BIOLOGY EXAM 3

Chapters 9 and 10

energy flow

• energy flows into an ecosystem as sunlight & leaves as heat

• photosynthesis generates O2 & organic molecules, which are used in cellular respiration

• cells use chemical energy stored in organic molecules to regenerate ATP, which powers work

catabolic pathways and production of ATP

the breakdown of organic molecules is exergonic (spontaneous; catabolic; deltaG<0)

• aerobic respiration consumes organic molecules and O2 and yields ATP

• anaerobic respiration is similar to aerobic respiration but consumes compounds without O2

• fermentation is a partial degradation of sugars that occurs without O2

• cellular respiration includes both aerobic and anaerobic respiration but is often used to refer to aerobic respiration (NEEDS O2 AND MITOCHONDRIA)

although carbohydrates, fats, and proteins are all consumed as fuel, it is helpful to trace cellular respiration with the sugar glucose:
C6H12O6 + 6O2 ——> 6CO2 + 6H2O + energy (ATP)

the principle of redox

chemical reactions that transfer e- between reactants are called oxidation-reduction reactions, or redox reactions

• in oxidation, a substance loses e-, or is oxidized

• in reduction, a substance gains e-, or is reduced (the amount of positive charge is reduced)

memory trick: OIL RIG (oxidation is loss, reduction is gain)

during cellular respiration, the organic fuel (such as glucose) is oxidized (loses e-), and O2 is reduced (gains e-)

• H atoms can be equated to e- movement (1 H atom = 1 e-, 1 p+)

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

• high energy e- from organic compounds are usually first transferred to NAD+, an electron carrier that assists the enzyme dehydrogenase (want to carry hydrogens high energy to somewhere that ATP can be made)

• each NADH (the reduced form of NAD+) represents stored energy - carries 2 high-energy electrons - that will be tapped to synthesize ATP

  • FAD —> FADH2 works similarly

electron carriers:

carry 2 high energy e- to the ETC

NAD+ —→ (reduce) NADH = H+

←— (oxidize)

NADH and FADH2 pass e- to the electron transport chain (ETC)

• ETC passes e- in controlled series of steps instead of one explosive reaction

• O2 pulls e- down the chain in an energy-yielding tumble (“falling down the staircase”) = oxygen must be present!

• energy yielded from the e- movement in the ETC is used to generate ATP in chemiosmosis

reduction of NAD+ → NADH (NAD+ gains 2 e- and 1p+) allows e- to lose very little potential energy

• electron carriers (NAD+ and FAD) can accept 2 high energy e-, transfer them and most of their energy, to other molecules

ETC is used to break the fall of the e- to O2 into several energy-releasing steps

• e- move from protein complex to protein complex, losing a small amount of energy with each step, until they reach O2 at the end, which serves as the final/terminal e- acceptor

• O2 is reduced to H2O in this process

the stages of cellular respiration

harvesting energy from glucose has 3 stages:

1. glycolysis (breaks down glucose into 2 molecules of pyruvate)

2. citric acid cycle (completes the breakdown of glucose, releasing e-)

3. oxidative phosphorylation (accounts for most of the ATP synthesis in ETC and chemiosmosis)

cellular respiration: oxidative phosphorylation

oxidative phosphorylation generates almost 90% of the ATP (powered by redox reactions)

smaller amounts of ATP formed in glycolysis & the citric acd cycle by substrate-level phosphorylation

for each molecule of glucose degraded to CO2 the cell makes up to 32 ATP total by the end of complete cellular respiration

Stage 1: glycolysis

glycolysis - oxidizes glucose to pyruvate, harvesting energy

• glycolysis (“sugar splitting”) breaks down glucose into 2 molecules of pyruvate

occurs in the cytoplasm & has 2 major phases:

1. energy investment phase (uses 2 ATP)

2. energy payoff phase (makes 4 ATP)

glycolysis occurs whether or not O2 is present!

glycolysis net results:

• 2 pyruvate

• 2 NADH + 2H+

• 2 ATP

Stage 1.5: Oxidation of Pyruvate to Acetyl-CoA

there is a transition step between glycolysis and the citric acid cycle!

• before the CAC can begin, pyruvate must be converted to acetyl-CoA (acetyl Coenzyme A)

• pyruvate enters the mitochondrion by active transport (ATP is used) - as it moves into the matrix it is oxidized

• oxidation of pyruvate is carried out by a multi-enzyme complex that catalyzes 3 reactions as it is transported into the mitochondrial matrix

  • 2 pyruvate → 2 acetyl-CoA

  • also results in 2 NADH + 2H+

1. carboxyl group of pyruvate is removed and given off as CO2

2. remaining 2-C fragment is oxidized forming acetate. NADH is formed in the process

3. coenzyme A attaches to the acetate to become acetyl-CoA, which has high potential energy

Stage 2: The Citric Acid Cycle

Citric acid cycle, also called the Krebs Cycle, completes the breakdown of pyruvate to CO2

• Acetyl-CoA is what enters the CAC

• oxidizes organic fuel derived from pyruvate, generating:

  • 1 ATP

  • 3 NADH + 3H+

  • 1 FADH2

  • 2 CO2

per single turn of the cycle

• the CAC has 8 steps, each catalyzed by a specific enzyme

• Co-A stripped off Acetyl-CoA

• acetyl group joins the cycle by combining with oxaloacetate (already present in the matrix), forming citrate (hence the cycle name)

• the next 7 steps decompose the citrate back to oxaloacetate, making the process a cycle

• electron carrier FAD now makes an appearance

  • FAD (also called FADH) reduces to FADH2

• NADH and FADH2 produced by the cycle carry e- extracted from glucose to the ETC

• after 2 turns of the cycle (due to 2 acetyl-CoA):

  • 6 NADH + 6H+

  • 2 FADH2

  • 2 ATP

  • 4 CO2

Stage 3: Oxidative Phosphorylation

during oxidative phosphorylation, chemiosmosis couples e- transport to ATP synthesis using H+

2 processes contribute to oxidative phosphorylation:

1. Electron Transport Chain (ETC)

2. Chemiosmosis

ETC - oxidative, chemiosmosis - phosphorylation

NADH and FADH2 donate e- to the ETC, which powers ATP synthesis

• NADH and FADH2 account for most of the energy extracted from glucose

ETC:

• ETC is in the inner membrane (cristae). most of the chain’s components are cytochrome proteins, which exist in 4 multi-protein complexes

• ETC proteins alternate reduced & oxidized states as they accept & donate e-

• e- drop in free as they go through the chain & energy is passed, forming H2O

• e- are transferred NADH and the ETC

• e- are passed through proteins to the terminal e- acceptor

• ETC does not directly generate ATP

• ETC breaks the large free-energy drop from glucose to O2 into smaller steps that release energy in manageable amounts

CHEMIOSMOSIS:

• chemiosmosis: movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient. the concentration gradient is a form of potential energy that can drive work

• e- transfer in ETC causes proteins to pump H+ from the mitochondrial matrix to the intermembrane space

• then, H+ moves back across the membrane (down its concentration gradient), passing through ATP synthase (a transport protein; a proton “pump”)

• ATP synthase uses the exergonic flow of H+ to energize the phosphorylation of ATP = chemiosmosis

• H+ ions flow down their concentration gradient & enter binding sites on the rotor, changing the shape of each subunit (cooperativity)

• rotor spins in the membrane

• each H+ makes 1 complete turn before leaving the rotor and passing into the mitochondrial matrix

• turning of rotor & rod activated catalytic sites in the knob that produce ATP from ADP & Pi

• the energy stored in a H+ gradient across a membrane couples the redox reactions of the ETC to ATP synthesis (remember H+ = a proton)

• H+ gradient is referred to as a proton-motive force, emphasizing its capacity to do work (chemiosmosis is work)

an accounting of ATP production by cellular respiration

during cellular respiration, most energy (e-) flows in this sequence:

glucose → NADH/FADH2 —> ETC → chemiosmosis (proton-motive force) → O2 (terminal electron acceptor)

• about 34% of energy in glucose is transferred to ATP during cellular respiration, making about 30-32 ATP total

• some reasons why exact number of ATP is not known:

  • losses due to leaky membranes

  • cost of moving pyruvate & ADP into the mitochondrial matrix

fermentation and anaerobic respiration

fermentation & anaerobic respiration enable cells to produce ATP without the use of oxygen

• without O2, the ETC will cease to operate (causing NAD+ and FAD to no longer be available for e-), therefore, glycolysis now couples with fermentation or anaerobic respiration to produce ATP

organisms use of cellular respiration and fermentation:

• obligate anaerobes carry out fermentation or anaerobic respiration & some cannot survive in the presence of O2 (ex. clostridium botulinum (botulism))

• yeasts and many bacteria are facultative anaerobes, meaning that they can survive either fermentation or respiration

  • in a facultative anaerobe (similar muscle cells), pyruvate is a fork in the metabolic road that leads to 2 alternative catabolic routes (ex. E. Coli and Staphylococci)

types of fermentation:

• fermentation uses substrate-level phosphorylation instead of an ETC/Chemiosmosis to generate ATP

• fermentation consists of glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis

• 2 common types: alcohol fermentation and lactic acid fermentation

alcohol fermentation:

• pyruvate is converted to ethanol & releases CO2

• alcohol fermentation by yeast is used in brewing, winemaking, and baking

lactic acid fermentation:

• pyruvate reduced to NADH, forming lactate as an end-product, with no release of CO2

• used by some bacteria that we use to make cheese and yogurt

• used by human muscle cells to generate ATP when O2 is scarce

regulation of cellular respiration via feedback mechanisms

feedback inhibition is the most common mechanism for control of reactions

• if ATP concentration begins to drop, aerobic respiration speeds up (also links to breathing rate)

• when there is plenty of ATP, aerobic respiration slows down (also links to breathing rate)

• control of catabolism is based mainly on regulating the activity of enzymes at strategic points in the pathway

regulation:

• allosteric enzymes respond to inhibitors & activators

• phosphofructokinase is stimulated by AMP (adenosine monophosphate) but is inhibited by ATP and citrate

• this adjusts the rate of respiration as the cells catabolic and anabolic demands change

COMPARING FERMENTATION WITH AEROBIC RESPIRATION

SAME: glycolysis (always 2 net ATP) to oxidize glucose & harvest chemical energy of food

SAME: NAD+ accepts e- during glycolysis as it is reduced to NADH

DIFFERENT: final e- acceptors

• organic molecule (such as pyruvate) used in fermentation

• O2 in cellular respiration

DIFFERENT: total ATP yield

• cellular respiration produces 32 ATP per glucose molecule

• fermentation produces 2 ATP per glucose molecule

evolutionary significance of glycolysis

• ancient prokaryotes are thought to have used glycolysis long before there was oxygen in the atmosphere

• very little O2 was available until about 2.7 billion years ago, so early prokaryotes likely used only glycolysis to generate ATP

• glycolysis is a very ancient process that gives evidence fo cellular evolution

• all cells can do glycolysis to yield ATP

the process that feeds the biosphere: photosynthesis

photosynthesis: the process that converts solar energy into chemical energy

• directly or indirectly, photosynthesis nourishes almost the entire living world

autotrophs sustain themselves without eating anything derived from other organisms

• autotrophs are the producers of the biosphere, producing organic molecules from CO2 and other inorganic molecules

• almost all plants are photoautotrophs, using the energy of sunlight to make organic molecules

heterotrophs: obtain their organic material from other organisms

• heterotrophs are the consumers of the biosphere

• almost all heterotrophs, including humans, depend on photoautotrophs for food and O2

the importance of photosynthesis:

• the energy entering chloroplasts as sunlight gets stored as chemical energy in organic compounds (mainly sugars)

• sugar made in the chloroplasts supplies chemical energy and carbon skeletons to synthesize the organic molecules of cells

• plants store excess sugar as starch in structures like roots, tubers, seeds, and fruits

• in addition to food production, photosynthesis produces the O2 in our atmosphere

photosynthesis

• photosynthesis converts light energy to chemical energy of food

• chloroplasts are structurally similar to, and likely evolved from, photosynthetic bacteria

• the structural organization allows for the chemical reaction of photosynthesis

reaction equation:

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

chloroplasts: the site of photosynthesis in plants

• leaves are the major locations of photosynthesis

• their green color is from chlorophyll, the green pigment within chloroplasts

• chloroplasts are found mainly in cells of the mesophyll, the interior tissue of the leaf

• each mesophyll cell contains 30-40 chloroplasts

• CO2 enters and O2 exits the leaf through microscopic pores called stomata (stoma = 1)

• the chlorophyll is in the membranes of thylakoids (connected sacs in the chloroplast)

• thylakoids may be stacked in columns called grana

• chloroplasts also contain stroma, a dense interior fluid

STROMA - cytoplasm-like material

STOMA - pore in the side of the cell

light

• light is a form of electromagnetic energy. the electromagnetic spectrum is the entire range of electromagnetic energy.

• visible light consists of wavelengths that produce colors we can see

• light consists of discrete particles called photons

the nature of sunlight

• photons travel in rhythmic waves

• wavelength is the distance between crests of waves. wavelength determines the type of electromagnetic energy (& color)

• wavelengths that are absorbed are reflected

photosynthetic pigments: the light receptors

• pigments - molecules that absorb visible light

  • 3 different pigments in reaction centers of thylakoids allow plants to absorb light energy at different wavelengths

  • leaves appear green because chlorophyll reflects green light

  • they absorb all colors of light except for what color you see, which is reflected

• chlorophyll a is the main photosynthetic pigment

• accessory pigments, such as chlorophyll b, broaden the spectrum used for photosynthesis

  • accessory pigments called carotenoids also absorb excessive light that would damage chlorophyll

chlorophyll

• most of the molecule is the porphyrin ring: consists of C=C & C=N bonds

  • bonds let the central ring absorb energy and reorganiez to accommodate extra e- (switch bonds around in the ring as it absorbs energy)

• long hydrophobic tail sticks off and anchors the chlorophyll molecule in the thylakoid membrane so that they can be exposed to sunlight

• Mg2+ ion is in the center of the ring to give green color

a spectrophotometer measures a pigment’s ability to absorb various wavelengths

• this machine sends light through pigments and measures the fraction of light transmitted at each wavelength

absorption spectrum is a graph plotting a pigment’s light absorption vs wavelength

• absorption spectrum of chlorophyll a suggests that violet-blue and red light work best for photosynthesis

action spectrum profiles the relative effectiveness of different wavelengths of radiation in driving a process (summation of all wavelengths)

excitation of chlorophyll by light:

• when a pigment absorbs light, its e- go from ground state to excited state, which is unstable

• when excited e-’s fall back to the ground state, photons are given off resulting in an afterglow called fluorescence

photosynthesis equation

photosynthesis is a complex series of reactions that can be summarized as the following equation:

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

the splitting of water

chloroplasts split H2O into H and O2

• incorporated the e- of H’s into sugar

• releases O2 as a byproduct

photosynthesis: a redox process

• photosynthesis reverses the direction of e- flow compared to cellular respiration

• Photosynthesis is a redox process in which H2O is oxidized and CO2 is reduced

• photosynthesis is an endergonic process; the energy boost is provided by light

two stages of photosynthesis

photosynthesis consists of:

1. light reactions (the photo part)

2. Calvin cycle (the synthesis part)

light reactions of photosynthesis:

• the light reactions occur in the thylakoids

  • split H2O

  • release O2

  • reduce NADP+ to NADPH

  • generate ATP from ADP by photophosphorylation

• NADP+ is the electron carrier in photosynthesis

  • when reduced, NADPH carries 2e-

• light reactions convert solar energy to the chemical energy of ATP and NADPH

• chloroplasts and their thylakoids are solar-powered chemical factories

calvin cycle of photosynthesis:

• calvin cycle occurs in the chloroplast’s stroma and forms sugar from CO2, using ATP and NADPH

  • also referred to as the dark reactions

• calvin cycle begins with carbon fixation, incorporating CO2 into organic molecules (sugars)

light reaction photosystems

a photosystem consists of a reaction-center complex (protein complex) surrounded by light-harvesting complexes

• the light-harvesting complexes are pigment molecules bound to proteins that transfer the energy of light (photons) to the reaction center

• a primary electron acceptor in the reaction center accepts the excited e- (is reduced)

• transfer of excited e- from reaction center chlorophyll-a molecule to the primary electron acceptor is the 1st step of the light reactions

• 2 photosystems in the thylakoid membrane

  • photosystem II (PS II) functions first and is best at absorbing a wavelength of 680 nm

    • thus, the chlorophyll a reaction center of PS II is called P680

  • photosystem I (PS I) is best at absorbing a wavelength of 700 nm (called P700)

light reaction electron flow

• during the light reactions, there are 2 possible routes for e- flow:

1. cyclic electron flow

2. linear electron flow ( the primary pathway; involves both photosystems, & produces ATP and NADPH using light energy)

PS II → PS I → Calvin Cycle

linear electron flow: PS II

• photon hits a pigment & its energy is passed among surrounding pigment molecules until it excites P680

• an excited e- from P680 is transferred to the primary electron acceptor. we now call it P680+ (lost e- gives + charge)

• P680 is easily reduced and can gain more e-

• H2O is split by enzymes, and the e- are transferred from the H atoms to P680+, thus reducing it to P680

• O2 is released as a byproduct of this reaction

• e- falls down an ETC from PS II to PS I

• energy released drives creation of a proton (H+) gradient across the thylakoid membrane (H+ moved to thylakoid space)

• diffusion of H+ across the membrane to the stroma through ATP synthase creates ATP from ADP + Pi (proton-motive force of H+ ions drives chemiosmosis)

linear electron flow: PS II → PS I

• P700+ (P700 that is missing an e-) accepts e- passed down from PS II via the ETC

• in PS I transferred light energy excites P700, which loses an e- to a primary electron acceptor (like PS II)

linear electron flow: ETC PS I

• PS I e- falls down a short ETC from the primary e- acceptor to ferredoxin (Fd)

• e- transferred from Fd to NADP+ (which reduces it to NADPH)

  • ATP is not produced in this ETC, the energy is in the form of NADPH

• e- on NADPH are now available for the reactions of the calvin cycle

• Terminal e- acceptor in linear flow is NADP+

cyclic electron flow:

• cyclic electron flow uses only PS I and produces ATP

  • only uses a part of the ETC from PS II to return e- to PS I’s reaction center

• No O2 is released, no NADPH made

• cyclic electron flow generates surplus ATP in the stroma, satisfying the higher demand of the Calvin Cycle

light reactions: SUMMARY

• ATP and NADPH are produced on the side facing the stroma, where the Calvin Cycle takes place

• light reactions generate ATP and increase the potential energy of e- by moving them from H2O to NADPH (linear e- flow)

the calvin cycle

• the calvin cycle uses the chemical energy of ATP & NADPH to reduce CO2 to sugar

• calvin cycle (like the CAC) regenerates its starting material after molecules enter and leave the cycle

• calvin cycle builds sugar from smaller molecules by using ATP & the power of e- carried by NADPH

• carbon enters the cycle as CO2 & leaves as a sugar named G3P (glyceraldehyde 3-phosphate)

  • glucose is not the molecule that leaves the cycle!

• for net synthesis of 1 G3P (sugar), the cycle must fix 3 molecules of CO2

• the calvin cycle has 3 phases

1. Carbon fixation

2. reduction

3. regeneration of RuBP

calvin cycle in a nutshell

• RuBP present as a CO2 acceptor (1 CO2 enters Calvin Cycle & joins RuBP (a 6-C compound))

• CO2 + RuBP + Rubisco (enzyme) → 2 PGA molecules

• PGA needs ATP to phosphorylate it & needs NADPH to reduce it to form G3P

• REPEAT the above steps with 2 more CO2 molecules

• net gain after 3CO2 = 6 G3P molecules & 1 G3P exits the cycle

• remaining 5 G3P used to rebuild RuBP using ATP

• cycle needs 6 CO2 to make 2 G3P leave & form glucose or other sugars in the cytoplasm

calvin cycle phases

1. carbon fixation

• 3 CO2 + 3RuBP + 3 Rubisco = 6 PGAs (total of 6 ATP used)

2. reduction

• PGAs phosphorylated by ATP & reduced by NADPH = G3Ps (total of 6 G3P are fomed per 3 CO2)

  • 6 ATP used, 6 NADH used

  • 6 PGA → 6 G3P

• 1 G3P leaves the cycle and the chloroplast to form glucose or other sugars in the cytoplasm

3. regeneration

• RuBP regenerates from remaining 5 G3P molecules (uses 3 ATP)

• 5 G3P → RuBP

G3P leaves the chloroplast and moves into the cytoplasm

G3P + G3P = glucose

importance of G3P

• G3P is the end product of the calvin cycle

• G3P moves into the cytoplasm to:

  • make glucose or other sugars

  • make starches

  • make cellulose

  • make sucrose (glucose + fructose)

  • help make fatty acids

  • help make amino acids

chloroplast vs mitochondria: chemiosmosis

chloroplasts and mitochondria generate ATP by chemiosmosis, but use different sources of energy

mitochondria transfer chemical energy from food to ATP

chloroplasts transform light energy into the chemical energy of ATP (and sugar)

spatial organization of chemiosmosis differs between chloroplasts and mitochondria, but also shows similarities

comparison of chemiosmosis:

• in mitochondria, protons (H+) are pumped to the intermembrane space and drive ATP synthesis as they diffuse back into the mitochondrial matrix

• in chloroplasts, protons (H+) are pumped into the thylakoid space and drive ATP synthesis as they diffuse back into the stroma