Category: My Classroom Material

Chromatography of Pigments Write Up

Chromatography of Pigments Write Up

Introduction:

  • Explain paper chromatography
  • Describe the Greek origins of the word chromatography
  • Explain how paper chromatography is used
  • Explain how chromatography separates liquids into their individual components
  • Explain the purpose of the paper
  • Explain what is used as the developer
  • Explain how the separation process actually takes place
  • Explain the movement of the different components up the paper
  • Tell what a chromatogram is
  • What is the Rf value and give the formula for obtaining this value
  • How do scientists use Rf values

Hypothesis:

  • Write a statement explaining the lab objective of using paper chromatography to separate pigments

Materials:

  • In sentence form, write a statement listing the materials required for this lab.

Procedure:

  • In paragraph form, write the procedures for completing this lab

Results:

  • Include your chromatography strip. 
  • Complete Data Table 1
  • Write out and answer the questions on the lab. Remember to write and underline the question, but do NOT underline the answer

Conclusion (Write in paragraph form):

  • Restate your hypothesis
  • Tell the distance traveled by the solvent and by each color
  • Compare the Rf value for each color and explain any similarities and differences
  • Explain why some colors moved further than others
  • Explain any errors you might have made in lab that could have affected your results

Chapter 9 – Cellular Respiration

Chapter 9    Cellular Respiration: Harvesting Chemical Energy    Lecture Outline

Overview

·         To perform their many tasks, living cells require energy from outside sources.

·         Energy enters most ecosystems as sunlight and leaves as heat.

·         Photosynthesis generates oxygen and organic molecules that the mitochondria of eukaryotes use as fuel for cellular respiration.

·         Cells harvest the chemical energy stored in organic molecules and use it to regenerate ATP, the molecule that drives most cellular work.

·         Respiration has three key pathways: glycolysis, the citric acid cycle, and oxidative phosphorylation.

A. The Principles of Energy Harvest

1. Cellular respiration and fermentation are catabolic, energy-yielding pathways.

·         The arrangement of atoms of organic molecules represents potential energy.

·         Enzymes catalyze the systematic degradation of organic molecules that are rich in energy to simpler waste products with less energy.

·         Some of the released energy is used to do work; the rest is dissipated as heat.

·         Catabolic metabolic pathways release the energy stored in complex organic molecules.

·         One type of catabolic process, fermentation, leads to the partial degradation of sugars in the absence of oxygen.

·         A more efficient and widespread catabolic process, cellular respiration, consumes oxygen as a reactant to complete the breakdown of a variety of organic molecules.

°         In eukaryotic cells, mitochondria are the site of most of the processes of cellular respiration.

·         Cellular respiration is similar in broad principle to the combustion of gasoline in an automobile engine after oxygen is mixed with hydrocarbon fuel.

°         Food is the fuel for respiration. The exhaust is carbon dioxide and water.

·         The overall process is:

°         organic compounds + O2 à CO2 + H2O + energy (ATP + heat).

·         Carbohydrates, fats, and proteins can all be used as the fuel, but it is most useful to consider glucose.

°         C6H12O6 + 6O2 à 6CO2 + 6H2O + Energy (ATP + heat)

·         The catabolism of glucose is exergonic with a D G of −686 kcal per mole of glucose.

°         Some of this energy is used to produce ATP, which can perform cellular work.

2. Redox reactions release energy when electrons move closer to electronegative atoms.

·         Catabolic pathways transfer the electrons stored in food molecules, releasing energy that is used to synthesize ATP.

·         Reactions that result in the transfer of one or more electrons from one reactant to another are oxidation-reduction reactions, or redox reactions.

°         The loss of electrons is called oxidation.

°         The addition of electrons is called reduction.

·         The formation of table salt from sodium and chloride is a redox reaction.

°         Na + Cl à Na+ + Cl−

°         Here sodium is oxidized and chlorine is reduced (its charge drops from 0 to −1).

·         More generally: Xe− + Y à X + Ye−

°         X, the electron donor, is the reducing agent and reduces Y.

°         Y, the electron recipient, is the oxidizing agent and oxidizes X.

·         Redox reactions require both a donor and acceptor.

·         Redox reactions also occur when the transfer of electrons is not complete but involves a change in the degree of electron sharing in covalent bonds.

°         In the combustion of methane to form water and carbon dioxide, the nonpolar covalent bonds of methane (C—H) and oxygen (O=O) are converted to polar covalent bonds (C=O and O—H).

°         When methane reacts with oxygen to form carbon dioxide, electrons end up farther away from the carbon atom and closer to their new covalent partners, the oxygen atoms, which are very electronegative.

°         In effect, the carbon atom has partially “lost” its shared electrons. Thus, methane has been oxidized.

·         The two atoms of the oxygen molecule share their electrons equally. When oxygen reacts with the hydrogen from methane to form water, the electrons of the covalent bonds are drawn closer to the oxygen.

°         In effect, each oxygen atom has partially “gained” electrons, and so the oxygen molecule has been reduced.

°         Oxygen is very electronegative, and is one of the most potent of all oxidizing agents.

·         Energy must be added to pull an electron away from an atom.

·         The more electronegative the atom, the more energy is required to take an electron away from it.

·         An electron loses potential energy when it shifts from a less electronegative atom toward a more electronegative one.

·         A redox reaction that relocates electrons closer to oxygen, such as the burning of methane, releases chemical energy that can do work.

3. The “fall” of electrons during respiration is stepwise, via NAD+ and an electron transport chain.

·         Cellular respiration does not oxidize glucose in a single step that transfers all the hydrogen in the fuel to oxygen at one time.

·         Rather, glucose and other fuels are broken down in a series of steps, each catalyzed by a specific enzyme.

°         At key steps, electrons are stripped from the glucose.

°         In many oxidation reactions, the electron is transferred with a proton, as a hydrogen atom.

·         The hydrogen atoms are not transferred directly to oxygen but are passed first to a coenzyme called NAD+ (nicotinamide adenine dinucleotide).

·         How does NAD+ trap electrons from glucose?

°         Dehydrogenase enzymes strip two hydrogen atoms from the fuel (e.g., glucose), oxidizing it.

°          The enzyme passes two electrons and one proton to NAD+.

°          The other proton is released as H+ to the surrounding solution.

·         By receiving two electrons and only one proton, NAD+ has its charge neutralized when it is reduced to NADH.

°         NAD+ functions as the oxidizing agent in many of the redox steps during the catabolism of glucose.

·         The electrons carried by NADH have lost very little of their potential energy in this process.

·         Each NADH molecule formed during respiration represents stored energy. This energy is tapped to synthesize ATP as electrons “fall” from NADH to oxygen.

·         How are electrons extracted from food and stored by NADH finally transferred to oxygen?

°         Unlike the explosive release of heat energy that occurs when H2 and O2 are combined (with a spark for activation energy), cellular respiration uses an electron transport chain to break the fall of electrons to O2 into several steps.

·         The electron transport chain consists of several molecules (primarily proteins) built into the inner membrane of a mitochondrion.

·         Electrons released from food are shuttled by NADH to the “top” higher-energy end of the chain.

·         At the “bottom” lower-energy end, oxygen captures the electrons along with H+ to form water.

·         Electron transfer from NADH to oxygen is an exergonic reaction with a free energy change of −53 kcal/mol.

·         Electrons are passed to increasingly electronegative molecules in the chain until they reduce oxygen, the most electronegative receptor.

·         In summary, during cellular respiration, most electrons travel the following “downhill” route: food à NADH à electron transport chain à oxygen.

B. The Process of Cellular Respiration

1. These are the stages of cellular respiration: a preview.

·         Respiration occurs in three metabolic stages: glycolysis, the citric acid cycle, and the electron transport chain and oxidative phosphorylation.

·         Glycolysis occurs in the cytoplasm.

°         It begins catabolism by breaking glucose into two molecules of pyruvate.

·         The citric acid cycle occurs in the mitochondrial matrix.

°         It completes the breakdown of glucose by oxidizing a derivative of pyruvate to carbon dioxide.

·         Several steps in glycolysis and the citric acid cycle are redox reactions in which dehydrogenase enzymes transfer electrons from substrates to NAD+, forming NADH.

·         NADH passes these electrons to the electron transport chain.

·         In the electron transport chain, the electrons move from molecule to molecule until they combine with molecular oxygen and hydrogen ions to form water.

·         As they are passed along the chain, the energy carried by these electrons is transformed in the mitochondrion into a form that can be used to synthesize ATP via oxidative phosphorylation.

·         The inner membrane of the mitochondrion is the site of electron transport and chemiosmosis, processes that together constitute oxidative phosphorylation.

°         Oxidative phosphorylation produces almost 90% of the ATP generated by respiration.

·         Some ATP is also formed directly during glycolysis and the citric acid cycle by substrate-level phosphorylation.

°         Here an enzyme transfers a phosphate group from an organic substrate to ADP, forming ATP.

·         For each molecule of glucose degraded to carbon dioxide and water by respiration, the cell makes up to 38 ATP, each with 7.3 kcal/mol of free energy.

·         Respiration uses the small steps in the respiratory pathway to break the large denomination of energy contained in glucose into the small change of ATP.

°         The quantity of energy in ATP is more appropriate for the level of work required in the cell.

2. Glycolysis harvests chemical energy by oxidizing glucose to pyruvate.

·         During glycolysis, glucose, a six carbon-sugar, is split into two three-carbon sugars.

·         These smaller sugars are oxidized and rearranged to form two molecules of pyruvate, the ionized form of pyruvic acid.

·         Each of the ten steps in glycolysis is catalyzed by a specific enzyme.

·         These steps can be divided into two phases: an energy investment phase and an energy payoff phase.

·         In the energy investment phase, the cell invests ATP to provide activation energy by phosphorylating glucose.

°         This requires 2 ATP per glucose.

·         In the energy payoff phase, ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released by the oxidation of glucose.

·         The net yield from glycolysis is 2 ATP and 2 NADH per glucose.

°         No CO2 is produced during glycolysis.

·         Glycolysis can occur whether O2 is present or not.

3. The citric acid cycle completes the energy-yielding oxidation of organic molecules.

·         More than three-quarters of the original energy in glucose is still present in the two molecules of pyruvate.

·         If oxygen is present, pyruvate enters the mitochondrion where enzymes of the citric acid cycle complete the oxidation of the organic fuel to carbon dioxide.

·         After pyruvate enters the mitochondrion via active transport, it is converted to a compound called acetyl coenzyme A or acetyl CoA.

·         This step is accomplished by a multienzyme complex that catalyzes three reactions:

1.       A carboxyl group is removed as CO2.

2.       The remaining two-carbon fragment is oxidized to form acetate. An enzyme transfers the pair of electrons to NAD+ to form NADH.

3.       Acetate combines with coenzyme A to form the very reactive molecule acetyl CoA.

·         Acetyl CoA is now ready to feed its acetyl group into the citric acid cycle for further oxidation.

·         The citric acid cycle is also called the Krebs cycle in honor of Hans Krebs, who was largely responsible for elucidating its pathways in the 1930s.

·         The citric acid cycle oxidizes organic fuel derived from pyruvate.

°         The citric acid cycle has eight steps, each catalyzed by a specific enzyme.

°         The acetyl group of acetyl CoA joins the cycle by combining with the compound oxaloacetate, forming citrate.

°         The next seven steps decompose the citrate back to oxaloacetate. It is the regeneration of oxaloacetate that makes this process a cycle.

°         Three CO2 molecules are released, including the one released during the conversion of pyruvate to acetyl CoA.

·         The cycle generates one ATP per turn by substrate-level phosphorylation.

°         A GTP molecule is formed by substrate-level phosphorylation.

°         The GTP is then used to synthesize an ATP, the only ATP generated directly by the citric acid cycle.

·         Most of the chemical energy is transferred to NAD+ and FAD during the redox reactions.

·         The reduced coenzymes NADH and FADH2 then transfer high-energy electrons to the electron transport chain.

·         Each cycle produces one ATP by substrate-level phosphorylation, three NADH, and one FADH2 per acetyl CoA.

4. The inner mitochondrial membrane couples electron transport to ATP synthesis.

·         Only 4 of 38 ATP ultimately produced by respiration of glucose are produced by substrate-level phosphorylation.

°         Two are produced during glycolysis, and 2 are produced during the citric acid cycle.

·         NADH and FADH2 account for the vast majority of the energy extracted from the food.

°         These reduced coenzymes link glycolysis and the citric acid cycle to oxidative phosphorylation, which uses energy released by the electron transport chain to power ATP synthesis.

·         The electron transport chain is a collection of molecules embedded in the cristae, the folded inner membrane of the mitochondrion.

°         The folding of the cristae increases its surface area, providing space for thousands of copies of the chain in each mitochondrion.

°         Most components of the chain are proteins bound to prosthetic groups, nonprotein components essential for catalysis.

·         Electrons drop in free energy as they pass down the electron transport chain.

·         During electron transport along the chain, electron carriers alternate between reduced and oxidized states as they accept and donate electrons.

°         Each component of the chain becomes reduced when it accepts electrons from its “uphill” neighbor, which is less electronegative.

°         It then returns to its oxidized form as it passes electrons to its more electronegative “downhill” neighbor.

·         Electrons carried by NADH are transferred to the first molecule in the electron transport chain, a flavoprotein.

·         The electrons continue along the chain that includes several cytochrome proteins and one lipid carrier.

°         The prosthetic group of each cytochrome is a heme group with an iron atom that accepts and donates electrons.

·         The last cytochrome of the chain, cyt a3, passes its electrons to oxygen, which is very electronegative.

°         Each oxygen atom also picks up a pair of hydrogen ions from the aqueous solution to form water.

°         For every two electron carriers (four electrons), one O2 molecule is reduced to two molecules of water.

·         The electrons carried by FADH2 have lower free energy and are added at a lower energy level than those carried by NADH.

°         The electron transport chain provides about one-third less energy for ATP synthesis when the electron donor is FADH2 rather than NADH.

·         The electron transport chain generates no ATP directly.

·         Its function is to break the large free energy drop from food to oxygen into a series of smaller steps that release energy in manageable amounts.

·         How does the mitochondrion couple electron transport and energy release to ATP synthesis?

°         The answer is a mechanism called chemiosmosis.

·         A protein complex, ATP synthase, in the cristae actually makes ATP from ADP and Pi.

·         ATP uses the energy of an existing proton gradient to power ATP synthesis.

°         The proton gradient develops between the intermembrane space and the matrix.

·         The proton gradient is produced by the movement of electrons along the electron transport chain.

·         The chain is an energy converter that uses the exergonic flow of electrons to pump H+ from the matrix into the intermembrane space.

·         The protons pass back to the matrix through a channel in ATP synthase, using the exergonic flow of H+ to drive the phosphorylation of ADP.

·         Thus, the energy stored in a H+ gradient across a membrane couples the redox reactions of the electron transport chain to ATP synthesis.

·         From studying the structure of ATP synthase, scientists have learned how the flow of H+ through this large enzyme powers ATP generation.

·         ATP synthase is a multisubunit complex with four main parts, each made up of multiple polypeptides:

1.       A rotor in the inner mitochondrial membrane.

2.       A knob that protrudes into the mitochondrial matrix.

3.       An internal rod extending from the rotor into the knob.

4.       A stator, anchored next to the rotor, which holds the knob stationary.

·         Protons flow down a narrow space between the stator and rotor, causing the rotor and its attached rod to rotate.

°         The spinning rod causes conformational changes in the stationary knob, activating three catalytic sites in the knob where ADP and inorganic phosphate combine to make ATP.

·         How does the inner mitochondrial membrane generate and maintain the H+ gradient that drives ATP synthesis in the ATP synthase protein complex?

°         Creating the H+ gradient is the function of the electron transport chain.

°         The ETC is an energy converter that uses the exergonic flow of electrons to pump H+ across the membrane from the mitochondrial matrix to the intermembrane space.

°         The H+ has a tendency to diffuse down its gradient.

·         The ATP synthase molecules are the only place that H+ can diffuse back to the matrix.

°         The exergonic flow of H+ is used by the enzyme to generate ATP.

°         This coupling of the redox reactions of the electron transport chain to ATP synthesis is called chemiosmosis.

·         How does the electron transport chain pump protons?

°         Certain members of the electron transport chain accept and release H+ along with electrons.

°         At certain steps along the chain, electron transfers cause H+ to be taken up and released into the surrounding solution.

·         The electron carriers are spatially arranged in the membrane in such a way that protons are accepted from the mitochondrial matrix and deposited in the intermembrane space.

°         The H+ gradient that results is the proton-motive force.

°         The gradient has the capacity to do work.

·         Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work.

·         In mitochondria, the energy for proton gradient formation comes from exergonic redox reactions, and ATP synthesis is the work performed.

·         Chemiosmosis in chloroplasts also generates ATP, but light drives the electron flow down an electron transport chain and H+ gradient formation.

·         Prokaryotes generate H+ gradients across their plasma membrane.

°         They can use this proton-motive force not only to generate ATP, but also to pump nutrients and waste products across the membrane and to rotate their flagella.

5. Here is an accounting of ATP production by cellular respiration.

·         During cellular respiration, most energy flows from glucose à NADH à electron transport chain à proton-motive force à ATP.

·         Let’s consider the products generated when cellular respiration oxidizes a molecule of glucose to six CO2 molecules.

·         Four ATP molecules are produced by substrate-level phosphorylation during glycolysis and the citric acid cycle.

·         Many more ATP molecules are generated by oxidative phosphorylation.

·         Each NADH from the citric acid cycle and the conversion of pyruvate contributes enough energy to the proton-motive force to generate a maximum of 3 ATP.

°         The NADH from glycolysis may also yield 3 ATP.

·         Each FADH2 from the citric acid cycle can be used to generate about 2 ATP.

·         Why is our accounting so inexact?

·         There are three reasons that we cannot state an exact number of ATP molecules generated by one molecule of glucose.

1.       Phosphorylation and the redox reactions are not directly coupled to each other, so the ratio of number of NADH to number of ATP is not a whole number.

°         One NADH results in 10 H+ being transported across the inner mitochondrial membrane.

°         Between 3 and 4 H+ must reenter the mitochondrial matrix via ATP synthase to generate 1 ATP.

°         Therefore, 1 NADH generates enough proton-motive force for synthesis of 2.5 to 3.3 ATP.

°         We round off and say that 1 NADH generates 3 ATP.

2.       The ATP yield varies slightly depending on the type of shuttle used to transport electrons from the cytosol into the mitochondrion.

°         The mitochondrial inner membrane is impermeable to NADH, so the two electrons of the NADH produced in glycolysis must be conveyed into the mitochondrion by one of several electron shuttle systems.

°         In some shuttle systems, the electrons are passed to NAD+, which generates 3 ATP. In others, the electrons are passed to FAD, which generates only 2 ATP.

3.       The proton-motive force generated by the redox reactions of respiration may drive other kinds of work, such as mitochondrial uptake of pyruvate from the cytosol.

°         If all the proton-motive force generated by the electron transport chain were used to drive ATP synthesis, one glucose molecule could generate a maximum of 34 ATP by oxidative phosphorylation plus 4 ATP (net) from substrate-level phosphorylation to give a total yield of 36–38 ATP (depending on the efficiency of the shuttle).

·         How efficient is respiration in generating ATP?

°         Complete oxidation of glucose releases 686 kcal/mol.

°         Phosphorylation of ADP to form ATP requires at least 7.3 kcal/mol.

°         Efficiency of respiration is 7.3 kcal/mol times 38 ATP/glucose divided by 686 kcal/mol glucose, which equals 0.4 or 40%.

°         Approximately 60% of the energy from glucose is lost as heat.

§         Some of that heat is used to maintain our high body temperature (37°C).

·         Cellular respiration is remarkably efficient in energy conversion.

C. Related Metabolic Processes

1. Fermentation enables some cells to produce ATP without the help of oxygen.

·         Without electronegative oxygen to pull electrons down the transport chain, oxidative phosphorylation ceases.

·         However, fermentation provides a mechanism by which some cells can oxidize organic fuel and generate ATP without the use of oxygen.

°         In glycolysis, glucose is oxidized to two pyruvate molecules with NAD+ as the oxidizing agent.

°         Glycolysis is exergonic and produces 2 ATP (net).

°         If oxygen is present, additional ATP can be generated when NADH delivers its electrons to the electron transport chain.

·         Glycolysis generates 2 ATP whether oxygen is present (aerobic) or not (anaerobic).

·         Anaerobic catabolism of sugars can occur by fermentation.

·         Fermentation can generate ATP from glucose by substrate-level phosphorylation as long as there is a supply of NAD+ to accept electrons.

°         If the NAD+ pool is exhausted, glycolysis shuts down.

°         Under aerobic conditions, NADH transfers its electrons to the electron transfer chain, recycling NAD+.

·         Under anaerobic conditions, various fermentation pathways generate ATP by glycolysis and recycle NAD+ by transferring electrons from NADH to pyruvate or derivatives of pyruvate.

·         In alcohol fermentation, pyruvate is converted to ethanol in two steps.

°         First, pyruvate is converted to a two-carbon compound, acetaldehyde, by the removal of CO2.

°         Second, acetaldehyde is reduced by NADH to ethanol.

°         Alcohol fermentation by yeast is used in brewing and winemaking.

·         During lactic acid fermentation, pyruvate is reduced directly by NADH to form lactate (the ionized form of lactic acid) without release of CO2.

°         Lactic acid fermentation by some fungi and bacteria is used to make cheese and yogurt.

°         Human muscle cells switch from aerobic respiration to lactic acid fermentation to generate ATP when O2 is scarce.

§         The waste product, lactate, may cause muscle fatigue, but ultimately it is converted back to pyruvate in the liver.

·         Fermentation and cellular respiration are anaerobic and aerobic alternatives, respectively, for producing ATP from sugars.

°         Both use glycolysis to oxidize sugars to pyruvate with a net production of 2 ATP by substrate-level phosphorylation.

°         Both use NAD+ as an oxidizing agent to accept electrons from food during glycolysis.

·         The two processes differ in their mechanism for oxidizing NADH to NAD+.

°         In fermentation, the electrons of NADH are passed to an organic molecule to regenerate NAD+.

°         In respiration, the electrons of NADH are ultimately passed to O2, generating ATP by oxidative phosphorylation.

·         More ATP is generated from the oxidation of pyruvate in the citric acid cycle.

°         Without oxygen, the energy still stored in pyruvate is unavailable to the cell.

°         Under aerobic respiration, a molecule of glucose yields 38 ATP, but the same molecule of glucose yields only 2 ATP under anaerobic respiration.

·         Yeast and many bacteria are facultative anaerobes that can survive using either fermentation or respiration.

°         At a cellular level, human muscle cells can behave as facultative anaerobes.

·         For facultative anaerobes, pyruvate is a fork in the metabolic road that leads to two alternative routes.

°         Under aerobic conditions, pyruvate is converted to acetyl CoA and oxidation continues in the citric acid cycle.

°         Under anaerobic conditions, pyruvate serves as an electron acceptor to recycle NAD+.

·         The oldest bacterial fossils are more than 3.5 billion years old, appearing long before appreciable quantities of O2 accumulated in the atmosphere.

°         Therefore, the first prokaryotes may have generated ATP exclusively from glycolysis.

·         The fact that glycolysis is a ubiquitous metabolic pathway and occurs in the cytosol without membrane-enclosed organelles suggests that glycolysis evolved early in the history of life.

2. Glycolysis and the citric acid cycle connect to many other metabolic pathways.

·         Glycolysis can accept a wide range of carbohydrates for catabolism.

°         Polysaccharides like starch or glycogen can be hydrolyzed to glucose monomers that enter glycolysis.

°         Other hexose sugars, such as galactose and fructose, can also be modified to undergo glycolysis.

·         The other two major fuels, proteins and fats, can also enter the respiratory pathways used by carbohydrates.

·         Proteins must first be digested to individual amino acids.

°         Amino acids that will be catabolized must have their amino groups removed via deamination.

°         The nitrogenous waste is excreted as ammonia, urea, or another waste product.

·         The carbon skeletons are modified by enzymes and enter as intermediaries into glycolysis or the citric acid cycle, depending on their structure.

·         Catabolism can also harvest energy stored in fats.

·         Fats must be digested to glycerol and fatty acids.

°         Glycerol can be converted to glyceraldehyde phosphate, an intermediate of glycolysis.

°         The rich energy of fatty acids is accessed as fatty acids are split into two-carbon fragments via beta oxidation.

°         These molecules enter the citric acid cycle as acetyl CoA.

·         A gram of fat oxides by respiration generates twice as much ATP as a gram of carbohydrate.

·         The metabolic pathways of respiration also play a role in anabolic pathways of the cell.

·         Intermediaries in glycolysis and the citric acid cycle can be diverted to anabolic pathways.

°         For example, a human cell can synthesize about half the 20 different amino acids by modifying compounds from the citric acid cycle.

°         Glucose can be synthesized from pyruvate; fatty acids can be synthesized from acetyl CoA.

·         Glycolysis and the citric acid cycle function as metabolic interchanges that enable cells to convert one kind of molecule to another as needed.

°         For example, excess carbohydrates and proteins can be converted to fats through intermediaries of glycolysis and the citric acid cycle.

·         Metabolism is remarkably versatile and adaptable.

3. Feedback mechanisms control cellular respiration.

·         Basic principles of supply and demand regulate the metabolic economy.

°         If a cell has an excess of a certain amino acid, it typically uses feedback inhibition to prevent the diversion of intermediary molecules from the citric acid cycle to the synthesis pathway of that amino acid.

·         The rate of catabolism is also regulated, typically by the level of ATP in the cell.

°         If ATP levels drop, catabolism speeds up to produce more ATP.

·         Control of catabolism is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway.

·         One strategic point occurs in the third step of glycolysis, catalyzed by phosphofructokinase.

·         Allosteric regulation of phosphofructokinase sets the pace of respiration.

°         This enzyme catalyzes the earliest step that irreversibly commits the substrate to glycolysis.

°         Phosphofructokinase is an allosteric enzyme with receptor sites for specific inhibitors and activators.

°         It is inhibited by ATP and stimulated by AMP (derived from ADP).

§         When ATP levels are high, inhibition of this enzyme slows glycolysis.

§         As ATP levels drop and ADP and AMP levels rise, the enzyme becomes active again and glycolysis speeds up.

·         Citrate, the first product of the citric acid cycle, is also an inhibitor of phosphofructokinase.

°         This synchronizes the rate of glycolysis and the citric acid cycle.

·         If intermediaries from the citric acid cycle are diverted to other uses (e.g., amino acid synthesis), glycolysis speeds up to replace these molecules.

·         Metabolic balance is augmented by the control of other enzymes at other key locations in glycolysis and the citric acid cycle.

·         Cells are thrifty, expedient, and responsive in their metabolism.

 

 

Chromatography of Plant Pigments 3

 

 

Chromatography of Plant Pigments

 

 

Introduction:

 

Can chromatography be used to separate mixtures of chemical substances? The purpose of this experiment is to answer this question. In paper chromatography, a liquid sample flows down a vertical strip of absorbent paper, on which the components of a mixture are deposited in specific directions and locations. Chromatography is a tool used to examine and separate mixtures of chemical substances. Chromatography is essential to the separation of pure substances from complex mixtures. Separation results in a chromatographically pure substance. Chromatography allows you to determine the properties of chemical substances.

The relationship between the chromatography paper, mixture, and the solvent is very important in all chromatographic separations. The solvent has to dissolve the mixture that should be separated. The paper must also absorb the components of the mixtures selectively and reversibly. The substances making up the mixture must be evenly dispersed in the water. Chromatography is a simple and inexpensive tool for separating and identifying chemical mixtures if all these things are done.

 

Hypothesis:

 

Paper can be used to separate mixed chemicals.

 

Materials:

 

The materials used in this lab are filter paper, test tube, rubber stopper, paper clip, metric ruler, black felt-tip pen, pencil, calculator, and water.

 

Methods:

 

First, bend a paper clip so that it’s straight with a hook at one end. Push the straight end of the paper clip into the bottom of a cork stopper. Then, hang a thin strip of filter paper on the hooked end of the paper clip and insert the paper strip into the test tube. The paper should not touch the sides and should almost touch the bottom of the test tube. Next, remove the paper strip from the test tube. Now draw a solid 5-mm-wide band about 25 mm from the bottom of the paper, using a black felt tip pen. After this, use a pencil to draw a line across the paper strip 10 cm above the black band. Then, put the filter paper back into the test tube with the bottom of the paper in the water and the black band above the water. Observe what happens as the liquid travels up the paper and record the changes you see. When the solvent has reached the pencil line, remove the paper from the test tube. Let the paper dry on the desk. Finally, with a metric ruler, measure the distances from the starting point to the top edge of each color. Record the data in a data table and calculate a ratio for each color by dividing the distance, the color traveled by the distance the solvent traveled.

 

Results:

 

The results of the chromatography experiment are shown in a chart and a graph.

 

Color of ink (list in order) Distance traveled by each color (mm) Distance solvent traveled (mm) Ratio traveled = distance color moved divided by distance solvent moved
Yellow 70 108 0.65
Orange  

85

  

108

  

0.79
Pink 95  

108

  

0.88
Violet 102  

108

  

0.94
Blue 108  

108

  

1.00

 

 

 

Questions:

1. How many colors separated from the black ink? Five colors separated from the ink: yellow, orange, pink, violet, and blue.

 

2. What served as the solvent for the ink? Water served as the solvent for the ink.

 

3. As the solvent traveled up the paper, which color of ink appeared first? Dark blue appeared first.

 

4. List the colors in order from top to bottom that separated from the black ink? The colors separated in the order of: blue, violet, pink, orange, and yellow.

 

5. In millimeters, how far did the solvent travel? The solvent traveled 108 mm.

 

6. From your results, what can you conclude is true about black ink? Black ink is a mixture of several different colors.

 

7. Why did the inks separate? The inks separated because black ink is a mixture of different pigments that are soluble in water, have different molecular characteristics, and travel different distances.

 

8. Why did some inks move a greater distance? Some inks move a greater distance because molecules in ink have different characteristics, like how readily they are absorbed by paper. This means that the ink least readily absorbed by paper will travel farthest from the starting mark and the ink most readily absorbed by paper will be the closest to the starting mark. All of the different color inks that were separated were different in how readily they are absorbed by paper.

Error Analysis:

 

There are a few errors that could have changed the results. First, there could be inaccurate measurements of how far every color traveled or how far the water traveled up the filter paper. Another error could occur when calculating the ratio traveled, Rf value. Also, a longer test tube could have been used by different groups which would make the filter strip longer. This means that a group could have detected another color because they had more room on their filter paper. This also could have affected the ratios. Finally, the groups could have put different amounts of black ink on the filter paper.

 

Conclusion:

 

The hypothesis that paper can be used to separate mixed chemicals was correct. The different colored inks mixed together give the black its color. The five colors that separated from the black ink were blue, violet, pink, orange, and yellow. Blue appeared first and then was followed by violet, pink, orange, and yellow. The colors separated the way they did because they have different molecular characteristics, like how readily they were absorbed by the paper and their solubility in water. Blue was most readily absorbed by the paper and soluble by water, while yellow was the least.

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Chapter 4 – Carbon and the Molecular Diversity of Life – Lecture Outline

Chapter 4    Carbon and the Molecular Diversity of Life    Lecture Outline

Overview: Carbon – The Backbone of Biological Molecules

·         Although cells are 70–95% water, the rest consists mostly of carbon-based compounds.

·         Carbon is unparalleled in its ability to form large, complex, and diverse molecules.

·         Carbon accounts for the diversity of biological molecules and has made possible the great diversity of living things.

·         Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inorganic material are all composed of carbon atoms bonded to each other and to atoms of other elements.

·         These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P).

 

Concept 4.1 Organic chemistry is the study of carbon compounds

·         The study of carbon compounds, organic chemistry, deals with any compound with carbon (organic compounds).

·         Organic compounds can range from simple molecules, such as CO2 or CH4, to complex molecules such as proteins, which may weigh more than 100,000 daltons.

·         The overall percentages of the major elements of life (C, H, O, N, S, and P) are quite uniform from one organism to another.

·         However, because of carbon’s versatility, these few elements can be combined to build an inexhaustible variety of organic molecules.

·         Variations in organic molecules can distinguish even between individuals of a single species.

·         The science of organic chemistry began in attempts to purify and improve the yield of products obtained from other organisms.

·         Initially, chemists learned to synthesize simple compounds in the laboratory, but had no success with more complex compounds.

·         The Swedish chemist Jons Jacob Berzelius was the first to make a distinction between organic compounds that seemed to arise only in living organisms and inorganic compounds that were found in the nonliving world.

·         This led early organic chemists to propose vitalism, the belief that physical and chemical laws did not apply to living things.

·         Support for vitalism began to wane as organic chemists learned to synthesize complex organic compounds in the laboratory.

·         In the early 1800s, the German chemist Friedrich Wöhler and his students were able to synthesize urea from totally inorganic materials.

·         In 1953, Stanley Miller at the University of Chicago set up a laboratory simulation of chemical conditions on the primitive Earth and demonstrated the spontaneous synthesis of organic compounds.

·         Such spontaneous synthesis of organic compounds may have been an early stage in the origin of life.

·         Organic chemists finally rejected vitalism and embraced mechanism, accepting that the same physical and chemical laws govern all natural phenomena including the processes of life.

·         Organic chemistry was redefined as the study of carbon compounds regardless of their origin.

·         Organisms do produce the majority of organic compounds.

·         The laws of chemistry apply to inorganic and organic compounds alike.

 

Concept 4.2 Carbon atoms can form diverse molecules by bonding to four other atoms

·         With a total of 6 electrons, a carbon atom has 2 in the first electron shell and 4 in the second shell.

·         Carbon has little tendency to form ionic bonds by losing or gaining 4 electrons to complete its valence shell.

·         Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent bonds.

·         This tetravalence by carbon makes large, complex molecules possible.

·         When carbon forms covalent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedron with bond angles of 109.5°.

·         In molecules with multiple carbons, every carbon bonded to four other atoms has a tetrahedral shape.

·         However, when two carbon atoms are joined by a double bond, all bonds around those carbons are in the same plane and have a flat, three-dimensional structure.

·         The three-dimensional shape of an organic molecule determines its function.

·         The electron configuration of carbon makes it capable of forming covalent bonds with many different elements.

·         The valences of carbon and its partners can be viewed as the building code that governs the architecture of organic molecules.

·         In carbon dioxide, one carbon atom forms two double bonds with two different oxygen atoms.

·         In the structural formula, O=C=O, each line represents a pair of shared electrons. This arrangement completes the valence shells of all atoms in the molecule.

·         While CO2 can be classified as either organic or inorganic, its importance to the living world is clear.

·         CO2 is the source of carbon for all organic molecules found in organisms. It is usually fixed into organic molecules by the process of photosynthesis.

·         Urea, CO(NH2)2, is another simple organic molecule in which each atom forms covalent bonds to complete its valence shell.

Variation in carbon skeletons contributes to the diversity of organic molecules.

·         Carbon chains form the skeletons of most organic molecules.

·         The skeletons vary in length and may be straight, branched, or arranged in closed rings.

·         The carbon skeletons may include double bonds.

·         Atoms of other elements can be bonded to the atoms of the carbon skeleton.

·         Hydrocarbons are organic molecules that consist of only carbon and hydrogen atoms.

·         Hydrocarbons are the major component of petroleum, a fossil fuel that consists of the partially decomposed remains of organisms that lived millions of years ago.

·         Fats are biological molecules that have long hydrocarbon tails attached to a nonhydrocarbon component.

·         Petroleum and fat are hydrophobic compounds that cannot dissolve in water because of their many nonpolar carbon-to-hydrogen bonds.

·         Isomers are compounds that have the same molecular formula but different structures and, therefore, different chemical properties.

·         For example, butane and isobutane have the same molecular formula, C4H10, but butane has a straight skeleton and isobutane has a branched skeleton.

·         The two butanes are structural isomers, molecules that have the same molecular formula but differ in the covalent arrangement of atoms.

·         Geometric isomers are compounds with the same covalent partnerships that differ in the spatial arrangement of atoms around a carbon–carbon double bond.

·         The double bond does not allow atoms to rotate freely around the bond axis.

·         The biochemistry of vision involves a light-induced change in the structure of rhodopsin in the retina from one geometric isomer to another.

·         Enantiomers are molecules that are mirror images of each other.

·         Enantiomers are possible when four different atoms or groups of atoms are bonded to a carbon.

·         In this case, the four groups can be arranged in space in two different ways that are mirror images.

·         They are like left-handed and right-handed versions of the molecule.

·         Usually one is biologically active, while the other is inactive.

·         Even subtle structural differences in two enantiomers have important functional significance because of emergent properties from specific arrangements of atoms.

·         One enantiomer of the drug thalidomide reduced morning sickness, the desired effect, but the other isomer caused severe birth defects.

·         The L-dopa isomer is an effective treatment of Parkinson’s disease, but the D-dopa isomer is inactive.

 

Concept 4.3 Functional groups are the parts of molecules involved in chemical reactions

·         The components of organic molecules that are most commonly involved in chemical reactions are known as functional groups.

·         If we consider hydrocarbons to be the simplest organic molecules, we can view functional groups as attachments that replace one or more of the hydrogen atoms bonded to the carbon skeleton of the hydrocarbon.

·         Each functional group behaves consistently from one organic molecule to another.

·         The number and arrangement of functional groups help give each molecule its unique properties.

·         As an example, the basic structure of testosterone (a male sex hormone) and estradiol (a female sex hormone) is the same.

·         Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the rings.

·         These functional groups interact with different targets in the body.

·         There are six functional groups that are most important to the chemistry of life: hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, and phosphate groups.

·         All are hydrophilic and increase the solubility of organic compounds in water.

·         In a hydroxyl group (—OH), a hydrogen atom forms a polar covalent bond with an oxygen atom, which forms a polar covalent bond to the carbon skeleton.

·         Because of these polar covalent bonds, hydroxyl groups increase the solubility of organic molecules.

·         Organic compounds with hydroxyl groups are alcohols, and their names typically end in -ol.

·         A carbonyl group (>CO) consists of an oxygen atom joined to the carbon skeleton by a double bond.

·         If the carbonyl group is on the end of the skeleton, the compound is an aldehyde.

·         If the carbonyl group is within the carbon skeleton, then the compound is a ketone.

·         Isomers with aldehydes versus ketones have different properties.

·         A carboxyl group (—COOH) consists of a carbon atom with a double bond to an oxygen atom and a single bond to the oxygen of a hydroxyl group.

·         Compounds with carboxyl groups are carboxylic acids.

·         A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H+).

·         An amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and the carbon skeleton.

·         Organic compounds with amino groups are amines.

·         The amino group acts as a base because the amino group can pick up a hydrogen ion (H+) from the solution.

·         Amino acids, the building blocks of proteins, have amino and carboxyl groups.

·         A sulfhydryl group (—SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone.

·         This group resembles a hydroxyl group in shape.

·         Organic molecules with sulfhydryl groups are thiols.

·         Two sulfhydryl groups can interact to help stabilize the structure of proteins.

·         A phosphate group (—OPO32−) consists of a phosphorus atom bound to four oxygen atoms (three with single bonds and one with a double bond).

·         A phosphate group connects to the carbon backbone via one of its oxygen atoms.

·         Phosphate groups are anions with two negative charges, as two protons have dissociated from the oxygen atoms.

·         One function of phosphate groups is to transfer energy between organic molecules.

·         Adenosine triphosphate, or ATP, is the primary energy-transferring molecule in living cells.

These are the chemical elements of life.

·         Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur and phosphorus.

·         These elements are linked by strong covalent bonds.

·         Carbon, with its four covalent bonds, is the basic building block in molecular architecture.

·         The great diversity of organic molecules with their special properties emerges from the unique arrangement of the carbon skeleton and the functional groups attached to the skeleton.

Chapter 50 AP Obj – Intro to Ecology

 

 

Chapter 50    Introduction to Ecology & the Biosphere
Objectives
The Scope of Ecology
1. Define ecology. Identify the two features of organisms studied by ecologists.
2. Describe the relationship between ecology and evolutionary biology.
3. Distinguish between abiotic and biotic components of the environment.
4. Distinguish among organismal ecology, population ecology, community ecology, ecosystem ecology, and landscape ecology.
5. Clarify the difference between ecology and environmentalism.
Interactions Between Organisms and the Environment Affect the Distribution of Species
6. Define biogeography.
7. Describe the questions that might be asked in a study addressing the limits of the geographic distribution of a particular species.
8. Describe the problems caused by introduced species and illustrate with a specific example.
9. Explain how habitat selection may limit distribution of a species within its range of suitable habitats.
10. Describe, with examples, how biotic and abiotic factors may affect the distribution of organisms.
11. List the four abiotic factors that are the most important components of climate.
12. Distinguish between macroclimate and microclimate patterns.
13. Provide an example of a microclimate.
14. Explain, with examples, how a body of water and a mountain range might affect regional climatic conditions.
15. Describe how an ecologist might predict the effect of global warming on distribution of a tree species.
16. Name three ways in which marine biomes affect the biosphere.
Aquatic and Terrestrial Biomes
17. Describe the characteristics of the major aquatic biomes: lakes, wetlands, streams, rivers, estuaries, intertidal biomes, oceanic pelagic biomes, coral reefs, and marine benthic biomes.
18. Define the following characteristics of lakes: seasonal turnover, thermal stratification, thermocline, photic zone.
19. Explain why the following statement is false: “All communities on Earth are based on primary producers that capture light energy by photosynthesis.”
20. Describe the characteristics of the major terrestrial biomes: tropical forest, desert, savanna, chaparral, temperate grassland, coniferous forest, temperate broadleaf forest, and tundra.
21. Give an example of a biome characterized by periodic disturbance.
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