blb12 ch24 lecture

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Chapter 24

The Chemistry of

Life: Organic and

Biological Chemistry

Lecture Presentation

John D. Bookstaver

St. Charles Community College

Cottleville, MO© 2012 Pearson Education, Inc.



Organic and

BiologicalChemistry

Organic Chemistry

• Organic chemistry is the chemistry

of carbon compounds.

• Carbon has the ability to formlong chains.

• Without this property, large

biomolecules such as proteins,

lipids, carbohydrates, and nucleicacids could not form.

© 2012 Pearson Education, Inc.



Organic and

BiologicalChemistry

Structure of Carbon Compounds

• There are three hybridization states and

geometries found in organic compounds:

– sp3

tetrahedral – sp2 trigonal planar

– sp linear




Organic and

BiologicalChemistry

Hydrocarbons

• There are four basic

types of hydrocarbons:

– Alkanes – Alkenes

– Alkynes

– Aromatic hydrocarbons




Organic and

BiologicalChemistry

Alkanes

• Alkanes contain only single bonds.

• They are also known as saturated hydrocarbons.

– They are ―saturated‖ with hydrogens.




Organic and

Biological

Chemistry

Formulas

• Lewis structures of alkanes look like this

(Figure 24.3).

• They are also called structural formulas.• They are often not convenient, though…,




Organic and

Biological

Chemistry

Formulas

…so more often condensed formulas are used.




Organic and

Biological

Chemistry

Properties of Alkanes

• The only van der Waals force is theLondon dispersion force.

• The boiling point increases with the length

of the chain.




Organic and

Biological

Chemistry

Structure of Alkanes

• Carbons in alkanes

are sp3 hybrids.

• They have atetrahedral

geometry and

109.5 bond angles.




Organic and

Biological

Chemistry

Structure of Alkanes

• There are only

-bonds in alkanes.

• There is freerotation about the

C—C bonds.




Organic and

Biological

Chemistry

Isomers

Isomers havethe same

molecular

formulas, but

the atoms are

bonded in a

different order.




Organic and

Biological

Chemistry

Organic Nomenclature

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

longest continuous chain.




Organic and

Biological

Chemistry




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




Organic and

Biological

Chemistry




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

– Prefix: This tells what groups are attached to

the chain.




Organic and

Biological

Chemistry

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 thecarbon(s) to which they

are attached.




Organic and

Biological

Chemistry

How to Name a Compound

If there is more than

one type of

substituent in themolecule, list them

alphabetically.




Organic and

Biological

Chemistry

Cycloalkanes

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

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

– Smaller rings are quite strained.




Organic and

Biological

Chemistry

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.




Organic and

Biological

Chemistry

Alkenes

• Alkenes contain at least one carbon –carbondouble bond.

• They are unsaturated.

– That is, they have fewer than the maximum number

of hydrogens.




Organic and

Biological

Chemistry

Structure of Alkenes

• Unlike alkanes, alkenes cannot rotate freely

about the double bond.

– The side-to-side overlap in the -bond makes thisimpossible without breaking the -bond.




Organic and

Biological

Chemistry

Structure of Alkenes

This creates geometric isomers, which differ

from each other in the spatial arrangement of

groups about the double bond.




Organic and

Biological

Chemistry

Nomenclature of Alkenes

• The chain is numbered so the double bond gets thesmallest 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 onopposite sides of the molecule.




Organic and

Biological

Chemistry

Reactions of Alkenes

• One reaction of alkenes is the addition reaction. – In it, two atoms (e.g., bromine) add across the

double bond.

– One -bond and one -bond are replaced by

two -bonds; therefore, H is negative.




Organic and

Biological

Chemistry

Mechanism of Addition Reactions

• It is a two-step mechanism:

– The first step is the slow, rate-determining step.

– The second step is fast.




Organic and

Biological

Chemistry


In the first step, the

-bond breaks and

the new C—H bondand a cation form.




Organic and

Biological

Chemistry


In the second step,

a new bond forms

between the negative

bromide ion and thepositive carbon.




Organic and

Biological

Chemistry

Alkynes

• Alkynes contain at least one carbon –carbon

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

• They are also unsaturated.




Organic and

Biological

Chemistry

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




Organic and

Biological

Chemistry

Reactions of Alkynes

• Alkynes undergo many of the same reactions

alkenes do.

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




Organic and

Biological

Chemistry

Aromatic Hydrocarbons

• Aromatic hydrocarbons are cyclic hydrocarbonsthat 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.




Organic and

Biological

Chemistry

Aromatic Nomenclature

Many aromatic hydrocarbons are known

by their common names.




Organic and

Biological

Chemistry

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.




Organic and

Biological

Chemistry


• Due to this stabilization, aromatic compounds

do not undergo addition reactions; they

undergo substitution.

• In substitution reactions, hydrogen isreplaced by a substituent.




Organic and

Biological

Chemistry

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.




Organic and

Biological

Chemistry


Reactions of aromatic compounds often

require a catalyst.




Organic and

Biological

Chemistry

Functional

Groups The term functional

group is used to

refer to parts of

organic moleculeswhere reactions

tend to occur.




Organic and

Biological

Chemistry

Alcohols

• Alcohols contain one or morehydroxyl groups, —OH.

• They are named

from the parent

hydrocarbon; thesuffix is changed to

- ol and a number

designates the carbon

to which the hydroxyl

is attached.




Organic and

Biological

Chemistry

Alcohols

• Alcohols are much more acidic than hydrocarbons. – pK a ~15 for most alcohols.

– Aromatic alcohols have pK a ~10.




Organic and

Biological

Chemistry

Ethers

• Ethers tend to be quite unreactive.

• Therefore, they are good polar solvents.




Organic and

Biological

Chemistry

Aldehydes

In an aldehyde, at least one hydrogen isattached to the carbonyl carbon.




Organic and

Biological

Chemistry

Ketones

In ketones, there are two carbons bonded to

the carbonyl carbon.




Organic and

Biological

Chemistry

Carboxylic Acids

• Acids have a hydroxyl group bonded to

the carbonyl group.

• They are tart tasting.

• Carboxylic acids are weak acids.




Organic and

Biological

Chemistry

Esters

• Esters are the products of reactions between

carboxylic acids and alcohols.

• They are found in many fruits and perfumes.




Organic and

Biological

Chemistry

Amides

Amides are formed by the reaction of

carboxylic acids with amines.




Organic and

Biological

Chemistry

Amines

• Amines are organic bases.

• They generally have strong, unpleasant odors.




Organic and

Biological

Chemistry

Chirality

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

• These are optical isomers, or stereoisomers.

• If one stereoisomer is ―right-handed,‖ itsenantiomer is ―left-handed.‖




Organic and

Biological

Chemistry

Chirality

• Many pharmaceuticals

are chiral.

• Often only one

enantiomer isclinically active.




Organic and

Biological

Chemistry

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.




Organic and

Biological

Chemistry


• Hydrogen bondingin peptide chains

causes coils and

helices in the chain.

• Kinking and foldingof the coiled chain

gives proteins a

characteristic shape.




Organic and

Biological

Chemistry


• Most enzymesare proteins.

• The shape of the

active site

complements theshape of the

substrate on which

the enzyme acts;

hence, the ―lock-

and-key‖ model.




Organic and

Biological

Chemistry

Carbohydrates

Simple sugars are

polyhydroxy aldehydes

or ketones.




Organic and

Biological

Chemistry

Carbohydrates

• In solution, they form cyclic structures.

• These structures can form chains of sugars

that form structural molecules such as starch

and cellulose.




Organic and

Biological

Chemistry

Lipids

• Lipids are a broadclass of nonpolar

organic molecules.

• The fats known astriglycerides are

lipids made from

carboxylic acids

and glycerol.




Organic and

Biological

Chemistry

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).




Organic and

Biological

Chemistry

Nucleic Acids

These combine witha phosphate to form

a nucleotide.




Organic and

Biological

Nucleic Acids

Nucleotides combine to formthe familiar double-helix form

of the nucleic acids.

blb12 ch24 lecture

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