Mr. Ramos Bioenergetics Study Guide

Students, here is a study guide for the Bioenergetics Test. Read it and study it carefully in conjunction with your class & book notes. The Bioenergetics test has 50 Multiple Choice questions worth 50% of your total class grade. The test is curved. Also, take advantage of this generous study guide. I will NOT always do these nice things for you all.

EnzymesSC.912.L.18.11 Explain the role of enzymes as catalysts that lower the activation energy of biochemical reactions. Identify factors, such as pH and temperature, and their effect on enzyme activity.

IntroductionEnzymes are proteins known as biological catalysts.

In chemistry, a catalyst is a substance that speeds up a chemical reaction but is not consumed in the reaction.

However, since this is not chemistry, we call them enzymes instead. We also call them enzymes because they are inside your body.

Activation Energy

Enzymes speed up chemical reactions by lowering the energy of activation.

The energy of activation (aka activation energy) is the amount of energy needed to get a reaction going.

In simple terms, imagine that you need to climb a very steep mountain. The amount of energy that you need to go over the mountain is the energy of activation. Now, imagine having a good friend called “enzyme.” Your friend, enzyme, has the ability of lowering the mountain-top. Thus, you will now go over the mountain without having to sweat about it.

This mountain is so high! Please enzyme, bring it down! Activation Energy

Enzyme Naming

Enzymes are specific to the reaction that they catalyze (speed up). Therefore, their names have something to do with the reaction that they catalyze.

Lactase, for example, is the enzyme that breaks down the sugar in milk, lactose. Lactase only works for this type of reaction. Other reactions need their own specialized enzymes.

Amylase is another type of enzyme that is present in human saliva. It is in charge of breaking down starch into simple sugars.

Notice that both lactase and amylase end with the suffix –ase. This is true for the majority of enzymes. If you see the “-ase” ending, then it is an enzyme.

Keep in mind that every rule has an exception. Not all enzymes end in –ase. Pepsin is an enzyme found in your stomach that does not end in –ase.Trypsin is an enzyme found in your small intestines that does not end in –ase.

Enzymatic Activity

Enzymes attach themselves to a substance called the substrate.

The enzyme and the substrate combine in a way similar to a lock-and-key. This is called the enzyme-substrate complex. There is a slight change in enzyme shape as it attaches to the substrate. This slight enzymatic change is known as an induced fit.

Only a part of the enzyme called the active site catalyzes a reaction. By the way, the fancy words catalyzes, catalysis, catalyst, etc…just mean speed up a chemical reaction.

The substrate will bind to the enzyme’s active site to perform catalysis.

Factors Affecting Reaction Rates

Many things can affect enzymatic activity, but we will focus on three things: temperature, pH, and the amount of enzyme or substrate.

Enzymes happen to work best at certain temperatures. For example, the enzymes in your body work best at 37°C or 98.6°F. This is called the optimal temperature for these particular enzymes found in your body. It is the temperature where these enzymes are working at their best (optimum). If you have a very high fever, the enzymes will speed up, but then they may stop working.

Heat increases enzymatic activity. But too much heat denatures the enzymes (looses 3D shape).

On the other hand, cooling an enzyme may simply put the enzyme in a “sleep-like” state (inactive).

Enzymes also work better under optimal pH concentrations. Remember that pH is a measurement of the acid/base. The enzyme pepsin, found in your stomach, has an optimal pH of about 1 or 2. Pepsin may not work if the pH increases to become basic.

When an enzyme is outside its temperature and pH range, it may lose its 3-dimensional protein shape and become denatured.

Normally, a reaction will speed up if there are more enzymes to get the job done. The converse is also true (less enzymes = slower reaction).

Sometimes reaction rates can increase when you add substrates to a reaction because it becomes easier for an enzyme to attach itself to the substrate since there are so many of them. Thus, adding more substrates may increase the reaction rate. However, if you continue adding more substrates, the enzyme will come to a point where it cannot work any faster, and the reaction continues at a steady speed.

EnergySC.912.L.18.10 Connect the role of adenosine triphosphate (ATP) to energy transfers within a cell.

SC.912.P.10.1Differentiate among the various forms of energy and recognize that they can be transformed from one form to others.

Introduction

The first law of thermodynamics states that the energy in the universe cannot be created nor destroyed. Energy in the universe is constant.

The second law of thermodynamics is the law of entropy. Entropy is a fancy word for disorder. A system tends to want to be in disorder. For example, an ice cube placed on a kitchen top could represent a system. Eventually the ice-cube begins to melt causing a mess in your kitchen.

This disorder, or entropy, is a result of heat being released. Every chemical reaction produces some heat that is lost to the surrounding.

Energy is constantly changing forms. For example, plants harvest the energy from sunlight and transfer it to chemical energy found within sugars. Then, an animal, such as a cow, may eat the plant and gather its chemical energy. Finally, the cow is able to transform the chemical energy from the plant into mechanical energy, which allows the cow to move around. In addition, the cow will release heat to the environment.

ATP

ATP stands for adenosine triphosphate.

ATP is a high energy molecule composed of a ribose sugar, an adenine base, and three high energy phosphate groups.

The energy in ATP is found in the bonds that connect each phosphate. Energy is released when a phosphate is broken off.

ATP – 1 phosphate = ADP (adenosine diphosphate)ADP – 1 phosphate = AMP (adenosine monophosphate)

(Most Energy) ATP …………ADP…………AMP (Least Energy)

ATP is the energy currency of the cell. Cell’s use ATP to carry out all biological process, such as breathing, movement, talking, etc…

PhotosynthesisSC.912.L.18.7 Identify the reactants, products, and basic functions of photosynthesis.

Introduction

Photosynthesis is a process by which plants, green algae, cyanobacteria, and some protists use to convert sunlight into chemical energy.

For this biology class we will focus on plant photosynthesis only.

6CO2 + 6H2O + sunlight C6H12O6 + O2 (memorize this formula)

carbon dioxide + water + sunlight sugar + oxygen

Photosynthesis mainly occurs in the leaves of plants in an organelle called the chloroplast. Inside the chloroplast is a special pigment called chlorophyll. Pigments absorb light.

Chlorophyll is capable of absorbing red, violet, and blue. Chlorophyll, however, cannot absorb green! Whatever is not absorbed will be reflected. This is why plants are mainly green because green is reflected onto your eyes.

There are two reactions that occur during photosynthesis: light-dependent reaction and light-independent reaction.

The light-dependent reaction of photosynthesis occurs within the chloroplast in disk-like structures called thylakoids.

The light-independent reaction of photosynthesis (sometimes called the dark reaction) occurs within the chloroplast’s jelly-like substance called the stroma.

The general concept of photosynthesis begins in the

thylakoids. (Light-dependent reaction)*Water and light enter the thylakoids. The light splits the water into oxygen gas, which is released as a byproduct, and ATP & NADPH are formed.

The second part of photosynthesis will now continue in the stroma (Light-independent reaction)*The ATP and NADPH made in the light-dependent reaction are used in conjunction with carbon dioxide to power the Calvin cycle.* Once the Calvin cycle is powered, sugars are made. Since the energy in ATP and NADPH has been used, these molecules are recycled as ADP and NADP+.

Do not confuse the words stroma and stoma

The Light-dependent Reaction: Photoysystem II and Photosystem I

The light-dependent reaction occurs in the thylakoids of the chloroplast and is made possible by a machinery of pigments and proteins called photosystem II and photosystem I. Notice that photosystem II occurs first.

The products of the light-dependent reaction are oxygen, ATP, and NADPH.

PS IILight and water enter the thylakoids within the photosystem II machinery. The light is absorbed by a special chlorophyll pigment which absorbs light at 680 nanometers. We call this pigment P680.

Light-dependent

The light splits the water, which causes the release of oxygen. This process also produces hydrogen ions (H+ ions) and high energy electrons.

The high energy electrons are then passed down an electron transport chain to produce energy in the form of ATP. As electrons pass down the electron transport chain, hydrogen ions are pulled into the thylakoids space. The high concentration of H+ ions are then forced out of an enzyme called ATP synthase. When H+ ions pass through the ATP synthase, energy is formed by combining a phosphate group to ADP to produce ATP. This process of going from ADP to ATP with the help of light is called photophosphorylation.

PS I

By the time the electrons from photosystem II reach photosystem I, they have very little energy. A second light source must re-charge these electrons when they reach photosystem I. The pigment that absorbs light in photosystem I is called P700 because it absorbs light at 700 nanometers.

The electrons are now energized and ready to pass a second and shorter electron transport chain. The electrons are picked up by NADP+ in the stroma, along with H+. This produces the final product of the light-dependent reaction, NADPH.

Please LOOK at the picture below and try to see what is happening as you read the information above

The Light-independent Reaction: The Calvin cycle

The light-independent reaction is sometimes called the dark reaction or the Calvin cycle. We do not call it the dark reaction anymore because it is misleading. It does not need to be dark for it to happen.

During the light-independent reaction, ATP, NADPH, and carbon dioxide are used to make high-energy sugars.

The Calvin cycle: C3 Pathway

Carbon dioxide enters the Calvin cycle and mixes with a sugar called Ribulose Bisphosphate (RuBP). This occurs because of the enzyme RuBisCo (Ribulose Bisphosphate Carboxylase).

The first organic compound to be formed in the Calvin cycle is PGA, a 3 carbon molecule.

PGA is then energized by ATP and NADPH to produce a higher-energy molecular state called PGAL or G3P.

Since G3P is the first product made, and it contains 3 carbons, this form of photosynthesis is called the C3

pathway. Many plants undergo the C3 pathway.

Notice that glucose is NOT the first sugar made. The first sugar made is G3P, which is later turned into a variety of sugars, such as glucose, sucrose, etc.

Photorespiration

Plants close their stomata when it is too hot in order to conserve water. Therefore, carbon dioxide is not able to enter the plant, and the oxygen made is stuck in the plant. This is not good news.

At this point, the plant’s enzyme, RuBisCo, will bind to the oxygen. This method does not produce any energy at all (it actually wastes energy).

No sugars are produced either.

In summary, photorespiration is bad for plants. It takes their energy and does not really do anything good for plants.

Evolutionarily speaking, some plants have adapted ways to deal with intense light, high temperatures, and low carbon dioxide levels.

C4 Pathway

The C4 pathway occurs in plants that are under intense light, high temperatures, and low carbon dioxide.

The C4 pathway requires extra energy in the form of ATP, and it is common in corn, sugarcane, and sorghum.

The C4 pathway uses two cells to perform photosynthesis: Mesophyll cell and Bundle-sheath cell.

Carbon dioxide and PEP combine thanks to the enzyme PEP carboxylase to form a 4 carbon molecule called Oxaloacetate. The

Oxaloacetate is later converted to another 4 carbon molecule called Malate. This all happens in the Mesophyll cell. Because Malate is a 4 carbon molecule, we call this the C4 pathway.

The Malate is then transferred to the bundle-sheath cell where it is broken down into carbon dioxide and pyruvate. The carbon dioxide is used to power the Calvin cycle while pyruvate is recycled back to the Mesophyll cell to later be turned back into PEP.

Crassulacean Acid Metabolism (CAM) Photosynthesis

CAM plants are similar to C4 plants because they are adapted to very hot and dry environments.

Examples of CAM plants include pineapple trees and many desert cacti.

CAM plants allow air to go in only at night when they open their stomata. At night, carbon dioxide is combined with organic acids and stored in the plant. During the day when the stomata are closed, these acids release the carbon dioxide into the Calvin cycle to produce carbohydrates.

Cellular Respiration SC.912.L.18.8 Identify the reactants, products, and basic functions of aerobic and anaerobic cellular respiration.

SC.912.L.18.6Discuss the role of anaerobic respiration in living things and in human society

Introduction

All organisms get energy from food. The energy in food is expressed in a unit called the calorie.

Cellular respiration is the process by which energy is released from food in the presence of oxygen.

C6H12O6 + O2 6CO2 + 6H2O + ATP (memorize this formula)

sugar + oxygen carbon dioxide + water + energy

Notice that the formula for cellular respiration is the same as photosynthesis but backwards. Also notice that the energy in photosynthesis is solar while in cellular respiration it is chemical energy.

Cellular respiration can occur aerobically (with oxygen) or anaerobically (without oxygen).

The process of glycolysis is always first and is present in aerobic and anaerobic respiration.

GlycolysisOXYGEN

Krebs cycle (citric acid cycle)

Electron Transport chain &

Oxidative phosphorylation

Fermentation

Lactic Acid Fermentation

Alcoholic Fermentation

No OXYGEN

Aerobic Respiration (with oxygen)

If oxygen is present, cellular respiration will begin with glycolysis, form an intermediate called acetyl CoA, enter the Krebs cycle, and finish with the electron transport chain and oxidative phosphorylation.

Technically speaking, glycolysis does not need oxygen to function, so it is anaerobic. Memorize this. It is usually asked on all tests.

Glycolysis occurs in the cytoplasm of cells where 1 molecule of glucose is broken down into pyruvic acid (aka pyruvate), ATP, and NADH.

Notice that in photosynthesis we dealt with NADPH and NADP+, but in cellular respiration we deal with NADH and NAD+.

After glycolysis, the pyruvic acid is converted into acetyl CoA, which then enters the Krebs cycle.

The Krebs cycle takes place in the matrix of the mitochondria of eukaryotic cells.

Acetyl CoA mixes with Oxaloacetate to produce citric acid (aka citrate). Since citric acid is the first product, we also call the Krebs cycle the citric acid cycle.

The Krebs cycle produces very little energy, some carbon dioxide (which you breathe out), and a lot of electron carriers (NADH, FADH2) which will later be used to make a lot of energy.

The electron carries NADH and FADH2 are ready to dump their electrons onto the inner membrane of the mitochondria called the cristae. This is where the electron transport chain is found.

The electrons that are dumped on the electron transport chain are passed on from protein to protein. As this is happening, the intermembrane space of the mitochondria becomes filled with hydrogen ions. These hydrogen ions are then forced to go back

into the matrix through the enzyme ATP synthase. Energy (ATP) is producedin the process when ADP is attached to a phosphate. This is called phosphorylation. Since

oxygen is the final electron acceptor in the chain, we specifically call this step oxidative phosphorylation.The electron transport chain and oxidative phosphorylation together produce the most amount of energy (about 36 molecules of ATP from 1 sugar in eukaryotes).

Keep in mind that while not all organisms perform photosynthesis, ALL organisms perform cellular respiration, including plants (ALL ORGANISMS)

One last thing to note is that while eukaryotes perform cellular respiration in their mitochondria, bacterial cells do not contain mitochondria! So how do they do cellular respiration? They perform the same functions in their cell membrane.

Anaerobic Respiration (without oxygen)

What happens where there is no oxygen?

Glycolysis will continue to run, since it is an anerobic process. It will produce the same products, pyruvic acid, energy, and NADH. Unfortunately, we cannot have all this high energy NADH running around, so we need something to bring it back to its lower energy state, NAD+.

In alcoholic fermentation, the products of glycolysis are turned into an alcohol called ethanol, carbon dioxide, and NAD+ (look we managed to bring that high energy NADH back down to NAD+). Unfortunately, no ATP is produced =( ….but at least we get alcohol and bread =)

By the way, humans cannot do alcoholic fermentation. This is done by the fungus yeast.

In lactic acid fermentation, the products of glycolysis are turned into lactic acid and NAD+ (look we managed to bring that high energy NADH back down to NAD+). The lactic acid may cause muscle

Notice how the electrons force the H+ to go to the intermembrane space.

Then notice how the H+ is forced back into the matrix of the mitochondria by the “red” enzyme ATP synthase. This produces ATP.

soreness after you exercise. More fascinating though, bacteria use lactic acid fermentation to produce cheese, yogurt, buttermilk, and sour-cream. COOL!Comparing photosynthesis and cellular respirationSC.912.L.18.9 Explain the interrelated nature of photosynthesis and cellular respiration.

Photosynthesis Equation:6CO2 + 6H2O + sunlight C6H12O6 + O2

Cellular Respiration Equation:C6H12O6 + O2 6CO2 + 6H2O + ATP

Photosynthesis removes carbon dioxide from the environment while cellular respiration puts it back in the environment.

Keep in mind that animals cannot do photosynthesis. Only plants, some bacteria, and some protists can perform photosynthesis.

Also, keep in mind that ALL organisms can perform cellular respiration. Plants are fortunate because they can do both photosynthesis and respiration.

Some factors affect the rate of photosynthesis. These factors include light intensity, temperature, and water. If photosynthesis is affected, so will cellular respiration.

For the most part, high light intensity and temperature increases photosynthesis (and thus respiration). The reverse is also true. Low light and low temperatures stop photosynthesis (and thus respiration).

One last thing, fungi cannot perform photosynthesis! I know these little guys look like plants but they are not plants. Fungi are decomposers; they are Heterotrophs (consumers not producers).

Notice that these are the same equations but in reverse to each other.

In photosynthesis we have solar energy while in respiration we have chemical energy (ATP)