Metabolism:



Chapter 6 Metabolism: Fueling Cell Growth

 

Fundamental Tasks for Growth

♣         Method of ______________  ______________ to invest in

♣         Biosynthetic processes

♣         Transporting nutrients / other molecules

♣         Continual ___________________ of new cell components

♣         Cell walls, membranes, ribosomes, nucleic acids, other

♣         Replacing worn or damaged components

♣         Accumulating enough components so that cell can divide

(growth = increase in cell number)

 

Principles of Metabolism

♣         ______________ is coupled to ______________

♣         Energy from breakdown of molecules is invested into buildup of new molecules

♣         ______________ reactions are coupled to ______________ reactions

 

Energy

♣         ______________ energy – stored energy

♣         Stored due to position (rock on a hill, water behind a dam)

♣         Stored due to chemical bonds

♣         ______________ energy – energy of motion

♣         Potential energy ______________ to kinetic

♣         But some is lost as ______________

♣    (random energy = entropy)

♣         Kinetic energy ______________ to potential

♣         Again, some is lost as ______________

♣         Lost energy must be replaced

 

 

 

 

 

Methods of Acquiring Energy

♣         Phototrophs

♣         Harvest energy in __________________

♣         Power synthesis of organic molecules

♣   e.g. glucose

♣         Chemoorganotrophs

♣         Harvest energy from __________________ molecules

♣   Depend on __________________ to synthesize high energy organic molecules

 

Free Energy

♣         __________________ energy released when bonds are broken

♣         Does not include heat

♣         __________________ reactions

♣         If more free energy in reactants

♣         __________________ reactions

♣         If more free energy in products

♣         Multiple ___________ allows slow release of free energy

♣         Less is lost as heat

♣         “Metabolic pathways”

 

Metabolic __________________

♣         Ordered sequence of steps resulting in an end-product

♣         Starts with reactants

♣         Continues with series of __________________

♣   May be in dissociated form (e.g. pyruvate)

♣   May be in undissociated form (e.g. pyruvic acid)

♣         Ends with __________________  __________________

♣         Pathway may be _________________, _________________, or _______________

 

 

 

 

Key Components of Metabolic Pathways

♣         Enzymes

♣         ATP

♣         Energy sources

♣         Redox reactions

♣         Electron carriers

♣         Precursor metabolites

Enzymes

♣         Enzymes ______________ on substrates

♣         Turn substrates into products

♣         Facilitate reactions – “__________________”

♣         Do not participate directly in reaction

♣         Without enzymes, some catabolic reactions would go very slowly

♣         Enzymes speed up reaction

♣         Enzymes lower the __________________ of __________________

♣         Even exergonic reactions

 

ATP Couples Energy Production with Energy Investment

♣         ________ donates energy to reactions

♣         Cycles to ___________

♣         ADP accepts energy

♣         Cycles to ATP

♣         ADP + Pi

♣         Cell constantly recycles ATP

 

Phosphorylation

♣         Ways to add Pi to ADP

♣         __________________ -level phosphorylation

♣         __________________ / proton motive force

♣   __________________ phosphorylation

Using redox reactions

♣   _______________phosphorylation

♣         Photoautotrophs only

♣         Sources of energy for phosphorylation

♣         All require __________________ reactions

♣         Transfer 1 or more electrons from one substance to another

♣         Prokaryotes very versatile

♣   e.g. Glucose

♣   e.g. Ammonia

 

Redox Reactions

♣         When substance is __________________

♣         Loses an electron

♣         When substance is __________________

♣         Gains an electron

♣         Where electrons go, protons __________________

♣         Lose e- & H+ = lose H atom = oxidation = dehydrogenation

♣         Gain e- & H+ = gain H atom = reduction = hydrogenation

♣         If e- removed to e- carrier

♣         H+ may go, too

♣         H+ may go into aqueous solution

♣         Often ignore the H+ when writing biological reactions, but it’s there!

 

e- Carriers that Diffuse Easily

♣         NAD+ reduces to __________________

♣         FAD+ reduces to __________________

♣         NADP+ reduces to NADPH

♣         (reduced = becomes less positive)

♣         Reduced form has __________________  __________________

♣         NADH & FADH2 reduce other carriers

♣         Drives proton motive force

♣         Proton motive force drives ATP production

♣         NADPH reduces molecules in __________________

Precursor Metabolites

♣         __________________ in catabolic reactions

♣         Link catabolic reactions to __________________ reactions

♣         Some are broken down further

♣         Some are siphoned off for anabolic rxns.

♣         e.g. pyruvate

♣   Oxidized further

♣   Convert to alanine

Use of Precursor Metabolites by E. coli

 

Central Metabolic Pathways

♣         3 key pathways to gradually oxidize glucose

♣         __________________

♣         “Embden-Meyerhoff pathway”

♣         “Glycolytic pathway”

♣         __________________  __________________ pathway

♣         ________ cycle

♣         “Tricarboxylic acid cycle”

♣         “Krebs cycle”

♣         “Citric Acid cycle”

Central Metabolic Pathways

♣         Glycolysis

♣         Most __________________ to initiate sugar breakdown

♣         End products are ATP & NADH & pyruvate

♣         __________________ into Krebs TCA cycle

♣         Pentose Phosphate pathway

♣         Alternative pathway to make pyruvate

♣         Operates in conjunction with glycolysis

♣         __________________ feeds into TCA cycle

♣         Usually feeds into biosynthesis pathways

♣         [Entner-Douderoff pathway]

♣         Add’l alternative to glycolysis

♣         Some bacteria

♣         Less ATP

Fate of Pyruvate

♣         __________________ to TCA cycle from glycolysis, Entner-Douderoff, or Pentose Phosphate

♣         Pyruvate ⋄ Acetate + CO2

♣         3C ⋄ 2C + C

♣         __________________ CoA enters __________________ cycle

♣         2 pyruvates for each glucose that started

 

Respiration

♣         Uses reducing power of __________________ and __________________ produced in glycolysis and transition step

♣         Powers __________________ phosphorylation

♣         Electrons from NADH and FADH2 enter e- transport

♣         ________ pumped to other side of membrane

♣         Produces proton __________________

♣         Drives proton motive force

♣         Terminal e- acceptor _________   ______ O2 or other

 

Catabolic Processes of Chemoorganoheterotrophs

♣         __________________ respiration – ___________ ATP

♣         __________________ respiration – ___________ ATP

♣         __________________– _____________ ATP

 

Energy Yields

♣         Energy yields theoretical, as __________________ may be siphoned off to biosynthesis

♣         Calculated approximately with a theoretical __________________

♣         __________________ -level phosphorylation slow

♣         Little ATP produced

♣         __________________ phosphorylation fast

♣         Much ATP produced

Energy Yields in Glycolysis

♣         Glucose (6C) + 2 NAD+ + 2 ADP + 2 Pi

♣         ⋄ 2 pyruvate (3C) + 2 NADH + 2 H+ 2 ATP (net gain)

♣         Also produces precursor molecules (used by E. coli)

 

Yields from Glycolysis

♣         Energy expended ---  ______ ATP per glucose

♣         Energy harvested ---  ______ ATP

♣         Net gain -------------   ______ ATP

♣         Reducing power ----- ______ NADH

♣         __________________ metabolites (reduce energy yield) --- ______ (based on E. coli) plus pyruvate

♣         ATP produced by ------- __________________ level __________________

 

Yields from Pentose Phosphate Pathway

♣         Energy yield ---- __________________ amts ATP

♣         Reducing power ---- __________________ amts NADH

♣         Precursor metabolites --- ______ plus pyruvate

♣         Most of the products of the Pentose Phosphate Pathway are used as precursors in biosynthesis

♣         ATP produced by ------- __________________ level __________________

 

Yields of the Transition Step and TCA Cycle

♣         Transition step (yield per glucose)

♣         Reducing power --- ______ NADH 

♣         Precursor metabolites --- ______ Acetyl CoA

♣         TCA Cycle (yield per glucose)

♣         Energy yield --- ______ ATP

♣   GTP in step 5 converts to ATP

♣         Reducing power --- ______ NADH + ______ FADH2

♣         Precursor metabolites --- ______ (based on E. coli)

♣         ATP produced by __________________ level __________________

 

Electron Carriers in the Plasma Membrane

♣         Electron carriers embedded in the __________________  __________________

♣         Where in eukaryotes?

♣         Electron transport goes from ______________ energy to _________ energy carriers

♣         Some carry H+, too

♣         Some push H+ to other side of membrane

♣         FADH2 __________________ chain __________________ than NADH

♣         Less __________________ results from FADH2

♣         Terminal e- acceptor ________ ______ ½ O2

♣         If anaerobic, then ________ ½ O2

 

Oxidative Phosphorylation

♣         Chemiosmotic __________________ (proton motive force) drives ATP synthesis

♣         H+ flow back across membrane through ion __________________ in ________ __________________

♣         Called “__________________” even if O2 not terminal e- acceptor

♣         Still oxidizing!

♣         Very __________________ amounts of ATP made

♣         Variation in _______   __________________ allows differential testing

♣         Oxidase test detects cytochrome c

 

Theoretical Energy Yields from Oxidative Phosphorylation

♣         All theoretical

♣         Not precise conversion

♣         Siphoning off of precursor metabolites reduces yield from theoretical max

♣         Based on reducing power from other steps

♣         Assume ______ ATP / NADH

♣         Assume ______ ATP / FADH2

♣         Reducing power from:

♣         Glycolysis

♣         ______ NADH ⋄ ______ ATP

♣         Transition step

♣         ______ NADH ⋄ ______ ATP

♣         TCA cycle

♣         ______ NADH ⋄ _______ ATP

♣         ______ FADH2 ⋄ ______ ATP

♣         ________ ATP total

♣         Maximum for oxidative phosphorylation

 

Maximum Theoretical Energy Yields for Aerobic Respiration = ________ ATP

♣         Substrate level

phosphorylation – ______ ATP

♣         Glycolysis ⋄ ______ ATP

♣         TCA cycle ⋄ ______ ATP

♣         Oxidative

phosphorylation – ________ ATP

♣         Reducing power from glycolysis ⋄ ______ ATP

♣         Reducing power from transition step ⋄ ______ ATP

♣         Reducing power in TCA cycle ⋄ ________ ATP

 

 

Anaerobic Pathways

♣         Two types

♣         __________________   __________________

♣         __________________

♣         Both use glycolysis & pentose phosphate pathway

♣         Differ in __________________ e- __________________

♣         Differ in what happens to __________________

♣         Anaerobic respiration

♣         Terminal e- acceptor not O2 and not organic

♣         __________________ reducers (NO3-) or _________________ reducers (SO42-)

♣         Pyruvate oxidized to _____________

♣         Fermentation

♣         __________________ ⋄ terminal e- acceptor

  

Anaerobic Respiration

♣         __________________ (NO3-) reduced to nitrite (NO2-)

♣         Or to nitrous oxide (N2O)

♣         Or to nitrogen gas (N2)

♣         __________________ (SO42-) reduced to hydrogen sulfide (H2S)

♣         __________________ efficient than aerobic respiration

 

Fermentation

♣         Fermentation pathways used by

♣         __________________   __________________ (e.g. E. coli)

♣         __________________ species

♣   Lactic acid bacteria ferment only – never respire

♣   Obligate fermenters that are not harmed by O2

♣         __________________   __________________ that ferment

♣   Harmed by O2

♣         ATP comes only from __________________

♣          Other steps recycle NADH from NAD+

♣         __________________ or derivative used as e- __________________

 

End Products of Fermentation

♣         __________________ Acid

♣         Pyruvate is terminal e- acceptor

♣         e.g. Lactic acid bacteria

♣   Streptococcus & Lactobacillus spp.

♣   Yogurt, pickles, cheeses, cured sausages

♣   Acid ⋄ tooth decay

♣   Food spoilage

♣         __________________

♣         CO2 removed ⋄ EtOH + CO2

♣         e.g. Saccharomyces spp. (yeast)

♣   Wine, beer, bread

♣         __________________ Acid

♣         e.g. Clostridium spp.

♣         __________________ Acid

♣         CO2 removed ⋄ modification ⋄ propionate

–     Propionibacterium spp

♣   Swiss cheese

♣         2, 3 – __________________

♣         Differentiates members of Enterobacteriaceae

♣   e.g. Klebsiella spp., Enterobacter spp.

♣         Voges-Proskauer test detects acetoin

♣         Mixed __________________

♣         Various pathways branched

♣         Methyl red test differentiates E. coli from other Enterobacteriaceae

 

Catabolism of Other Compounds

♣         Compounds other than glucose

♣    Broken down by hydrolytic enzymes

♣    May then enter cycles at various points

♣         __________________

♣         Lipases break down to precursor metabolites

♣    Enter various pathways

♣         __________________

♣         Proteases break peptide bonds

♣         Deaminases remove amino group

♣         Precursor metabolites enter various pathways

♣         __________________

♣         Amylase breaks down amylose

♣         Cellulase breaks down cellulose

♣    e.g. fungi

♣    e.g. bacteria in rumen of many herbivores & termites

♣         β-galactosidase breaks down lactose ⋄ glucose & fructose

♣         Glucose enters glycolysis directly

♣         Other monosaccharides modified first

 

 

Categories of Organisms by Energy and Carbon Sources

Chemolithotrophs

♣         Use __________________ source of energy

♣         ________ – hydrogen sulfide

♣         ________ – ammonia

♣         Products of anaerobic respiration __________________

♣         Fix __________________ into organic molecules from CO2

♣          = Chemolithoautotrophs

 

Photoautotrophs

♣         Use photosynthesis to

♣         Harvest energy from __________________

♣         Fix __________ into organic molecules

♣         6 CO2 + 12 H2X     [pic]      C6H12O6 + 12 X + 6 H2O

♣         ______ depends on source of electrons

♣         Two stages

♣         Light __________________– __________________

♣         Light __________________ (“dark”) – carbon __________________

 

Photophosphorylation

♣         Light energy harvested in __________________ complexes

♣         Many __________________ absorb light

♣         Pass __________________ to reaction-center chlorophyll

♣         Excited electrons pass along electron transport chain in membrane e- carriers

♣         __________________

♣         Generates proton motive force and _________

♣         _______________________

♣         Generates __________________ power

♣         NADPH generates reducing power for e- transport

 

  

 

Electron Sources in Photosynthesis

♣         Source of __________________ determines if __________ is produced

♣         __________________ photosynthesis

♣         Plants, algae, cyanobacteria

♣         __________________ is source of electrons

♣         O2 is generated

♣         __________________ photosynthesis

♣         Green and purple bacteria

♣         ___________,  ________ gas is source of electrons (not water)

♣         _____ O2 is generated

 

Carbon Fixation

♣         Conversion of _________ to organic form

♣         __________________– requires input of much energy (__________)

♣         Several cycles

♣         Calvin cycle most common

♣         Uses ribulose bisphosphate carboxylase

♣   “__________________”

♣         __________________ abundant / important enzyme on earth

♣         3 turns of the cycle

♣         ⋄ one glyceraldehyde–3–phosphate (___________, a 3-carbon sugar)

♣         6 turns of the cycle

♣         ⋄ one molecule of 6-__________________ sugar (e.g. fructose 6-phosphate)

♣         Consume 18 ATP & 12 NADPH + H+

 

Calvin Cycle

__________________ Pathways

Using __________________ Molecules

♣         Variation in ability to utilize substrates

♣         Variation in ability to synthesize intermediates

♣         Basis of selective media

♣         Basis of differential media

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