Chapter 5 - Microbial Metabolism
Where to start with this chapter. This is a hard chapter to teach due to the fact that all of you seem to come in at a slightly different level of comfort with the core material. So let us look at the nuts and bolts first.
All metabolism is about the cycling of resources (materials, energy, wastes, etc.). No life-form on this planet exist in isolation, they are all connected in some way to an network of other organisms that either supply energy and/or materials for it or derive energy and/or resources from it. In this chapter we are going to be looking at the various ways in which a microorganism can either produces energy or utilizes energy.
The first part of the chapter deals with the idea of a chemical reaction. A chemical reaction is when molecules interact and form new molecules. This reaction can either release energy (exothermic or exergonic) or require energy (endothermic or endergonic). The key point to this idea is that the release or absorption of energy is a net measurement. All chemical reactions require energy to start (activation energy) and whether they produce less or more energy than this activation energy is the determining factor as to whether they are exothermic or endothermic. Say you need to borrow money from a friend to buy lunch. If the friend gives you five dollars but lunch only cost three, you will absorb the additional two dollars (endothermic), but if lunch cost seven you will have to give an additional two to pay (exothermic). I know it isn't the best example, but I'll try to come up with a new one.
The second part of the chapter deals with the concept of catalysts and enzymes. Catalyst lower the activation energy of a reaction (i.e. make it easier to start). Most importantly, they do not change the starting or final energy of a reaction, just the activation energy. In other words, an exothermic reaction is always exothermic and an endothermic reaction is always endothermic. Enzymes are biological catalysts, typically proteins. While almost all enzymes are proteins, not all proteins are enzymes.
more to come...
I. Catabolic and Anabolic Reactions
A. Definitions
1. Metabolism the sum of all chemical reactions within a living organism
2. Catabolism the breakdown of complex organic molecules into simpler ones.
3. Anabolism the building of complex organic molecules from simpler ones.
4. Metabolic Pathways sequences of chemical reactions in a specific biological role.
B. Reactions in biology are typically coupled (ie catabolic reactions provide the energy or building blocks for anabolic reactions)
1. Coupling of reactions is possible due to the presence of an energy-carrier in cells, ATP
2. ATP, adenosine triphosphate, is a molecule with an unstable third phosphate bond.
3. Energy can be stored in the terminal bond of ATP and then released through cleavage of that bond.
ATP ΰ ADP + Pi + Energy
ADP + Pi + Energy ΰ ATP
II. Enzymes
A. Definitions
1. Collision Theory theory stating that all molecules, atoms, and ions are in constant motion and are therefore constantly colliding with each other.
2. Activation Energy The amount of energy that is need to initiate a chemical reaction.
3. Exergonic Reaction A reaction that has a net production of energy.
4. Endergonic Reaction A Reaction that requires a net influx of energy.
5. Reaction Rate The frequency at which molecules collide with sufficient energy to initiate a reaction.
6. Energy The capacity to do work
7. Kinetic Energy The energy of movement
8. Potential Energy Stored energy
9. Entropy Useless, random energy (i.e. friction, waste heat)
B. Chemical Theory of Reactions
1. All chemical reactions are governed by the Laws of Thermodynamics
a. First Law of Thermodynamics Conservation of energy, in a closed system the amount of energy present in a chemical reaction is the same through out the reaction.
b. Second Law of Thermodynamics Every chemical reaction results in a loss of energy to Entropy.
2. Reactions on Earth are not in a closed system, the Sun is constantly pumping a large amount of energy into the system.
3. Collision theory shows that as temperatures increase the reaction rate increases, but at biologically relevant temperatures even spontaneous reactions are too slow for biological organisms.
C. Enzymes and Chemical Reactions
1. Definitions
a. Catalysts Materials that lower the activation energy of a reaction, but does not become altered or get used up in the reaction.
b. Enzymes Biological catalysts that can be made of proteins or RNA.
c. Substrate The materials that enzymes act upon.
d. Enzyme-substrate complex The temporary binding of substrate to enzyme in a high energy transitional state.
e. Transition state The peak of the energy diagram, where the substrates are in a chemical state between the beginning and final products, enzymes stabilize this state.
2. The power of the enzymes lies in their three-dimensional shapes, which promote binding of substrates in a way as to promote the transition state.
3. The site of binding in an enzyme is a pocket with the electrical properties that promote binding of substrates; this is called the active site.
4. The lowering of activation energies by enzymes allow for biological reactions to happen at moderate temperatures.
D. Enzyme Specificity and Efficiency
1. The specificity of an enzyme is driven by the unique three-dimensional structure.
2. Enzymes are efficient, increasing the rate of reactions by as much as 108 and 109 times.
3. Enzyme efficiency is measured in turnover numbers (substrate conversions per second).
E. Naming Enzymes
1. Enzyme names add in ase.
2. Classes of enzymes.
a. Oxidoreductase oxidation/reduction the gain or loss of hydrogen and oxygen.
b. Transferase transfer of functional groups
c. Hydrolase hydrolysis (addition of water)
d. Lyase Removal of atoms without hydrolysis
e. Isomerase rearrangement of atoms within a molecule
f. Ligase Joining of two molecules
F. Enzyme Components
1. Definitions
a. Apoenzyme the protein component of most enzymes
b. Cofactor the nonprotein component of most enzymes (not all enzymes have cofactors)
c. Coenzyme if the cofactor is an organic molecule
d. Holoenzyme the apoenzyme combined with the cofactor.
2. Apoenzymes are not active without their cofactors.
3. Many cofactors are products of vitamins.
G. Mechanism of Enzymatic Action
1. The substrate(s) contacts the enzymes active sites.
2. The temporary enzyme-sustrate complex forms at the active site.
3. The activation energy hump is overcome and the substrate(s) is transformed to its new state.
4. The transformed substrate is released from the enzyme.
5. The enzyme returns to its initial state and the cycle can begin again.
H. Factors Influencing Enzymatic Activity
1. Temperature the enzyme is a protein and as such is subject to denaturation at high temperatures.
2. pH Dramatic changes to the pH of a solution results in significant changes to the three-dimensional shape of a protein.
3. Substrate Concentration under situations of extremely high load a maximum rate for the enzyme is attained, a condition termed saturation.
4. Inhibitors
a. Competitive Inhibitors a situation where a similarly shaped compound competes for the active site of an enzyme.
b. Noncompetitive Inhibition (allosteric inhibition) a molecule that looks nothing like the substrate binds at a site on the enzyme other than the active site. This binding changes the active site such that the substrate can no longer bind.
I. Feedback Inhibition
1. Feedback inhibition is where the end product of an enzymatic reaction or pathway then serves as an inhibitor for the enzyme.
2. Typically the interaction is through an allosteric site.
J. Ribozymes unique types of RNA that form catalyzing structures.
III. Energy Production
A. Definition
1. Oxidation the removal of electrons from an atom or molecule.
2. Reduction the gaining of one or more electrons to atoms or molecules.
3. Oxidation-Reduction Reaction coupling of the two reaction types. (redox reactions)
4. Dehydrogenation the removal of hydrogen atoms, a common situation in biological oxidation.
Organic Cmpd. + NAD+ ΰ Oxidized Organic Cmpd. + NADH + H+
B. The Generation of ATP
1. Phosphorylation the addition of a phosphate group to a molecule.
2. Substrate-level Phophorylation Transfer of a phosphate from a phosphrylated carbon molecules to ADP.
C-P +ADP ΰ C + ATP
3. Oxidative Phosphorylation The passage of electrons through a number of compounds that result in the production of ATP.
4. Photophosphorylation The passage of light energy through a number of carriers to produce ATP, which is then used to produce glucose.
C. Metabolic Pathways of Energy Production
IV. Carbohydrate Catabolism
A. Carbohydrate Catabolism the breakdown of carbohydrate molecules for energy.
B. To produce energy from glucose microbes use two pathways
1. Respiration
a. Glycolysis The oxidation of glucose to pyruvic acid with some production of ATP and NADH
i. A net gain of 2 ATP
ii. A net gain of 2 NADH
b. Krebs Cycle generates NADH and FADH2 for Electron Transport Chain.
c. Electron Transport Chain The oxidation of NADH and FADH2 to produce a large amount of ATP.
2. Alternatives to Glycolysis
a. Pentose Phosphate Pathway allows the breakdown of five-carbon sugars
i. Allows a pathway to produce nucleic acids, some amino acids, and sugars through photosynthesis.
ii. Produces a net gain of one ATP.
iii. Operates at the same time as Glycolysis.
b. Enter-Doudoroff Pathway a pathway to metabolize glucose that does not involve glycolysis or the pentose phosphate pathway
i. Net gain of one ATP
ii. Clinically relevant as a test for the genus Pseudomonas.
3. Cellular Respiration
a. Definitions
i. Cellular Respiration The ATP-generating process by which molecules are oxidized and the final electron acceptor is (almost always) an inorganic molecule (i.e. CO2)
ii. Aerobic Respiration Respiration where the final electron acceptor is O2 (generating CO2), organisms that accomplish are termed aerobes.
iii. Anaerobic Respiration Respiration where the final electron receptor is an inorganic compound other than O2 (rarely an organic compound), these organisms are called anaerobes and they may be killed by the presence of O2.
b. Krebs Cycle
i. The oxidative of acetyl CoA (a derivative of pyruvic acid) to carbon dioxide with the production of some ATP, NADH, and FADH2.
ii. Generates 8 NADH, 2 FADH2, and 2 ATP for each molecule of Glucose.
c. Electron Transport Chain
i. A series of membrane bound proteins capable of coupled oxidation-reduction reactions.
ii. A step-wise release of captured energy (in NADH and FADH2) that drives the production of ATP
iii. Final electron acceptor is an irreversible reaction and represents the terminal electron receptor for the organism.
iv. Located on the mitochondrian membrane in eukaryotes and on the plasma membrane on prokaryotes.
d. Summary of Aerobic respiration
1 C6H12O6 + 6 O2 + 38 ADP +38 Pi ΰ 6 CO2 + 6 H20 + 38 ATP
e. In anaerobic respiration any number of reactions can occur at the terminal step (i.e. SO4-2 ΰ H2S), but they never generate as many ATP as aerobic respiration, leading to slower growth.
f. Fermentation any metabolic process that releases energy from a sugar or other organic compound, does not require oxygen or an electron chain system, and uses an organic compound as the final electron receptor.
i. Used to regenerate cofactors (NAD+ and NADP+) for Glycolysis.
ii. ATP is only produced during Glycolysis.
iii. The end products are determined by the microorganism and the substrates used, but are varied and useful in identification.
g. Catabolism of other macromolecule classes are possible, though they all get fed into Glycolysis and the Krebs cycle eventually.
4. Biochemical tests much of microbial identification (almost all up till the 1980s) are dependent on tests that judge positive negative reactions to a number of catabolic or anabolic reactions.
V. Photosynthesis
A. The fixation of carbon with sunlight.
B. Common equation for plants, algae, and cyanobacteria
6 CO2 + 12 H20 + Light Energy ΰ C6H12O6 + 6H20 +6 O2
C. Common equation for purple sulfur and green sulfur bacteria
6 CO2 + 12 H2S + Light Energy ΰ C6H12O6 + 6 H20 + 12 S
VI. Metabolic Diversity among Organisms
A. When you try to identify an organism one of the first test you do is try to determine what type of metabolism it has, this narrows you field quite a bit.
B. Chemotroph/Phototroph
1. Chemotroph depend on oxidation-reduction of organic or inorganic compounds for energy.
2. Phototroph depend on sunlight for energy.
C. Autotroph/Heterotroph
1. Autotroph its primary source of carbon is CO2
2. Heterotroph its primary source of carbon is organic compounds
D. These main classes combine into four subgroups
1. Chemoheterotroph an organism that derives its carbon from organic compounds and relies on the oxidation-reduction of organic compounds for energy.
2. Chemoautotroph an organism that derives its carbon from CO2 and relies on the oxidation-reduction of organic compounds for energy.
3. Photoheterotroph - an organism that derives its carbon from organic compounds and relies on sunlight for energy.
4. Photoautotroph - an organism that derives its carbon from CO2 and relies on sunlight for energy.
E. The groups can further be split along whether they have anaerobic, aerobic, or fermentative metabolisms.
F. These divisions are not purely academic in that they tell a lot about the organisms environment of choice. For example, would an anaerobic chemoheterotroph be present in a patients upper airway?