CH 11: Micro Exam 3

photo litho autotroph: energy source, electron source, carbon source

energy: light

electron: inorganic compounds

carbon: carbon dioxide, CO2

** also known as photoautotrophs, primary producer

can bacteria and archaea oxidize hydrogen

yes, several do, they reduce NAD+ or donate the e- directly to ETC

nitrifying bacteria

• found in soil and water

• nitrification

• oxidiation ammonia NH3 → nitrate NO3-

• two step process from two different or one microbe

lipid catabolism

triglycerides hydrolyzed by lipases into glycerol and fatty acids

• glycerol: degraded via glycolytic pathway as dihydroxyacetone phosphate → glyceraldehyde-3P

• fatty acids: oxidized via β-oxidation pathway and shortened by 2 C → acetyl CoA

protein catabolism

proteases hydrolyze proteins into amino acids (proteolysis)

amino acid catabolism

• deamination followed by transamination

• organic acids → pyruvate, acetyl CoA, TCA cycle intermediate

catabolism of carbohydrates

• carbohydrates: can be supplied external or internal

• monosaccharides

• disaccharides or polysaccharides: hydrolases (outside) and phosphorylases (inside)

3 things that work w/o ETC

1. fermentation: end products efflux

2. facultative anaerobes: pmf redox-loop mechanisms

3. strictly fermentative conditions: F₁F₀-ATP synthase operates reversibly

dissimilatory nitrate reduction or denitrification

• under anoxic conditions by P. denitrificans, Pseudomonas, Bacillus

• NO3- → NO2- → NO → N2O → N2

Paracoccus denitrificans

gram neg, facultative anaerobic soil bacteria, non-fermenting

anaerobic respiration

• final e- acceptor not O2

• less energy yield because of acceptor and a shorter ETC

• all three domains

• e- acceptors oxidized but once they gain an e- they become reduced

aerobic respiration in E. coli ETC chain

e- donor →

dehydrogenase →

quinone →

cytochrome bo oxidase → high O2

or

cytochrome bd oxidase → low O2

** eggs done quick can high bo or low bd

anaerobic respiration in E. coli ETC chain

e- donor →

dehydrogenase →

quinone →

fumarate reductase → fumarate → succinate

or

nitrate reductase → NO3- → NO2- → NH4+

** eggs done quick further reduce fumes stink or not reduce

can maximum ATP yield be calculated

yes and this also includes P/O ratios of NADH (2.5) and FADH2 (1.5)

neumonic for TCA intermediate

Can- Citrate

I- Isocitrate

Keep- ⍺-Ketogluturate

Selling- succinyl CoA

Substances- succinate

For- fumurate

Money- malate

Officer- oxaloacetate

theoretical maximum total yield of ATP

• aerobic: 32 ATP

• max in eukaryotes: 30 ATP

• there is less in prokaryotes due to a shorter ETC and lower P/O ratio

F₁F₀ATP synthase

• mitochondria, bacteria and chloroplast

• can catalyze ATP hydrolysis

• pmf drives ATP synthesis using this synthase

• F₀: proton conducting channel

• F₁: complex that catalyzes ATP synthesis

ΔE’_° between NADH and O2

1.14 Volts

ETC

• makes most ATP as NADH and FADH2 reoxidized

• uses series of e- carriers from more neg reduction potential to more pos

tricarboxylic acid cycle, TCA

• citric acid cycle, krebs cycle

• common in aerobic bacteria, free-living protozoa, most algae, most fungi

• source of carbon skeletons for biosynthesis

TCA cycle overview

1. pyruvate → CO2, NADH, Acetyl-CoA (precursor metabolite)

2. 2 C of Acetyl-CoA combined 4 C of oxaloacetate → 6 C citrate

3. rearrangement to isocitric acid

4. oxidative decarboxylation (also step 1) removes C → CO2, NADH, ⍺-ketoglutarate (precursor metabolite)

5. last C released, same as 4, → CO2, NADH, succinyl-CoA (precursor metabolite)

6. CoA cleaved from succinyl-CoA, energy released → GTP (make ATP or translation)

7. succinate oxidized → fumarate

8. fumarate + H2O → malate

9. malate oxidized → NADH, regenerate oxaloacetate (precursor metabolite)

hydrolysis of thioester Acetyl-CoA bond in TCA

yields lots of energy, also same w/ succinyl-CoA

what oxidizes and cleaves pyruvate in step one of TCA

PDH- pyruvate dehydrogenase complex

entner-doudoroff pathway, ED

• gram neg soil bacteria, some gram pos

• many aerobic

• E. coli and Enterococcus faecalis

• not used by eukaryotes

• replaces 6 C phase of EMP

ED pathway overview

glucose → glucose 6-p → 6-phosphogluconate → KDPG (2-keto-3-deoxy-6-phosphogluconate) → pyruvate and glyceraldehyde 3-p

glyceraldehyde 3-p futher catabolised by EMP

pentose phosphate pathway, PPP

• oxidizes glucose 6-p → ribulose-5p + CO2, and is major NADPH source

• not O dependent

• works alongside ED or EMP

• not in archaea

• needed biosynthesis and catabolism

• produces: E4P, ribose-5-p and intermediates can be used for ATP

PPP overview 3 steps

1. glucose 6-p (from EMP) oxidized → 6-phosphogluconate + NADPH

2. 6-phosphogluconate oxidized and decarboxylated → CO2 +NADPH

3. sugar transformation rxns catalyzed by enzymes transaldolase and transketolase → regeneration glucose 6-p, biosynthesis, or catabolized to pyruvate

PPP overview rxn

3 glucose 6-p + 6 NADP⁺ + 3 H2O → 2 fructose 6-p + glyceraldehyde 3-p + 3 CO2 + 6 NADPH + 6 H⁺

PPP intermediates

• degraded to pyruvate by EMP enzymes

• regenerate glucose-6p by gluconeogenesis

PPP other name

hexose monophosphate pathway

embden-meyerhof pathway, EMP

• most common pathway for glucose degradation to pyruvate

• provides precursor metabolites NADH and ATP

• presence or absence of O2

• two phases: 6 C phase (uses ATP), and 3 C phase (makes ATP)

EMP pathway overview

6 C: glucose → glucose 6-p → fructose 6-p → fructose 1,6-bis-p

3 C: DHAP splits into → 2 glyceraldehyde 3-p → 1,3-bis-p-glycerate

SLP: → 3-p-glycerate → 2-p-glycerate → p-enolpyruvate → 2 pyruvate, 2 ATP, 2 NADH

EMP, ED, PPP all …

convert glucose to glyeraldehyde 3-p which is oxidized to pyruvate the same way in all 3

aerobic respiration CO2

completely catabolize an organic energy source to CO2 through

1. glycolytic pathways, produce pyruvate, NADH, FADH2

2. TCA cycle, pyruvate oxidized CO2, GTP, NADH, FADH2

3. ETC, O is final acceptor

and produce ATP and high energy e- carriers

energy sources

most pathways generate glucose or intermediates, and glycolytic intermediates must be synthesized

ex. TCA cycle

fermentation

• partial oxidation organic compounds or energy source

• endogenous e- acceptor like pyruvate or derivative

• oxidation of NADH produced by glycolysis and NADH is converted back to NAD+

• no ETC, no PMF, no OP, no need for O2

• uses SLP- substrate level phosphorylation to form ATP

respiration

etc to external e- acceptor; pmf fuels oxidative phosphorylation

chemoorganotroph fueling process

oxidized organic energy source releases e- that are accepted by NADH/ FADH2

chemo litho troph respiration type

aerobic and anaerobic, no fermentation bc there is no organic molecule to oxidize

chemolithotrophy electron donors and acceptors

donors: H2, H2S, Fe²⁺, NH4+, etc.

acceptors: S⁰, SO4^2-, NO3-, O2

chemoorganotrophy electron donors and acceptors

donors: organics

acceptors: S⁰, SO4^2-, NO3-, O2, organics

3 basic needs of organisms

1. ATP as energy

2. reducing power for e- for chem rxns

3. precursor metabolites for biosynthesis

can organisms change major nutritional categories

yes, depending on environment

phototrophs

use light as energy source

chemotrophs

use oxidation of chemical compounds as energy source

organotrophs

use organic compounds as electron source

lithotrophs

use reduced inorganic substances as electron source

heterotrophs

use organic molecules as carbon source and are often same as energy source

autotrophs

use CO2 molecules as carbon source

photo organo heterotroph: energy source, electron source, carbon source

energy: light

electron: organic compounds

carbon: organic compounds

chemo litho autotroph: energy source, electron source, carbon source

energy: inorganic compounds; H2, reduced N, reduced S, Fe2+ directly donated to ETC

electron: inorganic compounds; oxygen, sulfate, nitrate

carbon: carbon dioxide, CO2 fixation pathways

** oldest microbes, primary producer, also called chemo litho trophs

chemo litho heterotroph: energy source, electron source, carbon source

energy: inorganic compounds

electron: inorganic compounds

carbon: organic carbon

chemo organo heterotroph: energy source, electron source, carbon source

energy: organic compounds, oxidized

electron: organic compounds

carbon: organic carbon

** catabolism, anabolism

another term for chemo organo heterotrophs

chemo organo trophs, chemo heterotrophs

what includes majority of human pathogenic microbes

chemo organo trophs

for which nutritional type class can a single organic nutrient satisfy all three requirements

chemo organo heterotrophs

reducing power

molecules that serve as a supply of electrons for chemical reactions; NADPH and NADH

can chemo organo trophs perform both fermentation and respiration

yes, they also perform aerobic and anaerobic respiration

respiration: e- donated to etc

fermentation: e- donated to endogenous acceptor

can chemo organo trophs perform metabolic processes that include endogenous electron acceptors

yes

fermentation involve endogenous or exogenous electron acceptor

endogenous electron acceptor

does respiration utilizes ETC

yes

during aerobic respiration is glucose fully catabolized and oxidized

yes

products of aerobic respiration

ATP and CO2

true or false: aerobic respiration involves formation of pmf which fuels generation of ATP through OP

true

does EMP function only in the presence of O2

no, also in the absence

where is EMP found

in all domains of life

is CO2 an EMP product

no

how does the step from 1,3-bisphosphoglycerate to 3-phosphoglycerate produce ATP

via SLP

is ED pathway oxidative or reductive

oxidative

does ED pathway generate less or more ATP than EMP per one glucose

less ATP

does ED pathway synthesize both NADPH and NADH

yes

true or false: ED pathway involves a key intermediate KDPG that is cleaved into pyruvate and glyceraldehyde 3-phosphate

true

what part of ED pathway is SLP involved in

G3P’s conversion to pyruvate

products of PPP

ribose 5-P

erythrose 4-P

NADPH

CO2

do EMP, PPP, and ED all involve glucose 6-phosphate and produce precursor metabolites and reducing power

yes

do EMP or ED occur at the same time as PPP

yes

can PPP’s intermediates be fed into glycolysis

yes

amphibolic pathways

• include metabolic pathways that function both catabolically and anabolically

• include EMP/ gluconeogenesis, TCA, PPP

what can determine which direction the amphibolic pathway proceeds

regulation of pacemaker enzymes such as PFK glycolysis

where does the TCA cycle occur in bacteria

cytoplasm

does the TCA cycle produce NADH and precursor metabolites

yes

does TCA cycle involve hydrolysis of thioester bonds

yes

another term for TCA cycle

krebs

does the PDH complex involve oxidative decarboxylation

yes

what does the PDH complex use to generate CO2

NAD+

what does the PDH complex use to generate acetyl-CoA

pyruvate

flavoproteins

Contains prosthetic group flavin and can carry 2 electrons & 2 protons

cytochrome c

Have iron bound to heme and carries 1 electron

coupling sites

complex I, III, IV

mitochondrial ETC

overview

bacterial and archaeal ETC

overview

prokaryotic vs eukaryotic ETCs

differ in location, e- carriers, branching, length, P/O ratio

complex I name

NADH-ubiquinone oxidoreductase

complex II name

succinate dehydrogenase

complex III name

ubiquinol-cytochrome c oxidoreductase

complex IV name

cytochrome c oxidase

what connects complex I and III and II and III

CoQ

what connects complex III and IV

Cyt c

what does complex IV facilitate

formation of water, and transfers e- to O2

true or false: As the electrons move through the ETC, Ca2+ ions are transported across the IMM

false, H+ ions