Learn more about the Electron Transport Chain on this subpage.

Metabolism- The sum total of all chemical reations and physical workings occurring in a cell

OVERVIEW

• Rules of metabolism
• Catabolism and Anabolism
• Enzymes
• Oxidation and Reduction
• Metabolic Pathways

Rules of Metabolism

1. Metabolism has to do with acquiring and using energy efficiency
2. Survival of the fittest. The most effective and efficient energy users survive and reproduce
3. Metabolism follows unbreakable physical laws
   1. First Law of Thermodynamics- energy cannot be created or destroyed (however it can change forms, during each conversion energy is lost as heat.)
      • Energy exsists in many forms: mechanical, sound, light, electric, heat and chemical. All forms can be converted into heat.
   2. Second Law of Thermodynamics- disorder in closed systems is continuously increasing (organization requires energy and disorder happens spontaneously)
      • Entrophy- is a measure of the disorder of a system

Anabolism and Catabolism

• Catabolic- reactions are energy releasing (exergonic) reactions which breakdown more complex molecules into simpler molecules. (ATP generated; some lost at heat)
  • exergonic- is a reaction that releases energy as it goes forward, it is considered free because it is available for doing cellular work.
  • Hydrolysis-another term for digestion because the breaking of bonds require the input of water
• Anabolic- reactions are energy-requiring (endergonic) and build more complex molecules from smaller simple molecules. (ATP required)
  • endergonic- they use energy as a reaction occurs
• Condensation reactions-anabolic reations require enzymes (ligases) to form covalent bonds between smaller substrate molecules
  • Synthesis reaction typically require ATP and always release one water molecule for each bond

The energy for anabolic reactions is provided by catabolic reactions; they are ALWAYS linked. Cells do NOT make energy they simply harness the energy released and made from bonds breaking and forming.


Enzymes

In order for a reation to occur the reaction must have enough energy input, called activation energy, in order to start

• There are three ways for activaion energy to occur:
  1. Increasing thermal energy (heating) to increase molecular velocity
  2. increase the concentration of reactants
  3. adding by catalysts
• Enzyme-chemicals that increase the rate of a chemical reaction without becoming part of the product or being comsumed in the reaction.
• All enzymes are composed of protiens call amino acids. The amino acids are arranged in a linear chain which is bonded together by covalent bond called peptide bonds. Amino acids differ from there side chains which determines their chemical nature.
• Enzymes can be classified as simple or conjucted.
  • Conjuncted enzymes are a combination of protiens and one or more cofactors.
  • Cofactors are organic molecules (called coenzymes) or inorganic elements.
• Each enzyme has a specific surface configuration know as its primary, secondary and teriaty structures. This unique configuration enables each enzyme to find its specific substrate.

Enzymes and Chemical Reactions

• 
  
• Catalysts- can speed up a chemical reation without being permanently altered (also know as an enzyme)
• Enzymes are organic catalysts. They act on specific substances called substrates, and each enzyme catalyzes only one reaction.
• 
  
• When a substrate matches with a specific enzyme the substrate will bind to the active site. This is when the enzyme will catalyze (break or form a bond) the substrate. The enzyme will change shape and is now ready for the next reaction.
• Active site (catalytic site)- is where the substrate binds to a crevice on the enzyme.
  • (The lock and key mechanism)

The union between an enzyme and its substrate is called the enzyme substrate complex. When a substrate is bound to the active site particular chemical bonds are weakened. This has the effect of lowering the activation energy to the point that heat in the enviorment is sufficient enough to supply the activation energy to initiate the reaction

Cofactors

• Cofactors- are organic compounds that work in conjuction with an apoenzyme to perform a necessary alteration to a substrate.
  • Cofactors are a nonprotien component. (ex. iron, copper, magnesium, manganese, zinc, cobalt, and selenium
• Apoenzymes- protien portion of an enzyme
• If the cofactor is an organic molecule it is call a coenzyme.
  • The general function of a coenzyme is to remove a functional group from one substrate molecule and add it to another molecule.
  • Two important coenzymes are nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP)
  • Both of these coenzymes function as electron carriers. Although NAD is primarily involved with catabolic (energy-yielding) reactions, NADP is involved with anabolic (energy-requiring) reactions.
• Apoenzymes are inactive by themselves.They must be activated by cofactors, and together the apoenzyme and the cofactor form a holoenzyme (active enzyme)
  • If the cofactor is removed than the apoenzyme will not function.
  • Vitamin deficiencies prevent a complete holoenzyme from forming
• Exoenzymes- transported extracellulary, where they breakdown (hydrolyze) large food molecules or harmful chemicals
  • Examples: cellulase, amylase, and penicillanase
  • Many pathogens secrete unique exoenzymes that help them avoid host defencestp promote their multiplication in tissues.
• Endoenzymes- retained intracellularly and function there
  • Constitutive enzymes- always present and in relatively constant amount regrdles the amount of substrate.
  • Induced enzyme- not constantly present and is produced only when its substrate is present.

Enzyme Inhibitors
An effective way to control the growth of bacteria is to control their enzymes. Certian poisons, such as cyanide, arsenic, and mercury, combine with enzymes and prevent them from functioning. As result the cells stop functioning and die.

• There are two major catagories of enzyme inhibitors:
  • Competitive and Noncompetitive
• Competitive Inhibitors- fill the active site and compete with the normal substrate for the active site
  • Some competitive inhibitors bind permently to amino acids within the active site which prevents any further interactions with the substrate.
  • Other competitive inhibitors bind reversibly, alternating leaving and occupying the active site, slowing the enzymes interaction with the substrate
    • Reversible competitive inhibitors can be overcome by increasing the substrate concentration
    • Examples of competitive inhibitors are: AZT which blocks an importat enzyme of the HIV virus, Sulfa drugs which prevent the synthesis of folic acid by bacteria,and penicillian which blocks a bacterial enzyme that form a crucial bond in peptidoglycan
• Noncompetitive Inhibitors- do not compete with the substrate for the enzymes active site; instead, they interact with another part of the enzyme
  • There are two classes of noncompetitive inhibitors: Nonspecific noncompetitive enzyme inhibitors and Noncompetitive specific inhibitors
    • 
      
    • Nonspecific noncompetitive enzyme inhibitors- denature or inhibit a lot if different enzymes which include things like heavy metals (lead, mercury, cadmium, and nickel), cyanide, and carbon monoxide

Denaturing- a process by which the weal bonds that collectively maintain the native shape of the apoenzyme are broken
Labile- when an enzyme is unstable because of forced changes in its enviorment

• Noncompetitive specific enzyme inhibitors (allosteric inhibition)- (organic molecules)the inhibitor binds to a site other than the substrates binding site called the allosteric site. This binding causes the active site to change its shape, making it nonfunctional.
• Feedback Inhibition- when an allosteric inhibitor can temporarily stop the action of that enzyme
• In many anabolic pathways, the final product can allosterically inhibit the activity of one of the products earlier in the pathway this is know as feedback inhibition
  • Feedback inhibition generally acts on the first enzyme in a metabolic pathway.
    • Because the enzyme is inhibited, the product of the first enzymatic reaction is not sythesized. That unsythesized would normally be the substrate for the second enzyme in the pathway, the second reation stops as well. Even though only the first enzyme in the pathway was inhibited, the entire pathway shuts down and no new end-product is formed

• Enzyme repression- a means to stop further synthesis of an enzyme somewhere along its pathway
• Enzyme induction- enzymes appear (are induced) only when a suitable substrate is present
• Negitive feedback- when the process is inhibited by the product
• Positive feedback- when the process is stimulated by the product

Oxidation-Reduction Reaction

• Oxidation-is the removal of electrons from an atom or a molecule (a reaction that often produces energy)
  • the loss of hydrogen (proton) atoms from a substrate
  • electrons are typically lost together with the hydrogen atoms
  • the addition of oxygen is also termed oxidation
  • molecule has given up energy
• Reduction- has a gain of of one or more electrons
  • the gain of electrons and hydrogen atoms by a substrate
  • the loss of oxygen is also called reduction
  • energy rich
• Oxidation and reduction reactions are always coupled meaning: each time one substance is oxidized the other is stimultaneously reduced.
  • The pairing of these reactions is called redox reaction (oxidation-reduction)
  • Dont forget OIL RIG
• Most biological oxidation involves the loss of of hydrogen atoms which is also called dehydrogenation reactions
  • Example: An organic molecule is oxidized by the loss of two hydrogen atoms, and a molecule of NAD+ is reduced. NAD+ assists enzymes by accepting hydrogen atoms from substrates (organic molecule). NAD+ accepts two electrons and one proton. One proton (H+) is left over and is released into the surrounding medium. The reduced coenzyme, NADH, contains more energy than NAD+.
  • * Remember that in biological oxidation-reduction reactions cells use them in catabolism to extract energy from nutrient molecules
    • Cells take nutrients, some of which serve as high energy sources, and degrade them from highly reduced compounds to highly oxidized compounds.

Metabolic Pathways

The Metabolic Pathway- is a sequence of enzymatically catalyzed chemical reactions occuring in a cell.
Organisms release and store energy from organic molecules by a series of controlled reactions. If the energy was released all at once the energy could not be efficiently used and would umltimatly damage the cell. Extracting energy from organic compounds and storing it in a chemical form the organisms must pass electrons from one compound to another through a series of oxidation-reduction reactions.

Most microorganisms oxidize carbohydrates as their main source of cellular energy. Carbohydrate catabolism is the breakdown of carb molecules to produce energy. Glucose is the most common carb energy source used by cells. *Also some microorganisms can catabolize various lipids and protiens for energy production. To produce energy microorganisms use two general processes: cellular respreration, which includes glycolysis, krebs cycle and the electron transport chain, and fermentation.



Glycolysis

Glycolysis (aka Embden-Meyerhof pathway) literally means "sugar splitting." It is the most common pathway for the breakdown or oxidation of glucose into pyruvic acid this is typically the first stage of carbohydrate catabolism.

• In gycolysis enzymes catalyze glucose, a 6 carbon sugar, into 3 carbon sugars. The sugars are than further oxidized, releaseing energy, making their atoms to rearrange into 2 molecules of pyruvic acid. During glycolysis NAD+ is reduced to NADH, and there is a net production of 2 ATP by substrate-level phosphorylation.
  • Glycolysis does NOT require oxygen; it can occur whether oxygen is present or not.
• Glycolysis consists of two basic stages; the preparatory stage (where ATP is used to reconstruct (phosphorylated) a 6 carbon glucose molecule and split-it it into a 3 carbon molecules (this stage consists of steps 1-5)) and the energy conserving stage (where the 3 carbon molecule are oxydized into 2 molecules of pyruvic acid (this stage consists of steps 6-10))
• Steps of Glycolysis
  • Prepertory Stage
    1. Glucose enters the cell and is reconstructed by ATP in a 6- carbon glucose phosphate molecule.
    2. Glucose 6- phosphate is rearranged to form fructose 6- phosphate.
    3. The P from another ATP molecule is used to from the fructose. * note: 6- diphosphate is still a 6- carbon compound.
    4. An enzyme splits the sugar into 2 3-carbon molecules. (dihydroxyacetone phostphate (DHAP) and glyceraldehyde 3- phosphate (GP))
    5. DHAP is readily converted into GP (the reverse action may also occur)
  • Energy Conserving Stage
    1. The next enzyme converts GP to another 3 carbon compound (3-diphosphoglyceric). GP is oxidized by the transfer of 2 hydrogen atoms to NAD+ to form NADH.
    2. The high energy P is moved to ADP, forming ATP, the first ATP production of glycolysis.
    3. An enzyme relocates the remainign P of 3-phosphoglyceric acid to form 2-phosphoglyceric acid to prepare for the next step.
    4. By the loss of a water molecule , 2-phosphoglyceric acid is converted to phosphoenolpyruvic acid (PEP). In the process the phosphate bond is upgraded into a high energy bond.
    5. This high energy P is transferred from PEP to ADP, forming ATP.
       • For each initial glucose molecule, the result of htis step is 2 molecules of ATP and 2 molecules of a 3-carbon compound called Pyruvic Acid
  • The net gain is two molecules of ATP for each glucose molecule that is oxidized.
  Krebs Cycle (Aerobic Respiration)

After the breakdown glucose to pyruvic acid the pyruvic acid can be further channeled by either cellular respiration or fermentation.

• Cellular Respiration- is an ATP generating process in which molecules are oxidized and the final electron acceptor is an inorganic molecule.
• Two types of respiration: Aerobic- uses oxygen and the final electron acceptor is O2. Anaerobic- (which does not use oxygen and may be killed by it) the final electron acceptor in an inorganic molecule other than O2 or organic molecule.
  • 
    
• The Krebs Cycle is also known as the TCA cycle or the Citric Acid Cycle. In this cycle, a series of oxidation and reduction reactions transfer potential energy, in the form of electrons, to electron carrier coenzymes (mainly NAD+).
  • Pyruvic acid derivatives are oxidized; the coenzymes are reduced.
• The Preparatory Step: In order for Pyruvic acid to enter the Kreb cycle it needs to lose one molecule of CO2 and become a two carbon compound. (This is known as decarboxylation) The two carbon compound (called acetyl group) attaches to coenzyme A by a high energy bond. Also pyruvic acid is oxidized and NAD+ is reduced to NADH.
• Step 2:As soon as the acetyl CoA enters the krebs cycle CoA will detach and the remaining acetyl group will attach to a four carbon compound (oxaloacetic acid) forming the six carbon citric acid molecule.
• Step 3: A molecule of water is removed and another one is adde back.Isocitric acid is the result of the conversion of citric acid to isomer.
• Step 4: The substrate loses CO2 molecule and the remaining five carbon compound is oxidized reducing NAD+ to NADH plus H+.
• Step 5: CO2 is lost and the remaining four carbon compound is oxidized by the transfer of electrons to NAD+ to NADH plus H+, and then is attached to CoA by an unstable bond.
• Step 6: CoA is displaced by a phosphate group which is transfer to GDP to GTP (guanosine triphosphate) ***NOTE: GTP is similar to ATP, which is formed when GTP donates a phosphate group to ADP.
• Step 7: Oxydative step, two hydrogens are transferred to FAD to from FADH2. ***NOTE: This coenzyme is similar to that of NADH plus H+, but FADH2 stores less energy.
• Step 8: Bonds in the substrate are rearranged in this step by the addition of a water molecule.
• Step 9: Last oxidative step produces another molecule of NAD plus H+and regenerates oxaloaetic acid. Which accepts a two carbon fragment from acetyl CoA for another term in the cycle.
• As result the Krebs cycle has a net gain of 6 molecules of NADH, 2 molecules of FADH2, and 2 molecules ATP. Also 4 molecules of CO2 are givem off.

Electron Transport Chain
The electron transport chain- consists of a sequence of carrier molecules that are capable of oxidation and reduction. The final oxidation is irreversible.

• In eukaryotic cells, the electron transport chain is found in the inner membrane of the mitochondria; In prokaryotic cells, it is found in the plasma membrane.
• There are three classes of carrier molecules.
  1. Flavoprotiens- which contain flavin, are coenzymes that are derived from riboflavin, are capable of performing alternating oxidations and reductions (FMN)
  2. Cytochromes- protiens with an iron containing group (heme) is capable of existing alternately as a reduced (Fe2+) form and an oxidized (Fe3+) form.
  3. Ubiquinones or coenzyme Q (symbolized as Q)- these are small nonprotien carriers.
• Steps of the Electron Transport Chain.
  1. Involves the transfer of high energy electrons from NADH to FMN, the first carrier in the chain.
     • This transfer actually involves the passage of a hydrogen atom with two elestrons to FMN, which than picks up an additional H+. As a result of the first transfer NADH is oxidized to NAD+; and FMN is reduced to NADH2.
  2. In the second step FMNH2 passes 2H+ to the other side of the mitochondrial membrane and passes two electrons to Q. As result FMNH2 is oxidized to FMN. Q also picks up an additional 2H+ and releases it on the other side of the membrane.
  3. The third step involves the cytochromes. Electrons are passed successively from Q to cytochromes and each cytochrome is reduced as it picks up electrons and is oxidized as it gives up electrons. The last cytochrome passes it electrons to molecular oxygen (O2), which becomes negitively charged and than picks up protons to form H2O.

Chemiosmotic Mechanism of ATP Generation

• Chemiosmosis- is the mechanism of ATP synthesis used in the Electron Transport Chain.
  • ***Recall: substances diffuse passively across membranes from areas of high concentration to areas of low concentrations; this diffusion yields energy. Also the movement of substances agianst such a concentration gradient requires energy and the required energy is usually provided b ATP.
• In chemiosmosis, the energy released when a substance (protons) moves along a gradient is used to synthesize ATP.
• In respiration, chemiosmosis is responsible fro most of the ATP that is generated.
• Steps of chemiomosis are:
  1. As electrons pass down the chain some of the carriers in the chain pump (actively transport by proton pumps) protons across the membrane.
  2. The phospholipid membrane is usually impermeable to protons, so the pumping creates a proton gradient. There is also an electrical charge gradient. The remaining H+ on one side of the membrane makes it have a positive charge compared to the other side.The resulting electrochemical gradient has a potential energy called proton motive force.
  3. The higher proton concentration on the one side of the membrane can diffuse across the membrane through special proton channels that contain the enzyme ATP synthase. When this flow occurs, energy is released and is used by the enzyme to synthesize ATP from ADP and P.
• The total net gain for teh electron transport chain is 34 ATP. Where 30 comes from NADH and 4 come from FADH2.

Fermetation- is the enzymatic degradation of carbs in which the final electron acceptor is an organic molecule, ATP synthesized by substrate-level phosphorylation, an O2 is not required.
Energy
Energy is the capacity to do work or to make something happen. There are two types of energy, Potential energy and Kinetic energy.
Potential energy is the same as stored energy. Think of a big boulder at the top of a mountain. Sitting there it is potential energy because at the time it is not doing anything, but if it drops it will be active, or kinetic, energy.
Kinetic energy comes from the Greek language as the meaning of move. Kinetic energy is the motion of an object. The faster something is moving, the more kinetic energy it has. Endergonic reactions consume energy. They are anabolic and the products have more energy that the reactants.
Exergonic reactions release energy. They are catabolic and the products have less energy than the reactants.


Metabolic Strategies Among Heterotrophic Microorganisms

Scheme	Pathways Involved	Final Electron Acceptor	Products	Chief Microbe Type
Aerobic respiration	Glycolysis, TCA cycle, electron transport	O2	ATP, CO2, H2O	Aerobes; facultative anaerobes
Anaerobic metabolism Fermentative	Glycolysis	Organic molecules	ATP, CO2, ethanol, lactic acid	Facultative, aerotolerant, strict anaerobes
Respiration	Glycolysis, TCA cycle, electron transport	Various inorganic salts	CO2, ATP, organic acids, H2S, CH4, N2	Anaerobes; some facultatives

flash cards for this chapter are at www.flashcardexchange.com under Kevin Youngs micro chapter 8

Chapter 8 Questions
1. What is a catalyst?
a. synthesis of cell molecules and structures
b. A substance that speeds up a reaction
c. where the substrate binds to on an enzyme
d. organic compound that alters a substrate

2. An active site is:
a. also known as a catalytic site
b. removes excess metallic cofacters from the enzyme
c. where the substrate binds to the enzyme
d. b & c
e. a & c


3. Another word for biosythesis is_______.
a. catabolism
b. anabolism
c. metabolism
d. catalyst

4. Catabolism is a form of metabolism in which ________ molecules are converted into _______ molecules.
a. large, small
b. small, large
c. amino acid, protein
d. food, storage

5. An enzyme _______ the activation energy required for a chemical reaction.
a. increases
b. converts
c. lowers
d. catalyzes

6. An enzyme
a. becomes part of the final products
b. is nonspecific for substrate
c. is consumed by the reaction
d. is the heat and pH labile

7. Any process that breaks bonds of the larger molecules into smaller molecules
a. Anabolism b. Biosynthesis
c. Catabolism
d. Redox

8.There are 3 ways for activation energy to occur except

a. Decrease the concentration of reactants
b. Increasing the concentration of reactants
c. Adding a catalyst
d. Increasing thermal energy (heating) to increase molecular velocity

9. What often controls enzyme repression

a. end-products
b. molecular mimics
c. substrates
d. reactants
e. bio energetics

10. Which answer best describes enzymes?
a. a carrier molecule that resembles a shuttle that are alternately loaded and unloaded.
b. a general term for the totality of chemical and physical processes occurring in a cell.
c. a protein biocatalyst that facilitates metabolic reactions
d. They raise the activation energy required for a chemical reaction to proceed

11. Exergonic reactions
a. release potential energy
b. consume energy
c. form bonds
d. occur only outside the cell

12. What is responsible for the overall direction of protein synthesis?
a. DNA
b. RNA
c. carbohydrates
d. both a & b

13. Which of the following compounds has the greatest amount of energy for a cell?
a. CO2
b. ATP
c. O2
d. O2
e. lactic acid