1. Nutrition = how an organism obtains
energy and
a carbon source to build the organic molecules of cells.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

2. Metabolism & energetics
Metabolism – sum total of all chemical reactions occurring in living organisms.
Anabolic pathways – synthesize compounds, generally endergonic.
Catabolic pathways – break down compounds, usually exergonic.
Many reactions also involve conversion of energy from one form to another.
Energy can exist as potential energy or kinetic energy.

3. There are many kinds of energy that can interconvert from one form to another.

4. How does a cell maintain & regulate its metabolism?
How does a cell garner & utilize energy?
From where does this energy come?

5. Organisms within the biosphere exchange molecules and energy
Energy of sunlight
Useful chemical bond energy
(e.g. some bacteria, animals, humans)
complex carbon,
glucose, amino acids
CO2, H2O
Autotrophs:
Phototrophs
& chemotrophs
Heterotrophs
Chemical oxidations
(via iron & sulfur bacteria)
Light (via plants)
Need 9 amino acids & 15 vitamins from outside sources
1st Law of Thermodynamics:
In any process, the total energy of the universe remains constant.

6. How do we get energy and carbon?
Ways to obtain energy:
phototrophs use light energy
chemotrophs get energy from chemicals.
Ways to obtain Carbon
autotrophs only need only CO2 (inorganic C)
Heterotrophs need organic carbon sources
How do we get energy and carbon?
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

7. Several ways to generate energy!
All organisms
Includes: Animals, bacteria, fungi
Includes: plants, bacteria
Chemotrophs
(use chemical compounds as 10 energy source)
Phototrophs
(use light as 10 energy source)
Chemolithotrophs
(use inorganic chem)
Chemoorganotrophs
(use organic chem)

8. Copyright © 2002 Pearson Education, Inc
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

9. What is the main role for enzymes? Metabolism
1) All biochemical reactions are integrated.
3) Energetics and the reactions in the pathways are important.
Emphasize:
1. All biochemical reactions are interrelated, integrated
2. General discussion: bacteria to humans
3. Strategies important:
1) reactions in pathways
2) energetics important
2) All living organisms have similar metabolic pathways.
pp. 375

10. The Tokyo subway system is much like cellular metabolism.

11. Anabolic (biosynthetic) pathways
Food molecules:
complex carbohydrates, etc.
Molecules that form the cell: lipids, proteins, etc.
Useful forms of energy
Anabolic (biosynthetic) pathways
Catabolic pathways
Building blocks for biosynthesis: sugars, amino acids, etc.
Adapted from Molecular Biology of the Cell, 4th ed.

12. Heterotrophic metabolism: Interconversion of material and energy
Catabolism (breakdown):
Yields energy, precursors
Anabolism (synthesis):
Requires energy, precursors
coupled
How are catabolism and anabolism coupled?

14. ATP couples energy between catabolism and anabolism
ADP
ATP
+ Pi
Energy from food (fuel molecules) or from photosynthesis
Energy available for work & chemical synthesis (e.g. movement, signal amplification, etc.
ATP is the principal carrier of chemical energy in the cell!
Major activities promoted by ATP:
-locomotion
-membrane transport
-signal transduction
-keeping materials in the cell
-nucleotide synthesis
They produce an activated carrier molecule or some other useful energy store.
pp. 381

15. ATP: the universal currency of free energy;
ATP: the universal currency of free energy; “high energy” phosphate compound
ATP +
H2O
ADP + Pi + H+
Go’ = -7.3 kcal/mol
(G in cells = -12 kcal/mol)
ADP +
H2O
AMP + Pi + H+
Go’ = -7.3 kcal/mol
ATP
ADP
Molecular Biology of the Cell, 3rd ed. Fig. 2-28

16. ATP is an intermediate “high energy” compound
Why ATP? It’s not the highest energy compound…
 It (and other nucleotide triphosphates) are stable
& the high free energy of hydrolysis
pp. 380

17. Another source of energy is the coupling of Oxidation & Reduction reactions
NAD+ (and NADP+) carry high-energy electrons and hydrogen atoms.
catabolism
Reduced fuel
Oxidized Fuel
NAD+(oxidized)
NADH(reduced)
Reduced Products
Oxidized Precursors
anabolism
“LEO the lion goes GER.”
Losing Electrons (is) Oxidation … Gaining Electrons (is) Reduction.

18. Nicotinamide adenine dinucleotide
NAD+(oxidized)
NADH(reduced)
Nicotinamide adenine dinucleotide
H: (hydride ion)
(PO4)
NADP+ NADPH
pp. 383

19. Summary Metabolism consists of many coupled & connecting reactions
• Major source of energy = oxidation of carbon fuels
• ATP = major carrier of energy
Few kinds of reactions; many recurring themes
Two major activated carrier molecules couple catabolism/anabolism reactions:
ATP/ADP couples energy (through hydrolysis)
NAD+/NADH couples oxidation/reduction (by carrying electrons & hydrogen atom)
ATP & NADH are activated carrier molecules.
pg. 373

20. Cellular Metabolism Acetyl CoA Citric acid cycle ATP Part 1:
Breakdown of large macromolecules to simple subunits
Part 2:
Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH
Part 3:
Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP in mitochondrion
fats
fatty acids and glycerol
polysaccharides
simple sugars
proteins
amino acids
Acetyl CoA
glucose
Citric acid cycle
CoA
2 CO2
8 e-
(Reducing power as NADH)
oxidative phosphorylation O2
H2O
ATP
glycolysis
pyruvate
NADH
Adapted from MBOC4, fig & pp. 383

21. Respiration The 3 types of bacterial respiration
Aerobic - require oxygen for their growth and existence
Anaerobic – do not require oxygen for any respiration
Anaerobes - prefer growing in the presence of oxygen, but can continue to grow without it

22. Catabolism - Respiration, fermentation
Glycolysis
Krebs/Tricarboxylic acid (TCA) Cycle
Electron transport chain & oxidative phosphorylation
Fermentation:
Glycolysis followed by NAD+ regeneration reactions.

23. Cellular Metabolism Acetyl CoA Citric acid cycle ATP Part 1:
Breakdown of large macromolecules to simple subunits
Part 2:
Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH
Part 3:
Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP in mitochondrion
fats
fatty acids and glycerol
polysaccharides
simple sugars
proteins
amino acids
Acetyl CoA
glucose
Citric acid cycle
CoA
2 CO2
8 e-
(Reducing power as NADH)
oxidative phosphorylation O2
H2O
ATP
glycolysis
pyruvate
NADH
Adapted from MBOC4, fig & pp. 383

24. Cellular Metabolism Acetyl CoA Citric acid cycle ATP Part 1:
Breakdown of large macromolecules to simple subunits
Part 2:
Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH
Part 3:
Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP in mitochondrion
fats
fatty acids and glycerol
polysaccharides
simple sugars
proteins
amino acids
Acetyl CoA
glucose
Citric acid cycle
CoA
2 CO2
8 e-
(Reducing power as NADH)
oxidative phosphorylation O2
H2O
ATP
glycolysis
pyruvate
NADH
Adapted from MBOC4, fig & pp. 383

25. Glucose catabolism + 6O2 3 stages involved: 1) Glycolysis
(a sugar)
C6H12O6 +
6 CO2
Carbon dioxide
6 H2O
water
(requires O2)
+ 6O2
oxidation
reduction
DG= -686 kcal/mol
Exergonic rxn
3 stages involved:
1) Glycolysis
2) TCA (citric acid) cycle
3) Electron transport/oxidative phosphorylation
Food = electron donor
Oxygen = terminal electron acceptor

26. Regulation of Energy Metabolism
Part 1:
Breakdown of large macromolecules to simple subunits
Part 2:
Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH
Part 3:
Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP in mitochondrion
fats
fatty acids and glycerol
polysaccharides
simple sugars
proteins
amino acids
Acetyl CoA
glucose
Citric acid cycle
CoA
2 CO2
8 e-
(Reducing power as NADH)
oxidative phosphorylation O2
H2O
ATP
glycolysis
pyruvate
NADH
glycolysis
TCA cycle
electron transport &
ox. phosphorylation
Adapted from MBOC4, fig & pp. 383

27. Glucose catabolism 3 stages involved: 1) Glycolysis
C6H12O6
6 CO2 +
6 H2O
(requires O2)
glucose
(a sugar)
Carbon dioxide
water
Go’ = -686 kcal/mol
3 stages involved:
1) Glycolysis
2) TCA (citric acid) cycle
3) Electron transport/oxidative phosphorylation
glucose
lactate (muscle)
ethanol (yeast)
no O2 required
Glycolysis:
What organisms use glycolysis?
1. Anaerobes (grow without O2)
2. Facultative organisms (grow with & without O2)
3. Aerobes (grow only with O2)

28. Cellular Metabolism Glycolysis Acetyl CoA Citric acid cycle ATP
Part 1:
Breakdown of large macromolecules to simple subunits
Part 2:
Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH
Part 3:
Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP in mitochondrion
fats
fatty acids and glycerol
polysaccharides
simple sugars
proteins
amino acids
Acetyl CoA
glucose
Citric acid cycle
CoA
2 CO2
8 e-
(Reducing power as NADH)
oxidative phosphorylation O2
H2O
ATP
glycolysis
pyruvate
NADH
Adapted from MBOC4, fig & pp. 383

29. Glycolysis
Splitting of glucose: yield of 2 pyruvate molecules from one glucose molecule. (Also H2O.)
ATP invested in early steps, energy generated in later steps. Net energy yield: 2 ATP, 2 NADH + 2 H+.

30. Cellular Metabolism Acetyl CoA Citric acid cycle ATP Part 1:
Breakdown of large macromolecules to simple subunits
Part 2:
Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH
Part 3:
Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP in mitochondrion
fats
fatty acids and glycerol
polysaccharides
simple sugars
proteins
amino acids
Acetyl CoA
glucose
Citric acid cycle
CoA
2 CO2
8 e-
(Reducing power as NADH)
oxidative phosphorylation O2
H2O
ATP
glycolysis
pyruvate
NADH
Adapted from MBOC4, fig & pp. 383

31. Krebs Cycle
Transition step required after pyruvate enters mitochondrion; pyruvate converted to Acetyl CoA. (NAD+ reduced to NADH during this process.)
Krebs cycle doesn’t directly need oxygen, but won’t occur without it.
Krebs cycle involves decarboxylation, oxidation to generate NADH, FADH2, ATP. CO2 is byproduct of these steps.
NADH, FADH2 will relay electrons to electron transport chain.

32. Cellular Metabolism Acetyl CoA Citric acid cycle ATP Part 1:
Breakdown of large macromolecules to simple subunits
Part 2:
Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH
Part 3:
Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP in mitochondrion
fats
fatty acids and glycerol
polysaccharides
simple sugars
proteins
amino acids
Acetyl CoA
glucose
Citric acid cycle
CoA
2 CO2
8 e-
(Reducing power as NADH)
oxidative phosphorylation O2
H2O
ATP
glycolysis
pyruvate
NADH
Adapted from MBOC4, fig & pp. 383

33. Electron transport system
Electron transport chain and oxidative phosphorylation produce ATP from products of glycolysis, Krebs.
Electron transport chain = protein complexes with prosthetic groups in/on inner mitochondrial membrane. (Some groups are able to move! E.g. Cyt C)
ETC facilitates series of redox reactions, with oxygen as final electron acceptor.
ATP formation uses proton motive force - voltage across membrane (ion gradient) that results from high [H+] in intermembrane space.

34. Redox reactions E.g. Na + Cl -> Na+ + Cl-
Many energy transfers involve transfer of electrons (or hydrogen atoms).
Oxidation and reduction occur together.
Loss of electrons from one substance = oxidation.
Addition of electrons to a substance = reduction.
Oxidizing agent - accepts electrons.
Reducing agent - gives up electrons.
E.g. Na + Cl -> Na+ + Cl-
reduction
oxidation

35. Electron transport chain - series of redox reactions
Cells release energy in stages.

36. Electron transport system

37. Development of Proton Motive Force from Chemiosmosis

38. Formation of ATP from Proton Motive Force and ATP Synthase

39. ATP Production during Aerobic Respiration by Oxidative Phosphorylation involving Electron Transport System and Chemiosmosis

40. Bacterial electron transport
ASM digital image collection:

41. Bacterial chemiosmotic ATP generation

42. Cellular Metabolism Acetyl CoA Citric acid cycle ATP Part 1:
Breakdown of large macromolecules to simple subunits
Part 2:
Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH
Part 3:
Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP in mitochondrion
fats
fatty acids and glycerol
polysaccharides
simple sugars
proteins
amino acids
Acetyl CoA
glucose
Citric acid cycle
CoA
2 CO2
8 e-
(Reducing power as NADH)
oxidative phosphorylation O2
H2O
ATP
glycolysis
pyruvate
NADH
Adapted from MBOC4, fig & pp. 383

43. Cellular Metabolism Acetyl CoA Citric acid cycle ATP Part 1:
Breakdown of large macromolecules to simple subunits
Part 2:
Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH
Part 3:
Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP in mitochondrion
fats
fatty acids and glycerol
polysaccharides
simple sugars
proteins
amino acids
Acetyl CoA
glucose
Citric acid cycle
CoA
2 CO2
8 e-
(Reducing power as NADH)
oxidative phosphorylation O2
H2O
ATP
glycolysis
pyruvate
NADH
Adapted from MBOC4, fig & pp. 383

46. Fermented … food? Yogourt Bread Kimchee
Fermented milk, fermentation carried out by lactic acid bacteria.
Bread
Simple fermentation of sugar to alchohol and CO2 by bread yeast Saccharomyces cerevisiae. CO2 makes bread rise.
Kimchee
Cabbage and other veggies fermented by lactic acid bacteria.
Even some meat & fish products!
E.g. Country-cured ham, Katsuobushi (tuna)

47. Unusual catabolism CONTAMINATION!!!!!
Badger Ammunitions Plant provided weapons for the military and handled large quantities of explosive nitroglycerin (NG).
CONTAMINATION!!!!!

48. How can we clean the NG up?
Organisms capable of degrading NG?
Microorganisms: e.g. Pseudomonas fluorescens, Pseudomonas putida
Pseudomonads only convert NG to mononitroglycerin (MNG). Other microbes in soil degrade MNG to glycerol. Glycerol can be converted to glyceraldehyde-3-phosphate and further metabolized.

49. Amazing enzyme
P. fluorescens & P. putida use single enzyme: xenobiotic reductase.
Nonspecific enzyme, recognizes many molecules carrying nitro group (like trinitrotoluene: TNT).
Many bacteria important in bioremediation!

50. Two nutritional modes are unique to prokaryotes
Chemoautotrophs
use CO2 as a carbon source, but they obtain energy by oxidizing inorganic substances,
Inorganic energy sources = hydrogen sulfide (H2S), ammonia (NH3), and ferrous ions (Fe2+).
E.g. Nitrobacter - key in N-cycle converts ammonia (NH4) to nitrate (NO3)
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51. Photoheterotrophs
use light to generate ATP but obtain their carbon in organic form.
This mode is restricted to prokaryotes.
E.g. purple bacteria - make salt flats purple & red
E.g. green bacteria
Where does “red herring” come from?
dead herring have salt coating: halophiles grow on salt (red color; smelly); dragged around by animal rights activists to stop fox hunts
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

52. Carbon cycle The majority of known prokaryotes are chemoheterotrophs.
parasites, which absorb nutrients from the body fluids of living hosts.
saprobes, decomposers that absorb nutrients from dead organisms,
Almost any organic molecule is food for one of the many chemoheterotrophic bacteria (like oil)
If it can’t be broken down by bacteria its called nonbiodegradable.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

53. Nitrogen Cycle Eukaryotes can only use organic nitrogen, NO3 or NH4.
Diverse prokaryotes can metabolize most nitrogenous compounds.
Prokaryotes are essential to converting N into usable forms for eukaryotes
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

54. Prokaryotes are responsible for the key steps in the cycling of nitrogen through ecosystems.
Some chemoautotrophic bacteria convert ammonium (NH4+) to nitrite (NO2-).
Others “denitrify” nitrite or nitrate (NO3-) to N2, returning N2 gas to the atmosphere.
A diverse group of prokaryotes, including cyanobacteria, can use atmospheric N2 directly.
During nitrogen fixation, they convert N2 to NH4+, making atmospheric nitrogen available to other organisms for incorporation into organic molecules.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

55. Cyanobacteria fix N and C (photosynthesis)
= most self-sufficient of all organisms.
Only need: light, CO2, N2, water and some minerals to grow.
Fig
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56. Cyanobacteria thought to put 02 in atmosphere.
= Massive change in the world
Great for aerobes (who require O2)
Deadly for anerobes (who are poisoned by o2)
Forced to live in remaining anerobic environments
Prokaryotes can be facultative or obligate aerobes or anerobes
Eukaryotes are all aerobic
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

57. 2. Photosynthesis evolved early in prokaryotic life
First prokaryotes were probably heterotrophs
Ate the primordial soup of early earth
But photosynthesis (harnessing the sun) shows up early in the fossil record)
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

58. Similarity in complex machinery suggests photosynthesis evolved once.
= most parsimonious hypothesis,
Thus:heterotrophic groups represent a loss of photosynthetic ability during evolution.
Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings