organic compounds carbon containing compounds carbon containing compounds form covalent form...

Organic CompoundsOrganic CompoundsCarbon containing compounds Carbon containing compounds

Form Form covalent covalent

bondsbonds with with(usually) other(usually) othercarbon orcarbon orhydrogen hydrogen

atomsatoms

By virtue of its By virtue of its 4 valence 4 valence electronselectrons::

Can form Can form single, double, single, double, or tripleor triple covalent bonds covalent bonds with itself (and other with itself (and other atoms) atoms)

Can form a Can form a variety of variety of shapesshapes (chains, rings, (chains, rings, branches sheets, etc.)branches sheets, etc.)

Carbon MoleculesCarbon Molecules

AromaticsAromatics

BuckyballBuckyball

• HydrocarbonsHydrocarbons – Organic – Organic molecules consisting only of molecules consisting only of carbon and hydrogen; carbon and hydrogen; energy-energy-richrich

• Functional GroupsFunctional Groups - Groups of - Groups of molecules that have definite molecules that have definite chemical properties they retain chemical properties they retain no matter where they occurno matter where they occur..

MacromoleculesMacromolecules““largelarge” molecules ” molecules

synthesized by living thingssynthesized by living thingsMany are “organic” (Many are “organic” (contain contain

a carbon corea carbon core))Most have “functional Most have “functional

groups” attached to carbon groups” attached to carbon core (core (determine function of determine function of moleculemolecule))

Biological Biological MacromoleculesMacromoleculesCarbohydratesCarbohydratesLipidsLipidsProteinsProteinsNucleic AcidsNucleic AcidsATPATP

Building MacromoleculesBuilding Macromolecules

Most organic Most organic macromolecules are macromolecules are polymerspolymers made by using made by using enzymes to help link together enzymes to help link together smaller smaller monomersmonomers. Done in a . Done in a process called process called dehydration dehydration synthesissynthesis (or condensation). (or condensation).

This process removes This process removes one Hone H++ from one molecule from one molecule and one OHand one OH-- from another from another molecule (Hmolecule (H220) and 0) and

cause the two to link cause the two to link togethertogether

Diversity in polymers isAchieved by arrangingThe same monomers inDifferent waysThese different arrangementsAre called ISOMERS

Breaking Breaking macromolecules uses the macromolecules uses the reverse process called reverse process called hydrolysishydrolysis; process in ; process in which water is added to which water is added to break apart polymers into break apart polymers into monomers.monomers.

CarbohydratesCarbohydratesCarbohydrates Carbohydrates

are a loosely are a loosely defined group of defined group of molecules that molecules that contain carbon, contain carbon, hydrogen, and hydrogen, and oxygen in a oxygen in a 1:2:11:2:1 ratio (ratio (CHCH22OO))

Serve as Serve as energy storing energy storing moleculesmolecules and structural and structural elementselements

Energy is stored in the Energy is stored in the C-H C-H bondsbonds; when the bond is ; when the bond is broken, energy is released.broken, energy is released.

Named according to Named according to size size and structureand structure (triose, (triose, pentose, hexose) pentose, hexose)

MonosaccharidesMonosaccharides – – ““simplesimple” sugars; ” sugars; glucose, fructose, glucose, fructose, galactosegalactose3-6 carbon sugar3-6 carbon sugarCC66HH1212OO66 is the common is the common fuel source for cellsfuel source for cells

Many monosaccharides Many monosaccharides have the have the same empirical same empirical formulaformula, but different , but different arrangement of double arrangement of double bonds &/or OH- groups. bonds &/or OH- groups. This causes their This causes their properties to be properties to be different.different.

Sugar IsomersSugar Isomers - - Alternative forms of the Alternative forms of the same chemical formula.same chemical formula.GlucoseGlucoseFructoseFructoseGalactoseGalactose

RiboseGlyceraldehyde(building blocks) (RNA) (DNA)

(Plants)(ENERGY)

DisaccharidesDisaccharides – created – created when 2 monosaccharides are when 2 monosaccharides are joined by dehydration joined by dehydration synthesis. (Csynthesis. (C1212HH2222OO1111))PurposePurpose: so sugars can be : so sugars can be transported w/i an organism transported w/i an organism without being metabolized.without being metabolized.

Ex: glucose + glucose = Ex: glucose + glucose = maltosemaltose

glucose + fructose glucose + fructose = = sucrosesucrose

glucose + glucose + galactose = galactose = lactoselactose

PolysaccharidesPolysaccharides – formed from – formed from assembled disaccharides into an assembled disaccharides into an insoluble form and then stored.insoluble form and then stored.StorageStorage: : starchstarch (plant (plant polysaccharide), polysaccharide), glycogenglycogen (animal starch stored in liver (animal starch stored in liver and muscles)and muscles)

StructuralStructural: : pectinpectin and and cellulosecellulose (plant polysaccharides used to (plant polysaccharides used to make plant cell walls), make plant cell walls), chitinchitin (animal structural sugar)(animal structural sugar)

StarchStarch – chains of glucose – chains of glucose produced by plants, coil in produced by plants, coil in water, are rendered insoluble. water, are rendered insoluble. EnzymesEnzymes can cleave them can cleave them randomly into smaller, more randomly into smaller, more soluble, fragments and then cut soluble, fragments and then cut into smaller disaccharides of into smaller disaccharides of maltose and then smaller maltose and then smaller monosaccharides of glucose for monosaccharides of glucose for cell metabolism. cell metabolism.

GlycogenGlycogen – produced by – produced by animals; length and number animals; length and number of branches are larger than of branches are larger than plant starches.plant starches.

When the animal body When the animal body needs energy, it looks needs energy, it looks to the liver to to the liver to hydrolizehydrolize glycogen and release glycogen and release the resulting the resulting monosaccharides to monosaccharides to the cells. the cells.

From there, the cells, From there, the cells, through respiration through respiration release release the energythe energy stored in the stored in the bonds of the bonds of the monosaccharide molecule. monosaccharide molecule. The energy is converted to The energy is converted to another energy compound – another energy compound – ATPATP..

CelluloseCellulose and Pectinand Pectin - - Chain of glucose Chain of glucose molecules that consists of molecules that consists of all all beta-glucosebeta-glucose subunits. subunits.Cleavage of subunits Cleavage of subunits requires an enzymerequires an enzyme most organisms lackmost organisms lack

Why Fiber?Why Fiber?We can’t break fiber We can’t break fiber

down but we need itdown but we need itIt makes us salivateIt makes us salivateFeel fullFeel fullGo to the bathroomGo to the bathroomPrevents colon cancerPrevents colon cancer

Cows, for example, have Cows, for example, have bacteria and protistsbacteria and protists in their in their gut that have the necessary gut that have the necessary enzymes for digesting the enzymes for digesting the cellulose of grasses and cellulose of grasses and grains. Therefore cows can grains. Therefore cows can get energy from this food – get energy from this food – we cannot. This makes we cannot. This makes cellulose a good structural cellulose a good structural material.material.

PectinPectin – branched – branched polysaccharide produced by polysaccharide produced by plants (plants (citruscitrus); sugars are ); sugars are cross-linked to form a mesh cross-linked to form a mesh of glucose which can only be of glucose which can only be broken down by a specific broken down by a specific enzyme. Different plants have enzyme. Different plants have different mesh sizes. (Used different mesh sizes. (Used as gelling agents & diarrhea as gelling agents & diarrhea management)management)

ChitinChitin - Modified form of cellulose - Modified form of cellulose with nitrogen group added to the with nitrogen group added to the glucose units.glucose units.Structural unit in many insects.Structural unit in many insects.

More carb trivia –More carb trivia –Sugars have either Sugars have either aldehyde or ketone aldehyde or ketone functional groupsfunctional groups

Sugars can be recognized Sugars can be recognized by their “ose” endingsby their “ose” endings

Most sugars form rings in Most sugars form rings in aqueous solutionsaqueous solutions

ARE ALL FATS ARE ALL FATS BAD?BAD?

LipidsLipidsMonomers are Monomers are fatty acids and fatty acids and

glycerolglycerolCompounds with Compounds with > 2:1 H:O> 2:1 H:O ratio ratio

and large numbers of C-H and large numbers of C-H bondsbonds

C-H bonds are C-H bonds are nonpolarnonpolar and and hydrophobichydrophobic; fat molecules ; fat molecules tend to cluster and are tend to cluster and are insolubleinsoluble

Lipids store energy well Lipids store energy well because of the C-H bondsbecause of the C-H bondsMost lipids have more Most lipids have more than 40 carbonsthan 40 carbons

9 kcal of energy for fats 9 kcal of energy for fats compared to 4 kcal of compared to 4 kcal of energy for carbohydrates.energy for carbohydrates.

People gain weight People gain weight because their energy because their energy levels drop as they get levels drop as they get older, but their food older, but their food intake doesn’tintake doesn’t

Types of lipids:Types of lipids:PhospholipidsPhospholipids – used in cell – used in cell

membranes; one fatty acid is membranes; one fatty acid is replaced with a polar replaced with a polar phosphate head.phosphate head.

Triglycerides (Fats, Triglycerides (Fats, Oils)Oils)FatsFats – composed of a – composed of a backbone glycerol backbone glycerol molecule and 3 fatty molecule and 3 fatty acid chains (long acid chains (long hydrocarbon chains – hydrocarbon chains – triglyceridetriglyceride). ).

Fatty acids can be of Fatty acids can be of varying lengths; 14-20 varying lengths; 14-20 carbons are averagecarbons are averageSaturated fatsSaturated fats – all – all carbons on the internal carbons on the internal structure have Hstructure have H++ bonded to thembonded to them

These fats (which These fats (which come mostly from come mostly from animals) tend to be animals) tend to be solid at room temp; solid at room temp; ex: Crisco; tropical ex: Crisco; tropical oils (palm and oils (palm and coconut)coconut)

Unsaturated fatsUnsaturated fats – – some Hsome H++ are are lacking on internal lacking on internal carbons and carbons and double bonds are double bonds are in its placein its place

Polyunsaturated fatsPolyunsaturated fats – more – more than one missing Hthan one missing H++ and and more than one double bondmore than one double bondTend to have low melting Tend to have low melting point because chains bend point because chains bend at double bonds.at double bonds.

Usually liquid at room Usually liquid at room temperature.temperature.

Based on the double bonds, what kind of fat is this?

Saturated FatsSaturated FatsA.A. SolidSolid at room at room

temp.temp.

(except palm & (except palm & coconut oil)coconut oil)

B. All B. All singlesingle bondsbonds

C-C-C-C-C-C-C-CC-C-C-C-C-C-C-C

C. Increases C. Increases CholesterolCholesterol

Unsaturated Unsaturated FatsFats

A.A. Usually Usually liquidliquid

B.B. One or more One or more doubledouble bonds bonds

C-C=C-C=C-C-CC-C=C-C=C-C-C

C. Found in C. Found in ArticArtic animalsanimals

HydrogenatingHydrogenating (adding hydrogen) (adding hydrogen) unsaturated fats to unsaturated fats to make them solid make them solid (peanut butter and (peanut butter and margarine) are just as margarine) are just as unhealthy as unhealthy as saturated fatssaturated fats

Unhydrogenated Peanut ButterUnhydrogenated Peanut Butter

Animal fats are Animal fats are saturated, while most saturated, while most plant fats are plant fats are unsaturated.unsaturated.Can convert oil into Can convert oil into solid fat through solid fat through hydrogenation (adding hydrogenation (adding hydrogen).hydrogen).

Steroids Steroids – 4 carbon ring – 4 carbon ring lipid (ex: cholesterol), used lipid (ex: cholesterol), used to make hormones like to make hormones like testosterone and estrogentestosterone and estrogen

TerpenesTerpenes – long lipid – long lipid chains that contain chains that contain pigments (ex: chlorophyll, pigments (ex: chlorophyll, rhodopsin, rubber)rhodopsin, rubber)

ProstaglandinsProstaglandins – 5 carbon – 5 carbon ring head and 2 nonpolar ring head and 2 nonpolar tails; act as chemical tails; act as chemical messengers; used in messengers; used in muscle contractions, blood muscle contractions, blood vessel dilation, ovulation, vessel dilation, ovulation, uterine contraction, blood uterine contraction, blood clotting, inflammatory clotting, inflammatory responses; aspirin inhibits responses; aspirin inhibits prostaglandin productionprostaglandin production

Men need 4-7% body fatMen need 4-7% body fatWomen need 9-16% body fatWomen need 9-16% body fatGoing below these Going below these

percentages is harmful since percentages is harmful since your body can’t perform all its your body can’t perform all its normal functionsnormal functions

Low Carb Diets?Low Carb Diets? Carbs are needed to synthesize glycogen which Carbs are needed to synthesize glycogen which

are needed for effective workoutsare needed for effective workouts Without glycogen, you cannot burn as much fatWithout glycogen, you cannot burn as much fat Body uses fuel in this order (Glycogen, Fat, Body uses fuel in this order (Glycogen, Fat,

Muscle)Muscle) Low calorie diets make your body burn muscle Low calorie diets make your body burn muscle

which causes a loss in total calorie burning which causes a loss in total calorie burning potential – muscle cells have more mitochondria) potential – muscle cells have more mitochondria)

Weight comes off because of lost muscle but Weight comes off because of lost muscle but comes back as fat (NOT GOOD)comes back as fat (NOT GOOD)

Good Things About FatGood Things About FatMore energy than carbs or More energy than carbs or

proteinsproteinsHelps absorb Vitamins A, C, Helps absorb Vitamins A, C,

etc.etc.Healthy skinHealthy skinGives us fatty acids for growthGives us fatty acids for growth

The Good – Omega-3 FatsThe Good – Omega-3 Fats

Lower blood Lower blood pressurepressure

Decrease risk of Decrease risk of heart attackheart attack

Protect against Protect against irregular irregular heartbeatsheartbeats

How much should you eat?How much should you eat?

YUM!

You should consume 20 to 30% You should consume 20 to 30% of your total calories from fatof your total calories from fat

No more than 10% should be No more than 10% should be saturated fatssaturated fats

Too much or too little Too much or too little can be a health risk!can be a health risk!

Nucleic AcidsNucleic Acids(Information Molecules(Information Molecules))

Nucleic acidsNucleic acids are are information information storage storage devicesdevices, and serve as , and serve as templates to produce templates to produce precise copies of precise copies of themselves.themselves.

Nucleic acids are polymers Nucleic acids are polymers made of monomers called made of monomers called ““nucleotidesnucleotides””

Nucleotide consists ofNucleotide consists ofSugarSugar (deoxyribose or ribose) (deoxyribose or ribose)PhosphatePhosphateNitrogenNitrogen containing “base” containing “base”

(adenine, guanine, cytosine, (adenine, guanine, cytosine, thymine)thymine)

ATPATPAdenosine TriphosphateAdenosine Triphosphate

Nucleotide derivative (adenine)Nucleotide derivative (adenine)Cell batteryCell batteryManufactured in the Manufactured in the

mitochondria of cell as a result of mitochondria of cell as a result of the breakdown of glucosethe breakdown of glucose

Energy of the molecule is stored Energy of the molecule is stored in the bonds that hold the in the bonds that hold the phosphates togetherphosphates together

Pop QuizPop Quiz1) What does hydrolysis do?1) What does hydrolysis do?

2) What are the building 2) What are the building blocks of lipids?blocks of lipids?

3) Why is cellulose difficult to 3) Why is cellulose difficult to digest?digest?

4) How do animals store 4) How do animals store glucose?glucose?

5) “Double helix” describes 5) “Double helix” describes what?what?

6) Phospholipids always 6) Phospholipids always orient so their tails face:orient so their tails face:

7) How is sucrose 7) How is sucrose (disaccharide) created from (disaccharide) created from glucose and galactose (both glucose and galactose (both monosaccharides)monosaccharides)

Proteins are Proteins are polymers of amino polymers of amino acids.acids.Covalent bond linking two amino Covalent bond linking two amino

acids = acids = peptide bond.peptide bond.Proteins composed of one or Proteins composed of one or more long chains = more long chains = polypeptidespolypeptides

Polypeptides composed of Polypeptides composed of amino acids linked by amino acids linked by peptide peptide bondsbonds..

ProteinsProteins

Amino AcidAmino Acid

Can act as base(Accept H+)

Amino Acids Build ProteinsAmino Acids Build ProteinsAmino acids – molecules that Amino acids – molecules that

contain an contain an amino groupamino group (-NH (-NH22) )

or or carboxyl groupcarboxyl group (-COOH), a (-COOH), a HH++,, and a and a functional (R) groupfunctional (R) group all bonded to a central carbonall bonded to a central carbon

Amino acids determine the Amino acids determine the shapeshape of the protein of the protein

20 common amino acids20 common amino acids in in nature (Make tens of nature (Make tens of thousands of proteins in thousands of proteins in human)human)

The functional (side) groups The functional (side) groups give the amino acid its give the amino acid its unique chemical propertiesunique chemical properties and thus the protein and thus the protein propertiesproperties

20 Common Amino Acids 20 Common Amino Acids grouped into five chemical grouped into five chemical classes, based on functional (R) classes, based on functional (R) groups:groups:Nonpolar amino acidsNonpolar amino acidsPolar uncharged amino acidsPolar uncharged amino acidsIonizable amino acidsIonizable amino acidsAromatic amino acidsAromatic amino acidsSpecial-function aminoSpecial-function amino acids acids

Nonpolar – contain –CHNonpolar – contain –CH22 or or

–CH–CH3 3 ((HydrophobicHydrophobic))

Polar uncharged – Contain Polar uncharged – Contain O or only –H (O or only –H (HydrophilicHydrophilic))

Ionizable – acid (R groups are negative) Ionizable – acid (R groups are negative) or base groups (R groups = +)or base groups (R groups = +)

AromaticAromatic – contain – contain rings with rings with alternating alternating single and single and double double bondsbonds

Special Special functionsfunctions – cause – cause chaining, chaining, linking, or linking, or bending bending of protein of protein moleculemolecule

2 categories of proteins:2 categories of proteins:StructuralStructural – fibrous; – fibrous; muscle hair, cell markersmuscle hair, cell markers

FunctionalFunctional – globular; – globular; enzymes, antibodies, enzymes, antibodies, venom, peptide venom, peptide messengers, globulins, messengers, globulins, hormoneshormones

Protein FunctionsProtein FunctionsEnzyme Catalysis - catalaseEnzyme Catalysis - catalaseDefense - antibodiesDefense - antibodiesTransport – cell membranesTransport – cell membranesSupport - cytoskeletonSupport - cytoskeletonMotion – cilia, flagellaMotion – cilia, flagellaRegulation – receptor proteinsRegulation – receptor proteins

Proteins consist of long Proteins consist of long amino acid chains folded into amino acid chains folded into complex shapes.complex shapes.Primary StructurePrimary Structure – 1 – 1oo - - Specific amino acid Specific amino acid sequencesequence; chains; ; chains; characteristic of structural characteristic of structural proteinsproteins

Secondary StructureSecondary Structure - 2 - 2oo - - Folding of amino acid chain Folding of amino acid chain by by hydrogen bondinghydrogen bonding into into coils (coils (alphaalpha) and pleats ) and pleats ((betabeta); characteristic of ); characteristic of structural proteinsstructural proteinsMotifMotif – variations on – variations on secondary structure; ex: secondary structure; ex: barrel, Beta-alpha-beta)barrel, Beta-alpha-beta)

MotifsMotifs

Water helps to position Water helps to position motifs and also helps to fold motifs and also helps to fold nonpolar side groups into nonpolar side groups into the interior.the interior.Stability of a protein is Stability of a protein is influenced by how well its influenced by how well its interior fits together.interior fits together.

Spider silkSpider silk

Bullet-proof clothing Bullet-proof clothing Wear-resistant lightweight clothing Wear-resistant lightweight clothing Ropes, nets, seat belts, parachutes Ropes, nets, seat belts, parachutes Rust-free panels on motor vehicles or boats Rust-free panels on motor vehicles or boats Biodegradable bottles Biodegradable bottles Bandages, surgical thread Bandages, surgical thread Artificial tendons or ligaments, supports for weak Artificial tendons or ligaments, supports for weak

blood vessels. blood vessels.

Tertiary StructureTertiary Structure - 3 - 3o -o - Final Final folded shape due tofolded shape due tohydrophobic interactionshydrophobic interactions with with waterwater

hydrogenhydrogen and and ionic bondingionic bonding between R groupsbetween R groups

disulfide bridgesdisulfide bridges..bonding determined by bonding determined by primary structure (types of primary structure (types of amino acids and side groups) amino acids and side groups)

Quaternary StructureQuaternary Structure - 4 - 4oo– – When When 2 or more 2 or more polypeptide chains joinpolypeptide chains join to to form a functional protein. form a functional protein. Ex: Hemoglobin is Ex: Hemoglobin is composed of 2 composed of 2 chains chains and 2 and 2 chains. chains.

Tertiary StructureTertiary Structure

Substitution of amino Substitution of amino acids due to acids due to mutationsmutations, , can interfere with can interfere with protein stabilityprotein stability

Characteristic of Characteristic of functional proteinsfunctional proteins

11oo and 2 and 2oo are usually are usually structuralstructural proteins proteins

33oo and 4 and 4oo are usually are usually functionalfunctional (globular) (globular) proteins.proteins.

How Proteins FoldHow Proteins FoldNormal cells contain special Normal cells contain special

proteins (proteins (chaperoninschaperonins) that help ) that help new proteins fold correctly.new proteins fold correctly.Exact workings are Exact workings are

controversial.controversial.Chaperonin deficiencies Chaperonin deficiencies (and, therefore, improper (and, therefore, improper protein folding) may play protein folding) may play role in certain diseases.role in certain diseases.

How Proteins UnfoldHow Proteins Unfold

Alteration of a protein’s Alteration of a protein’s environment may cause environment may cause denaturation.denaturation.Usually renders protein Usually renders protein biologically inactive.biologically inactive.

pH extremes, pH extremes, temperature, ionic temperature, ionic concentration (salt) of concentration (salt) of protein’s environmentprotein’s environment

Some denaturation is Some denaturation is reversible; most are reversible; most are not.not.

Pop QuizPop Quiz1) Term for a “large molecule 1) Term for a “large molecule

made of similar subunits”?made of similar subunits”?2) Building blocks of proteins?2) Building blocks of proteins?3) Hair is made of protein. What 3) Hair is made of protein. What

category of protein? category of protein? 4) Which protein structure is not 4) Which protein structure is not

affected by denaturing heat?affected by denaturing heat?5) What are the monomers of 5) What are the monomers of

protein?protein?

Helpful WebsitesHelpful Websites

Kinetics Tutorial Arizona University Maricopa Atoms and Periodic TableKinetics Tutorial Arizona University Maricopa Atoms and Periodic Table

Chemistry Review Molecules ReviewChemistry Review Molecules Review

MathemoleSite; MathemoleSite; Covalent Bonds Water Chemistry Covalent Bonds Water Chemistry Animated Animated

Molecules, MassMolecules, Mass Water Water TutorialTutorial

Water and pHWater and pH pH Tutorial pH Tutorial Chemistry of pH Chemistry of pH pH Scale pH Scale

pH/pOH GamepH/pOH Game Functional Groups Amino Acids Functional Groups Amino Acids Carbon Carbon FactsFacts

Monosaccharide Macromolecules Protein ExplorerMonosaccharide Macromolecules Protein Explorer

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