+ Chapter 4: Carbon and the Molecular Diversity of Life

•+Chapter 4: Carbon and the Molecular Diversity of Life

•+Overview: Carbon: The Backbone of Life

• Cells 70–95% water BUT the rest mostly carbon-based compounds

• “Carbon is unparalleled in its ability to form large, complex, and diverse molecules”• Why?

• Important Carbon Compounds:• Proteins • DNA • Carbohydrates, • Molecules that

distinguish living

Carbon-rich Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

•+Concept 4.1: Organic chemistry is the study of carbon compounds

• Organic chemistry: study of compounds that contain carbon• Simple molecules to colossal ones• Organic compounds usually contain hydrogen

too Vitalism: idea that organic compounds

arise only in organisms disproved when chemists synthesized these

compounds Mechanism: the view that all natural

phenomena are governed by physical and chemical laws

Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

•+Concept 4.2: Carbon atoms can form diverse molecules by bonding to four other atoms Electron configuration = key to an atom’s characteristics

Electron configuration determines: the kinds of bond number of bonds with other atoms (MANY)

Tetravalence: Carbon has FOUR valence electrons FOUR covalent bonds can be formed This makes large, complex molecules possible

Tetrahedral shape: molecules with multiple carbons, when each carbon bonded to four other atoms

HOWEVER, two carbon with double bond flat shape “Building code that governs architecture of living molecule:

Valences of carbon Its most frequent

partners (hydrogen, oxygen, and nitrogen)


O = C = O

•+Fig. 4-3

NameMolecular Formula

Structural Formula

Ball-and-StickModel

Space-FillingModel

(a) Methane

(b) Ethane

(c) Ethene (ethylene)

•+Fig. 4-4

Hydrogen(valence = 1)

Oxygen(valence = 2)

Nitrogen(valence = 3)

Carbon(valence = 4)

H O N C

•+Fig. 4-UN1

Urea

•+Molecular Diversity Arising from Carbon Skeleton Variation

Carbon chains form skeletons of most organic molecules length and shape

Hydrocarbons: organic molecules consisting of only carbon and hydrogen Many organic molecules have hydrocarbon components Can undergo reactions that release a large amount of energy

Which organic molecules do you think has a lot of hydrocarbons then?


•+Fig. 4-6

(a) Mammalian adipose cells (b) A fat molecule

Fat droplets (stained red)

100 µm

•+ Isomers

Isomers: compounds with the same molecular formula but different structures and properties: Structural isomers:

different covalent arrangements of their atoms

Geometric isomers: the same covalent arrangements but differ in spatial arrangements

Enantiomers: isomers that are mirror images of each other


•+

Enantiomers are Important in the pharmaceutical industry Two enantiomers of a drug may have different effects organisms

are sensitive to even subtle variations in molecules


•+ Concept 4.3: A small number of chemical groups are key to the functioning of biological molecules

Distinctive properties depend on the carbon skeleton molecular components attached to it

Can be more than one Functional groups: the components of organic molecules

that are most commonly involved in chemical reactions Number + arrangement of functional groups = unique properties


•+

Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group


Seven Most Important FUNctional groups in Chemistry of Life

•+Fig. 4-10a

HydroxylCHEMICALGROUP

STRUCTURE

NAME OF COMPOUND

EXAMPLE

FUNCTIONALPROPERTIES

Carbonyl Carboxyl

(may be written HO—)

In a hydroxyl group (—OH), ahydrogen atom is bonded to anoxygen atom, which in turn isbonded to the carbon skeleton ofthe organic molecule. (Do notconfuse this functional groupwith the hydroxide ion, OH–.)

When an oxygen atom isdouble-bonded to a carbonatom that is also bonded toan —OH group, the entireassembly of atoms is calleda carboxyl group (—COOH).

Carboxylic acids, or organicacids

Ketones if the carbonyl group iswithin a carbon skeleton

Aldehydes if the carbonyl groupis at the end of the carbonskeleton

Alcohols (their specific namesusually end in -ol)

Ethanol, the alcohol present inalcoholic beverages

Acetone, the simplest ketone Acetic acid, which gives vinegarits sour taste

Propanal, an aldehyde

Has acidic propertiesbecause the covalent bondbetween oxygen and hydrogenis so polar; for example,

Found in cells in the ionizedform with a charge of 1– andcalled a carboxylate ion (here,specifically, the acetate ion).

Acetic acid Acetate ion

A ketone and an aldehyde maybe structural isomers withdifferent properties, as is thecase for acetone and propanal.

These two groups are alsofound in sugars, giving rise totwo major groups of sugars:aldoses (containing analdehyde) and ketoses(containing a ketone).

Is polar as a result of theelectrons spending more timenear the electronegative oxygen atom.

Can form hydrogen bonds withwater molecules, helpingdissolve organic compoundssuch as sugars.

The carbonyl group ( CO)consists of a carbon atomjoined to an oxygen atom by adouble bond.

•+Fig. 4-10b

CHEMICALGROUP

STRUCTURE

NAME OFCOMPOUND

EXAMPLE


Amino Sulfhydryl Phosphate Methyl

A methyl group consists of acarbon bonded to threehydrogen atoms. The methylgroup may be attached to acarbon or to a different atom.

In a phosphate group, aphosphorus atom is bonded tofour oxygen atoms; one oxygenis bonded to the carbon skeleton;two oxygens carry negativecharges. The phosphate group(—OPO3

2–, abbreviated ) is anionized form of a phosphoric acidgroup (—OPO3H2; note the twohydrogens).

P

The sulfhydryl groupconsists of a sulfur atombonded to an atom ofhydrogen; resembles ahydroxyl group in shape.

(may bewritten HS—)

The amino group(—NH2) consists of anitrogen atom bondedto two hydrogen atomsand to the carbon skeleton.

Amines Thiols Organic phosphates Methylated compounds

5-Methyl cytidine

5-Methyl cytidine is acomponent of DNA that hasbeen modified by addition ofthe methyl group.

In addition to taking part inmany important chemicalreactions in cells, glycerolphosphate provides thebackbone for phospholipids,the most prevalent molecules incell membranes.

Glycerol phosphate

Cysteine

Cysteine is an importantsulfur-containing aminoacid.

Glycine

Because it also has acarboxyl group, glycineis both an amine anda carboxylic acid;compounds with bothgroups are called amino acids.

Addition of a methyl groupto DNA, or to moleculesbound to DNA, affectsexpression of genes.

Arrangement of methylgroups in male and femalesex hormones affectstheir shape and function.

Contributes negative chargeto the molecule of which it isa part (2– when at the end ofa molecule; 1– when locatedinternally in a chain ofphosphates).

Has the potential to reactwith water, releasing energy.

Two sulfhydryl groupscan react, forming acovalent bond. This“cross-linking” helpsstabilize proteinstructure.

Cross-linking ofcysteines in hairproteins maintains thecurliness or straightnessof hair. Straight hair canbe “permanently” curledby shaping it aroundcurlers, then breakingand re-forming thecross-linking bonds.

Acts as a base; canpick up an H+ fromthe surroundingsolution (water, in living organisms).

Ionized, with acharge of 1+, undercellular conditions.

(nonionized) (ionized)

•+Fig. 4-10c

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Carboxyl

Acetic acid, which gives vinegar its sour taste

Carboxylic acids, or organic acids

Has acidic propertiesbecause the covalent bond between oxygen and hydrogen is so polar; for example,

Found in cells in the ionized form with a charge of 1– and called a carboxylate ion (here, specifically, the acetate ion).

Acetic acid Acetate ion

•+Fig. 4-10d

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Amino

Because it also has a carboxyl group, glycine is both an amine anda carboxylic acid; compounds with both groups are called amino acids.

Amines

Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms).

Ionized, with a charge of 1+, under cellular conditions.

(ionized)(nonionized)

Glycine

•+Fig. 4-10e

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Sulfhydryl

(may be written HS—)

Cysteine

Cysteine is an important sulfur-containing amino acid.

Thiols

Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure.

Cross-linking ofcysteines in hairproteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers, then breakingand re-forming thecross-linking bonds.

•+Fig. 4-10f

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Phosphate

In addition to taking part in many important chemical reactions in cells, glycerol phosphate provides the backbone for phospholipids, the most prevalent molecules in cell membranes.

Glycerol phosphate

Organic phosphates

Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule; 1– when located internally in a chain of phosphates).

Has the potential to react with water, releasing energy.

•+Fig. 4-10g

STRUCTURE

EXAMPLE

NAME OFCOMPOUND


Methyl

5-Methyl cytidine is a component of DNA that has been modified by addition of the methyl group.

5-Methyl cytidine

Methylated compounds

Addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes.

Arrangement of methyl groups in male and female sex hormones affectstheir shape and function.

•+ATP: An Important Source of Energy for Cellular Processes

Adenosine triphosphate (ATP): phosphate molecule that is the primary energy-transferring molecule in the cell adenosine attached to a string of three phosphate groups What did YOU use it for today? How did you get it?


•+Fig. 4-UN4

P P P P i P PAdenosine Adenosine Energy

ADPATP Inorganic phosphate

Reacts with H2O

•+Fig. 4-UN6

•+You should now be able to:

1. Explain how carbon’s electron configuration is key to its ability to form large, complex, diverse organic molecules

2. Describe how carbon skeletons may vary and explain how this variation contributes to the diversity and complexity of organic molecules

3. Distinguish among the three types of isomers: 1. structural 2. geometric3. enantiomer

4. Name the major functional groups found in organic molecules; describe the basic structure of each functional group and outline the chemical properties of the organic molecules in which they occur

5. Explain how ATP functions as the primary energy transfer molecule in living cells


Documents

+ Chapter 4: Carbon and the Molecular Diversity of Life