Monday February 24, 1999
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Lecture notes:

Metabolic Pathway

A metabolic pathway is a series of orderly reactios that operates under the following rules:

1. Each step is "catalyzed" (quickened) by a specific enzyme.
2. Pathways can be linear, cyclic, or branched.
3. Major pathways are:
   a. catabolic (degradative) These reactions break down large molecules into smaller ones.
   (proteins------------------------->amino acids)
   b. anabolic (biosynthetic) These reactions make large molecules from smaller ones.
   (amino acids--------------------->proteins)
4. The compounds used in reactions must be in sufficient concentration to permit reactions, but low enough to prevent disruptive side reactions.
   
   *****This is why it can be dangerous to take "mega" doses of vitamins or other metabolites without a prescription. They stop acting as a "vitamin" (or mineral, etc.) and start acting as a drug.
5. Most reactions are reversible. Glucose<-------->fructose
   
   The rate of the reaction in either direction depends upon the concentration of the reactants.
   
   Reversible reactions try to reach "equilibrium" - (when the forward and reverse reactions are occurring at the same rate)
   
   There is no NET change in the concentration of products or reactants what a reaction is at equilibrium.
   
   Reactions that are not reversible-often involve regulatory enzymes.
   1 enzyme for forward run. 1 enzyme for reverse run.

1. Almost all enzymes are proteins. (a few are RNA)
2. Enzymes are catalysts. They make a reaction happen faster.
3. They do not determine (in reversible reactions) the direction of a reaction.
4. They are selective. They work on specific "substrates". (molecules involved in a reaction)
5. Enzymes have active sites where there is a complementary fit between an enzyme and its substrate.
6. Increasing temperature will increase the rate of a reaction up to a point. A very high temperature will denature the enzyme.
7. Ph 7 is ideal for most enzyme functions. (exceptions: digestive enzymes) Too high or too low pH will denature the protein.
8. There are a lot of controls on enzymes. Adjustments can be made in seconds.
   Activation/inactivation (on/off switch)
   inhibition/enhancement
   feedback mechanisms
   feedforward mechanisms
9. Some enzymes need co-factors to help run certain reactions. Coenzymes are not proteins. (examples: metal ions and B vitamins) "Coenzyme" generally refers to "vitamins". Co-factor generally refers to metal ions.
10. Enzymes are not permanately altered or consumed in a reaction.

When an enzyme is not made or is made incorrectly, this can lead to diseases known as Inborn Errors of Metabolism.

A missing or incorrectly made enzyme results in a disturbance in a metabolic pathway.

Problems arise in two ways:
1. Build up of a substance in the middle of the pathway and/or
2. Lack of a final product.

Examples: Lactose intolerance-enzyme to break down lactose is deficient or missing.
Galactosemia-the enzyme to change galactose into glucose is misssing.
PKU-enzyme to break down phenylalanine is missing.

Over 2,000 inborn errors in metabolism have been identified.

1. Cells can't use the energy stored in large biomolecules (lipids, carbohydrates, etc.) directly.
2. The energy must be transformed into a form that can be used in chemical reactions inside the cell.
3. Some energy is transformed into ATP-adenosine triphosphate (ribose-adenine-and 3 phosphates)
4. This energy can be used to drive reactions in the cell.
5. Most ATP is made when electrons from catabolic reactions are used in a series of reactions that creates enough energy to make ATP's

Points to ponder:

1. Where does the carbon come from in organic compounds?
2. 2. How do those "air" bubbles appear on under water plants/
3. Does the oxygen released during photosynthesis come from the CO₂ of the H₂0?
4. How does the energy inherent in carbon compounds become available to do cellular wor]k?
5. Where does the energy come from to make these carbon compunds?

Photosynthesis is the primary way that living organisms are able to capture solar energy and convert it to chemical energy. It occurs in the chloroplasts in Eukaryotes.

Light Dependent phase:

1. Sunlight is trapped by pigment molecules (chlorophyll, mostly)
2. Light activated chlorophyll splits water (H₂0) molecules into oxygen gas (O₂) and hydrogen (H).
3. The hydrogen is split into protons and electrons (H- and e+)
4. These protons and electrons are used to make NADPH in a manner similar to the electron transport chain in aerobic respiration.
5. There are two possible paths for electrons to follow:
   a. a cyclic path which produces only ATP
   b. a non-cyclic path which produces both ATP and NADPH.
   12H₂O + light ----------------------> 12 NADPH + 6O₂

In the light dependent phase of photosynthesis, plants manufacture the energy needed to make sugar.

The NADPH is used as a source of H atoms in making sugar. (+ electrons)

Light Independent phase: (this used to be called the "dark" phase)

1. Carbon dioxide is "fixed" by reacting with a 5 carbon sugar.
2. The new 6 carbon sugar goes through a cyclic metabolic pathway called the Calvin-Benson cycle.
3. For every 6 CO₂'s that enter the cycle, one 6 carbon sugar leaves.
4. Six molecules of water (H₂0) are produced also.
5. The light independent phase uses the 12 NADPH's and the ATP formed in the light dependent phase as the energy source to make the sugar and water made in the light independent phase.
   6CO₂ + 18 ATP + 12 NADPH------------------->C₆H₁₂O6 + 6H₂0 + 12 NADP + 18 ADP