Bioenergetics

The study of how cells accomplish this is called bioenergetics.

Thermodynamics

Energy cannot be created or destroyed, it can be only be transferred.

• First Law of Thermodynamics: Cells cannot take energy out of thin air. It must harvest it from somewhere.

• Second Law of Thermodynamics: It states that energy transfer leads to less organization. That means the universe tends toward disorder (entropy). In order to power cellular processes, energy input must exceed energy loss to maintain order. Cellular processes that release energy can be coupled with cellular processes that require an input of energy.

Types of Reactions

• Exergonic reactions are those in which the products have less energy than the reactants.

• The course of a reaction can be represented by an energy diagram. You’ll notice that energy is represented along the y-axis.

• Reactions that require an input of energy are called endergonic reactions. You’ll notice that the products have more energy than the reactants.

Enzymes

• A catalyst is something that speeds something up.

• Enzymes are biological catalysts that speed up reactions which is by lowering the activation energy and helping the transition state to form.

• Enzymes do NOT change the energy of the starting point or the ending point of the reaction. They only lower the activation energy.

Enzyme Specificity

• Each enzyme catalyzes only one kind of reaction. This is known as enzyme specificity.

• Enzymes are usually named after the molecules they target. In enzymatic reactions, the targeted molecules are known as substrates.

Enzyme-Substrate Complex

• During a reaction, the enzyme’s job is to bring the transition state about by helping the substrate(s) get into position. It accomplishes this through a special region on the enzyme known as an active site.

• The enzyme temporarily binds one or more of the substrates to its active site and forms an enzyme-substrate complex.

• Enzymes Do: increase the rate of a reaction by lowering the reaction’s activation energy form temporary enzyme-substrate complexes remain unaffected by the reaction

• Enzymes Don’t: change the reaction make reactions occur that would otherwise not occur at all

Induced-fit

• Enzymes and substrates don’t fit together quite so seamlessly. Enzymes have to change its shape slightly to accommodate the shape of the substrates. This is called induced-fit.

• Because the fit between the enzyme and the substrate must be perfect, enzymes operate only under a strict set of biological conditions.

Enzymes Don’t Always Work Alone

• Enzymes sometimes need a little help in catalysing a reaction. Those factors are known as cofactors. Cofactors can be either organic molecules called coenzymes or inorganic molecules or ions.

• Inorganic cofactors are usually metal ions (Fe2+, Mg2+).

• Vitamins are examples of organic coenzymes

Factors Affecting Reaction Rates

• Enzymatic reactions can be influenced by a number of factors, such as temperature and pH. The concentrations of enzyme and substrate will also determine the speed of the reaction.

Temperature

• The rate of a reaction increases with increasing temperature.

• An increase in the temperature of a reaction increases the frequency of collisions among the molecules. But too much heat can damage an enzyme and becomes denatured.

• Enzyme denaturation is reversible if the original optimal environmental conditions of the enzyme are restored.

pH

• Enzymes also function best at a particular pH.

• At an incorrect pH, the hydrogen bonds can be disrupted and the structure of the enzyme can be altered

Relative Concentration of Substrates and Products

• The relative concentration of substrates and products can also affect the rate of an enzyme-catalysed reaction.

• An increase in substrate concentration will initially speed up the reaction. However, once all of the enzyme in solution is bound by substrate, the reaction can no longer speed up.

• This concentration of substrate where all of the enzyme in a reaction is bound by substrate is called the saturation point. Additional substrate past this point will no longer increase the speed of the reaction.

Enzyme Regulation

• A cell can control enzymatic activity by regulating the conditions that influence the shape of the enzyme.

• Enzymes can be turned on or off by things that bind to them. Sometimes these things can bind at the active site, and sometimes they bind at other sites, called allosteric sites.

• If the substance has a shape that fits the active site of an enzyme it can compete with the substrate and block the substrate from getting into the active site. This is called competitive inhibition. You can always identify a competitive inhibitor based on what happens when you flood the system with lots of substrate.

• If the inhibitor binds to an allosteric site, it is an allosteric inhibitor and it is noncompetitive inhibition. A noncompetitive inhibitor generally distorts the enzyme shape so that it cannot function. The substrate can still bind at the active site, but the enzyme will not be able to catalyze the reaction.

Reaction Coupling and ATP

• The cell gets its energy through adenosine triphosphate (ATP).

• ATP consists of a molecule of adenosine bonded to three phosphates. Enormous amount of energy is packed into those phosphate bonds.

• When a cell needs energy, it takes one of these potential-packed molecules of ATP and splits off the third phosphate, forming adenosine diphosphate (ADP) and one loose phosphate (Pi ), while releasing energy in the process. ATP → ADP + Pi + energy

• Organisms can use exergonic processes that increase energy, like breaking down ATP, to power endergonic reactions, like building organic macromolecules.

Sources of ATP

• ATP comes from a process called cellular respiration.

• Cellular respiration is a process of breaking down sugar and making ATP.

• In autotrophs, the sugar is made during photosynthesis.

• In heterotrophs, glucose comes from the food we eat.

Photosynthesis

• Photosynthesis is the process by which light energy is converted to chemical energy.

• 6CO2 + 6H2O C6H12O6 + 6O2

• You’ll notice from this equation that carbon dioxide and water are the raw materials used to manufacture simple sugars. Oxygen is one of the products of photosynthesis.

• There is strong evidence that prokaryotic photosynthesis contributed to the production of oxygen in the atmosphere. Furthermore, prokaryotic photosynthesis pathways laid the evolutionary foundation for eukaryotic photosynthesis to develop.

• There are two stages in photosynthesis: the light reactions (also called the light-dependent reactions) and the dark reactions (also called the light- independent reactions).

  • The whole process begins when photons (energy units) of sunlight strike a leaf, activating chlorophyll and exciting electrons.

  • The activated chlorophyll molecule then passes these excited electrons down to a series of electron carriers, ultimately producing ATP and NADPH.

  • Both of these products, along with carbon dioxide, are then used in the dark reactions (light-independent) to make carbohydrates.

  • Along the way, water is also split and oxygen gets released.

Chloroplast Structure

• The leaves of plants contain lots of chloroplasts, which are the primary sites of photosynthesis.

• If you split the membranes of a chloroplast, you’ll find a fluid-filled region called the stroma. Inside the stroma are structures that look like stacks of coins. These structures are the grana.

• The many disk-like structures that make up grana are called thylakoids. They contain chlorophyll, a light-absorbing pigment that drives photosynthesis, as well as enzymes involved in the process.

• The very inside of a thylakoid is called the thylakoid lumen.

• Many light-absorbing pigments participate in photosynthesis. Some of the more important ones are chlorophyll a, chlorophyll b, and carotenoids. These pigments are clustered in the thylakoid membrane into units called antenna complexes.

• All of the pigments within a unit are able to “gather” light, but they’re not able to “excite” electrons. The other pigments, called antenna pigments, “gather” light and “bounce” energy to the reaction center.

• There are two types of reaction centers:

  • photosystem I (PS I) and photosystem II (PS II). T

• The principal difference between the two is that each reaction center has a specific type of chlorophyll—chlorophyll a—that absorbs a particular wavelength of light.

• Autotrophs are using light and ADP and phosphates (that’s phosphorylation) to produce ATP. An absorption spectrum shows how well a certain pigment absorbs electromagnetic radiation. Light absorbed is plotted as a function of radiation wavelength. This spectrum is the opposite of an emission spectrum, which gives information on which wavelengths are emitted by a pigment.

• Carotenoids absorb light on the blue-green end of the spectrum, but not on the other end. This is why plants rich in carotenoids are yellow, orange, or red.

The Light Reactions

• When a leaf captures sunlight, the energy is sent to P680, the reaction center for photosystem II.

• The activated electrons are trapped by P680 and passed to a molecule called the primary acceptor, and then they are passed down to carriers in the electron transport chain.

• To replenish the electrons in the thylakoid, water is split into oxygen, hydrogen ions, and electrons. That process is called photolysis.

• The electrons from photolysis replace the missing electrons in photosystem II. As the energized electrons from photosystem II travel down the electron transport chain, they pump hydrogen ions into the thylakoid lumen. A proton gradient is established. As the hydrogen ions move back into the stroma through ATP synthase, ATP is produced.

• After the electrons leave photosystem II, they go to photosystem I. The electrons are passed through a second electron transport chain until they reach the final electron acceptor NADP+ to make NADPH. Photosystem I and photosystem II were numbered in order of their discovery, not the order they are used in photosynthesis.

The Light-Independent Reactions

• The dark reactions use the products of the light reactions—ATP and NADPH—to make sugar.

• We now have energy to make glucose, Their carbon source is CO2. Carbon fixation means is that CO2 from the air is converted into carbohydrates.

• This step occurs in the stroma of the leaf. The dark reactions are also called the Calvin-Benson Cycle

Plants that live in hot climates have evolved two different ways around this:

• CAM plants deal with this problem by temporally separating carbon fixation and the Calvin cycle.

• They open their stomata at night and incorporate CO2 into organic acids.

• During the day, they close their stomata and release CO2 from the organic acids while the light reactions run.

• In contrast, C4 plants have slightly different leaf anatomy that allows them to perform CO2 fixation in a different part of the leaf from the rest of the Calvin cycle. This prevents photorespiration.

• C4 plants produce a four- carbon molecule as the first product of carbon fixation and perform cyclic electron flow in the light reactions.

Cellular Respiration

• C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP

• You can break cellular respiration down into two different approaches:

• aerobic respiration and anaerobic respiration.

• If ATP is made in the presence of oxygen, we call it aerobic respiration. If oxygen

• If it isn’t present, we call it anaerobic respiration.

Introduction to Aerobic Respiration

Aerobic respiration consists of four stages containing a series of coupled reactions that establish an electrochemical gradient across membranes:

1. glycolysis

2. formation of acetyl-CoA

3. the Krebs (citric acid) cycle

4. oxidative phosphorylation (the electron transport chain + chemiosmosis)

Stage 1: Glycolysis

• The first stage begins with glycolysis, the splitting of glucose

  • Glucose is a six-carbon molecule that is broken into two three- carbon molecules called pyruvic acid.

  • This breakdown of glucose also results in the net production of two molecules of ATP and two molecules of NADH.

  • Glucose + 2 ATP + 2NAD+ → 2 Pyruvic acid + 4 ATP + 2NADH

  • Glycolysis also creates two NADH, which result from the transfer of electrons to the carrier NAD+, which then becomes NADH.

  • NAD+ and NADH are constantly being turned into each other as electrons are being carried and then unloaded.

There are four important tidbits to remember regarding glycolysis:

• occurs in the cytoplasm

• net of 2 ATPs produced

• 2 pyruvic acids formed

• 2 NADH produced

Stage 2: Formation of Acetyl-CoA

• Pyruvic acid is transported to the mitochondrion.

• Each pyruvic acid (a three-carbon molecule) is converted to acetyl-coenzyme

• A (a two-carbon molecule, usually just called acetyl-CoA) and CO2 is released.

• 2 Pyruvic acid + 2 Coenzyme A + 2NAD+ → 2 Acetyl-CoA + 2CO2 + 2NADH

• From two 3- carbon molecules to now two 2-carbon molecules.

• The extra carbons leave the cell in the form of CO2. Once again, two molecules of NADH are also produced for each glucose you started with.

• This process of turning pyruvic acid into acetyl-CoA is catalyzed by an enzyme complex called the pyruvate dehydrogenase complex (PDC).

Stage 3: The Krebs Cycle

• Also known as the citric acid cycle.

  • The Krebs cycle begins with each molecule of acetyl-CoA produced from the second stage of aerobic respiration combining with oxaloacetate, a four-carbon molecule, to form a six-carbon molecule, citric acid or citrate.

  • In the mitochondria, pyruvate is turned into acetyl- CoA and 1 NADH is made; double this if you are counting per glucose.

  • The Krebs cycle occurs in the mitochondrial matrix.

  • It begins with acetyl-CoA joining with oxaloacetate to make citric acid and ends with oxaloacetate, 1 ATP, 3 NADH, and 1 FADH2; double this if you are counting per glucose.

  • Citrate gets turned into several other things, and because the cycle begins with a four-carbon molecule, oxaloacetate, it eventually gets turned back into oxaloacetate to maintain the cycle by joining with the next acetyl-CoA coming down the pipeline.

• With each turn of the cycle, three types of energy are produced:

  • 1 ATP

  • 3 NADH

  • 1 FADH2

• To figure out the total number of products per molecule of glucose, we simply double the number of products.

Stage 4: Oxidative Phosphorylation

Electron Transport Chain

• As electrons are removed from a molecule of glucose, they carry much energy that was originally stored in their chemical bonds.

• These electrons are transferred to readied hydrogen carrier molecules.

• In the case of cellular respiration, these charged carriers are the coenzymes NADH and FADH2.

• We now have:

  • 2 NADH molecules from glycolysis

  • 2 NADH from the production of acetyl-CoA

  • 6 NADH from the Krebs cycle

  • 2 FADH2 from the Krebs cycle

• That gives us a total of 12 electron or energy carriers altogether.

• These electron carriers—NADH and FADH2—“shuttle” electrons to the electron transport chain, the resulting NAD+ and FADH can be recycled to be used as carriers again, and the hydrogen atoms are split into hydrogen ions and electrons.

• The high-energy electrons from NADH and FADH2 are passed down a series of protein carrier molecules that are embedded in the cristae; thus, it is called the electron transport chain.

• Some of the carrier molecules in the electron transport chain are NADH dehydrogenase and cytochrome C.

• Each carrier molecule hands down the electrons to the next molecule in the chain.

• The electrons travel down the electron transport chain until they reach the final electron acceptor, oxygen. Oxygen combines with these electrons (and some hydrogens) to form water.

• This explains the “aerobic” in aerobic respiration. If oxygen weren’t available to accept the electrons, they wouldn’t move down the chain at all, thereby shutting down the whole process of electron transport.

Chemiosmosis

• The energy released from the electron transport chain is used to pump hydrogen ions across the inner mitochondrial membrane from the matrix into the inter-membrane space.

• The pumping of hydrogen ions into the inter-membrane space creates a pH gradient, or proton gradient.

• The hydrogen ions really want to diffuse back into the matrix. The potential energy established in this gradient is responsible for the production of ATP.

• This pumping of ions and diffusion of ions to create ATP is chemiosmosis

• Overall, this process is called oxidative phosphorylation because when electrons are given up it is called “oxidation” and then ADP is “phosphorylated” to make ATP.

• You’re also expected to know the following two things for the AP Biology Exam:

• Every NADH from glycolysis yields 1.5 ATP and all other NADH molecules yield 2.5 ATP.

• Every FADH2 yields 1.5 ATP.

You will also want to make sure you remember the major steps of cell respiration, and the outcome of each steM

Photosynthesis vs. Cell Respiration

• In both cases, ATP production is driven by a proton gradient, and the proton gradient is created by an electron transport chain.

• In respiration, protons are pumped from the mitochondrial matrix to the intermembrane space, and they return to the matrix through an ATP synthase down their concentration gradient.

• In photosynthesis, protons are pumped from the stroma into the thylakoids compartment, and they return to the stroma through an ATP synthase down their concentration gradient.

• The Krebs cycle seeks to oxidize carbohydrates to CO2, while the Calvin cycle seeks to reduce CO2 to carbohydrates.

Anaerobic Respiration

• When oxygen is not available, the anaerobic version of respiration occurs.

  • The electron transport chain stops working, and electron carriers have nowhere to drop their electrons.

  • The mitochondrial production of acetyl- CoA and the Krebs cycle cease too.

  • Glycolysis, however, can continue to run. This means that glucose can be broken down to give net two ATP. Only two instead of 30!

  • Glycolysis also gives two pyruvates and two NADH. The pyruvate and NADH make a deal with each other, and pyruvate helps NADH get recycled back into NAD+ and takes its electrons.

  • The pyruvate turns into either lactic acid (in muscles) or ethanol (in yeast).

  • Since these two things are toxic at high concentrations, this process, called fermentation, is done only in emergencies. Aerobic respiration is a better option

• What types of organisms undergo fermentation?

  • Yeast cells and some bacteria make ethanol and carbon dioxide. Other bacteria produce lactic acid.

Your Muscle Cells Can Ferment

• A cramp was possibly the consequence of anaerobic respiration.

• When you exercise, your muscles require a lot of energy.

• To get this energy, they convert enormous amounts of glucose to ATP.

• As you continue to exercise, your body doesn’t get enough oxygen to keep up with the demand in your muscles. This creates an oxygen debt.

• Muscles switch over to anaerobic respiration.

• Pyruvic acid produced from glycolysis is converted to lactic acid.