.

Chapter 4: Life is based on molecules

with carbon (organic molecules)

organic compounds

isomers

functional groups

.

Much of the chemistry of life is

based on organic compounds

organic compounds have at least one carbon atom covalently bound to either:

another carbon atom

or to hydrogen

the chemistry of organic molecules is organized around the carbon atom

.

• Discuss the chemistry of carbon. How

does it typically bond? What does it

typically bond to? What sort of shapes,

angles, freedoms, etc. are associated

with the bonds that it makes?

• Draw a tetrahedron.

.

Organic Compounds

carbon atoms have six electrons –

2 in level 1

4 in their valence (outer) shell (level 2)

carbon is not a strongly electron seeking element, and it does not readily give up its electrons; therefore:

carbon does not readily from ionic bonds

it almost always forms covalent bonds

carbon can form up to 4 covalent bonds (and typically does form all four)

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Organic Compounds

wide diversity in organic compounds

over 5 million identified

variety partially because carbon tends to bond to carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus

hydrocarbons – contain only hydrogen and carbon

single carbon-carbon bonds allow rotation around them and lend flexibility to molecules

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Organic Compounds

building of organic macromolecules also leads to diversity

carbon works well as a molecular “backbone” for forming long chain molecules

stronger carbon-carbon bonds can be made with double and triple covalent bonds

carbon chains can branch

.

Organic Compounds

the shape of a molecule is important in determining its chemical and biological properties

When 4 separate bonds are formed by carbon…

formed at 109.5 degree angles

form a pyramid with a triangular base called a tetrahedron

When double bonds are formed…

angles are 120 or 180 degrees apart, and they all lie in the same plane

.

Organic Compounds

bond angles for carbon play a critical role in determining the shape of molecules

generally there is freedom to rotate around carbon to carbon single bonds but not double (or triple) bonds

.

• Discuss the chemistry of carbon. How

does it typically bond? What does it

typically bond to? What sort of shapes,

angles, freedoms, etc. are associated

with the bonds that it makes?

• Draw a tetrahedron.

.

Chapter 4: Life is based on molecules

with carbon (organic molecules)

organic compounds

isomers

functional groups

.

• Discuss isomers. What are they? What

is the difference between structural

isomers and stereoisomers? Between

cis-trans isomers and enantiomers?

• Draw an example of each of these:

structural isomers

cis-trans isomers

enantiomers

.

• What type of isomer situation is this?

How do you know?

.

• What type of isomer situation is this?

How do you know?

.

• What type of isomer situation is this?

How do you know?

.

• What type of isomer situation is this?

How do you know?

.

• What type of isomer situation is this?

How do you know?

.

• What type of isomer situation is this?

How do you know?

.

Isomers

have the same molecular formula

have different structures

there are two kinds of isomers

structural isomers

stereoisomers

.

Isomers

structural isomers - substances with the same molecular formula that differ in the covalent arrangement of their atoms

example: ethanol and dimethyl ether (C2H6O)

.

Isomers stereoisomers - substances with the same

arrangement of covalent bonds, but the order in which the atoms are arranged in space is different

two types: enantiomers and diastereomers

.

Isomers cis-trans isomers – diastereomers associated with

compounds that have carbon-carbon double bonds

since there is no rotation around the double bond the other atoms attached to the carbons are stuck in place in relationship to each other

larger items together = cis; larger items opposite = trans

examples: trans-2-butene and cis-2-butene

.

Isomers

enantiomers – substances that are mirror images of each other and that cannot be superimposed on each other

sometimes called optical isomers (kind of a loose term, though)

.

Isomers

typically, only one form of an enatiomer pair is found in and/or used by organisms

the enantiomers are given designations such as

[(+)- vs. (−)-] or [D- vs. L-] or [(R)- vs. (S)-]

biologically important enantiomers include

amino acids (found in proteins) – most are L-amino acids

(e.g. L-leucine, L-alanine, etc)

sugars – most are D-sugars

(e.g. D-glucose, D-fructose, etc.)

.

• Discuss isomers. What are they? What

is the difference between structural

isomers and stereoisomers? Between

cis-trans isomers and enantiomers?

• Draw an example of each of these:

structural isomers

cis-trans isomers

enantiomers

.

Chapter 4: Life is based on molecules

with carbon (organic molecules)

organic compounds

isomers

functional groups

.

• What is a functional group, and why is it

useful to know them? Quiz each other

on the names and chemistry of the

functional groups in the notes.

.

Functional Groups

functional groups determine most of the reactive properties (functions) of organic molecules

functional groups are groups of atoms covalently bonded to a carbon backbone that give properties different from a C-H bond

the properties of the major classes of organic compounds (carbohydrates, lipids, proteins, and nucleic acids) are determined mostly by their functional groups

learn the seven functional groups on the following slides

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Functional Groups

.

Functional Groups

hydroxyl group: polar; found in alcohols

carbonyl group: polar; found in aldehydes and ketones

carboxyl group: weakly acidic; found in organic acids (such as amino acids)

.

Functional Groups

amino group: weakly basic; found in such things as amino acids

sulfhydryl group: essentially nonpolar; found in some amino acids

phosphate group: weakly acidic; found in such things as phospholipids and nucleic acids

methyl group: nonpolar (thus hydrophobic); found in such things as lipids, other membrane components

P