the structure & function of...

The Structure & The Structure & The Structure & The Structure & The Structure & The Structure & The Structure & The Structure &

Function of Function of Function of Function of Function of Function of Function of Function of

MacromoleculesMacromoleculesMacromoleculesMacromoleculesMacromoleculesMacromoleculesMacromoleculesMacromolecules

Chapter 5Chapter 5

Polymer PrinciplesPolymer PrinciplesPolymer PrinciplesPolymer PrinciplesPolymer PrinciplesPolymer PrinciplesPolymer PrinciplesPolymer Principles

�� Macromolecules Macromolecules –– large biological large biological moleculesmolecules

�� Polymer Polymer –– long molecule consisting of long molecule consisting of many similar building block linked by many similar building block linked by covalent bondscovalent bonds

�� Monomer Monomer –– repeated units that serve as repeated units that serve as building blocks of polymersbuilding blocks of polymers

Condensation / Condensation / Condensation / Condensation / Condensation / Condensation / Condensation / Condensation /

Dehydration ReactionDehydration ReactionDehydration ReactionDehydration ReactionDehydration ReactionDehydration ReactionDehydration ReactionDehydration Reaction

�� Formation of polymeric macromoleculesFormation of polymeric macromolecules

�� 2 molecules are covalently bonded together 2 molecules are covalently bonded together through loss of water moleculethrough loss of water molecule

�� Each monomer contributes part of the water Each monomer contributes part of the water moleculemolecule

�� One provides a hydroxyl (One provides a hydroxyl (--OH) and other a OH) and other a hydrogen (hydrogen (--H)H)

�� Requires cellular energy and aid of enzymesRequires cellular energy and aid of enzymes

Example of dehydrationExample of dehydrationExample of dehydrationExample of dehydrationExample of dehydrationExample of dehydrationExample of dehydrationExample of dehydration

Hydrolysis ReactionHydrolysis ReactionHydrolysis ReactionHydrolysis ReactionHydrolysis ReactionHydrolysis ReactionHydrolysis ReactionHydrolysis Reaction

�� Breakdown of polymeric macromoleculesBreakdown of polymeric macromolecules�� Reverse of dehydrationReverse of dehydration�� Bonds between monomers are broken Bonds between monomers are broken

with water moleculeswith water molecules�� hydrogen from water attaches to one hydrogen from water attaches to one

monomer and hydroxyl attaches to monomer and hydroxyl attaches to adjacent monomeradjacent monomer

�� Ex. DigestionEx. Digestion

Example of HydrolysisExample of HydrolysisExample of HydrolysisExample of HydrolysisExample of HydrolysisExample of HydrolysisExample of HydrolysisExample of Hydrolysis

CarbohydratesCarbohydratesCarbohydratesCarbohydratesCarbohydratesCarbohydratesCarbohydratesCarbohydrates

�� Sugars and starchesSugars and starches

�� MonosaccharidesMonosaccharides –– simple sugarssimple sugars

�� Molecular formula multiples of CHMolecular formula multiples of CH22OO

�� Serve as source of cellular energy & raw Serve as source of cellular energy & raw material for synthesis of other organic material for synthesis of other organic moleculesmolecules

�� Classifying sugars:Classifying sugars:1.Location of carbonyl group 1.Location of carbonyl group –– if at end sugar if at end sugar

is known as an is known as an aldosealdose or if in middle sugar is or if in middle sugar is known as a known as a ketoseketose

�� 2. size of carbon 2. size of carbon skeletonskeleton�� HexosesHexoses –– 66

�� TriosesTrioses –– 33

�� PentosesPentoses -- 55

�� 3. spatial 3. spatial arrangement of their arrangement of their parts around parts around asymmetrical asymmetrical carbonscarbons

�� Most sugars form Most sugars form rings in aqueous rings in aqueous solutionssolutions

�� DisaccharidesDisaccharides –– double sugarsdouble sugars

�� 2 2 monosaccharidesmonosaccharides joined by a joined by a glycosidicglycosidiclinkage linkage –– covalent bond formed between covalent bond formed between 2 2 monosaccharidesmonosaccharides by dehydration by dehydration reactionreaction

�� Joins carbon 1 of a monomer to carbon 4 Joins carbon 1 of a monomer to carbon 4 of anotherof another

�� Sucrose = glucose + fructoseSucrose = glucose + fructose

�� Maltose = glucose + glucoseMaltose = glucose + glucose

�� Lactose = Lactose = galactosegalactose + glucose+ glucose

GlycosidicGlycosidicGlycosidicGlycosidicGlycosidicGlycosidicGlycosidicGlycosidic LinkageLinkageLinkageLinkageLinkageLinkageLinkageLinkage

http://www.wwnorton.com/chemistry/tutorials/ch12.htm

�� PolysaccharidesPolysaccharides

�� Contain hundreds to thousands of Contain hundreds to thousands of monomers joined by monomers joined by glycosidicglycosidic linkageslinkages

�� Serve as storage materials or building Serve as storage materials or building materialsmaterials

�� Function determined by its sugar Function determined by its sugar monomers & position of monomers & position of glycosidicglycosidiclinkageslinkages

�� StarchStarch�� Storage polysaccharide of plantsStorage polysaccharide of plants

�� Consists of glucose monomers Consists of glucose monomers

�� Angle of linkages makes molecule helicalAngle of linkages makes molecule helical

�� AmyloseAmylose –– simplest starch; simplest starch; unbranchedunbranched

�� AmylopectinAmylopectin –– complex starch; branchedcomplex starch; branched

�� Stored in plastids of plantsStored in plastids of plants

�� GlycogenGlycogen�� Polysaccharide stored by animals in muscle Polysaccharide stored by animals in muscle

& liver cells& liver cells

�� Extensively branched polysaccharideExtensively branched polysaccharide

�� Hydrolysis of stored glycogen provides Hydrolysis of stored glycogen provides sugar on demandsugar on demand

�� CelluloseCellulose�� Building polysaccharide of plants Building polysaccharide of plants –– cell wallcell wall

�� Polymer of glucose but the Polymer of glucose but the glycosidicglycosidiclinkages are different than in starchlinkages are different than in starch

�� Two different ring structures of glucoseTwo different ring structures of glucose

�� Alpha glucose: 1 Alpha glucose: 1 –– 4 linkage is below the 4 linkage is below the planeplane

�� Beta glucose: 1 Beta glucose: 1 –– 4 linkage is above the 4 linkage is above the planeplane

�� Cellulose molecule is straight & Cellulose molecule is straight & unbranchedunbranched

Starch / Cellulose Starch / Cellulose Starch / Cellulose Starch / Cellulose Starch / Cellulose Starch / Cellulose Starch / Cellulose Starch / Cellulose

StructuresStructuresStructuresStructuresStructuresStructuresStructuresStructures

LipidsLipidsLipidsLipidsLipidsLipidsLipidsLipids

�� Do not contain polymersDo not contain polymers

�� Include waxes, oils, fats, phospholipids & Include waxes, oils, fats, phospholipids & steroidssteroids

�� Composed of fatty acids & glycerolComposed of fatty acids & glycerol

�� Fatty acids Fatty acids –– long hydrocarbon chain w/ long hydrocarbon chain w/ carboxyl group at end; 16 carboxyl group at end; 16 –– 18 carbons18 carbons

�� Glycerol Glycerol –– alcohol with 3 carbonsalcohol with 3 carbons

Dehydration of LipidsDehydration of LipidsDehydration of LipidsDehydration of LipidsDehydration of LipidsDehydration of LipidsDehydration of LipidsDehydration of Lipids

�� H removed from OH of glycerolH removed from OH of glycerol�� OH removed from carboxyl of fatty acidOH removed from carboxyl of fatty acid�� Ester linkage forms between oxygen of glycerol Ester linkage forms between oxygen of glycerol

and carboxyl of fatty acidand carboxyl of fatty acid�� Triglyceride Triglyceride –– 3 fatty acids linked to one 3 fatty acids linked to one

glycerolglycerol

�� http://www2.nl.edu/jste/lipids.htmhttp://www2.nl.edu/jste/lipids.htm

Types of Fatty AcidsTypes of Fatty AcidsTypes of Fatty AcidsTypes of Fatty AcidsTypes of Fatty AcidsTypes of Fatty AcidsTypes of Fatty AcidsTypes of Fatty Acids

�� Saturated Saturated –– all single bonds between all single bonds between carbon atoms of hydrocarbon ; derived carbon atoms of hydrocarbon ; derived from animal products ; unhealthyfrom animal products ; unhealthy

�� Unsaturated Unsaturated –– one or more double bonds one or more double bonds in hydrocarbon; derived from plant seed in hydrocarbon; derived from plant seed oils; healthyoils; healthy

�� Fats provide energy storage (greater Fats provide energy storage (greater than than carbscarbs) , cushion organs & insulate) , cushion organs & insulate

�� Phospholipids Phospholipids –– 2 fatty acids rather than 2 fatty acids rather than 33

�� Phosphate group joins to third hydroxyl of Phosphate group joins to third hydroxyl of glycerolglycerol

�� Part is Part is hydophilichydophilic –– head (carboxyl of head (carboxyl of fatty acid which is polar)fatty acid which is polar)

�� Part is hydrophobic Part is hydrophobic –– tails (hydrocarbon tails (hydrocarbon of fatty acid which is of fatty acid which is nonpolarnonpolar))

�� Micelle Micelle –– phosphate heads directed to outside phosphate heads directed to outside in contact with water; tails directed inward in contact with water; tails directed inward away from wateraway from water

�� BilayerBilayer –– heads face aqueous environment heads face aqueous environment inside & outside cell; tails point to interior of inside & outside cell; tails point to interior of membranemembrane

�� Steroids Steroids –– carbon carbon skeleton consists of skeleton consists of 4 fused rings4 fused rings

�� Cholesterol Cholesterol

�� HormonesHormones

ProteinsProteinsProteinsProteinsProteinsProteinsProteinsProteins

�� Most important compound to living thingsMost important compound to living things

�� Functions: ( Table 5.1 page 72)Functions: ( Table 5.1 page 72)�� Structural Structural

�� StorageStorage

�� TransportTransport

�� ReceptorReceptor

�� DefenseDefense

�� MovementMovement

�� EnzymesEnzymes

�� Polypeptides Polypeptides –– polymers of amino acidspolymers of amino acids

�� Proteins Proteins –– one or more polypeptides one or more polypeptides folded or coiled togetherfolded or coiled together

Amino Acid StructureAmino Acid StructureAmino Acid StructureAmino Acid StructureAmino Acid StructureAmino Acid StructureAmino Acid StructureAmino Acid Structure

�� Alpha carbon is at centerAlpha carbon is at center

�� 4 attachment groups 4 attachment groups –– amine, carboxyl, amine, carboxyl, hydrogen and a variable group hydrogen and a variable group symbolized by R (also called side chain)symbolized by R (also called side chain)

�� Physical & chemical properties of side Physical & chemical properties of side chain determine characteristics of amino chain determine characteristics of amino acidacid

�� Side chains can be Side chains can be nonpolarnonpolar, polar or , polar or electrically chargedelectrically charged

�� Figure 5.15 page 72Figure 5.15 page 72

NonpolarNonpolarNonpolarNonpolarNonpolarNonpolarNonpolarNonpolar Side ChainsSide ChainsSide ChainsSide ChainsSide ChainsSide ChainsSide ChainsSide Chains

Polar & Electrically Polar & Electrically Polar & Electrically Polar & Electrically Polar & Electrically Polar & Electrically Polar & Electrically Polar & Electrically

Charged Side ChainsCharged Side ChainsCharged Side ChainsCharged Side ChainsCharged Side ChainsCharged Side ChainsCharged Side ChainsCharged Side Chains

DEHYDRATION OF AMINO DEHYDRATION OF AMINO DEHYDRATION OF AMINO DEHYDRATION OF AMINO DEHYDRATION OF AMINO DEHYDRATION OF AMINO DEHYDRATION OF AMINO DEHYDRATION OF AMINO

ACIDSACIDSACIDSACIDSACIDSACIDSACIDSACIDS

�� OH removed from carboxyl of one amino acidOH removed from carboxyl of one amino acid

�� H removed from amine of adjacent amino acidH removed from amine of adjacent amino acid

�� Peptide bond forms between exposed C and NPeptide bond forms between exposed C and N

�� Polypeptides have free carboxyl group at one Polypeptides have free carboxyl group at one end (end (CC--terminusterminus) and free amino at the other ) and free amino at the other end (end (NN--terminusterminus))

�� http://www2.nl.edu/jste/proteins.htmhttp://www2.nl.edu/jste/proteins.htm

4 Levels of Protein 4 Levels of Protein 4 Levels of Protein 4 Levels of Protein 4 Levels of Protein 4 Levels of Protein 4 Levels of Protein 4 Levels of Protein

StructureStructureStructureStructureStructureStructureStructureStructure

�� Function of a protein depends Function of a protein depends on its ability to recognize & on its ability to recognize & bind to some other moleculebind to some other molecule

�� 1. Primary Structure 1. Primary Structure –– amino amino acid sequenceacid sequence

�� Determined by inherited Determined by inherited genetic informationgenetic information

�� Change in primary sequence Change in primary sequence can lead to inability to function can lead to inability to function (sickle cell anemia)(sickle cell anemia)

2.2.2.2.2.2.2.2. Secondary Structure Secondary Structure –– repeated coiled or folded patterns of repeated coiled or folded patterns of proteinprotein ’’s overall conformations overall conformationInvolves only backbone, not side chainsInvolves only backbone, not side chainsHydrogen of amine has an attraction to the oxygen o f the peptideHydrogen of amine has an attraction to the oxygen o f the peptidebond bond

�� Alpha helix Alpha helix –– coil held together by coil held together by hydrogen bonding between every 4hydrogen bonding between every 4thth

amino acidamino acid

�� Beta pleated sheet Beta pleated sheet –– 2 or more regions 2 or more regions lie parallel to each otherlie parallel to each other

�� 3. Tertiary Structure 3. Tertiary Structure –– consists of irregular contortions consists of irregular contortions from interactions of side chainsfrom interactions of side chains

�� Hydrophobic interactions Hydrophobic interactions –– amino acids w/ hydrophobic amino acids w/ hydrophobic side chains end up in core (interior) of proteinside chains end up in core (interior) of protein

�� Van Van derder Waals Waals –– weak hydrogen interactions occur weak hydrogen interactions occur between polar side chainbetween polar side chain

�� Disulfide bridges Disulfide bridges –– strong covalent bonds between strong covalent bonds between amino acids w/ amino acids w/ sulfhydrylsulfhydryl groupsgroups

�� Ionic Bonds Ionic Bonds –– between positive & negative charged between positive & negative charged side chainsside chains

�� 4. Quaternary 4. Quaternary Structure Structure –– overall overall structure due to structure due to association of two or association of two or more polypeptidesmore polypeptides

Problem of Protein FoldingProblem of Protein FoldingProblem of Protein FoldingProblem of Protein FoldingProblem of Protein FoldingProblem of Protein FoldingProblem of Protein FoldingProblem of Protein Folding

�� Most proteins go through several Most proteins go through several intermediate states on their way to stable intermediate states on their way to stable conformationconformation

�� ChaperoninsChaperonins (chaperone proteins) (chaperone proteins) ––assist the proper folding of proteins by assist the proper folding of proteins by keeping polypeptide separated from bad keeping polypeptide separated from bad influences in influences in cytoplasmiccytoplasmic environmentenvironment

Nucleic AcidsNucleic AcidsNucleic AcidsNucleic AcidsNucleic AcidsNucleic AcidsNucleic AcidsNucleic Acids

�� Informational polymersInformational polymers

�� DNA and RNADNA and RNA

�� Long chains of monomers called Long chains of monomers called nucleotidesnucleotides

�� Nucleotides composed of pentose sugar, Nucleotides composed of pentose sugar, nitrogen base & phosphate groupnitrogen base & phosphate group

�� Nitrogen bases exist in 2 familiesNitrogen bases exist in 2 families

�� PyrimidinesPyrimidines –– 6 6 memberedmembered ring of carbon ring of carbon & nitrogen ; includes cytosine, thymine & nitrogen ; includes cytosine, thymine and and uraciluracil

�� PurinesPurines –– 6 6 memberedmembered ring fused to a 5 ring fused to a 5 memberedmembered ring ; adenine and guaninering ; adenine and guanine

DNADNA�� DeoxyriboseDeoxyribose sugar sugar ––

5 carbon sugar 5 carbon sugar lacking an oxygen on lacking an oxygen on carbon 2carbon 2

�� A,T,C,GA,T,C,G

�� Double HelixDouble Helix

RNARNA�� Ribose sugarRibose sugar

�� A,U,C,GA,U,C,G

�� Single polynucleotide Single polynucleotide chainchain

Double HelixDouble HelixDouble HelixDouble HelixDouble HelixDouble HelixDouble HelixDouble Helix

�� Watson & CrickWatson & Crick�� Sugar & phosphate backbone Sugar & phosphate backbone –– covalent bond covalent bond

called called phosphodiesterphosphodiester linkage bonds linkage bonds phosphate of one nucleotide to sugar of phosphate of one nucleotide to sugar of anotheranother

�� Complementary base pairs; A to T and C to GComplementary base pairs; A to T and C to G�� Weak hydrogen bond holds together nitrogen Weak hydrogen bond holds together nitrogen

base pairsbase pairs�� Van Van derder Waals interactions between stacked Waals interactions between stacked

nitrogen basesnitrogen bases