1

Chapter 4 Carbon and the Molecular Diversity of Life

Outline

I. Organic compoundsII. Bonding with CarbonIII. IsomersIV. Functional Groups

Organic Compounds

What is organic We think of organic produce “natural”

In chemistry organic refers to molecules that have a carbon backbone, covalently bound to each other

Early chemists thought of organic as coming from plants and animals and inorganic coming from minerals

Overview: Carbon: The Backbone of Life

Living organisms consist mostly of carbon-based compounds

Carbon is unparalleled in its ability to form large, complex, and diverse molecules

Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds

© 2011 Pearson Education, Inc.

Organic Molecules and the Origin of Life on Earth

Stanley Miller’s classic experiment demonstrated the abiotic synthesis of organic compounds

Experiments support the idea that abiotic synthesis of organic compounds, perhaps near volcanoes, could have been a stage in the origin of life

© 2011 Pearson Education, Inc.

Figure 4.2 EXPERIMENT“Atmosphere”

Electrode

Condenser

CH4Water vapor

Cooled “rain”containingorganicmolecules

Cold water

Sample for chemical analysis

H2O “sea”

2

Carbon

Carbon has four electrons in its outer shell. It needs eight electrons to be stable

So, carbon can form up to four covalent bonds.

Carbons can link together to form a backbone – many other elements can bond to this backbone

Carbon – carbon bonds are strong

Carbon compounds

Carbons can form single, double or triple bonds.

Hydrocarbons are made of carbon and hydrogen

Carbons can form chains or rings

Figure 4.3

Name andComment

MolecularFormula

(a) Methane

(b) Ethane

CH4

Ball-and-Stick Model

Space-FillingModel

(c) Ethene(ethylene)

C2H6

C2H4

StructuralFormula

Figure 4.5

(a) Length

Ethane 1-Butene

(c) Double bond position

2-ButenePropane

(b) Branching (d) Presence of rings

Butane 2-Methylpropane(isobutane)

Cyclohexane Benzene

Carbon atoms can partner with atoms other than hydrogen; for example:

Carbon dioxide: CO2

Urea: CO(NH2)2

© 2011 Pearson Education, Inc.

Urea

Isomers

Isomers: compounds with the same molecular formulas, but different structures

Structural isomers Geometric isomers Enantiomers

Isomers do not have identical physical, chemical, or biological properties

3

Figure 4.7 (a) Structural isomers

(b) Geometric isomers

(c) Enantiomers

cis isomer: The two Xsare on the same side.

trans isomer: The two Xsare on opposite sides.

CO2HCO2H

CH3

H NH2

L isomer

NH2

CH3

H

D isomer

Structural Isomers

Molecule have different arrangement of their carbon skeleton but still have the same molecular formula:

Geometric Isomers

Have the same arrangement of atoms but the spatial arrangement of the atoms are different.

An example is cis vs trans arrangements across a double bond (cis = large groups are on same side, trans = large groups on opposite side

Enantiomers

Isomers that are mirror images of each other

Must be a chiral molecule –where a carbon is bonded to four different molecules

Referred to as: + or – R or L

Fig. 3.2

Enantiomers

4

Web sites

http://scholar.hw.ac.uk/site/chemistry/topic5.asp?outline=no

http://webhost.bridgew.edu/fgorga/Stereochem/default.htm

http://www.mhhe.com/physsci/chemistry/carey/student/olc/ch07enantiomers.html

Why do we care

The function of a protein is determined by its shape.

Usually only one form of an isomer is active in biological systems.

Why do we care

Biological organisms usually synthesize only one form.

However, chemical synthesis usually produces equal amounts of the two enantiomers

Enantiomers are important in the pharmaceutical industry

Two enantiomers of a drug may have different effects

Usually only one isomer is biologically active

Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

© 2011 Pearson Education, Inc.

© 2011 Pearson Education, Inc.

Animation: L-DopaRight-click slide / select “Play”

Figure 4.8

Drug

Ibuprofen

Albuterol

Condition EffectiveEnantiomer

IneffectiveEnantiomer

Pain;inflammation

Asthma

S-Ibuprofen R-Ibuprofen

R-Albuterol S-Albuterol

5

Example: The drug albuterol (e.g., Proventil®) contains equal amounts of two enantiomers.

Another more expensive drug is levalbuterol (Xopenex®) it only contains the active form of the drug, it has fewer side effects

This is an example of what kind of isomer?

1. Geometric2. Enantiomers3. Structural4. None of the above

Geo

metric

Enantio

mers

Structu

ral

Non

e of th

e abo

ve

25% 25%25%25%

Functional Groups

Functional groups are the components of organic molecules that are most commonly involved in chemical reactions

The number and arrangement of functional groups give each molecule its unique properties

© 2011 Pearson Education, Inc.

Figure 4.UN02

Estradiol

Testosterone

Functional Groups

Groups of atoms; determines the types of chemical reactions and associations

1. Hydroxyl2. Carbonyl3. Carboxyl 4. Amino5. Sulfhydryl6. Phosphate7. Methyl

Polarity

Remember that C-H and C-C bonds are non polar

S, N, and O are electronegative atoms and can make a molecule more polar.

Polar and ionic functional groups are hydrophilic, and strongly associate with water

6

Fig. 3.1 Fig. 3.1

Properties of functional Groups

1. Hydroxyl – polar, can form hydrogen bonds

2. Carbonyl – polar, can form hydrogen bonds

3. Carboxyl – very polar, weakly acidic and can ionize to become -COO- + H+

Important in amino acids

4. Amino - Polar and weakly basic, can accept a H+ to become –NH3

+

Important in amino acids and nucleic acids

Properties of functional Groups

5. Sulfhydryl – also called thiol, polar, important in proteins, can form strong S-S bonds that stabilize structure

6. Phosphate – polar and weakly acidic. Can dissociate to –PO4

-2

Important in nucleic acids and some lipids

7. Methyl – nonpolar hydrocarbon

Figure 4.9a

STRUCTURE

EXAMPLE

Alcohols(Their specificnames usuallyend in -ol.)

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

(may be written HO—)

Ethanol

• Is polar as a resultof the electronsspending moretime near theelectronegativeoxygen atom.

• Can form hydrogenbonds with watermolecules, helpingdissolve organiccompounds suchas sugars.

Hydroxyl

Figure 4.9bCarbonyl

STRUCTURE

EXAMPLE

Ketones if the carbonylgroup is within acarbon skeleton

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Aldehydes if the carbonylgroup is at the end of thecarbon skeleton

• A ketone and analdehyde may bestructural isomerswith different properties,as is the case foracetone and propanal.

Acetone

Propanal

• Ketone and aldehydegroups are also foundin sugars, giving riseto two major groupsof sugars: ketoses(containing ketonegroups) and aldoses(containing aldehydegroups).

7

Carboxyl

STRUCTURE

EXAMPLE

Carboxylic acids, or organicacids

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Acetic acid

• Acts as an acid; candonate an H+ because thecovalent bond betweenoxygen and hydrogen is sopolar:

• Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion.

Nonionized Ionized

Figure 4.9c

Amino

Amines

Glycine

STRUCTURE

EXAMPLE • Acts as a base; canpick up an H+ from thesurrounding solution(water, in livingorganisms):

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

• Found in cells in theionized form with acharge of 1.

Nonionized Ionized

Figure 4.9d

Sulfhydryl

Thiols

(may bewritten HS—)

STRUCTURE

EXAMPLE • Two sulfhydryl groups canreact, forming a covalentbond. This “cross-linking”helps stabilize proteinstructure.

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

• Cross-linking of cysteinesin hair proteins maintainsthe curliness or straightnessof hair. Straight hair can be“permanently” curled byshaping it around curlersand then breaking andre-forming the cross-linkingbonds.

Cysteine

Figure 4.9e Figure 4.9f

Phosphate

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Organic phosphates

Glycerol phosphate

• Contributes negativecharge to the moleculeof which it is a part(2– when at the end ofa molecule, as at left;1– when locatedinternally in a chain ofphosphates).

• Molecules containingphosphate groups havethe potential to reactwith water, releasingenergy.

Figure 4.9g

Methyl

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

Methylated compounds

5-Methyl cytidine

• Addition of a methyl groupto DNA, or to moleculesbound to DNA, affects theexpression of genes.

• Arrangement of methylgroups in male and femalesex hormones affects theirshape and function.

Carboxyl functional groups are:

1. Polar2. Acidic3. Nonpolar4. Polar and acidic

Polar

Acid

ic

Non

polar

Polar an

d acid

ic

25% 25%25%25%

8

Important Concepts Read Chapters 5 for next lecture

Know the vocabulary of the lecture

Understand the importance of carbon in organic molecules

Understand Stanley Miller’s experiments

What are the different types of isomers, be able to identify examples of each type of isomer?

What is the structure and the properties of the common functional groups?