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TULANE / Biology / CELL 01 / What are the four parts of aerobic metabolism?

What are the four parts of aerobic metabolism?

What are the four parts of aerobic metabolism?

Description

School: Tulane University
Department: Biology
Course: Intro to Cell & Molec Biology
Professor: Meenakshi vijayaraghavan
Term: Spring 2017
Tags:
Cost: 25
Name: Cell biology chapter 7 notes - part two
Description: Part 2 of chapter 7 notes - Krebs cycle and oxidative phosphorylation
Uploaded: 04/03/2017
9 Pages 51 Views 3 Unlocks
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Chapter 7 ­ Cellular Respiration and Fermentation


What are the four parts of aerobic metabolism?



Notes Part 2 ­ citric acid cycle and oxidative phosphorylation

4 steps of aerobic respiration involving glucose 

1.) Glycolysis

2.) Breakdown of pyruvate

3.) Citric acid cycle 

4.) Oxidative phosphorylation 

Citric Acid Cycle

● Citric acid is the first product produced

● Also known as “Krebs Cycle,” or Tricarboxylic Acid (TCA) cycle

● The process is a metabolic cycle → organic molecules are regenerated  

with each turn of the cycle If you want to learn more check out What are the factors that gave rise to southeast asia?

○ Particular molecules enter the cycle while others leave

● Involves the breakdown of carbohydrates to CO2


What does isocitrate dehydrogenase do?



● Complete oxidation of carbons takes place here

● There are 2 rounds of the Kreb cycle per 1 glucose molecule 

○ 4 carbons from 1 glucose molecule enter Krebs (2 per molecule of  Don't forget about the age old question of How is ar receivable information evaluated?

Acetyl CoA from breakdown of pyruvate)

● 3 phases: Priming phase → preparing for breakdown (1-2), Oxidation 

phase (3­4), Regeneration phase (5­8)

● Key: Enzyme, substances released or consumed, final product. Don't forget about the age old question of What makes p680 special from other pigments?

      Process of ONE cycle: 

● **Oxaloacetate (4C) is the starting and ending compound of the Kreb cycle 1. Acetyl CoA (2C) from the breakdown of pyruvate enters the Krebs Cycle. The 


What is the role of succinate dehydrogenase?



acetyl group (CH3CO) attaches to oxaloacetate (4C) with the help of citrate synthetase, 

forming citrate aka citric acid (6C). CoA­SH is released from the Acetyl CoA molecule. a. Highly exergonic reaction

2. Aconitase rearranges citrate into an isomer called Isocitrate (6C), in a two step 

process that involves:

a. Releasing one molecule of H2O

b. Consuming one molecule of H2O

3. Isocitrate dehydrogenase oxidizes isocitrate (6C) into ?­ketoglutarate (5C),  releasing one CO2 and forming one NADH molecule (NAD+ + 2e- + 2H+ →  NADH + H+)We also discuss several other topics like When did native american assimilation end?

a. Highly exergonic 

b. **first energy compound (NADH) in Kreb cycle is produced 

here!

c. When CO2 is released, a hydronium ion is also released, forming 

NADH

4. ?­ketoglutarate dehydrogenase oxidizes ­ketoglutarate (5C) and   attaches it to CoA­SH, forming succinyl CoA (4C), releasing one CO2 and forming one 

NADH molecule

a. Highly exergonic reaction

b. Attaching the CoA­SH compound helps stabilize the molecule

5. Succinyl CoA synthetase breaks down succinyl CoA into succinate (4C), 

releasing the CoA­SH attachment. 

a. This exergonic reaction drives formation of GTP from GDP and 

Pi, which then gives a phosphate to ADP forming ATP

i. ***this step (formation of succinate from 

succinyl CoA) is the only step in the Krebs cycle where ATP is 

produced

6. Succinate dehydrogenase oxidizes succinate (4C) into fumarate (4C), producing 

FADH2

7. Fumarase helps fumarate(4C) to combine with water, forming malate (4C). a. **only step where net one water molecule comes in If you want to learn more check out How did pco2 affect respiration rate?

8. Malate dehydrogenase oxidizes malate into oxaloacetate (4C) → the starting  compound of the krebs cycle, forming one NADH. The cycle begins again and  repeats itself! (2 cycles per glucose molecule)

    

      Final product (per 1 cycle) 

1. 2 CO2

2. 1 ATP

3. 1 FADH

4. 3 NADH

Per glucose:

Pathway/cycle

CO2

ATP

NADH

FADH2

Glycolysis

­­­­­­­

2

2

­­­­­­

Breakdown of  Pyruvate

2

______

2

______

Kreb Cycle

4

2

6

2

Don't forget about the age old question of Why did marge piercy write barbie doll?

Oxidative Phosphorylation

● Process by which high­energy electrons are removed from NADH and FADH2 to 

produce more ATP

● Typically requires oxygen (last electron acceptor in ETC)

○ “Oxidative” → high energy electrons from NADH and  

FADH2 are removed via oxidation in electron transport chain 

○ “Phosphorylation” → ATP is created by the  

phosphorylation of ADP via ATP synthase 

Electron transport chain (ETC) → first step of oxidative  phosphorylation.  

● ETC: group of protein complexes and small organic molecules embedded in inner mitochondrial membrane. 

Structure 

● Protein complexes involved in ETC:

I. NADH dehydrogenase → proton pump 

II. Succinate reductase 

III. Cytochrome b­c­1 → proton pump 

IV. Cytochrome oxidase → proton pump 

● Mobile electron carriers involved in ETC:

Q. Ubiquinone (coenzyme Q) 

○ Organic molecule

CyC. Cytochrome c 

○ Protein

Process 

● Electrons passed from NADH and FADH2 → ETC → oxygen ○ e­ are passed linearly from one component to the next in a series 

of redox reactions

 1a) NADH is oxidized to NAD+ → releasing 2e-

◆ One electron at a time, e­ are transferred to I. 

◆ I. uses part of electron’s energy to pump H+ from mitochondrial 

matrix (low concentration) to intermembrane space (high concentration), 

establishing proton gradient

◆ e­ are then transferred to Q 

      1b) FADH2 is oxidized to FAD

◆ e­ are transferred to II. 

● Because FADH is found in inner mitochondrial 

membrane right next to II.

◆ e­ are then transferred to Q 

2. Q accepts the partly de­energized electrons from complex I. and electrons from 

complex II. and delivers them to complex III. 

◆ III. uses part of electron’s energy to pump H+ from mitochondrial 

matrix (low concentration) to intermembrane space (high concentration), 

establishing proton gradient

◆ e­ are then transferred to CyC 

3. CyC carries e­ from III to IV 

◆ IV. uses part of electron’s energy to pump H+ from mitochondrial 

matrix (low concentration) to intermembrane space (high concentration), 

establishing proton gradient

◆ e- are then transferred to O2 → water is produced

Function 

● Movement of electrons across ETC is an exergonic process (negative free energy) ○ Some free energy is harnessed to pump H+ ions into 

intermembrane space, ultimately generating an H+ electrochemical (proton) 

gradient across the inner mitochondrial membrane

● Gradient is source of potential energy that helps drive ATP synthesis later

******possible test questions******

● Q: how many proton pumps are involved in electron transfer from NADH? ○ A: 3 pumps (NADH dehydrogenase, Cytochrome b­c­1,  

Cytochrome oxidase)

● Q: how many proton pumps are involved in electron transfer from FADH2? ○ A: 2 pumps (Cytochrome b­c­1, Cytochrome oxidase)

● Q: similarities and differences between Ubiquinone (coenzyme Q) and 

Cytochrome c?

○ A: both are mobile electron carriers. Ubiquinone is an organic 

molecule, while  Cytochrome c is a protein. Ubiquinone carries electrons from I. 

and II. to III., while Cytochrome c carries electrons from  III to IV.

● Q: what is the role of succinate reductase (II) in the ETF, if it is not a proton 

pump?

○ A: II. is simply located near FADH2 in the intermembrane space, 

so it is convenient for FADH2 electrons to be transferred to Q from II

Racker and Stoeckenius Experiment

● Artificial vesicle made in lab

● Insert bacteriorhodopsin into vesicle membrane

○ light­driven H+ pump —> pumps protons from outside of vesicle 

to inside vesicle in the presence of light

● Insert ATP synthase into vesicle membrane

○ helps protons move from inside of vesicle to outside of vesicle, 

down the concentration gradient

● ADP and Pi added on the outside of vesicle

○ One sample in light (H+ pump activated): showed ATP was made

○ One sample in dark (H+ pump not activated): showed no ATP was 

made

● Result/conclusion: ATP synthase directly requires an H+ proton electrochemical  gradient to synthesize ATP

ATP Synthesis → second step of oxidative phosphorylation ● ATP synthase: enzyme embedded in inner membrane of mitochondria that  synthesizes ATP.

Process 

● ETC creates H+ electrochemical gradient across inner mitochondrial membrane ○ High concentration of H+ in intermembrane space

○ Low concentration of H+ in mitochondrial matrix

● Passive movement of H+ down gradient is an exergonic process

○ ATP synthase allows H+ to pass through lipid bilayer (usually 

impermeable to ions)

○ ATP synthase harnesses energy released as ions flow through 

membrane

Function 

● Free energy is used to synthesize ATP from ADP and iP

○ Energy conversion: energy from H+ gradient converted to 

chemical bond energy in ATP

○ Chemiosmosis: the movement or “push” of H+ ions down their 

gradient, resulting in ATP synthesis

Structure 

○ ATP synthase is a rotary machine

○ ATP synthase is made of a membrane ( F0) and matrix embedded (

F1) unit 

■ Membrane embedded unit:

● c subunits (9-12) → create proton  

channel ring

● a subunit (1) → connects c units to  

b units

● b subunits (2) → connect  

membrane embedded units to matrix embedded units

■ Matrix embedded unit:

● ε subunit (1) → binds to c subunits

● Ɣ subunit (1) → long central stalk.  

Connected to c subunits, and α/β ring. Rotates clockwise  

(when viewed from the inter membrane space) in 3 sets of  120 degrees to synthesize ATP. Causes β subunits to  

change conformation

● β subunits (3) → forms ring with 3 α

subunits. Each contains catalytic site where ATP is made.  

Changes conformation each time Ɣ subunit rotates 120  

degrees.

1. Conformation 1 → ADP  

and Pi bind with good affinity

2. Conformation 2 →  

Squishes to bind ADP and Pi tightly enough to make  

ATP

3. Conformation 3 → ATP  

binds weakly, ATP is released

● α subunits (3) → forms ring with 3 β

subunits

● ẟ subunit (1) → connects α/β ring to

two b subunits

Yoshida and Kinosita Experiment

● Examined the  ­ 3­ 3 protein complex of ATP synthase on a glass slide so the  Ɣ α β Ɣ subunit was pointing upward

● Attached large, fluorescent actin filament to   subunit so it could be seen with  Ɣ

fluorescent mic

● Added ATP to glass slide

○ (ATP synthase can work backwards to hydrolyze ATP)

○ Observed that   subunit was rotating counterclockwise Ɣ

● Result/conclusion:   subunit of ATP synthase rotates clockwise when  Ɣ synthesizing ATP

Regulating Aerobic Respiration

● It is important for our bodies to regulate aerobic respiration, so we don’t waste 

energy creating unneeded amounts of ATP.

● Rate of aerobic respiration is largely regulated by the availability of substrates 

and feedback inhibition 

○ Glycolysis: regulated by rate limiting enzyme 

phosphofructokinase 

■ Involved in the third step of glycolysis →  

the rate-limiting step

■ Levels of ATP, AMP, and citrate regulate 

activation/inhibition of phosphofructokinase

○ Pyruvate oxidation: regulated by rate limiting enzyme

pyruvate decarboxylase. 

■ Levels of NADH and ATP regulate 

activation/inhibition of pyruvate decarboxylase

■ Pyruvate dehydrogenase is also activated by its  

substrate, pyruvate, and inhibited by its product, acetyl CoA. 

○ Krebs Cycle: regulated by rate limiting enzyme isocitrate  

dehydrogenase. 

■ Levels of ATP and NADH regulate 

activation/inhibition of isocitrate dehydrogenase

○ Oxidative phosphorylation: regulated by availability of ETC 

substrates and rate limiting enzyme cytochrome oxidase (complex IV) ■ Levels of NADH and O2 regulate rate of ETC

■ ATP/ADP ratio regulate activation/inhibition of 

cytochrome oxidase

● High levels of ATP → ATP  

binds to IV and inhibits it, inhibiting oxidative phosphorylation ● High levels of ADP →  

stimulates IV, and provides more substrate to produce ATP,  stimulating oxidative phosphorylation

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