Bio 112 Carbon and molecular diversity of life. Organic chemistry is the study of carbon compounds Vitalism Mechanism.

Bio 112

Carbon and molecular diversity of life

Organic chemistry is the study of carbon compoundsVitalismMechanism

Carbon atoms can form diverse molecules by bonding with up to 4 other atoms

4 valence electrons (tetravalent)Completes its outer energy shell by

sharing its valence electrons in 4 covalent bonds.

Covalent compatibility with many different elements (Carbon’s three best friends = H, O, and N)

Large complex molecules are possible

Variation in carbon skeletons contributes to diversity of molecules.Carbon skeletons may vary in:

LengtghShapeNumber and location of double bondsOther elements covalently bonded to the

carbons

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

Hydrocarbons are organic molecules consisting of only carbon and hydrogen

Many organic molecules, such as fats, have hydrocarbon components

Hydrocarbons can undergo reactions that release a large amount of energy

Isomers

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

arrangements of their atomsGeometric isomers have the same covalent

arrangements but differ in spatial arrangements. Result from the fact that double bonds will not allow the atoms they join to freely rotate about the bond axis.

Enantiomers are isomers that are mirror images of each other(usually one form is biologically active and its mirror image is

not)

Animation: IsomersAnimation: Isomers Animation: Isomers-DopaAnimation: Isomers-Dopa

Fig. 4-7

Pentane

(a) Structural isomers

(b) Geometric isomers

2-methyl butane

cis isomer: The two Xs areon the same side.

trans isomer: The two Xs areon opposite sides.

(c) Enantiomers

L isomer D isomer

Functional groupsFunctional 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

The seven functional groups that are most important in the chemistry of life:Hydroxyl groupCarbonyl groupCarboxyl groupAmino groupSulfhydryl groupPhosphate groupMethyl group

Fig. 4-10aHydroxyl

CHEMICALGROUP

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 skeletonAldehydes 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)