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9/29/17

General, Organic, and Chapter 6: Chapter Opener CHAPTER 6: HYDROCARBONS & STRUCTURE • Our relatively diverse diet is remarkably simple at the chemical level: ü Carbohydrates ü Lipids ü ü Nucleic acids ü Vitamins/micronutrients

• The chemical composition of all these biomolecules is

Chapter 1: Measurement, , and MANY ELEMENTS….ONLY A FEW BUILDING BLOCKS TO BIOMOLECULES

Hydrocarbons

General, Organic, and Biochemistry Chapter 6 SIMPLE ORGANIC STRUCTURAL CLASSES • Hydrocarbons can be arranged in a remarkable variety of ways due to the flexible bonding available to carbon atoms • The simplest classification system is based on the type of bond formed between carbon atoms

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General, Organic, and Biochemistry Chapter 6 COMMON PROPERTIES OF HYDROCARBONS

• Nonpolar: Natural Gas Ø Composed of all nonpolar bonds

• Poor water solubility: Ø Hydrophobic = “water fearing” Ø Hydrophilic = “water loving” Petroleum Products

General, Organic, and Biochemistry Chapter 6 – SINGLE BONDED CARBONS • Alkanes are the simplest class of hydrocarbons Ø Composed of carbons sharing only SINGLE bonds Ø Can form (very!) long chains • Each carbon will form 4 separate covalent bonds

Ø The molecular geometry around each carbon is tetrahedral

General, Organic, and Biochemistry Chapter 6 ALKANES NOMENCLATURE • Nomenclature: 1. Number of carbons: specific root for each number 2. Bond structure: always end with –ane

Number of Root Alkane Molecular Carbons Prefix Name Formula

1 Meth CH4

2 Eth Ethane C2H6

3 Prop Propane C3H8

4 But Butane C4H10

5 Pent Pentane C5H12

6 Hex Hexane C6H14

7 Hept Heptane C7H16

8 Oct Octane C8H18

9 Non Nonane C9H20

10 Dec Decane C10H22

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General, Organic, and Biochemistry Chapter 6 ALKANES ARE FLEXIBLE MOLECULES • Single bonds allow for rotation between adjacent carbon atoms

• Alkanes are highly flexible molecules!

General, Organic, and Biochemistry Chapter 6 BRANCHED CHAIN ALKANES • Alkanes do NOT have to be linear….

• Branched alkanes are like trees

• Branching dramatically increases the variety of organic molecules

General, Organic, and Biochemistry Chapter 6 STRUCTURAL • Structural isomers are molecules with the same number & type of atoms, but different bond arrangements

Consider a family of 5 carbon structural isomers

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General, Organic, and Biochemistry Chapter 6 REPRESENTING ALKANE STRUCTURES • Organic chemists use condensed ways of drawing hydrocarbons to simplify structures

• There are three ways to represent hydrocarbons:

Complete Structural Formulas

Condensed Structural Formulas

Skeleton Line Structures

General, Organic, and Biochemistry Chapter 6 NOMENCLATURE FOR BRANCHED ALKANES • Branched alkane nomenclature depends on: 1. Number of atoms in the longest C-C chain 2. The length of side-chains with an –yl on the end 3. The location of side-chains

4-methyl-heptane

General, Organic, and Biochemistry Chapter 6 – DOUBLE BONDED CARBONS • Alkenes contain C=C double bonds Ø Hydrocarbons with double bonds have fewer atoms, and are therefore unsaturated • Carbons with double bonds have only three groups to consider in their shape: Ø molecular geometry is trigonal planar

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General, Organic, and Biochemistry Chapter 6 ALKENE NOMENCLATURE • Alkene Nomenclature: 1. Number of carbons: specific root for each number 2. Bond structure: always end with –ene

Number of Root Alkane Molecular Carbons Prefix Name Formula 1 Meth - -

2 Eth Ethene C2H4

3 Prop Propene C3H6

4 But Butene C4H8

5 Pent Pentene C5H10

6 Hex Hexene C6H12

7 Hept Heptene C7H14

8 Oct Octene C8H16

9 Non Nonene C9H18

10 Dec Decene C10H20

General, Organic, and Biochemistry Chapter 6 ALKENE ROTATION IS CONSTRAINED • Double bonds prevent rotation between adjacent carbon atoms: Ø Such bonds are said to be constrained

• Consider two closely related molecules:

An alkane: An alkene: Butane Butene

C4H10 C4H8

General, Organic, and Biochemistry Chapter 6 ALKENES FORM GEOMETRIC ISOMERS • Geometric Isomers are molecules with opposite rotations around a C=C double bond

• Naming of each depends on arrangement of priority groups around the C=C bond

cis isomer trans isomer (same side) (opposite sides)

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General, Organic, and Biochemistry Chapter 6: Figure 6.12 GEOMETRIC ISOMERS ARE BIOLOGICALLY IMPORTANT FOR VISION

General, Organic, and Biochemistry Chapter 6: Figure 6.12 GEOMETRIC ISOMERS ARE BIOLOGICALLY IMPORTANT FOR VISION

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General, Organic, and Biochemistry Chapter 6 – TRIPLE BONDED CARBONS • Alkynes contain C C triple bonds Ø Composed of carbons with 6 shared • Carbons with triple bonds have only two electron groups to consider in their geometry: Ø Molecular geometry is linear

C2H2

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General, Organic, and Biochemistry Chapter 6 NOMENCLATURE FOR BRANCHED ALKANES • Double and triple bonds take priority in naming branched hydrocarbons: Ø Number of atoms in the longest C-C chain that also contains the double or triple bond

How do we name this ? 2-ethyl-1-butene

General, Organic, and Biochemistry Chapter 6 MAKING RINGS WITH CARBON • HydrocarbonsHydrocarbons do do NOT NOT have have to to be be linear linear….or branched…. • Cyclic hydrocarbons (“rings”) are another type of commonly found in hydrocarbons

Ø Cyclic hydrocarbons are unsaturated Ø Note how the backbone of cyclic alkanes is “kinked” (not flat)

General, Organic, and Biochemistry Chapter 6 BOND STRAIN IN CYCLIC HYDROCARBONS • The # of carbons in a ring affects bond angles Ø Typical cyclic hydrocarbons have 5-8 carbons

• Fewer or more carbons are possible, but create

“ring strain” cyclopropane

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General, Organic, and Biochemistry Chapter 6 NOMENCLATURE FOR CYCLIC HYDROCARBONS• Hydrocarbon rings simply use the prefix cyclo- in front of the alkane name to denote the structure: Ø All C-C single bonds: cyclo____ane Ø Containing a C=C double bond: cyclo_____ene Pentane (C H ) 5 12 Cyclopentane (C5H10)

Note how the C:H ratio helps to identify a cyclic hydrocarbon from a linear or branched hydrocarbon H = 2C + 2 H = 2C

General, Organic, and Biochemistry Chapter 6 CARBON RINGS WITH DOUBLE BONDS • Cyclic hydrocarbons with C=C double bonds in addition to C-C single bonds are more unsaturated: Ø Cyclopentane C5H10 C H Ø Cyclopentene 5 8 • Aromatic rings are formed when all carbons in a ring share C=C double bonds: Ø All carbons in the ring have trigonal planar geometry

This makes aromatic rings very flat

General, Organic, and Biochemistry Chapter 6 COMPLEX CYCLIC HYDROCARBONS • Carbon rings can have their remaining hydrogen atoms substituted with other chemical groups Ø These are called functional groups (Chapter 7) Ø Impart new shapes & chemical properties to organic rings 6-carbon aromatic ring

Functional groups can be added at any carbon

Remember your nomenclature rules!

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General, Organic, and Biochemistry Chapter 6 EMBRACING THE COMPLEXITY • Biologically relevant molecules (biomolecules) are complex organic chemical units Ø Carbon “backbone” decorated with a variety of functional groups

Ø Functional groups (-OH, -NH2, etc) can add new properties (e.g. polarity) to the hydrocarbon backbone

What sort of hydrocarbon Cholesterol shapes are present in this molecule?

What sort of functional groups are attached?

General, Organic, and Biochemistry Chapter 6 SHAPE MATTERS!! • Simple changes to biological hydrocarbons can have dramatic effects on physical properties

• Biochemistry is largely a study of how small chemical changes alter shape & function of biomolecules:

Palmitic acid Linolenic acid

Unsaturated Saturated fatty acid fatty acid

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