Chapter 4

*Molecules are important for biological function*Carbon is the molecular backbone of life

The Main Molecules of Life

Carbon Hydrogen Oxygen Nitrogen Sulfur Phosphorus

Carbon

• Organic – means that it contains carbon

• Although cells are 70–95% water, the rest consists mostly of carbon-based compounds

Why is carbon so versatile?

Tetravalence – can bind to four other molecules

Fig. 4-5

Ethane Propane1-Butene 2-Butene

(c) Double bonds

(d) RingsCyclohexane Benzene

Butane 2-Methylpropane(commonly called isobutane)

(b) Branching

(a) Length

Hydrocarbons – organic molecules consisting of only C and H

Draw C5H12 on your notes

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

arrangements of their atoms Geometric isomers have the same covalent

arrangements but differ in spatial arrangements

Enantiomers are isomers that are mirror images of each other

Fig. 4-7a

(a) Structural isomers

2-methyl butanePentane

–Structural isomers have different covalent arrangements of their atoms

Fig. 4-7b

(b) Geometric isomers

cis isomer: The two Xs areon the same side.

trans isomer: The two Xs areon opposite sides.

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

Fig. 4-7c

(c) EnantiomersL isomer D isomer

Enantiomers are isomers that are mirror images of each other

Fig. 4-8

Drug

Ibuprofen

Albuterol

Condition

Pain;inflammation

Asthma

EffectiveEnantiomer

S-Ibuprofen

R-Albuterol

R-Ibuprofen

S-Albuterol

IneffectiveEnantiomer

Zyrtec (cetirizine) is both enantiomers and xyzal (levocetirizine) is only the left handed enantiomer

Functional Groups

The groups (molecules) off of the carbon skeleton that give that molecule its properties

Read/look over the functional groups on page 64 and draw them in your notes. Then we will play the white board game.

Fig. 4-10aHydroxylCHEMICAL

GROUP

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. 4-10bCHEMICALGROUP

STRUCTURE

NAME OFCOMPOUND

EXAMPLE

FUNCTIONALPROPERTIES

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-UN3

Adenosine

Fig. 4-UN4

P P P P i P PAdenosine Adenosine Energy

ADPATP Inorganic phosphate

Reacts with H2O

Macromolecules

Large molecules of life Carbohydrates Proteins Nucleic acids lipids

Polymers

Polymers (such as carbohydrates, proteins, and nucleic acids) are made up of monomers

Fig. 5-2

Short polymer

HO 1 2 3 H HO H

Unlinked monomer

Dehydration removes a watermolecule, forming a new bond

HO

H2O

H1 2 3 4

Longer polymer

(a) Dehydration reaction in the synthesis of a polymer

HO 1 2 3 4 H

H2OHydrolysis adds a watermolecule, breaking a bond

HO HH HO1 2 3

(b) Hydrolysis of a polymer