lecture notebook to accompany principles of life
TRANSCRIPT
Sinauer Associates, Inc. W. H. Freeman and Company
Lecture Notebook to accompany
Copyright © 2012 Sinauer Associates, Inc. Cover photograph © Fred Bavendam/Minden Pictures.
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© 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)
© 2012 Sinauer Associates, Inc.
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)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 4
POL HillisSinauer AssociatesMorales Studio Figure In Text 02.02 Date 06-22-10
–+
+–
++
–+
+
–+
+–
++
–+
+––
+
+
–
++–
+ +
–+
+
–
++ –
++
+
AnionCation
Watermolecules
IN-TEXT ART (Page 19)
Principles of LIFE Sadava Sinauer AssociatesMorales Studio Figure 02.03 Date 06-21-10
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)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 5
POL HillisSinauer AssociatesMorales Studio Figure 02.04 Date 06-22-10
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)
POL HillisSinauer AssociatesMorales Studio Figure In Text 02.03 Date 06-22-10
O
H
δ+
δ−
δ−
δ+
Bohr model Space-filling model
H
Unshared electrons
OH
HPolarcovalentbonds
IN-TEXT ART (Page 21)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 6
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)
POL HillisSinauer AssociatesMorales Studio Figure 02.05 Date 06-22-10
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)
POL HillisSinauer AssociatesMorales Studio Figure In Text 02.06 Date 06-22-10
Solid water (ice)
Liquid water
IN-TEXT ART (Page 22)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 7
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)
LIFE The Science of Biology 9E Sadava Sinauer AssociatesMorales Studio Figure 3.1 Date 04-08-09
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)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 8
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
LIFE The Science of Biology 9E Sadava Sinauer AssociatesMorales Studio Figure 02.08 Date 04-27-09
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)
IN-TEXT ART (Page 23)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 9
POL HillisSinauer AssociatesMorales Studio Figure 02.09 Date 06-22-10
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)
POL HillisSinauer AssociatesMorales Studio Figure In Text 02.05 Date 06-22-10
H2OO
1 +
CH2OH
OH
HO2
CH2OH
CH2OH
H
HO
O
1
CH2OHHO
2
CH2OH
CH2OH
O
Glucose Fructose
Formationof linkage
Glucose FructoseSucrose
IN-TEXT ART (Page 25)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 10
POL HillisSinauer AssociatesMorales Studio Figure 02.10 Date 06-22-10
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)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 11
POL HillisSinauer AssociatesMorales Studio Figure 02.11 Date 06-22-10
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)
Principles of LIFE Sadava Sinauer AssociatesMorales Studio Figure 02.12 Date 06-21-10
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)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 12
POL HillisSinauer AssociatesMorales Studio Figure 02.13 Date 06-22-10
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)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 13
POL HillisSinauer AssociatesMorales Studio Figure 02.14 Date 06-22-10
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
Time course of reaction
Free
ene
rgy
Products
Amount ofenergyrequired
Reactants
Time course of reaction
Time course of reaction
FIGURE 2.14 Energy Changes in Reactions (Page 30)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 14
POL HillisSinauer AssociatesMorales Studio Figure 02.15 Date 06-22-10
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)
© 2012 Sinauer Associates, Inc.
Chapter 2 | Life Chemistry and Energy 15
Principles of LIFE Sadava Sinauer AssociatesMorales Studio Figure 02.16 Date 06-21-10
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)