AP Biology Notes Outline Enduring Understanding 2.A

L. Carnes

Big Idea 2: 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.

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

– (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.

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.

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.

Bozeman Instruction Videos: http://www.bozemanscience.com/ap-biology/ 2.A.1 - #012: Life Requires Free Energy 2.A.2 - #013: Photosynthesis & Respiration 2.A.3 - #014: Environmental Matter Exchange

Required Readings: Textbook Chapters – Life Requires Free Energy: 8.2; 40.1; 40.2; 40.3; 40.4; 55.1; 51.3; 53.3; 53.4; 55.2; 55.3; 8.1; 8.2; 8.3 Textbook Chapters – Photosynthesis & Respiration: 10.1; 10.2; 10.3; 9.1; 9.2; 9.3; 9.4; 9.5 Textbooks Chapters – Environmental Matter Exchange: 4.1; 4.2; 4.3; 3.1; 3.2; 6.2; 11.5 Article: Surface Area-to-Volume Ratio in Cells Article: Eutrophication & Algal Blooms

Animated Content Review Videos:

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

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

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

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

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

Electron Transport & Chemiosmosis: http://highered.mcgraw-

hill.com/sites/0072507470/student_view0/chapter25/animation__electron_transport_system_and_atp_synthesis__quiz_1_.html

Light Reactions of Photosynthesis: http://highered.mheducation.com/olc/dl/120072/bio13.swf

Dark Reactions/Calvin Cycle: http://highered.mheducation.com/sites/0070960526/student_view0/chapter5/animation_quiz_1.html

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

Surface Area to Volume Ratio in Cells: https://www.youtube.com/watch?v=wuXSEOKNxN8

Practicing Biology Homework Questions: Questions #1-20

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

Living systems require energy to maintain order, grow and reproduce. In accordance with the laws of thermodynamics, to offset entropy, energy input must exceed energy lost from and used by an organism to maintain order. Organisms use various energy-related strategies to survive; strategies that include different metabolic rates, physiological changes, and variations in reproductive and offspring-raising strategies. Not only can energy deficiencies be detrimental to individual organisms, but changes in free energy availability can also affect population size and cause disruptions at the ecosystem level. 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 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.

• 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.

Energy is the capacity to cause change. Energy cannot be created or destroyed, but can be converted from one form to another. 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.

Thermodynamics is the study of energy transformations. A closed system 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. According to the first law of thermodynamics (principle of conservation of energy), the energy of the universe is constant: energy can be transferred and transformed, but it cannot be created or destroyed. 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 cells unavoidably convert organized forms of energy to heat. Spontaneous processes occur without energy input; they can happen quickly or slowly. For a process to occur without energy input, it must increase the entropy of the universe. Living systems do not violate the second law of thermodynamics, which states that entropy increases over time:

• Energy flows into an ecosystem in the form of light and exits in the form of heat. Order is maintained by coupling cellular processes that increase entropy (and so have negative changes in free energy) with those that decrease entropy (and so have positive changes in free energy).

• Energy input must exceed free energy lost to entropy to maintain order and power cellular processes. Cells create ordered structures from less ordered materials. Organisms also replace ordered forms of matter and energy with less ordered forms.

• 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. Living systems increase the entropy of their surroundings, as predicted by thermodynamic law. Therefore, the evolution of biological order is perfectly consistent with the laws of thermodynamics. Biological Example: An animal obtains starch, proteins, and other complex molecules from the food it eats. As catabolic pathways break down these molecules, the animal releases carbon dioxide and water (small molecules that possess less energy than the food did). The depletion of chemical energy is accounted for by heat generated during metabolism.

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

The free-energy change of a reaction is a measure of whether or not the reaction occurs spontaneously. To understand which reactions require inputs of energy, biologists 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.

• 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. • G system’s quantity of free energy; H system’s total energy; T absolute temperature in Kelvin; S system’s total

entropy • So, for a process to occur spontaneously, the system must either give up energy (decrease H), give up order (increase S), or

both. The change in G must be negative.

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. 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).

Exergonic Reaction: ΔG < 0…reaction proceeds with a net RELEASE of free energy…these reactions occur spontaneously. Endergonic Reaction: ΔG > 0…reaction proceeds with an ABSORPTION of free energy…these reactions are not spontaneous.

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

ATP powers cellular work by coupling exergonic reactions to endergonic reactions. To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one. Most energy coupling in cells is mediated by ATP using the chemical potential energy stored in the bonds of an ATP molecule. ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP). The energy to phosphorylate ADP comes from catabolic reactions in the cell. In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction. Overall, the coupled reactions are exergonic. 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.

Energy-related pathways in biological systems are sequential and may be entered at multiple points in the pathway. Organisms use free energy to maintain organization, grow and reproduce. Illustrative Examples include:

• Strategies to regulate body temperature • Strategies for reproduction & rearing of offspring • Metabolic rate and size • Excess acquired free energy • Insufficient acquired free energy

Bioenergetics is a field in biochemistry that studies energy flow through living systems. This flow ultimately limits the animal’s behavior, growth, and reproduction – which determines how much food it needs.

Animals harvest chemical energy from the food they eat. Once food has been digested, the energy-containing molecules are usually used to make ATP, which powers cellular work. After the energetic needs of staying alive are met any remaining molecules can be used in biosynthesis. Excess acquired free energy versus required free energy expenditure results in energy storage or growth. Insufficient acquired free energy versus required free energy expenditure results in loss of mass and, ultimately, the death of the organism.

Organisms use various strategies to regulate body temperature and metabolism. 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.

• Minimum metabolic rate is measured differently for endotherms and ectotherms. For endotherms: comfortable temperature range; for ectotherms: specific temperature range because changes in the environmental temperature alter body temperature and therefore metabolic rate.

In many species of thermogenic plants, the temperature of their flowers can increase up to 35°C above the surroundings. Heat production occurs by rapid respiration in the thermogenic cells of the flowers. A few species of plants actually exhibit temperature regulation, which is the maintenance of a relatively constant temperature in the flower, regardless of external air temperature.

In these cases, the respiratory rate increases almost linearly as the ambient temperature drops below 30°C, and the mean temperature of the flower is almost constant.

Temperature regulation appears to be important for proper floral development and pollination success. Research indicates that artificially-enforced low temperatures reduce fertilization and seed set in many thermoregulatory plant species.

It is also likely that an increase in floral temperature helps to speed the diffusion of floral scent – thus increasing/attracting pollinators to the plant.

Different organisms use various reproductive strategies in response to energy availability. Reproduction and rearing of offspring require free energy beyond that used for maintenance and growth. The ways in which animals use the chemical energy of food depend on environment, behavior, size, and thermoregulation.

Timely reproduction is the essence of success for plants as individuals, populations or species. One of the major differences in life history strategies among plants is how long they take to complete their life cycles. Plant life cycles are attuned to cyclic seasonal environments. Illustrative Example: Short and Long Cycles:

Annuals - take advantage of short-lived desirable environmental conditions that favor reproduction / success of offspring. Seeds germinate in the spring, all individuals flower during the summer, and drop seeds in the fall. These plants live only a single year. Because they have only a single chance to reproduce, annual plants produce large numbers of seeds; often only a few of these many seeds survive.

Perennials - adaptive to survive seasonal climate extremes. Perennials flower and produce seeds for many growing seasons. Since they have multiple chances to reproduce, they may produce fewer seeds which have a better chance of survival.

Biennials - store energy and build a strong root system the first year, over winter as a low rosette of leaves, then flower and produce seeds during their second summer. After they produce seeds, the plants die.

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. One hypothesis regarding the inverse relationship of metabolic rate per unit of body mass to body size is that for endotherms, the smaller the animal, the greater the energy cost of maintaining a stable body temperature.

In effect, the smaller an animal is, the greater its surface-to-volume ratio is and thus the faster it loses heat to (or gains heat from) its surroundings.

BUT – this hypothesis does NOT explain why this trend is also observed in ectotherms, which do not use metabolic heat to maintain body temperature.

Regardless of cause, the relationship of metabolic rate to size profoundly affects energy consumption by body cells and tissues.

The energy it takes to maintain each gram of body weight is INVERSELY related to body size. Each gram of mouse, for example, requires about 20 times as many calories as a gram of an elephant, even though the whole elephant uses far more calories than the whole mouse.

The smaller animal’s higher metabolic rate requires greater rate of oxygen delivery, a higher breathing rate, blood volume, and heart rate. It must eat MUCH MORE food per unit of body mass.

Changes in free energy availability can result in changes in population size and disruption to an ecosystem: • Change in the producer level can affect the number and size of other trophic levels. • Change in energy resource levels such as sunlight can affect the number and size of the trophic levels.

Ecologists study the transformations of energy and matter within their system, and use these studies to suggest the health of an ecosystem. Energy and nutrients pass from primary producers (autotrophs) to primary consumers (herbivores) to secondary consumers (carnivores) to tertiary consumers (carnivores that feed on other carnivores). Each food chain in a food web is usually only a few links long. Two hypotheses attempt to explain food chain length: the energetic hypothesis and the dynamic stability hypothesis.

• The energetic hypothesis suggests that length is limited by inefficient energy transfer.

• The dynamic stability hypothesis proposes that long food chains are less stable than short ones.

• Most data support the energetic hypothesis. Population fluctuations at lower trophic levels are generally magnified at higher levels – potentially causing the local extinction of top predators. In a variable environment, top predators must be able to recover from environmental shocks that can reduce the food supply all the way up the food chain. The longer the chain, the more slowly top predators recover from environmental setbacks. So…food chains should be shorter in unpredictable environments. Any loss of producers within the food chain affects the consumers. If there is no grass for the rabbit to eat, the rabbit must leave the ecosystem to hunt for food. With no rabbits, the snakes must find other food. Eventually every link within the food chain leaves a particular ecosystem and that ecosystem no longer exists and is lost. A loss of a producer can make the ecosystem change. Biogeochemists calculate this changing of the ecosystem with a mass balance equation that helps them determine the state of an ecosystem. A dramatic loss of one consumer within a food chain affects the ecosystem. For example, if the snake population within the food chain drops dramatically, the population of rabbits will increase. The increase in the rabbit population will eventually bring another carnivore into the ecosystem that wasn't there before. Another carnivore may not be a producer for the hawk. Without a producer for the hawk, the hawk will be lost to the ecosystem.

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

Several means to capture, use and store free energy have evolved in organisms. Cells can capture free energy through photosynthesis and chemosynthesis. Autotrophs capture free energy from the environment, including energy present in sunlight and chemical sources, whereas heterotrophs harvest free energy from carbon compounds produced by other organisms. Through a series of coordinated reaction pathways, photosynthesis traps free energy in sunlight that, in turn, is used to produce carbohydrates from carbon dioxide and water. Cellular respiration and fermentation use free energy available from sugars and from interconnected, multistep pathways (i.e., glycolysis, the Krebs cycle and the electron transport chain) to phosphorylate ADP, producing the most common energy carrier, ATP. The free energy available in sugars can be used to drive metabolic pathways vital to cell processes. The processes of photosynthesis and cellular respiration are interdependent in their reactants and products.

Autotrophs capture free energy from physical sources in the environment.

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

• 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

• 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

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 in eukaryotes involves a series of coordinated enzyme-catalyzed reactions that harvest free energy from

simple carbohydrates. Cellular respiration includes both aerobic and anaerobic respiration but is often used to refer to aerobic

respiration. Although carbohydrates, fats, and proteins are all consumed as fuel, it is helpful to trace cellular respiration with the

sugar glucose. During cellular respiration, the fuel (such as glucose) is oxidized, and O2 is reduced:

The transfer of electrons during chemical reactions releases energy stored in organic molecules. This released energy is ultimately

used to synthesize ATP. In cellular respiration, glucose and other organic molecules are broken down in a series of steps. Cellular

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

carbohydrates. 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.

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

Cellular respiration has three 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

Mitochondria have a DOUBLE MEMBRANE that allows COMPARTMENTALIZATION of reactions. The OUTER MEMBRANE is smooth, but INNER MEMBRANE is highly convoluted, forming folds called cristae. Cristae contain enzymes important to ATP production; cristae also increase the surface area for ATP production.

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

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.

• Glycolysis harvests chemical energy by oxidizing glucose to two molecules of pyruvate – it is the first stage of cellular respiration.

• Glycolysis occurs in the cytoplasm and has two major phases: an energy investment phase and an energy payoff phase.

• 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), so there is a net production of 2 ATPs.

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

+ to the coenzyme NAD

+.

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).

WATCH IT http://highered.mcgraw-

hill.com/sites/0072507470/student_view0/chapter25/animation__how_the_krebs_cycle_works__quiz_1_.html 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.

• 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.

• Electrons that are extracted in the series of Krebs cycle reactions are carried by NADH and FADH2 to the electron transport chain.

WATCH IT http://highered.mcgraw-

hill.com/sites/0072507470/student_view0/chapter25/animation__electron_transport_system_and_atp_synthesis__quiz_1_.html The electron transport chain captures free energy from electrons in a series of coupled reactions that establish an electrochemical gradient across membranes.

Electron transport chain reactions occur across the Christae of the mitochondria (inner membrane).

Electrons delivered by NADH and FADH2 are passed to a series of electron acceptors as they move toward the terminal electron acceptor, OXYGEN.

Most of the chain’s components are proteins. The carriers alternate reduced and oxidized states as they accept and donate electrons. Electrons drop in free energy as they go down the chain and are finally passed to the terminal electron acceptor, O2, forming H2O. The electron transport chain generates no ATP. The chain’s function is to break the large free-energy drop from food to O2 into smaller steps that release energy in manageable amounts

The passage of electrons is accompanied by the formation of a PROTON GRADIENT (H+) 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 the membrane-bound enzyme ATP synthase by chemiosmosis generates ATP from ADP and inorganic phosphate.

ATP synthase uses the exergonic flow of H+ to drive phosphorylation of ATP. This is an example of chemiosmosis, the use of

energy in a H+ gradient to drive cellular work.

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 Fermentation consists of glycolysis plus reactions that regenerate NAD

+, which can be

reused by glycolysis. Two common types are alcohol fermentation and lactic acid fermentation.

In alcohol fermentation, pyruvate is converted to ethanol in two steps, with the first releasing CO2. Alcohol fermentation by yeast is used in brewing, winemaking, and baking.

In lactic acid fermentation, pyruvate is reduced to NADH, forming lactate as an end product, with no release of CO2. Lactic acid fermentation by some fungi and bacteria is used to make cheese and yogurt. Human muscle cells use lactic acid fermentation to generate ATP when O2 is scarce.

The ONLY ATP produced during fermentation are the TWO ATP produced during glycolysis – all other steps regenerate NAD+ so that glycolysis can occur over and over!

Both fermentation and cellular respiration 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 • Glycolysis is common to fermentation AND respiration. The end product of glycolysis is pyruvate…represents a fork in the

catabolic pathways of glucose oxidation. In a cell capable of both respiration and fermentation, pyruvate is committed to one of those two pathways, usually depending on the presence of oxygen.

• The Evolutionary Significance of Glycolysis: Glycolysis occurs in nearly all organisms. Glycolysis probably evolved in ancient prokaryotes before there was oxygen in the atmosphere.

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. 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 • 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. It is likely that photosynthesis first evolved in prokaryotic organisms! There is scientific evidence that prokaryotic photosynthesis was responsible for an oxygenated atmosphere (the oxygen revolution)…and that these pathways were the foundation of eukaryotic photosynthesis (endosymbiosis). Chloroplasts are chemical factories powered by the sun…their thylakoids transform light energy into the chemical energy of ATP and NADPH.

Chloroplasts have a double outer membrane that creates a compartmentalized structure – which supports its function. This structure allows cells to capture the energy available in sunlight and convert it to chemical bond energy via photosynthesis.

Thylakoid - saclike structure in chloroplasts made of photosynthetic membranes – these sacs are made up of lipid bilayers (energy-capturing reactions occur here)

Granum - a stack of thylakoids (produce ATP and NADPH2)

Stroma - aqueous region outside of the thylakoid membranes

Chlorophyll - molecules are embedded in the thylakoid membrane – capture energy from sunlight to power photosynthesis

An absorption spectrum indicates the relative amount of light absorbed across a range of wavelengths. Chlorophyll does not absorb all the wavelengths of visible light equally.

• Chlorophyll a, the most important light-absorbing pigment in plants, does not absorb light in the green part of the spectrum. Light in this range of wavelengths is reflected. This is the reason why chlorophyll is green and also why plants (which contain a lot of chlorophyll) are also green. Note in the graph that the absorption of light by chlorophyll a is at a maximum at two points on the graph 430 and 662 nm.

• The rate of photosynthesis at the different wavelengths of visible light also shows two peaks which roughly correspond to the absorption peaks of chlorophyll a.

• Plants do not depend only on chlorophyll a in their light harvesting machinery but also have other pigments (accessory pigments) which absorb light of different wavelengths (Chlorophyll b, xanthophyll, carotenoids, phycobilins, etc.)

The 2

nd graph to the right represents the pigment commonly found in purple photosynthetic

bacteria, bacteriorhodopsin. Bacteriorhodopsin has been found in aquatic organisms whose ancestors existed before the ancestors of plants evolved in the same environment.

During photosynthesis, chlorophylls absorb free energy from light, boosting electrons to a higher energy level in photosystems I and II.

• Photosystems I and II are embedded in the internal membranes of chloroplasts (thylakoids) and are connected by the transfer of higher free energy electrons through and electron transport chain (ETC).

• Photosystems are light-harvesting complexes in the thylakoid membranes of chloroplasts.

• Each photosystem consists of a reaction center containing chlorophyll a and a region of many atenna pigment molecules that funnel energy into chlorophyll a.

The reactions that occur 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 – use energy in ATP and NADPH to covert CO2 to sugar…PRODUCE SUGAR

BOTH REACTIONS REQUIRE LIGHT (SOMEWHAT): Even the dark reactions in most plants occurs during daylight – because that is the only time the light reactions can operate AND the dark reactions depend on the light reactions!!!

WATCH IT http://highered.mheducation.com/olc/dl/120072/bio13.swf

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). • When a photon strikes a pigment molecule, the energy

is passed from molecule to molecule until it reaches the reaction center in a chlorophyll a molecule.

• Energy is absorbed by PS II. Electrons from the double bonds in the head of chlorophyll a become energized and move to a higher energy level. They are captured by a primary electron acceptor.

• Photolysis – water gets split apart, providing electrons to replace those lost from chlorophyll a in PS II. Photolysis splits water into two electrons, two protons, and one oxygen atom. Two oxygen atoms combine to produce one O2 molecule, which is released into the air as waste.

• Electron Transport Chain – Electrons from PS II pass along an electron transport chain consisting of a complex of proteins and ultimately are shuttled to PS I. This flow of electrons is exergonic and provides energy to produce ATP by chemiosmosis. Because this ATP synthesis is powered by light, it is called PHOTOPHOSPHORYLATION.

• Photosystem I – energy is absorbed by PS I. Electrons from the head of chlorophyll a become energized and are captured by a primary electron receptor. Electrons that escape from chlorophyll a are replaced with electrons from PS II (instead of water) – these electrons are shuttled from PSII to PSI by an enzyme carrier. This electron chain ends with the production of NADPH, not ATP.

• Remember: the light reactions use solar power to generate ATP and NADPH, which provide chemical energy and reducing power, to the sugar-making reactions of the Calvin Cycle.

During photosynthesis, chlorophylls absorb free energy from light, boosting electrons to a higher energy level in photosystems I and II. Photosystems I and II are embedded in the internal membranes of chloroplasts (thylakoids) and are connected by the transfer of higher free energy electrons through an electron transport chain. When electrons are transferred between molecules in a sequence of reactions as they pass through the ETC, an electrochemical gradient of hydrogen ions (protons) across the thylakoid membrane is established. The formation of the proton gradient is a separate process, but it is linked to the synthesis of ATP from ADP and inorganic phosphate via ATP synthase.

The ETC of the Chloroplast: Protons that were released from water during photolysis (into the stroma) are actively pumped by the thylakoid membrane (B6f complex) into the lumen (thylakoid space) – the energy from the free fall of electrons is used for this active transport mechanism. ATP is formed as these protons diffuse down the gradient from the thylakoid space, through ATP-synthase channels, and into the stroma. The ATP produced here provides the energy to power the Calvin cycle. NADP becomes reduced when it picks up the two protons that were released from water in PS II. Newly formed NADPH carries hydrogen to the Calvin cycle. NOTE: the terminal electron acceptor here is NADP

+, whereas oxygen was used

in cellular respiration!

Figure 10.15 Comparison of Chemiosmosis in Mitochondria and Chloroplasts http://bcs.whfreeman.com/thelifewire/content/chp08/0802002.html • BOTH processes involve establishing a concentration gradient across a

membrane to power the production of ATP. • BOTH processes involve an energy-capturing processes but use DIFFERENT

types of electron acceptors. • In BOTH processes, the passage of electrons is accompanied by the

formation of a proton gradient across either the inner mitochondrial membrane or the thylakoid membrane, with the membranes separating a region of high proton concentration from a region of low proton concentration.

• In prokaryotes, the passage of electrons is accompanied by the outward movement of protons across the plasma membrane.

WATCH IT http://highered.mheducation.com/sites/0070960526/student_view0/chapter5/animation_quiz_1.html

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!!! Calvin cycle can be divided into 3 phases:

• Phase 1: Carbon Fixation – CO2 is incorporated and attached to RuBP (catalyzed by enzyme rubisco). – Product of reaction is 6-carbon intermediate so unstable that it splits in

half to form two molecules of 3-phosphoglycerate.

• Phase 2: Reduction – Each molecule of 3-phosphoglycerate receives additional phosphate group

from ATP to become 1,3 bisphosphoglycerate. – A pair of electrons donated from NADPH reduces 1,3 bisphosphoglycerate

into Glyceraldehide-3-phosphate (a sugar). – One of the G3P molecules is exported and used to build glucose.

• Phase 3: Regeneration of CO2 Acceptor (RuBP) – In a series of complex reactions, the carbon skeletons of 5 molecules of

G3P are rearranged by the last steps of the Calvin cycle into three molecules of RuBP.

– The RuBP is now prepared again to receive CO2…and the cycle continues. – The regeneration phase requires ATP.

STUDENTS DO NOT NEED TO MEMORIZE THE DETAIL OF THE THREE

PHASES…A GENERAL OVERVIEW WILL SUFFICE!

Essential Knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization.

Organisms must exchange matter with the environment to grow, reproduce and maintain organization. The cellular surface-to-volume ratio affects a biological system’s ability to obtain resources and eliminate waste products. Water and nutrients are essential for building new molecules. Carbon dioxide moves from the environment to photosynthetic organisms where it is metabolized and incorporated into carbohydrates, proteins, nucleic acids or lipids. Nitrogen is essential for building nucleic acids and proteins; phosphorus is incorporated into nucleic acids, phospholipids, ATP and ADP. In aerobic organisms, oxygen serves as an electron acceptor in energy transformations. 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 • A model of nutrient cycling includes main reservoirs of elements and processes

that transfer elements between reservoirs. All elements cycle between organic and inorganic reservoirs – arrows indicate the processes that move nutrients between reservoirs.

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; AND major ways in which humans impact the cycles….be sure you can discuss both short and long term effects! FIGURE 55.14a: The Water Cycle Water is essential to all organisms – and its availability influences the rates at which primary production and decomposition occur.

FORMS: liquid water is the phase used by plants – frozen water can limit availability in terrestrial ecosystems.

97% of the biosphere’s water is contained in the oceans, 2% is in glaciers and polar ice caps, and 1% is in lakes, rivers, and groundwater

Water moves by the processes of evaporation, transpiration, condensation, precipitation, and movement through surface and groundwater

HUMAN IMPACT: overuse, pollution, increased run-off, etc. FIGURE 55.14b: The Carbon Cycle Carbon-based organic molecules are essential to all organisms – carbon forms the framework of the organic molecules essential to living things.

FORMS: atmospheric CO2 is incorporated during photosynthesis and converted to organic forms that are used by consumers.

Carbon reservoirs include fossil fuels, soils and sediments, solutes in oceans, plant and animal biomass, and the atmosphere

CO2 is taken up and released through photosynthesis and respiration; additionally, volcanoes and the burning of fossil fuels contribute CO2 to the atmosphere

HUMAN IMPACT: increase in CO2 concentration by burning fossil fuels. Decreased photosynthesis when removing vast areas of forests. FIGURE 55.14c: The Nitrogen Cycle Nitrogen is a component of amino acids, proteins, and nucleic acids – and is often a limiting plant nutrient.

FORMS: plants can use ammonium (NH4+) and nitrate (NO3

-) – various bacteria convert atmospheric N2 into these forms.

The main reservoir of nitrogen is the atmosphere (gaseous N2), though this nitrogen must be converted to NH4+ or NO3

– for uptake by plants, via nitrogen fixation by bacteria.

Organic nitrogen is decomposed to NH4+ by ammonification, and NH4

+ is decomposed to NO3– by nitrification.

Denitrification converts NO3– back to N2.

HUMAN IMPACT: addition of nitrogen into ecosystems by overusing fertilizers. FIGURE 55.14d: The Phosphorus Cycle Phosphorus is a major constituent of nucleic acids, phospholipids, and ATP

FORMS: Phosphate (PO43–) is the most important inorganic form of phosphorus – absorbed by plants and used in the synthesis of compounds.

The largest reservoirs are sedimentary rocks of marine origin, the oceans, and organisms

Phosphate binds with soil particles, and movement is often localized – weathering of rocks gradually adds phosphate to soil and some may leach into groundwater and eventually reach the sea.

HUMAN IMPACT: removal of phosphorus (dirt/rock) from one ecosystem to another. Addition of phosphates into aquatic ecosystems.

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. • 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.

Agriculture and Nitrogen Cycling The quality of soil varies with the amount of organic material it contains, and agriculture removes from ecosystems nutrients that would ordinarily be cycled back into the soil. • Nitrogen is the main nutrient lost through

agriculture; thus, agriculture greatly affects the nitrogen cycle.

• Plowing: mixes soil and speeds up decomposition of organic matter – applying fertilizer makes up for lost nitrogen when crops are harvested….harvesting of plants causes nitrogen from fertilizers to be leached from the ecosystem.

READ ARTICLE: Eutrophication & Algal Blooms!

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

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: (1) Cohesive/Adhesive behavior; (2) Ability to moderate temperature; (3) Expansion upon freezing; and (4) Versatility as a solvent The water molecule is a polar molecule, meaning that 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. Adhesion is the clinging of one substance to another. 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.

High Specific Heat 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.

• The world is covered mostly by water. Large bodies of water can absorb and store a huge amount of heat from the sun in the daytime and during summer while warming up only a few degrees. Gradually cooling water warms air at night.

• Organisms are made primarily of water, so these properties help to maintain body temperatures. This is vital because many biologically important chemical reactions take place in a very narrow temperature range.

• A large body of water can absorb and store a huge amount of heat from the sun in the daytime and during summer while warming up only a few. THE HIGH SPECIFIC HEAT OF WATER TENDS TO STABILIZE OCEAN TEMPERATURES – CREATING A FAVORABLE ENVIRONMENT FOR LIFE.

• The 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. This minimizes temperature fluctuations to within limits that permit life

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: this helps stabilize temperatures in

organisms and bodies of water. • Evaporation of sweat from human skin dissipates body heat and helps prevent overheating on a hot day or when excess

heat is generated by strenuous activity. The Density Anomaly Ice floats in liquid water because hydrogen bonds in ice are more “ordered,” making ice less dense. Water reaches its greatest density at 4°C.

If ice sank, all bodies of water would eventually freeze solid, making life impossible on Earth

Due to geometry of water molecule, they must move slightly apart to maintain the max number of H bonds in a stable structure.

So at Zero degrees Celsius, an open latticework is formed, allowing air in – thus ice becomes less dense than liquid water floats on top of the water.

The Universal Solvent 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. 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). http://www.sumanasinc.com/webcontent/animations/content/propertiesofwater/water.html If a spoonful of salt (or other ionic substance) is placed in water, the ions in the salt and the water molecules have a mutual affinity owing to the attraction between opposite charges. O is negative and attracts to positive sodium. H is positive and attracts to negative chlorine. As a result, water will surround the individual sodium and chloride ions, separating and shielding them from one another (called a hydration shell). WATER IS THE SOLVENT OF LIFE – molecules within a living system must be broken down in order to be used by the system!

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. 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 and acidification of the oceans; this leads to a decrease in the ability of corals to form calcified reefs.

WATCH IT https://www.youtube.com/watch?v=wuXSEOKNxN8

Surface area-to-volume ratios affect a biological system’s ability to obtain necessary resources or eliminate waste products. Metabolic requirements impose upper limits on cell size – the surface area-to-volume ratio of a cell is critical.

• 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 n

3, so small cells have a greater surface

area relative to volume. • These limitations restrict cell size

As these cubes illustrate the surface area to volume ratio of a small object is larger than that of a large object of similar shape. This ratio limits how large cells can be. Therefore, the smaller the object, the greater its ratio of surface area to volume.

Illustrative Example: 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.

Illustrative Example: 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.

Illustrative Example: Microvilli and 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. Surface-area-to-volume ratio requires that cells be small: a. As cells get larger in volume, relative surface area actually decreases b. This limits how large actively metabolizing cells can become c. Cells needing greater surface area use modifications such as folding