Ch. 11: Catabolism Energy Release and Conservation

what requirement is often satisifed together in organic compounds?

C, H, and O

metabolic flexibility

ability to switch between different energy sources

• depends on environment (pH, temperature, osmolarity)

what are the two types of energy sources

phototrophs

chemotrophs

phototrophs use

light

chemotrophs use

[energy from oxidation of] chemical compounds

what are the two types of electron sources

organotrophs

lithotrophs

organotrophs

organic compounds

lithotrophs

reduced inorganic substances

what are the two types of carbon sources

heterotrophs

autotrophs

heterotrophs

organic molecules

autotrophs

single carbon molecule (CO2)

photolithoautotroph

energy source: light

electron source: inorganic e- donor

carbon source: CO2

ex: purple and green sulfur bacteria, cyanobacteria, diatoms

photoorganoheterotroph

energy source: light

electron source: organic e- donor

carbon source: organic carbon

ex: purple and green nonsulfur bacteria

chemolithoautroph

energy source: inorganic chemicals

electron source: inorganic e- donor

carbon source: CO2

ex: sulfur-oxidizing bacteria, hydrogen-oxizidizing bacteria, methanogens, nitrifying bacteria, iron-oxidizing bacteria

chemolithoheterotroph

energy source: inorganic chemicals

electron source: inorganic e- donor

carbon source: organic carbon

some sulfur-oxidizing bacteria (Beggiatoa spp.)

chemoorganoheterotroph

energy source: organic chemicals, often same as C source

electron source: organic e- donor, often same as C source

carbon source: organic carbon

ex: most nonphotosynthetic microbes, including most pathogens, fungi, and many protists and archaea

majority of microorganisms known are

• photolithoautotrophs/photoautotrophs

• chemolithoautotrophs

• chemoorganoheterotrophs / chemoheterotrophs / chemoorganotrophs

these 3 are primary producers that produce what other organisms use

what nutritional type is the majority of pathogens

• chemoorganoheterotrophs / chemoheterotrophs / chemoorganotrophs

• simple organic nutrient can satisfy all 3 requirements

some organisms can change categories of nutritional types depending on…

environment

what are the same basic needs all organisms have

1. ATP as an energy source

2. reducing power to supply e- for chemical rxns

3. precursor metabolites for biosynthesis

chemoorganotrophs can do…

• fermentation

• aerobic respiration

• anaerobic respiration

chemolithotrophs can only do…

• aerobic respiration

• anaerobic respiration

lack donor (NADH) and acceptor (organic molecule) for fermentation

how does chemoorganoheterotrophs etc,. get energy?

oxidizing organic compounds

*** chemotrophs: energy from oxidation of chemical compounds

(they lose e-

resp - which go to ETC and powers ATP synthesis via OP)

chemoorganoheterotrophs etc., release…

energy (catabolism), provides carbon and e- for anabolism

chemoorganotrophic fueling processes include

• aerobic respiration

• anaerobic respiration

• fermentation

oxidized organic energy source releases ____ which are accepted by ____

1. electrons

2. NADH/FADH2

if electrons are donated to ETC, what is it?

respiration

if electrons are donated to endogenous acceptor, what is it?

fermentation

respiration involves the use of…

an ETC

what is generated in respiration?

pmf

what are the 2 types of respiration

aerobic respiration

anaerobic respiration

what is the final e- acceptor in aerobic respiration

oxygen

what is the final e- acceptor in anaerobic respiration

exogenous acceptors like

• NO3-, SO42-, CO2, Fe3+, SeO42-

what type of respiration is oxidative phosphorylation?

aerobic respiration

what does OP use to produce ATP?

pmf

what type of e- acceptor does fermentation use?

endogenous

ex: pyruvate

unlike respiration, fermentation does not involve the use of…

ETC

unlike respiration, fermentation does not generate

pmf

is there oxidative phosphorylation in fermentation?

No

what does fermentation use instead of OP to generate ATP?

SLP

most pathways generate…

glucose or intermediates

• must still synthesize glycolytic intermediates

aerobic respiration starts with…

glucose oxidation

aerobic respiration produces…

ATP and high energy electron carriers

what are the 3 steps to completely catabolize an organic energy source to CO2?

1. glycolytic pathways (glycolysis)

2. tri-carboxylic acid (TCA) cycle

3. electron transport chain (ETC)

glycolysis location

cytoplasm in eukaryotes and prokaryotes

TCA cycle location

eukaryotes: mitochondrial matrix

prokaryotes: cytoplasm

ETC location

eukaryotes: inner mitochondrial membrane

prokaryotes: plasma membrane

1. glycolytic pathways (glycolysis)

glucose breaks down to produce pyruvate

• 3 pathways in microbes

• in the prokaryotic cytoplasm

2. tri-carboxylic acid (TCA) cycle

pyruvate is completely oxidized to CO2

• in the prokaryotic cytoplasm

3. electron transport chain (ETC)

oxygen is the final e- acceptor

associated with OP

• in the eukaryotic inner plasma membrane

what are the 6 carbon skeletons in EMP?

1. Glucose-6-phosphate

2. Fructose-6-phosphate

3. Glyceraldehyde-3-phosphate

4. 3-phosphoglycerate

5. Phosphoenolpyruvate (PEP)

6. Pyruvate

what are the 2 carbon skeletons in PPP?

1. Erythrose-4-phosphate (E4P)

2. Ribose-5-phosphate

what are the 4 carbon skeletons in TCA?

1. Acetyl CoA

2. Alpha-ketoglutarate

3. Succinyl CoA

4. Oxaloacetate

What is the main role of central metabolic pathways?

To provide the precursor metabolites for all other pathways.

what are the 3 common routes from glucose to pyruvate

• Embden-Meyerhof pathway (EMP)

• Entner-Doudoroff pathway (ED)

• Pentose phosphate pathway (PPP)

What is another name for the Embden-Meyerhof pathway?

Glycolysis (EMP is the main glycolytic pathway)

what do all 3 pathways (EMP, ED, PPP) do?

convert glucose to glyceraldehyde 3-P

What happens to glyceraldehyde 3-phosphate (G3P) in all three pathways (EMP, ED, PPP)?

It is oxidized to pyruvate in the same way

What is another name for glyceraldehyde 3-phosphate?

Phosphoglyceraldehyde (PGALD)

what is the most common pathway for glucose degradation to pyruvate?

Embden-Meyerhof Pathway (EMP)

EMP can function in the presence or absence of…

O2

Is there oxidative phosphorylation in EMP?

No, but there is some SLP

what are the two phases in EMP?

6 carbon phase

3 carbon phase

what occurs in 6 carbon phase?

• ATP is used

• rearranges glucose and adds phosphate to turn glucose 6-phosphate into fructose 6-phosphate

• glucose (6C)

  ↓ ATP used

• glucose 6-phosphate

• fructose 6-phosphate

  ↓ ATP used

• fructose 1,6-bisphosphate (6C)

what occurs in 3 carbon phase?

• ATP is made

• fructose 1,6-bisphosphate split into two glyceraldehyde 3-phosphate

• Glyceraldehyde 3-phosphate (G3P) (3C)
  ↓ oxidation + phosphorylation
  (NAD⁺ is reduced to NADH, Pi added)

• 1,3-BPG
  ↓ SLP: ADP → ATP (+1)

• 3-phosphoglycerate (3PG)

  ↓

  ↓

• phosphoenolpyruvate

  ↓ generates ATP (+1)

• pyruvate (3C)

  • pyruvate will get used in TCA

what does the oxidation step in EMP generate?

NAD+ → NADH (reducing power)

when does the oxidation step in EMP occur?

when G3P is oxidized and phosphorylated

what can NADH synthesize via OP?

ATP

net gain per 1 glucose molecule in EMP?

2 ATP, 2 NADH, 2 pyruvate

(produces 4 ATP total, but the 6 C phase uses 2)

what uses Entner-Doudoroff Pathway (ED)?

gram-negative soil bacteria

• E. coli and Enterococcus faecalis

NO eukaryotes

is ED under anaerobic or aerobic conditions?

mostly aerobic

what does ED pathway replace?

first phase of the EMP

what does the first phase of ED yield?

pyruvate and glyceraldehyde 3-phosphate

what is produced instead of NADH in the first (oxidative) phase of ED

NADPH

• glucose 6-phosphate
  ↓ NADP⁺ → NADPH + H⁺

• 6-phosphogluconate

what does 2-keto-3-deoxy-6-phosphogluconate (KDPG) generate in the first phase of ED

pyruvate and glyceraldehyde 3-phosphate

further catabolism of G3P in ED is done by…

enzymes of the EMP

(same pathway as 3 C phase)

what is unique to ED pathway?

2-keto-3-deoxy-6-phosphogluconate (KDPG)

net yield per glucose of ED pathway

• 1 ATP

• 1 NADH

• 1 NADPH

• 2 pyruvate

what is another name for the pentose phosphate pathway (PPP)

hexose monophosphate pathway

what is produced when glucose-6P is oxidized in PPP pathway

ribulose-5P + CO2

does PPP require oxygen to function?

no - it is aerobic and anaerobic — working simultaneously with ED or EMP

why can PPP work with ED or EMP

all 3 pathways start with glucose-6-phosphate (G6P), it can be diverted to EMP/ED if needed, intermediates of PPP can re-enter EMP, it can contribute to ED when G3P goes through EMP steps

— which can be given to PPP for NADPH and biosynthesis

where is PPP not found

archaea, though it can be found in most prokaryotes

• because archaea are extremophiles and have different needs

what is PPP needed for

biosynthesis (anabolism) and catabolism

…

EMP and ED: catabolism

TCA: amphibolic

what is PPP a major source of

NADPH

PPP intermediates generate

ATP via SLP

PPP is degraded by EMP enzymes to generate

pyruvate

• glyceraldehyde-3-P → pyruvate

  • via EMP enzymes (3 C phase)

what do PPP intermediates regenerate by gluconeogenesis

glucose-6P

• G3P and fructose-6P can run in reverse via gluconeogenesis to form G6P

• G6P can reenter PPP to continue the cycle

  • important when cell needs more NADPH or ribose than ATP

net yield per glucose of PPP

2 NADPH

1 CO2

** no NADH

what is an amphibolic pathway

both an anabolic and catabolic process (forward and backwards)

how does an amphibolic pathway pick whether it is anabolic or catabolic

levels of ATP, PEP, and F6P

what pathways are involved in amphibolic pathways

• EMP/gluconeogenesis

• TCA cycle

• PPP

what is the link reaction

connection between EMP and TCA

what is tricarboxylic acid cycle (TCA) also known as

citric acid cycle/krebs cycle

what is TCA common in

aerobic bacteria, free-living protozoa, most algae, and fungi

TCA is a source of carbon skeletons for use in…

biosynthesis

where does TCA occur in eukaryotes

mitochondrial matrix

where does TCA occur in prokaryotes

cytoplasm

how is acetyl-coa made in TCA

pryuvate dehydrogenase complex (PDH) oxidizes and cleaves pyruvate

**yields 2 NADH, 2 acetyl-coa — per 1 glucose

• 1 NADH, 1 acetyl-coa — per 1 pyruvate

• 1 glucose = 2 pyruvate

pyruvate (3C)

↓ loss of 1C and e-

acetyl-CoA (2C)

hydrolysis of _____ yields a lot of energy in TCA

thioester bond of acetyl-CoA