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Carbon and the Carbon and the Molecular Diversity Molecular Diversity

of Lifeof Lifechapter 4chapter 4

Site: wikipedia.org

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Carbon—The Backbone of Carbon—The Backbone of Biological MoleculesBiological Molecules

Cells 70–95% water – remainder mostly Cells 70–95% water – remainder mostly carbon-based compoundscarbon-based compounds Unparalleled ability to form large, complex, Unparalleled ability to form large, complex,

diverse moleculesdiverse molecules

Proteins, DNA, carbohydrates, and other Proteins, DNA, carbohydrates, and other molecules that distinguish living matter molecules that distinguish living matter are all composed of carbon compoundsare all composed of carbon compounds

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Organic chemistry -- the Organic chemistry -- the study of carbon study of carbon

compoundscompounds Organic compounds -- simple Organic compounds -- simple

molecules to colossal onesmolecules to colossal ones simplest -- hydrogen atoms in addition simplest -- hydrogen atoms in addition

to carbon atomsto carbon atoms

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Carbon atoms form Carbon atoms form diverse molecules by diverse molecules by bonding to up to four bonding to up to four

other atomsother atoms

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LE 2-8LE 2-8

Firstshell

Hydrogen

1H

Lithium

3Li

Secondshell

Thirdshell

Sodium

11Na

Beryllium

4Be

Magnesium

12Mg

Boron

5B

Aluminum

12AlSilicon

14Si

Carbon

6CNitrogen

7N

Phosphorus

15P

Oxygen

8O

Sulfur

16SChlorine

17Cl

Fluorine

9FNeon

10Ne

Argon

18Ar

Helium

2HeAtomic number

Element symbol

Electron-shelldiagram

Atomic mass

2He4.00

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Carbon and partners (hydrogen, Carbon and partners (hydrogen, oxygen, and nitrogen) -- building oxygen, and nitrogen) -- building blocks of organic moleculesblocks of organic molecules

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

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Components of Carbon Components of Carbon DiversityDiversity

Skeleton VariationSkeleton Variation IsomerizationIsomerization Functional GroupsFunctional Groups

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Each carbon bonded to four other Each carbon bonded to four other atoms has a tetrahedral shapeatoms has a tetrahedral shape Two carbon atoms joined in a double Two carbon atoms joined in a double

bond, the molecule is flatbond, the molecule is flat

LE 4-3LE 4-3

MolecularFormula

StructuralFormula

Ball-and-StickModel

Space-FillingModel

Methane

Ethane

Ethene (ethylene)

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Molecular Diversity Molecular Diversity Arising from Carbon Arising from Carbon Skeleton VariationSkeleton Variation

Carbon chains form the skeletons of Carbon chains form the skeletons of most organic moleculesmost organic molecules

Carbon chains vary in length and Carbon chains vary in length and shapeshape single, double, or triplesingle, double, or triple straight or branched chainsstraight or branched chains ringsrings

Bond with many different elementsBond with many different elements

LE 4-5LE 4-5

LengthEthane Propane

Butane 2-methylpropane(commonly called isobutane)

Branching

Double bonds

Rings

1-Butene2-Butene

CyclohexaneBenzene

13Fig. 3-1, p. 46

Cyclopentane

Ethane

1-Butene

Isobutane

Propane

2-Butene

Isopentane Histidine (an amino acid)

Benzene

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IsomersIsomers Isomers are compounds with the same Isomers are compounds with the same

molecular formula but different molecular formula but different structures and propertiesstructures and properties Structural isomers -- different covalent Structural isomers -- different covalent

arrangements of their atomsarrangements of their atoms

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Dimethyl ether (C2H6O)Ethanol (C2H6O)

IsomersIsomers Structural isomersStructural isomers

different covalent arrangementsdifferent covalent arrangements

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IsomersIsomers Isomers are compounds with the same Isomers are compounds with the same

molecular formula but different molecular formula but different structures and propertiesstructures and properties Structural isomers -- different covalent Structural isomers -- different covalent

arrangements of their atomsarrangements of their atoms Geometric isomers -- covalent Geometric isomers -- covalent

arrangements but differ in spatial arrangements but differ in spatial arrangementsarrangements

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IsomersIsomers Geometric isomersGeometric isomers ( (ciscis––trans trans

isomers)isomers) different spatial arrangementsdifferent spatial arrangements

cis-2-butenetrans-2-butene

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IsomersIsomers Isomers are compounds with the same Isomers are compounds with the same

molecular formula but different molecular formula but different structures and propertiesstructures and properties Structural isomers -- different covalent Structural isomers -- different covalent

arrangements of their atomsarrangements of their atoms Geometric isomers -- covalent Geometric isomers -- covalent

arrangements but differ in spatial arrangements but differ in spatial arrangementsarrangements

Enantiomers -- mirror images of each Enantiomers -- mirror images of each otherother

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IsomersIsomers

EnantiomersEnantiomers mirror imagesmirror images

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Important in the pharmaceutical industryImportant in the pharmaceutical industry Different enantiomers may have different Different enantiomers may have different

effectseffects Organisms are sensitive to even subtle Organisms are sensitive to even subtle

variationsvariations

EnantiomersEnantiomers

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LE 4-7LE 4-7

Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane.

Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon.

cis isomer: The two Xsare on the same side.

trans isomer: The two Xsare on opposite sides.

L isomer D isomer

Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.

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IsomersIsomers Isomers are compounds with the same Isomers are compounds with the same

molecular formula but different structures molecular formula but different structures and propertiesand properties Structural isomers -- different covalent Structural isomers -- different covalent

arrangements of their atomsarrangements of their atoms Geometric isomers -- covalent arrangements Geometric isomers -- covalent arrangements

but differ in spatial arrangementsbut differ in spatial arrangements Enantiomers -- mirror images of each otherEnantiomers -- mirror images of each other

SHAPESHAPE -- critical -- critical

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Molecular Shape and Molecular Shape and FunctionFunction

shape shape veryvery important (can be important (can be critical) to functioncritical) to function

shape determined by the shape determined by the positions of its atoms’ valence positions of its atoms’ valence orbitalsorbitals

In a covalent bond, the In a covalent bond, the ss and and pp orbitals may hybridize, creating orbitals may hybridize, creating specific molecular shapesspecific molecular shapes

LE 2-16aLE 2-16a

s orbitalz

x

y

Three p orbitalsFour hybrid orbitals

Tetrahedron

Hybridization of orbitals

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Biological molecules (Biological molecules (especially especially proteinsproteins) recognize and interact ) recognize and interact with each other with a specificity with each other with a specificity based on molecular shapebased on molecular shape

Molecules with similar shapes Molecules with similar shapes can have similar biological can have similar biological effectseffects

LE 2-17aLE 2-17a

Naturalendorphin

Morphine

Carbon

Hydrogen

Nitrogen

Sulfur

Oxygen

Structures of endorphin and morphine

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Functional groups -- Functional groups -- involved in chemical involved in chemical

reactionsreactions

Distinctive properties Distinctive properties depend not only on the carbon depend not only on the carbon

skeleton skeleton depend on the molecular depend on the molecular

components attached to itcomponents attached to it

LE 4-9LE 4-9

Estradiol

Testosterone

Male lion

Female lion

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Functional GroupsFunctional Groups

Properties depend on Properties depend on functional functional groupsgroups: : Polar -- hydroxyl and carbonyl groupsPolar -- hydroxyl and carbonyl groups Non-polar -- alkylNon-polar -- alkyl Acidic and BasicAcidic and Basic

o carboxyl and phosphate groups (acidic)carboxyl and phosphate groups (acidic)o amino groups (basic)amino groups (basic)

Most important Functional Most important Functional GroupsGroups

Hydrocarbons -- Alkyl most common Hydrocarbons -- Alkyl most common Alkenyl and AlkynylAlkenyl and Alkynyl

Hydroxyl group -- ROHHydroxyl group -- ROH Carbonyl group -- RCOR′ Carbonyl group -- RCOR′

Aldehyde group -- RCOHAldehyde group -- RCOH Carboxyl group -- RCOOHCarboxyl group -- RCOOH

Ester group -- RCOOR′Ester group -- RCOOR′ Amino groupAmino group Phosphate groupPhosphate group Sulfhydryl groupSulfhydryl group

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HydrocarbonsHydrocarbons

Organic compoundsOrganic compounds nonpolarnonpolar carbon and hydrogen onlycarbon and hydrogen only hydrophobic hydrophobic

Methyl groupMethyl group

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Polar and Ionic Polar and Ionic Functional Groups Functional Groups

Partial charges on atomsPartial charges on atoms at opposite ends of a bondat opposite ends of a bond interact with one anotherinteract with one another hydrophilichydrophilic

HydroxylHydroxyl and and carbonylcarbonyl groups groups

LE 4-10aaLE 4-10aa

STRUCTURE

(may be written HO—)

NAME OF COMPOUNDS

Alcohols (their specific names

usually end in -ol)

Ethanol, the alcohol present in

alcoholic beverages

FUNCTIONAL PROPERTIES

Is polar as a result of the

electronegative oxygen atom

drawing electrons toward itself.

Attracts water molecules, helping

dissolve organic compounds such

as sugars (see Figure 5.3).

LE 4-10abLE 4-10ab

STRUCTURE

NAME OF COMPOUNDS

Ketones if the carbonyl group is

within a carbon skeleton

EXAMPLE

Acetone, the simplest ketone

A ketone and an aldehyde may

be structural isomers with

different properties, as is the case

for acetone and propanal.

Aldehydes if the carbonyl group is

at the end of the carbon skeleton

Acetone, the simplest ketone

Propanal, an aldehyde

FUNCTIONAL PROPERTIES

RCOR′

RCOH

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Acidic and Basic GroupsAcidic and Basic Groups

AcidicAcidic release hydrogen ions release hydrogen ions become negatively chargedbecome negatively charged carboxylcarboxyl and and phosphatephosphate groupsgroups

LE 4-10acLE 4-10ac

STRUCTURE

NAME OF COMPOUNDS

Carboxylic acids, or organic acids

EXAMPLE

Has acidic properties because it isa source of hydrogen ions.

Acetic acid, which gives vinegarits sour taste

FUNCTIONAL PROPERTIES

The covalent bond betweenoxygen and hydrogen is so polarthat hydrogen ions (H+) tend todissociate reversibly; for example,

Acetic acid Acetate ion

In cells, found in the ionic form,which is called a carboxylate group.

RCOOH -- /carboxyl group makes acidsRCOOR′ -- Ester group

LE 4-10bcLE 4-10bc

STRUCTURE

NAME OF COMPOUNDS

Organic phosphates

EXAMPLE

Glycerol phosphate

FUNCTIONAL PROPERTIES

Makes the molecule of which it

is a part an anion (negatively

charged ion).

Can transfer energy between

organic molecules.

ATP – Adenosine TriPhosphate

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Acidic and Basic GroupsAcidic and Basic Groups

AcidicAcidic release hydrogen ions release hydrogen ions become negatively chargedbecome negatively charged carboxylcarboxyl and and phosphatephosphate groupsgroups

BasicBasic release hydroxide ionsrelease hydroxide ions become positively chargedbecome positively charged aminoamino group group

LE 4-10baLE 4-10ba

STRUCTURE

NAME OF COMPOUNDS

Amine

EXAMPLE

Because it also has a carboxyl

group, glycine is both an amine and

a carboxylic acid; compounds with

both groups are called amino acids.

FUNCTIONAL PROPERTIES

Acts as a base; can pick up a

proton from the surrounding

solution:

(nonionized)

Ionized, with a charge of 1+,under cellular conditions

Glycine

(ionized)

STRUCTURE

(may be written HS—)

NAME OF COMPOUNDS

Thiols

EXAMPLE

Ethanethiol

FUNCTIONAL PROPERTIES

Two sulfhydryl groups can

interact to help stabilize protein

structure (see Figure 5.20).

LE 4-10bbLE 4-10bb

41Table 3-1a, p. 49

Also RCOOR′

42Table 3-1b, p. 49

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ATP: An Important Source ATP: An Important Source of Energy for Cellular of Energy for Cellular

ProcessesProcesses One phosphate molecule, adenosine One phosphate molecule, adenosine

triphosphate (ATP), is the primary triphosphate (ATP), is the primary energy-transferring molecule in the cell energy-transferring molecule in the cell

ATP consists of an organic molecule ATP consists of an organic molecule called adenosine attached to a string of called adenosine attached to a string of three phosphate groupsthree phosphate groups

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The Chemical Elements The Chemical Elements of Life: of Life: A ReviewA Review

The versatility of carbon makes The versatility of carbon makes possible the great diversity of organic possible the great diversity of organic moleculesmolecules

Variation at the molecular level lies at Variation at the molecular level lies at the foundation of all biological diversitythe foundation of all biological diversity