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Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

PowerPoint® Lecture Presentations for

Biology

Eighth Edition

Neil Campbell and Jane Reece

Lectures by Chris Romero, updated by Erin Barley with contributions from Joan Sharp

BIG IDEA II Biological systems utilize free energy and molecular building blocks

to grow, to reproduce and to maintain dynamic homeostasis.

Enduring Understanding 2.A

Growth, reproduction and maintenance of the organization

of living systems require free energy and matter.

Essential Knowledge 2.A.1

All living systems require a constant input of free energy.


Essential Knowledge 2.A.1: All living systems require a constant input of free energy.

• Learning Objectives:

– (2.1) The student is able to explain how biological

systems use free energy based on empirical data

that all organisms require constant energy input to

maintain organization, to grow and to reproduce.

– (2.2) The student is able to justify a scientific claim

that free energy is required for living systems to

maintain organization, to grow or to reproduce, but that

multiple strategies exist in different living systems.

– (2.3) The student is able to predict how changes in

free energy availability affect organisms, populations

and ecosystems.

Fig. 9-2

Light energy

ECOSYSTEM

Photosynthesis in chloroplasts

CO2 + H2O

Cellular respiration in mitochondria

Organic molecules

+ O2

ATP powers most cellular work

Heat energy

ATP


Life requires a highly ordered system.

• The living cell is a chemical factory in miniature, where

thousands of reactions occur within a microscopic space.

– Order is maintained by constant free energy input into the

system.

– Loss of order or free energy flow results in death.

– Increased disorder and entropy are offset by biological

processes that maintain or increase order.

• The concepts of metabolism help us to understand how

matter and energy flow during life’s processes and how

that flow is regulated in living systems.


Metabolism

• Metabolism is the totality of an organism’s chemical

reactions:

– An organism’s metabolism transforms matter and

energy, subject to the laws of thermodynamics.

• Metabolism is an emergent property of life that arises from

interactions between molecules within the cell.

• A metabolic pathway begins with a specific molecule and

ends with a product, whereby each step is catalyzed by a

specific enzyme.

• Bioenergetics is the study of how organisms manage their

energy resources.


Enzyme 1 Enzyme 2 Enzyme 3

D C B A Reaction 1 Reaction 3 Reaction 2

Starting molecule

Product

Overview: A Metabolic Pathway


• Catabolic pathways release energy by breaking

down complex molecules into simpler compounds:

– Cellular respiration, the breakdown of glucose

in the presence of oxygen, is an example of a

pathway of catabolism.

• Anabolic pathways consume energy to build

complex molecules from simpler ones:

– The synthesis of protein from amino acids is

an example of anabolism.

Catabolism and Anabolism


Forms of Energy

• Energy is the capacity to cause change.

• Energy exists in various forms, some of which can perform

work:

– Kinetic energy is energy associated with motion.

– Heat (thermal energy) is kinetic energy associated with

random movement of atoms or molecules.

– Potential energy is energy that matter possesses because

of its location or structure.

– Chemical energy is potential energy available for release in

a chemical reaction.

• Energy cannot be created or destroyed, but it can be

converted from one form to another.

Climbing up converts the kinetic

energy of muscle movement

to potential energy.

A diver has less potential

energy in the water

than on the platform.

Diving converts

potential energy to

kinetic energy.

A diver has more potential

energy on the platform

than in the water.


The Laws of Energy Transformation

• Thermodynamics is the study of energy

transformations.

• A closed system, such as that approximated by

liquid in a thermos, is isolated from its

surroundings.

• In an open system, energy and matter can be

transferred between the system and its

surroundings.

• Organisms are open systems.


The First Law of Thermodynamics

• According to the first law of thermodynamics,

the energy of the universe is constant:

– Energy can be transferred and transformed,

but it cannot be created or destroyed.

• The first law is also called the principle of

conservation of energy.


The Second Law of Thermodynamics

• During every energy transfer or transformation,

some energy is unusable, and is often lost as heat.

• According to the second law of thermodynamics:

– Every energy transfer or transformation

increases the entropy (disorder) of the

universe.


Living systems do not violate the second law of thermodynamics, which states that entropy increases over time.


Biological Order and Disorder

• Cells create ordered structures from less ordered

materials.

• Organisms also replace ordered forms of matter and

energy with less ordered forms.

• Energy flows into an ecosystem in the form of light

and exits in the form of heat.

• The evolution of more complex organisms does

not violate the second law of thermodynamics.

• Entropy (disorder) may decrease in an organism,

but the universe’s total entropy increases.


Free-Energy Change, G https://paul-andersen.squarespace.com/gibbs-free-energy

• The free-energy change of a reaction tells us

whether or not the reaction occurs spontaneously.

• Biologists often want to know which reactions

occur spontaneously and which require input of

energy.

• To do so, they need to determine energy changes

that occur in chemical reactions.

• A living system’s free energy is energy that can

do work when temperature and pressure are

uniform, as in a living cell.

https://paul-andersen.squarespace.com/gibbs-free-energy








• The change in free energy (∆G) during a process

is related to the change in enthalpy, or change in

total energy (∆H), change in entropy (∆S), and

temperature in Kelvin (T):

∆G = ∆H – T∆S

• Only processes with a negative ∆G are

spontaneous.

• Spontaneous processes can be harnessed to

perform work.

Free-Energy Change, G


Free Energy, Stability, and Equilibrium

• Free energy is a measure of a system’s instability,

its tendency to change to a more stable state.

• During a spontaneous change, free energy

decreases and the stability of a system increases.

• Equilibrium is a state of maximum stability.

• A process is spontaneous and can perform work

only when it is moving toward equilibrium.

(a) Gravitational motion (b) Diffusion (c) Chemical reaction

• More free energy (higher G)

• Less stable

• Greater work capacity

In a spontaneous change

• The free energy of the system

decreases (∆G < 0) • The system becomes more

stable

• The released free energy can

be harnessed to do work

• Less free energy (lower G)

• More stable • Less work capacity


Free Energy and Metabolism

• The concept of free energy can be applied to the

chemistry of life’s processes:

– An exergonic reaction proceeds with a net

release of free energy and is spontaneous (∆G

is negative).

– An endergonic reaction absorbs free energy

from its surroundings and is nonspontaneous

(∆G is positive).

Reactants

Energy

Fre

e e

ne

rgy

Products

Amount of energy released (∆G < 0)

Progress of the reaction

(a) Exergonic reaction: energy released

Products

Reactants

Energy

Fre

e e

ne

rgy

Amount of energy required

(∆G > 0)

(b) Endergonic reaction: energy required

Progress of the reaction

(a) An isolated hydroelectric system

∆G < 0 ∆G = 0

(b) An open hydroelectric system ∆G < 0

∆G < 0

∆G < 0

∆G < 0

(c) A multistep open hydroelectric system


H2O

ATP & Energy Coupling https://www.youtube.com/watch?v=AhuqXwvFv2E

Energetically favorable exergonic reactions, such as ATPADP, that

have negative change in free energy can be used to maintain or

increase order in a system by being coupled with reactions that have

a positive free energy exchange.

https://www.youtube.com/watch?v=AhuqXwvFv2E


Structure of ATP

• The bonds between the phosphate groups of ATP’s tail can be broken

by hydrolysis

• Energy is released from ATP when the terminal phosphate bond is

broken

• This release of energy comes from the chemical change to a state of

lower free energy, not from the phosphate bonds themselves

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=J305bZLCfvLzIM&tbnid=bw3Cv2lgaZSsRM:&ved=0CAUQjRw&url=http%3A%2F%2Favonapbio.pbworks.com%2Fw%2Fpage%2F9429326%2FChapter%25208&ei=aJRBUv6zKIr68gSMuIDQBg&bvm=bv.52434380,d.eWU&psig=AFQjCNHjk5tPkwYOFwsdU15MCwtgg8a29Q&ust=1380115891118701

(b) Coupled with ATP hydrolysis, an exergonic reaction

Ammonia displaces the phosphate group, forming glutamine.

(a) Endergonic reaction

(c) Overall free-energy change

P

P

Glu

NH3

NH2

Glu i

Glu ADP +

P

ATP +

+

Glu

ATP phosphorylates glutamic acid, making the amino acid less stable.

Glu

NH3

NH2

Glu +

Glutamic acid

Glutamine Ammonia

∆G = +3.4 kcal/mol

+ 2

1

(b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzed

Membrane protein

P i

ADP

+

P

Solute Solute transported

P i

Vesicle Cytoskeletal track

Motor protein Protein moved

(a) Transport work: ATP phosphorylates transport proteins

ATP

ATP


Energy-related pathways in biological systems are sequential and may be entered at multiple points in the pathway.

• Illustrative Examples include:

– Glycolysis

– Krebs cycle

– Calvin cycle

– Fermentation


Organisms use free energy to maintain organization, grow and reproduce.

• Demonstrated understanding includes a

knowledge of:

– Strategies to regulate body temperature

– Strategies for reproduction & rearing of

offspring

– Correlation between metabolic rate and size

– Excess acquired free energy (storage/growth)

– Insufficient acquired free energy (death)


• Animals use the chemical energy in food to sustain

form and function.

• All organisms require chemical energy for growth,

repair, physiological processes, regulation, and

reproduction.

• The flow of energy through an animal, its

bioenergetics, ultimately limits the animal’s behavior,

growth, and reproduction – which determines how

much food it needs.

• Studying an animal’s bioenergetics tells us a great

deal about the animal’s adaptations.

Bioenergetics of Animals

Bioenergetics of an Animal


• An animal’s metabolic rate is the amount of energy it uses

in a unit of time.

• An animal’s metabolic rate is closely related to its

bioenergetic strategy – which determines nutritional

needs and is related to an animal’s size, activity, and

environment:

– The basal metabolic rate (BMR) is the metabolic rate of a non-

growing, unstressed endotherm at rest with an empty stomach.

– The standard metabolic rate (SMR) is the metabolic rate of a

fasting, non-stressed ectotherm at rest at a particular temperature.

– For both endotherms and ectotherms, size and activity has a large

effect on metabolic rate.

Quantifying Energy Use


Organisms use various strategies to regulate body temperature and metabolism.



Elevated Floral Temperature in Some Plant Species


Different organisms use various reproductive strategies in response to energy availability.


Seasonal Reproduction in Plants


• There is a relationship between metabolic rate per

unit body mass and the size of multicellular

organisms – generally, the smaller the organism,

the higher the metabolic rate.

• Larger animals have more body mass and

therefore require more chemical energy.

• Remarkably, the relationship between overall

metabolic rate and body mass is constant across

a wide range of sizes and forms.

Metabolic Rate and Size of Organisms


Metabolic Rate and Size of Organisms


• For example, a change in the producer level can affect the

number and size of other trophic levels.

• A change in energy resource levels such as sunlight can

affect the number and size of the trophic levels.

Changes in free energy availability can result in changes in population size and disruption to an ecosystem.



Biology

Eighth Edition









Organisms capture and store free energy for use in biological processes.


Essential Knowledge 2.A.2: Organisms capture and store free energy for use in biological processes.


– (2.4) The student is able to use representations to

pose scientific questions about what mechanisms

and structural features allow organisms to capture,

store and use free energy.

– (2.5) The student is able to construct explanations of

the mechanisms and structural features of cells that

allow organisms to capture, store or use free energy.


Autotrophs capture free energy from physical sources in the environment.

• Photosynthetic organisms capture free energy

present in sunlight.

– 6CO2 + 6 H2O + light energy C6H12O6 + 6 O2 + 6 H2O

– carbon dioxide + water + light energy sugar + oxygen + water

• Chemosynthetic organisms capture free energy

from small inorganic molecules present in their

environment, and this process can occur in the

absence of oxygen.

– 6H2S + 6 H2O + 6 CO2 + 6 O2 C6H12O6 + 6 H2SO4

– hydrogen sulfide + water + carbon dioxide + oxygen sugar + sulfuric acid


Photosynthesis and Chemosynthesis


Heterotrophs capture free energy present in carbon compounds produced by other organisms.

• Heterotrophs may metabolize carbohydrates,

lipids and proteins by hydrolysis as sources of free

energy.

– C6H12O6 + 6 O2 6CO2 + 6 H2O + energy (ATP + heat)

– organic compounds + oxygen carbon dioxide + water + energy

• Fermentation produces organic molecules,

including alcohol and lactic acid, and it occurs in

the absence of oxygen.

– C6H12O6 yeast 2 CH3CH2OH + 2 CO2 + heat

– sugar yeast ethanol + carbon dioxide + heat


Respiration and Fermentation


Different energy-capturing processes use different types of electron acceptors.

• An electron acceptor is a chemical entity that

accepts electrons transferred to it from another compound.

• It is an oxidizing agent that, by virtue of its accepting

electrons, is itself reduced in the process.

– For example, NADP+ in photosynthesis

– For example, oxygen in cellular respiration

• Chemical reactions that transfer electrons between

reactants are called oxidation-reduction reactions, or redox

reactions.


Catabolic Pathways & ATP Production

• Catabolic Pathways yield energy by oxidizing organic fuels.

• Several processes are central to cellular respiration and

related pathways.

• The breakdown of organic molecules is exergonic:

– Fermentation is a partial degradation of sugars that occurs without O2.

– Aerobic respiration consumes organic molecules and O2 and yields ATP.

– Anaerobic respiration is similar to aerobic respiration but consumes compounds other than O2.



• Cellular respiration includes both aerobic and

anaerobic respiration but is often used to refer to

aerobic respiration.

• Although carbohydrates, fats, and proteins can all

be consumed as fuel, it is helpful to trace cellular

respiration with the sugar glucose:

• C6H12O6 + 6 O2 6 CO2 + 6 H2O + Energy (ATP + heat)

– The transfer of electrons during chemical reactions releases

energy stored in organic molecules.

– This released energy is ultimately used to synthesize ATP.


Cellular respiration in eukaryotes involves a series of coordinated enzyme-catalyzed reactions that harvest free energy from simple carbohydrates.


Oxidation of Organic Fuel Molecules During Cellular Respiration

• During cellular respiration, the fuel (such as glucose)

is oxidized, and O2 is reduced:



Stepwise Energy Harvest via NAD+ and the Electron Transport Chain

• In cellular respiration, glucose and other organic molecules

are broken down in a series of steps.

– Electrons from organic compounds are usually first

transferred to NAD+, a coenzyme.

– As an electron acceptor, NAD+ functions as an oxidizing

agent during cellular respiration.



The Stages of Cellular Respiration: A Preview

• WATCH IT! http://www.sumanasinc.com/webcontent/animations/content/cellularrespiration.html

• Cellular respiration has three MAIN stages:

– Glycolysis (breaks down glucose into two molecules of

pyruvate) – occurs in cytosol.

– The citric acid cycle (completes the breakdown of

glucose) – occurs in mitochondrial matrix.

– Electron Transport/Oxidative Phosphorylation

(accounts for most of the ATP synthesis) – occurs

across inner membrane of mitochondria.


http://www.sumanasinc.com/webcontent/animations/content/cellularrespiration.html

Figure 9.16 Review: how each molecule of glucose yields many ATP molecules during cellular respiration:

http://www.wadsworthmedia.com/biology/0495119814_starr/big_picture/ch07_bp.html

http://www.wadsworthmedia.com/biology/0495119814_starr/big_picture/ch07_bp.html


• The process that generates most of the ATP during cellular

respiration is called oxidative phosphorylation because it is

powered by redox reactions of an electron transport chain.

• Oxidative phosphorylation accounts for almost 90% of the ATP

generated by cellular respiration.


Oxidative Phosphorylation


• A smaller amount of

ATP is formed in

glycolysis and the citric

acid cycle by

substrate-level

phosphorylation.


Substrate-Level Phosphorylation


Mitochondrion Structure & Function


Visual Overview of Cellular Respiration


Glycolysis rearranges the bonds in glucose molecules, releasing free energy to form ATP from ADP and inorganic phosphate, and resulting in the production of pyruvate.

• WATCH IT! http://highered.mcgraw-

hill.com/sites/0072507470/student_view0/chapter25/anima

tion__how_glycolysis_works.html

• Glycolysis harvests chemical energy by oxidizing glucose

to pyruvate – it is the first stage of cellular respiration.

• This means that glycolysis “splits sugar” into two molecules

of pyruvate.

• Glycolysis occurs in the cytoplasm and has two major

phases:

– Energy investment phase

– Energy payoff phase


http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_glycolysis_works.html





Glycolysis “Need to Know”

• Glycolysis occurs WITH or WITHOUT oxygen.

• The first step is the phosphorylation of glucose (glucose molecule gains 2 inorganic phosphates) – this ACTIVATES the glucose to split.

• The second step is the splitting of glucose – breaking it down into (2) 3-carbon molecules called pyruvic acid.

– This process is achieved by stripping electrons and hydrogens from the unstable 3-C molecules (as well as the borrowed phosphates).

• 2 ATPs are needed to produce 4 ATPs (energy investment and energy payoff phases).

• A second product in glycolysis is 2 NADH, which results from the transfer of e- and H+ to the coenzyme NAD+.

– Occurs in the cytoplasm

– Net of 2 ATPs produced

– 2 pyruvic acids formed

– 2 NADH produced

Fig. 9-8

Energy investment phase

Glucose

2 ADP + 2 P 2 ATP used

formed 4 ATP

Energy payoff phase

4 ADP + 4 P

2 NAD+ + 4 e– + 4 H+ 2 NADH + 2 H+

2 Pyruvate + 2 H2O

2 Pyruvate + 2 H2O Glucose

Net

4 ATP formed – 2 ATP used 2 ATP

2 NAD+ + 4 e– + 4 H+ 2 NADH + 2 H+


The “Intermediate” Step

• The pyruvate produced during glycolysis is transported from the cytoplasm to the mitochondrion, where further oxidation occurs.

• The conversion of pyruvate to acetyl CoA is the junction between glycolysis (step 1) and the Krebs cycle (step 2).

• If oxygen is present, Pyruvate (3 C each) from glycolysis enters the mitochondrion.

• Using Coenzyme A, each pyruvate is converted into a molecule of Acetyl CoA (2 C each).

Fig. 9-10

CYTOSOL MITOCHONDRION

NAD+ NADH + H+

2

1 3

Pyruvate

Transport protein

CO2 Coenzyme A Acetyl CoA


• In the Krebs cycle, carbon dioxide is released from

organic intermediates.

• ATP is synthesized from ADP and inorganic

phosphate via substrate level phosphorylation and

electrons are captured by coenzymes (NAD+ & FAD+).

• The citric acid (Krebs) cycle completes the energy-

yielding oxidation of organic molecules – and its

events take place within the mitochondrial matrix.

• The cycle oxidizes organic fuel derived from pyruvate,

generating 1 ATP, 3 NADH, and 1 FADH2 per turn.


The Citric Acid Cycle http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_krebs_cycle_works__quiz_1_.html

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_krebs_cycle_works__quiz_1_.html



Fig. 9-11

Pyruvate

NAD+

NADH

+ H+ Acetyl CoA

CO2

CoA

CoA

CoA

Citric acid cycle

FADH2

FAD

CO2 2

3

3 NAD+

+ 3 H+

ADP + P i

ATP

NADH


Chemiosmosis & Electron Transport http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__electron_transport_system_and_atp_synthesis__quiz_1_.html

• Following the Krebs cycle, the electrons captured by NADH and FADH2 are passed to the electron transport chain:

– The electron transport chain uses the high-energy electrons from the Krebs cycle to convert ADP to ATP.

– Every time high energy electrons are transported down the ETC, their energy is used to transport H+ across the inner membrane of the mitochondria…this creates a (+) charge on the inside of the membrane and a (–) charge in the matrix of the mitochondria.

– As a result of this charge difference, H+ ions escape through channel proteins called ATP synthase causing it to rotate.

– Each time it rotates, the enzyme ATP synthase grabs a low energy ADP and attaches a phosphate, forming high-energy ATP.


http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__electron_transport_system_and_atp_synthesis__quiz_1_.html



NADH

NAD+ 2

FADH2

2 FAD

Multiprotein

complexes FAD

Fe•S

FMN

Fe•S

Q

Fe•S

Cyt b

Cyt c1

Cyt c

Cyt a

Cyt a3

IV

50

40

30

20

10 2

(from NADH

or FADH2)

0 2 H+ + 1/2 O2

H2O

e–

e–

e–

• The electron transport chain captures free energy from electrons in a series of coupled reactions that

establish an electrochemical gradient across membranes.

• Electrons delivered by NADH and FADH2 are passed to a series of electron acceptors as they move

toward the terminal electron acceptor, oxygen.

• The passage of electrons is accompanied by the formation of a proton gradient (a type of

electrochemical gradient) across the inner mitochondrial membrane, with the membrane separating a

region of high proton concentration from a region of low proton concentration.

• The flow of protons back through membrane-bound ATP synthase by chemiosmosis generates ATP

from ADP and inorganic phosphate (Pi).

Fig. 9-14

INTERMEMBRANE SPACE

Rotor

H+ Stator

Internal rod

Cata- lytic knob

ADP +

P ATP i

MITOCHONDRIAL MATRIX

Fig. 9-16

Protein complex of electron carriers

H+

H+ H+

Cyt c

Q

V

FADH2 FAD

NAD+ NADH

(carrying electrons from food)

Electron transport chain

2 H+ + 1/2O2 H2O

ADP + P i

Chemiosmosis

Oxidative phosphorylation

H+

H+

ATP

synthase

ATP

2 1

Fig. 9-17

Maximum per glucose: About 36 or 38 ATP

+ 2 ATP + 2 ATP + about 32 or 34 ATP

Oxidative phosphorylation: electron transport

and chemiosmosis

Citric acid cycle

2 Acetyl CoA

Glycolysis

Glucose 2

Pyruvate

2 NADH 2 NADH 6 NADH 2 FADH2

2 FADH2

2 NADH CYTOSOL Electron shuttles

span membrane

or

MITOCHONDRION


Fermentation/Anaerobic Respiration

• Fermentation and anaerobic respiration enable cells to

produce ATP without the use of oxygen

• Most cellular respiration requires O2 to produce ATP

• Glycolysis can produce ATP with or without O2 (in aerobic

or anaerobic conditions)

• In the absence of O2, glycolysis couples with fermentation

or anaerobic respiration to produce ATP

– Anaerobic respiration uses an electron transport chain with

an electron acceptor other than O2, for example sulfate

– Fermentation uses phosphorylation instead of an electron

transport chain to generate ATP


Fig. 9-18

2 ADP + 2 Pi 2 ATP

Glucose Glycolysis

2 NAD+ 2 NADH

2 Pyruvate

+ 2 H+

2 Acetaldehyde 2 Ethanol

(a) Alcohol fermentation

2 ADP + 2 Pi 2 ATP

Glucose Glycolysis

2 NAD+ 2 NADH

+ 2 H+ 2 Pyruvate

2 Lactate

(b) Lactic acid fermentation

2 CO2


Fermentation and Aerobic Respiration Compared

• Both processes use glycolysis to oxidize glucose

and other organic fuels to pyruvate.

• The processes have different final electron

acceptors: an organic molecule (such as pyruvate

or acetaldehyde) in fermentation and O2 in cellular

respiration.

• Cellular respiration produces 38 ATP per glucose

molecule; fermentation produces 2 ATP per

glucose molecule.



• Obligate anaerobes carry out fermentation or

anaerobic respiration and cannot survive in the

presence of O2.

• Yeast and many bacteria are facultative

anaerobes, meaning that they can survive using

either fermentation or cellular respiration:

– In a facultative anaerobe, pyruvate is a fork in

the metabolic road that leads to two alternative

catabolic routes.


The Anaerobes

Fig. 9-19

Glucose

Glycolysis

Pyruvate

CYTOSOL

No O2 present:

Fermentation

O2 present:

Aerobic cellular

respiration

MITOCHONDRION

Acetyl CoA Ethanol or

lactate

Citric acid cycle


The Versatility of Catabolism

• Glycolysis and the citric acid cycle are major

intersections to various catabolic and anabolic

pathways.

• Catabolic pathways funnel electrons from many

kinds of organic molecules into cellular respiration.

• Glycolysis accepts a wide range of carbohydrates.

• In addition to carbohydrates, heterotrophs may

metabolize lipids and proteins by hydrolysis as

sources of free energy.


Fig. 9-20

Proteins Carbohydrates

Amino acids

Sugars

Fats

Glycerol Fatty acids

Glycolysis

Glucose

Glyceraldehyde-3-

Pyruvate

P

NH3

Acetyl CoA

Citric acid cycle

Oxidative phosphorylation

Fig. 9-21 Glucose

Glycolysis

Fructose-6-phosphate

Phosphofructokinase

Fructose-1,6-bisphosphate

Inhibits

AMP

Stimulates

Inhibits

Pyruvate

Citrate

Acetyl CoA

Citric

acid cycle

Oxidative

phosphorylation

ATP

+

– –


H2O

Energy Coupling

Following cellular respiration or fermentation, free energy becomes

available for metabolism by the conversion of ATPADP, which is coupled

to many steps in metabolic pathways.


Photosynthesis is the process whereby light energy is converted to chemical energy and carbon is fixed into organic compounds.

• In the presence of light, plants transform carbon dioxide and water into carbohydrates and release oxygen:

– Photosynthesis uses the energy of sunlight to convert water and CO2 into O2 and high energy sugars

– 6 CO2 + 6 H2O + light → C6H12O6 + 6 O2

– carbon dioxide + water + light → sugar + oxygen

• Plants then use the sugars to produce complex carbohydrates such as starches:

– Plants obtain carbon dioxide from the air or water in which they grow.

Inside a Chloroplast


Photosynthetic Pigments

• Photosynthetic pigments absorb light energy and use it to provide energy to carry out photosynthesis.

– Chlorophylls (absorb light in the red, blue, and violet range):

• Chlorophyll a - directly involved in transformation of photons to chemical energy

• Chlorophyll b - helps trap other wavelengths and transfers it to chlorophyll a

– Carotenoids (absorb light in the blue, green, and violet range):

• xanthophyll - Yellow

• beta carotene - Orange

• Phycobilins – Red

– Chlorophyll b, the carotenoids, and the phycobilins are known as ANTENNA PIGMENTS – they capture light in other wavelengths and pass the energy along to chlorphyll a.

– Chlorophyll a is the pigment that participates directly in the light reactions of photosynthesis!

During photosynthesis, chlorophylls absorb free energy from light,

boosting electrons to a higher energy level in photosystems I and II.


Different types of organisms use different photosynthetic pigments to harvest energy.

Figure 10.9 Location and structure of chlorophyll molecules in plants

The pigment molecules have a

large head section that is

exposed to light in the surface of

the membrane; the hydrocarbon

tail anchors the pigment

molecules into the lipid bilayer.


Photosystems


Stages of Photosynthesis

• The reaction that occurs during photosynthesis can be

broken into 2 stages:

1. Light Dependent Reactions

• Take place within the thylakoid membranes inside a

chloroplast

• “PHOTO” phase – make ATP & NADPH…USE LIGHT

ENERGY TO PRODUCE ATP & NADPH

2. Light Independent Reactions (Calvin Cycle)

• Take place in the stroma of the chloroplast

• “SYNTHESIS” phase – coverts CO2 to sugar…PRODUCE

SUGAR

Light Reactions:

-carried out by molecules in thylakoid

membranes

-convert light E to chemical E of ATP and

NADPH

-split H2O and release O2 to the atmosphere

Calvin Cycle Reactions:

-take place in stroma

-use ATP and NADPH to convert CO2

into the sugar G3P

-return ADP, inorganic phosphate, and

NADP+ to the light reactions


Light Dependent Reactions - Overview

• The light-dependent reactions of photosynthesis in

eukaryotes involve a series of coordinated reaction

pathways that capture free energy present in light to

yield ATP and NADPH, which power the production of

organic molecules in the Calvin cycle (dark reactions).

– require presence of light

– occur in thylakoids of chloroplasts

– use energy from light to produce ATP and NADPH (a

temporary, mobile energy source that helps store even more

energy)

– water is split during the process to replace electrons lost from

excited chlorophyll

– oxygen gas is produced as a by-product


Light Independent Reactions - Overview

• The energy captured in the light reactions as

ATP and NADPH powers the production of

carbohydrates from carbon dioxide in the Calvin

cycle.

– do not require light directly – so also known as the

Dark Reactions or the Calvin Cycle

– take place in the stroma of chloroplasts

– ATP and NADPH produced during light dependent

reactions are used to make glucose

LIGHT REACTIONS: How electron flow during the light reactions generates ATP and NADPH

Section 8-3

Figure 8-10 Light-Dependent

Reactions

Go to

Section:

Figure 10.15 Comparison of chemiosmosis in mitochondria and chloroplasts http://bcs.whfreeman.com/thelifewire/content/chp08/0802002.html


The Dark Reactions (Calvin cycle)

• Calvin cycle can be divided into 3 phases:

– Phase 1: Carbon Fixation

– Phase 2: Reduction

– Phase 3: Regeneration of CO2 Acceptor (RuBP)

• REMEMBER: The Calvin cycle is an ANABOLIC process – and therefore requires ENERGY – this energy is provided by the ATP and NADPH made during the light reactions!!!

Figure 10.17 The Calvin Cycle



Biology

Eighth Edition









Organisms must exchange matter with the environment

to grow, reproduce and maintain organization.


Essential Knowledge 2.A.3: Organisms must exchange matter

with the environment to grow, reproduce and maintain organization.


– (2.6) The student is able to use calculated surface area-to-volume

ratios to predict which cell(s) might eliminate wastes or procure

nutrients faster by diffusion.

– (2.7) The student is able to explain how cell size and shape affect

the overall rate of nutrient intake and the rate of waste elimination.

– (2.8) The student is able to justify the selection of data regarding

the types of molecules that an animal, plant or bacterium will take up

as necessary building blocks and excrete as waste products.

– (2.9) The student is able to represent graphically or model

quantitatively the exchange of molecules between an organism and

its environment, and the subsequent use of these molecules to build

new molecules that facilitate dynamic homeostasis, growth and

reproduction.


Molecules and atoms from the environment are necessary to build new molecules.

• Carbon moves from the environment to organisms

where it is used to build carbohydrates, proteins,

lipids or nucleic acids. Carbon is used in storage

compounds and cell formation in all organisms.

• Nitrogen moves from the environment to

organisms where it is used in building proteins and

nucleic acids.

• Phosphorus moves from the environment to

organisms where it is used in nucleic acids and

certain lipids.


Biological and geochemical processes cycle nutrients between organic and inorganic parts of an ecosystem.

• Life depends on recycling chemical elements.

• Nutrient circuits in ecosystems involve biotic and

abiotic components and are often called

biogeochemical cycles:

– Gaseous carbon, oxygen, sulfur, and nitrogen occur in the atmosphere and cycle globally.

– Less mobile elements such as phosphorus, potassium, and calcium cycle on a more local level.

Fig. 55-13 Reservoir A Reservoir B

Organic materials available

as nutrients Fossilization

Organic materials

unavailable as nutrients

Reservoir D Reservoir C

Coal, oil, peat

Living organisms, detritus

Burning of fossil fuels

Respiration, decomposition, excretion

Assimilation, photosynthesis

Inorganic materials available

as nutrients

Inorganic materials

unavailable as nutrients

Atmosphere,soil, water

Minerals in rocks

Weathering, erosion

Formation of sedimentary rock


• In studying cycling of water, carbon, nitrogen, and

phosphorus, ecologists focus on four factors:

– Each chemical’s biological importance

– Forms in which each chemical is available or

used by organisms

– Major reservoirs for each chemical

– Key processes driving movement of each

chemical through its cycle

– How humans are impacting each cycle

Biogeochemical Cycles

Fig. 55-14a

Precipitation

over land

Transport over land

Solar energy

Net movement of water vapor by wind

Evaporation from ocean

Percolation through soil

Evapotranspiration from land

Runoff and groundwater

Precipitation over ocean

Fig. 55-14b

Higher-level consumers Primary

consumers

Detritus

Burning of

fossil fuels

and wood

Phyto-

plankton

Cellular respiration

Photo- synthesis

Photosynthesis

Carbon compounds in water

Decomposition

CO2 in atmosphere

Fig. 55-14c

Decomposers

N2 in atmosphere

Nitrification

Nitrifying bacteria

Nitrifying bacteria

Denitrifying bacteria

Assimilation

NH3 NH4 NO2

NO3

+ –

–

Ammonification

Nitrogen-fixing soil bacteria

Nitrogen-fixing bacteria

Fig. 55-14d

Leaching

Consumption

Precipitation

Plant uptake of PO4

3–

Soil

Sedimentation

Uptake

Plankton

Decomposition

Dissolved PO43–

Runoff

Geologic uplift

Weathering of rocks


Decomposition and Nutrient Cycling Rates

• Decomposers (detritivores) play a key role in the

general pattern of chemical cycling.

• Rates at which nutrients cycle in different

ecosystems vary greatly, mostly as a result of

differing rates of decomposition.

• The rate of decomposition is controlled by

temperature, moisture, and nutrient availability.

• Rapid decomposition results in relatively low

levels of nutrients in the soil.

Fig. 55-15 Ecosystem type EXPERIMENT

RESULTS

Arctic

Subarctic

Boreal

Temperate

Grassland

Mountain

P

O

D

J

R Q

K

B,C

E,F H,I

L N U S

T

M

G

A

A

80

70

60

50

40

30

20

10

0 –15 –10 –5 0 5 10 15

Mean annual temperature (ºC)

Pe

rce

nt

of

ma

ss

lo

st

B

C

D

E

F

G H

I

J

K

L M

N

O

P

Q

R

S

T

U

Fig. 55-16

1965

(c) Nitrogen in runoff from watersheds

Nit

rate

co

nce

ntr

ati

on

in

ru

no

ff

(mg

/L)

(a) Concrete dam and weir

(b) Clear-cut watershed

1966 1967 1968

Control

Completion of tree cutting

Deforested

0

1

2

3

4

20

40

60

80


Human activities now dominate most chemical cycles on Earth.

• As the human population has grown, our activities

have disrupted the trophic structure, energy flow,

and chemical cycling of many ecosystems

• In addition to transporting nutrients from one

location to another, humans have added new

materials, some of them toxins, to ecosystems

• Disruptions that deplete nutrients in one area and

increase them in other areas can be detrimental

to ecosystem dynamics.


Fig. 55-17: Agriculture & Nitrogen Cycling


Algae Blooms & Eutrophication

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=lnGAc-NK9yQDbM&tbnid=nSrtXmxuUPhN4M:&ved=0CAUQjRw&url=http%3A%2F%2Fwww.ecy.wa.gov%2FPrograms%2Feap%2FNitrogen%2FEffects.html&ei=xWFVUs6KB4fy8ATAjoGwAg&bvm=bv.53760139,d.eWU&psig=AFQjCNHRdbd_xLnIt2LFSH4mG6W8BDfp3g&ust=1381413687478413

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=i6u1oBDiJm0JhM&tbnid=GpDZ9p2DrFPztM:&ved=0CAUQjRw&url=http%3A%2F%2Fsciencebitz.com%2F%3Fpage_id%3D597&ei=7mFVUqz8OoLs8wT-oYCQBw&bvm=bv.53760139,d.eWU&psig=AFQjCNHRdbd_xLnIt2LFSH4mG6W8BDfp3g&ust=1381413687478413

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=pacdtaRQD1ISEM&tbnid=azN5h6AA3gRtsM:&ved=0CAUQjRw&url=http%3A%2F%2Fwww.macalester.edu%2Facademics%2Fenvironmentalstudies%2Fthreerivers%2Fstudentprojects%2FENVI_133_Spr_08%2FPhosphorus%2FPhosphorus%2520Effects%2520Webpage.html&ei=hmJVUrDlFIfu8ATMy4CYBg&bvm=bv.53760139,d.eWU&psig=AFQjCNHRdbd_xLnIt2LFSH4mG6W8BDfp3g&ust=1381413687478413

http://www.google.com/url?sa=i&rct=j&q=&esrc=s&frm=1&source=images&cd=&cad=rja&docid=pacdtaRQD1ISEM&tbnid=azN5h6AA3gRtsM:&ved=0CAUQjRw&url=http%3A%2F%2Fwww.macalester.edu%2Facademics%2Fenvironmentalstudies%2Fthreerivers%2Fstudentprojects%2FENVI_133_Spr_08%2FPhosphorus%2FPhosphorus%2520Effects%2520Webpage.html&ei=hmJVUrDlFIfu8ATMy4CYBg&bvm=bv.53760139,d.eWU&psig=AFQjCNHRdbd_xLnIt2LFSH4mG6W8BDfp3g&ust=1381413687478413


The Role of Matter in Living Organisms

• What is an appropriate title for this graph?

• What was the IV of this experiment? The DV?

• What variables should have been controlled during this experiment?

• The photosynthetic pattern of this plant species is unusual. Explain.

• A useful control for the experiment would have included what?

Experiments were carried out to determine the

plant’s photosynthetic capacity by measuring the

net uptake of carbon dioxide and changes in tissue

starch concentration over a 32-hour period with 8

hours of dark at the start and end of the

measurement period and 16 hours of moderate

light between the two dark periods.

The changes in the rate of carbon dioxide uptake

and the concentration of tissue starch are shown

graph.

Epiphytic Plant from Rain Forest Canopy


Living systems depend on properties of water that result from its polarity and hydrogen bonding.

• Four of water’s properties that facilitate an environment for life are:

– Cohesive/Adhesive behavior

– Ability to moderate temperature

– Expansion upon freezing

– Versatility as a solvent

– http://www.sumanasinc.com/webcontent/animations/content/propertiesofwater/water.html


http://www.sumanasinc.com/webcontent/animations/content/propertiesofwater/water.html



The polarity of water molecules results in hydrogen bonding.

• The water molecule is a polar

molecule: The opposite ends

have opposite charges

• Polarity allows water

molecules to form hydrogen

bonds with each other

– Water is polar because the

oxygen atom has a stronger

electronegative pull on

shared electrons in the

molecule than do the

hydrogen atoms



Cohesion & Adhesion

• Collectively, hydrogen bonds hold water

molecules together, a phenomenon called

cohesion

– the attraction of water molecules to other water molecules as a

result of hydrogen bonding

– Cohesion due to hydrogen bonding contributes to the transport of

water and dissolved nutrients against gravity in plants

• Adhesion is the clinging of one substance to

another

– Adhesion of water to cell walls by hydrogen bonds helps to counter

the downward pull of gravity on the liquids passing through plants


Fig. 3-3

Water-conducting

cells

Adhesion

Cohesion

150 µm

Direction

of water

movement

Cohesion and adhesion work

together to give capillarity – the

ability of water to spread through fine

pores or to move upward through

narrow tubes against the force of

gravity.


Moderation of Temperature

• Water moderates air temperature by absorbing

heat from air that is warmer and releasing the

stored heat to air that is cooler

• Water can absorb or release a large amount of

heat with only a slight change in its own

temperature

• The ability of water to stabilize temperature stems

from its relatively high specific heat

– This is the amount of heat that must be absorbed or lost

for 1g of a substance to change its temperature by 1°C



• Water’s high specific heat can be traced to hydrogen bonding

– Heat is absorbed when hydrogen bonds break

– Heat is released when hydrogen bonds form

• High specific heat of water is due to hydrogen bonding – H-bonds tend to restrict molecular movement, so when we add heat energy to water, it must break bonds first rather than increase molecular motion.

– A greater input of energy is required to raise the temperature of water than the temperature of air!

– Minimizes temperature fluctuations to within limits that permit life

Water’s High Specific Heat


Evaporative Cooling

• Evaporation is transformation of a substance from liquid to gas

• Heat of vaporization is the heat a liquid must absorb for 1 g to be converted to gas

• As a liquid evaporates, its remaining surface cools, a process called evaporative cooling

• The high amount of energy required to vaporize water has a wide range of effects:

– Helps stabilize temperatures in organisms and bodies of water


Fig. 3-6

Hydrogen

bond Liquid water

Hydrogen bonds break and re-form

Ice

Hydrogen bonds are stable

Insulation of Bodies of Water by Floating Ice


The Solvent of Life

• A solution is a liquid that is a homogeneous

mixture of substances

– Solvent (dissolving agent)

– Solute (substance that is dissolved)

• An aqueous solution is one in which water is the

solvent


Hydration Shell http://www.sumanasinc.com/webcontent/animations/content/propertiesofwater/water.html

• A hydration shell refers to the sphere of water

molecules around each dissolved ion in an

aqueous solution

– Water will work inward from the surface of the

solute until it dissolves all of it (provided that

the solute is soluble in water)



Threats to Water Quality on Earth

• Acid precipitation refers to rain, snow, or fog with

a pH lower than 5.6.

• Acid precipitation is caused mainly by the mixing

of different pollutants with water in the air and can

fall at some distance from the source of pollutants.

• Acid precipitation can damage life in lakes and

streams.

• Effects of acid precipitation on soil chemistry are

contributing to the decline of some forests.


Fig. 3-10

More acidic

0

Acid rain Acid rain

Normal rain

More basic

1

2

3

4

5

6

7

8

9

10

11

12

13

14


• Human activities such as burning fossil fuels

threaten water quality

• CO2 is released by fossil fuel combustion and

contributes to:

– A warming of earth called the “greenhouse”

effect

– This can cause acidification of the oceans;

leads to a decrease in the ability of corals to

form calcified reefs

Threats to Water Quality on Earth

Fig. 3-11

EXPERIMENT

RESULTS

[CO32–] (µmol/kg)

150 200 250 300

0

20

40


Surface area-to-volume ratios affect a biological system’s ability to obtain necessary resources or eliminate waste products.

• As cells increase in volume, the relative surface area

decreases and demand for material resources increases;

more cellular structures are necessary to adequately

exchange materials and energy with the environment.

• As the surface area increases by a factor of n2, the volume

increases by a factor of n3 - small cells have a greater surface

area relative to volume.

• These limitations restrict cell size. Illustrative examples

include:

– Root hairs

– Cells of the alveoli

– Microvilli

Fig. 6-8: Limits to Cell Size Surface area increases while

total volume remains constant

5

1

1

6 150 750

125 125 1

6 6 1.2

Total surface area

[Sum of the surface areas

(height width) of all boxes

sides number of boxes]

Total volume

[height width length

number of boxes]

Surface-to-volume

(S-to-V) ratio

[surface area ÷ volume]


Root Hairs

• An increased surface area to volume

ratio means increased exposure to

the environment. The higher the

SA:Volume ratio for a cell, the more

effective the process of diffusion.

• Root hairs are long, thin hair-like

cells that emerge from the root tip to

form an important surface over which

plants absorb most of their water and

nutrients via diffusion.

• They present a large surface area to

the surrounding soil, which makes

absorbing both water and minerals

more efficient using osmosis.


Cells of the Alveoli

• The ratio between the surface area

and volume of cells and organisms

has an enormous impact on their

biology. Individual organs in animals

are often shaped by requirements of

surface area to volume ratio.

• The numerous internal branchings of

the lung and alveoli increase the

surface area through which oxygen is

passed into the blood and carbon

dioxide is released from the blood.

• Human lungs contain millions of

alveoli, which together have a

surface area of about 100m2, fifty

times that of the skin.


Microvilli & Other Cell Types

• Large animals require specialized organs

(lungs, kidneys, intestines, etc.) that

effectively increase the surface area

available for exchange processes, and a

circulatory system to move material and heat

energy between the surface and the core of

the organism.

• The intestine has a finely wrinkled internal

surface, increasing the area through which

nutrients are absorbed by the body.

• A wide and thin cell, such as a nerve cell, or

one with membrane protrusions such as

microvilli has a greater surface-area-to-

volume ratio than a spheroidal one.

• Likewise a worm has proportionately more

surface area than a rounder organism of the

same mass does.


The Plasma Membrane

• The surface area of the plasma membrane must be large

enough to adequately exchange materials;

• Smaller cells have a more favorable surface area-to-

volume ratio for exchange of materials with the

environment.

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