Chapter 5

Metabolism -- The sum of all chemical reaction within a cell. It can also be described as catabolism + anabolism.

Chemical Reactions
Some reactions require energy. Energy must be added in order to make these reactions happen and the product(s) will be at a higher energy level than the reactants. In metabolism, many anabolic reactions fall into this category. Anabolic reactions require energy. Catabolic reactions release energy.

Not all energetically favored reactions are spontaneous. Many times some energy of activation needs to be added. For example, paper (cellulose = C6H12O6) exists stably in the presence of oxygen. Even though the rapid oxidation of the cellulose to form CO2, H2O and C is energetically favored, the paper won't burn (burning = the rapid oxidation of cellulose) unless activation energy (heat) is applied.

I. ENZYMES
In the cell, the energy needed to drive anabolic reactions as well as the activation energy needed to get many catabolic reactions going cannot be directly applied as heat. Instead, cells use enzymes to lower the amount of energy needed to cause the reactions to occur. Thus enzymes are called catalysts because the facilitate reactions and speed them up but they don't enter into the reactions.

Enzymes lower the activation energy of reactions because enzymes are able to (1) bind to the reactants (substrate), (2) force the reactants (substrate molecules) very close to each other and (3) bend the substrate molecules and destabilize their electron configurations. This makes the molecules unstable and reactive.

E + S <---> E-S <---> E + P

II. Components of an Enzyme:

• The place on the enzyme where substrate binds is called the substrate binding site or the active site of the enzyme. Allosteric site is a site other than the active site.
• Apoenzyme = the protein portion
• Cofactors = are non-protein atoms or molecules which bind to the apoenzyme. They are divided into organic molecules = coenzymes, and inorganic elements = metal ions.
• Coenzymes= NAD+ (nicotinamide adenine dinucleotide), FAD (flavin adenine dinucleotide), CoA (coenzyme A)
• Metal ions = Iron, copper, calcium, zinc, magnesium.
• Holoenzyme = Apoenzyme + Cofactor

1) pH
2) Temperature
3) Substrate concentration
4) Enzyme concentration

IV. Enzyme Inhibition:
a) Competitive Inhibition: A molecule with similar structure to the normal substrate can occupy (and block) the enzyme's active site. Can be reversed by adding more substrate. E.g. folic acid synthetase binds PABA ---> folic acid. The drug sulfanilamide has a chemical structure very similar to PABA and the drug will bind to the active site of the enzyme. Folic acid synthetase however is incapable of converting sulfanilamide into anything.

b) Non-competive Inhibition: Inhibitors (e.g. lead or other metals) can bind to the allosteric site changing the shape of the enzyme. Now, the active site is different and can't bind to the substrate.

ENERGY FLOW IN METABOLISM
Energy in metabolism often flows in terms of electrons. If electrons ARE LOST, this is called oxidation. If electrons ARE GAINED, this is called reduction. Oxidation is coupled to reduction; that is, if something gets oxidized, then something else gets reduced (remember the first and second laws of thermodinamics!).

In most of the oxidations and reductions which we will study, electrons (e-) will be moved with protons (H+). Watching the hydrogens therefore provides a convenient way to tell if a molecule has been oxidized or reduced.

Also, in many of the oxidation-reduction reactions we will look at, the molecule nicotinamide adenine dinucleotide (NAD) which serves as an electron-shuttle. NAD can become REDUCED to NADH₂, and then carry the electrons to some other reaction and become OXIDIZED back to NAD. In other words, NAD can pick up electrons from one reaction and carry them to another.

Note that when a molecule gets OXIDIZED IT LOSES ENERGY. Also, the more reduced a molecule is the more energy it contains. (See pgs 121 - 122, figs. 5.8 and 5.9 for descriptions of NAD and oxidation-reduction reactions.)

The ultimate goal in many instances of catabolism will be to take energy from a (food source) molecule, trap the energy and store it as ATP.

There are three ways to make ATP:

1.) Substrate level phosphorylation- where a high energy phosphate from an intermediate phosphorylated metabolic molecule gets transferred directly onto ADP in a catabolic pathway converting it to ATP.

2.) Oxidative phosphorylation - where a (food source) molecule is oxidized and the energy is extracted from the electrons by an electron transport chain. The extracted energy is then used to make ATP by a process known as chemiosmosis.

3.) Photophosphorylation - This is seen only in cells carrying out photosynthesis. In here, light energy is used to generate electrons and then the energy is extracted from the electrons by an electron transport chain. As in oxidative phosphorylation, the extracted energy is used to make ATP by chemiosmosis.
 

BACTERIAL METHODS OF OBTAINING ENERGY

• Aerobic respiration, in which oxygen is the final electron acceptor
• Anaerobic respiration, in which an inorganic molecule other than oxygen is the final electron acceptor
• Fermentation, in which an organic molecule is the final electron acceptor, and
• Photosynthesis, during which radiant energy is converted into chemical energy

1. AEROBIC RESPIRATION
The respiration of glucose (carbohydrate metabolism) as a fuel source occurs in 3 stages: glycolysis, Krebs cycle and electron transport chain.

Glucose + 6O₂ ----> 6CO₂ + 6H₂O + energy

(a) GLYCOLYSIS - or Embden Meyerhof Pathway

• The partial breakdown (oxidation) of a glucose molecule (a 6-C molecule) into 2 pyruvic acid molecules (3-C molecules).
• Uses 2 ATP's and makes 4 ATP's. So, there is a net gain of 2 ATP's
• Makes 2 NADH₂

• Further oxidation of carbon molecules
• Pyruvic acid ---> acetyl-CoA + CO2
• Regeneration by oxaloacetic acid (4C) + acetyl-CoA (2C)
• A lot of NADH produced and 6 molecules of CO2 released.

It is a series of enzymes imbedded in a membrane. These enzymes use the membrane to set up a chemiosmotic gradient of hydrogen ions. This gradient of hydrogen ions is called a proton motive force and this force supplies the energy for an ATP synthetase.

The electron transport chain enzymes are a series of oxidation-reduction electron carrier molecules and proton pumps. These enzymes use the energy in the electrons from glycolysis and Krebs cycle to move protons against a concentration gradient to form the proton motive force.

In the mitochondria of eukaryotes, 3 pairs of protons are "pumped out" between the inner and outer mitochondrial membranes during a single run down the electron transport system and their re-entry generates the formation of 3 molecules of ATP. However, in prokaryotes, often less protons are transported across the membrane in a single run (2 pairs in E. coli) so less ATP's are generated (2 in E. coli). The principle is however, the same.

(2) FERMENTATION:

• Metabolism of pyruvic acid and uses an organic molecule as final electron acceptor
• Does not require oxygen
• Regeneration of NAD+ and NADP+
• Very little energy is produced (1 or 2 ATP's mostly from glycolysis)
• End products are: lactic acid, CO2, ethanol, butanediol, propionic acid, succinic acid, acetic acid, etc.
• No Krebs cycle or electron transport chain
• Found only in anaerobic and facultative bacteria

• Complete oxidation of glucose to CO2 and H2O
• Final electron acceptor is oxygen
• Both the electron transport chain and the krebs cycle operate

 

 

A lot of ATP is produced from NADH2 and FADH2

Comparison between Fermentation and Aerobic respiration.
 

	Pathways Involved	Final Electron acceptor	Net Products
Fermentation	glycolysis	organic molecules	2 ATP, CO2, ethanol,  lactic acid, etc
Respiration	glycolysis, Krebs cycle,  electron transport chain	oxygen	38 ATP, CO2, H2O

Summary of Aerobic respiration:

• Remember this is for one glucose molecule!
• NADH is going to produce 3 ATP molecules
• FADH is going to produce 2 ATP molecules

Summary of Metabolism:

• Remember we only look at carbohydrate metabolism but the metabolism of fatty acids and proteins pretty much follows the same catabolic pathways.
• We also did not look any anabolic pathways, pathways that are used to make complex molecules from simple components.

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Lecture 4.

CLASSIFICATION OF ORGANISMS BY NUTRITIONAL PATTERN:

Energy is the ability to do work. Bacteria require energy for motility, active transport of nutrients into the cell, and biosynthesis of cell components such as nucleotides, RNA, DNA, proteins, peptidoglycan, etc. In other words, energy is required to drive various chemical reactions.

To get energy, bacteria (chemoheterotrophs) take energy-rich compounds such as glucose into the cell and enzymatically break them down to release their energy. Therefore, the bacterium needs a way to trap that released energy so it is not wasted as heat and store the energy in a form that can be utilized by cells. Principally, energy is trapped and stored in the form of adenosine triphosphate or ATP. Much ATP is needed for normal growth. For example, a typical growing E. coli cell must synthesize approximately 2.5 million molecules of ATP per second to support its energy needs.

1) ENERGY SOURCE

• light -- phototroph
• oxidation -reduction of organic & inorganic compounds -- chemotroph
 2) CARBON SOURCE
• carbon dioxide -- autotroph (Self -feeders)
• organic compounds -- heterotroph
EXAMPLES:
 
• Chemoheterotrophs= energy and carbon from organic molecules
• Chemoautotrophs= energy from reduced inorganic compounds and CO2 as source of carbon. 

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