?2. What determines a substance’s state?3. At what temperatures does the state of water change?4. Explain what happens to molecules of matter when matter changes state from a liquid to a gas.5. What is the law of conservation of mass?

Review Answers

1. A gas is a state of matter in which atoms or molecules have enough energy to move freely and to spreadthroughout its container. A liquid is a state of matter in which atoms or molecules are constantly in contactbut have enough energy to keep changing positions relative to one another and to spread to take the shape ofits container, not the volume. A solid is a state of matter in which atoms or molecules do not have enoughenergy to move, they are constantly in contact and in fixed positions relative to one another. They neither takethe shape nor the volume of its container.

2. A substance’s state is partially determined by temperature and air pressure.3. Below 0 degrees Celsius, water exists as a solid. Above 100 degrees Celsius, water exists as a gas. And

between 0-100 degrees Celsius, water exists as a liquid.4. When molecules of matter are heated to their boiling point, energy pulls them apart from one another so they

no longer have contact. The liquid molecules vaporize and become vapor molecules.5. The law of conservation of mass states that the mass of an isolated system will remain constant over time.

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1.3. Chemical Reactions - Advanced www.ck12.org

1.3 Chemical Reactions - Advanced

• Describe what happens in a chemical reaction, and identify types of chemical reactions.

Understanding chemistry is essential to fully understand biology. Why?

A general understanding of chemistry is necessary to understand biology. Essentially, our cells are just thousandsof chemicals —made of elements like carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur —in just the rightcombinations. And these chemicals combine through chemical reactions.

What are Chemical Reactions?

A chemical compound may be very different from the substances that combine to form it. For example, the elementchlorine (Cl) is a poisonous gas, but when it combines with sodium (Na) to form sodium chloride (NaCl), it is nolonger toxic. You may even eat it on your food. Sodium chloride is just table salt. What process changes a toxicchemical like chlorine into a much different substance like table salt?

A chemical reaction is a process that changes some chemical substances into other chemical substances. Thesubstances that start a chemical reaction are called reactants. The substances that form as a result of a chemicalreaction are called products. During the reaction, the reactants are used up to create the products. For example,when methane burns in oxygen, it releases carbon dioxide and water. In this reaction, the reactants are methane(CH4) and oxygen (O2), and the products are carbon dioxide (CO2) and water (H2O).

Chemical Equations

A chemical reaction can be represented by a chemical equation. Using the same example, the burning of methanegas can be represented by the equation:

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CH4 + 2 O2 → CO2 + 2 H2O.

The arrow in a chemical equation separates the reactants from the products and shows the direction in which thereaction occurs. If the reaction could also occur in the opposite direction, then two arrows, one pointing in eachdirection, or one arrow pointing in both directions, would be used. On each side of the arrow, a mixture of chemicalsis indicated by the chemical symbols joined by a plus sign (+). The numbers preceding some of the chemical symbols(such as 2 O2) indicate how many molecules of the chemicals are involved in the reaction. (If there is no number infront of a chemical symbol, it means that just one molecule is involved.)

In a chemical reaction, the quantity of each element does not change. There is the same amount of each element atthe end of the reaction as there was at the beginning. This is reflected in the chemical equation for the reaction. Theequation should be balanced. In a balanced equation, the same number of atoms of a given element appear on eachside of the arrow. For example, in the equation above, there are four hydrogen atoms on each side of the arrow.

Types of Chemical Reactions

In general, a chemical reaction involves the breaking and forming of chemical bonds. In the methane reaction above,bonds are broken in methane and oxygen, and bonds are formed in carbon dioxide and water. A reaction like this, inwhich a compound or element burns in oxygen, is called a combustion reaction. This is just one of many possibletypes of chemical reactions. Other types of chemical reactions include synthesis, decomposition, and substitutionreactions.

• A synthesis reaction occurs when two or more chemical elements or compounds unite to form a more complexproduct. For example, nitrogen (N2) and hydrogen (H2) unite to form ammonia (NH3):

N2 + 3 H2 → 2 NH3.

• A decomposition reaction occurs when a compound is broken down into smaller compounds or elements.For example, water (H2O) breaks down into hydrogen (H2) and oxygen (O2):

2 H2O → 2 H2 + O2.

• A substitution reaction occurs when one element replaces another element in a compound. For example,sodium (Na+) replaces hydrogen (H) in hydrochloric acid (HCl), producing sodium chloride (NaCl) andhydrogen gas (H2):

2 Na+ + 2 HCl → 2 NaCl + H2.

Redox Rections

Reduction-oxidation reactions, or redox reactions include all chemical reactions in which atoms have their oxidationstate changed. This can be either a simple redox process, such as the oxidation of carbon into carbon dioxide or thereduction of carbon by hydrogen into methane, or a complex process such as the oxidation of glucose through aseries of complex electron transfer processes during cellular respiration. Oxidation is the loss of electrons or anincrease in oxidation state by a molecule, atom, or ion. Reduction is the gain of electrons or a decrease in oxidationstate by a molecule, atom, or ion.

Redox Reactions in Biology

Many important biological processes involve redox reactions, which frequently store and release energy. Forexample, photosynthesis involves the reduction of carbon dioxide into glucose and the oxidation of water into

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1.3. Chemical Reactions - Advanced www.ck12.org

oxygen. This process stores the energy of sunlight in the bonds of sugars. The reverse reaction, cellular respiration,converts the energy in glucose into ATP. Cellular respiration involves the oxidation of glucose to carbon dioxide andthe reduction of oxygen gas to water. This process depends on the reduction of NAD+ to the electron carrier NADH,and the reverse oxidation of NADH to NAD+. The reduction of NAD+ leads to the formation of a proton (H+)gradient, which drives the synthesis of ATP. NADH (nicotinamide adenine dinucleotide) and NADPH (Nicotinamideadenine dinucleotide phosphate) are electron carriers in biological systems. The term redox state is often used todescribe the balance between NAD+/NADH and NADP+/NADPH (Nicotinamide adenine dinucleotide phosphate).

Vocabulary

• chemical reaction: A process that changes some chemical substances into other chemical substances.

• combustion reaction: Type of chemical reaction in which a compound or element burns in oxygen.

• decomposition reaction: Type of chemical reaction in which a compound is broken down into smallercompounds or elements.

• oxidation: The loss of electrons or an increase in oxidation state by a molecule, atom, or ion.

• product: Substance that forms as a result of a chemical reaction.

• reactant: Substance involved in a chemical reaction that is present at the beginning of the reaction.

• redox reaction: A chemical reaction in which atom(s) have their oxidation state changed.

• redox state: Describes the balance between NAD+/NADH and NADP+/NADPH.

• reduction: The gain of electrons or a decrease in oxidation state by a molecule, atom, or ion.

• substitution reaction: Type of chemical reaction in which one element replaces another element in a com-pound.

• synthesis reaction: Type of chemical reaction in which elements or compounds unite to form a more complexproduct.

Summary

• A chemical reaction is a process that changes some chemical substances into others. It involves breakingand forming chemical bonds. Types of chemical reactions include synthesis reactions and decompositionreactions.

Review

1. Identify the roles of reactants and products in a chemical reaction.2. Describe each type of chemical reaction.3. What is wrong with the following chemical equation? How could you fix it? CH4 + O2 → CO2 + 2H2O4. What type of reaction is represented by the following chemical equation? Explain your answer. 2Na + 2HCl

→ 2NaCl + H2

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Review Answers

1. A reactant is a substance involved in a chemical reaction that is present at the beginning of the reaction. Aproduct is a substance that forms as a result of a chemical reaction.

2. A synthesis reaction occurs when two or more chemical elements or compounds unite to form a more complexproduct. A decomposition reaction occurs when a compound is broken down into smaller compounds orelements. A substitution reaction occurs when one element replaces another element in a compound.

3. There were originally two oxygen atoms in the reactants, but four oxygen atoms in the products. The correctedequation should look like: CH4 + 2O2 → CO2 + 2H2O

4. This type of reaction is a substitution reactions because one element replaces another element in the compound.The sodium replaces the hydrogen in the hydrochloric acid.

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1.4. Chemical Reactions and Energy - Advanced www.ck12.org

1.4 Chemical Reactions and Energy - Ad-vanced

• Explain the role of energy in chemical reactions, and define activation energy.

How do you change one thing into another?

The bonds between the atoms need to be rearranged. That is the definition of a chemical reaction. And all chemicalsections need energy to get started.

Chemical Reactions and Energy

All chemical reactions involve energy. Some chemical reactions consume energy, whereas other chemical reactionsrelease energy. Chemical reactions can be either spontaneous, which do not require an input of energy, or non-spontaneous, which does require an input of some type of energy. Energy may be in the form of heat, light orelectricity. Each of the energy changes that occur during a reaction are graphed in Figure 1.3. In the reaction on theleft, energy is released. In the reaction on the right, energy is consumed.

Bill Nye discusses chemical reactions at http://www.youtube.com/watch?v=66kuhJkQCVM (2:05).

MEDIAClick image to the left or use the URL below.URL: http://www.ck12.org/flx/render/embeddedobject/201

Thermodynamics

Chemical reactions follow the laws of thermodynamics. The First Law of Thermodynamics states that energy canbe changed from one form to another, but it cannot be created or destroyed. This law is also known as the Law of

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FIGURE 1.3The exothermic reaction on the left re-leases energy. The endothermic reactionon the right consumes energy.

Conservation of Energy. The Second Law of Thermodynamics states the energy available after a chemical reactionis always less than that at the beginning of a reaction. This is also commonly referred to as entropy. Entropy canbe described as the degree of disorder in a system. That is, as energy is transferred from one form to another, someof the energy is lost as heat, and the amount of available energy decreases. As the energy decreases, the disorder inthe system increases, and, by definition, the entropy increases. Ice melting provides an example in which entropyincreases. Entropy essentially is a measure of the tendency of a process, such as a chemical reaction, to proceed in aparticular direction.

Reactions can proceed by themselves if they are exergonic or exothermic, that is if they release energy. Theassociated free energy of the reaction is composed of two different thermodynamic quantities, enthalpy and entropy.Enthalpy is a measure of the total energy of a thermodynamic system. The change in enthalpy is positive inendothermic reactions, and negative in exothermic processes.

Exothermic Reactions

Chemical reactions that release energy are called exothermic reactions. An example is the combustion of methanedescribed at the beginning of this lesson. In organisms, exothermic reactions are called catabolic reactions.Catabolic reactions break down molecules into smaller units. An example is a decomposition reaction, such asthe breakdown of glucose molecules for energy. Exothermic reactions can be represented by the general chemicalequation:

Reactants → Products + Heat.

Endothermic Reactions

Chemical reactions that consume energy are called endothermic reactions. Energy is usually absorbed fromthe surroundings as heat. An example is the synthesis of ammonia, described above. In organisms, endothermicreactions are called anabolic reactions. Anabolic reactions construct molecules from smaller units. An exampleis the synthesis of proteins from amino acids. Endothermic reactions can be represented by the general chemicalequation:

Reactants + Heat → Products.

Endothermic Organisms

In biological systems, the term endothermic is a metabolic term related to maintenance of body temperature. Anendothermic animals is an organism that produces heat through internal means, a process known as endothermy.Animals may do this through muscle shivering or increasing metabolism. These animals do to absorb heat fromtheir surroundings, so the term endothermic has distinct uses related to chemical reactions or maintenance of body

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1.4. Chemical Reactions and Energy - Advanced www.ck12.org

FIGURE 1.4This pack gets cold due to an endothermic reaction.

temperature. The opposite of endothermy is ectothermy. Ectothermic animals (cold-blooded) do absorb heat fromtheir surroundings.

Vocabulary

• anabolic reaction: Endothermic reaction that occurs in organisms; chemical reaction that builds new moleculesand/or stores energy.

• catabolic reaction: Chemical reaction that breaks down more complex organic molecules into simpler sub-stances; usually releases energy.

• decomposition reaction: Type of chemical reaction in which a compound is broken down into smallercompounds or elements.

• endothermic reaction: Any chemical reaction that consumes energy.

• enthalpy: A measure of the total energy of a thermodynamic system.

• entropy: A measure of the tendency of a process, such as a chemical reaction, to proceed in a particulardirection.

• exothermic reaction: Any chemical reaction that releases energy.

Summary

• Chemical reactions follow the laws of thermodynamics.• Some chemical reactions are exothermic, which means they release energy. Other chemical reactions are

endothermic, which means they consume energy.• Catabolic and anabolic reactions occur in cells/organisms.

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Explore More

Use this resource to answer the questions that follow. Assignment Discovery: Chemical Reactions at http://www.discovery.com/tv-shows/other-shows/videos/assignment-discovery-shorts-chemical-reactions.htm

MEDIAClick image to the left or use the URL below.URL: http://www.ck12.org/flx/render/embeddedobject/139421

1. What is the chemical reaction definition used in this video?2. How does a chemical reaction form new substances?3. What is a balanced equation? Give an example.4. Define a single replacement reaction.5. Give an example of a double replacement reaction.6. What is a redox reaction?7. Define oxidation and reduction.

Explore More Answers

1. A chemical reaction is a process in which one or more substances are converted into new substances withdifferent physical and chemical properties.

2. A balanced equation is an equal amount of specific atoms on each side of the reaction. An example is: Mg +2HCl → MgCl2 + H2

3. A single replacement reaction displaces one element with another.4. An example of a double replacement reaction is: 2KI + Pb(NO3)2 → PbI2 + 2KNO35. A redox reaction is a chemical reaction involving both reduction and oxidation, which results in changes in

oxidation numbers of atoms included in the reaction.6. Oxidation refers to the loss of electrons and reduction refers to the gain of electrons.

Review

1. Compare and contrast each of the following:

a. The first and seconds laws of thermodynamics.b. Entropy and enthalpy.c. Endothermic and exothermic reactions.d. Anabolic and catabolic reactions.

Review Answers

1. Sample answers:

a. The first law of thermodynamics is the Law of Conservation of Energy which states that energy can bechanged from one form to another, but it cannot be created or destroyed. The second law of thermody-namics states the energy available after a chemical reaction is always less than that at the beginning of areaction- entropy.

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1.4. Chemical Reactions and Energy - Advanced www.ck12.org

b. Entropy refers to as energy is transferred from one form to another, some of the energy is lost as heat,and the amount of available energy decreases. Entropy also is a measure of the tendency of a process toproceed in a particular direction. Enthalpy is a measure of the total energy of a thermodynamic system.The associated free energy of the reaction is composed of both entropy and enthalpy.

c. Endothermic reactions are any chemical reaction that consumes energy. Exothermic reactions are anychemical reaction that releases energy.

d. Anabolic reactions construct molecules from smaller units, producing endothermic chemical reactions.Catabolic reactions break down molecules into small units, producing exothermic chemical reactions.

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www.ck12.org Chapter 1. Biochemistry - Advanced

1.5 Enzymes and Activation Energy - Ad-vanced

• Explain the importance of enzymes in organisms, and describe how enzymes work.• State factors that affect the rate of chemical reactions.

What is the energy needed for biochemical reactions?

Is it light or heat? It could be either. But whatever form energy takes, every single biochemical reaction in your body- and there are trillions of these reactions (or more) every split second, needs energy to start or activate. And that isknown as activation energy.

Activation Energy

Regardless of whether reactions are exothermic reactions or endothermic reactions, they all need energy to getstarted. This energy is called activation energy. Activation energy is like the push you need to start moving downa slide. The push gives you enough energy to start moving. Once you start, you keep moving without being pushedagain. Activation energy is defined as the energy that must be overcome in order for a chemical reaction to occur, orthe minimum energy required to start a chemical reaction. The concept of activation energy is illustrated in Figure1.5.

An overview of activation energy can be viewed at http://www.youtube.com/watch?v=VbIaK6PLrRM (1:16).

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1.5. Enzymes and Activation Energy - Advanced www.ck12.org

FIGURE 1.5To start this reaction, a certain amount ofenergy is required, called the activationenergy. How much activation energy isrequired depends on the nature of the re-action and the conditions under which thereaction takes place. Activation energycan be thought of as the height of theenergy barrier between the reactants andthe products.

Why do reactions need energy to get started? In order for reactions to occur, three things must happen, and they allrequire energy:

• Reactant molecules must collide. To collide, they must move, so they need kinetic energy.• Unless reactant molecules are positioned correctly, intermolecular forces may push them apart. To overcome

these forces and move together requires more energy.• If reactant molecules collide and move together, there must be enough energy left for them to react.

Rates of Chemical Reactions

The rates at which chemical reactions take place in organisms are very important. Chemical reactions in organismsare involved in processes ranging from the contraction of muscles to the digestion of food. For example, when youwave goodbye, it requires repeated contractions of muscles in your arm over a period of a couple of seconds. A hugenumber of reactions must take place in that time, so each reaction cannot take longer than a few milliseconds. If thereactions took much longer, you might not finish waving until sometime next year.

Factors that help reactant molecules collide and react speed up chemical reactions. These factors include theconcentration of reactants and the temperature at which the reactions occur.

• Reactions are usually faster at higher concentrations of reactants. The more reactant molecules there are in agiven space, the more likely they are to collide and react.

• Reactions are usually faster at higher temperatures. Reactant molecules at higher temperatures have moreenergy to move, collide, and react.

Vocabulary

• activation energy: Energy needed for a chemical reaction to get started.

• endothermic reaction: Any chemical reaction that consumes energy.

• exothermic reaction: Any chemical reaction that releases energy.

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www.ck12.org Chapter 1. Biochemistry - Advanced

• product: Substance that forms as a result of a chemical reaction.

• reactant: Substance involved in a chemical reaction that is present at the beginning of the reaction.

Summary

• All chemical reactions require activation energy, which is the energy needed to get a reaction started.• Rates of chemical reactions depend on factors such as the concentration of reactants and the temperature at

which reactions occur. Both factors affect the ability of reactant molecules to react.

Explore More

Use this resource to answer the questions that follow.

• Activation Energy at http://www.sophia.org/activation-energy--2/activation-energy–5-tutorial?pathway=thermochemistry

1. In this video, what does A + B represent?2. In this video, what does P + Q represent?3. What is the activation energy?4. Why is one activation energy lower than the other?5. What is the main difference between an endothermic and exothermic reaction?

Review

1. What is activation energy?2. Why do all chemical reactions require activation energy?

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1.6. Enzymes and Biochemical Reactions - Advanced www.ck12.org

1.6 Enzymes and Biochemical Reactions - Ad-vanced

• Explain the importance of enzymes in organisms, and describe how enzymes work.

What is a biological catalyst?

This super fast train can obviously reach great speeds. And there’s a lot of technology that helps this train go fast.Speaking of helping things go fast brings us to enzymes. Life could not exist without enzymes. Essentially, enzymesare biological catalysts that speed up biochemical reactions.

Enzymes and Biochemical Reactions

Most chemical reactions within organisms would be impossible under the normal conditions within cell. Forexample, the body temperature of most organisms is too low for reactions to occur quickly enough to carry outlife processes. Reactants may also be present in such low concentrations that it is unlikely they will meet andcollide. Therefore, the rate of most biochemical reactions must be increased by a catalyst. A catalyst is a chemicalthat speeds up chemical reactions. In organisms, catalysts are called enzymes.

Like other catalysts, enzymes are not reactants in the reactions they control. They help the reactants interact butare not used up in the reactions. Instead, they may be used over and over again. Unlike other catalysts, enzymesare usually highly specific for a particular chemical reaction. They generally catalyze only one or a few types ofreactions.

Enzymes are extremely efficient in speeding up biochemical reactions. They can catalyze up to several millionreactions per second. As a result, the difference in rates of biochemical reactions with and without enzymes may beenormous. A typical biochemical reaction might take hours or even days to occur under normal cellular conditionswithout an enzyme, but less than a second with the enzyme.

An overview of enzymes can be viewed at http://www.youtube.com/watch?v=E90D4BmaVJM (9:43).

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How Enzymes Work

How do enzymes speed up biochemical reactions so dramatically? Like all catalysts, enzymes work by lowering theactivation energy of chemical reactions. This is illustrated in Figure 1.6. The biochemical reaction shown in thefigure requires about three times as much activation energy without the enzyme as it does with the enzyme.

An animation of how enzymes work can be seen at http://www.youtube.com/watch?v=CZD5xsOKres (2:02).

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FIGURE 1.6The reaction represented by this graphis a combustion reaction involving the re-actants glucose (C6H12O6) and oxygen(O2). The products of the reaction arecarbon dioxide (CO2) and water (H2O).Energy is also released during the reac-tion. The enzyme speeds up the reactionby lowering the activation energy neededfor the reaction to start. Compare theactivation energy with and without the en-zyme.

Enzymes generally lower activation energy by reducing the energy needed for reactants to come together and react.For example:

• Enzymes bring reactants together so they don’t have to expend energy moving about until they collide atrandom. Enzymes bind both reactant molecules (called substrates), tightly and specifically, at a site on theenzyme molecule called the active site (Figure 1.7). This forms an enzyme-substrate complex.

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1.6. Enzymes and Biochemical Reactions - Advanced www.ck12.org

• By binding reactants at the active site, enzymes also position reactants correctly, so they do not have toovercome intermolecular forces that would otherwise push them apart. This allows the molecules to interactwith less energy.

• Enzymes may also allow reactions to occur by different pathways that have lower activation energy.

FIGURE 1.7This enzyme molecule binds reactantmolecules—called substrate—at its activesite, forming an enzyme-substrate com-plex. This brings the reactants togetherand positions them correctly so the re-action can occur. After the reaction, theproducts are released from the enzyme’sactive site. This frees up the enzyme so itcan catalyze additional reactions.

The activities of enzymes also depend on the temperature, ionic conditions, and the pH of the surroundings. Someenzymes work best at acidic pHs, while others work best in neutral environments.

• Digestive enzymes secreted in the acidic environment (low pH) of the stomach help break down proteins intosmaller molecules. The main digestive enzyme in the stomach is pepsin, which works best at a pH of about1.5). These enzymes would not work optimally at other pHs. Trypsin is another enzyme in the digestivesystem which break protein chains in the food into smaller parts. Trypsin works in the small intestine, whichis not an acidic environment. Trypsin’s optimum pH is about 8.

• Biochemical reactions are optimal at physiological temperatures. For example, most biochemical reactionswork best at the normal body temperature of 98.6˚F (37˚C). Many enzymes lose function at lower and highertemperatures. At higher temperatures, an enzyme’s shape deteriorates, and only when the temperature comesback to normal does the enzyme regain its shape and normal activity.

Importance of Enzymes

Enzymes are involved in most of the chemical reactions that take place in organisms. About 4,000 such reactions areknown to be catalyzed by enzymes, but the number may be even higher. In animals, an important function of enzymesis to help digest food. Digestive enzymes speed up reactions that break down large molecules of carbohydrates,proteins, and fats into smaller molecules the body can use. Without digestive enzymes, animals would not be able tobreak down food molecules quickly enough to provide the energy and nutrients they need to survive.

Vocabulary

• active site: Site on the enzyme where the reaction occurs.

• biochemical reaction: Chemical reaction within a cell or organism; usually controlled by an enzyme.

• enzyme: Chemical, usually a protein, that speeds up chemical reactions in organisms; a biological catalyst.

• pepsin: The main digestive enzyme in the stomach; degrades food proteins into peptides.

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www.ck12.org Chapter 1. Biochemistry - Advanced

• reactant: Substance involved in a chemical reaction that is present at the beginning of the reaction.

• substrates: The reactants in an enzyme catalyzed reaction.

• trypsin: Digestive enzyme which break protein chains in food into smaller peptide fragments; a serineprotease, cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine, exceptwhen either is followed by proline.

Summary

• Enzymes are needed to speed up chemical reactions in organisms. They work by lowering the activationenergy of reactions.

• Enzymes position substrates into active sites.• Various conditions affect enzyme function. Pepsin and trypsin are two digestive enzymes that work in

contrasting environments.

Review

1. In general, how do enzymes speed up chemical reactions?2. How do enzymes bring reactants together? How is it beneficial?3. Explain why organisms need enzymes to survive.4. What are the conditions necessary for enzymes to perform optimally?5. What are pepsin and trypsin?

Review Answers

1. Enzymes speed up chemical reactions by lowering the activation energy needed for reactants to come togetherand react.

2. Enzymes bind both reactant molecules at an active site forming an enzyme substrate complex. By holding ontothe substrates and positioning them, they are able to overcome intermolecular forces that would otherwise pushthem apart. Thus allowing molecules to interact with less energy.

3. Organisms need enzymes to survive because without enzymes, animals would not be able to break down foodmolecules quickly enough to provide the energy and nutrients needed for survival.

4. The optimal conditions necessary for enzymes to perform depend on the temperature, ionic conditions and thepH of the surroundings.

5. Pepsin is the main digestive enzyme in the stomach that degrades food proteins into peptides. Trypsin is adigestive enzyme which breaks protein chains from food into smaller peptide fragments.

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1.7. References www.ck12.org

1.7 References

1. Laura Guerin. CK-12 Foundation . CC BY-NC 3.02. Christopher Auyeung. CK-12 Foundation . CC BY-NC 3.03. CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.04. Julie Magro. Ice Pack . CC BY 2.05. CK-12 Foundation. CK-12 Foundation . CC BY-NC 3.06. Hana Zavadska. Enzyme Action . CC BY-NC 3.07. Laura Guerin. CK-12 Foundation . CC BY-NC 3.0

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