The Backbone of Biological Molecules

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

• Carbon is unparalleled in its ability to form large, complex and diverse molecules

• Proteins, lipids, DNA, carbohydrates and other molecules that distinguish living matter are all composed of carbon compounds

Organic chemistry is the study of carbon compounds

• Organic compounds range from simple molecules to colossal ones

• Most organic compounds contain hydrogen atoms in addition to carbon atoms

• Vitalism, the idea that organic compounds arise only in organisms, was disproved when chemists synthesized the compounds in the lab

Water vapor

H 2NH

3

“Atmosphere”

Electrode

Condenser

Coldwater

Cooled watercontainingorganicmolecules

Sample forchemical analysis

H2O“sea”

EXPERIMENT

CH4

Carbon atoms can form diverse molecules by bonding to four other atoms

• Electron configuration is the key to an atom’s characteristics

• Electron configuration determines the kinds and number of bonds an atom will form with other atoms

The Formation of Bonds with Carbon

• With four valence electrons, carbon can form four covalent bonds with a variety of atoms

• This tetravalence makes large, complex molecules possible

• In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape

• However, when two carbon atoms are joined by a double bond, the molecule has a flat shape

NameMolecular Formula

Structural Formula

Ball-and-StickModel

Space-FillingModel

(a) Methane

(b) Ethane

(c) Ethene (ethylene)

• The electron configuration of carbon gives it covalent compatibility with many different elements

• The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the “building code” that governs the architecture of living molecules

Hydrogen

(valence = 1)

Oxygen

(valence = 2)

Nitrogen

(valence = 3)

Carbon

(valence = 4)

Molecular Diversity Arising from Carbon Skeleton Variation

• Carbon chains form the skeletons of most organic molecules

• Carbon chains vary in length and shape

LengthEthane Propane

Butane 2-methylpropane(commonly called isobutane)

Branching

Double bonds

Rings

1-Butene 2-Butene

Cyclohexane Benzene

• Carbon atoms can partner with atoms other than hydrogen; for example:

– Carbon dioxide: CO2

– Urea: CO(NH2)2

O = C = O

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

A fat molecule Mammalian adipose cells

100 µm

Fat droplets (stained red)

Isomers

• 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

(a) Structural isomers

2-methyl butanePentane

(b) Geometric isomers

cis isomer: The two Xs areon the same side.

trans isomer: The two Xs areon opposite sides.

(c) Enantiomers

L isomer D isomer

• Enantiomers are important in the pharmaceutical industry

• Two enantiomers of a drug may have different effects

• Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

L-Dopa(effective againstParkinson’s disease)

D-Dopa(biologicallyInactive)

Drug

Ibuprofen

Albuterol

Condition

Pain;inflammation

Asthma

EffectiveEnantiomer

S-Ibuprofen

R-Albuterol

R-Ibuprofen

S-Albuterol

IneffectiveEnantiomer

Functional groups are the parts of molecules involved in chemical reactions

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

• Certain groups of atoms are often attached to skeletons of organic molecules

The Functional Groups Most Important in the Chemistry of Life

• 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

Estradiol

Testosterone

Male lion

Female lion

• The six 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

STRUCTURE

(may be written HO—)

NAME OF COMPOUNDS

Alcohols (their specific names

usually end in -ol)

Ethanol, the alcohol present in

alcoholic beverages

FUNCTIONAL PROPERTIES

Is polar as a result of the

electronegative oxygen atom

drawing electrons toward itself.

Attracts water molecules, helping

dissolve organic compounds such

as sugars (see Figure 5.3).

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

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.

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)

STRUCTURE

(may be written HS—)

NAME OF COMPOUNDS

Thiols

EXAMPLE

Ethanethiol

FUNCTIONAL PROPERTIES

Two sulfhydryl groups can

interact to help stabilize protein

structure (see Figure 5.20).

Methyl group ( CH3)

Methylated compound

5-Methyl cytosine, acomponent of DNA that hasbeen modified by addition ofa methyl group

Figure 3.21d

Hydrogenbond

Disulfidebridge

Polypeptidebackbone

Hydrophobicinteractions andvan der Waalsinteractions

Ionic bond

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.

Phosphate groups

Ribose

Adenine

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

P P P P i P PAdenosine Adenosine Energy

ADPATP Inorganic phosphate

Reacts with H2O

Animations and Videos

• Bozeman - Molecules of Life

• Bozeman - Biological Molecules

• Building Biomolecules

• Properties of Biomolecules

• Biochemical Pathway

• A Biochemical Pathway

• Functional Groups – 1

• Functional Groups - 2

Animations and Videos

• Chapter Quiz Questions – 1

• Chapter Quiz Questions – 2

What was the first organic molecule to be synthesized in the laboratory?

• ammonium cyanate

• hydrogen cyanide

• urea

• acetic acid

• methane

What was the first organic molecule to be synthesized in the laboratory?

• ammonium cyanate

• hydrogen cyanide

• urea

• acetic acid

• methane

Carbon is an unusual atom in that it can form multiple bonds. Which statement is NOT true?

a) A carbon-to-carbon cis double bond is the type found in nature and is associated with cardiovascular health.

b) A carbon-to-carbon trans double bond is made artificially in food processing and is associated with poor cardiovascular health.

c) Multiple carbon-to-carbon double bonds located near each other can absorb light, so they are found in molecules in the eye or in chloroplasts.

d) Multiple carbon-to-carbon bonds are stronger than single bonds.

e) Saturated fats are those that have a carbon-to-carbon double bond and are associated with good health.

Carbon is an unusual atom in that it can form multiple bonds. Which statement is NOT true?

a) A carbon-to-carbon cis double bond is the type found in nature and is associated with cardiovascular health.

b) A carbon-to-carbon trans double bond is made artificially in food processing and is associated with poor cardiovascular health.

c) Multiple carbon-to-carbon double bonds located near each other can absorb light, so they are found in molecules in the eye or in chloroplasts.

d) Multiple carbon-to-carbon bonds are stronger than single bonds.

e) Saturated fats are those that have a carbon-to-carbon double bond and are associated with good health.

What type of chemical bond joins a functional group to the carbon skeleton of a large molecule?

• covalent bond

• hydrogen bond

• ionic bond

• double bond

• disulfide bond

What type of chemical bond joins a functional group to the carbon skeleton of a large molecule?

• covalent bond

• hydrogen bond

• ionic bond

• double bond

• disulfide bond

Which of the following is NOT one of the seven functional groups found in biological molecules?

• amino

• hydroxyl

• carboxyl

• cyanate

• phosphate

Which of the following is NOT one of the seven functional groups found in biological molecules?

• amino

• hydroxyl

• carboxyl

• cyanate

• phosphate

Which functional group behaves as a weak acid in organic molecules?

• amino

• carboxyl

• carbonyl

• sulfhydryl

• hydroxyl

Which functional group behaves as a weak acid in organic molecules?

• amino

• carboxyl

• carbonyl

• sulfhydryl

• hydroxyl

Which functional group behaves as a weak base in organic molecules?

• amino

• carboxyl

• carbonyl

• sulfhydryl

• hydroxyl

Which functional group behaves as a weak base in organic molecules?

• amino

• carboxyl

• carbonyl

• sulfhydryl

• hydroxyl

Which type of molecule always contains phosphate groups?

• carbohydrates

• lipids

• proteins

• nucleic acids

• none of the above

Which type of molecule always contains phosphate groups?

• carbohydrates

• lipids

• proteins

• nucleic acids

• none of the above

What type of isomer is propanal compared to acetone?

• cis-trans isomer

• structural isomer

• enantiomer

• none of the above; these are not isomers

What type of isomer is propanal compared to acetone?

• cis-trans isomer

• structural isomer

• enantiomer

• none of the above; these are not isomers

Which type of molecule may contain sulfhydryl groups?

• carbohydrate

• lipid

• protein

• nucleic acid

• all of the above

Which type of molecule may contain sulfhydryl groups?

• carbohydrate

• lipid

• protein

• nucleic acid

• all of the above

Which functional group is best known for its ability to change the shape of a molecule without affecting its reactivity?

• amino

• carboxyl

• sulfhydryl

• phosphate

• methyl

Which functional group is best known for its ability to change the shape of a molecule without affecting its reactivity?

• amino

• carboxyl

• sulfhydryl

• phosphate

• methyl

Scientific Skills Questions

The table below gives the molar ratios of some of the products from Stanley Miller’s abiotic synthesis of organic molecules experiment. What is the molar ratio of serine?• 1 mole of serine per mole of glycine

• 3.0 x 102 moles of serine per mole of glycine

• 3.0 x 102 moles of glycine per mole of serine

• 1 mole of serine per 3.0 x 102 moles of glycine

The table below gives the molar ratios of some of the products from Stanley Miller’s abiotic synthesis of organic molecules experiment. What is the molar ratio of serine?• 1 mole of serine per mole of glycine

• 3.0 x 102 moles of serine per mole of glycine

• 3.0 x 102 moles of glycine per mole of serine

• 1 mole of serine per 3.0 x 102 moles of glycine

The table below gives the molar ratios of some of the products from Stanley Miller’s abiotic synthesis of organic molecules experiment. Which amino acid is present in higher amounts than glycine?

• serine

• methionine

• alanine

• serine and methionine

The table below gives the molar ratios of some of the products from Stanley Miller’s abiotic synthesis of organic molecules experiment. Which amino acid is present in higher amounts than glycine?

• serine

• methionine

• alanine

• serine and methionine

Based on these results, how many molecules of methionine are present per mole of glycine?

• 1.08 x 1070 molecules

• 1.8 x 103 molecules

• 1.08 x 1021 molecules

• 6.02 x 1023 molecules

Based on these results, how many molecules of methionine are present per mole of glycine?

• 1.08 x 1070 molecules

• 1.8 x 103 molecules

• 1.08 x 1021 molecules

• 6.02 x 1023 molecules

The synthetic atmosphere in this experiment contained H2S instead of water vapor. Which of these amino acids could not have been produced in Miller’s original abiotic synthesis experiment?

• serine

• methionine

• alanine

• glycine

The synthetic atmosphere in this experiment contained H2S instead of water vapor. Which of these amino acids could not have been produced in Miller’s original abiotic synthesis experiment?

• serine

• methionine

• alanine

• glycine