BIO100 Exam 2 Chapter 9

Which source of energy fuels ATP generation?

chemical energy stored in food

Photosynthesis rxn

visible light → organic molecules + O_² (byproduct)

animal catabolic rxn

ingested plant → broken down organic molecules + ATP + CO₂, H₂O, heat (byproducts)

Relationship btwn byproducts of plant photosynthesis and animal ATP synthesis

Animals produce CO₂ and H₂O which support photosynthesis in plants

Plants produce O₂ which supports ATP synthesis in animals

What form of cellular work does produced ATP power?

complex molecule synthesis

where does complex molecule synthesis occur?

mitochondria of animal cells

How does mitochondrion’s double membrane system support cellular respiration

allows for compartmentalization of mitochondrial matrix and inter membrane space; compartmentalization allows for specialization of each part of mitochondria in producing ATP

Function of mitochondria’s outer membrane in ATP production

contains porins allowing for passage of small molecules and ions (based on size, only)

Function of mitochondria’s intermembrane space in ATP production

contains solute and pH conditions similar to cytosol; establishes strong electrochemical gradient w/ matrix

Function of mitochondria’s inner membrane in ATP production

highly selective, permeable membrane acts as a barrier to most solutes; folds into Cristae, increasing surface area and allowing for protein complexes to embed

Function of protein complexes embedded in inner membrane

supports oxidative phosphorylation; required

Catabolic pathway mechanism in releasing stored energy in organic molecules

oxidation

oxidation + catalyzing enzyme

dehydrogenation: removal/loss of H⁺ and e^- and catalyzed by dehydrogenase

reduction + catalyzing enzyme

hydrogenation: addition/gain of H⁺ and e^- and catalyzed by hydrogenase and reductase

What processes must occur simultaneously in order for a redox rxn to occur

oxidation and reduction

reducing agent

substance losing electrons (charge becomes more positive)

oxidizing agent

substance gaining electrons (charge becomes more negative)

in an oxidation rxn, protons and electrons are on the ___ side of the equation

products

in a reduction rxn, protons and electrons are on the ___ side of the rxn

reactants

LEO in “Leo the lion says ger”

Loss of Electrons is Oxidation

GER in “Leo the lion says ger”

Gain of Electrons is Reduction

ATP production is an ender/exogonic process

endergonic

cellular respiration rxn

C₆H₁₂O₆ + O₂ → 6CO₂ + 6H₂O + energy

which reactant is oxidized in cellular respiration? and to what?

C₆H₁₂O₆ or glucose → 6CO₂ or carbon dioxide

which reactant is reduced in cellular respiration? and to what?

O₂ or oxygen → 6H₂O or water

redox rxn of glucose in cellular respiration

glucose is oxidized → donates e^-; reducing agent

redox rxn of oxygen in cellular respiration

oxygen is reduced → accepts e^-; oxidizing agent

two pathways of ATP production

aerobic (aka cellular respiration) and anaerobic respiration

aerobic/cellular respiration

• uses oxygen and glucose to produce ATP

• O₂ is the final e^- acceptor

• Generates CO₂ and H₂O as byproducts and lots of ATP

anaerobic respiration

• doesn’t use oxygen to produce ATP

• occurs in some bacteria and other prokaryotes

• not the same as fermentation

Cellular respiration processes of oxidation rxn’s

(1) Dehydrogenation (by dehydrogenase): H⁺ and 2e^- are removed from substrate by NAD⁺ to form NADH and release proton into solution

(2) NADH carries e^- to ETC (electron transport chain) in mitochondria

(3) NADH donates its collected e^- to ETC, powering proton pump

NAD⁺ functions as an electron carrier

• electron accepter; functions as oxidizing agent during substrate oxidation

• reduced to NADH, which stores energy for proton pump after transport to ETC

How do cells capture energy instead of losing it as heat? what is the rxn?

via electron transfer (NAD⁺ + 2e^- + H⁺ → NADH)

What processes involve NAD⁺ ?

Glycolysis

Pyruvate oxidation

Krebs (citric acid) cycle

Components of NAD⁺

Adenine nucleotide (structural support) and Nicotinamide (oxidized form; functional, e^- accepting/reactive part derived from Vitamin B₃ or niacin)

NAD⁺ (coenzyme) concentration level

low

Why is glucose a favorable source of energy? Delta-G in kcal/mol?

its oxidation is highly exergonic in the presence of oxygen, at -686 kcal/mol

impact of oxidation process (step-wise vs all at once) on total energy released + differences

unaffected; total energy released is the same either way.

EA is larger for all-at-once oxidation process and all free energy is released as heat (thermal/useless energy); none is stored.

EA is smaller for step-wise oxidation process and activated carrier molecules store more energy

Why are step-wise oxidation processes more favorable in living organisms?

easily overcame at body temperature

usable energy is released and transferred to activated carriers to be stored in ATP

used In cellular respiration for more efficiency + control over process and usable energy conservation

Three processes of cellular respiration

Glycolysis

Pyruvate oxidation

Kreb’s (Citric Acid) cycle

Glycolysis conversion

glucose → pyruvate and little ATP via substrate-level phosphorylation

Pyruvate oxidation conversion

pyruvate → acetyl-CoA

Kreb’s (Citric Acid) cycle conversion

substrate-level phosphorylation → ATP and NADH + FADH₂ (reduced e^- carriers)

Where does glycolysis occur?

cytosol of mitochondrion

Where does pyruvate oxidation occur?

mitochondrial matrix

where does Kreb’s (Citric acid) cycle occur?

mitochondrial matrix

where does oxidative phosphorylation occur?

multiple mitochondrial components; Matrix, inner membrane, and intermembrane space

oxidative phosphorylation

• involves e^- transport and chemiosmosis

• Uses electrons from NADH and FADH₂ (reduced e^- carriers) to power ATP synthesis

• Yields more ATP than substrate-level phosphorylation

substrate-level phosphorylation

phosphate group is transferred directly to ATP from phosphate-containing intermediate substrate

Which enzyme facilitates the phosphate group transfer in the substrate-level phosphorylation? How?

kinase

Intermediate (organic molecule generated during glucose breakdown) and ADP bind to active site of Kinase

In which of the three cellular respiration processes does substrate-level phosphorylation occur in?

glycolysis and Kreb’s (citric acid) cycle

glycolysis process

breakdown of glucose molecule into two smaller molecules

partial oxidation of glucose (w/o oxygen) + conservation of some usable energy → NADH + little ATP

Initiating process of glucose oxidation; process includes later stages such as Kreb’s cycle and oxidative phosphorylation

Two phases of glycolysis + net result

energy investment: two ATP molecules are invested into beginning glycolysis

energy payoff: 4 ATP, 2 NADH, and 2 pyruvate molecules are produced

net result: 2 ATP, 2 NADH, 2 pyruvate molecules

how many electrons does one NADH carry

2

what form of energy do the pyruvate molecules produced in glycolysis contain?

potential energy

Energy investment phase steps 1-2: first investment

(1) ATP consumption + glucose phosphorylation: ATP + glucose → ADP + glucose-6-phosphate; catalyzed by hexokinase. Traps glucose in cell.

(2) isomerization of glucose-6-phosphate: glucose-6-phosphate → fructose-6-phosphate, catalyzed by phosphoglucoisomerase. Eases addition of 2nd phosphate by better exposing hydroxyl (reactive) group.

Kinase specificity

group-level; phosphorylates other hexoses as well besides just glucose

Energy investment phase steps 3-5: 2nd investment

(3) commitment step of glycolysis: 2nd ATP molecule + fructose-6-phosphate → ADP + fructose-1,6-biphosphate, catalyzed by phosphofructokinase (PFK)

(4) aldolase cleavage/split of fructose-1,6-biphosphate → 2 3-carbon sugar (G3P and DHAP) isomers

(5) DHAP conversion into G3P: allows glycolysis pathway to continue w/ 2 G3P molecules. Catalyzed by isomerase enzyme

energy, reversibility, and rate of 2nd investment of ATP’s phosphate group

highly exergonic, irreversible, rate-limiting

PFK is an example of which type of feedback?

negative; highly regulated

Energy payoff phase steps 6-7

occurs twice/glucose molecule

(6) continuous oxidation of molecule: catalyzed by dehydrogenase highly specific to G3P only (Not DHAP). Some energy released reduces NAD⁺ → NADH. 2 P_i will phosphorylate triose sugars → 1,3-bisphosphoglycerate; double phosphorylated, high energy product

(7) 1st energy payoff (1st instance of substrate level phosphorylation): 1,3-bisphosphoglycerate + ADP → ATP + 3-phosphoglycerate, catalyzed by phosphoglycerokinase

Which group does 3-phosphoglycerate belong to?

carboxylic acid

What process do cells undergo to extract energy from glucose?

conversion of glucose → pyruvate via glycolysis

Under aerobic conditions (oxygen is present), pyruvate undergoes… by… (hint: prep-step 2 krebs)

Pyruvate oxidation: pyruvate is oxidized to acetyl-CoA in mitochondrial matrix and its stored energy is released.

Kreb’s cycle function and location

Completes energy-yielding oxidation of organic molecules

Occurs in mitochondrial matrix

Why must pyruvate be converted to acetyl-CoA?

only a 2-carbon acetyl group (such as acetyl-CoA) can combine w/ oxaloacetate to enter Krebs cycle

step by step process of pyruvate oxidation → acetyl-CoA

(1) pyruvate exits cytosol → via porin (outer membrane) and proton-pyruvate symporter (inner membrane) → enters mitochondrial matrix

(2) conversion of pyruvate → acetyl-CoA, catalyzed by pyruvate dehydrogenase complex; beginning of Krebs cycle.

What are the enzymatic steps of pyruvate conversion to Acetyl-CoA?

enzyme subunits hand off intermediates to one another w/o releasing them:

(1) one carbon removed as CO₂; 2-carbon molecule remains

(2) e^- transfer to NAD⁺ → NADH

(3) resulting acetyl group transferred to coenzyme A → acetyl-CoA

Citric Acid cycle steps

(1) 2-carbons of Acetyl-CoA + 4 oxaloacetate → 6 citrate

(2) citrate undergoes 2 decarboxylation steps → 2CO₂; balance of incoming and outgoing carbon losses + NADH generation

(3) 4x oxidation: 3NAD⁺ → 3NADH and 1FAD → 1FADH₂

(4) substrate-level phosphorylation produces 1 ATP (or GTP in animal cells which is converted into ATP)

(5) cycle repeats 2x/glucose molecule as oxaloacetate is regenerated

main goal of citric acid cycle + mnemonic for products

generate large amounts of reduced enzymes, NADH and FADH₂, which feed into ETC to drive ATP synthesis.

3-1-1: 3NADH, 1ATP, 1FADH₂

substrate-level phosphorylation of Krebs cycle

succinyl-CoA → succinate, producing ATP thru breakage of high energy bond btwn succinyl group and coenzyme A

What coupled rxn’s does the energy obtained from substrate-level phosphorylation drive?

GDP + P_i → GTP

GTP + ADP → ATP; phosphate transfer

oxidative phosphorylation

NADH and FADH₂ donate high-energy electrons from glucose to inner membrane (ETC or Chemiosmosis) to drive ATP production

Two components of inner membrane dealing with oxidative phosphorylation

(1) ETC: protein complexes transferring e^-’s to power the pumping of H⁺ ions across inner membrane

(2) chemiosmosis: diffusion of H⁺ ions back thru membrane via ATP synthase; process in which most of ATP is produced in cellular respiration

Functions of Electron transport chain (ETC)

located along inner membrane; its increased surface area allows for more ETC’s

As electrons move along ETC, what changes are observed in the electron’s free energy and along the chain’s EN?

e^-’s free energy decreases as e^- flows from high → low energy state

Chain EN increases along chain as each component has stronger pull on e^-’s than the one before

What characteristics of the ETC allows electrons to efficiently pass thru ETC?

(1) multi-protein complexes alternate btwn reduced and oxidized

(2) proteins arranged based on reduction potential (ability to attract e^-), from lowest to highest

Why is oxygen the final electron acceptor of this step-wise process? What is the rxn?

strong affinity for e^-; powerful oxidizing agent

O₂ + 4e^- + 4H⁺ → 2H₂O (byproduct)

ETC: electron flow + proton pumping

(1) e^-’s from NADH enter complex 1 and are transferred to CoQ; complex 1 uses energy from transfer to pump H⁺ into intermembrane

(2) e^-’s from FADH₂ enter complex 2 and are transferred to CoQ

(3) complex 3 collects e^-s from CoQ and passes them to cytochrome C, which also pumps H⁺

(4) complex 4 receives e^-s from cytochrome c and transfers them to O₂, which forms water (byproduct). complex 4 also pumps more H⁺

How is the energy released during stepwise ETC rxn’s used?

it builds a proton gradient across membrane, supporting ATP production

What is coenzyme Q (ubiquinone)

non-protein, mobile e^- carrier in membrane’s interior

What makes complex 2 different from 1, 3, and 4?

not a transmembrane protein; doesn’t pump protons

what is cytochrome C?

peripheral protein/electron carrier from complex 3 to complex 4; attached to outer layer of membrane, outside mitochondria

how are the functions of complexes 1, 3, and 4 powered?

they use energy from e^- transfers to pump H⁺ into intermembrane space

What is the purpose of pumping protons into intermembrane space?

creates electrochemical gradient across inner mitochondrial membrane which stores PE

components of electrochemical gradient/proton motive force

voltage gradient: matrix → negative and intermembrane space → positive

pH gradient: intermembrane space + H⁺ → acidic and matrix → H⁺ and basic

What pathway does the electrochemical gradient power for ATP production?

Chemiosmosis

What quality of the inner membrane maintains the electrochemical gradient?

inner membrane is not freely permeable to protons

What enzyme catalyzes chemiosmosis and what are its components

ATP synthase: rotary enzyme anchored into the inner mitochondrial membrane

composed of membrane-bound portion containing H⁺ channel and rotating internal rod + catalytic knob that both extend into mitochondrial matrix

how is chemiosmosis catalyzed?

Flow of H⁺ ions down their gradient provides mechanical energy used to power internal rod rotation, activating catalytic knob that joins ADP + P_i → ATP

What qualities of chemiosmosis differentiate it from substrate-level phosphorylation?

• not dependent on organic substrate to donate phosphate group

• ADP and P_i are readily available in matrix

• enzyme is powered by electrochemical gradient and not chemical rxn w/ substrate; much more ATP is produced w/ oxidative phosphorylation

Summarized energy flow sequence thru cellular respiration

Glucose → NADH → ETC → electrochemical gradient → ATP

Efficiency level of cellular respiration + composition of produced ATP

not 100%; 30-32 ATP per glucose molecule

• 2 from glycolysis (substrate-level phosphorylation)

• 2 from Krebs cycle (substrate-level phosphorylation)

• 26-28 from oxidative phosphorylation (chemiosmosis)

Three causes of variety in total ATP produced

(1) # of ATP molecules produced per NADH is unfixed; depends on how electrons enter ETC. electron transfer uses energy, lowering ATP yield

(2) electron carriers differ in atp output: NADH → 2.5 ATP and FADH₂ → 1.5 ATP

(3) not all protons in gradient are used for ATP synthesis; some is utilized for other cellular work

What availability does pyruvate conversion depend on, and what are the pathways that it follows accordingly?

O₂ presence: aerobic respiration in mitochondrion

O₂ absence: fermentation (dependent on organism; ex. ethanol or lactate production)

Difference between glycolysis and fermentation

Glycolysis produces pyruvate

fermentation uses pyruvate, but not as a part of glycolysis

Goal of fermentation

regenerate oxidized e^- carriers (NAD⁺ and FAD) to supply and promote continuation of glycolysis in the absence of oxygen

role of fermentation in ATP synthesis

ATP from fermentation comes only from glycolysis, not fermentation itself; produces e^- carriers that support glycolysis functions

Ethanol fermentation process + active ingredient

involves yeast

(1) decarboxylation of pyruvate → removal of CO₂, forming acetaldehyde

(2) acetaldehyde accepts e^- from NADH generated during glycolysis; acetaldehyde’s 2-carbon molecule structure allows it to accept electrons.

(3) reduction of acetaldehyde → ethanol and oxidation of NADH → NAD⁺; ethanol is byproduct of fermentation

What causes yeast to rise in bread?

release of CO₂