Carbon and the Molecular Diversity of Life chapter 4

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Carbon and the Molecular Diversity of
Lifechapter 4
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CarbonThe Backbone of Biological Molecules

• Cells 7095 water remainder mostly
  carbon-based compounds
• Unparalleled ability to form large, complex,
  diverse molecules
• Proteins, DNA, carbohydrates, and other molecules
  that distinguish living matter are all composed
  of carbon compounds

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Organic chemistry -- the study of carbon compounds

• Organic compounds -- simple molecules to colossal
  ones
• simplest -- hydrogen atoms in addition to carbon
  atoms

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Carbon atoms form diverse molecules by bonding to
up to four other atoms
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LE 2-8
Helium 2He
Hydrogen 1H
2 He 4.00
Atomic number
Atomic mass
Element symbol
First shell
Electron-shell diagram
Lithium 3Li
Beryllium 4Be
Boron 5B
Carbon 6C
Nitrogen 7N
Oxygen 8O
Fluorine 9F
Neon 10Ne
Second shell
Sodium 11Na
Magnesium 12Mg
Aluminum 12Al
Silicon 14Si
Sulfur 16S
Chlorine 17Cl
Argon 18Ar
Phosphorus 15P
Third shell
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• Carbon and partners (hydrogen, oxygen, and
  nitrogen) -- building blocks of organic molecules

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Components of Carbon Diversity

• Skeleton Variation
• Isomerization
• Functional Groups

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• Each carbon bonded to four other atoms has a
  tetrahedral shape
• Two carbon atoms joined in a double bond, the
  molecule is flat

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LE 4-3
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Molecular Diversity Arising from Carbon Skeleton
Variation

• Carbon chains form the skeletons of most organic
  molecules
• Carbon chains vary in length and shape
• single, double, or triple
• straight or branched chains
• rings
• Bond with many different elements

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LE 4-5
Ethane
Propane
Length
2-methylpropane (commonly called isobutane)
Butane
Branching
1-Butene
2-Butene
Double bonds
Cyclohexane
Benzene
Rings
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Ethane
Propane
Cyclopentane
Benzene
1-Butene
2-Butene
Isopentane
Isobutane
Histidine (an amino acid)
Fig. 3-1, p. 46
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Isomers

• Isomers are compounds with the same molecular
  formula but different structures and properties
• Structural isomers -- different covalent
  arrangements of their atoms

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Isomers

• Structural isomers
• different covalent arrangements

Dimethyl ether (C2H6O)
Ethanol (C2H6O)
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Isomers

• Isomers are compounds with the same molecular
  formula but different structures and properties
• Structural isomers -- different covalent
  arrangements of their atoms
• Geometric isomers -- covalent arrangements but
  differ in spatial arrangements

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Isomers

• Geometric isomers (cistrans isomers)
• different spatial arrangements

cis-2-butene
trans-2-butene
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Isomers

• Isomers are compounds with the same molecular
  formula but different structures and properties
• Structural isomers -- different covalent
  arrangements of their atoms
• Geometric isomers -- covalent arrangements but
  differ in spatial arrangements
• Enantiomers -- mirror images of each other

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Isomers

• Enantiomers
• mirror images

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Enantiomers

• Important in the pharmaceutical industry
• Different enantiomers may have different effects
• Organisms are sensitive to even subtle variations

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LE 4-7
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Isomers

• Isomers are compounds with the same molecular
  formula but different structures and properties
• Structural isomers -- different covalent
  arrangements of their atoms
• Geometric isomers -- covalent arrangements but
  differ in spatial arrangements
• Enantiomers -- mirror images of each other
• SHAPE -- critical

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Molecular Shape and Function

• shape very important (can be critical) to
  function
• shape determined by the positions of its atoms
  valence orbitals
• In a covalent bond, the s and p orbitals may
  hybridize, creating specific molecular shapes

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LE 2-16a
Four hybrid orbitals
z
Three p orbitals
s orbital
x
y
Tetrahedron
Hybridization of orbitals
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• Biological molecules (especially proteins)
  recognize and interact with each other with a
  specificity based on molecular shape
• Molecules with similar shapes can have similar
  biological effects

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LE 2-17a
Carbon
Nitrogen
Hydrogen
Sulfur
Natural endorphin
Oxygen
Morphine
Structures of endorphin and morphine
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Functional groups -- involved in chemical
reactions

• Distinctive properties
• depend not only on the carbon skeleton
• depend on the molecular components attached to it

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LE 4-9
Estradiol
Female lion
Testosterone
Male lion
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Functional Groups

• Properties depend on functional groups
• Polar -- hydroxyl and carbonyl groups
• Non-polar -- alkyl
• Acidic and Basic
• carboxyl and phosphate groups (acidic)
• amino groups (basic)

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Most important Functional Groups

• Hydrocarbons -- Alkyl most common
• Alkenyl and Alkynyl
• Hydroxyl group -- ROH
• Carbonyl group -- RCOR'
• Aldehyde group -- RCOH
• Carboxyl group -- RCOOH
• Ester group -- RCOOR'
• Amino group
• Phosphate group
• Sulfhydryl group

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Hydrocarbons

• Organic compounds
• nonpolar
• carbon and hydrogen only
• hydrophobic
• Methyl group

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Polar and Ionic Functional Groups

• Partial charges on atoms
• at opposite ends of a bond
• interact with one another
• hydrophilic
• Hydroxyl and carbonyl groups

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LE 4-10aa
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LE 4-10ab
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Acidic and Basic Groups

• Acidic
• release hydrogen ions
• become negatively charged
• carboxyl and phosphate groups

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LE 4-10ac
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LE 4-10bc
ATP Adenosine TriPhosphate
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Acidic and Basic Groups

• Acidic
• release hydrogen ions
• become negatively charged
• carboxyl and phosphate groups
• Basic
• release hydroxide ions
• become positively charged
• amino group

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LE 4-10ba
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LE 4-10bb
EXAMPLE
STRUCTURE
(may be written HS)
Ethanethiol
FUNCTIONAL PROPERTIES
NAME OF COMPOUNDS
Two sulfhydryl groups can interact to help
stabilize protein structure (see Figure 5.20).
Thiols
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Also RCOOR'
Table 3-1a, p. 49
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Table 3-1b, p. 49
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ATP An Important Source of Energy for Cellular
Processes

• One phosphate molecule, adenosine triphosphate
  (ATP), is the primary energy-transferring
  molecule in the cell
• ATP consists of an organic molecule called
  adenosine attached to a string of three phosphate
  groups

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The Chemical Elements of Life A Review

• The versatility of carbon makes possible the
  great diversity of organic molecules
• Variation at the molecular level lies at the
  foundation of all biological diversity