MOLECULAR MODEL BUILDINGAP Bio Lab

Activity

Fig. 4-5a

(a) Length

Ethane Propane

Fig. 4-5b

(b) Branching

Butane 2-Methylpropane(commonly called

isobutane)

Fig. 4-5c

(c) Double bonds

1-Butene 2-Butene

Fig. 4-7a

(a) Structural isomers

2-methyl butanePentane

Fig. 4-7b

(b) Geometric isomers

cis isomer: The two Xs areon the same side.

trans isomer: The two Xs areon opposite sides.

The seven functional groups that are most important in the chemistry of life: Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group

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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)

Fig. 4-10c

STRUCTURE

EXAMPLE

NAME OFCOMPOUND

FUNCTIONALPROPERTIES

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

FUNCTIONALPROPERTIES

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

FUNCTIONALPROPERTIES

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

FUNCTIONALPROPERTIES

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

FUNCTIONALPROPERTIES

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

One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell

ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups

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Fig. 4-UN3

Adenosine

Fig. 4-UN4

P P P P i P PAdenosine

Adenosine

Energy

ADPATP Inorganic phosphate

Reacts with H2O

Fig. 5-3

Dihydroxyacetone

Ribulose

Keto

ses

Al d

oses

Fructose

Glyceraldehyde

Ribose

Glucose Galactose

Hexoses (C6H12O6)Pentoses (C5H10O5)Trioses (C3H6O3)

Though often drawn as linear skeletons, in aqueous solutions many sugars form rings

Monosaccharides serve as a major fuel for cells and as raw material for building molecules

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

Fig. 5-4

(a) Linear and ring forms (b) Abbreviated ring structure

Fig. 5-4a

(a) Linear and ring forms

A disaccharide is formed when a dehydration reaction joins two monosaccharides

This covalent bond is called a glycosidic linkage

Animation: Disaccharides

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Fig. 5-5

(b) Dehydration reaction in the synthesis of sucrose

Glucose Fructose Sucrose

MaltoseGlucoseGlucose

(a) Dehydration reaction in the synthesis of maltose

1–4glycosidic

linkage

1–2glycosidic

linkage

POLYSACCHARIDES

Polysaccharides, the polymers of sugars, have storage and structural roles

The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

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