AP Bio Nickel OKM

Unit 1 -Chemistry of Life

Deadline: ____________________________________________

To Do Checklist:

1. Reading Guides Chapter 1-5 (page 1-15) ______

2. Bozeman Biology Videos (page 16) ______

3. Prezis ______

AP Bio- Introductory Presentation on Prezi

AP Bio- Chemistry 1: Atoms, Water, & Carbon on Prezi (3 days)

AP Bio- Chemistry 2: Macromolecules on Prezi (2 days)

4. Labs/Activities ______a) Properties of Water Stations (page 17-18)b) Paper Moleculesb) Pipe Cleaner Proteins (page 19-21)

5. Vocab (page 22-24) ______

6. Review – Macromolecules Table (page 25-26) ______

7. Student Objectives (page 27-28) ______

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AP Bio Nickel OKM

Chapter 1Introduction: Themes in the Study of Life

1. Why do Biology courses build their content around themes and major concepts?

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2. List each major theme and briefly describe.

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g. _____________________________________________________________________

3. List and briefly describe the properties of life.

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b. ____________________________________________________________________

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d. _____________________________________________________________________

e. _____________________________________________________________________

f. _____________________________________________________________________

g. _____________________________________________________________________

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AP Bio Nickel OKM4. What is the primary model for regulation?

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5. List and give an example of the three domains.

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6. How does biology account for the unity and diversity of life?

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7. What is meant by the statement that science is a process?

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AP Bio Nickel OKMChapter 2 Guided Reading – REVIEW!!!!!!!!!!!!!

This chapter is a review of basic chemistry – we will be going through this chapter very quickly. 1. Contrast the term element with compound.

2. Label the diagram below and define the terms that you label.

3. Contrast the terms atomic mass and atomic number.

4. What is the difference between the terms atomic mass and atomic weight?

5. What is an isotope and what is “special” about radioactive isotopes?

6. Explain how radioactive tracers are used in science?

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AP Bio Nickel OKM7. Explain how the movement of electrons relates to the concept of potential energy – use the diagram

below to help answer the question.

8. What determines interactions between atoms? Why are valence electrons important?

9. Define the following terms:a. Chemical bond

b. Covalent bond

c. Single bond

d. Double bond

e. Valence

f. Electronegativity

g. Nonpolar covalent bond

h. Polar covalent bond

10. What is the difference between a structural and molecular formula?

11. How do ionic bonds compare with covalent bonds?

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AP Bio Nickel OKM12. Compare and contrast hydrogen bonds and van der Waals interactions.

13. Based on the reading, what is an example, in a living system, of how molecular shape is critical?

14. Define a dynamic chemical equilibrium in terms of quantities of reactants and products.

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AP Bio Nickel OKMChapter 3 Guided Reading

1. Why is water considered a polar molecule?

2. For each of the below listed properties of water – briefly define the property and then explain how water’s polar nature and polar covalent bonds contribute to the water special property. Include an example in nature of each property also.a. Cohesion

b. Adhesion

c. Surface tension

d. High specific heat

e. Heat of vaporization

f. Evaporative cooling

3. What is special about water and density?

4. Define the following terms:a. Solute

b. Solvent

c. Aqueous solution

d. Hydrophilic

e. Hydrophobic

f. Colloid

g. Hydration shell

h. Molarity

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AP Bio Nickel OKM5. Label the diagram below to demonstrate the dissociation of the water molecule and then relate this

diagram to pH.

6. What defines an acid and a base?

7. Why are “apparently” small changes in pH so important in biology?

8. What is acid precipitation and why is it important to living organisms?

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AP Bio Nickel OKMChapter 4 Guided Reading

1. Why is organic chemistry so important in the study of biology?

2. Why was the Urey-Miller experiment so important?

3. What is special about carbon that makes it the central atom in the chemistry of life?

4. Use the diagram below to label and contrast the three types of isomers.

5. Create a table below: after each functional group – draw the structure, name the compound, write and example and note the functional properties – (doesn’t this look like great quiz material?)

a. Hydroxyl

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AP Bio Nickel OKM

b. Carbonyl aldehyde

c. Carbonyl ketone

d. Carboxyl

e. Amino

f. Sulfhydryl

g. Phosphate

Chapter 5 Guided Reading

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1. Label the diagram below – identify a monomer, polymer, condensation reaction, and hydrolysis.

2. What are the three hexose monosaccharides?

3. What is a glycosidic linkage?

4. Compare and contrast the two storage polysaccharides.

5. Compare and contrast the two structural polysaccharides.

6. Why are lipids grouped together?

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7. What are the building blocks of fats?

8. Contrast saturated and unsaturated fats – how does this relate to the concept that structure and function are linked?

9. Label and identify the molecule below.

10. How would you recognize a basic steroid molecule?

11. List the eight types of proteins and their basic function.

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AP Bio Nickel OKM12. What are the names for the monomers and polymers of proteins?

13. Label the diagram below concerning the catalytic cycle of an enzyme -

14. Draw two amino acids – note the amino group, the carboxyl group and the alpha carbon, circle the water molecule to be removed and then note the peptide bond formed when the two are joined.

15. Explain the four levels of protein structure – a. Primary

b. Secondary

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AP Bio Nickel OKMc. Tertiary

d. Quaternary

16. How does the characteristics of an amino acid – nonpolar, polar, acidic or basic relate to the issue of tertiary and quaternary structure?

17. What does denaturation mean and why is it important?

18. What are chaperonins and what is their role in protein structure?

19. What are the roles of nucleic acids?

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AP Bio Nickel OKM20. Label the blank diagram below:

21. What is meant by the term that DNA is anti-parallel?

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AP Bio Nickel OKMBozeman Biology Videos Chapter 1 Biology - 4 key Ideas Three Domains of Life

Chapter 2 Chemistry Background For Biology (good refresh if you are weak in Chemistry)This lesson reviews chemistry concepts that are necessary for the study of biology. You will get an overview of atoms and isotopes, electron energy levels, and chemical bonds.

Chapter 3 - Water A Polar Molecule Mr. Andersen explains why water is a polar molecule. He also explains why this gives water properties like cohesion, high specific heat, less dense ice, and the ability to act as a solvent. All of these properties are due to hydrogen bonding.

Chapter 5 042 - Biological Molecules

Paul Andersen describes the four major biological molecules found in living things. He begins with a brief discussion of polymerization. Dehydration synthesis is used to connect monomers into polymers and hydrolysis breaks them down again. The major characteristics of nucleic acids are described as well as their directionality from 3' to 5' end. Protein structure is describes as well as the structure of its monomers; amino acids. The carboxyl and amino ends of a protein are described. The major groups of lipids are included with a brief discussion of saturated, unsaturated and trans-fats. Finally carbohydrates and their sugar monomers are discussed.

Properties of Water Lab

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AP Bio Nickel OKMProceduresStation #1: Freeze!

1. Observe the differences between a can of soda that was frozen, and a can of soda that remained at room temperature

Station #2: Dish-and-ClipsMaterials: paper clip, petri dish, tweezers, water in a beaker, paper towels

1. After drying off the paperclip with a paper towel, use the tweezers to gently set the paperclip onto the surface of the water.

2. When finished, refill the dish if necessary; place the paper clip on the paper towel to dry.

Station #3: Stir It UpMaterials: stirring rod, graduated cylinder, water in a beaker

1. Pour water from the beaker along the stirring rod and down into the graduated cylinder2. Pour the water back into the beaker

Station #4: Sink or SwimMaterials: tongs, ice cubes (d=0.917 g/mL), beaker of water, beaker of ethanol (d=0.789 g/mL)CAUTION: ETHANOL IS HIGHLY POISONOUS! DO NOT DRINK

1. Using tongs, place an ice cube in each beaker2. When finished, leave materials as you found them. If more ice cubes are needed notify your

teacher

Station #5: Stop on a DimeMaterials: dropper, dime, beaker of water

1. Make a prediction of how many drops of water will "fit" on the dime before it spills over the edge

2. Counting drops as you go, use the dropper to carefully add drops of water to the top of the dime.

3. Continue to add drops until water spills over the edge. Record the total number of drops.

Station #6: Much Color-ado About NothingMaterials: food coloring, 2 test tubes, 2 10mL graduated cylinders, water in a beaker, oil in a beaker

1. Measure and add 5mL of water to one test tube and 5mL of oil to the other test tube.2. Add 2-3 drops of food coloring to each test tube. Do not shake the test tubes. 3. When finished, pour the test tube with water and food coloring down the sink, and pour the

test tube with oil and food coloring into the garbage can.

Station #7: To Wax Philosophic Materials: wax paper, dropper, water in beaker

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AP Bio Nickel OKM1. Using the dropper, form a small puddle (about the size of a dim) on the wax paper2. Place the tip of the dropper in the center of the puddle and slowly drag the tip of the dropper

around the wax paper.3. When finished, dump the water back into the beaker.

Station #8: Anit-GravityMaterials: paper towel, shallow dish of water, stapler

1. Fold a paper towel in half, then roll it into a tube which has a diameter smaller than that of the dish.

2. Stand the rolled paper town in the dish and observe.

Station #9: Loony BallooneyMaterials: paper towels, balloon, water in buret, buret stand, beaker of water

1. Rub the balloon with the paper towel.2. Open the buret so a stream of water flows.3. Bring the balloon near (but not touching) the stream of water.4. When finished, refill the buret with water

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AP Bio Nickel OKM

Pipe-Cleaner ProteinsYour Instructions…

1. Work with a partner. One partner gets two long pieces of pipe cleaner from the teacher, and the other gets 8 felt pens. You’ll need the following 8 colours: red, yellow, brown, green, orange, blue, purple, pink. Each partner will colour one of the pipe cleaners.

2. Starting at one end of the pipe cleaner, colour a 2 cm segment with one of the colours of felt pen (choose any colour you like to start with). Then leave a 3 cm space and colour another 2 cm segment a different colour, then continue on in the same fashion down the whole length of the pipe cleaner. Again, the order of colours is up to you (don’t use the order listed in step 1 though), but only use each colour once. Make sure that the order you choose is NOT the same as your partners. Write out the order in the boxes below:

Strand 1

Strand 23. Once coloured from end to end, what you have represents a chain of amino acids. The coloured

segments represent the amino acids, and the uncoloured segments represent the bonds.a. In the box to the right, draw an amino acid

and label the groups on it.

b. How many kinds of R groups are there?

c. Draw a dipeptide, and colour the bond that forms between the two amino acids red.

d. What is the name of the bond that forms between two amino acids?

e. What type of bond is this, and what is special about it?

f. What do you call a chain of 8 amino acids?

g. The straight chain that you’ve just made represents what level of protein structure?

4. Wrap the pipecleaner around a pencil to form a spiral shape.a. Draw the shape in the box to the right

b. What is the name of this shape?

c. What causes it?

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AP Bio Nickel OKMd. What level of protein structure does it

represent?

5. Suppose that there is an attraction between the blue and the orange amino acids. Let’s also suppose that a “disulfide bridge” (a covalent bond that forms between sulfur atoms in “R” groups) forms between the red and green amino acid. Let’s further suppose that there is repulsion between the purple and yellow amino acids. Make your amino acid chain assume the shape that would seem the most logical, based on the information above.

a. What level of protein structure does the chain represent now?

b. Compare the shape of your protein chain to that of your partners, as well as that of two other people in the class. Are they the same? What is responsible for the difference?

c. Make a sketch of your chain in the box to the right.

6. Join your amino acid chain to the one that your partner made, in a way that makes sense based on the information given in step 5. Show your completed protein to your teacher.

a. What level of protein structure does this represent now?

b. Now that you have made your protein, what conclusions can you form about the effect of the primary structure on the shape of the protein?

c. Exactly what determines the function of a protein?

d. What does it mean to denature a protein?

e. List 3 ways that proteins can be denatured. 1

2

3

f. Summarize the functions of proteins in the table to the right.

Examples of Structural Functions

Metabolic Functions

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AP Bio Nickel OKM1 1

2 2

3 3

4

5

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Chapter 1BIOLOGYBIOSPHERECELLCOMMUNITYCONSUMER (HETEROTROPH)CONTROLLED EXPERIMENTDATADEDUCTIVE REASONINGDOMAIN ARCHAEADOMAIN BACTERIADOMAIN EUKARYAECOSYSTEMEMERGENT PROPERTIES

EUKARYOTIC CELLGENEGENOMEHYPOTHESISINDUCTIVE REASONINGKINGDOM ANIMALIAKINGDOM PLANTAEKINGDOM FUNGIMODELMOLECULENEGATIVE FEEDBACKORGAN

ORGAN SYSTEMORGANELLEORGANISMPOPULATIONPOSITIVE FEEDBACKPRODUCER (AUTOTROPH)PROKARYOTIC CELLREDUCTIONISMSYSTEMS BIOLOGYTECHNOLOGYTHEORYTISSUE

bio= life (biology: scientific study of life; biosphere: all the environments on Earth inhabited by life)eu= true (eukaryotic cell has a true nucleus ell= small (organelle: small, formed body with a specialized function found in the cytoplasm of eukaryotic cells)pro = before; karyo= nucleus (prokaryotic cell a cell that has no nucleus)

Chapter 2ANIONATOMATOMIC MASSATOMIC NUCLEUSATOMIC NUMBERCATIONCHEMICAL BONDCHEMICAL EQUILIBRIUMCHEMICAL REACTIONCOMPOUNDCOVALENT BONDCHEMICAL BONDCHEMICAL EQUILIBRIUMCHEMICAL REACTIONCOMPOUNDCOVALENT BONDDALTONDOUBLE BOND

ELECTRONELECTRON SHELLELECTRONEGATIVITYELEMENTENERGYENERGY LEVELHYDROGEN BONDIONIONIC BONDIONIC COMPOUNDISOTOPEMASS NUMBERMATTERMOLECULAR FORMULAMOLECULENEUTRONNONPOLAR COVALENT BOND

ORBITALPERIODIC TABLE OF THE ELEMENTSPOLAR COVALENT BONDPOTENTIAL ENERGYPRODUCTPROTONRADIOACTIVE ISOTOPEREACTANTSALTSINGLE BONDSTRUCTURAL FORMULATRACE ELEMENTVALENCEVALENCE ELECTRONVALENCE SHELLVan der Waals INTERACTIONS

co- = together; -valent = strength (covalent bond: an attraction between atoms that share one or more pairs of outer-shell electronselectro- = electricity (electronegativity: the tendency for an atom to pull electrons toward itselfiso- = equal (isotope: an element having the same number of protons and electrons but a different number of neutrons)neutr- = neither (neutron: a subatomic particle with a neutral electric charge

Chapter 3ACIDADHESIONAQUEOUS SOLUTIONBASEBUFFERCalorie (cal)Calorie (kcal)

HEATHEAT OF VAPORIZATIONHYDRATION SHELLHYDROGEN IONHYDROPHILICHYDROPHOBICHYDROXIDE ION

MOLE (mol)MOLECULAR MASSpHPOLAR MOLECULESOLUTESOLUTIONSOLVENT

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AP Bio Nickel OKMCELSIUS SCALECOHESIONCOLLOIDEVAPORATIVE COOLING

JOULEKILOCALORIE (kcal)KINETIC ENERGYMOLARITY

SPECIFIC HEATSURFACE TENSIONTEMPERATURE

hydro- = water; -philos = loving; -phobos = fearing (hydrophilic: having an affinity for water: hydrophobic: having an aversion to water)kilo = a thousand (kilocalorie: a thousand calories)

Chapter 4ADENOSINE TRIPHOSPHATE (ATP)AMINO GROUPCARBONYL GROUPCARBOXYL GROUP

ENANTIOMERFUNCTION GROUPGEOMETRIC ISOMERHYDROCARBONHYDROXYL GROUP

ISOMERORGANIC CHEMISTRYPHOSPHATE GROUPSTRUCTURAL ISOMERSULFHYDRYL GROUP

carb- = coal; (carboxyl group: a functional group present in organic acids, consisting of a carbon atom double-bonded to an oxygen atom and a hydroxyl group

enanti- = opposite (enantiomer: molecules that are mirror images of each other)iso- = equal (isomer: one of several organic compounds with the same molecular formula, but different structures and, therefore, different properties)sulf- = sulfur (sulfhydryl group: a functional group that consists of a sulfur bonded to an atom of hydrogenthio- = sulfur (thiol: organic compounds containing sulfhydryl groups)

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Chapter 5ALPHA (α) HELIXAMINO ACIDANTIPARALLELBETA (ß) PLEATED SHEETCARBOHYDRATECATALYSTCELLULOSECHAPERONINCHITINCHOLESTEROLCONDENSATION REACTIONDEHYDRATION REACTIONDEOXYRIBONUCLEIC ACID(DNA)DEOXYRIBOSEDISACCHARIDEDISULFIDE BRIDGEDOUBLE HELIX

ENZYMEFATFATTY ACIDGENEGLYCOGENGLYCOSIDIC LINKAGEHYDROLYSISHYDROPHOBIC INTERACTIONLIPIDMACROMOLECULEMONOMERMONOSACCHARIDENUCLEIC ACIDNUCLEOTIDEPEPTIDE BONDPHOSPHOLIPIDPOLYMERPOLYNUCLEOTIDE

POLYPEPTICEPOLYSACCHARIDEPRIMARY STRUCTUREPROTEINPURINEPYRIMIDINEQUATERNARY STRUCTURERIBONUCLEIC ACID (RNA)RIBOSESATURATED FATTY ACIDSECONDARY STRUCTURESTARCHSTEROIDTERTIARY STRUCTURETRIACYLGLYCEROLUNSATURATED FATTY ACIDX-RAY CRYSTALLOGRAPHY

di- = two (disaccharide: two monosaccharides joined together

glycol- = sweet (glycogen: a polysaccharide sugar used to store energy in animals

hydro- = water; lyse- = break (hydrolysis: breaking chemical bonds by adding water)

macro- = large (macromolecule: a large molecule)

meros- = part (polymer: chain made from smaller organic molecules)

mono- = single; sacchar = sugar (monosaccharide: simplest type of sugar)

poly- = many (polysaccharide: many monosaccharides joined together)

tri- = three (triacylglycerol: three fatty acids linked to one glycerol molecule)

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AP Bio Nickel OKM

The Principal Biological Molecules

Group Name Main Elements Subunit Examples Location Function

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AP Bio Nickel OKM

Bio 12 – The Principal Biological Molecules

Group Name Main Elements Subunit Examples Location Function

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Biochemistry Student Objectives

Enduring understanding 2.A: Growth, reproduction and maintenance of the organization of living systems require free energy and matter.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.3. Phosphorus moves from the environment to organisms where it is used in nucleic acids and certain lipids.student objectives:  4. Living systems depend on properties of water that result from its polarity and hydrogen bonding.To demonstrate understanding of this concept, be able to explain water’s:

Cohesion Adhesion High specific heat capacity Universal solvent supports reactions Heat of vaporization Heat of fusion thermal conductivity

Student objectives: why is matter necessary for biological systems? explain the uses of carbon, hydrogen, oxygen, nitrogen, phosphorous and sulfur in biological systems. Diagram the exchange of matter between organisms and the environment. what function does nitrogen serve in proteins?  In nucleic acids? what function does phosphorus serve in nucleic acids?  In phospholipids? Why do biological systems need water? How does the structure of a water molecule relate to its function(s)? How does the polarity of water lead to the emergence of unique properties in liquid water?

Enduring understanding 4.A: Interactions within biological systems lead to complex properties.Essential knowledge 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.Evidence of student learning is a demonstrated understanding of each of the following:

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. 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. 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.

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AP Bio Nickel OKM

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.

b. Directionality influences structure and function of the polymer.Evidence of student learning is a demonstrated understanding of each of the following:

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 (NH2) 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.

Student objectives: Compare the synthesis and decomposition of biological macromolecules. Where does the energy needed to drive the synthesis of biological macromolecules come from? How does the structure of <polysaccharides, proteins, nucleic acids> influence the function of those

molecules? How does the structure of DNA contribute to it’s roles in protein synthesis and heritability? Why is DNA a good molecule for information storage? How do the differences in the structure of DNA and RNA contribute to the difference in the functions of

those molecules? Explain how the sequence of amino acids in a protein determines each level of that protein’s structure. Explain how the conditions of the environment that a protein is in affect the structure and function of that

protein. Explain how the structure of lipids determines the polarity of the molecule. If the chemistry of water occurs in aqueous solution, why are lipids useful in biological systems? Why is starch easily digested by animals, while cellulose isn’t? Explain how directionality influences structure and function of the following polymer:

1.  Nucleic acids2. Proteins3.  Carbohydrates

Learning Objectives: The student is able to explain the connection between the sequence and the subcomponents of a biological

polymer and its properties. 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. 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.

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