Metabolism and Energy: The images have big font size and reduced background color. Useful for smartphones, classroom and printouts. The rest is standard stuff.

1. Molecular Biology 1-6
put together by: Linda Fahlberg-Stojanovska
Disclaimer: I put these together for my kid for his smartphone.
However, I found most images had very small type and increased the font
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2. Contents
• Metabolism
• Energy
Living organisms exchange energy and matter
in order to maintain a dynamic equilibrium
separate from changes in its environment.

3. Metabolism
• Metabolism is the set of chemical reactions that happen in
the cells of living organisms to sustain life.
• Key biochemicals in metabolism
– Amino acids and proteins
– Lipids
– Carbohydrates
– Nucleotides
– Coenzymes
– Minerals and cofactors
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4. Major Types of Reactions in Metabolism
• oxidation-reduction (electron transfer)
• group transfer reactions (functional group changes from
donor to recipient or vice- versa )
• hydrolysis (bond cleavage, water released)
• nonhydrolytic cleavage (bond cleavage without water)
• isomerization/rearrangement (carbon skeleton change)
• bond formation reactions using ATP energy
Notice that these 6 reaction types directly correspond
to the enzyme classification!
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5. Metabolism of Heterotrophs vs. Autotrophs
Autotrophs - "make their own food“ - photosynthesis
The metabolism of autotrophs is based on their ability to
generate high energy molecules from simpler
substances using the energy of light.
Heterotrophs – “eat their food” – cellular respiration
The metabolism of heterotrophs is much simpler and is
based on their ability to break complex molecules down
into simpler substances releasing energy from this
chemical breakdown for life processes.
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6. Metabolism of Heterotrophs
High Energy Biological
Nutrients Macromolecules
carbohydrates polysaccharides
lipids lipids
proteins nucleic acids
Chemical proteins
Energy
catabolism anabolism
ATP
Low Energy NADPH Precursor
End Products molecules
CO2 monosaccharides
H2 O fatty acids
NH3 nucleotides
amino acids
M. Dolinar, uni-lj 6

7. Characteristics of a Biological System
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cannot find source

8. Anabolism – Synthesis – USE ATP
Anabolism is the set of metabolic pathways that
• construct molecules from smaller units
– releases H2O - condensation reaction
• requires energy – usually ATP
– powered by catabolism (uses ATP made in catabolism)
•Anabolic processes “build up” organs and tissues
– growth and differentiation of cells and
– increase in body size,
– synthesis of complex molecules.
•Example: growth and mineralization of bone
•Example: increases in muscle mass
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9. Catabolism – Decomposition – MAKE ATP
Catabolism is the set of metabolic pathways that
• breaks down large molecules into smaller units
– absorbs H2O - hydrolysis reaction
• releases energy which is then used to MAKE ATP
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10. Catabolism - 2
• Catabolic processes include
– glycolysis,
– Kreb’s cycle,
– breakdown of muscle protein
to use amino acids as substrates for gluconeogenesis
– breakdown of fat in adipose tissue to fatty acids.
• Cells use monomers to construct new polymer or
further degrade to waste products.
• Cellular wastes include lactic acid, acetic acid, carbon
dioxide, ammonia, and urea.
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11. ATP → ADP + P + ENERGY
Same in both anaerobic and aerobic
– breaks phosphoanhydride bond (ATP → ADP)
– releases energy (and phosphate)
– is an anabolic (condensation) process
uses released energy to synthesize
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12. ATP – adenosine triphosfate
ATP - composed of an adenine ring and a ribose sugar
and 3 phosphate groups (triphosphate)
• 10 C, 16 H, 5 N, 13 O and 3 P.
phosphoanhydride bonds
adenine ring
triphosphate
ribose
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13. ADP – adenosine diphosfate
ADP - composed of an adenine ring and a ribose sugar
and 2 phosphate groups (diphosphate)
adenine ring
diphosphate
ribose
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14. ADP + Pi → ATP
DIFFERENT for anaerobic and aerobic
– catabolic (hydrolysis) process
decomposes food and stores their energy in ATP
• ATP is produced and used continuously.
• The entire amount of ATP in an organism is recycled once
per minute.
• Most cells maintain only a few seconds supply of ATP.
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15. ADP + Pi → ATP - Anaerobic
• Step 1: Glycolysis - Anaerobic or Aerobic
1 glucose → +2ATP (net) + 2 pyruvate acid molecules
• Step 2: Fermentation - Anaerobic
Yeast Fermentation or Homolactic Fermentation
Fermentation → 2ATP + lactate or ethanol + CO2
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16. ADP + Pi → ATP - Anaerobic
Anaerobic catabolism
–Glycolysis
–Fermentation
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http://getyournotes.blogspot.com/2012_01_01_archive.html

17. ADP + Pi → ATP - Aerobic
Aerobic catabolism = CELLULAR RESPIRATION
up to 19 times more efficient than anaerobic
Steps
–1. Glycolysis
–2. Pyruvate decarboxylation
–3. Kreb’s Cycle Aerobic
–4. ETC (Electron Chain Transport)
Chemiosmosis
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18. Aerobic Steps in Forming ATP
http://163.16.28.248/bio/activelearner/07/ch7c1.html 18

19. Aerobic Steps in Forming ATP
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20. Glycolysis - 1 - Anaerobic or Aerobic
• Glycolysis is 1st step in respiration.
• It occurs in both aerobic and anaerobic.
• Glycolysis is the metabolic pathway that converts glucose
C6H12O6, into pyruvate, CH3COCOO− + H+.
• The free energy released in this process is used to form the
high-energy compounds ATP (adenosine triphosphate) and
NADH (reduced nicotinamide adenine dinucleotide).
• We think it is one of the most ancient known metabolic
pathways.
• It occurs in the cytosol – the intracellular fluid of the cell.
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21. Glycolysis: Steps 1-5
cannot find source 21

22. Glycolysis: Steps 6-10
-2 ATP +4 ATP = net gain of 2 ATP
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23. Glycolysis - 2
• Glycolysis is a definite sequence of ten reactions involving
ten intermediate compounds (one of the steps involves two
intermediates). The intermediates provide entry points to
glycolysis.
• Most monosaccharides, such as fructose, glucose, and
galactose, can be converted to one of these intermediates.
• The intermediates may also be directly useful. For example,
the intermediate dihydroxyacetone phosphate (DHAP) is a
source of the glycerol that combines with fatty acids to form
fat.
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24. Pyruvate decarboxylation - 1
• 2nd step in aerobic respiration (formation of ATP)
• Catalyzed by pyruvate dehydrogenase reaction
• → 2 pyruvate molecules (from glycolysis) + CoA
– 1 C and 2 O atoms are removed, releasing CO2
– a molecule of the coenzyme NAD+ becomes NADH
– remaining molecule CH3CO - Acetyl coenzyme A.
• occurs in the mitochondria
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25. Pyruvate decarboxylation - 2
• Acetyl coenzyme A or acetyl-CoA is an important molecule
in metabolism,
• Its main function is to convey the carbon atoms within the
acetyl group to the citric acid cycle (Krebs cycle) to be
oxidized for energy production.
• Acetyl-CoA is produced during the 2nd step of aerobic
cellular respiration, pyruvate decarboxylation, which
occurs in the matrix of the mitochondria.
• Acetyl-CoA then enters Kreb’s Cycle (3rd step).
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26. Acetyl coenzyme A or acetyl-CoA
Coenzyme A
http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/krebs.htm
http://www.chm.bris.ac.uk/motm/acetylcoa/acoah.htm 26

27. Kreb’s Cycle
Kreb’s Cycle is the 3rd step in aerobic respiration
Kreb’s Cycle = Citric Acid Cycle
Kreb’s cycle is amphibolic (both anabolic and catabolic)
•Aerobic (requires oxygen)
•occurs in the mitochondria
•results in the formation of 2 ATP and
•results in the formation of other high energy redox
compounds which undergo further reactions to form more
ATP (in the ETC).
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28. Kreb’s Cycle
→ Acetyl coenzyme A enters binds with oxaloacetic acid (7)
1. citric acid → H2O
2. isocitric acid NAD+→NADH and → CO2
3. α-ketoglutaric acid:
NAD+→NADH → CO2 and ATD→ATP ← H2O
4. succinic acid : FAD → FADH2
5. fumaric acid: ← H2O
6. malic acid: NAD+→ NADH
7. oxaloacetic acid
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29. 29
http://library.thinkquest.org/27819/ch4_6.shtml

30. Kreb’s Cycle - ATP
• Krebs cycle produces 2 ATP directly.
• It also produces the high energy redox compounds:
6 NADH and 2 FADH2
– NAD+ →NADH is a redox reaction occurs 3 times in the
Kreb’s cycle (and in other reactions). NADH≈2.5 ATP
– FAD→FADH2 is another redox reaction.
It occurs in step 8 of Kreb’s cycle. FADH2≈1.5 ATP
• These are then used to power the formation of additional
≈34 ATP through the electron transport chain (ETC).
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31. NAD+ → NADH and FAD→FADH2
• Nicotinamide adenine dinucleotide, abbreviated NAD+, is a
coenzyme found in all living cells.
• In metabolism, NAD+ is involved in redox reactions, carrying
electrons from one reaction to another.
• NAD+ is an oxidizing agent, i.e. an electron acceptor .
It accepts electrons from other molecules and becomes
reduced to form NADH.
• NADH is thus a reducing agent, i.e. an electron donor.
• Similarly FAD is an oxidizing agent that accepts electrons to
become the reducing agent FADH2.
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32. Electron Transport Chain - ETC
• ETC is the 4th and final cellular mechanism in aerobic
(oxidative) respiration.
(Glycolysis, Pyruvate dehydoxylation, Kreb’s Cycle, ETC)
– In the ETC, the 6NADH and 2FADH2 from the Kreb’s cycle
are catabolized to produce the energy storing ATP.
• Electron transport chain (ETC) couples electron transfer
between an electron donor (such as NADH) and an electron
acceptor (such as O2) and
• It uses the movement of these electrons (e-) to pump
H+ ions (protons) across a membrane.
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33. ETC in Mitochondria
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http://wikidoc.org/index.php/Chemiosmosis

34. ETC – Active Transport System
• The transfer of H+ ions (protons) in the ETC in the
opposite direction of the concentration gradient is called the
active transport system
• Example: The NADH (from Kreb’s Cycle) take their 2 electrons
(and energy) to Complex I of the ETC.
• The electrons are transferred to an electron acceptor and
NAD+ is regenerated as the NADH gives up its electrons.
• These electrons are now transported along - releasing energy.
• This energy is utilized to pump H+ ions (protons) across the
inner mitochondrial membrane in the Active Transport S.
http://www.austincc.edu/~emeyerth/electrontrans.htm 34

35. ETC – Active Transport System
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http://wikidoc.org/index.php/Chemiosmosis

36. Electrochemical Gradient - Chemiosmosis
• The energy released by electrons from redox agents such
as NADH and FADH2 is used by ETC to pump protons
across the inner mitochondrial membrane in the Active
Transport System
• This generates potential energy in the form of a pH
gradient or a proton gradient and an electrical potential
across this membrane.
• A large enzyme called ATP synthase provides a channel
for the protons to flow back across the membrane and
down this gradient. This flow is called chemiosmosis.
• The energy in this gradient is used to make ATP.
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37. Electrochemical Gradient - Chemiosmosis
• Hydrogen ions (protons) diffuse from an area of high proton
concentration to an area of lower proton concentration
creating a gradient of protons (more → less).
This process is “similar”
to osmosis, (the
diffusion of water across
a semi-permeable
membrane), which is
why it is called
chemiosmosis.
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http://wikidoc.org/index.php/Chemiosmosis

38. Oxidative Phosphorylation
• The ATP synthase enzyme provides a channel for the
protons to flow back across the membrane, down this
proton gradient and back into the inner mitochondrial
space.
• This flow is with the concentration gradient.
• ATP synthase uses this energy to generate ATP from ADP in
a phosphorylation reaction (adding of phospate group).
– oxidative phosphorylation is from redox reactions, such as the
oxidation of sugars (e.g. glucose) in respiration in heterotrophs.
– photophosphorylation from sunlight in photosynthesis in
autotrophs and mainly uses a pH gradient.
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39. Oxidative Phosphorylation
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http://wikidoc.org/index.php/Chemiosmosis

40. Photophosphorylation - Autotrophs
• In photophosphorylation, the energy of sunlight is used to
create a high-energy electron donor and an electron acceptor.
– Cyclic photophosphorylation (plants and bacteria)
– Non-cyclic photophosphorylation (only plants)
• In chloroplasts, light drives the conversion of water to oxygen
and NADP+ to NADPH with transfer of H+ ions across
chloroplast membranes.
• NADP+ is a coenzyme with redox agent NADPH
(The coenzyme NAD+ is converted into NADP+; the chemistry of this related
coenzyme is similar to that of NAD+ but with additional phosphate group.)
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41. Photophosphorylation
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42. Electron Transport Chain of Photosystems
http://wikidoc.org/index.php/Thylakoid
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