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114 Terms

1

kinetic energy

The energy of motion

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potential energy

The energy matter possesses bc of its location or structure

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oxidation

chemical reaction in which electrons are lost

think leo: loss of electron oxidation

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reduction

chemical reaction in which electrons are added

think ger - gain electron reduction

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5

anabolism

Metabolic pathways that consume energy to build complicated molecules from simpler ones (ex: synthesis of amino acids from simpler molecules)

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catabolism

Metabolic pathways that release energy by breaking down complex molecules to simpler compounds (ex: cellular respiration: breaks down glucose and other organic fuels in presence of oxygen to carbon dioxide and water)

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7

Explain the First Law of Thermodynamics and its relationship to biological systems.

The First Law of Thermodynamics states that the energy of the universe is constant. In other terns, it states that energy can be transferred and transformed but not created or destroyed. An example of how this relates to biological systems is that plants convert sunlight to chemical energy but do not produce or destroy it.

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Explain the Second Law of Thermodynamics and its relationship to biological systems

The Second Law of Thermodynamics states that every energy transfer or transformation increases the entropy of the universe. In simpler terms, it says that as energy is transferred or transformed, wasted energy (such as energy lost as heat) is increased. An example of how it relates to biological systems is that consumers only get a small percent of the energy stored in their food because energy is released as heat between trophic levels.

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9

what is meant by change in free energy?

free energy is energy that can do work when temperature and pressure are uniform, as in a living cell; measure of a systems instability, its tendency to change to a more stable state

free energy change of a reaction tells us whether or not the reaction occurs spontaneously

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exergonic reactions

energy is released into surroundings, spontaneous

<p>energy is released into surroundings, spontaneous</p>
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endergonic reactions

energy is absorbed from surroundings

<p>energy is absorbed from surroundings</p>
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what is a catalyst?

chemical agent that speeds up a reaction without being consumed by the reaction

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13

what is activation energy (EA)?

The minimum amount of energy needed to cause specific reaction or process; often in the form of thermal energy that the reactant molecules absorb from surroundings

<p>The minimum amount of energy needed to cause specific reaction or process; often in the form of thermal energy that the reactant molecules absorb from surroundings</p>
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what effect does an enzyme have on EA?

an enzyme makes the EA lower

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<p>label <span style="font-family: Times, serif">Δ</span><em><span style="font-family: Times New Roman, serif">G</span></em><span style="font-family: Times New Roman, serif">. Is it positive or negative?</span></p>

label ΔG. Is it positive or negative?

negative

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How is ΔG affected by the enzyme?

unaffected

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what is the substrate?

the reactant the enzyme acts on

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<p>A</p>

A

total energy in presence if enzyme

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<p>B</p>

B

EA with enzyme

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<p>C</p>

C

activation energy without enzyme

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<p>D</p>

D

ΔG (unaffected by enzyme)

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<p>E</p>

E

Total energy without enzyme

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enzyme

catalytic protein

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active site

area on enzyme where substrate fits

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cofactors

nonprotein helpers for enzyme catalytic activity, often for chemical processes like electron transfers that cannot easily be carried out by amino acids in proteins

may be bound tightly rot the enzyme as permanent residents or bind loosely and reversible along with substrate

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coenzyme

organic molecule serving as a cofactor (ex: many vitamins are coenzymes in metabolic reactions)

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how does ATP couple reactions?

Coupling reactions in biological systems refer to the coordination of chemical reactions in which the energy released from one reaction is used to drive another reaction. These coupled reactions are essential in various cellular processes to maintain the energy balance and perform work within living organisms.

The role of ATP (adenosine triphosphate) in coupling reactions is fundamental. ATP acts as an energy carrier molecule in cells. It contains high-energy phosphate bonds that, when broken (hydrolyzed), release energy. This released energy is utilized to power endergonic (energy-absorbing) reactions in cells, making them energetically favorable.

energy coupling: use of exergonic process to drive endergonic one

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competitive inhibitors

bind to the active site of an enzyme, competing with the substrate

<p>bind to the active site of an enzyme, competing with the substrate</p>
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noncompetitive inhibitors

bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

<p>bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective</p>
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examples of inhibitors

toxins, poisons, pesticides, antibiotics

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31
<p>what is the substrate that initiates this metabolic pathway?</p>

what is the substrate that initiates this metabolic pathway?

threonine

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<p>what is the inhibitor molecule?</p>

what is the inhibitor molecule?

isoleucine

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<p>what type of inhibitor is it?</p>

what type of inhibitor is it?

allosteric inhibitor

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<p>what type of metabolic control is this?</p>

what type of metabolic control is this?

negative feedback

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what does it mean to be spontaneous? which type of metabolic pathway is spontaneous?

occurs without energy input; they can happen quickly or slowly

catabolic; must increase entropy of universe; a process is spontaneous and can perform work only when it is moving towards equilibrium

spontaneous processes are energetically favorable

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when is change in G negative and positive?

it is negative in catabolic reactions (releases energy) and positive in anabolic reactions (requires energy)

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heat (thermal energy)

kinetic energy + random movement of atoms or molecules

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chemical energy

potential energy for release in chemical reaction

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thermodynamics

study of energy transformations

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isolated vs open system

isolated: such as that approximated by liquid in a thermos, is unable to exchange energy or matter with its surroundings

open system: energy and matter can be transferred between the system and its surroundings (ex: organisms)

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change in free energy equation

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 units (T)

∆G = ∆H - T∆S

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<p>interpret image</p>

interpret image

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ATP structure

ribose (sugar), adenine (nitrogenous base), three phosphate groups

<p>ribose (sugar), adenine (nitrogenous base), three phosphate groups </p>
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three types of cellular work

mechanical, transport, chemical

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phosphorylation

ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant

recipient molecule now called phosphorylated intermediate

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47

ATP hydrolysis

the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

Overall, the coupled reactions are exergonic

<p>the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction</p><p><span data-name="black_small_square" data-type="emoji">▪</span> Overall, the coupled reactions are exergonic</p>
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how does the enzyme lower EA barrier?

  • orienting substrates correctly

  • straining substrate bonds

  • providing a favorable microenvironment

  • covalently bonding to substrate

<ul><li><p>orienting substrates correctly</p></li><li><p>straining substrate bonds</p></li><li><p>providing a favorable microenvironment</p></li><li><p>covalently bonding to substrate </p></li></ul>
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allosteric regulation

may either inhibit or stimulate an enzymes activity

allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the proteins function at another side

<p>may either inhibit or stimulate an enzymes activity</p><p>allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the proteins function at another side</p>
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cooperativity

form of allosteric regulation that can amplify enzyme activity

one substrate mol primes an enzyme to act on additional substrate moles more readily

cooperativity is allosteric bc binding by a substrate to one active site affects catalysis in a different active site

<p>form of allosteric regulation that can amplify enzyme activity</p><p>one substrate mol primes an enzyme to act on additional substrate moles more readily</p><p>cooperativity is allosteric bc binding by a substrate to one active site affects catalysis in a different active site</p>
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noncompetitive inhibition vs allosteric inhibition

  • Allosteric Inhibition: may either inhibit or stimulate an enzyme’s activity, occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site

  • Noncompetitive Inhibition: bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

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substrate-level phosphorylation

A mode of ATP synthesis in which an enzyme transfers a phosphate group from a substrate molecule to ADP rather than addicting an inorganic phosphate to ADP as in oxidative phosphorylation. This form creates less ATP than oxidative phosphorylation

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oxidative phosphorylation

A mode of ATP synthesis in which energy derived from the redox reactions of an electron transport chain is used; creates more ATP than substrate-level phosphorylation

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54

4 stages of cellular respiration

glycolysis

pyruvate oxidation

the krebs cycle/citric acid cycle

electron transport chain

<p>glycolysis</p><p>pyruvate oxidation</p><p>the krebs cycle/citric acid cycle</p><p>electron transport chain</p>
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glycolysis

location: cytoplasm

starts with: breaking down glucose into two molecules of pyruvate (2 3 carbon compounds)

produces: pyruvate, 2 ATP

produces ATP through: substrate-level phosphorylation

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oxidation of pyruvate

location: mitochondria matrix

starts with: pyruvate first converted into acetyl coenzyme A (acetyl CoA)

produces: CO2, NADH, acetyl CoA (2c)

<p>location: mitochondria matrix</p><p>starts with: pyruvate first converted into acetyl coenzyme A (acetyl CoA)</p><p>produces: CO2, NADH, acetyl CoA (2c)</p>
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krebs cycle/citric acid cycle

location: mitochondria matrix

starts with: two carbons (red) enter in the relatively reduced form of an acetyl group, the acetyl group of acetyl CoA joins the cycle by combining with the compound oxaloacetate, forming citrate

produces: (1 ATP, 3 NADH, 1 FADH2 per turn)x2 for total

produces ATP through: substrate-level phosphorylation

major function: completes breakdown of glucose

the roles of NAD+ and FAD in respiration: electron acceptors that carry them to electron transport chain

<p>location: mitochondria matrix</p><p>starts with: two carbons (red) enter in the relatively reduced form of an acetyl group, the acetyl group of acetyl CoA&nbsp;joins the cycle by combining with the compound oxaloacetate, forming citrate</p><p>produces: (1 ATP, 3 NADH, 1 FADH2 per turn)x2 for total</p><p>produces ATP through: substrate-level phosphorylation</p><p>major function: completes breakdown of glucose</p><p>the roles of NAD+ and FAD in respiration: electron acceptors that carry them to electron transport chain</p>
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electron transport chain

location: mitochondria inner membrane

starts with: donation of electrons by NADH (nicotinamide adenine dinucleotide) and FADH2 (flavin adenine dinucleotide) to the first protein complex in the chain, known as Complex I or NADH dehydrogenase

produces: 26/28 ATP, NAD+, FAD, water

produces ATP through: oxidative phosphorylation

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59

How is Glycolysis regulated? Name of the enzyme, where does it act and regulate and what does it control? When does it regulate?

Glycolysis is regulated by the enzyme, phosphofructokinase. It is in the cytoplasm. It regulates glycolysis through allosteric inhibition, and through doing so regulates the rate of glycolysis. It slows down the process when there is excess ATP and speeds the process back up when there is not enough ATP.

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60

what is the final electron acceptor in the electron transport chain?

oxygen

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61

Describe the role of the Electron Transport Chain. What happens to the electrons and H+?

It produces the most ATP in cellular respiration. The electrons and H+ move through channels down the concentration gradient and produce ATP.

<p><span style="font-family: Calibri, sans-serif">It produces the most ATP in cellular respiration. The electrons and H+ move through channels down the concentration gradient and produce ATP.</span></p>
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62

what is chemiosmosis and how is it generated?

chemiosmosis is the use of energy in a H+ gradient to drive cellular work. It is generated by the flow of electrons down the electron transport chain.

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63

explain why respiration is considered exergonic

it is accompanied by the release of ATP

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64

alcoholic fermentation converts glucose to

ethanol and carbon dioxide

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alcoholic fermentation is utilized by what organisms

yeast, bacteria

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lactic acid fermentation converts glucose to what

lactic acid

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lactic acid fermentation is utilized by what organisms?

yogurt bacteria, human muscle cells

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68

Which process produces more ATP Aerobic, Anaerobic respiration or fermentation?

aerobic respiration

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69

where does substrate phosphorylation take place?

glycolysis, citric acid cycle

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where does oxidative phosphorylation take place?

electron transport chain, chemiosmosis

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difference between two phosphorylations

Substrate-level phosphorylation occurs when enzymes remove a high-energy phosphate from a substrate and directly transfer it to ADP. Oxidative phosphorylation occurs when electrons move through an ETC and proficient a proton-motive force that drives ATP synthesis. Both processes produce ATP from ADP and Pi.

<p><span style="font-family: Calibri, sans-serif">Substrate-level phosphorylation occurs when enzymes remove a high-energy phosphate from a substrate and directly transfer it to ADP. Oxidative phosphorylation occurs when electrons move through an ETC and proficient a proton-motive force that drives ATP synthesis. Both processes produce ATP from ADP and Pi.</span></p>
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72

how is carbon dioxide made, which cycle(s) do you see this happening?

carbon dioxide is made through the breakdown of pyruvate; occurs in citric acid cycle

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73

what happens to the carbon that is released from pyruvate that becomes Acetyl CoA? where else in the central metabolic pathway do you see this?

the carbon that is released from pyruvate is released as carbon dioxide

this also occurs in the citric acid cycle

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74

what is the outcome of ATP, NADH, in glycolysis and citric acid cycle?

glycolysis: 2 ATP, 2 NADH

citric acid cycle: 2 ATP, 6 NADH (TOTAL)

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75

how many ATPs are made in ETP? What happens to the NADH - oxidized or reduced?

ETC makes 26/28 ATP. The NADH is oxidized to NAD+

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76

which enzyme helps in making ATP? where is it located, how many protons are needed for one ATP and where are the protons?

ATP synthase

located in mitochondria, and about 3.33 protons are needed for one ATP

the protons are also located in the mitochondria inner membrane space

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77

how is water made in the ETC? who is the electron acceptor? which part of the hydrogen is forming water (electrons or protons)?

water is made by adding H+ ions to O2

the electron acceptor is oxygen

the part of hydrogen forming water is the protons

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fermentation

partial degradation of sugars that occurs without O2

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79

aerobic respiration

(aka cellular respiration) consumes organic molecules and O2 and yields ATP

cellular respiration includes both aerobic and anaerobic respiration but is often used to refer to aerobic respiration

<p>(aka cellular respiration) consumes organic molecules and O2 and yields ATP</p><p>cellular respiration includes both aerobic and anaerobic respiration but is often used to refer to aerobic respiration</p>
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80

anaerobic respiration

similar to aerobic respiration but consumes compounds other than O2

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81

redox reactions

oxidation and reduction

transfer or electrons during chemical reactions releases energy stored in organic moles

this released energy is used to synthesize ATP

<p>oxidation and reduction</p><p>transfer or electrons during chemical reactions releases energy stored in organic moles</p><p>this released energy is used to synthesize ATP</p>
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reducing agent

electron donor

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electron acceptor

oxidizing agent

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84

during cellular respiration, the fuel (such as glucose) is ___, and O2 is ___

oxidized, reduced

<p>oxidized, reduced</p>
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function of NAD+ in cellular respiration

electron acceptor, oxidizing agent

each NADH (reduced form of NAD+ represents stored energy that is tapped to synthesize ATP)

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86

reduction is to _ as oxidation is to _

hydrogenation, dehydration

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87

in the ETC, __ pulls down chain in an energy yielding tumble

O2, energy yielded used to regenerate ATP

<p>O2, energy yielded used to regenerate ATP</p>
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substrate level phosphorylation

This mode of ATP synthesis occurs when an enzyme transfers a phosphate group from a substrate molecule to ADP, rather than adding an inorganic phosphate to ADP as in oxidative phosphorylation.

<p>This mode of ATP synthesis occurs when an enzyme transfers a phosphate group from a substrate molecule to ADP, rather than adding an inorganic phosphate to ADP as in oxidative phosphorylation.</p>
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89

true or false: glycolysis only occurs if O2 is present

false

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glycolysis: energy investment phase vs energy payoff phase

energy investment: cell spends ATP

energy payoff: ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by electrons released from oxidation of glucose

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91

does pyruvate oxidation require O2?

yes

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92

steps of citric acid cycle

acetyl group of acetyl CoA joins cycle by combining with oxaloacetate, forming citrate

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

NADH and FADH2 produced by cycle relay electrons extracted from food to electron transport chain

<p>acetyl group of acetyl CoA joins cycle by combining with oxaloacetate, forming citrate</p><p>next seven steps decompose citrate back to oxaloacetate, making the process a cycle</p><p>NADH and FADH2 produced by cycle relay electrons extracted from food to electron transport chain </p>
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93

free energy outcome in ETC

electrons drop in free energy as they go down the chain and are finally passed to O2, forming H2O

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94

does the ETC chain generate ATP directly?

no

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95

chemiosmosis steps

Electron transfer in the electron transport chain causes proteins to pump H+ from the mitochondrial matrix to the intermembrane space

H+ then moves back across the membrane, passing through the protein complex, ATP synthase

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

the energy stored in H+ gradient across membrane couples redox reactions of electron transport chain to ATP synthesis - this H+ gradient is called a proton-motive force

<p>Electron transfer in the electron transport chain causes proteins to pump H+ from the mitochondrial matrix to the intermembrane space</p><p><span data-name="black_small_square" data-type="emoji">▪</span> H+ then moves back across the membrane, passing through the protein complex, ATP synthase</p><p><span data-name="black_small_square" data-type="emoji">▪</span> ATP synthase uses the exergonic flow of H+ to drive phosphorylation of ATP</p><p><span data-name="black_small_square" data-type="emoji">▪</span> This is an example of chemiosmosis, the use of energy in a H+ gradient to drive cellular work</p><p>the energy stored in H+ gradient across membrane couples redox reactions of electron transport chain to ATP synthesis - this H+ gradient is called a proton-motive force</p>
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96

energy flow sequence in cellular respiration

glucose —> NADH —> electron transport chain —> proton-motive force —> ATP

<p>glucose —&gt; NADH —&gt; electron transport chain —&gt; proton-motive force —&gt; ATP</p>
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97

can the ETC work without oxygen

no, without O2 the ETC will cease to operate - in that case glycolysis couples with anaerobic respiration or fermentation to make ATP

anaerobic respiration uses ETC with final electron acceptor other than O2 (like sulfate)

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98

what phosphorylation is used by fermentation instead of an ETC

substrate-level phosphorylation

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99

what are the steps in alcohol fermentation that convert pyruvate to ethanol (2 steps)?

-release of CO2

-production of ethanol

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100

lactic acid fermentation

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

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