lecture notebook to accompany principles of life

Sinauer Associates, Inc. W. H. Freeman and Company

Lecture Notebook to accompany

Copyright © 2012 Sinauer Associates, Inc. Cover photograph © Fred Bavendam/Minden Pictures.

This document may not be modified or distributed (either electronically or on paper) without the permission of the publisher, with the following exception: Individual users may enter their own notes into this document and may print it for their own personal use.

© 2012 Sinauer Associates, Inc.

Life Chemistry and Energy 2

2

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Principles of LIFE Sadava Sinauer AssociatesMorales Studio Figure inline 2.1 Date 06-21-10

–

–

+

+

Each proton has a mass of 1 and a positive charge.

Each neutron has a mass of 1 and no charge.

Each electron has negligible mass and a negative charge.

Nucleus

POL HillisSinauer AssociatesMorales Studio Figure 02.01 Date 06-22-10

Hydrogen (H)

Phosphorus (P)

Carbon (C)

–––

–

––

–

–

––

––––

––

––

––

––

Third shell(8 electrons maximum)

Second shell(8 electrons maximum)

First shell(2 electrons maximum)

Sulfur (S)

Oxygen (O)Nitrogen (N)

16+

8+7+

––––

– –

–

––––

– ––

–

–

–

––––

––

––

––

––

––

Nucleus

6+

1+

15+

FIGURE 2.1 Electron Shells (Page 18)

IN-TEXT ART (Page 17)

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Atomic Structure Recap The mass of a proton serves as a standard unit of measure called the dalton. A single proton or neutron has a mass of about 1 dalton. An electron is even tinier. The mass of an electron is about 1/2000th of the mass of a proton or neutron. The mass of an electron is usually ignored when chemical measurements and calculations are made. Ex: Atomic number= number of protons Mass number= number of protons + number of neutrons Oxygen's mass number is 18, Carbon's is 12. Electrons determine how an atom will react. Electrons reside around the nucleus of an atom on shells or orbits. The behaviors of electrons determine whether a chemical bond will form and the shape of that bond. Electrons have a negative charge and protons have a positive charge. Atoms tend to follow the octet rule.....acquiring 8 electrons in the outer shell for stability.

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The energy level of an electron is higher in a shell farther from the nucleus. Atoms that do not have a full outer shell of 2 or 8 electrons will react with other elements.


Chapter 2 | Life Chemistry and Energy 3

TABLE 2.1 Chemical Bonds and Interactions NAmE BASIS oF INTErACTIoN STruCTurE BoNd ENErGYa

Ionic attraction Attraction of opposite charges 3–7

Covalent bond Sharing of electron pairs 50–110

Hydrogen bond Sharing of H atom 3–7

Hydrophobic interaction Interaction of nonpolar substances in the presence of polar substances (especially water) 1–2

van der Waals interaction Interaction of electrons of nonpolar substances 1

aBond energy is the amount of energy (Kcal/mol) needed to separate two bonded or interacting atoms under physiological conditions.

Principles of LIFE Sadava Sinauer AssociatesMorales Studio Table 02.01 Date 06-21-10

N C

H O

H

H O Cδ+ δ–

N

HH

HH

CC

H

HH

CCH

H

H

H

H

N

O

CH O+ –

CH

H

H

HH H

(Page 18)

Principles of LIFE Sadava Sinauer AssociatesMorales Studio Figure 02.02 Date 06-21-10

The atoms are now electrically charged ions. Both have full electron shells and are thus stable.

Chlorine “steals” an electron from sodium.

+ –

Sodium atom (Na)(11 protons, 11 electrons)

Chlorine atom (Cl)(17 protons, 17 electrons)

Sodium ion (Na+)(11 protons, 10 electrons)

Chloride ion (Cl– )(17 protons, 18 electrons)

Ionicbond

FIGURE 2.2 Ionic Bond between Sodium and Chlorine (Page 19)

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Ionic bonds form cations which are positively charged and anions that are negatively charged.



POL HillisSinauer AssociatesMorales Studio Figure In Text 02.02 Date 06-22-10

–+

+–

++

–+

+

–+

+–

++

–+

+––

+

+

–

++–

+ +

–+

+

–

++ –

++

+

AnionCation

Watermolecules



Each electron is attracted to the other atom’s nucleus…

…but the nucleus still attracts its own electron.

The atoms move closer togetherand share the electron pair in a covalent bond.

Hydrogen molecule (H2)

Hydrogen atoms (2 H)

H

H

H

H

H

H

Covalentbond

FIGURE 2.3 Electrons Are Shared in Covalent Bonds (Page 20)

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Because ionic attractions are weak, salts dissolve in water, the ions separate from one another and become surrounded by water molecules. The waters molecules are turned with their negative poles nearest the cations and their positive poles nearest to the anions.

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Covalent Bonds consist of shared pairs of electrons. A covalent bond forms when two atoms attain stable electron numbers in their outer shell by sharing one or more pairs of electrons.




Carbon can complete its outer shell by sharing the electrons of fourhydrogen atoms, forming methane.

This model shows the shape methane presents to its environment.

The hydrogen atoms form corners of a regular tetrahedron.

Each line or pair of dots represents a shared pair of electrons.

Methane (CH4)1 C and 4 H

H

(A)

(B)

C

H

H

Hor HC

H

H

HHH

H

H

H

H

H

HH

H

H

H

H

H

H

H

Structural formulas Ball-and-stick model

Covalent bond

Space-filling model

Bohr models

CC

C C

FIGURE 2.4 Covalent Bonding (Page 20)


O

H

δ+

δ−

δ−

δ+

Bohr model Space-filling model

H

Unshared electrons

OH

HPolarcovalentbonds


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Multiple Covlent Bonds - a single bond involves the sharing of a single pair of electrons such as H-H or C-H -a double bond involves the sharing of 4 electrons or two pairs: C=C -a triple bond shows six shared electrons or 3 pairs, which is Nitrogen

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Unequal sharing of electrons can happen when two atoms are different and the sharing of electrons is not equal. One nucleus may exert a greater attractive force on the electron pair than the other nucleus, so that the pair tends to be closer to that atom. The attractive force that atomic nucleus exerts on electrons in a covalent bond is called electro-negativity. If two atoms are close together in electronegativity they will share electrons equally in what is called a non polar covalent bond they will usually be hydrophobic. When electrons are drawn to one nucleus of an atom more than the other, the result is a polar covalent bond which is hydrophilic. Example: Oxygen and hydrogen. The oxygen end has a slightly negative end. We use a delta negative sign to denote this. The hydrogen will have a slightly end. It will be a polar molecule.



TABLE 2.2 Some Electronegativities ELEmENT ELECTroNEGATIvITY

Oxygen (O) 3.4

Chlorine (Cl) 3.2

Nitrogen (N) 3.0

Carbon (C) 2.6

Phosphorus (P) 2.2

Hydrogen (H) 2.2

Sodium (Na) 0.9

Potassium (K) 0.8

(Page 21)


H

N

O

C

Hydrogenbonds

Two water molecules Two parts of one large molecule(or two large molecules)

O

O

H H

H

H

δ+ δ+

δ+

δ+δ−

δ−

δ−

δ+

δ+ δ−

(A) (B) Complex molecule

FIGURE 2.5 Hydrogen Bonds Can Form between or within Molecules (Page 21)


Solid water (ice)

Liquid water


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Electronegativity differences: Ionic: > 1.70 Polar covalent: 0.4-1.70 Non polar covalent: 0.0-0.4

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Hydrogen bonds can form between or within molecules. The bond forms between the two molecules because of the attraction between a negatively charged atom on one molecule and a positively charged hydrogen atom on a second molecule. Hydrogen bonds can form between different parts of the same large molecule.

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Water has a high heat capacity. Raising the temperature of liquid water takes a lot of heat, because much of the heat is used to break the hydrogen bonds. A water molecule forms and average of 3.4 hydrogen bonds with other water molecules. Water also has a high heat of vaporization. Water has cohesive strength which is the capactiy of water molecules to resist coming apart from one another when placed under tension. The property allows water molecules to move through narrow columns against gravity. This happens in plants.



LIFE The Science of Biology 9E Sadava Sinauer AssociatesMorales Studio Figure 02.12 Date 04-03-09

Water is polar.

Polar molecules areattracted to water.

Nonpolar molecules are more attracted to one another than to water.

(A) Hydrophilic (B) Hydrophobic

δδδδδδδδδδδδδδδδδδδδ+++++++++

δ–δ–

δ+

FIGURE 2.6 Hydrophilic and Hydrophobic (Page 22)


O –O

OH

O

O –

P

CC

H

H

H

H

OHH

C

H

O

C

H

H

H

H

O

C

O

CC

H

H

H

H

HH C

O

C

OH

O

C

H

H

H

O–

O

N

H

H

C

H

H

H N

H

H

C

C

H

H O–O

O

O–

P

H OH

C

O– O

SH CC

H

H

H

H

HO SH

C

C

Class of compoundsand an example Properties

Ethanol

Alcohols

Aldehydes

Ketones

Hydroxyl

AcetaldehydeAldehyde

AcetoneKeto

Acetate

Amines

Carboxylic acids

Carboxyl

MethylamineAmino

3-PhosphoglyceratePhosphate

Mercaptoethanol

Thiols

Organic phosphates

Sulfhydryl

Functional group

R

R R

R

R

R

R

R

Polar. Hydrogen bonds with water to help dissolve molecules. Enables linkage to other molecules by condensation.

C==O group is very reactive. Important in building molecules and in energy-releasing reactions.

C==O group is important in carbohydrates and in energy reactions.

Acidic. Ionizes in living tissues to form —COO– and H+. Enters into conden-sation reactions by giving up —OH. Some carboxylic acids important in energy-releasing reactions.

Basic. Accepts H+ in living tissues to form —NH3 Enters into condensation reactions by giving up H+.

Negatively charged. Enters into condensation reactions by giving up —OH. When bonded to another phos-phate, hydrolysis releases much energy.

By giving up H, two —SH groups can react to form a disulfide bridge (S—S), thus stabilizing protein structure.

+.

FIGURE 2.7 Functional Groups Important to Living Systems (Page 23)

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Functional Groups are found together in very different biological molecules. Functional groups have very different properties and when they attach to larger molecules they can change the property of that molecule. Example: The glucose molecule can attract the functional group amino and become glucosamine. Large molecules are called macromolecules and are formed by covalent linkages of smaller molecules. 4 kinds of macromolecules: proteins lipids carbohydrates nucleic acids



Principles of LIFE Sadava Sinauer AssociatesMorales Studio Figure inline 2.4 Date 06-21-10

Living tissues are70% water by weight.

Every living organism contains about these same proportions of the four kinds of macromolecules.

Nucleicacids

ProteinsMacromolecules

Ions andsmall molecules

Carbohydrates(polysaccharides)

Lipids

Water


Water is removedin condensation.

Water is addedin hydrolysis.

A covalent bond forms between monomers.

A covalent bond between monomers is broken.

H OH H OH

H OHH

H

OH

OH

H OH

H2O

H2O

H2O

H2O

H OH H OH

H OH H OH

Monomer

(A) Condensation (B) Hydrolysis

+

++

+

FIGURE 2.8 Condensation and Hydrolysis of Polymers (Page 24)


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: formed from different combinations of amino acids

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: formed from nucleotide monomers linked in a long chain

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: can be giant molecules formed by linking together chemically similar sugar molecules

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large structures formed through noncovalent forces maintain the interactions between lipid monomers. Polymers are formed and broken down by a series of reactions involving water: condensation-removal of water links monomers together hydrolysis-the addition of water breaks a polymer into monomers

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Polymers are formed and broken down by a series of reactions called condensation (dehydration synthesis; the removal of water links monomers together. In hydrolysis the addition of water breaks a polymer into monomers. See animation http://www.biotopics.co.uk/as/condensation_and_hydrolysis.html




H2OH

H H

OH

H

H

H OH

OH

HO

C

C

C

CC

C

3

4

5

2

1

6

O

Glucose

11

3

4

5

2

6

3

4

5

2

65

4

3 2

5

14

3 2

6

5

4 3

2

1

1

H2OHH2OHH2OHH2OH

H2OH

OH H

OH

H

H

H OH

OH

H

H

OH

H2OH

HH

HO

H H

OH

HO

OH

H

OH

HH

H

H

OH

H

OH

HH

OH

H

OH

OH

OHH

H

H

O OO O O

C

C

C

C

C

C

C

C

C

C

C

C

C

CC

CC

C

CC C

C

C

CC

C CC

Five-carbon sugars (pentoses) Six-carbon sugars (hexoses)

Mannose Galactose FructoseRibose Deoxyribose

These hexoses all have the formula C6H12O6, but each has distinct biochemical properties.

Ribose and deoxyribose each have five carbons, but very different chemical properties and biological roles.

FIGURE 2.9 Monosaccharides (Page 25)


H2OO

1 +

CH2OH

OH

HO2

CH2OH

CH2OH

H

HO

O

1

CH2OHHO

2

CH2OH

CH2OH

O

Glucose Fructose

Formationof linkage

Glucose FructoseSucrose


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Carbohydrates are large groups of molecules that have similar characteristics but differ in size and chemistry.

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1. Store energy 2. Transport stored energy 3. Function as structural molecules 4. Recognition of signaling molecules

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Monosaccharides are simple sugars. Pentoses are five carbon sugars. Examples are RNA and DNA. The hexoses have 6 carbons and the the formula C6H12O6. glucose, fructose, mannose and galactose The disaccharides, oligosaccharides and polysaccharides are all constructed from monosaccharides through condensation reactions that form glycosidic linkages. Sucrose (table sugar) is a dissacharide form from glucose and fructose.

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Remember a water molecule is released in a condensation reaction.

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Polysaccharides are large polymers of monosaccharides connected by glycosidic linkages. Starches polysaccharides of glucose.

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Glycogen is a water soluble, highly branched polymer of glucose. It is a major energy storing molecule in mammals. Both starch and glycogen are readily hydrolyzed into glucose monomers, which can be broken down to use their stored energy. Cellulose is a polysaccharide of glucose, but its chemical arrangement makes it very stable. Cellulose is an excellent structural material that can withstand harsh environments. It is the most abundant carbon based material in the world and is a source of biofuel.




Hydrogen bonding to other cellulose molecules can occur at these points.

Branching occurs here.

HOH H

H OH

H

O

H

O

CH2OH

HOH H

H OH

H

O

H

O

CH2

HOH H

H OH

H

O

HHOH H

H OH

H

O

HHOH H

H OH

H

O

H

HOH H

H

H

H

O HOH

H

H

OHH

HOH H

H

H

HO

O HOH

H

H

OHH

OH HO

CH2OH

CH2OH

CH2OH

CH2OHCH2OH CH2OH

CH2OH

OO

O

OO

O

OO

O

OH OH

Linear (cellulose) Branched (starch) Highly branched (glycogen)

(B) Macromolecular structure

(C) Polysaccharides in cells

Starch and glycogen

Cellulose

(A) Molecular structure

Cellulose is an unbranched polymer of glucose with linkages that are chemically very stable.

Glycogen and starch are polymers of glucose, with branching at carbon 6 (see Figure 2.9).

Parallel cellulose molecules form hydrogen bonds, resulting in thin fibrils.

Branching limits the number of hydrogen bonds that can form in starch molecules, making starch less compact than cellulose.

The high amount of branching inglycogen makes its solid depositsmore compact than starch.

Layers of cellulose fibrils, as seen inthis scanning electron micrograph, give plant cell walls great strength.

Within these potato cells, starch deposits (colored purple in this scanning electron micrograph) have a granular shape.

The dark clumps in this electron micrograph are glycogen deposits in a monkey liver cell.

FIGURE 2.10 Polysaccharides (Page 26)




The bonding of glycerol and fatty acids releases water and thus is a condensation reaction.

O H

H2C

O H

CH2

O H

C

CO

OH

CH2

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH3

H2C

CH2

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH3

H2C

CH2

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH3

H2C

CH2

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH3

H2C

CH2

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH3

H2C

CH2

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CH3

H2C

CO

OH

CO

OH CO

H

O

H2C CH2C

O O

H

CO CO

Triglyceride

3 H2O+

Glycerol(an alcohol)

3 Fatty acidmolecules

FIGURE 2.11 Synthesis of a Triglyceride (Page 27)


All bonds between carbon atoms are single in a saturated fatty acid (chain is straight).

The straight chain allows a molecule to pack tightly among other similar molecules.

Double bonds between two carbons make an unsaturated fatty acid (carbon chain has kinks).

Kinks prevent close packing.

The straight cha

CO

OH

CH2

CH2

H2C

CH2

H2C

CH2

H2C

CH2

H2C

CO

OH

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH2

CH3

CH2

CH2

CH2

CH2

HC

HC

HC

HC

CH2

H2C

CH2

H2C

CH3

H2C

Oxygen

HydrogenCarbon

(A) Palmitic acid (B) Linoleic acid

FIGURE 2.12 Saturated and Unsaturated Fatty Acids (Page 28)

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Lipids are hydrophobic molecules Lipids, called fats, are hydrocarbons that are insoluble in water because of their nonpolar covalent bonds. Remember nonpolar covalent bonds have an equal sharing of electrons. Lipid molecules will aggregate together away from water molecules. Lipids: store energy in C-C- and C-H bonds play important structural roles in the cell membrane provide thermal insulation Fats and oils are triglycerides or simple lipids Triglycerides that are solids at room temperature are called fats; liquids at room temperature are oils. A triglyceride contains 3 fatty acids and one glycerol molecule.

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3 hydroxyl groups (-OH) alcohol

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long nonpolor hydrocarbon attached to a polor carboxyl (-COOH) this makes it a carboylic acid It is very hydrophobic because of its many C-C and C_H bonds

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Synthesis of triglycerides involves 3 condensation reactions. This results in very little polarity and extremely hydrophobic. Think about oil and water not mixing. Saturated fatty acid- all available bonds are saturated hydrogen atoms, only single bonds. Rigid and straight molecules that pack together. Unsaturated fatty acid-hydrocarbon chains contain one or more double bonds. The molecule has kinks in the chain making it harder to stack. Naturally these are better for you. Unsaturated fats can be artificially hydrogentated to make them saturated fats. This results in trans fats which are unhealthy for coronary systems.




The hydrophilic “head” is attracted to water, which is polar.

In an aqueous environment, “tails”stay away from water and “heads”interact with water, forming a bilayer.

The hydrophobic “tails” arenot attracted to water.

P O–O

O

CHH2C

H3C N+

CH2

CH2

O

CH2

CH2

O

C O

CH3

CH2

C O

O

CH3

Choline

Hydrophilichead

Phosphate

Glycerol

Hydrocarbonchains

Positivecharge

Negativecharge

Hydrophobictail

Hydrophilic“heads”

Hydrophilic“heads”

Hydrophobicfatty acid “tails”

Water

Water

+–

+–

(A) Phosphatidylcholine

(B) Phospholipid bilayer

FIGURE 2.13 Phospholipids (Page 28)

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Amphipathic means the membrane is made of a hydophilic and hydrophobic area.

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+

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-

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This bilayer allows for passages of certain molecules into and out of the cell. These will be dicussed in chapter 5.




In an exergonic reaction, energy is as the reactants form lower-

energy products.

Energy must be added for an endergonic reaction, in which reactants are converted to products with a higher energy level.

released

(B) Exergonic reaction

(A) Endergonic reaction

Reactants

Amount ofenergyreleased

Products

Time course of reaction

Free

ene

rgy


Free

ene

rgy

Products

Amount ofenergyrequired

Reactants



FIGURE 2.14 Energy Changes in Reactions (Page 30)

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Key terms for section 2.5 chemical reaction reactants products metabolism- sum total of chemical reactions in a biological system What is energy? potential energy kinetic energy Anabolic reactions-require an input of energy or endergonic or endothermic reactions Catabolic reactions- energy is released or exergonic or exothermic The energy released in catabolic reactions in oftern used to drive anabolic reactions. That is why fat accumulates if you eat foods in excess of your energy needs.




If we delete the balance in (B) I’m assuming it should be deleted in (A) too.

(A)

(B)

Free energy

The First Law of Thermodynamics The total amount of energy before a transformation equals the total amount after a transformation. No new energy is created, and no energy is lost.

The Second Law of Thermodynamics Although a transformation does not change the total amount of energy within a closed system (one that is not exchanging matter or energy with the surroundings), after any transformation the amount of energy available to do work is always less than the original amount of energy.

Another statement of the second law is that in a closed system, with repeated energy transformations, free energy decreases and unusable energy (disorder) increases—a phenomenon known as the increase in entropy.

Unusable energy after

Energybefore

Energybefore

Usable energy after(free energy)

Energytransformation

Unusable energy after

Energyafter

FIGURE 2.15 The Laws of Thermodynamics (Page 30)




Go to yourBioPortal.com for original citations, discussions,and relevant links for all INVESTIGATION figures.

The chemical building blocks of life could have been generated in the probable atmosphere of early Earth.

Organic chemical compounds can be generated under conditions similar to those that existed in the atmosphere of primitive Earth.

FIGURE 2.16 Synthesis of Prebiotic Molecules in an Experimental Atmosphere With an increased understanding of the atmospheric conditions that existed on primitive Earth, the researchers devised an experiment to see if these conditions could lead to the formation of organic molecules.

ANALYZE THE DATA

The following data show the amount of energy impinging on Earth in different forms.

INVESTIGATION

A condenser coolsthe “atmospheric”gases in a “rain”containing newcompounds. The compounds collect in an “ocean.”

Electrical sparks simulating lightningprovide energy forsynthesis of new compounds.

3

Collect and analyze condensed liquid.

4

2

Heat a solution of simple chemicals to produce an “atmos-phere.”

1“Atmospheric”compartment

Coldwater

Condensation

N2

H2CO2

CH4

NH3

H2O

“Oceanic”compartment

Heat

Reactions in the condensed liquid eventually formed organic chemicalcompounds, including purines, pyrimidines, and amino acids.

Source Energy (cal cm–2 yr–1)

Total radiation from sun 260,000Ultraviolet light Wavelength <2500 nm 570 Wavelength <2000 nm 85 Wavelength <1500 nm 3.5Electric discharges 4Cosmic rays 0.0015Radioactivity 0.8Volcanoes 0.13

A. Only a small fraction of the sun’s energy is ultraviolet light (less than 2500 nm). What is the rest of the solar energy?

B. The molecules CH4, H2O, NH3, and CO2 absorb light at wavelengths less than 2000 nm. What fraction of total solar radiation is in this range?

C. Instead of electric discharges, what other sources of energy could be used in these experiments?

HYPOTHESIS

METHOD

CONCLUSION

RESULTS

For more, go to Working with Data 2.1 at yourBioPortal.com.

(Page 32)

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