chapter 4 lecture-5

8/3/2019 Chapter 4 Lecture-5

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Chapter 4 Lecture

Organic Chemistry


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Although ce

lls are 70-95% water, the restconsists most ly of carbon-based compounds.

P roteins, DN A , carbohydrates, and other mo lecu les that distinguish l iving matter frominorganic materia l are a ll composed of carbonatoms bonded to each other and to atoms of other e lements.

These other e lements common ly inc lude hydrogen(H), oxygen (O), nitrogen (N), su lfur (S), and

phosphorus ( P ).

Introduction

Copyright 2002 P earson Education, Inc., pub l ishing as Benjamin Cummings


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The study of carbon compounds, organicchemistry, focuses on any compound withcarbon (organic compounds). Whi le the name, organic compounds, imp l ies that

these compounds can on ly come from bio logica l processes, they can be synthesized by non- l ivingreactions.

Organic compounds can range from the simp le (CO 2or CH 4) to comp lex mo lecu les, l ike proteins, that mayweigh over 100,000 da l tons.

1. Organic chemistry is the study of carbon compounds



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The overa ll percentages of the major e lementsof l ife (C, H, O, N, S, and P ) are quite uniformfrom one organism to another.However, because of carbons versati l ity, thesefew e lements can be combined to bui ld an

inexhaustib le variety of organic mo lecu les.Whi le the percentages of major e lements do notdiffer within or among species, variations in

organic molecu

les can distinguish even betweenindividua ls of a sing le species.



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Support for vita l ism began to wane as organicchemists learned to synthesize more comp lexorganic compounds in the laboratory. In the ear ly 1800s the German chemist Friedrich

Wh ler and his students were ab le to synthesize urea

from totall

y inorganic starting materials.

In 1953, Stan ley Mi ll er at theUniversity of Chicago was ab leto simu late chemica l conditionson the primitive Earth todemonstrate the spontaneoussynthesis of organic compounds.

Copyright 2002 P earson Education, Inc., pub l ishing as Benjamin CummingsF ig. 4.1


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Organic chemists fina ll y rejected vita l ism andembraced mechanism . Under mechanism, a ll natura l phenomena, inc luding

the processes of l ife, are governed by the same physica l and chemica l laws.

Organic chemistry was redefined as the study of carbon compounds regard less of origin. Sti ll , most organic compounds in an amazing

diversity and comp lexity are produced byorganisms.

However, the same ru les app ly to inorganic andorganic compounds a l ike.



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With a tota l of 6 e lectrons, a carbon atom has 2 inthe first she ll and 4 in the second she ll . Carbon has l itt le tendency to form ionic bonds by

loosing or gaining 4 e lectrons. Instead, carbon usua ll y comp letes its va lence she ll by

sharing e lectrons with other atoms in four cova lent bonds.

This tetravalence by carbon makes large, comp lexmo lecu les possib le.

2 . Carbon atoms are the most versatilebuilding blocks of molecules



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When carbon forms cova lent bonds with four other atoms, they are arranged at the corners of an imaginary tetrahedron with bond ang les near 109 o. Whi le drawn f lat, they are actua ll y three-dimensiona l .

When two carbon atoms are joined by a doub le bond, a ll bonds around the carbons are in thesame p lane.

They have a f lat, three-dimensiona

lstructure.



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F ig. 4. 2


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The e lectron configuration of carbon gives itcompatibi l ity to form cova lent bonds with manydifferent e lements.The va lences of carbon and its partners can beviewed as the bui lding code that governs the

architecture of organic mo lecu les.


F ig. 4.3


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In carbon dioxide, one carbon atom forms twodoub le bonds with two different oxygen atoms.

The structura l formu la, O = C = O, shows that eachatom has comp leted its va lence she ll s.

Whi le CO 2 can be c lassified at either organic or inorganic, its importance to the l iving wor ld is c lear.

CO 2 is the source for a ll organic mo lecu les in organisms viathe process of photosynthesis.

Urea, CO(NH 2) 2, is another simp le organic mo lecu le in

which each atom has enoughcova lent bonds to comp leteits va lence she ll .



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Carbon chains form the ske letons of most

organic molecu

les. The ske letons may vary in length and may be

straight, branched, or arranged in c losed rings. The carbon ske letons may a lso inc lude doub le bonds.

3. Variation in carbon skeletonscontributes to the diversity of organic

molecules



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F ig. 4.4


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H ydrocarbons are organic mo lecu les thatconsist of on ly carbon and hydrogen atoms. Hydrocarbons are the major component of petro leum. P etro leum is a fossi l fue l because it consists of the

partia ll y decomposed remains of organisms that l ived

mill

ions of years ago.Fats are bio logica l mo lecu les that havelong hydrocarbontai ls attached to anon-hydrocarboncomponent.

F ig. 4.5


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Isomers are compounds that have the samemo lecu lar formu la but different structures and

therefore different chemica l properties. For examp le, butane and isobutane have the same

mo lecu lar formu la C 4H10, but butane has a straightske leton and isobutane has a branched ske leton.

The two butanes are structural isomers ,mo lecu les with the same mo lecu lar formu la butdiffer in the cova lent arrangement of atoms.


Fig. 4.6a


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G eometric isomers are compounds with thesame cova lent partnerships that differ in their spatia l arrangement around a carbon-carbondoub le bond. The doub le bond does not a ll ow atoms to rotate

freely around the bond axis.

The biochemistry of vision invo lves a l ight-inducedchange in the structure of rhodopsin in the retinafrom one geometric isomer to another.


F ig. 4.6b


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E nantiomers are mo lecu les that are mirror images of each other Enantiomers are possib le if there are four different

atoms or groups of atoms bonded to a carbon. If this is true, it is possib le to arrange the four groups

in space in two different ways that are mirror images. They are l ike

left-handed andright-handed

versions. Usua ll y one is

bio logica ll y active,the other inactive.


F ig. 4.6c


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Even the subt le structura l differences in twoenantiomers have important functiona l significance because of emergent propertiesfrom the specific arrangements of atoms. One enantiomer of the drug tha l idomide reduced

morning sickness, its desired effect, but the other isomer caused severe birth defects.

The L-Dopa isomer

is an effective treatmentof P arkinsons disease,

but the D-Dopa isomer is inactive.

Copyright 2002 P earson Education, Inc., pub l ishing as Benjamin CummingsF ig. 4.7


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The components of organic mo lecu les that aremost common ly invo lved in chemica l reactionsare known as functional groups . Functiona l groups are attachments that rep lace one or

more hydrogen atoms to the carbon ske leton of thehydrocarbon.

Each functiona l groups behaves consistent ly fromone organic mo lecu le to another.The number and arrangement of functiona l groupshe l p give each mo lecu le its unique properties.

1. F unctional groups contribute tothe molecular diversity of life



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The basic structure of testosterone (ma lehormone) and estradio l (fema le hormone) isidentica l .

Both are steroids with four fused carbon rings, but theydiffer in the functiona l groups attached to the rings.

These then interact with different targets in the body.


Fig. 4.8


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There are six functiona l groups that are mostimportant to the chemistry of l ife: hydroxy l ,carbony l , carboxy l , amino, su lfhydry l , and

phosphate groups. All are hydrophi l ic and increase so lubi l ity of organic

compounds in water.



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In a hydroxyl group (-OH), a hydrogen atomforms a po lar cova lent bond with an oxygenwhich forms a po lar cova lent bond to thecarbon ske leton. Because of these po lar cova lent bonds hydroxy l

groups improve the solubi

lity of organic mo

lecu

les.

Organic compounds with hydroxy l groups arealcohols and their names typica ll y end in -o l.



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A carbonyl group (=CO) consists of an oxygenatom joined to the carbon ske leton by a doub le

bond. If the carbony l group is on the end of the ske leton,the compound is an aldelhyde .

If not, then the compound is a ketone .

Isomers with aldehydes versus ketones have different properties.



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A carboxyl group (-COOH) consists of a carbonatom with a doub le bond with an oxygen atomand a sing le bond to a hydroxy l group. Compounds with carboxy l groups are carboxylic

acids . A carboxy l group acts as an acid because the

combined e lectronegativities of the two adjacentoxygen atoms increase the dissociation of hydrogenas an ion (H +).



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A n amino group (-NH 2) consists of a nitrogenatom attached to two hydrogen atoms and the

carbon ske leton. Organic compounds with amino groups are amines . The amino group acts as a base because ammonia

can pick up a hydrogen ion (H +) from the so lution.

A

mino acids, the building b

locks of proteins, haveamino and carboxy l groups.



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A sulfhydryl group (-SH) consists of a su lfur atom bonded to a hydrogen atom and to the

backbone. This group resemb les a hydroxy l group in shape. Organic mo lecu les with su lfhydry l groups are

thiols . Su lfhydry l groups he l p stabi l ize the structure of

proteins.



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A phosphate group (-O P O32-) consists of phosphorus bound to four oxygen atoms (threewith sing le bonds and one with a doub le bond). A phosphate group connects to the carbon backbone

via one of its oxygen atoms. P hosphate groups are anions with two negative

charges as two protons have dissociated from theoxygen atoms.

One function of phosphate groups is to transfer energy between organic mo lecu les.



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Living matter consists mainly of carbon, oxygen,hydrogen, and nitrogen, with sma ll er amounts of

su lfur and phosphorus.These e lements are l inked by strong cova lent

bonds.Carbon with its four cova lent bonds is the basic

bui lding b lock in mo lecu lar architecture.The great diversity of organic mo lecu les withtheir specia l properties emerge from the uniquearrangement of the carbon ske leton and the

functiona l groups attached to the ske leton.

2 . The chemical elements of life: a review


chapter 4 lecture-5

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