SPRING 2015 Chemical Principles: Carbon. Chapter 4: Carbon: The Backbone of Life Although cells are mostly% water, the rest consists mostly of carbon-based.

SPRING 2015

Chemical Principles:

Carbon

Chapter 4: Carbon: The Backbone of Life

• Although cells are mostly% water, the rest consists 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

• What is so special about carbon?

The electron configuration of carbon gives it the ability to:

• make more covalent bonds than other elements

• make single, double or triple bonds

• bond with many other elements

• impart shape to molecules

NameMolecular Formula

Structural Formula

Ball-and-StickModel

Space-FillingModel

(a) Methane

(b) Ethane

(c) Ethene (ethylene)

Carbon can form up to four covalent bonds

Sharing one pair of electrons = single covalent bond

Sharing two pairs = double covalent bond

Carbon can form covalent bonds with other elements

• Carbon dioxide: CO2

Carbon shares four pairs of electrons with oxygen (highest oxidation state)

• Urea

Carbon shares two pairs of electrons

with oxygen and two with nitrogen

Carbon’s bonding properties can impart shape to molecules like these hydrocarbons

Ethane Propane1-Butene 2-Butene

(c) Double bonds

(d) RingsCyclohexane Benzene

Butane 2-Methylpropane(commonly called isobutane)

(b) Branching

(a) Length

Isomers provide many different shapes

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

Drug

Ibuprofen

Albuterol

Condition

Pain;inflammation

Asthma

EffectiveEnantiomer

S-Ibuprofen

R-Albuterol

R-Ibuprofen

S-Albuterol

IneffectiveEnantiomer

A small number of chemical groups are key to the functioning of biological molecules

• Distinctive properties of organic molecules depend not only on the carbon skeleton but also on the molecular components attached to it

• A number of characteristic groups are often attached to skeletons of organic molecules

• 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

Example-Different functional groupsmake a difference at the biological level

EstradiolTestosterone

• The seven functional groups that are most important in the chemistry of life:

– Hydroxyl group: -OH

– Carbonyl group: -C=O

– Carboxyl group: -COOH

– Amino group: -NH2

– Sulfhydryl group: -SH

– Phosphate group: -PO4

– Methyl group: -CH3

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.

CHEMICALGROUP

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)

•Hydroxyl

•Carbonyl

•Carboxylic

•Amino

•Sulfhydryl

•Phosphate

•Methyl

Why is carbon special for life?

• Carbon was thought to have supernatural properties that placed it at the center of living systems

• Reflected in the name of the branch of chemistry that deals with carbon: organic chemistry

• Vitalism was the idea that carbon compounds could only be produced by living organisms,

• Vitalism dropped out of the picture when chemists first synthesized organic compounds in their labs

• Mechanism is the view that all natural phenomena are governed by the same physical and chemical laws

• The mechanistic view allows scientists to take a reductionist approach to the study of living systems (and to this course)

What makes carbon “special”?

•makes more bonds than other elements

•makes single, double or triple bonds

•bonds with many other elements

•imparts shape to molecules

These properties are the result of electron configuration-not magic!