Ch 4 Molecular Basis of Living Organisms

• After water, cells consists mostly of carbon-based compounds= organic molecules

• • Examples

• Carbohydrates, lipids, proteins, nucleic acids (DNA, RNA)

Carbon Bonds

• Four valence electrons--> allows 4 covalent single bonds

• Or 2 double bonds

• Consequence:– Potential to form complex molecules

LE 4-3

MolecularFormula

StructuralFormula

Ball-and-StickModel

Space-FillingModel

Methane

Ethane

Ethene (ethylene)

• Tetrahedron– When C bonded to 4 other groups

• Groups can rotate around single bonds

• Linear/Flat/Planar– When C is double bonded to another C

• Unable to rotate

Shape of carbon complex

• Hydrogen

• Oxygen

• Nitrogen

Common Carbon Bonding Partners in Biological Molecules

Molecular Diversity of Organic Molecules

Due in part to• Formation of carbon chain

• Differences in length and organizationof chain

LE 4-5

LengthEthane Propane

Butane 2-methylpropane(commonly called isobutane)

Branching

Double bonds

Rings

1-Butene 2-Butene

Cyclohexane Benzene

Note: molecularabbreviation

Isomers• Compounds with same molecular formula but

different structures/ properties

Structural isomers

different covalent arrangements of atoms

Geometric isomers

same covalent arrangements;different spatial arrangements

Enantiomers mirror images of each other

LE 4-7

Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane.

Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon.

cis isomer: The two Xsare on the same side.

trans isomer: The two Xsare on opposite sides.

L isomer D isomer

Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.

Structural isomer

Geometric

EnantiomersStereoisomersMirror images

LE 4-8

L-Dopa(effective againstParkinson’s disease)

D-Dopa(biologicallyInactive)

Enantiomers

• Molecules attached to carbon chains that are involved in reactions

• Determine distinctive properties of organic molecule

Functional Groups

LE 4-9

Estradiol

Testosterone

Male lion

Female lion

• The six functional groups that are most important in the biological chemistry:

– Hydroxyl group– Carbonyl group– Carboxyl group– Amino group– Phosphate group– Sulfhydryl group

LE 4-10aa

STRUCTURE

NAME OF COMPOUNDS

Alcohols (their specific names

usually end in -ol)

Ethanol, the alcohol present in

alcoholic beverages

FUNCTIONAL PROPERTIES

polar as a result of the

electronegative oxygen atom

drawing electrons toward itself.

Attracts water molecules, helping

dissolve organic compounds such

as sugars

LE 4-10ab

STRUCTURE

NAME OF COMPOUNDS

Ketones if the carbonyl group is

within a carbon skeleton

EXAMPLE

Acetone, the simplest ketone

A ketone and an aldehyde may

be structural isomers with

different properties, as is the case

for acetone and propanal.

Aldehydes if the carbonyl group is

at the end of the carbon skeleton

Acetone, the simplest ketone

Propanal, an aldehyde

FUNCTIONAL PROPERTIES

LE 4-10ac

STRUCTURE

NAME OF COMPOUNDS

Carboxylic acids, or organic acids

EXAMPLE

Has acidic properties because it isa source of hydrogen ions.

Acetic acid, which gives vinegarits sour taste

FUNCTIONAL PROPERTIES

The covalent bond betweenoxygen and hydrogen is so polarthat hydrogen ions (H+) tend todissociate reversibly; for example,

Acetic acid Acetate ion

In cells, found in the ionic form,which is called a carboxylate group.

LE 4-10ba

STRUCTURE

NAME OF COMPOUNDS

Amine

EXAMPLE

Because it also has a carboxyl

group, glycine is both an amine and

a carboxylic acid; compounds with

both groups are called amino acids.

FUNCTIONAL PROPERTIES

Acts as a base; can pick up a

proton from the surrounding

solution:

(nonionized)

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

Glycine

(ionized)

LE 4-10bc

STRUCTURE

NAME OF COMPOUNDS

Organic phosphates

EXAMPLE

Glycerol phosphate

FUNCTIONAL PROPERTIES

Makes the molecule of which it

is a part an anion (negatively

charged ion).

Can transfer energy between

organic molecules.

LE 4-10bb

STRUCTURE

(may be written HS—)

NAME OF COMPOUNDS

Thiols

EXAMPLE

Ethanethiol

FUNCTIONAL PROPERTIES

Two sulfhydryl groups can

interact to help stabilize protein

Structure.

LE 4-10bc

Questions?

Cccccccccc

ccccccc

ccc

OH

COOH

SH

PO4_

Ch 5 Overview: The Molecules of Life

• Within cells– small organic molecules bond together to form

larger molecules

• Macromolecules– large molecules composed of thousands of

covalently connected atoms

Polymer

long molecule consisting of similar building blocks called monomers

• Three of the four classes of life’s organic molecules are polymers:– Carbohydrates– Proteins– Nucleic acids

What is the structure of most organic macromolecules?

LE 5-2

Short polymer Unlinked monomer

Dehydration removes a watermolecule, forming a new bond

Dehydration reaction in the synthesis of a polymer

Longer polymer

Hydrolysis adds a watermolecule, breaking a bond

Hydrolysis of a polymer

The Synthesis and Breakdown of Polymers

• Synthesis (Construction)– Monomers link together through

– dehydration reactions

• Breakdown

• Polymers disassemble to monomers by

hydrolysis (reverse of dehydration)

Carbohydrates

FunctionsFuelConstruction and support

StructureSimple sugars: monosaccharides

Formula CH2O

PolymersDisaccharides (relatively short)Polysaccharides (long)

LE 5-3Triose sugars

(C3H6O3)

GlyceraldehydeAld

ose

sK

eto

s es

Pentose sugars(C5H10O5)

Ribose

Hexose sugars(C5H12O6)

Glucose Galactose

Dihydroxyacetone

Ribulose

Fructose

• Monosaccharides• Functions

– major fuel for cells – raw material for building molecules

• Structures • linear ---> ring

LE 5-4

Linear andring forms

Abbreviated ringstructure

• Disaccharide– forms by a dehydration reaction between two monosaccharides

• Nomenclature of bond– glycosidic linkage

LE 5-5

Glucose

Maltose

Fructose Sucrose

Glucose Glucose

Dehydrationreaction in thesynthesis of maltose

Dehydrationreaction in thesynthesis of sucrose

1–4glycosidic

linkage

1–2glycosidic

linkage

Disaccharide formation

Polysaccharides

Storage Polysaccharides

• Starch– Fuel storage molecule in plants

• Polymer of glucose -glycosidic linkage

• Stored in chloroplasts and other plastids

LE 5-6aChloroplast Starch

1 µm

Amylose

Starch: a plant polysaccharide

Amylopectin

LE 5-7

Glucose

and glucose ring structures

Glucose

Starch: 1–4 linkage of glucose monomers.

Cellulose: 1–4 linkage of glucose monomers.

Starch

• Glycogen– storage polysaccharide in animals

– Stored in liver and muscle

LE 5-6bMitochondria Glycogen granules

0.5 µm

Glycogen

Glycogen: an animal polysaccharide

Structural Polysaccharides

– Cellulose found in plant cell walls

– Polymer of glucose

-glycosidic linkages

LE 5-7

Glucose

and glucose ring structures

Glucose

Starch: 1–4 linkage of glucose monomers.

Cellulose: 1–4 linkage of glucose monomers.

Cellulose

LE 5-8

Cellulosemolecules

Cellulose microfibrilsin a plant cell wall

Cell walls Microfibril

Plant cells

0.5 µm

Glucosemonomer

• Polymers of alpha glucose• helical

• Polymers with beta glucose • Straight• Pack together well in microfibrils• Stabilized by H-bonds• Strong

Structural difference of glucose isomers

Many animals-unable to breakdown cellulose-lack hydrolytic enzymes- in human: insoluble fiber results

• Some bacteria

– Possess enzymes to breakdown cellulose

– Live in symbiotic relationship in guts of animals (from cow to termite)

• Chitin– structural polysaccharide

– in the exoskeleton of arthropods– cell walls of many fungi

• Chitin – used as surgical thread!