Chapter 3: The Chemistry of Organic Molecules

Transcription

1 Chapter 3: The Chemistry of Organic Molecules AP Curriculum Alignment Chapter 3 merges components of all four of the Big Ideas that are found in the AP Biology Curriculum Framework. Biological interactions begin at the molecular level. Building upon the chemistry knowledge obtained in chapter 2, we now find that it organic chemistry molecules are the subcomponents of a biological polymers. These monomers determine properties of that polymer that provide cells with biochemical pathways that are part of a coordinated system that keeps cells alive, growing, and reproducing. Big Idea 1 explains that organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. The category of organic compounds known as nucleic acids can be found in all organisms and is evidence that supports the relatedness of all domains. The theory of natural origin of life on Earth begins with the organization of simple organic compounds that served as monomers for the complex polymers that formed the ability to replicate, store and transfer information. Big Idea 2 explains that this organization of organic molecules requires that all living systems have a constant input of free energy. The conversion of ATP to ADP is a favorable exergonic reaction can be used to maintain or increase order in a system by being coupled with reactions that have a positive free energy change. The ATP molecule is introduced in this chapter and free energy is detailed in Chapter 6. Details concerning enzymes and their functions are also included in Chapter 6. The elements that need to be obtained from the environment in order to build these essential organic compounds are outlined as part of Big Idea 2 but will also be addressed in Chapter 45 when the geochemical cycles are presented. Big Idea 3 is concerned with how the processing of genetic information is imperfect and is a source of genetic variation. The structure of DNA and RNA is explained in this chapter in order to lay the foundation for understanding how changes in the sequence of DNA can cause changes to proteins. These changes can lead to changes in a phenotype. The concepts outlined in Big Idea 4 explain how biological systems interact, and that these systems and their interactions possess complex properties. The parts of biological systems interact with each other and produce characteristics that are not found in the individual parts alone. Big Idea 4 directs student learning toward realizing that how the monomers of the four organic compounds are placed in the macromolecule determines how that molecule will function. These monomers are linked together via dehydration synthesis reactions and that changes in the sequence of these monomers affects their functionality. These four organic compounds that are found in all organisms are carbohydrates, lipids, proteins, and nucleic acids. Mader, Biology, 12 th Edition, Chapter 3 31

2 ALIGNMENT OF CONTENT TO THE CURRICULUM FRAMEWORK Big Idea 1: The process of evolution drives the diversity and unity of life. Enduring understanding (EU) 1.B: Organisms are linked by lines of descent from common ancestry. Essential knowledge (EK) 1.B.1: Organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. a. Structural and functional evidence supports the relatedness of all domains. 1. DNA and RNA are carriers of genetic information through transcription, translation and replication. 2. Major features of the genetic code are shared by all modern living systems. 3. Metabolic pathways are conserved across all currently recognized domains. Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, to reproduce and to maintain dynamic homeostasis. Enduring understanding (EU) 2.A: Growth, reproduction and maintenance of the organization of living systems require free energy and matter. Essential knowledge 2.A.1: All living systems require constant input of free energy. b. Living systems do not violate the second law of thermodynamics, which states that entropy increases over time. 3. Energetically favorable exergonic reactions, such as ATP ADP, that have a negative change in free energy can be used to maintain or increase order in a system by being coupled with reactions that have a positive free energy change. Essential knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization. a. Molecules and atoms from the environment are necessary to build new molecules. Evidence of student learning is a demonstrated understanding of each of the following: 1. Carbon moves from the environment to organisms where it is used to build carbohydrates, proteins, lipids or nucleic acids. Carbon is used in storage compounds and cell formation in all organisms. 2. Nitrogen moves from the environment to organisms where it is used in building proteins and nucleic acids. Phosphorus moves from the environment to organisms where it is used in nucleic acids and certain lipids. Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes. Enduring understanding (EU) 3.A: Heritable information provides for continuity of life. Essential knowledge (EK) 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information. a. Genetic information is transmitted from one generation to the next through DNA or RNA. b. DNA and RNA molecules have structural similarities and differences that define function. 1. Both have three components sugar, phosphate and a nitrogenous base 32 Mader, Biology, 12 th Edition Chapter 3

3 which form nucleotide units that are connected by covalent bonds to form a linear molecule with 3' and 5' ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone. 2. The basic structural differences include: i. DNA contains deoxyribose (RNA contains ribose). ii. RNA contains uracil in lieu of thymine in DNA. iii. DNA is usually double stranded, RNA is usually single stranded. iv. The two DNA strands in double-stranded DNA are antiparallel in directionality. 3. Both DNA and RNA exhibit specific nucleotide base pairing that is conserved through evolution: adenine pairs with thymine or uracil (A-T or A-U) and cytosine pairs with guanine (C-G). i. Purines (G and A) have a double ring structure. ii. Pyrimidines (C, T and U) have a single ring structure. Enduring understanding (EU) 3.C: The processing of genetic information is imperfect and is a source of genetic variation. Essential knowledge (EK) 3.C.1: Changes in genotype can result in changes in phenotype. a. Alterations in a DNA sequence can lead to changes in the type or amount of the protein produced and the consequent phenotype. Big Idea 4: Biological systems interact, and these systems and their interactions possess complex properties. Enduring understanding (EU) 4.A: Interactions within biological systems lead to complex properties. Essential knowledge (EK) 4.A.1: The subcomponents of biological molecules and their sequence determine the properties of that molecule. a. Structure and function of polymers are derived from the way their monomers are assembled. 1. In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (adenine, thymine, guanine, cytosine or uracil). DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions. The molecular structure of specific nucleotides is beyond the scope of the course and the AP Exam. 2. In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. The R group of an amino acid can be categorized by chemical properties (hydrophobic, hydrophilic and ionic), and the interactions of these R groups determine structure and function of that region of the protein. The molecular structure of specific amino acids is beyond the scope of the course and the AP Exam. Mader, Biology, 12 th Edition, Chapter 3 33

4 3. In general, lipids are nonpolar; however, phospholipids exhibit structural properties, with polar regions that interact with other polar molecules such as water, and with nonpolar regions where differences in saturation determine the structure and function of lipids. The molecular structure of specific lipids is beyond the scope of the course and the AP Exam. 4. Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. Illustrative examples include: cellulose versus starch. The molecular structure of specific carbohydrate polymers is beyond the scope of the course and the AP Exam. b. Directionality influences structure and function of the polymer 1. Nucleic acids have ends, defined by the 3' and 5' carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs (from 5' to 3'). 2. Proteins have an amino (NH 2 ) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers. 3. The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate, which then determines the secondary structure of the carbohydrate. Enduring understanding (EU) 4.C: Naturally occurring diversity among and between components within biological systems affects interactions with the environment. Essential knowledge (EK) 4.C.1: Variation in molecular units provides cells with a wider range of functions. a. Variations within molecular classes provide cells and organisms with a wider range of functions. To foster student understanding of this concept, instructors can choose an illustrative example such as: Different types of phospholipids in cell membranes Different types of hemoglobin MHC proteins Chlorophylls Molecular diversity of antibodies in response to an antigen Concepts covered in Chapter 3 also align to the learning objectives that provide a foundation for the course, an inquiry-based laboratory experience, class activities, and AP exam questions. Each learning objective (LO) merges required content with one or more of the seven science practices (SP), and one activity or lab can encompass several learning objectives. 34 Mader, Biology, 12 th Edition Chapter 3

5 The learning objectives and science practices from the Curriculum Framework that pertain to organic chemistry are shown in the table below. Note that other learning objectives may apply as well. LO 1.16 The student is able to justify the scientific claim that organisms share many conserved core processes and features that evolved and are widely distributed among organisms today. SP 6.1 The student can justify claims with evidence. LO 2.8 The student is able to justify the selection of data regarding the types of molecules that an animal, plant or bacterium will take up as necessary building blocks and excrete as waste products. SP 4.1; [Essential knowledge 2.A.3] LO 4.1 The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. SP 7.1 The student can connect phenomena and models across spatial and temporal scales. LO 4.2 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. SP 1.3 The student can refine representations and models of natural or manmade phenomena and systems in the domain. LO 4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule. SP 6.1 The student can justify claims with evidence. SP 6.4 The student can make claims and predictions about natural phenomena based on scientific theories and models. Key Concepts Summary Building blocks of macromolecules All organisms contain four categories of carbon-based (organic) compounds: carbohydrates, lipids, proteins, and nucleic acids. These compounds are composed of the elements sulfur, phosphorus, oxygen, nitrogen, carbon, and hydrogen that can be remembered by the acronym SPONCH. Each polymer is formed from specific smaller compounds called monomers that are small building block units. The dehydration synthesis reaction in which a water molecule is removed occurs to join the building blocks together to form the large macromolecules (polymers). Hydrolysis reactions or the addition of a water molecule break apart the monomers. Mader, Biology, 12 th Edition, Chapter 3 35

6 Carbohydrates Carbohydrates are formed from the elements C, O, and H in a ratio of C n H 2n O n. o Monosaccharides are the monomers for carbohydrates. o Their main function is energy storage. Plants store glucose as starch. Animals store glucose as glycogen. o Carbohydrates can also be important structural molecules. Cellulose is the most abundant organic compound and is found in all plant cell walls. Chitin is another structural carbohydrate that is found in the exoskeleton of arthropods. Lipids Lipids are also formed from the elements C, O, and H Lipids are used for energy storage and store 2x the energy of carbohydrates Lipids can also be used for structure (cell membranes), signal molecules (steroids), and protection (wax) Proteins Proteins are formed from the elements C, H, O, N, and S Made up of monomers called amino acids, of which there are 20 Important proteins include enzymes, transport proteins like hemoglobin, membrane proteins, structure, defense, signal molecules The structure of a protein exists in four levels: o primary: amino acid sequence o secondary: hydrogen bonding between amino acids for alpha helices and beta pleated sheets o tertiary: attractions between the R groups, polar attractions, covalent bonds o quaternary structure: several polymers joined together through hydrogen bonding o If a protein s structure is altered too far it is said to be denatured and it loses its ability to function Nucleic acids Nucleic acids are formed from the elements C, H, O, N, P The monomer of nucleic acids is a nucleotide and each nucleotide has a sugar, a phosphate group and a nitrogen base The two types of nucleic acids are DNA and RNA They store and transmit hereditary information The differences in DNA and RNA structure are that DNA has deoxyribose and a sugar, is usually double stranded and contains the bases guanine, cytosine, thymine and adenine while RNA contains the sugar ribose, is mainly single stranded and contains the bases, guanine, cytosine, uracil, and adenine 36 Mader, Biology, 12 th Edition Chapter 3

7 Key Terms cellulose chitin dehydration synthesis reaction denature deoxyribose functional group glycogen hydrolysis reaction inorganic chemistry isomers monomer monosaccharide organic chemistry organic molecules polymers ribose starch Teaching Strategies Most students have never taken an organic chemistry course but have probably been introduced to organic compounds in their first biology class. The focus for AP Biology is really to be able to predict which elements are cycled from the environment into the four categories of organic compounds that all organisms contain. AP Biology also wants student to be able to predict what would be the result in function of a change to one of these molecules and to understand what factors can cause changes in the molecules. Basic information about these organic compounds will enable students to be able to recognize and predict functionality in changes molecules. There is an app called MacroMole that students can download for free. It provides information about the four categories of organic compounds and their monomers. Students may enjoy having this study aid of their phone. Class Time: 5 days with 45 minute classes each day Day 1: Lecture on the nature of the four organic compounds found in all organisms (25 minutes). Macromolecules activity outlined below (20 minutes). Have students share their rules for identifying these macromolecules. Day 2: Lecture on dehydration synthesis and hydrolysis. (15 minutes). Demonstration for dehydration synthesis reaction and hydrolysis. (10 minutes). Students write an explanation and evaluation of the demonstration (20 minutes). Day 3: Students build proteins and fold the proteins in to shape by determining the interactions of the amino acids that they chose Day 4 and Day 5: Students conduct an inquiry enzyme lab and discuss their results. See College Board AP Lab Manual: Investigation 13: Enzyme Investigation. You do not have to complete this particular lab but a similar enzyme lab that provides an opportunity for students to conduct an open inquiry style of investigation should be conducted. Mader, Biology, 12 th Edition, Chapter 3 37

8 Suggested Approaches I have provided the activities that provide hands on learning experiences for you students. This approach facilitates the internalization of the organic chemistry concepts. In addition, the command terms from the learning objectives and science practices have be utilized by your students. The suggested daily activities provide a daily concept lecture followed by an activity. This should dispel a common student misconception that organic molecules are versatile enough that they can switch functions so that if one organic compound is destroyed, then another category of organic compound can take its place. Suggested Activities Attached are worksheets and directions for the following activities: 1. Macromolecule activity: students will fill out a table with the identifying features and characteristics of the four classes of macromolecules. 2. Dehydration/hydration reaction demonstration: students will participate in a teacher-led demonstration of how dehydration and hydration reactions work in proteins. 3. Protein folding activity: students will model how amino acid groups influence protein folding. Several variations of the activity are included. 38 Mader, Biology, 12 th Edition Chapter 3

9 Macromolecules Chart Macromolecule Elements Monomer Structure (describe and draw) Carbohydrate Develop a rule for recognizing carbohydrates: Protein Develop a rule for recognizing proteins: Lipid Function Examples (These are simple or complex carbohydrates) - Lactose - Sucrose - Starch (plants) - Glycogen (animals) - Cellulose (plants) - Enzymes - Antibodies - Hemoglobin - Actin and myosin - Collagen - Keratin - Oils - Fats - Steroids - Wax Develop a rule for recognizing lipids: Nucleic Acid Develop a rule for recognizing nucleic acids: Two types: - Deoxyribonuc leic Acid (DNA) - Ribonucleic Acid (RNA) Mader, Biology, 12 th Edition, Chapter 3 39

10 Dehydration Synthesis Reaction Demonstration I use several cut up sponges and generously wet them. Students form a circle around the room. Every student receives a wet sponge which they hold in their right hand. Each student represents a monomer. They are told to join hands to form a strong covalent bond with each student beside them. When they squeeze each other s hands to form the bond, water drips on the floor which symbolizes the dehydration synthesis reaction. While they are still holding hands, I toss a small amount of water at the students and the drop their held hands in order to avoid getting wet. This symbolizes the hydrolysis reaction. I ask each of them to write an explanation of how this simulation is like the actual dehydration synthesis and hydrolysis reactions. I ask each student to write an evaluation of how this simulation is different from the actual dehydration synthesis and hydrolysis reaction. In addition to learning about the reactions, the writing provides students with practice using two of the command terms that are frequently found in the Learning Objectives and Science Practices. Protein construction (from the Center for BioMolecular Modeling) The purpose of this activity is to explore the forces that drive protein folding with 15 tacks and a 4 foot toober or pipe cleaner. The color-coded tacks represent the sidechains of the following amino acids. Tack color Tack number Symbolizing: Blue 2 basic amino acids (+ charge) Red 2 acidic amino acids (- charge) Yellow 6 hydrophobic amino acids White 3 polar amino acids Green 2 cysteine amino acids Instructions 1. Distribute the 15 tacks randomly but evenly along the toober. By doing this, the tacked toober represents a protein made of 15 amino acids. 2. Instruct students to fold their protein, following the laws of chemistry that drive protein folding. 40 Mader, Biology, 12 th Edition Chapter 3

11 Basic Laws of Chemistry that Drive Protein Folding Stably folded proteins simultaneously satisfy several basic laws of chemistry including: 1. Hydrophobic sidechains (yellow tacks) will be buried on the inside of the globular protein, where they are hidden from polar water molecules. 2. Charged sidechains (blue and red tacks) will be on the surface of proteins where they often neutralize each other and form salt bridges. 3. Polar sidechains (white tacks) will be on the surface of the protein where they can hydrogen bond with water. 4. Cysteine sidechains (green tacks) often interact with each other to form covalent disulfide bonds that stabilize protein structure. Teaching Tips Students should have no trouble folding their toober so that all of the yellow, hydrophobic tacks are clustered together in the central core of the folded structure. However, it may be difficult to maintain this structure while simultaneously: pairing up blue and red tacks (positive and negative charges that neutralize each other) and pairing up green tacks that form disulfide bonds, and keeping all of the polar white tacks on the surface of the protein. After everyone has folded their toober, the teacher can point out: Every toober had a different random sequence of tacks (amino acids) and therefore each toober (protein) folded into a different structure. Some sequences of tacks were more easily folded into a reasonable structure than others. In fact, the 30,000 proteins encoded by the human genome have been selected from an enormous number of possible amino acid sequences based on their ability to spontaneously fold into a stable structure that simultaneously satisfies these basic laws of chemistry. Pipe cleaners can be used instead of Toobers or you can order Toobers from or call (414) Mader, Biology, 12 th Edition, Chapter 3 41

12 Variations There are many variations to the basic Toober folding exercise. Each one can be used to emphasize a different point related to molecular structure. Examples of variations are described below. Reversible Denaturation Many proteins undergo reversible denaturation, by re-folding into their original shape (native structure) following their complete unfolding (denaturation) by heating. 1. Have students document the native shape of their folded protein with a digital photo. 2. Ask the students to unfold their protein and then re-fold it. 3. Check the refolded protein against the photo of the native structure. Reverse Engineering Some students will randomly generate a sequence of tacks that is very difficult to fold into a shape that simultaneously satisfies all 3 (or 4) laws of chemistry. This is a good teaching moment in that the teacher can use these examples to emphasize that such proteins would not be selected from the enormous pool of possible protein sequences. How can students arrive at a perfectly optimized sequence of tacks that have been selected over evolutionary time to always fold into the same globular shape? ANSWER: By reverse engineering the sequence. 1. Have each group of students fold their toober into a compact globular shape without any tacks. 2. Have each group of students then add the tacks to the pre-folded toober, positioning them such that all of the laws of chemistry are satisfied in the folded structure. 3. Unfold the toober and document the sequence of tacks. 4. Have the students then re-fold the sequence into the original shape (see reversible denaturation, above). The Effect of Mutations Some mutations inactivate a protein by destabilizing its native shape. 1. Starting with the reverse engineered sequence of tacks as described above, mutate one of the hydrophobic amino acids (yellow tack) to a positively charged amino acid (blue tack). 2. Can the students fold this mutated sequence back into its native shape? 42 Mader, Biology, 12 th Edition Chapter 3

13 Student Edition Chapter Review Answers Answers to Assess Questions 1. d; 2. c; 3. a; 4. c; 5. c; 6. b; 7. b; 8. d; 9. d; 10. c; 11. d; 12. a; 13. b; 14. c; 15. d Answers to Applying the Big Ideas 1. Molecules evolve from simple to complex, with building block monomers often joining to form polymers with the ability to replicate, store, and transfer information. a) Describe TWO specific subcomponents that define nucleic acids. b) Explain how each of the subcomponents you described in part (a) contributes to the functionality of the polymer to replicate, store, and transfer information. Essential Knowledge Science Practice Learning Objective 1.D.1: There are several hypotheses about the natural origin of life on Earth, each with supporting scientific evidence. 1.2: The student can describe representations and models of natural or man-made phenomena and systems in the domain. 1.27: The student is able to describe a scientific hypothesis about the origin of life on Earth. 4 points maximum. Description of the appropriate subcomponent and the appropriately linked explanation of its connection to function of the polymer may include: Descriptions of monomer (1 point each) Nitrogen-containing base (specifically adenine, guanine, thymine and cytosine for DNA, and adenine, guanine, cytosine and uracil for RNA) those with single rings are pyrimidines (C, T, U); those with double rings are purines (A, G). Explanations of polymer function (1 point each) Bases raise the ph of a solution (making it more basic). A change in nucleic acid sequence (depending on order of purines and pyrimidines) often alters amino acid sequence, which may alter the structure and function of the protein produced, leading to a change within a species that is subject to natural selection. Mader, Biology, 12 th Edition, Chapter 3 43

14 It may be noted that if there is a mistake or change in the sequence of nitrogenous bases, this may alter the sequence of amino acids during translation, which may alter the folding and therefore function of a protein (making it not function as expected or needed). Phosphate molecule binds with the pentose sugar to form the backbone of the nucleic acid. Phosphate molecules are polar and acidic. According to the type of pentose sugar molecule, nitrogenous base and the number of phosphate groups, nucleotides differ. Nucleotides are joined into the polymer by a series of dehydration reactions. The resulting linear strand have a backbone with bases projecting to one side. This allows access to the bases by proteins that work in replication, transcription and translation. And the sugar-phosphate backbone helps to determine the shape of the molecule. While they may differ, nucleic acids seem to form the building blocks of all of life on Earth. Nucleotides are not only monomers of nucleic acids. They can also function as coenzymes or ATP. 2. Free energy from the sun and carbon from the environment contribute to the production of carbohydrates, essential polymers for fueling cells, as well as providing storage and structure. a) Describe TWO specific subcomponents that define carbohydrates. b) Explain how each of the subcomponents you described in part (a) contributes to the functionality of the polymer. Essential Knowledge Science Practice Learning Objective 2.A.2: Organisms capture and store free energy for use in biological processes. 6.2: The student can construct explanations of phenomena based on evidence produced through scientific practices. 2.5: The student is able to construct explanations of the mechanisms and structural features of cells that allow organisms to capture, store or use free energy. 44 Mader, Biology, 12 th Edition Chapter 3

15 4 points maximum. Description of the appropriate subcomponent and the appropriately linked explanation of its connection to function of polymers may include: Descriptions of subcomponents (1 point each) Carbohydrates are made up of carbon skeletons that form carbon rings in aqueous solutions. Sugar monomers contain carbonyl (C=O) and hydroxyl (-OH) groups. Location/position of hydroxyl groups is specific to each type of carbohydrate Explanations (1 point each) Hydrolyzing of the linkages in polysaccharides allows a sugar to be freed as needed for use by the cell. The carbon skeleton can be used by the cell in the synthesis of other biological molecules, such as amino acids. Sugar monomers can bond with each other (glycosidic linkage) by dehydration synthesis that occurs between two hydroxyl groups. Bonding allows for the building of polysaccharides. Hydrolyzing allows a sugar to be freed as needed for use by the cell. Positioning of hydroxyl groups affects the glycosidic linkage that occurs between monomers, which can mean the difference between function. For example, starch and cellulose are composed of the exact same atoms, but one hydroxyl group is flipped. This results in similar orientation of all components in a polymer of starch, but alternating orientation for those in cellulose. Starch is used for storage while cellulose provides structure. 3. One particular inherited blood disorder is caused by the substitution of valine (an amino acid with a nonpolar, hydrophobic side chain) for glutamic acid (an amino acid with a negatively-charged, hydrophilic side chain). a) Predict how this substitution impacts the structure and function of the globular proteins found in the blood of patients with this disorder. b) Explain why your predictions for part (a) are justified. Mader, Biology, 12 th Edition, Chapter 3 45

16 Essential Knowledge Science Practice Learning Objective 3.A.1: DNA, and in some cases RNA, is the primary source of heritable information. 6.4: The student can make claims and predictions about natural phenomena based on scientific theories and models. 3.6: The student can predict how a change in a specific DNA or RNA sequence can result in changes in gene expression. 4 points maximum. Description of predictions and corresponding justifications may include: Predictions (1 point each) Same length of chain with substitution, so secondary structure may not be affected. Substituting a hydrophobic side chain for a hydrophobic one might cause misfolding and exposing a hydrophobic region. It may no longer aggregate with other molecules due to new tertiary structure, or it might aggregate in a different formation. May no longer be able to perform its function as before, such as interacting with other molecules. Explanations (1 point each) The R group of an amino acid can be categorized by chemical properties (hydrophobic, hydrophilic, and ionic). The order of amino acids (determined by DNA) constitutes the primary structure of the protein. The secondary structure of the protein is determined by the backbone of the polypeptide chain, not the R groups. The interactions of these R groups, including hydrogen and ionic bonds, disulfide bridges, and hydrophobic and van der Waals interactions, determine structure and function of that local region of the protein. The overall shape of the polypeptide is known as tertiary structure. Quaternary structure is the association of multiple polypeptides to form a functional protein. Changes in the earlier structures of the protein can cause expected aggregations to not occur, or cause unexpected aggregations of other types. In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall 46 Mader, Biology, 12 th Edition Chapter 3

17 shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. This is the case with sickle-cell disease. The β subunit of the tertiary structure is misfolded, creating sickle-cell hemoglobin, which still aggregates with the α subunit, but now interacts with other β subunits in a new way. The capacity to carry oxygen is greatly reduced and the deformed red blood cells can impede blood flow through small vessels. 4. The subcomponents of biological molecules and their sequence determine the properties of that molecule. Proteins, of primary importance to cells, carry out many diverse functions in cells. Their sequence is dictated by amino acids. a) Describe TWO specific subcomponents that define amino acids. a) Explain how each of the subcomponents you described in part (a) contributes to the properties of the amino acids and proteins. Essential Knowledge Science Practice Learning Objective 4.A.1: The subcomponents of biological molecules and their sequence determine properties of that molecule. 7.1: The student can connect phenomena and models across spatial and temporal scales. 4.1: The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties 4 points maximum. Description of the appropriate subcomponent of amino acids and the appropriately linked explanation of its connection to function may include: Descriptions of subcomponents (1 point each) Side chain specific to each amino acid ( R group ) there are about 20 different side chains, and therefore about 20 common amino acids Explanation of properties (1 point each) According to the R group, amino acids can be categorized as being polar (and hydrophilic) or nonpolar (and hydrophobic), positively or negatively charged, etc. Because cells are 70-90% Mader, Biology, 12 th Edition, Chapter 3 47

18 All are made up of atoms C, H, O, N and S. Amine group ( NH 2 ) polar, basic, form hydrogen bonds. Carboxylic acid ( COOH) polar and acidic A peptide consists of two amino acids joined by a peptide bond (dehydration synthesis) between the amine group and the carboxylic acid (see the two groups defined above). water, the location and number of different types of R groups (hydrophobic vs. hydrophilic) can determine the structure and therefore function of the protein in the cell. This functional group always has the same chemical properties and therefore always reacts in the same way, regardless of the carbon skeleton it is attached to. The configuration of functional groups determines the properties of the biomolecule. The configuration of functional groups determines the properties of the biomolecule. In a watery environment, carboxyl groups tend to ionize and release hydrogen atoms in solution. A polypeptide is a long chain of amino acids. A protein is a polypeptide that has been folded into a particular shape and has a particular function. Mutations in DNA sequence could lead to changes in amino acid sequences that may increase, decrease, or have no effect on a protein s shape and function. Answers to Applying the Science Practices Questions Think Critically 1. pectin: 50 percent decrease in men, 33 percent in women; guar gum: 75 percent decrease in men, 50 percent in women; psyllium: 50 percent decrease in men and women 2. Soluble fiber appears to lower cholesterol levels. 48 Mader, Biology, 12 th Edition Chapter 3

19 Additional Questions for AP Practice 1. The environment of an enzyme that normally functions in a ph 5 has changed drastically to a ph of 8. Predict what will happen to the functioning of this enzyme at ph 8 and draw a diagram to help justify your answer. 2. Justify the claim that the organic compounds carbohydrates, lipids, nucleic acids, and proteins, are evidence of evolution. 3. Describe how the monosaccharides are linked together to form starch. 4. Complete the chart below: 5. Predict which organic compound(s) would be affected if the phosphorus in the environment was no longer available. Mader, Biology, 12 th Edition, Chapter 3 49

20 Grid-In Question 1. A scientist had a test tube of carbohydrates, a test tube of amino acids, and a test tube of nucleotides but the labels had faded off. To figure out which one was which, the scientist numbered the test tubes 1, 2, and 3, and used NMR spectral analysis to identify the following types of molecules present in each tube. What is the number of the test tube that contains nucleotides? Test Tube Molecules present 1 C, H, O, N 2 C, H, O, P, N 3 C, H, O 50 Mader, Biology, 12 th Edition Chapter 3

21 Answers to Additional Questions for AP Practice 1. The prediction is that at ph of 8, the enzyme is denatured and cannot function. In order for an enzyme to have functionality, it needs to have its active site in a particular shape. When the ph changes, the interactions that make up the secondary structure, hydrogen bonds, no longer occur. Some of the interactions that make up the tertiary structure would also no longer occur. This causes a change in shape and therefore the substrate can no longer bind to the enzyme. Student drawing should show a change in the secondary and tertiary structure of the enzyme. 2. All organisms on Earth today contain these four organic compounds. This is strong evidence that all organisms had a common ancestor. 3. Enzymes place the simple sugars in the best position for a dehydration synthesis reaction to occur. The bond between an OH on one molecule and an H+ of the second monosaccharide are broken and replaced with a bond that hold the two monosaccharides together. A water molecule is formed. This reaction is called a dehydration synthesis reaction Without phosphorus, cells would not be able to produce new DNA or RNA. Cells would be dependent of their food sources for phosphorus and these resources would eventually run out. Mader, Biology, 12 th Edition, Chapter 3 51

22 Answers to Grid-In Question 1. Chapter: 3 The Chemistry of Organic Molecules Topic: Macromolecule identification Answer: 2 52 Mader, Biology, 12 th Edition Chapter 3