organic and biological chemistry organic and biological chemistry

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Organic and Biological Chemistry Organic and Biological Chemistry

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Page 1: Organic and Biological Chemistry Organic and Biological Chemistry

Organic andBiologicalChemistry

Organic and Biological Chemistry

Page 2: Organic and Biological Chemistry Organic and Biological Chemistry

Organic andBiologicalChemistry

Organic Chemistry

• Organic chemistry is the chemistry of carbon compounds.

• Carbon has the ability to form long chains.

• Without this property, large biomolecules such as proteins, lipids, carbohydrates, and nucleic acids could not form.

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Structure of Carbon Compounds

• There are three hybridization states and geometries found in organic compounds:– sp3 Tetrahedral– sp2 Trigonal planar– sp Linear

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Hydrocarbons

• There are four basic types of hydrocarbons:– Alkanes– Alkenes– Alkynes– Aromatic hydrocarbons

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Properties of Alkanes

• The only van der Waals force is the London dispersion force.

• The boiling point increases with the length of the chain.

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Alkanes

• Alkanes contain only single bonds.• They are also known as saturated

hydrocarbons.– They are “saturated” with hydrogens.

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Formulas

• Lewis structures of alkanes look like this.• They are also called structural formulas.• They are often not convenient, though…

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Formulas

…so more often condensed formulas are used.

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Structure of Alkanes

• Carbons in alkanes are sp3 hybrids.• They have a tetrahedral geometry and 109.5°

bond angles.

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Structure of Alkanes

• There are only -bonds in alkanes.

• There is free rotation about the C—C bonds.

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Isomers

Isomers have the same molecular formulas, but the atoms are bonded in a different order.

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Organic Nomenclature

• There are three parts to a compound name:– Base: This tells how many carbons are in the

longest continuous chain.

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Organic Nomenclature

• There are three parts to a compound name:– Base: This tells how many carbons are in the

longest continuous chain.– Suffix: This tells what type of compound it is.

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Organic andBiologicalChemistry

Organic Nomenclature

• There are three parts to a compound name:– Base: This tells how many carbons are in the

longest continuous chain.– Suffix: This tells what type of compound it is.– Prefix: This tells what groups are attached to the

chain.

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How to Name a Compound

1. Find the longest chain in the molecule.

2. Number the chain from the end nearest the first substituent encountered.

3. List the substituents as a prefix along with the number(s) of the carbon(s) to which they are attached.

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How to Name a Compound

If there is more than one type of substituent in the molecule, list them alphabetically.

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Cycloalkanes

• Carbon can also form ringed structures.• Five- and six-membered rings are most stable.

– They can take on conformations in which their bond angles are very close to the tetrahedral angle.

– Smaller rings are quite strained.

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Reactions of Alkanes

• Alkanes are rather unreactive due to the presence of only C—C and C—H -bonds.

• Therefore, they make great nonpolar solvents.

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Alkenes

• Alkenes contain at least one carbon–carbon double bond.

• They are unsaturated.– That is, they have fewer than the maximum number of

hydrogens.

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Structure of Alkenes

• Unlike alkanes, alkenes cannot rotate freely about the double bond.– The side-to-side overlap in the -bond makes this

impossible without breaking the -bond.

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Structure of Alkenes

This creates geometric isomers, which differ from each other in the spatial arrangement of groups about the double bond.

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Properties of Alkenes

Structure also affects the physical properties of alkenes.

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Nomenclature of Alkenes• The chain is numbered so the double bond gets the

smallest possible number.• cis-Alkenes have the carbons in the chain on the

same side of the molecule.• trans-Alkenes have the carbons in the chain on

opposite sides of the molecule.

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Alkynes

• Alkynes contain at least one carbon–carbon triple bond.

• The carbons in the triple bond are sp-hybridized and have a linear geometry.

• They are also unsaturated.

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Nomenclature of Alkynes

• The method for naming alkynes is analogous to the naming of alkenes.

• However, the suffix is -yne rather than -ene.

4-methyl-2-pentyne

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Reactions of Alkynes

• Alkynes undergo many of the same reactions alkenes do.

• As with alkenes, the impetus for reaction is the replacement of -bonds with -bonds.

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Aromatic Hydrocarbons

• Aromatic hydrocarbons are cyclic hydrocarbons that have some particular features.

• There is a p-orbital on each atom.– The molecule is planar.

• There is an odd number of electron pairs in the -system.

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Aromatic Nomenclature

Many aromatic hydrocarbons are known by their common names.

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Reactions of Aromatic Compounds• In aromatic

compounds, unlike in alkenes and alkynes, each pair of -electrons does not sit between two atoms.

• Rather, the electrons are delocalized; this stabilizes aromatic compounds.

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Reactions of Aromatic Compounds

• Due to this stabilization, aromatic compounds do not undergo addition reactions; they undergo substitution.

• In substitution reactions, hydrogen is replaced by a substituent.

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Structure of Aromatic Compounds

• Two substituents on a benzene ring could have three possible relationships:– ortho-: On adjacent carbons.– meta-: With one carbon between them.– para-: On opposite sides of ring.

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Reactions of Aromatic Compounds

Reactions of aromatic compounds often require a catalyst.

Halogenation

Friedel-Crafts Reaction

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Functional Groups

The term functional group is used to refer to parts of organic molecules where reactions tend to occur.

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Alcohols

• Alcohols contain one or more hydroxyl groups, —OH.

• They are named from the parent hydrocarbon; the suffix is changed to -ol and a number designates the carbon to which the hydroxyl is attached.

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Alcohols

• Alcohols are much more acidic than hydrocarbons.– pKa ~15 for most

alcohols.– Aromatic alcohols

have pKa ~10.

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Ethers

• Ethers tend to be quite unreactive.• Therefore, they are good polar solvents.

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Carbonyl Compounds

• The carbonyl group is a carbon-oxygen double bond.

• Carbonyl compounds include many classes of compounds.

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AldehydesIn an aldehyde, at least one hydrogen is attached to the carbonyl carbon.

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Ketones

In ketones, there are two carbons bonded to the carbonyl carbon.

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Carboxylic Acids

• Acids have a hydroxyl group bonded to the carbonyl group.

• They are tart tasting.• Carboxylic acids are

weak acids.

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Esters

• Esters are the products of reactions between carboxylic acids and alcohols.

• They are found in many fruits and perfumes.

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Amides

Amides are formed by the reaction of carboxylic acids with amines.

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Amines

• Amines are organic bases.• They generally have strong, unpleasant

odors.

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Chirality

• Carbons with four different groups attached to them are handed, or chiral.

• These are optical isomers or stereoisomers.• If one stereoisomer is “right-handed,” its

enantiomer is “left-handed.”

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Chirality

• Many pharmaceuticals are chiral.• Often only one enantiomer is clinically

active.

S-ibuprofen

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Amino Acids and Proteins

• Proteins are polymers of -amino acids.

• A condensation reaction between the amine end of one amino acid and the acid end of another produces a peptide bond.

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Amino Acids and Proteins

• Hydrogen bonding in peptide chains causes coils and helices in the chain.

• Kinking and folding of the coiled chain gives proteins a characteristic shape.

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Amino Acids and Proteins

• Most enzymes are proteins.

• The shape of the active site complements the shape of the substrate on which the enzyme acts; hence, the “lock- and-key” model.

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Carbohydrates

Simple sugars are polyhydroxy aldehydes or ketones.

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Carbohydrates

• In solution, they form cyclic structures.

• These can form chains of sugars that form structural molecules such as starch and cellulose.

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Nucleic Acids

Two of the building blocks of RNA and DNA are sugars (ribose or deoxyribose) and cyclic bases (adenine, guanine, cytosine, and thymine or uracil).

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Nucleic Acids

These combine with a phosphate to form a nucleotide.

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Nucleic Acids

Nucleotides combine to form the familiar double-helix form of the nucleic acids.