the chemistry of life: organic and biological chemistry

Prof. T. L. Meeks

The Chemistry of Life: The Chemistry of Life: Organic and Biological Organic and Biological

ChemistryChemistry

The element carbon forms a vast The element carbon forms a vast number of compounds.number of compounds.

The study of carbon compounds The study of carbon compounds constitutes a separate branch of constitutes a separate branch of chemistry known as chemistry known as organic organic chemistrychemistry..

The study of living species is called The study of living species is called biological chemistry, or biochemistrybiological chemistry, or biochemistry

Prof. T. L. Meeks

A Look BackA Look Back

The shapes of organic molecules:The shapes of organic molecules:

The three dimensional structures The three dimensional structures of organic and biochemical of organic and biochemical molecules play an essential role in molecules play an essential role in determining their physical and determining their physical and chemical behaviors.chemical behaviors.

Carbon forms a tetrahedral Carbon forms a tetrahedral geometry normally.geometry normally.

Prof. T. L. Meeks


VSEPR model of carbon shows four VSEPR model of carbon shows four electron pairs.electron pairs.

All single bonds are tetrahedrally All single bonds are tetrahedrally spacedspaced

A double bond with 2 single bonds A double bond with 2 single bonds will be trigonal planarwill be trigonal planar

Two double bonds, or a triple bond, Two double bonds, or a triple bond, will be linearwill be linear

Prof. T. L. Meeks


The stabilities of organic substancesThe stabilities of organic substances

In chapter 8 we learned about the In chapter 8 we learned about the average strengths of various average strengths of various chemical bonds, including those chemical bonds, including those characteristic to organic chemistry.characteristic to organic chemistry.

- double bonds are normally - double bonds are normally stronger than single, stronger than single,

and triple and triple stronger than doublestronger than double

Prof. T. L. Meeks


The stabilities of organic substancesThe stabilities of organic substances

The reaction of a simple organic The reaction of a simple organic molecule with oxygen is highly molecule with oxygen is highly exothermic, however, many organic exothermic, however, many organic molecules are stable in air for molecules are stable in air for indeterminate amounts of time due indeterminate amounts of time due to the extremely high activation to the extremely high activation energy for combustion to begin.energy for combustion to begin.

Prof. T. L. Meeks


Solubility and Acid-Base propertiesSolubility and Acid-Base properties

Most organic compounds have Most organic compounds have prevalent C-C or C-H bonds which prevalent C-C or C-H bonds which are nonpolar. In general, the are nonpolar. In general, the molecules are nonpolar and do not molecules are nonpolar and do not dissolve well in water.dissolve well in water.

Prof. T. L. Meeks



Organic molecules that do dissolve Organic molecules that do dissolve in water are those that have polar in water are those that have polar groups on the surface of the groups on the surface of the molecule, such as glucosemolecule, such as glucose

Prof. T. L. Meeks



Many organic substances contain Many organic substances contain acidic or basic groups. The most acidic or basic groups. The most important acidic substances are important acidic substances are the carboxylic acids which bear the the carboxylic acids which bear the functional group -COOH.functional group -COOH.

Prof. T. L. Meeks



Basic organic substances are amines, Basic organic substances are amines, which bear the -NHwhich bear the -NH22, -NHR, or -NR, -NHR, or -NR22

groups.groups.

Amino acids contain both the Amino acids contain both the carboxylic acid group and the amino carboxylic acid group and the amino group, and are therefore amphotericgroup, and are therefore amphoteric

Prof. T. L. Meeks

Introduction to Introduction to HydrocarbonsHydrocarbons

The compounds of carbon are so The compounds of carbon are so numerous that it is convenient to numerous that it is convenient to organize them into families that organize them into families that exhibit similar structures.exhibit similar structures.

The simplest class of organic The simplest class of organic compounds is the hydrocarbons, compounds is the hydrocarbons, compounds composed only of carbon compounds composed only of carbon and hydrogen. Identified easily by and hydrogen. Identified easily by stable C-C bondsstable C-C bonds

Prof. T. L. Meeks


Hydrocarbons can be divided into 4 Hydrocarbons can be divided into 4 general typesgeneral typesalkanes - single bondsalkanes - single bondsalkenes - a double bondalkenes - a double bondalkynes - a triple bondalkynes - a triple bondaromatics - planar ring structurearomatics - planar ring structure

Prof. T. L. Meeks


Alkanes - single bonds onlyAlkanes - single bonds onlysaturated hydrocarbons, contain saturated hydrocarbons, contain

the largest possible number of the largest possible number of hydrogen atoms per carbonhydrogen atoms per carbon

general formula is Cgeneral formula is CnnHH2n+22n+2

Prof. T. L. Meeks


Alkenes - a double bond exists in Alkenes - a double bond exists in moleculemoleculeunsaturated hydrocarbons, do not unsaturated hydrocarbons, do not

contain the largest possible contain the largest possible number of hydrogen atoms per number of hydrogen atoms per carbon, double bond could be carbon, double bond could be broken to add two more hydrogensbroken to add two more hydrogens

general formula is Cgeneral formula is CnnHH2n2n

Prof. T. L. Meeks


Alkynes - a triple bond exists in Alkynes - a triple bond exists in moleculemoleculeunsaturated hydrocarbons, do not unsaturated hydrocarbons, do not

contain the largest possible contain the largest possible number of hydrogen atoms per number of hydrogen atoms per carbon, triple bond could be broken carbon, triple bond could be broken to add four more hydrogensto add four more hydrogens

general formula is Cgeneral formula is CnnHH2n-22n-2

Prof. T. L. Meeks


Aromatics - planar ring structureAromatics - planar ring structureconnected by both sigma and pi connected by both sigma and pi

bonds between carbon atomsbonds between carbon atomsgeneral formula is Cgeneral formula is CnnHH2n-62n-6

Prof. T. L. Meeks


Hydrocarbons are relatively nonpolar, Hydrocarbons are relatively nonpolar, thus are nearly insoluble in water, thus are nearly insoluble in water, but dissolve easily in nonpolar but dissolve easily in nonpolar solvents.solvents.

- melting points and boiling points - melting points and boiling points are determined by London dispersion are determined by London dispersion forces, in general, the larger the forces, in general, the larger the molecule the higher its boiling pointmolecule the higher its boiling point

Prof. T. L. Meeks

AlkanesAlkanes

Prof. T. L. Meeks

AlkanesAlkanes

Written two ways:Written two ways:

Lewis structureLewis structureCondensedCondensed

H H

H - C - HH - C - H CHCH44

HH

Prof. T. L. Meeks

AlkanesAlkanes

StructuresStructuresLewis structures and condensed Lewis structures and condensed

structural formulas do not tell us structural formulas do not tell us anything about the three dimensional anything about the three dimensional shapesshapes

must be predicted using AXE notation must be predicted using AXE notation based on VSEPR theorybased on VSEPR theory

Prof. T. L. Meeks

AlkanesAlkanes

Structural IsomersStructural IsomersThe alkanes listed in the table The alkanes listed in the table

are straight-chain hydrocarbons are straight-chain hydrocarbons because all the carbons are because all the carbons are joined in one continuous chainjoined in one continuous chain

alkanes consisting of four or alkanes consisting of four or more carbon atoms can also more carbon atoms can also form branched chainsform branched chains

Prof. T. L. Meeks

AlkanesAlkanes

Structural IsomersStructural IsomersCompounds with the same Compounds with the same

molecular formula but with molecular formula but with different bonding arrangements different bonding arrangements are called structural isomers.are called structural isomers.

Structural isomers differ slightly Structural isomers differ slightly from one another in physical from one another in physical propertiesproperties

Prof. T. L. Meeks

AlkanesAlkanes

NomenclatureNomenclature1892 IUP met to formulate rules 1892 IUP met to formulate rules

for systematic naming of organic for systematic naming of organic substancessubstances

Chemists everywhere subscribe Chemists everywhere subscribe to a common system for naming to a common system for naming compoundscompounds

Prof. T. L. Meeks

AlkanesAlkanesNomenclatureNomenclature

Find the longest continuous chain of Find the longest continuous chain of carbon atoms, and use the name of carbon atoms, and use the name of this chain as the base name of the this chain as the base name of the compoundcompound

Number the carbon chains in the Number the carbon chains in the longest chain, beginning with the longest chain, beginning with the end of the chain that is nearest a end of the chain that is nearest a substituentsubstituent

Prof. T. L. Meeks


Name and give the location of Name and give the location of each substituent groupeach substituent group

- a substituent - a substituent group that is formed by group that is formed by removing an H from an alkane is removing an H from an alkane is called an alkyl groupcalled an alkyl group

Prof. T. L. Meeks


When two or more substituents When two or more substituents are present, list them in are present, list them in alphabetical orderalphabetical order

Prof. T. L. Meeks

AlkanesAlkanesSample exercise: Name the following Sample exercise: Name the following

alkane:alkane:

CHCH33 - CH - CH - CH - CH33


CHCH33

Prof. T. L. Meeks


alkane:alkane:

CHCH33 - - CH - CHCH - CH33


CHCH33

pentanepentane

Prof. T. L. Meeks


alkane:alkane:

CHCH33 - - CH - CHCH - CH33


CHCH33

2,4 dimethyl pentane2,4 dimethyl pentane

Prof. T. L. Meeks

AlkanesAlkanesSample exercise: Write the Sample exercise: Write the

condensed structural formula for condensed structural formula for 2,3 2,3

dimethyl hexane. dimethyl hexane.

Prof. T. L. Meeks

AlkanesAlkanesSample exercise: Write the Sample exercise: Write the

condensed structural formula for condensed structural formula for 2,3 2,3

dimethyl hexane.dimethyl hexane.

CHCH33CHCH22CHCH22CHCH22CHCH22CHCH33

Prof. T. L. Meeks

AlkanesAlkanesSample exercise: Write the condensed Sample exercise: Write the condensed

structural formula for structural formula for 2,3 dimethyl hexane.2,3 dimethyl hexane.

CHCH33

CHCH33CHCHCHCHCHCH22CHCH22CHCH33

CHCH33

Prof. T. L. Meeks

AlkanesAlkanesCycloalkanes: alkanes can form not Cycloalkanes: alkanes can form not

only branched chains, but also ringsonly branched chains, but also rings or or cycles.cycles.

- sometimes drawn as a simple - sometimes drawn as a simple polygon in which each corner represents a polygon in which each corner represents a CHCH22 group group

- the amount of strain on the - the amount of strain on the

bonds increases in the smaller bonds increases in the smaller

ringsrings

Prof. T. L. Meeks

AlkanesAlkanesReactions of Alkanes: most alkanes are Reactions of Alkanes: most alkanes are

unreactiveunreactive

- at room temp, they do not react - at room temp, they do not react with acids, bases, or strong oxidizerswith acids, bases, or strong oxidizers

- they are not completely inert, a - they are not completely inert, a very important reaction is very important reaction is combustion in aircombustion in air

- when they do react, they will - when they do react, they will substitute another atom for a substitute another atom for a bonded hydrogen (ASS)bonded hydrogen (ASS)

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsThe presence of one or more The presence of one or more

multiple bonds makes unsaturated multiple bonds makes unsaturated hydrocarbons significantly different hydrocarbons significantly different from alkanes both in terms of their from alkanes both in terms of their structures and their activitystructures and their activity

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAlkenes: contain C=C bondAlkenes: contain C=C bond

Names of alkenes are based on the Names of alkenes are based on the longest continuous chain of carbon longest continuous chain of carbon atoms that contain the double bondatoms that contain the double bond

the location of the double bond along the chain is the location of the double bond along the chain is indicated by the number of the carbon atom indicated by the number of the carbon atom nearest the end of the chainnearest the end of the chain

Simplest alkene is ethene (ethylene)Simplest alkene is ethene (ethylene) it is a plant hormone, important in seed it is a plant hormone, important in seed

germination and fruit ripeninggermination and fruit ripening

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAlkenes: when the placement of Alkenes: when the placement of

alkyl groups differ in the geometric alkyl groups differ in the geometric attachment to double bond, attachment to double bond, geometric isomers occur geometric isomers occur

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAlkenes: Alkenes:

Cis isomer: the similar groups are Cis isomer: the similar groups are on the same side of the double on the same side of the double bondbond

Trans isomer: the similar groups are Trans isomer: the similar groups are on opposite sides of the double on opposite sides of the double bondbond

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAlkenes: geometric isomerism arises Alkenes: geometric isomerism arises

because double bonds are because double bonds are resistant to twistingresistant to twisting

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAlkynes: unsaturated hydrocarbons Alkynes: unsaturated hydrocarbons

containing one or more C C bondscontaining one or more C C bondsSimplest alkyne is acetylene, Simplest alkyne is acetylene,

CC22HH22

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAddition reactions: double and triple Addition reactions: double and triple

bonds markedly increases their bonds markedly increases their chemical reactivity. The most chemical reactivity. The most characteristic reactions are characteristic reactions are addition reactions.addition reactions.

- the bond is broken and the - the bond is broken and the reactant is added to the carbons reactant is added to the carbons that formed the multiple bondthat formed the multiple bond

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAddition reactions: halogenationAddition reactions: halogenation

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAddition reactions: hydrogenationAddition reactions: hydrogenation

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsSample exercise: Addition of HCl to Sample exercise: Addition of HCl to

an alkene leads to the formation of an alkene leads to the formation of 2- chloropropane. What is the 2- chloropropane. What is the alkene?alkene?

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsSample exercise: Addition of HCl to Sample exercise: Addition of HCl to

an alkene leads to the formation of an alkene leads to the formation of 2- chloropropane. What is the 2- chloropropane. What is the alkene?alkene?

propenepropene

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsMechanism of Addition Reaction:Mechanism of Addition Reaction:

An explanation of how the reaction occurs An explanation of how the reaction occurs is a reaction mechanismis a reaction mechanism

addition reactions occur in two basic stepsaddition reactions occur in two basic steps first step is the rate determining stepfirst step is the rate determining step the binary molecule being added transfers an the binary molecule being added transfers an

electron to one of the two carbonselectron to one of the two carbons second step involves the addition of the second step involves the addition of the

remaining half of the molecule to the second remaining half of the molecule to the second carboncarbon

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsMechanism of Addition Reaction:Mechanism of Addition Reaction:

An explanation of how the reaction An explanation of how the reaction occurs is a reaction mechanismoccurs is a reaction mechanism

addition reactions occur in two basic addition reactions occur in two basic stepssteps

a pair of electrons can also be donated to a pair of electrons can also be donated to form a new covalent bondform a new covalent bond

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAromaticsAromatics members of a large and important members of a large and important

class of hydrocarbonsclass of hydrocarbons simplest member of the series is simplest member of the series is

benzenebenzeneplanar, highly symmetricalplanar, highly symmetricalgreater stability is due to delocalization greater stability is due to delocalization

of electrons across the pi bondsof electrons across the pi bonds

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAromaticsAromatics each aromatic ring system is given each aromatic ring system is given

a common namea common name aromatic rings arearomatic rings are

written as hexagonswritten as hexagons

with circles in thewith circles in the

centercenter

Prof. T. L. Meeks

Unsaturated HydrocarbonsUnsaturated HydrocarbonsAromaticsAromatics although aromatics are although aromatics are

unsaturated, they do not readily unsaturated, they do not readily undergo addition reactionsundergo addition reactions

the delocalized electrons cause the delocalized electrons cause aromatics to behave differentlyaromatics to behave differently

aromatics undergo substitution aromatics undergo substitution reactionsreactions

Prof. T. L. Meeks

Functional Groups:Functional Groups: Alcohols and Ethers Alcohols and Ethers

The reactivity of organic compounds can The reactivity of organic compounds can be attributed to particular atoms or be attributed to particular atoms or groups of atomsgroups of atoms

A site of reactivity in an organic molecule A site of reactivity in an organic molecule is called a functional group because it is called a functional group because it controls how the molecule behaves or controls how the molecule behaves or functionsfunctions

Each distinct functional group often Each distinct functional group often undergoes the same kind of reactionundergoes the same kind of reaction

Prof. T. L. Meeks


Many of the functional groups contain Many of the functional groups contain other nonmetals such as O and Nother nonmetals such as O and N

Functional groups are represented as Functional groups are represented as being attached to an alkyl groupbeing attached to an alkyl group

R - HR - H

R - OHR - OH

R - COOHR - COOH

Prof. T. L. Meeks


Alcohols: R - OHAlcohols: R - OH name ends in -ol; e is changed to olname ends in -ol; e is changed to ol location is identified by number of location is identified by number of

carbon its attached to when necessarycarbon its attached to when necessary O-H is polar, so these molecules will O-H is polar, so these molecules will

dissolve in waterdissolve in water O-H can also participate in hydrogen O-H can also participate in hydrogen

bondingbonding

Prof. T. L. Meeks


Alcohols: R - OHAlcohols: R - OH Methanol - simplest and has many Methanol - simplest and has many

important usesimportant uses Ethanol - product of fermentation Ethanol - product of fermentation

of carbohydratesof carbohydrates Phenol - attached to an aromaticPhenol - attached to an aromatic

Prof. T. L. Meeks


Alcohols: R - OHAlcohols: R - OH Monohydroxy alcohols are named Monohydroxy alcohols are named

based on placement of OH on based on placement of OH on chainchainprimaryprimarysecondarysecondarytertiarytertiary

Prof. T. L. Meeks


Polyhydroxyl AlcoholsPolyhydroxyl Alcohols ethylene glycol - two OHethylene glycol - two OH glycerol - three OHglycerol - three OH

Prof. T. L. Meeks


EthersEthers created by the dehydration created by the dehydration

reaction of two primary alcoholsreaction of two primary alcohols also referred to as a condensation also referred to as a condensation

reactionreaction Ethers are used as solventsEthers are used as solvents

Prof. T. L. Meeks

Functional Functional Groups:Compounds with a Groups:Compounds with a

Carbonyl GroupCarbonyl GroupA carbonyl group is a double bonded A carbonyl group is a double bonded

oxygen attached to a carbon chainoxygen attached to a carbon chain aldehydesaldehydes ketonesketones carboxylic acidscarboxylic acids estersesters

Prof. T. L. Meeks


Carbonyl GroupCarbonyl GroupA carbonyl group is a double bonded A carbonyl group is a double bonded

oxygen attached to a carbon chainoxygen attached to a carbon chain aldehydes: attached to end of a chainaldehydes: attached to end of a chain ketones: attached to middle of a chainketones: attached to middle of a chain carboxylic acids: attached to end of carboxylic acids: attached to end of

chain with a hydroxy group on same chain with a hydroxy group on same carboncarbon

esters: condensation of alcohol and esters: condensation of alcohol and carboxylic acidcarboxylic acid

Prof. T. L. Meeks


Carbonyl GroupCarbonyl GroupAldehyde and KetonesAldehyde and Ketones R - CHO & R -CO - RR - CHO & R -CO - R prepared by carefully controlled prepared by carefully controlled

oxidation of alcoholsoxidation of alcohols oxidizing agents used are air, oxidizing agents used are air,

hydrogen peroxide, ozone, and hydrogen peroxide, ozone, and potassium dichromatepotassium dichromate

Prof. T. L. Meeks


Carbonyl GroupCarbonyl GroupCarboxylic AcidsCarboxylic Acids R - COOHR - COOH weak acids distributed throughout weak acids distributed throughout

naturenature produced by oxidation of alcoholsproduced by oxidation of alcohols

Prof. T. L. Meeks


Carbonyl GroupCarbonyl GroupEstersEsters R - COO - R’R - COO - R’ condensation reactions between condensation reactions between

carboxylic acid and alcoholcarboxylic acid and alcohol generally have pleasant odorsgenerally have pleasant odors breaking them apart will produce breaking them apart will produce

the alcohol and acidthe alcohol and acid

Prof. T. L. Meeks


Carbonyl GroupCarbonyl GroupAmineAmine organic basesorganic bases general formula Rgeneral formula R33NN

Prof. T. L. Meeks


Carbonyl GroupCarbonyl GroupAmideAmide amine reacting with a carboxylic amine reacting with a carboxylic

acids and undergoing a acids and undergoing a condensation reactioncondensation reaction

Prof. T. L. Meeks

Chirality in Organic Chirality in Organic ChemistryChemistry

A molecule possessing A molecule possessing nonsuperimposable mirror images nonsuperimposable mirror images is termed chiralis termed chiral

Chirality resides in the properties of Chirality resides in the properties of the branches - compounds the branches - compounds containing carbon atoms with four containing carbon atoms with four different attached groups are different attached groups are inherently chiralinherently chiral

Prof. T. L. Meeks


Example: BrExample: Br

CHCH33 - C - CH - C - CH22CHCH22CHCH33

HH

Prof. T. L. Meeks


Nonsuperimposable images are Nonsuperimposable images are called enantiomers.called enantiomers.Designated with labels of R and SDesignated with labels of R and Sidentical physical properties and identical physical properties and

identical chemical properties when identical chemical properties when they react with nonchiral reagents; they react with nonchiral reagents; only in a chiral environment will the only in a chiral environment will the differences showdifferences show

rotation of polarized lightrotation of polarized light

Prof. T. L. Meeks


Chirality is very common, yet not Chirality is very common, yet not often observedoften observedwhen organic molecules are created, when organic molecules are created,

they form the two enantiomers in they form the two enantiomers in equal quantitiesequal quantities

a mixture of these isomers is called a a mixture of these isomers is called a racemic mixtureracemic mixture

racemic mixtures do not rotate light due racemic mixtures do not rotate light due to presence of both enantiomersto presence of both enantiomers

Prof. T. L. Meeks


Finding a single enantiomer present Finding a single enantiomer present is difficultis difficultnaturally occurring substances are naturally occurring substances are

often found as just one enantiomeroften found as just one enantiomerExamples: tartaric acidExamples: tartaric acid

amino acidsamino acids

pharmaceuticals pharmaceuticals

Prof. T. L. Meeks

Introduction to Introduction to BiochemistryBiochemistry

The several types of organic The several types of organic molecules discussed generate a molecules discussed generate a vast array of molecules with very vast array of molecules with very specific chemical reactivities.specific chemical reactivities.

Nowhere is this specificity more Nowhere is this specificity more apparent then biochem apparent then biochem

Prof. T. L. Meeks

Introduction to Introduction to BiochemistryBiochemistry

General observations:General observations: biologically important molecules biologically important molecules

are quite largeare quite large synthesis of these is a very synthesis of these is a very

important aspect of biochemimportant aspect of biochem maintaining a high degree of order maintaining a high degree of order

places additional energetic places additional energetic requirements on organismsrequirements on organisms

Prof. T. L. Meeks

ProteinsProteinsProteins are macromolecular substances Proteins are macromolecular substances

present in all living things.present in all living things. Major structural components in animal Major structural components in animal

tissuetissue catalyze reactions, transport oxygen, serve catalyze reactions, transport oxygen, serve

as hormones and perform other tasksas hormones and perform other tasks all proteins are chemically similar, being all proteins are chemically similar, being

composed of the same basic building composed of the same basic building blocksblocks

Prof. T. L. Meeks

ProteinsProteinsAmino AcidsAmino Acids building blocks are building blocks are -amino acids-amino acids

amino group is located on the carbon amino group is located on the carbon atom immediately adjacent to the atom immediately adjacent to the carboxylic acid groupcarboxylic acid group

HH OO HH OO

HH22NN - - CC - - C - OHC - OH or or ++HH33NN - - CC - - C - OC - O--

R RR R

Prof. T. L. Meeks

ProteinsProteinsAmino AcidsAmino Acids differ in nature of their R groupsdiffer in nature of their R groups 20 needed amino acids - our bodies 20 needed amino acids - our bodies

synthesize 10, and 10 must be synthesize 10, and 10 must be found in naturefound in nature

amino acids are chiral - those found amino acids are chiral - those found in nature are primarily left handedin nature are primarily left handed

Prof. T. L. Meeks

ProteinsProteinsPolypeptides and proteinsPolypeptides and proteins amino acids are linked together by amino acids are linked together by

amide groupsamide groups links are created by peptide bondslinks are created by peptide bonds

a condensation reaction between the acid a condensation reaction between the acid of one amino acid and the amino group of of one amino acid and the amino group of anotheranother

the acid that furnishes the carboxyl group the acid that furnishes the carboxyl group is named first and ends in -ylis named first and ends in -yl

Prof. T. L. Meeks

ProteinsProteinsPolypeptides and proteinsPolypeptides and proteins polypeptides are formed when a polypeptides are formed when a

large number of amino acids are large number of amino acids are linked together by peptide bondslinked together by peptide bonds

proteins are linear with molecular proteins are linear with molecular weights ranging from 6000 to 50 weights ranging from 6000 to 50 million amumillion amu

Prof. T. L. Meeks

ProteinsProteinsProtein structureProtein structure the arrangement, or sequence, of the arrangement, or sequence, of

amino acids is called the amino acids is called the primary primary structurestructure

segments of the protein chain are segments of the protein chain are oriented in a regular fashion, called oriented in a regular fashion, called the the secondary structuresecondary structurea common secondary structure is the a common secondary structure is the

-helix -helix

Prof. T. L. Meeks

ProteinsProteinsFirst proposed by First proposed by Linus Pauling and Linus Pauling and R.B. CoreyR.B. Corey

Held in place by Held in place by hydrogen bond hydrogen bond interactions between interactions between N-H N-H bonds and the O bonds and the O of nearby of nearby carbonyl carbonyl groupsgroups

Prof. T. L. Meeks

ProteinsProteinsProtein structureProtein structure overall shape, determined by all the overall shape, determined by all the

bends and kinks, and sections of bends and kinks, and sections of rodlike rodlike -helical structure is called -helical structure is called tertiary structuretertiary structureone of the most important classes of one of the most important classes of

proteins are enzymes whose tertiary proteins are enzymes whose tertiary structures are very specific with structures are very specific with respect to the reactions they catalyzerespect to the reactions they catalyze

Prof. T. L. Meeks

CarbohydratesCarbohydratesAn important class of naturally An important class of naturally

occurring substances found in both occurring substances found in both plant and animal matter.plant and animal matter.

The name carbohydrate comes from The name carbohydrate comes from the formula of most of these the formula of most of these substances - carbon + watersubstances - carbon + water

Prof. T. L. Meeks

CarbohydratesCarbohydrates

GlucoseGlucose Most abundant carbohydrateMost abundant carbohydrate CC66HH1212OO66 C C66(H(H22O)O)66

these are not really hydrates of these are not really hydrates of carbon, rather they are aldehydes carbon, rather they are aldehydes or ketones with hydroxy groups or ketones with hydroxy groups added to same chainadded to same chain

Prof. T. L. Meeks


GlucoseGlucose Does not normally stay in a Does not normally stay in a

straight line chain, rather it will straight line chain, rather it will react with itself – 1react with itself – 1stst and 5 and 5thth carbons – to form a ring structurecarbons – to form a ring structure

Has two forms, OH’s are on same Has two forms, OH’s are on same side OR on opposite sidesside OR on opposite sides

Prof. T. L. Meeks


DisaccharidesDisaccharides Glucose and fructose, Glucose and fructose,

monosaccharides, cannot be broken monosaccharides, cannot be broken down into smaller moleculesdown into smaller molecules

Two monosaccharides can be linked Two monosaccharides can be linked together during a condensation together during a condensation reaction to form a single larger unit reaction to form a single larger unit called a disaccharidecalled a disaccharide

Prof. T. L. Meeks


DisaccharidesDisaccharides Sucrose and Lactose are two examplesSucrose and Lactose are two examples These sugars are all sweet however These sugars are all sweet however

they vary in the sweetness in a they vary in the sweetness in a randomness not easily explainedrandomness not easily explained

Disaccharides can be hydrolyzed to Disaccharides can be hydrolyzed to break apart into the smaller break apart into the smaller monosaccharidesmonosaccharides

Prof. T. L. Meeks


PolysaccharidesPolysaccharides Made up of many monosaccharide Made up of many monosaccharide

units to form longer chainsunits to form longer chains Starch, glycogen, and cellulose are Starch, glycogen, and cellulose are

the most importantthe most important

Prof. T. L. Meeks


StarchStarch Not a pure substanceNot a pure substance Found in plants and serve as food Found in plants and serve as food

storage in seeds and tubersstorage in seeds and tubers Some starch molecules are Some starch molecules are

branched, others are notbranched, others are not

Prof. T. L. Meeks

CarbohydratesCarbohydratesGlycogenGlycogen Starch-like substance synthesized in Starch-like substance synthesized in

the bodythe body Vary in molecular weightVary in molecular weight Acts as energy bank for body, found in Acts as energy bank for body, found in

high concentrations in the muscles high concentrations in the muscles and the liverand the liverMuscles – immediate energyMuscles – immediate energy

Liver – storage site where glucose levels can be maintainedLiver – storage site where glucose levels can be maintained

Prof. T. L. Meeks


CelluloseCellulose Major structural unit in plantsMajor structural unit in plants Consists of unbranched chain of Consists of unbranched chain of

glucose moleculesglucose molecules Looks very similar to starch, but Looks very similar to starch, but

bonds occur at different anglesbonds occur at different angles Has no caloric ability for body due Has no caloric ability for body due

to different bondingto different bonding

Prof. T. L. Meeks


StarchStarch

CelluloseCellulose

Prof. T. L. Meeks

Nucleic AcidsNucleic Acids

Nucleic acids are biopolymers that Nucleic acids are biopolymers that carry the genetic information of an carry the genetic information of an organismorganism

DNA are the larger molecule; RNA the DNA are the larger molecule; RNA the smallersmaller

DNA is found in the nucleus of the cell; DNA is found in the nucleus of the cell; RNA is found mostly in the cytoplasmRNA is found mostly in the cytoplasm

DNA stores genetic codes and controls DNA stores genetic codes and controls production of proteinsproduction of proteins

Prof. T. L. Meeks


Nucleic acidsNucleic acids Monomers are called nucleotides Monomers are called nucleotides

formed from these unitsformed from these unitsA phosphoric acid moleculeA phosphoric acid moleculeA five carbon sugarA five carbon sugarA nitrogen-containing organic baseA nitrogen-containing organic baseSugar in RNA is called ribose; in DNA Sugar in RNA is called ribose; in DNA

deoxyribosedeoxyribose

Prof. T. L. Meeks


Nucleic acidsNucleic acids 5 bases5 bases

Prof. T. L. Meeks


Nucleic acidsNucleic acids Polynucleotides formed by Polynucleotides formed by

condensation reactions between OH condensation reactions between OH of phosphoric acid of one group and of phosphoric acid of one group and OH group from sugar of anotherOH group from sugar of another

DNA consists of two polynucleotides DNA consists of two polynucleotides wound together in a double helixwound together in a double helix

Prof. T. L. Meeks


DNA consists of two polynucleotides DNA consists of two polynucleotides wound together in a double helixwound together in a double helix

Strands are held together by Strands are held together by attractions between basesattractions between bases

Attractions are London dispersion Attractions are London dispersion forces and hydrogen bondsforces and hydrogen bonds

the chemistry of life: organic and biological chemistry

Documents

organic chemistry

look backsolubility

simple organic molecule

study of carbon compounds

look backvsepr model

ch bonds

prevalent cc

vast number of compounds