PowerPoint Presentation

Carbon & The Molecular Diversity of Life

Note this is the third portion of the Biochemistry Unit. It is quite possible that your students know a bit of this, so use it as you see fit. It would be very appropriate to have them view the companion screencast prior to and outside of class and spend time simply answering questions. A good deal of this information will be prior knowledge for the AP Biology exam. BUT, be sure to emphasize the points that are unique to AP Biology as pointed out throughout these speaker notes. 1Carbon: The Backbone of LifeLiving organisms consist mostly of carbon-based compoundsCarbon is unparalleled in its ability to form large, complex, and diverse moleculesProteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds2

Note this is the third portion of the Biochemistry Unit. It is quite possible that your students know a bit of this, so use it as you see fit. It would be very appropriate to have them view the companion screencast prior to and outside of class and spend time simply answering questions. A good deal of this information will be prior knowledge for the AP Biology exam. BUT, be sure to emphasize the points that are unique to AP Biology as pointed out throughout these speaker notes.

2Carbon: Organic ChemistryCarbon is important enough to have its own branch of chemistry called Organic chemistry Organic compounds range from simple molecules to colossal onesMost organic compounds contain hydrogen atoms in addition to carbon atoms with O, N and P among others thrown in from time to time.

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Remind students that while carbon has six total electrons, two of them are in the 1st Energy level, leaving the other 4 electrons in the 2nd Energy level which is the valence level, thus only these 4 valence electrons are capable of forming bonds. Also remind them that carbon forms covalent bonds. 3Carbon has 4 valence electrons, thus makes 4 bondsWith four valence electrons, carbon can form four covalent bonds with a variety of atoms

This ability makes large, complex molecules possible

In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape4

Most likely prior knowledge if your students have had a Chemistry I course.4No need to memorize these!5

No need to memorize, simply an illustration of how the shape of the molecule changes as additional CH2 subunits are added vs. losing a pair of Hs each time an additional C-C bond is added to form a double or triple bonds. 5Carbon Skeletons VaryCarbon chains form the skeletons of most organic moleculesCarbon chains vary in length and shape

Again, no need to memorize! Just know that carbon can make ringed compounds as well as linear chains.6IsomersIsomers are compounds with the same molecular formula but different structures, thus different properties.Structural isomers have different covalent arrangements of their atomsCis-trans isomers have the same covalent bonds but differ in spatial arrangementsEnantiomers are isomers that are mirror images of each other & rotate light differently7The dreaded and ever so confusing I words: ion, isotope and isomer. Make sure that students can articulate the differences! Ions can be monatomic or polyatomic, but either way they have gained (negative ion, anion) or lost an electron (positive ion, cation). Isotopes have a different number of neutrons, but the same number of protons and electronscarbon-12, carbon-13 and carbon-14 are excellent examples. Isomers have the same chemical formula (#s of Cs and Hs and Os, etc.) but a different arrangement of said parts, thus function differently. 7More detail than you need, but cool none the less! 8

Linear vs. branched arrangements of the carbon skeleton. Different shapes result in different functions or physical properties!8More detail than you need, but cool none the less! 9

No need to memorize, just interesting! A nice opportunity to reinforce that the prefix trans- means across as in transmembrane proteins . In this case, across (opposite sides of) the double bond. These two molecules will exhibit different properties.9More detail than you need, but cool none the less! 10

My personal favorite! Enantiomer literally means opposite form. Some curious student is bound to ask, Whats the deal with the L-isomer vs. the D-isomer. Well, this is more than you probably want to know, butAn aqueous solution of one form of an optical isomerrotates the plane of polarization of a beam of polarized light in a counterclockwise direction (levorotatory), vice-versa for the (+) (dextrorotatory) optical isomer. 10Functional GroupsA few chemical groups are key to the functioning of moleculesDistinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to itA number of characteristic groups can replace the hydrogens attached to skeletons of organic molecules

11While a student shouldnt memorize these functional groups, it is helpful if they recognize them. 11Functional groups are the components of organic molecules that are most commonly involved in chemical reactionsThe number and arrangement of functional groups give each molecule its unique properties

12Functional Groups

This is just an introduction. Emphasize that structure relates to function and with each subtle molecular change, the IMFs are affected, thus molecular function is affected. 12

STRUCTUREEXAMPLEAlcohols(Their specificnames usuallyend in -ol.)NAME OFCOMPOUNDFUNCTIONALPROPERTIES(may be written HO)EthanolIs polar as a resultof the electronsspending moretime near theelectronegativeoxygen atom.

Can form hydrogenbonds with watermolecules, helpingdissolve organiccompounds suchas sugars.

Hydroxyl13Students may be confused. OH- is known as the hydroxide ion in inorganic chemistry and signifies a base, which is all they know at this point. They may or may not know that the OH group attached to a carbon skeleton forms an alcohol. Emphasize the polarity of an alcohol which is exactly why alcohols are water soluble.

CarbonylSTRUCTUREEXAMPLEKetones if the carbonylgroup is within acarbon skeletonNAME OFCOMPOUNDFUNCTIONALPROPERTIESAldehydes if the carbonylgroup is at the end of thecarbon skeletonA ketone and analdehyde may bestructural isomerswith different properties,as is the case foracetone and propanal.AcetonePropanalKetone and aldehydegroups are also foundin sugars, giving riseto two major groupsof sugars: ketoses(containing ketonegroups) and aldoses(containing aldehydegroups).14Dont stress over the names aldehyde or ketone, but rather emphasize that moving the -C=O group, alters the properties and reactivity of the molecules.

CarboxylSTRUCTUREEXAMPLECarboxylic acids, or organicacidsNAME OFCOMPOUNDFUNCTIONALPROPERTIESAcetic acidActs as an acid; candonate an H+ because thecovalent bond betweenoxygen and hydrogen is sopolar:Found in cells in the ionizedform with a charge of 1 andcalled a carboxylate ion. NonionizedIonized15Ah, this has many, many names thanks to inorganic and organic chemists that cant get along! The carboxyl group terminology is in most biology books, as in carboxylic acids which well see again as we build amino acids. The acetyl group as it is often known in inorganic chemistry.

AminoAminesGlycineSTRUCTUREEXAMPLEActs as a base; canpick up an H+ from thesurrounding solution(water, in livingorganisms):NAME OFCOMPOUNDFUNCTIONALPROPERTIESFound in cells in theionized form with acharge of 1.NonionizedIonized16Students should already know that ammonia, the NH3 molecule is a weak inorganic base. Emphasize that this is the amine portion of amino acid fame.

SulfhydrylThiols (may bewritten HS)STRUCTUREEXAMPLETwo sulfhydryl groups canreact, forming a covalentbond. This cross-linkinghelps stabilize proteinstructure.NAME OFCOMPOUNDFUNCTIONALPROPERTIESCross-linking of cysteinesin hair proteins maintainsthe curliness or straightnessof hair. Straight hair can bepermanently curled byshaping it around curlersand then breaking andre-forming the cross-linkingbonds.Cysteine17Not one of the more popular throughout the course, but handy to know once we get to protein structure as it relates to the formation of disulfide bridges.

PhosphateSTRUCTUREEXAMPLENAME OFCOMPOUNDFUNCTIONALPROPERTIESOrganic phosphatesGlycerol phosphateContributes negativecharge to the moleculeof which it is a part(2 when at the end ofa molecule, as at left;1 when locatedinternally in a chain ofphosphates).Molecules containingphosphate groups havethe potential to reactwith water, releasingenergy.18Heres a biggie! Students should know the phosphate ion from Chemistry I. Furthermore they should already know it has a -3 charge. In ATP we have three of those -3 ions stacked next to each other which is a great deal of negative ion-negative ion repulsion!

MethylSTRUCTUREEXAMPLENAME OFCOMPOUNDFUNCTIONALPROPERTIESMethylated compounds5-Methyl cytidineAddition of a methyl groupto DNA, or to moleculesbound to DNA, affects theexpression of genes.Arrangement of methylgroups in male and femalesex hormones affects theirshape and function.19An easy one! They should know methane from Chemistry I, so simply remove an H atom to make the methyl functional group. Dont skip past the DNA + gene expression comment on this slide. Its important later in the course!One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups20ATP: An Important Source of Energy for Cellular Processes

They most likely know this molecules general structure from their Biology I course. Emphasize yet again that breaking a bond requires energy (as in removing one of those phosphates) while bond formation releases energy.20The versatility of carbon makes possible the great diversity of organic molecules

Variation at the molecular level lies at the foundation of all biological diversity21Final ThoughtsIts all about carbon! 21

The Structure and Function of Macromolecules: Carbohydrates, Lipids & Phospholipids

A fair amount of this material will be new to students. Although some of this material is not directly tied to the framework, it is still fundamental to the understanding of

Big Idea 2, EK 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 for nucleic acids. Carbon is used in storage compounds and cell formation in all organisms. 22The FOUR Classes of Large BiomoleculesAll living things are made up of four classes of large biological molecules: Carbohydrates LipidsProteinNucleic Acids

Macromolecules are large molecules composed of thousands of covalently bonded atoms

Molecular structure and function are inseparable

23This lesson will deal with carbohydrates and lipids, with protein and nucleic acids coming in a separate lesson. Emphasize yet again that within the molecule, the intramolecular forces are covalent bonds, but the intermolecular forces (IMFs) between molecules will vary due to the polarity of the molecule as a whole.23The FOUR Classes of Large BiomoleculesMacromolecules are polymers, built from monomers A polymer is a long molecule consisting of many similar building blocks These small building-block molecules are called monomersThree of the four classes of lifes organic molecules are polymersCarbohydratesProteinsNucleic acids

24Emphasize that monomers join through covalent bonding (a pair, or more, of electrons is shared between two monomers). Take a moment to assess what students already know. Can they cite examples of carbohydrates, proteins and nucleic acids. If so, try to use the examples they came up with during your discussions. 24The synthesis and breakdown of polymersA dehydration reaction occurs when two monomers bond together through the loss of a water moleculePolymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction

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Ask if students know what dehydration means in a colloquial sense. Athletes drink a lot of water to prevent dehydration. Water exits when a covalent bond is formed (synthesis), water enters when a covalent bond is broken (decomposition). Scroll over the image to reveal the play command for the animation. 25Dehydration Synthesis26

Emphasize the ends of the molecule, one end has an OH group, the other has an H. Each group leaves an electron attached to the monomer or polymer and those 2 electrons form a covalent bond while the H and OH form a water molecule. 26Hydrolysis27

Hydrolysis literally means (water splitting). A water molecule adds across a covalent bond and cleaves off one monomer at a time. Drink lots of water if your goal is to disassemble fats! 27Carbohydrates Serve as Fuel & Building MaterialCarbohydrates include sugars and the polymers of sugars

The simplest carbohydrates are monosaccharides, or single sugars

Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks

28Ask them to name some sugars they remember from Biology I. See if they can really show off and give you the chemical formula for glucose or sucrose (or any other disaccharide from glucose-type monomers). Glucose: C6H12O6, sucrose: C12H22O11. Whats missing from a simple doubling of the subscripts on glucose? 2 Hs and an O! Thats a water molecule! It was released during the dehydration synthesis when the two monomers (monosaccharide in this case) bonded to form a dimer (disaccharide in this case).28

Sugars: MonosaccharidesMonosaccharides have molecular formulas that are usually multiples of CH2O (carbo-hydrate)

Glucose (C6H12O6) is the most common monosaccharide

Monosaccharides are classified by The location of the carbonyl groupThe number of carbons in the carbon skeleton

29Emphasize they are carbo-hydrates as in carbon-water as is evidenced from the (CH2O)n general formula. It is not necessary to emphasize how they are classified. 29Sugars: DisaccharidesA disaccharide is formed when a dehydration reaction joins two monosaccharides

This covalent bond is called a glycosidic linkage

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Ask students how these hexagons differ from the one in the previous slide. Point out to them that it is customary to leave Cs and even Hs off the art in the interest of focusing on what is really important with regard to a given bond formation. It is not necessary they know glycosidic linkage, its just necessary that they know a water was released and helpful to know that an oxygen remains in tact. 30Synthesizing Maltose & Sucrose31

No need to memorize! Just reemphasizing mono+mono = di saccharide through a dehydration synthesis. 31PolysaccharidesPolysaccharides, more than two sugars linked, have storage and structural roles

The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

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Same dehydration synthesis song, second verse. Scroll over the image to reveal the play command for the animation.32Types of Polysaccharides: StorageStarch, a storage polysaccharide of plants, consists entirely of glucose monomersPlants store surplus starch as granules within chloroplasts and other plastids The simplest form of starch is amylose

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Emphasize the link between structure and function. It is not necessary to memorize the names of starches. 33Types of Polysaccharides: StorageGlycogen is a storage polysaccharide in animals (animal starch)Humans and other vertebrates store glycogen mainly in liver and muscle cells34

Glycogen may have been referred to as animal starch in their middle school or Biology I course. 34Types of Polysaccharides: StructuralThe polysaccharide cellulose is a major component of the tough wall of plant cells

Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

35While cellulose may not be all that exciting, it is interesting that termites cannot digest it until they establish a symbiotic relationship with a protozoan that can! To digest cellulose, organisms must produce the enzymecellulase. Humans and termites are unable to produce cellulase themselves but termites have living in their gut simple organisms (protozoaandbacteria) which can produce the enzyme.This is an example ofmutualism- a relationship between two species in which both organisms benefit. The protoza and bacteria benefit by receiving a constant supply of food (wood) from the termite. The termite benefits from the energy-rich sugar released from the cellulose by the termites. Read more:http://wiki.answers.com/Q/Why_termites_can_digest_cellulose_but_human_cannot#ixzz23pblQhQb35Such Elegance!36

Emphasize the structural hierarchy from monomer to polymer to cellulose to a grouping of cellulose into a microfibril to the structure of the cell wall to the plant cell to the leaf. Whew!36Polysaccharide Random Acts of BiologyCellulose in human food passes through the digestive tract as insoluble fiberSome microbes use enzymes to digest celluloseMany herbivores, from cows to termites, have symbiotic relationships with these microbes

Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods (crunch!)

Chitin also provides structural support for the cell walls of many fungi

37Just site these as common examples of organisms that utilize carbohydrates.37Lipids Are HydrophobicLipids are a diverse group of hydrophobic moleculesLipids are the one class of large biological molecules that do not form polymersThe unifying feature of lipids is having little or no affinity for water (water fearing)Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bondsThe most biologically important lipids are fats, phospholipids, and steroids

38Hydrophobic means water fearing. If youre up for a demo, you can use a couple of clear containers (beakers, etc.) partway filled with water to demonstrate that neither oil nor shortening, etc. will dissolve in water. Also, since this is the first time steroid has appeared, you may want to take a moment and discuss anabolic (building up) versus catabolic (tearing down) processes and that the sum of these processes is metabolism. Also point out that testosterone and estrogen are steroids. 38Fats: Start with a Simple Little Glycerol MoleculeFats are constructed from two types of smaller molecules: glycerol and fatty acidsGlycerol is a three-carbon alcohol with a hydroxyl group attached to each carbonA fatty acid consists of a carboxyl group attached to a long carbon skeleton

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Remind students that an OH group attached to a hydrocarbon skeleton makes an alcohol, NOT A BASE! 39Dehydration Rxn 1: Add a Fatty Acid Next, add a fatty acid through a dehydration synthesis reactionWhat makes it an acid? The C double bond O, single bond OH!

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Glycerol is on its way to make a triglyceride, which they may have heard talk of if anyone in their family is struggling with too many triglycerides in their diet. 40Dehydration Rxn 2!!Next, add a SECOND fatty acid through a dehydration synthesis reaction

Sorry, the picture is not pretty, but it does convey the idea. One more fatty acid to add before this becomes a triglyceride.41Dehydration Reaction THREE!!!How many water molecules will it take to disassemble this molecule?

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No need to memorize ester linkage. Ask students how many water molecules it will take to disassemble this molecule! Ans: THREE!42Saturated or Unsaturated? Fats made from saturated fatty acids are called saturated fats, and are solid at room temperatureMost animal fats are saturated (lard)Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds

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Ask students saturated with what, exactly? Saturated with Hs. These diagrams have the fatty acid molecules with all single bonds so the tails are fairly straight. 43Saturated or Unsaturated? 44Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room temperaturePlant fats and fish fats are usually unsaturatedUnsaturated fatty acids have one or more double bonds

Unsaturated means a PAIR of Hs is now missing thus a double bond forms between neighboring Cs in the carbon chain of the fatty acid. Note this causes a bend or kink in the chain which alters the shape or conformation of the fat. Ask students what they think polyunsaturated fat means. 44Fats: Major function is storage!The major function of fats is energy storageHumans and other mammals store their fat in adipose cellsAdipose tissue also cushions vital organs and insulates the body

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Adipose tissue is from hormonally inert, adipose tissue has in recent years been recognized as a majorendocrine organ, as it produces hormones such as leptin, estrogen, and resistin. More than you need to have students know, but interesting none the less!45PhospholipidsWhen phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interiorThe structure of phospholipids results in a bilayer arrangement found in cell membranesPhospholipids are the major component of all cell membranes

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You know where this is headedbring on the cell membrane unit! 46

CholinePhosphateGlycerolFatty acidsHydrophilicheadHydrophobictails(c) Phospholipid symbol(b) Space-filling model(a) Structural formulaHydrophilic headHydrophobic tailsA Single Phospholipid Molecule47The structure of a phospholipid.Steroids

Steroids are lipids characterized by a carbon skeleton consisting of four fused ringsCholesterol, an important steroid, is a component in animal cell membranesAlthough cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease48See how many steroids your students can name. 48

The Structure and Function of Macromolecules Part II: Proteins & Nucleic Acids

A fair amount of this material will be new to students with the possible exception of the DNA-related material. Although some of this material is not directly tied to the framework, it is still fundamental to the understanding of the structure and function of proteins and nucleic acids as they relate to evolutionary mechanisms.

Big Idea 2, EK 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 for nucleic acids. Carbon is used in storage compounds and cell formation in all organisms. 49Proteins Come In Many Varieties!Proteins include a diversity of structures, resulting in a wide range of functions

Proteins account for more than 50% of the dry mass of most cells

Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances50Ask students what they already know about proteins and protein synthesis. Hopefully, they remember a few things from Biology I.50Enzymatic51

Enzymatic proteinsEnzymeExample: Digestive enzymes catalyze the hydrolysisof bonds in food molecules.Function: Selective acceleration of chemical reactions

Emphasize the specificity of enzymes. Also emphasize the catalytic nature of enzymes and that they function best in a unique set of pH and temperature conditions. Why is that? It is due to the shape of the enzyme molecule. That shape is held in place by IMFs and/or covalent or ionic bonding. Changes in pH or temperature often disrupt the electrostatic forces that are responsible for an enzymes specific shape.51Storage52

Storage proteinsOvalbuminAmino acidsfor embryoFunction: Storage of amino acidsExamples: Casein, the protein of milk, is the majorsource of amino acids for baby mammals. Plants havestorage proteins in their seeds. Ovalbumin is theprotein of egg white, used as an amino acid sourcefor the developing embryo.Ask students to identify other food sources that are proteins. One of my favorite quotes ever is from Bob Harper, a personal trainer from The Biggest Loser. Simply put, If the food in question had a mother, then its a protein!52Hormonal53

Hormonal proteinsFunction: Coordination of an organisms activitiesExample: Insulin, a hormone secreted by thepancreas, causes other tissues to take up glucose,thus regulating blood sugar concentrationHighblood sugarNormalblood sugarInsulinsecretedAsk students to give examples of hormonal proteins. They should easily come up with testosterone and estrogen among others.53Defensive54

Defensive proteinsVirusAntibodiesBacteriumFunction: Protection against diseaseExample: Antibodies inactivate and help destroyviruses and bacteria.Ask students which body system utilizes these types of proteins. 54Transport55

Transport proteinsTransportproteinCell membraneFunction: Transport of substancesExamples: Hemoglobin, the iron-containing protein ofvertebrate blood, transports oxygen from the lungs toother parts of the body. Other proteins transportmolecules across cell membranes.Ask which body system utilizes hemoglobin.55Receptor56

SignalingmoleculesReceptorproteinReceptor proteinsFunction: Response of cell to chemical stimuliExample: Receptors built into the membrane of anerve cell detect signaling molecules released byother nerve cells.Ask if they know any of the signaling molecules as well as which body system is involved in this process. Hopefully, they come up with the nervous system, the fight or flight response as it relates to adrenaline, etc. 56Structural57

60 mCollagenConnectivetissueStructural proteinsFunction: SupportExamples: Keratin is the protein of hair, horns,feathers, and other skin appendages. Insects andspiders use silk fibers to make their cocoons and webs,respectively. Collagen and elastin proteins provide afibrous framework in animal connective tissues.Emphasize collagens role in the aging process and its unfortunate consequences such as wrinkling! 57

More About Enzymes58Enzymes are a type of protein that acts as a catalyst to speed up chemical reactionsEnzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

This is a perfect time to bring out the water noodle enzyme models. You can extend this portion of the lesson to include competitive inhibition, etc. 58Amino Acids: Yet Another MonomerAmino acids are organic molecule protein monomers with carboxyl and amino groups

Amino acids differ in their properties due to differing side chains, called R groups

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Side chain (R group)AminogroupCarboxylgroup carbonThere are 23 amino acids (aas) but only 20 are biologically active. 59PolypeptidesPolypeptides are unbranched polymers built from the same set of 20 amino acidsA protein is a biologically functional molecule that consists of one or more polypeptides60

Ask, how many peptide bonds are formed. Ask how many amino acids are in this polypeptide. Additionally, emphasize the arrangement of the aas in this diagram. If one of the aas is flipped along the horizontal axis, its amine group no longer aligns with the neighboring aas carboxylic acid group, thus no dehydration reaction can occur. 60

Nonpolar side chains; hydrophobicSide chainGlycine(Gly or G)Alanine(Ala or A)Valine(Val or V)Leucine(Leu or L)Isoleucine(Ile or I)Methionine(Met or M)Phenylalanine(Phe or F)Tryptophan(Trp or W)Proline(Pro or P)Hydrophobic: Therefore retreat from water!61Absolutely no need to memorize these, but there is a need to recognize WHY these retreat from water. Point out that these R groups are very nonpolar as evidenced by the hydrocarbonish or CHX nature of the elements involved in the R groups. 62Hydrophilic: Therefore Are Attracted to Water

Absolutely no need to memorize these, but emphasize that while these R groups also look hydrocarbonish, that there are unpaired electrons left off this diagram. Each N, O or S atom has unshared electron pairs that make them polar and water soluble. 6263Hydrophilic: But Electrically Charged!

Again, no need to memorize these but students should know that ammonia (NH3) is a weak base from Chemistry I. Remove an H from ammonia and you have its cousin the amine group which is also basic. 63Peptide BondsAmino acids are linked by peptide bonds (dehydration synthesis)A polypeptide is a polymer of amino acidsPolypeptides range in length from a few to more than a thousand monomers (Yikes!)Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)

64Emphasize that the peptide bond forms as a consequence of a dehydration synthesis reaction. 64Peptide Bonds65

Peptide Bonds66

Protein Structure & FunctionAt first, all we have is a string of AAs bound with peptide bonds.Once the string of AAs interacts with itself and its environment (often aqueous), then we have a functional protein that consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shapeThe sequence of amino acids determines a proteins three-dimensional structureA proteins structure determines its function

6767Protein Structure: 4 LevelsPrimary structure consists of its unique sequence of amino acidsSecondary structure, found in most proteins, consists of coils and folds in the polypeptide chainTertiary structure is determined by interactions among various side chains (R groups)Quaternary structure results when a protein consists of multiple polypeptide chains

68Now is the time to explain that a string of aas is a polypeptide and NOT yet a protein. The protein forms once the secondary, tertiary and quaternary structures are established and that is usually facilitated in an aqueous environment. Also emphasize that conformation is the big people word for shape and that if the conformation changes, the function of the protein is affected.68

Primary StructurePrimary structure, the sequence of amino acids in a protein, is like the order of letters in a long word Primary structure is determined by inherited genetic information

Keep it simple. Explain to students that when they were about 3 years old, they would sing the alphabet song to anyone that would listen! They had no idea that one day theyd use that to spell or that they would use it to read, or write sentences, or paragraphs or research papers!

Also, remind them yet again that they have some prior knowledge regarding DNA and the process of protein synthesis.69Secondary StructureThe coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backboneTypical secondary structures are a coil called an helix and a folded structure called a pleated sheet

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Emphasize yet again that a H-bond is NOT a bonded H! Its an IMF, not a covalent bond, but rather an electrostatic force. H-bonds are fragile and easily interrupted by pH or temperature changes. 70Tertiary StructureTertiary structure is determined by interactions between R groups, rather than interactions between backbone constituentsThese interactions between R groups include actual ionic bonds and strong covalent bonds called disulfide bridges which may reinforce the proteins structure.IMFs such as London dispersion forces (LDFs a.k.a. and van der Waals interactions), hydrogen bonds (IMFs), and hydrophobic interactions (IMFs) may affect the proteins structure71Here we go again, the second bullet refers to actual chemical bondsthe sharing of a pair of electrons. The third bullet refers to intermolecular forces (IMFs) with LDFs that the biology books often refer to as van der Waals forces or interactions. H-bonds are a special case of dipole-dipole interactions. While none of these distinctions will be asked on the AP Biology exam, they certainly will on the AP Chemistry exam and should be taught in Chem I as well. Its not surprising that students are confused since the vocabulary is so different from book to book! Ugh!71Tertiary Structure72

Revisit the curly hair example for disulfide bridges. Folks with curly hair have more disulfide bridges and we often use heat to alter them 1.Use a hair dryer-brush-mechanically pull on the hair while applying heat to disrupt the S-S bridges. 2. Flat irons on dry hair 3. PermsA basic solution that reeks of ammonia (a base, thus a pH rather than thermal approach) is applied to hair that has been wound onto skinny curlers and left to sit for about 20 minutes to allow S-S to form.

72Quaternary StructureQuaternary structure results when two or more polypeptide chains form one macromolecule

Collagen is a fibrous protein consisting of three polypeptides coiled like a rope

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Emphasize that Quaternary structure involves a collection of polypeptides brought together into a new conformation. 73Four Levels of Protein Structure Revisited74

A nice visual summary!74Sickle-Cell Disease: A change in Primary StructureA slight change in primary structure can affect a proteins structure and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin75

Normal Red Blood CellsA perfect practical example of how a change in protein structure affects function. Be sensitive to the fact that you may have a student that suffers from sickle-cell disease. 75Sickle-Cell Disease: A change in Primary StructureA slight change in primary structure can affect a proteins structure and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin76

The sickled cells cannot move the blood vessels as effectively and can obstruct capillaries and restrict blood flow to an organ, resulting in pain, necrosis and often organ damage. Ask if students studied the connection between sickle-cell trait and malaria in Biology I. 76Sickle-Cell Disease: A change in Primary Structure77

What Determines Protein Structure?In addition to primary structure, physical and chemical conditions can affect structureAlterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravelThis loss of a proteins native structure is called denaturationA denatured protein is biologically inactive78Ask how EACH of the items mentioned could disrupt protein structure. 78Nucleic AcidsNucleic acids store, transmit, and help express hereditary information

The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene

Genes are made of DNA, a nucleic acid made of monomers called nucleotides79Ask questions to see what they already know about DNA structure. A good deal of this should be prior knowledge! 79Two Types of Nucleic AcidsThere are two types of nucleic acidsDeoxyribonucleic acid (DNA)Ribonucleic acid (RNA)DNA provides directions for its own replicationDNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesisProtein synthesis occurs on ribosomes

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Pause and let student examine both structures. WHERE exactly is the deoxy part of the name coming from? 80Figure 5.25-1

Synthesis ofmRNAmRNADNANUCLEUSCYTOPLASM181DNA mRNAFigure 5.25-2

Synthesis ofmRNAmRNADNANUCLEUSCYTOPLASMmRNAMovement ofmRNA intocytoplasm1282DNA m RNA what next?? (ribosome!)Figure 5.25-3

Synthesis ofmRNAmRNADNANUCLEUSCYTOPLASMmRNARibosomeAminoacidsPolypeptideMovement ofmRNA intocytoplasmSynthesisof protein12383DNA mRNA ribosome protein. Whats missing? See if they can supply the details about tRNA, etc. Try to connect to what they already know and correct any misconceptions.The Components of Nucleic AcidsEach nucleic acid is made of monomers called nucleotides

Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups84Again, most likely prior knowledge.84

Figure 5.26abSugar-phosphate backbone5 end5C3C5C3C3 end(a) Polynucleotide, or nucleic acid(b) NucleotidePhosphategroupSugar(pentose)NucleosideNitrogenousbase5C3C1C85Components of nucleic acids.Figure 5.26c

Nitrogenous basesCytosine (C)Thymine (T, in DNA)Uracil (U, in RNA)Adenine (A)Guanine (G)SugarsDeoxyribose (in DNA)Ribose (in RNA)(c) Nucleoside componentsPyrimidinesPurines86Ask about base pairing. Students most likely know A-T and G-C. Emphasize that the pairing is due to, you guessed it, H-bonding!

87Ask about base pairing. Students most likely know A-T and G-C. Emphasize that the pairing is due to, you guessed it, H-bonding! Note the formation of 2 H-bonds for AT and 3 H-bonds for GC. No need to memorize, just interesting to the student that makes you crazy with But, why? questions. The Devil is in the DetailsThere are two families of nitrogenous basesPyrimidines (cytosine, thymine, and uracil) have a single six-membered ringPurines (adenine and guanine) have a six-membered ring fused to a five-membered ring

In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose

88No need to memorize the 5 vs. 6 membered ring distinction. 88The Devil is in the DetailsAdjacent nucleotide backbone is joined by covalent bonds that form between the OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the nextThese links create a backbone of sugar-phosphate units with nitrogenous bases as appendagesThe sequence of bases along a DNA or mRNA polymer is unique for each gene

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Emphasize the backbone of the ladder is held together with actual covalent bonds (much stronger than an IMF). We number Cs in a ring starting with the O and going clockwise if anyone asks. 89The Devil is in the DetailsRNA molecules usually exist as single polypeptide chains DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helixIn the DNA double helix, the two backbones run in opposite 5 3 directions from each other, an arrangement referred to as antiparallelOne DNA molecule includes many genes

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Details they probably didnt get in Biology I.90The Devil is in the DetailsThe nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)Called complementary base pairingComplementary pairing can also occur between two RNA molecules or between parts of the same moleculeIn RNA, thymine is replaced by uracil (U) so A and U pair

91Probably prior knowledge.91

Sugar-phosphatebackbonesHydrogen bondsBase pair joinedby hydrogen bondingBase pair joinedby hydrogenbonding(b) Transfer RNA(a) DNA535392The single dotted line between base pairs is an oversimplification! Reiterate the sugar-phosphate backbones or sides of the ladder are held together with actual covalent chemical bonds. The rungs of the ladder or base pairs align the way they do because of H-bonding (an IMF) AND therefore are not as tightly held together. The elegance involves the ease of the unzipping or zipping of the molecule vs. the stability of the single strand when it is unzipped, thus vulnerable to damage. Link to EvolutionThe linear sequences of nucleotides in DNA molecules are passed from parents to offspring

Two closely related species are more similar in DNA than are more distantly related species

Molecular biology can be used to assess evolutionary kinship93Link Big Ideas together as often as possible!93

Created by:

Ren McCormickNational Math and Science Dallas, TX 94