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Life Chemistry and Energy 2
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Life Chemistry and Energy
2
Chapter 2 Life Chemistry and Energy
Key Concepts
• 2.1 Atomic Structure Is the Basis for Life’s Chemistry
• 2.2 Atoms Interact and Form Molecules
• 2.3 Carbohydrates Consist of Sugar Molecules
• 2.4 Lipids Are Hydrophobic Molecules
• 2.5 Biochemical Changes Involve Energy
Enduring Understanding
2.A. Growth, reproduction, and maintenance of the organization of living systems require free energy and matter. (The concept of free energy will be
discussed in detail during Chapter 6)
Essential Knowledge
2.A.1. All living systems require constant input of energy.
2.A.3. Organisms must exchange matter with the environment to grow, reproduce, and maintain organization.
Assessment
Test of Chapter 2
Word Roots
Like any profession, the study of biology has its own language.
Nouns constructed with components – prefixes and suffixes – of definite purpose and meaning.
What follows may be useful to you in understanding the construction and meaning of scientific vocabulary.
Word Roots
hydro - water; - philos loving; - phobos fearing (hydrophilic: having an affinity for water; hydrophobic: having an aversion to water)
kilo - a thousand (kilocalorie: a thousand calories)
Instructor’s Guide for Campbell/Reece Biology, Seventh Edition
Word Roots
carb - coal (carboxyl group: a functional group present in organic acids, consisting of a carbon atom double-bonded to an oxygen atom and a hydroxyl group)
enanti - opposite (enantiomer: molecules that are mirror images of each other)
hydro - water (hydrocarbon: an organic molecule consisting only of carbon and hydrogen)
Word Roots
iso - equal (isomer: one of several organic compounds with the same molecular formula but different structures and, therefore, different properties)
sulf - sulfur (sulfhydryl group: a functional group that consists of a sulfur atom bonded to an atom of hydrogen)
thio - sulfur (thiol: organic compounds containing sulfhydryl groups)
Word Roots
con - together (condensation reaction: a reaction in which two molecules become covalently bonded to each other through the loss of a small molecule, usually water)
di - two (disaccharide: two monosaccharides joined together)
Word Roots
glyco - sweet (glycogen: a polysaccharide sugar used to store energy in animals)
hydro - water; - lyse break (hydrolysis: breaking chemical bonds by adding water)
macro - large (macromolecule: a large molecule)
meros - part (polymer: a chain made from smaller organic molecules)
Word Roots
mono - single; - sacchar sugar (monosaccharide: simplest type of sugar)
poly - many (polysaccharide: many monosaccharides joined together)
tri - three (triacylglycerol: three fatty acids linked to one glycerol molecule)
Word Roots
bio- life (bioenergetics: the study of how organisms manage their energy resources)
endo- within (endergonic reaction: a reaction that absorbs free energy from its surroundings)
ex- out (exergonic reaction: a reaction that proceeds with a net release of free energy)
Word Roots
kinet- movement (kinetic energy: the energy of motion)
therm- heat (thermodynamics: the study of the energy transformations that occur in a collection of matter)
Word Roots
ana - up (anabolic pathway: a metabolic pathway that consumes energy to build complex molecules from simpler ones)
cata- down (catabolic pathway: a metabolic pathway that releases energy by breaking down complex molecules into simpler ones)
Chapter 2 Opening Question
Why is the search for water important in the search for life?
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Living and nonliving matter is composed of atoms.
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Like charges repel; different charges attract.
Most atoms are neutral because the number of electrons equals the number of protons.
Dalton—mass of one proton or neutron (1.7 × 10–24 grams)
Mass of electrons is so tiny, it is usually ignored.
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Element—pure substance that contains only one kind of atom
Living things are mostly composed of 6 elements:
Carbon (C) Hydrogen (H) Nitrogen (N)
Oxygen (O) Phosphorus (P) Sulfur (S)
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
• The number of protons identifies an element.
• Number of protons = atomic number
• For electrical neutrality, # protons = # electrons.
• Mass number—total number of protons and neutrons
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
A Bohr model for atomic structure—the atom is largely empty space, and the electrons occur in orbits, or electron shells.
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Actual atomic structure is far more complicated than the Bohr model - electron clouds, quantum mechanics, electron configurations, etc.
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Behavior of electrons
•determines whether a chemical bond will form
•and what shape the bond will have.
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Octet rule
•Atoms with at least two electron shells form stable molecules
•So they have eight electrons in their outermost (valence) shells.
Figure 2.1 Electron Shells
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Atoms with unfilled outer shells tend to undergo chemical reactions to fill their outer shells.
•Stability attained by sharing electrons with other atoms or by losing or gaining electrons.
•The atoms are then bonded together into molecules.
Concept 2.2 Atoms Interact and Form Molecules
Chemical bond
•An attractive force that links atoms together to form molecules.
There are several kinds of chemical bonds.
Table 2.1 Chemical Bonds and Interactions
Concept 2.2 Atoms Interact and Form Molecules
Ionic bonds
Ions are charged particle that form when an atom gains or loses one or more electrons.
Cations—positively charged ions
Anions—negatively charged ions
Ionic bonds result from the electrical attraction between ions with opposite charges.
The resulting molecules are called salts.
Figure 2.2 Ionic Bond between Sodium and Chlorine
Concept 2.2 Atoms Interact and Form Molecules
Ionic attractions are weak, so salts dissolve easily in water.
More about dissolving later…
Concept 2.2 Atoms Interact and Form Molecules
Covalent bonds
Covalent bonds form when two atoms share pairs of electrons.
• The atoms attain stability by having full outer shells.
• Each atom contributes one member of the electron pair.
Figure 2.3 Electrons Are Shared in Covalent Bonds
Covalent Bonds
http://ibchem.com/IB/ibnotes/full/bon_htm/4.2.htm
Animation – Ionic and Covalent Bonds
http://www.youtube.com/watch?v=QqjcCvzWwww&feature=related
Van der Waals Interactions
Van der Waals interactions• Occur when transiently positive and negative
regions of molecules attract each other
Van der Waals interactions
Molecules with partially negative and positive regions:
• Their electrons are constantly moving• Can be moments when electrons accumulate
by chance in one area of a molecule. • At that moment, a regions of negative charge
is created, and positive region opposite.
Van der Waals Interactions
Van der Waals Interactions
Van der Waals interactions
COMMON MISCONCEPTION
The simplified models of the atom electron shells, and covalent bonding can be confusing if you take them too literally. Please understand that:
• Atoms do not have defined surfaces.• Electrons do not travel in planetary orbits
around the nucleus of the atom.• Shared electron pairs are not paired spatially
in covalent bonds.• Electron shells represent energy levels rather
than the position of electrons.
Student Misconceptions
Concept 2.2 Atoms Interact and Form Molecules
Carbon
•Carbon atoms have four electrons in the outer shell
•Can form single covalent bonds with four other atoms.
Figure 2.4 Covalent Bonding (Part 1)
Figure 2.4 Covalent Bonding (Part 2)
Concept 2.2 Atoms Interact and Form Molecules
Properties of molecules are influenced by characteristics of the covalent bonds:
•Orientation—length, angle, and direction of bonds between any two elements are always the same.
Example: Methane always forms a tetrahedron.
Video 2.1 Methane: A three-dimensional model
Video 2.2 Starch: A three-dimensional model
Concept 2.2 Atoms Interact and Form Molecules
• Strength and stability—covalent bonds are very strong; it takes a lot of energy to break them.
• Multiple bonds
Single—sharing 1 pair of electrons
Double—sharing 2 pairs of electrons
Triple—sharing 3 pairs of electrons
C H
C C
N N
Concept 2.2 Atoms Interact and Form Molecules
Degree of sharing electrons is not always equal.
•Let’s review the implications of this in terms of • Electronegativity• Hydrogen bonds• Specific heat capacity• Polar and nonpolar covalent bonds• Cohesion and adhesion• Heat of vaporization• Solvent
Concept 2.2 Atoms Interact and Form Molecules
Degree of sharing electrons is not always equal.
•Electronegativity—the attractive force that an atomic nucleus exerts on electrons
• It depends on the number of protons and the distance between the nucleus and electrons.
Table 2.2 Some Electronegativities
Concept 2.2 Atoms Interact and Form Molecules
• If two atoms have similar electronegativities, they share electrons equally; a nonpolar covalent bond.
• If atoms have different electronegativities, electrons tend to be near the most attractive atom; a polar covalent bond
Concept 2.2 Atoms Interact and Form Molecules
Hydrogen bonds
• Attraction between the δ– end of one molecule and the δ+ hydrogen end of another molecule forms hydrogen bonds.
• Special kind of interactive force of attraction between a hydrogen atom, H, and the nonbonding electrons of a second, very electronegative F, O, or N
Concept 2.2 Atoms Interact and Form Molecules
Hydrogen bonds
• Do not involve the sharing or transfer of electrons.
• Relies on the attraction of partial opposite charges.
• Important in the structure of DNA and proteins.
Hydrogenbonds
+
+
H
H+
+
–
–
–
–
Concept 2.2 Atoms Interact and Form Molecules
Concept 2.2 Atoms Interact and Form Molecules
Hydrogen bonds
• Can occur between different molecules as long as there are areas of partial opposite charges.
Figure 2.5 Hydrogen Bonds Can Form between or within Molecules
Concept 2.2 Atoms Interact and Form Molecules
Hydrogen bonds
• Are weak bonds; roughly 1/20th the strength of a typical covalent bond.
• Are fleeting; they form and break with slight changes in the system’s energy.
• Have a collective strength, as you see in the formation of water ice.
Hydrogen bonds
“The bond lengths give some indication of the bond strength. A normal covalent bond is 0.96 Angstroms, while the hydrogen bond length is 1.97 A.”
http://www.elmhurst.edu/~chm/vchembook/161Ahydrogenbond.html
Hydrogen bonds
•At 0oC, water becomes locked into a crystalline lattice with each molecule bonded to the maximum of four partners.
Hydrogen bonds
•Remember – bond length of hydrogen bonds is roughly twice as much as typical covalent bond
Hydrogen bonds
•Resulting lattice structure finds molecules farther apart. As a result, the same amount of mass occupies more volume.
Hydrogen bonds
•Water ice is approximately 10% less dense that liquid water.
Concept 2.2 Atoms Interact and Form Molecules
• Since ice floats in water, Life can exist under
the frozen surfaces of lakes and polar seas
• So why is this oddity important to life?
Concept 2.2 Atoms Interact and Form Molecules
Concept 2.2 Atoms Interact and Form Molecules
If ice sank, eventually all ponds, lakes, and even the ocean would freeze solid from bottom up.
During the summer, only the upper few inches of the ocean would thaw.
Instead, the surface layer of ice insulates liquid water below, preventing it from freezing and allowing lifeto exist under the frozen surface.
Concept 2.2 Atoms Interact and Form Molecules
Hydrogen bonds
• Hydrogen bonds make possible water’s properties:
• freezing point,• cohesion and adhesion,• plus its ability to dissolve many
substances.
• Weak bonds like the hydrogen bond are vital in many biological processes
Animation – Hydrogen Bonds
Video- Hydrogen Bonds
http://www.youtube.com/watch?v=cgiNk94XyaI
Animation – Hydrogen Bonds
http://www.youtube.com/watch?v=LGwyBeuVjhU
Animation – Basilisk Lizard
http://www.youtube.com/watch?v=Spc9r4CHRDo&feature=related
Student Misconceptions
COMMON MISCONCEPTION
Students often believe that a hydrogen bond can occur between atoms in the same manner as ionic or covalent bonds instead of as a strong, yet transient attraction.
Student Misconceptions
COMMON MISCONCEPTIONS
Weak bonds play important roles in the chemistry of life, despite the transient nature of each individual bond.
• The compelling example of the gecko, able to walk on ceilings because of the van der Waals interactions between the ceiling and the hairs on the gecko’s toes.
• Strong and weak bonds are both important in the chemistry of life. Can you think of any examples?
Concept 2.2 Atoms Interact and Form Molecules
Water molecules form multiple hydrogen bonds with each other—this contributes to high specific heat capacity.
Concept 2.2 Atoms Interact and Form Molecules
A lot of heat is required to raise the temperature of water—the heat energy breaks the hydrogen bonds.
In organisms, presence of water shields them from fluctuations in environmental temperature.
Concept 2.2 Atoms Interact and Form Molecules
Water moderates air temperature
• By absorbing heat from air that is warmer and releasing the stored heat to air that is cooler
Why can water absorb or release relatively large amounts of heat with only a slight change in its own temperature?
Concept 2.2 Atoms Interact and Form Molecules
Distinguish Between Heat and Temperature
Heat Is a measure of the total amount of kinetic
energy due to molecular motion
Temperature Measures the intensity of heat due to the
average kinetic energy of molecules.
Concept 2.2 Atoms Interact and Form Molecules
Atoms and molecules have kinetic energy, the energy of motion, because they are always moving.
•Faster that a molecule moves, the more kinetic energy that it has.
•As the average speed of molecules increases, a thermometer will record an increase in temperature.
Heat and temperature are related, but not identical.
Concept 2.2 Atoms Interact and Form Molecules
FYI: There is no measure of cold in science – all objects have heat energy until the object is at absolute zero.
•Heat passes from the warmer object to the cooler until the two are the same temperature.
•Molecules in the cooler object speed up at the expense of kinetic energy of the warmer object.
•Ice cubes cool a drink by absorbing heat as the ice melts.
Concept 2.2 Atoms Interact and Form Molecules
Biology measure temperature on the Celsius scale (oC).
•At sea level, water freezes at Oo C and boils at 100o C.
•Human body temperature averages 37o C.
Concept 2.2 Atoms Interact and Form Molecules
Convenient unit of measurement of heat energy is the calorie (cal).
•One calorie is the amount of heat energy necessary to raise the temperature of one g of water by 1oC.
Concept 2.2 Atoms Interact and Form Molecules
Concept 2.2 Atoms Interact and Form Molecules
In biology, the kilocalorie (kcal), is even more convenient.
•A kilocalorie is the amount of heat energy necessary to raise the temperature of 1000g (1 kilogram or kg) of water by 1oC.
Another common energy unit, the joule (J), is equivalent to 0.239 cal.
Water has a relatively high specific heat
The specific heat of a substance
• Is the amount of heat that must be absorbed or lost for 1 gram of that substance to change its temperature by 1ºC Absorbing heat energy will increase temperature Releasing heat energy will decrease temperature
Concept 2.2 Atoms Interact and Form Molecules
Water has a high specific heat compared to other substances.
•Example: ethyl alcohol has a specific heat of 0.6 cal/g/oC
Less energy required to get a temperature increase in alcohol
•Specific heat of iron is 1/10th that of water.
Concept 2.2 Atoms Interact and Form Molecules
Due to high specific heat, water resists changes in temperature
•Takes relatively more heat energy to speed up its molecules
Or, water absorbs or releases a relatively large quantity of heat for each degree of change
Concept 2.2 Atoms Interact and Form Molecules
Water’s high specific heat is due to hydrogen bonding between each molecule of water
•Must absorb heat to break the hydrogen bonds
•Because so much energy must first be used to break hydrogen bonds…
Less energy is actually available to move the molecules faster – to increase its kinetic energy and therefore its temperature.
Concept 2.2 Atoms Interact and Form Molecules
When enough energy is added, enough bonds break…
•That’s when a liquid may change its state of matter – liquid to gas.
Concept 2.2 Atoms Interact and Form Molecules
Heating Curve of Water
It takes a lot of energy to force a change of water’s state of matter – solid to liquid to gas.
Why? Goes back to hydrogen bonds – added energy goes first to breaking hydrogen bonds before water can be evaporated.
Concept 2.2 Atoms Interact and Form Molecules
Environmental significance of high specific heat
Water’s high specific heat
• allows water to minimize temperature fluctuations to within limits that permit life.
Ever notice how it is cooler near at a beach?
Environmental significance of high specific heat
• Large bodies of water can absorb a large amount of heat from the sun in daytime and during the summer, while warming only a few degrees.
• At night and during the winter, the warm water will warm cooler air.
• Therefore, ocean temperatures and coastal land areas have more stable temperatures than inland areas.
Environmental significance of high specific heat
High specific heat impact individual organisms
• Organisms are mostly water.
• Water moderates changes in temperature better than if composed of a liquid with a lower specific heat.
Concept 2.2 Atoms Interact and Form Molecules
Transformation of a substance from a liquid to a gas known as vaporization
•Molecules now move fast enough to overcome the attraction of other molecules in the liquid.
•Even in a low temperature liquid (low average kinetic energy), some molecules are moving fast enough to evaporate.
•Heating a liquid increases the average kinetic energy and increases the rate of evaporation.
Concept 2.2 Atoms Interact and Form Molecules
Heat of vaporization
Quantity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas.
• Water has a relatively high heat of vaporization.• About 580 cal of heat to evaporate 1g of water at room
temperature.• That’s double the heat of vaporization of alcohol or
ammonia.
Why?
Why? I’ll tell you why!
Water’s many more hydrogen bonds must be broken before it can evaporate.
So why is a high heat of vaporization important to biology?
Heat of Vaporization
Concept 2.2 Atoms Interact and Form Molecules
Observe same quantities of water and isopropyl alcohol poured onto tables as a thin film.
What did you see?
The alcohol evaporated much faster than the water.
What does this say about alcohols heat of vaporization?
Concept 2.2 Atoms Interact and Form Molecules
As a liquid evaporates, the surface of the liquid that remains behind cools - evaporative cooling.
•Is due to water’s high heat of vaporization.
•Allows water to cool a surface.
•Cooling happens because the most energetic molecules are the most likely to evaporate, leaving the lower kinetic energy molecules behind.
So why is evaporative cooling important to biology?
Concept 2.2 Atoms Interact and Form Molecules
Remember, water has a high heat of vaporization—a lot of heat is required to change water from liquid to gaseous state.
Thus, evaporation has a cooling effect on the environment.
Sweating cools the body—as sweat evaporates from the skin, it transforms some of the adjacent body heat.
Concept 2.2 Atoms Interact and Form Molecules
Hydrogen bonds also give water cohesive strength, or cohesion—water molecules resist coming apart when placed under tension.
• Bonding of a high percentage of the molecules to neighboring molecules
• Due to hydrogen bonding
•Permits narrow columns of water to move from roots to leaves of plants.
Concept 2.2 Atoms Interact and Form Molecules
Helps pull water up through the microscopic vessels of plants
Water conducting cells
100 µm
Concept 2.2 Atoms Interact and Form Molecules
Cohesion and formation of a meniscus
Animation - Cohesion Transport
http://www.youtube.com/watch?v=Ns4vrocF99s
Surface tension
Related to cohesion, it is a measure of the force necessary to break the surface of a liquid.
Water has greater surface tension that most liquids.
The Solvent of Life
Water is a versatile solvent due to its polarity.
It can form aqueous solutions:
• Solution A liquid that is a completely homogeneous
mixture of two or more substances
• Aqueous solution A solution in which water is the solvent
• Solvent Dissolving agent
The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them.
Negative
oxygen regions
of polar water molecules
are attracted to sodium
cations (Na+).
+
+
+
+Cl –
–
–
–
–
Na+Positive hydrogen regions
of water molecules cling to chloride anions
(Cl–).
++
+
+
–
–
–
–
–
–Na+
Cl–
The Solvent of Life
Each dissolved ion is surrounded by a sphere of water molecules, a hydration shell.
Eventually, water dissolves all the ions, resulting in a solution with two solutes, sodium and chloride.
The Solvent of Life
Polar molecules are water soluble because they can form hydrogen bonds with water.
Even large molecules, like proteins, can dissolve in water if they have ionic and polar regions.
The Solvent of Life
Water can also interact with polar molecules such as proteins.
This oxygen is
attracted to a slight
positive charge on the
lysozyme molecule.
This oxygen is attracted to a slight
negative charge on the lysozyme molecule.
(a) Lysozyme molecule
in a nonaqueous
environment
(b) Lysozyme molecule (purple)
in an aqueous environment
such as tears or saliva
(c) Ionic and polar regions on the protein’s
Surface attract water molecules.
+
–
The Solvent of Life
Glucose molecules have polar hydroxyl (OH) groups in them and these attract the water to them. When sugar is in a crystal the molecules are attracted to the water and go into solution. Once in solution the molecules stay in solution at least in part because they become surrounded by water molecules. This layer of water molecules surrounding another molecule is called a hydration shell.
http://staff.jccc.net/pdecell/chemistry/hydrophilic.html
Dissolving leads to a hydration shell which bounds up water molecules – fewer free water molecules, less osmotic potential (more on osmosis in later chapter)
http://staff.jccc.net/pdecell/chemistry/hydrophilic.html
When a sucrose molecule is in water, it is immediately surrounded by water molecules. The sucrose has hydroxyl groups that have a slight negative charge. The positive charge of the oxygen found in the water molecule binds with the sugar. As the hydration shell forms around the sucrose molecule, the molecule is shielded from other sugar molecules so the sugar crystal does not reform.
http://www.bioinquiry.vt.edu/bioinquiry/water/waterpaid/waterhtmls/chem8.html
Assuming two solutions of the same molar concentration, one of glucose, the other of sucrose
Glucose, being a smaller molecule with therefore relatively greater surface area than sucrose, will bound up more water molecules.
http://www.bioinquiry.vt.edu/bioinquiry/water/waterpaid/waterhtmls/chem8.html
Concept 2.2 Atoms Interact and Form Molecules
Any polar molecule can interact with any other polar molecule through hydrogen bonds.
Hydrophilic (“water-loving”)—in aqueous solutions, polar molecules become separated and surrounded by water molecules
Nonpolar molecules are called hydrophobic (“water-hating”); the interactions between them are hydrophobic interactions.
Figure 2.6 Hydrophilic and Hydrophobic
Water: exists in nature as three states of matter
Concept 2.2 Atoms Interact and Form Molecules
Concept 2.2 Atoms Interact and Form Molecules
Concept 2.2 Atoms Interact and Form Molecules
Concept 2.2 Atoms Interact and Form Molecules
Concept 2.2 Atoms Interact and Form Molecules
Water: exists in nature as three states of matterConcept 2.2 Atoms Interact and Form Molecules
Water: exists in nature as three states of matterConcept 2.2 Atoms Interact and Form Molecules
Water: exists in nature as three states of matterConcept 2.2 Atoms Interact and Form Molecules
Chapter 2 Opening Question
Why is the search for water important in the search for life?
Overview
Three-quarters of the Earth’s surface is submerged in water.
The abundance of water is the main reason the Earth is habitable.
Concept 2.2 Atoms Interact and Form Molecules
Concept 2.2 Atoms Interact and Form Molecules
Water is most unusual
• Only pure substance that exists naturally as a gas, liquid and solid.
• Less dense as a solid than a liquid, unlike almost all other chemicals. Explains why ice floats.
Concept 2.2 Atoms Interact and Form Molecules
Water is the molecule that supports all of life
• Water is the biological medium here on Earth.
• All living organisms require water more than any other substance.
Concept 2.2 Atoms Interact and Form Molecules
Liquids essential to biochemistry because…
• Biochemical reactions need a liquid medium.• In a liquid, molecules can dissolve and
chemical reactions can occur.
• Liquid not stable; it can transport chemical from place to place within a cell, organism, or ecosystem. Imagine trying to transport vital nutrients
within a solid or a gas.
Concept 2.2 Atoms Interact and Form Molecules
Water is the best liquid
• The best solvent – it dissolves just about everything.
• Helps maintain the shape of enzymes – essential catalysts of biochemistry – no shape, no chemistry.
• If water wasn’t the essential liquid, if another liquid could take its place, why haven’t we seen it in any life forms?
Concept 2.2 Atoms Interact and Form Molecules
Ammonia! Ammonia!
Concept 2.2 Atoms Interact and Form Molecules
AP TIP
You should be able to describe the properties of water and why these properties are important to life.
Concept 2.2 Atoms Interact and Form Molecules
Functional groups—small groups of atoms with specific chemical properties
•Confer these properties to larger molecules, e.g., polarity.
•One biological molecule may contain many functional groups.
•Attachments that replace one or more hydrogen atoms to the carbon skeleton.
•Behave consistently from one organic molecule to another.
Concept 2.2 Atoms Interact and Form Molecules
Basic structure of testosterone (male hormone) and estradiol (female hormone) is identical.
CH3
OH
HO
O
CH3
CH3
OH
Estradiol
Testosterone
Female lion
Male lion
Concept 2.2 Atoms Interact and Form Molecules
Both are steroids with four fused carbon rings, but have different functional groups attached to the rings.
CH3
OH
HO
O
CH3
CH3
OH
Estradiol
Testosterone
Female lion
Male lion
Concept 2.2 Atoms Interact and Form Molecules
These functional groups then interact with different targets in the body.
CH3
OH
HO
O
CH3
CH3
OH
Estradiol
Testosterone
Female lion
Male lion
Male and female mallards
Male and female peacocks
Male and female sage grouse
Concept 2.2 Atoms Interact and Form Molecules
Six functional groups are important in the chemistry of life:
• Hydroxyl• Carbonyl• Carboxyl• Amino• Sulfhydryl• Phosphate
All are hydrophilic and increase the solubility of organic compounds in water.
-OH, a hydrogen atom forms a polar covalent bond with an oxygen atom, which forms a polar covalent bond to the carbon skeleton. Because of these polar covalent bonds,
hydroxyl groups improve the solubility of organic molecules.
Hydroxyl group
Organic compounds with hydroxyl groups are alcohols and their names typically end in -ol.
Hydroxyl group
>Carbonyl consists of an oxygen atom joined to the carbon skeleton by a double bond. If the carbonyl group is on the end of the
skeleton, the compound is an aldelhyde.
Carbonyl group
If not, then the compound is a ketone. Isomers with aldehydes versus ketones have
different properties.
Carbonyl group
-Carboxyl COOH consists of a carbon atom with a double bond to an oxygen atom and a single bond to a hydroxyl group. Compounds with carboxyl groups are
carboxylic acids.
Carboxyl group
Acts as an acid because the combined electronegativities of the two adjacent oxygen atoms increase the dissociation of hydrogen as an ion (H+).
Carboxyl group
-NH2 consists of a nitrogen atom attached to two hydrogen atoms and the carbon skeleton. Organic compounds with amino groups are
amines.
Amino group
Acts as a base because ammonia can pick up a hydrogen ion (H+) from the solution.
Amino acids, the building blocks of proteins, have amino and carboxyl groups.
Amino group
-SH consists of a sulfur atom bonded to a hydrogen atom and to the backbone. This group resembles a hydroxyl group in
shape.
Sulfhydryl group
Organic molecules with sulfhydryl groups are thiols.
Sulfhydryl groups help stabilize the structure of proteins.
Sulfhydryl group
-OPO32- consists of phosphorus bound to four
oxygen atoms (three with single bonds and one with a double bond). Connects to the carbon backbone via one of its
oxygen atoms.
Phosphate group
Anions with two negative charges as two protons have dissociated from the oxygen atoms.
One function of phosphate groups is to transfer energy between organic molecules.
Phosphate group
ATP (adenosine triphosphate) is a type of nucleotide that is the cell’s primary energy transferring molecule
Phosphate group
Figure 2.7 Functional Groups Important to Living Systems (Part 1)
Figure 2.7 Functional Groups Important to Living Systems (Part 2)
Concept 2.2 Atoms Interact and Form Molecules
AP TIP
You should be able to identify the functional groups most common in biological molecules and explain the characteristics that each functional group confers on molecules.
Concept 2.2 Atoms Interact and Form Molecules
Macromolecules
• Most biological molecules are polymers (poly, “many”; mer, “unit”), made by covalent bonding of smaller molecules called monomers.
Concept 2.2 Atoms Interact and Form Molecules
• Proteins: Formed from different combinations of 20 amino acids
• Carbohydrates—formed by linking similar sugar monomers (monosaccharides) to form polysaccharides
• Nucleic acids—formed from four kinds of nucleotide monomers
• Lipids—noncovalent forces maintain the interactions between the lipid monomers
Concept 2.2 Atoms Interact and Form Molecules
Polymers are formed and broken apart in reactions involving water.
•Condensation—removal of water links monomers together
•Hydrolysis—addition of water breaks a polymer into monomers
Figure 2.8 Condensation and Hydrolysis of Polymers (Part 1)
Figure 2.8 Condensation and Hydrolysis of Polymers (Part 2)
Concept 2.3 Carbohydrates Consist of Sugar Molecules
Carbohydrates
• Source of stored energy
• Transport stored energy within complex organisms
• Structural molecules that give many organisms their shapes
• Recognition or signaling molecules that can trigger specific biological responses
nn OHC )( 2
Concept 2.3 Carbohydrates Consist of Sugar Molecules
Monosaccharides are simple sugars.
Pentoses are 5-carbon sugars
Ribose and deoxyribose are the backbones of RNA and DNA.
Hexoses (C6H12O6) include glucose, fructose, mannose, and galactose.
Figure 2.9 Monosaccharides (Part 1)
Figure 2.9 Monosaccharides (Part 2)
Concept 2.3 Carbohydrates Consist of Sugar Molecules
Monosaccharides are covalently bonded by condensation reactions that form glycosidic linkages.
Sucrose is a disaccharide.
Concept 2.3 Carbohydrates Consist of Sugar Molecules
Oligosaccharides contain several monosaccharides.
Many have additional functional groups.
They are often bonded to proteins and lipids on cell surfaces, where they serve as recognition signals.
Concept 2.3 Carbohydrates Consist of Sugar Molecules
Polysaccharides are large polymers of monosaccharides; the chains can be branching.
Starches—a family of polysaccharides of glucose
Glycogen—highly branched polymer of glucose; main energy storage molecule in mammals
Cellulose—the most abundant carbon-containing (organic) biological compound on Earth; stable; good structural material
Figure 2.10 Polysaccharides (Part 1)
Figure 2.10 Polysaccharides (Part 2)
Figure 2.10 Polysaccharides (Part 3)
Video 2.3 Cellulose: A three-dimensional model
Concept 2.3 Carbohydrates Consist of Sugar Molecules
AP TIP
You should be able to describe structure and function of carbohydrates.
You should be able to explain how polysaccharides for energy storage differ from structural polysaccharides.
Concept 2.4 Lipids Are Hydrophobic Molecules
Lipids are hydrocarbons (composed of C and H atoms); they are insoluble in water because of many nonpolar covalent bonds.
When close together, weak but additive van der Waals interactions hold them together.
Concept 2.4 Lipids Are Hydrophobic Molecules
Lipids
• Store energy in C—C and C—H bonds
• Play structural role in cell membranes
• Fat in animal bodies serves as thermal insulation
Concept 2.4 Lipids Are Hydrophobic Molecules
Triglycerides (simple lipids)
Fats—solid at room temperature
Oils—liquid at room temperature
They have very little polarity and are extremely hydrophobic.
Concept 2.4 Lipids Are Hydrophobic Molecules
Triglycerides consist of:
• Three fatty acids—nonpolar hydrocarbon chain attached to a polar carboxyl group (—COOH) (carboxylic acid)
• One glycerol—an alcohol with 3 hydroxyl (—OH) groups
Synthesis of a triglyceride involves three condensation reactions.
Figure 2.11 Synthesis of a Triglyceride
Concept 2.4 Lipids Are Hydrophobic Molecules
Fatty acid chains can vary in length and structure.
Saturated fatty acids – hydrocarbon chains contain only single carbon-carbon bonds; they have the maximum number of hydrogen atoms (hence saturated).
Unsaturated fatty acids – hydrocarbon chains contain one or more double bonds. Results in kinks in the chain and prevents molecules from packing together tightly.
Figure 2.12 Saturated and Unsaturated Fatty Acids (Part 1)
Figure 2.12 Saturated and Unsaturated Fatty Acids (Part 2)
Video 2.4 Palmitic acid and linoleic acid: A three-dimensional model
Concept 2.4 Lipids Are Hydrophobic Molecules
Fatty acids are amphipathic; they have a hydrophilic end and a hydrophobic tail.
Concept 2.4 Lipids Are Hydrophobic Molecules
Phospholipid—two fatty acids and a phosphate compound bound to glycerol.
•Phosphate group has a negative charge, making that part of the molecule hydrophilic.
Figure 2.13 A Phospholipids
Figure 2.13 B Phospholipids
In an aqueous environment, phospholipids form a bilayer.
Figure 2.13 B Phospholipids
The nonpolar, hydrophobic “tails” pack together and the phosphate-containing “heads” face outward, where they interact with water.
Figure 2.13 B Phospholipids
Biological membranes have this kind of phospholipid bilayer structure.
Concept 2.4 Lipids are Hydrophobic Molecules
AP TIP
You should be able to describe structure and function of lipids.
You should be able to explain how lipids form biological membranes and describe why the degree of saturation in the fatty acid tail affects the structure of lipids.
Overview
The living cell Is a miniature factory where thousands of
reactions occur Converts energy in many ways
Overview
Some organisms Convert energy to light, as in bioluminescence
Figure 8.1
Overview
Graphic Organizer for Concept 2.5
Concept 2.5 Biochemical Changes Involve Energy
Chemical reactions occur when atoms have enough energy to combine, or change, bonding partners.
sucrose + H2O glucose + fructose
(C12H22O11) (C6H12O6) (C6H12O6)
reactants products
Concept 2.5 Biochemical Changes Involve Energy
Metabolism—the sum total of all chemical reactions occurring in a biological system at a given time
Metabolic reactions involve energy changes.
A metabolic pathway has many steps That begin with a specific molecule and end with
a product That are each catalyzed by a specific enzyme
Enzyme 1 Enzyme 2 Enzyme 3
A B C D
Reaction 1 Reaction 2 Reaction 3
Startingmolecule
Product
Concept 2.5 Biochemical Changes Involve Energy
Animation – Overview of Metabolic or Biochemical Pathways
http://highered.mcgraw-hill.com/olc/dl/120070/bio09.swf
Concept 2.5 Biochemical Changes Involve Energy
Two basic types of metabolism:
• Anabolic reactions
• Catabolic reactions
Metabolic Pathways
Catabolic pathways release energy by breaking down complex molecules into simpler
compounds. Energy stored in the chemical bonds is released. A major pathway of catabolism is cellular
respiration, in which the sugar glucose is broken down in
the presence of oxygen to carbon dioxide and water.
Metabolic Pathways
Anabolic pathways Build complicated molecules from simpler ones Consume energy; require energy input and
capturing of some of that energy in newly formed chemical bonds.
Also called biosynthetic pathways. The synthesis of protein from amino acids is an
example of anabolism. The energy released by catabolic pathways can
be stored and then used to drive anabolic pathways.
Concept 2.5 Biochemical Changes Involve Energy
All forms of energy can be considered as either:
• Potential—the energy of state or position, or stored energy
• Kinetic—the energy of movement (the type of energy that does work) that makes things change
Energy can be converted from one form to another.
Concept 2.5 Biochemical Changes Involve Energy
Chemical energy is a form of potential energy stored in
molecules because of the arrangement of their atoms.
Breaking or making chemical bonds – covalent or ionic – requires the release or absorption of energy during a chemical reaction
Chemical reactions can be classified as either exergonic or endergonic based on free energy.
Figure 2.14 Energy Changes in Reactions (Part 1)
Figure 2.14 Energy Changes in Reactions (Part 2)
An exergonic reaction Proceeds with a net release of free energy
and is spontaneous – negative ∆G
Reactants
Products
Energy
Progress of the reaction
Amount ofenergyreleased (∆G <0)
Fre
e e
ne
rgy
(a) Exergonic reaction: energy released
An exergonic reaction The greater the decrease in free energy, the
greater the amount of work that can be done
Reactants
Products
Energy
Progress of the reaction
Amount ofenergyreleased (∆G <0)
Fre
e e
ne
rgy
(a) Exergonic reaction: energy released
Concept 2.5 Biochemical Changes Involve Energy
For the overall reaction of cellular respiration: C6H12O6 + 6O2 -> 6CO2 + 6H2O
G = −686 kcal/molReactants
Products
Energy
Progress of the reaction
Amount ofenergyreleased (∆G <0)
Fre
e e
ne
rgy
(a) Exergonic reaction: energy released
Concept 2.5 Biochemical Changes Involve Energy
The products have 686 kcal less free energy than the reactants.
Reactants
Products
Energy
Progress of the reaction
Amount ofenergyreleased (∆G <0)
Fre
e e
ne
rgy
(a) Exergonic reaction: energy released
Concept 2.5 Biochemical Changes Involve Energy
An endergonic reaction Is one that absorbs free energy from its
surroundings and is nonspontaneous
Energy
Products
Amount ofenergyreleased (∆G>0)
Reactants
Progress of the reaction
Fre
e e
ne
rgy
(b) Endergonic reaction: energy required
Concept 2.5 Biochemical Changes Involve Energy
An endergonic reaction stores energy in molecules; G is positive.
Energy
Products
Amount ofenergyreleased (∆G>0)
Reactants
Progress of the reaction
Fre
e e
ne
rgy
(b) Endergonic reaction: energy required
Concept 2.5 Biochemical Changes Involve Energy
If cellular respiration releases 686 kcal, then photosynthesis, the reverse reaction, must require an equivalent investment of energy.
Energy
Products
Amount ofenergyreleased (∆G>0)
Reactants
Progress of the reaction
Fre
e e
ne
rgy
(b) Endergonic reaction: energy required
Concept 2.5 Biochemical Changes Involve Energy
For the conversion of carbon dioxide and water to sugar, G = +686 kcal/mol.
Figure 8.6
Energy
Products
Amount ofenergyreleased (∆G>0)
Reactants
Progress of the reaction
Fre
e e
ne
rgy
(b) Endergonic reaction: energy required
Concept 2.5 Biochemical Changes Involve Energy
Equilibrium and Metabolism
Reactions in a closed system Eventually reach equilibrium and can do no
work
(a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium.
∆G < 0 ∆G = 0
Equilibrium and Metabolism
Should a cell reach equilibrium, when G = 0, THAT CELL IS DEAD!
(a) A closed hydroelectric system. Water flowing downhill turns a turbine that drives a generator providing electricity to a light bulb, but only until the system reaches equilibrium.
∆G < 0 ∆G = 0
Equilibrium and Metabolism
Cells in our body Experience a constant flow of materials in and
out, preventing metabolic pathways from reaching equilibrium.
(b) An open hydroelectric system. Flowing water keeps driving the generator because intake and outflow of water keep the system from reaching equlibrium.
∆G < 0
Equilibrium and Metabolism
Metabolic disequilibrium is one of the defining features of life.
Cells maintain disequilibrium because they are open systems.
The constant flow of materials into and out of the cell keeps metabolic pathways from ever reaching equilibrium.
A cell continues to do work throughout its life.
Equilibrium and Metabolism
An analogy for cellular respiration
(c) A multistep open hydroelectric system. Cellular respiration is analogous to this system: Glucoce is brocken down in a series of exergonic reactions that power the work of the cell. The product of each reaction becomes the reactant for the next, so no reaction reaches equilibrium.
∆G < 0
∆G < 0
∆G < 0
Equilibrium and Metabolism
Some reversible reactions of respiration are constantly “pulled” in one direction, as the product of one reaction does not accumulate but…
becomes the reactant in the next step.
Sunlight provides a daily source of free energy for photosynthetic organisms.
Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic organisms in the form of organic molecules.
Student Misconceptions
COMMON MISCONCEPTION
Let’s double check if you fully grasp the concept of energy, and especially potential energy.
• Potential energy is not a substance or fuel that is somehow stored in matter.
• Potential energy is associated with an object’s ability to move to a lower-energy state, thus releasing some of the potential energy.
Concept 2.5 Biochemical Changes Involve Energy
The laws of thermodynamics apply to all matter and energy transformations in the universe.
First law: Energy is neither created nor destroyed.
Second law: Disorder (entropy) tends to increase. • When energy is converted from one form to
another, some of that energy becomes unavailable for doing work.
• That “lost” energy contributes to disorder or entropy.
Concept 2.5 Biochemical Changes Involve Energy
First law of thermodynamics Energy can be transferred and transformed. Energy cannot be created or destroyed.
Concept 2.5 Biochemical Changes Involve Energy
First law of thermodynamics The first law is also known as the principle of
conservation of energy Total energy in a system before a
transformation must equal the total energy in the system after the transformation
Concept 2.5 Biochemical Changes Involve Energy
First law of thermodynamics Plants do not produce energy; they transform
light energy to chemical energy Animals eat other organisms and catabolize
complex nutrient molecules into simple compounds, such as H2O and CO2
Quantity of energy does not change, but the quality of energy does change
Concept 2.5 Biochemical Changes Involve Energy
An example of energy conversion
First law of thermodynamics: Energy can be transferred or transformed but Neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b).
(a)
Chemicalenergy
Concept 2.5 Biochemical Changes Involve Energy
No process is 100% efficient in using potential energy to do work
During every transfer or transformation of energy, some energy is converted to heat,
which is the energy associated with the random movement of atoms and molecules
Energytotal = Energywork + Energylost as heat
Concept 2.5 Biochemical Changes Involve Energy
Concept 2.5 Biochemical Changes Involve Energy
Heat can still do work
A system can use heat to do work only when
there is a temperature difference that results in heat flowing from a warmer location to a cooler one.
a.k.a a temperature gradient
If temperature is uniform, as in a living cell, heat can only be used to warm the organism.
Concept 2.5 Biochemical Changes Involve Energy
Inherent inefficiency in energy transformations leads us to the second law of thermodynamics
Energy transfers and transformations make the universe more disordered due to this loss of usable energy.
Cue the cheetah
Concept 2.5 Biochemical Changes Involve Energy
According to the second law of thermodynamics Every energy transfer or transformation
increases the disorder of the universe.
Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.
(b)
Heat co2
H2O+
Concept 2.5 Biochemical Changes Involve Energy
According to the second law of thermodynamics Cheetah breaks down – catabolizes –
relatively more complex sugar molecules into simple CO2 and H2O.
Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.
(b)
Heat co2
H2O+
Concept 2.5 Biochemical Changes Involve Energy
We needed a better way to conceptualize the second law of thermodynamics and the disorder of the universe
Hence the concept of entropy
Concept 2.5 Biochemical Changes Involve Energy
Entropy
• Quantity used as a measure of disorder or randomness.
• The more random a collection of matter, the greater its entropy.
• Let’s update the cheetah
Concept 2.5 Biochemical Changes Involve Energy
• Every energy transfer or transformation increases the disorder (entropy) of the universe.
Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.
(b)
Heat co2
H2O+
Concept 2.5 Biochemical Changes Involve Energy
• Entropy increases because as the cheetah runs, it adds heat to its surroundings and releases simple by-products from the breakdown of complex chemicals
Second law of thermodynamics: Every energy transfer or transformation increasesthe disorder (entropy) of the universe. For example, disorder is added to the cheetah’ssurroundings in the form of heat and the small molecules that are the by-productsof metabolism.
(b)
Heat co2
H2O+
Concept 2.5 Biochemical Changes Involve Energy
The universe the cheetah lives in is a closed system (so far as we know).
Second law requires that the disorder or entropy of any closed system always increases.
Therefore, if there is at one point a decrease in entropy, there must also be somewhere an increase in entropy.
Concept 2.5 Biochemical Changes Involve Energy
If the second law of thermodynamics requires an increase in disorder, what form may that disorder take?
•Catabolism breaks complex molecules into simpler ones, increasing disorder (entropy)
•Each catabolic reaction will also release heat energy, increasing disorder (entropy)
•So there are two types of entropy• Material• Thermal
The Second Law of Thermodynamics
Combustion of the fuel releases heat, thereby increasing entropy. Automobiles convert only 25% of the energy in gasoline into motion; the rest is lost as heat.
Concept 2.5 Biochemical Changes Involve Energy
The Second Law of Thermodynamics
C8H18 + O2 CO2 + H2O + heat
There is both an increase in disorder materially – octane to carbon dioxide and water – and thermally – the release of heat energy
Concept 2.5 Biochemical Changes Involve Energy
Concept 2.5 Biochemical Changes Involve Energy
Here’s another way of defining entropy
Entropy is measured by the number of distinguishable arrangements by the particles of matter The fewer the number of distinguishable
arrangements, the lower the entropy The more distinguishable arrangements,
the greater the entropy
Concept 2.5 Biochemical Changes Involve Energy
An to illustrate distinguishable arrangements ..a card trick
How many possible five card hands can be dealt in poker?
Concept 2.5 Biochemical Changes Involve Energy
Each of the 2,598,960 five-card hands are a distinguishable arrangement
When happens when the number of cards is halved to 26?
Concept 2.5 Biochemical Changes Involve Energy
With 26 cards, only 65,780 five card arrangements can be made.
Now suppose those cards are atoms?
Concept 2.5 Biochemical Changes Involve Energy
With fewer atoms, few distinguishable arrangements can be made, the lower the entropy.
But then of course, if you increased the number of atoms in each arrangement, from 5 to 10
You get 5,311,735 distinguishable arrangements – fewer atoms but larger molecules – entropy is increased!
Concept 2.5 Biochemical Changes Involve Energy
Second law of thermodynamics
• Requires increasing entropy from any closed system
• Isolated from its surroundings, lacking any input of additional energy, the closed system will (eventually) increase its entropy
• All things will fall apart
Concept 2.5 Biochemical Changes Involve Energy
For a process to occur on its own, without outside help in the form of energy input, it must increase the entropy of the universe.
In other words, the process must be spontaneous
Spontaneous processes need not occur quickly.
•Some spontaneous processes are instantaneous, such as an explosion.
•Some are very slow, such as the rusting of an old car.
A spontaneous change is a change that has a tendency to occur without been driven by an external influence
e.g. the cooling of a hot metal block to the temperature of its surroundings
A non-spontaneous change is a change that occurs only when driven
e.g. forcing electric current through a metal block to heat it
The Second Law of ThermodynamicsConcept 2.5 Biochemical Changes Involve Energy
Concept 2.5 Biochemical Changes Involve Energy
So, another way to state the second law of thermodynamics is
•for a process to occur spontaneously, it must increase the entropy of the universe
•You will see that spontaneous processes are absolutely vital to biological processes
Diffusion and facilitated diffusion Osmosis and dissolution Evolution
Concept 2.5 Biochemical Changes Involve Energy
Let’s describe the second law mathematically S = entropy ∆S = change in entropy A spontaneous process will be a positive or
negative ∆S?positive
The Second Law of Thermodynamics
Enthalpy is the total potential energy of a system
H – the total enthalpy (in biological systems, equivalent to energy)
Enthalpy – the energy and matter within a system that may be exchanged with its surroundings.
The Second Law of Thermodynamics
Entropy is that fraction of enthalpy that cannot be used to do work – it is always lost to increasing disorder
So the amount of energy in any system that can do work is approximately the difference between the two
Total entropy change
entropy change of system
entropy change of surroundings
+=
Dissolving
disorder of solution
disorder of surroundings
• must be an overall increase in disorder for dissolving to occur
The Second Law of ThermodynamicsThe Second Law of Thermodynamics
Biological Order and Disorder
Now for the apparent paradox of life…
Don’t living systems increase order, violating the second law of thermodynamics?
50µm
Biological Order and Disorder
Living systems are open systems that absorb energy—light or chemical energy – in the form of organic molecules
50µm
Biological Order and Disorder
and release heat and metabolic waste products such as urea or CO2 to their surroundings.
50µm
Biological Order and Disorder
Living systems create ordered structures from less ordered starting materials.
The structure of a multicellular body is organized and complex.
50µm
Biological Order and Disorder
Example: amino acids are ordered into polypeptide chains
But living systems must use energy to maintain order.
50µm
Biological Order and Disorder
And, in using energy to maintain order an organism takes in organized forms of
matter and energy from its surroundings and replaces them with less ordered forms.
50µm
Biological Order and Disorder
Example: an animal consumes organic molecules as food and catabolizes them to low-energy carbon dioxide and water.
50µm
Biological Order and Disorder
So what is the answer to the paradox?
50µm
Biological Order and Disorder
While they can increase order locally and temporarily, there is an unstoppable trend toward randomization of the entire universe.
50µm
Biological Order and Disorder
“Living things preserve their low levels of entropy throughout time, because they receive energy from their surroundings in the form of food.”
50µm
Entropy in Biology,
Jayant Udgaonkar
Biological Order and Disorder
“They gain their order at the expense of disordering the nutrient they consume.”
50µm
Entropy in Biology,
Jayant Udgaonkar
Biological Order and Disorder
“Dust thou art, and unto dust thou shalt return" (Genesis 3:19)
Death is the inevitable result of increasing molecular entropy
50µm
Biological Order and Disorder
The entropy of a particular system, such as an organism, may decrease as long as
the total entropy of the universe—the system plus its surroundings—increases.
Think of organisms as islands of low entropy in an increasingly random universe.
The evolution of biological order is perfectly consistent with the laws of thermodynamics.
Biological Order and Disorder
Now how does entropy relate to evolution?
Over evolutionary time, complex organisms have evolved from simpler ones.
How does this happen?
Biological Order and Disorder
Second law of thermodynamics makes certain that a sequence of DNA cannot be maintained forever.
•Eventually it must fall to disorder and increase its entropy
•Small random changes in the DNA sequence is inevitable
Biological Order and Disorder
Sometime those changes – mutations – lead to changes in a gene
which leads to different proteins being produced,
which leads to different traits, which allows natural selection to determine
the advantageous traits, and so on and so on.
Biological Order and Disorder
Evolution therefore does not violate the second law of thermodynamics
Individuals and entire species are merely temporary and isolated examples of decreasing entropy
Entropy drives the processes of evolution, osmosis, diffusion and other spontaneous processes
Not a directed process; there is no goal Evolution is inevitable
Biological Order and Disorder
Let’s check your understanding of entropy using this model of osmosis.
Assume the dialysis bag contains a saline solution.
It is surrounded by pure water.
Which direction will the water tend – into or out of the bag?
Biological Order and Disorder
Water will tend to go into the bag
Osmosis requires water move from an area of high concentration – outside – to an area of low concentration until equilibrium is reached.
Now explain what happens in terms of entropy.
Biological Order and Disorder
First, we recognize the bag is an open system
Second, we know there will be a net flow of water into the bag
Third, we know this will be spontaneous
By definition, this will increase entropy in the beaker/bag system
But wait..there’s more!
Biological Order and Disorder
Salt water has greater entropy than pure water
Na+ and Cl- ions are spread out through the solution, creating greater disorder
Pure water is just water molecules bumping into other water molecules
Entropy will seek equilibrium until ∆S = 0
Biological Order and Disorder
Solutions have more distinguishable particles
With a solute(s), you can see more combinations between molecules of solute(s) and solvent, than just solvent
1. If we freeze water, disorder of the water molecules decreases , entropy decreases
( -ve S , -ve H)
2. If we boil water, disorder of the water molecules increases , entropy increases (vapour is highly disordered state)
( +ve S , +ve H)
Biological Order and DisorderBiological Order and Disorder
System in Dynamic EquilibriumSystem in Dynamic Equilibrium
A + B C + D
Dynamic (coming and going), equilibrium (no net change)
• no overall change in disorder
S 0 (zero entropy change)
Biological Order and DisorderBiological Order and Disorder
Biological Order and Disorder
Is the second law of thermodynamics responsible for time?
Well, not really. Second law and entropy do not require time in the equations, however…
Second does imply a direction of time All things must move toward a more
disordered state Known as Time’s Arrow
Biological Order and Disorder
Zero entropy13.7 billions years ago
Constantly increasing entropy in Universe
Biological Order and Disorder
Biological Order and Disorder
Biological Order and Disorder
Biological Order and Disorder
Biological Order and Disorder
Biological Order and Disorder
Biological Order and Disorder
Figure 2.15 The Laws of Thermodynamics (Part 2)
Figure 2.15 The Laws of Thermodynamics (Part 3)
Concept 2.5 Biochemical Changes Involve Energy
If a chemical reaction increases entropy, its products are more disordered or random than its reactants.
If there are fewer products than reactants, the disorder is reduced; this requires energy to achieve.
Concept 2.5 Biochemical Changes Involve Energy
As a result of energy transformations, disorder tends to increase.
•Some energy is always lost to random thermal motion (entropy).
Concept 2.5 Biochemical Changes Involve Energy
Metabolism creates more disorder (more energy is lost to entropy) than the amount of order that is stored.
Example:
•The anabolic reactions needed to construct 1 kg of animal body require the catabolism of about 10 kg of food.
Life requires a constant input of energy to maintain order.
Concept 2.5 Biochemical Changes Involve Energy
AP TIP
You should be able to predict the outcome of endergonic and exergonic reactions
You should be able to discuss the significance of the second law of thermodynamics.
Answer to Opening Question
One way to investigate the possibility of life on other planets is to study how life may have originated on Earth.
An experiment in the 1950s combined gases thought to be present in Earth’s early atmosphere, including water vapor. An electric spark provided energy.
Complex molecules were formed, such as amino acids. Water was essential in this experiment.
Figure 2.16 Synthesis of Prebiotic Molecules in an Experimental Atmosphere (Part 1)
Figure 2.16 Synthesis of Prebiotic Molecules in an Experimental Atmosphere (Part 2)
Life Chemistry and EnergyCGI Video Summation
2
Inner Lives of a Cell – Full version with musical score
We have reviewed the basics of biological molecules. This video shows those biological molecules in action. Can you, in your mind’s eye, see the bonds, the interactions?
http://www.youtube.com/watch?v=zrXykvorybo
Life Chemistry and EnergyPractice Questions
2
Atomic structure
The element magnesium has an atomic number of 12 and a mass number of 24. Working in pairs, and using the Bohr model for atomic structure, draw a magnesium atom.
Once you have drawn your magnesium atom, answer the following questions:
1. How many protons and neutrons are in the nucleus? How many electrons are in this atom?
2. Is the magnesium atom likely to bond with other atoms? Why or why not?
Take a few minutes to discuss, and then present your drawing and answers to the class.
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Select the false statement about elements:
a. An element contains only one kind of atom.
b. Isotopes are variants of an element with additional neutrons in the nucleus.
c. Atoms of different elements can have the same number of protons.
d. All the atoms of a particular element contain the same number of protons.
e. Carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur are the main elements found in living organisms.
Concept 2.1 Atomic Structure Is the Basis for Life’s Chemistry
Chemical bonds
Working in pairs, compare the following bonds with respect to their basis of interaction and strength:
• Ionic• Covalent• Hydrogen
Draw an example of each type of bond.
Concept 2.2 Atoms Interact and Form Molecules
Which of the following statements about water is false?
a. Water helps to prevent dramatic changes in body temperature because it has a high heat capacity.
b. Sweating cools the body because water has a high heat of vaporization.
c. Not counting bones, water makes up about 70% of the weight of your body.
d. During condensation, the addition of water breaks a polymer into monomers.
e. Molecules with polar covalent bonds are attracted to water.
Concept 2.2 Atoms Interact and Form Molecules
Carbohydrates
Working in pairs or small groups, discuss the polysaccharides starch, glycogen, and cellulose. In your discussion, consider the following questions:
1. Where are these polysaccharides found?
2. What biological role does each polysaccharide play?
3. What do these molecules have in common?
4. How do these molecules differ?
Present your answers to the class.
Concept 2.3 Carbohydrates Consist of Sugar Molecules
Carbohydrates
a. can have the same chemical formula, but distinct chemical properties and different biological roles.
b. such as polysaccharides are formed when monosaccharides are ionically bonded by condensation reactions.
c. are made of carbon, hydrogen, and oxygen.
d. are always linear, unbranched molecules.
e. Both a and c
Concept 2.3 Carbohydrates Consist of Sugar Molecules
Triglycerides
Working individually, compare saturated and unsaturated fatty acids with respect to the following characteristics:
1. Presence of double bonds between carbon atoms in the hydrocarbon chain
2. Ability to pack tightly together
3. State of lipid at room temperature
4. Melting point of lipid
5. Typical source
Compare your answers with your classmates and discuss.
Concept 2.4 Lipids Are Hydrophobic Molecules
Which of the following statements about phospholipids is false?
a. The phosphate functional group and glycerol form the hydrophobic head of a phospholipid.
b. A phospholipid has two fatty acids whereas a triglyceride has three fatty acids.
c. Phospholipids are amphipathic (i.e., they have two opposing chemical properties).
d. The phosphate functional group and glycerol form the hydrophilic head of a phospholipid.
e. Biological membranes are characterized by a phospholipid bilayer structure.
Concept 2.4 Lipids Are Hydrophobic Molecules
Chemical reactions
Working in pairs, consider the following chemical reaction and answer the questions below:
glucose + galactose lactose + water
1. Is this a condensation or hydrolysis reaction?
2. What are the reactants? What are the products?
3. Is this an anabolic or catabolic reaction?
4. Is energy required or released?
Concept 2.5 Biochemical Changes Involve Energy
Which of the following statements about energy is false?
a. Exergonic reactions release energy.
b. The energy released in anabolic reactions is often used to drive catabolic reactions.
c. Potential energy is stored energy.
d. Endergonic reactions require energy
e. Kinetic energy is the energy of movement.
Concept 2.5 Biochemical Changes Involve Energy
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Science, Technology and Society
• While waiting at an airport, Neil Campbell once overheard this claim:
– “It’s paranoid and ignorant to worry about industry or agriculture contaminating the environment with their chemical wastes. After all, this stuff is just made of the same atoms that were already present in our environment.”
• How would you counter this argument?
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Review – Online Quiz by Campell/Reece
http://www.hbwbiology.net/quizzes-ap-review-main.htm
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
2. You are studying a cellular enzyme involved in breaking down fatty acids for energy. Looking at theR groups of the amino acids in the following figures, what amino acids would you predict to occur in the parts of the enzyme that interact with the fatty acids? *
a. non-polar
b. polar
c. electrically charged
d. polar and electrically charged
e. all of these
Practice Problems
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The 20 Amino Acids of Proteins
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
The 20 Amino Acids of Proteins (cont.)
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Let’s begin with the condensation reaction that lead to the 1-4 glycosidic linkage
Scientific Inquiry
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
• Repeated many times results in a polysaccharide known as starch
Scientific Inquiry
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
H2O
Scientific Inquiry
• Hydrolysis breaks the glycosidic linkages, leaving behind glucose monomers, reinserting a water molecule
Note one hydrogen bonds with the oxygen of carbon-1; the remaining hydroxyl group OH bonds with the carbon 4
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
HCl
Scientific Inquiry
• If hydrochloric acid used to break glycosidic linkages..
The hydrogen will bond with carbon-1, as before, but the chlorine Cl- will bond with the carbon-4, resulting in only one glucose monomer, not two
Cl
Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings
Scientific Inquiry
