1 carbon and the molecular diversity of life chapter 4 site: wikipedia.org
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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