Ch. 11 - Catabolism Energy Release and Conservation

6 elements needed for survival

CHONPS

• carbon

• hydrogen

• oxygen

• nitrogen

• phosphorus

• sulfur

Energy source: Phototrophs vs. Chemotrophs

photo: use light as energy source

chemo: get energy from chem compounds

Electron source: Organotrophs vs. lithotrophs

organo: use organic compounds

litho: use reduced inorganic substances

Carbon source: Heterotrophs vs. Autotrophs

Hetero: use organic molecules

Auto: use single carbon molecule

What are most pathogens?

chemoorganotrophs

Primary producers

• photolithoautotroph

• chemolithoautotroph

Electron donors

• chemoogranotrophs

• chemolithotrophs

Chemoorganotrophs can do:

• fermentation

• aerobic respiration

• anaerobic respiration

Chemolithotrophs can do:

• aerobic respiration

• anaerobic respiration

Why is it harder for chemolithotrophs to make energy?

because they are at the bottom of the e- donor tower

T/F Chemolitho and chemoorgano tell you who the donor is, but not the acceptor

true

What is the final e- acceptor for aerobic respiration? anaerobic?

aerobic: oxygen

anaerobic: something other than oxygen

Chemoorganotroph alternative names

• chemoorganotrophs

• chemoheterotrophs

• chemoorganoheterotrophs

T/F the difference between respiration and fermentation has to do with the presence of oxygen

False; has to do with the use of ETC

Does respiration use the ETC? Fermentation?

respiration: uses ETC

fermentation: does not use ETC

Respiration pathway

1. energy goes through energy source and collects e-

2. e- is donated to NAD+ & FAD+ to make NADH and FADH2

3. those e- will then be donated to ETC

4. as e- go through the ETC, creates pmf which pumps protons out

5. high concentration of protons outside want to come back inside

6. Use ATP-sympae to allow protons back in

7. As protons come in, energy is harvest to phosphorylate ADP into ATP

T/F pmf and oxidative phosphorylation is unique to respiration

True because fermentation doesn’t use the ETC

Which gives more energy aerobic or anaerobic respiration?

aerobic bc oxygen is the final e-

Fermentation pathway

1. energy goes through energy source and collects e- to donate to NADH

   1. but no ETC for NADH to donate to

2. NADH usually donates to pyruvate

3. uses SLP to make ATP

3 energy sources

• breakdown of polysaccharides into monosaccharides

• breakdown of polypeptides into amino acids

• breakdown of phospholipids into glycerol and fatty acids

Breakdown of polysaccharides into monosaccharides process

1. makes glucose, glycolysis then breaks down glucose

2. breakdown of glucose from 6 carbon molecule to 3 carbon molecule releases energy in form of ATP through SLP

3. collects e- and NAD+ turns into NADH

4. for respiration: pyruvate turns to acetyl-CoA and loses a carbon

   1. also lose e- to make another NADH

5. go through TCA cycle (rotate twice per glucose) and fully oxidize whatever you started with

6. removed e- will go to ETC with help of NADH

Breakdown of polypeptides into amino acids pathway

• amino acids deaminated to lose amino group

  • pump amino group into glycolysis or TCA cycle depending on group

Breakdown of phospholipids into glycerol and fatty acids pathway

• glycerol is 3 carbon molecule → goes to glycolysis

• fatty acids go through beta oxidation

What is beta-oxidation?

removes 2 carbons at a time

3 main parts of aerobic respiration

• glycolysis

• TCA cycle

• ETC

What is the main job of glycolysis?

breakdown of glucose into pyruvate

What is the main job of the TCA cycle?

oxidize pyruvate into CO2

What is the main job of the ETC?

e- passes through series of redox reactions to release energy

Where is glycolysis in a prokaryote? Eukaryote?

cytoplasm for both

Where is the TCA cylce in a prokaryote? Eukaryote?

prokaryote: cytoplasm

eukaryote: mitochondria (matrix)

Where is the ETC in a prokaryote? Eukaryote?

prokaryote: cell membrane

eukaryote: mitochondria (matrix)

What are the products of glycolysis?

2 pyruvate for every 1 glucose

What are the products for the TCA cycle?

for every acetyl CoA molecule:

• 2 CO2

• 3 NADH

• 1 FADH2

• 1 ATP

for every glucose molecule:

• 4 CO2

• 6 NADH

• 2 FADH2

• 2 ATP

3 pathways for glucose to pyruvate

• Embden-Meyerhof pathway (EMP, glycolysis)

• Entner-Duodoroff pathway (ED)

• Pentose phosphate pathway (PPP)

Products of EMP

• 2 pyruvate

• 2 NADH

• 2 ATP

Products of ED

• 1 pyruvate

• 1 glyceraldehyde 3-P

• 1 ATP

• 1 NADH

• NADPH

Products of PPP

• 1 ATP

• 2 NADPH

• makes diff molecules that don’t have the usual 2,3, or 6 carbons

Can eukaryotes use ED pathway?

no only some bacteria

What intermediate does ED create?

KDO

Who uses PPP?

most organisms; but not usually archaea

T/F PPP happens at the same time as EMP or ED

true

T/F PPP is used to make building blocks for nucleotides

true; makes 5 carbon skeletons

All 3 pathways:

• convert glucose to glyceraldehyde 3P

• glyceraldehyde 3-P is oxidized to pyruvate the same way

2 phases of EMP (glycolysis)

• 6 carbon phase: uses ATP

• 3 carbon phase: makes ATP

6 carbon phase steps

1. glucose → glucose 6-P (uses ATP)

2. glucose 6-P → fructose 6-P (no ATP used)

3. use another ATP to add phosphate & end up with 6 carbons and 2 phosphates

4. cut in half to go to 3 carbon phase

3 carbon phase steps (identical for EMP, ED, and PPP)

1. 6 carbon cut in half into glyceraldehyde 3-P

2. glyceraldehyde 3-P oxidized (loses e-)

   1. reduces NAD+

3. intermediate donates 1 phosphate to ADP to make ATP (ex. of SLP)

   1. creates 3-phosphoglycerate

4. 3-phosphoglycerate modified into PPP (phosphoenolpyruvate)

5. PPP donates e- to ADP to make ATP and pyrvuate

Net gain of ATP in EMP

2 ATP

• uses 2 ATP

• makes 4 ATP

T/F 6 of 12-carbon skeletons come from glycolysis

true

• glucose 6-P

• fructose 6-P

• glyceraldehyde 3-P

• 3-phosphoglycerate

• PPP

• pyruvate

ED is used by?

gram negative soil bacteria; not eukaryotes

When does ED usually occur?

under aerobic conditions

ED steps

1. glucose → glucose 6-P

2. glucose 6-P gets oxidized (loses e-)

   1. creates NADPH (reducing power) and KDPG intermediate

3. KDPG (6 carbon molecule) gets cleaved

   1. produces 1 pyruvate and 1 glyceraldehyde 3-P

4. undergoes same 3 carbon phase as EMP

Net ATP gain for ED

1 ATP

What happens if ED uses group translocation?

end product will be glucose 6-P; don’t have to use ATP for first step (conserves some ATP)

PPP pathways

1. oxidize glucose 6P

   1. also makes NADPH

2. creates intermediate to be further oxidized

3. oxidize intermediate to lose carbon to make ribulose 5P

   1. also makes NADPH

4. modified into ribose 5P (12 C skeleton)

5. transaldolase modifies ribose 5P into glyceraldehyde 3P & 7 carbon molecule

6. another enzyme breaks it down into fructose 6P and erythrose 4P (E4P) (both 12 C skeletons)

7. diff enzymes can take the 4 and 5 carbon and break them down into 6 and 3 to make pyruvate

   1. also makes ATP and NADH but self feeds back into system

amphibolic pathway

can do both catabolism and anabolism

Which are amphibolic pathways?

EMP, TCA cycle, and PPP

T/F glycolysis happens in both respiration and fermentation

True; doesn’t depend on oxygen

TCA cycle steps

1. pyruvate loses 1 carbon and becomes acetyle-CoA (5 carbon)

   1. donated e- goes to NAD making NADH

   2. PDH helps this process

      1. removes carbon and adds thioester bond and coenzyme A

         1. this bond and enzyme are what moves TCA cycle in first half

2. break thioester bond to make citrate (6 carbons)

3. At end of 6 carbon stage, lose another carbon and CO2 released

   1. NAD+ accepts e- to make NADH

   2. becomes alpha-ketoglutarate (5 carbon)

      1. intermediate in adding amino groups to 12 carbon skeletons to make amino acids and nitrogenous bases

4. remove carbon from pyruvate to create succinyl CoA (4 carbon)

   1. thioester bond restored

5. succinyl CoA powers 2nd half of cycle

6. break thioester bond, there will be SLP

   1. becomes succinate

7. oxidations and reductions to go back to acetyl acetate (whole process will start again)

What is acetyl CoA needed to make?

fatty acids for lipids

What is the goal of the TCA cycle?

to fully oxidize the energy source

What are the products of the TCA cycle?

• 3 CO2

• 4 NADH

• 1 FADH

• 1 ATP

ETC pathway

complex 1 → CoQ → complex 3 → cytochrome C → complex 4

Complex 2 pathway

e- from succinate or FADH → complex 2 → CoQ → complex 3 → cytochrome C → complex 4

Coupling site

movement of protons

Which complexes are coupling sites?

1, 3, and 4

Why is complex 2 not a coupling site?

bc its not pumping protons

What is the only place in the mitochondria that can go in reverse?

• CoQ; if it can’t donate to the next complex, then goes back to complex 1

• NAD+ becomes NADH and causes ROS

Why do protons go back inside matrix after being pumped out?

• once pumped into IMS, higher concentration than matrix

  • IMS more acidic bc of protons

  • go back inside matrix with help of complex 5 (ATP synthase)

    • as ATP synthase rotates, make ATP from ADP and inorganic phosphate

Lipase

enzyme that breaks down lipids into glycerol and fatty acids

beta oxidation

remove 2 carbons at a time

Beta oxidation of fatty acids creates what?

Acetyle CoA

Prokaryotic vs. Eukaryotic ETC: location

prokaryotic: cell membrane

eukaryotic: IMM

Prokaryotic vs. Eukaryotic ETC: pathways

prokaryotic: can be branched

eukaryotic: linear

Prokaryotic vs. Eukaryotic ETC: length

prokaryotic: can be shorter

eukaryotic: longer

Prokaryotic vs. Eukaryotic ETC: P/O ratio

prokaryotic: lower P/O ratio (how much proton needed per ATP)

eukaryotic: higher P/O ratio

T/F a higher P/O ratio is better

true

T/F you want the ETC to be longer

True; bc being longer allows more protons to pumped out (more coupling sites), which means more energy

Where does CoQ go in E. Coli ETC when oxygen concentration is low? How many H does it pump out?

bd branch; 2H

Where does CoQ go in E. Coli ETC when oxygen concentration is high? How many H does it pump out?

bo branch; 4H

Does the bd branch produces enough H to make ATP? bo branch?

bd: no

bo: yes

What makes something a strict anaerobe?

lack of sod and catalase

Can E.Coli do fermentation? Can Paracoccus denitrificans do fermentation?

E. Coli: yes

Paracoccus denitrificans: no

What can Paracoccus denitrificans grow in besides oxygen?

methanol

Paracoccus denitrificans methanol growing pathway?

donate to cytrochrome C → donates to another complex

How many coupling sites does Paracoccus denitrificans ETC have when growing in methanol?

1 instead of usual 3

Two parts of ATP synthesis

F0 & F1

F0

in membrane; proton conducting channel

F1

complex that catalyzes ATP synthesis

How does F1 catalyze ATP synthesis?

• comes close to pos charge amino acid; towards it

• comes close to neg charge amino acid; pulls away from it

• as pushes and pulls diff rings, rotates to put inorganic phosphate with ADP to make ATP

T/F F1 is the oxidative part of oxidative phosphorylation

False; is phosphorylation part

Theoretical maximum ATP yield during aerobic respiration

32 ATP

T/F the actual ATP yield is never as high as the theoretical yield

True

Eukaryotic max ATP yield? Why?

30; because pyruvate has to move from cytoplasm to matrix for TCA (has to go across 2 membranes)

Why do prokaryotes not reach the theoretical yield?

because they have a shorter ETC and lower P/O ratio

Glycolysis yields how many ATPs? Net gain?

4; 2

How many NADH are made in glycolysis? Where do they go?

2; go to ETC

Pyruvate and acetyl CoA make what products? Where do they go?

2 NADH to ETC

TCA cycle products per glucose? per 1 Acetyl-CoA?

glucose:

• 6 NADH

• 2 FADH

• 2 ATP

Acetyl CoA

• 3 NADH

• 1 FADH

• 1 ATP

T/F anaerobic respiration is done by all 3 domains

true

Generalized bacterial ETC pathway for anaerobic respiration

e- donor → dehydrogenase → quinone → branches depending on whats available