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A hydrogen bond is a strong intermolecular force created by the relative positivity of hydrogen atoms.
Learning Objectives
• Describe the properties of hydrogen bonding.
Key Points
• Hydrogen bonds are strong intermolecular forces created when a hydrogen atom bonded to an electronegative atom approaches a nearby electronegative atom.
• Greater electronegativity of the hydrogen bond acceptor will lead to an increase in hydrogen-bond strength.
• The hydrogen bond is one of the strongest intermolecular attractions, but weaker than a covalent or an ionic bond.
• Hydrogen bonds are responsible for holding together DNA, proteins, and other macromolecules.
Key Terms
• electronegativity: The tendency of an atom or molecule to draw electrons towards itself, form dipoles, and thus form bonds.
• hydrogen bond: The attraction between a partially positively charged hydrogen atom attached to a highly electronegative atom (such as nitrogen, oxygen, or fluorine) and another nearby electronegative atom.
• intermolecular: A type of interaction between two different molecules.
Forming a Hydrogen Bond
A hydrogen bond is the electromagnetic attraction created between a partially positively charged hydrogen atom attached to a highly electronegative atom and another nearby electronegative atom. A hydrogen bond is a type of dipole-dipole interaction; it is not a true chemical bond. These attractions can occur between molecules (intermolecularly) or within different parts of a single molecule (intramolecularly).
Hydrogen Bond Donor
A hydrogen atom attached to a relatively electronegative atom is a hydrogen bond donor. This electronegative atom is usually fluorine, oxygen, or nitrogen. The electronegative atom attracts the electron cloud from around the hydrogen nucleus and, by decentralizing the cloud, leaves the hydrogen atom with a positive partial charge. Because of the small size of hydrogen relative to other atoms and molecules, the resulting charge, though only partial, is stronger. In the molecule ethanol, there is one hydrogen atom bonded to an oxygen atom, which is very electronegative. This hydrogen atom is a hydrogen bond donor.
Hydrogen Bond Acceptor
A hydrogen bond results when this strong partial positive charge attracts a lone pair of electrons on another atom, which becomes the hydrogen bond acceptor. An electronegative atom such as fluorine, oxygen, or nitrogen is a hydrogen bond acceptor, regardless of whether it is bonded to a hydrogen atom or not. Greater electronegativity of the hydrogen bond acceptor will create a stronger hydrogen bond. The diethyl ether molecule contains an oxygen atom that is not bonded to a hydrogen atom, making it a hydrogen bond acceptor.
Hydrogen bond donor and hydrogen bond acceptor: Ethanol contains a hydrogen atom that is a hydrogen bond donor because it is bonded to an electronegative oxygen atom, which is very electronegative, so the hydrogen atom is slightly positive. Diethyl ether contains an oxygen atom that is a hydrogen bond acceptor because it is not bonded to a hydrogen atom and so is slightly negative.
A hydrogen attached to carbon can also participate in hydrogen bonding when the carbon atom is bound to electronegative atoms, as is the case in chloroform (CHCl3). As in a molecule where a hydrogen is attached to nitrogen, oxygen, or fluorine, the electronegative atom attracts the electron cloud from around the hydrogen nucleus and, by decentralizing the cloud, leaves the hydrogen atom with a positive partial charge.
Interactive: Hydrogen Bonding: Explore hydrogen bonds forming between polar molecules, such as water. Hydrogen bonds are shown with dotted lines. Show partial charges and run the model. Where do hydrogen bonds form? Try changing the temperature of the model. How does the pattern of hydrogen bonding explain the lattice that makes up ice crystals?
Applications for Hydrogen Bonds
Hydrogen bonds occur in inorganic molecules, such as water, and organic molecules, such as DNA and proteins. The two complementary strands of DNA are held together by hydrogen bonds between complementary nucleotides (A&T, C&G). Hydrogen bonding in water contributes to its unique properties, including its high boiling point (100 °C) and surface tension.
In biology, intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids. The hydrogen bonds help the proteins and nucleic acids form and maintain specific shapes. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.02%3A_Chemical_Bonds/2.2.03%3A_Hydrogen_Bonding.txt |
The mole is represented by Avogadro’s number, which is 6.022 × 1023 atoms or molecules per mol.
Learning Objectives
• Define and memorize Avogadro’s number
Key Points
• The mole allows scientists to calculate the number of elementary entities (usually atoms or molecules ) in a certain mass of a given substance.
• Avogadro’s number is an absolute number: there are 6.022 × 1023elementary entities in 1 mole. This can also be written as 6.022 × 1023mol-1.
• The mass of one mole of a substance is equal to that substance’s molecular weight. For example, the mean molecular weight of water is 18.015 atomic mass units (amu), so one mole of water weight 18.015 grams.
Key Terms
• mole: The amount of substance of a system that contains as many elementary entities as there are atoms in 12 g of carbon-12.
The chemical changes observed in any reaction involve the rearrangement of billions of atoms. It is impractical to try to count or visualize all these atoms, but scientists need some way to refer to the entire quantity. They also need a way to compare these numbers and relate them to the weights of the substances, which they can measure and observe. The solution is the concept of the mole, which is very important in quantitative chemistry.
Avogadro’s Number
Amadeo Avogadro first proposed that the volume of a gas at a given pressure and temperature is proportional to the number of atoms or molecules, regardless of the type of gas. Although he did not determine the exact proportion, he is credited for the idea.
Avogadro’s number is a proportion that relates molar mass on an atomic scale to physical mass on a human scale. Avogadro’s number is defined as the number of elementary particles (molecules, atoms, compounds, etc.) per mole of a substance. It is equal to 6.022 × 1023 mol-1and is expressed as the symbol NA.
Avogadro’s number is a similar concept to that of a dozen or a gross. A dozen molecules is 12 molecules. A gross of molecules is 144 molecules. Avogadro’s number is 6.022 × 1023molecules. With Avogadro’s number, scientists can discuss and compare very large numbers, which is useful because substances in everyday quantities contain very large numbers of atoms and molecules.
The Mole
The mole (abbreviated mol) is the SI measure of quantity of a “chemical entity,” such as atoms, electrons, or protons. It is defined as the amount of a substance that contains as many particles as there are atoms in 12 grams of pure carbon-12. So, 1 mol contains 6.022×1023 elementary entities of the substance.
Chemical Computations with Avogadro’s Number and the Mole
Avogadro’s number is fundamental to understanding both the makeup of molecules and their interactions and combinations. For example, since one atom of oxygen will combine with two atoms of hydrogen to create one molecule of water (H2O), one mole of oxygen (6.022 × 1023 of O atoms) will combine with two moles of hydrogen (2 × 6.022 × 1023 of H atoms) to make one mole of H2O.
Another property of Avogadro’s number is that the mass of one mole of a substance is equal to that substance’s molecular weight. For example, the mean molecular weight of water is 18.015 atomic mass units (amu), so one mole of water weight 18.015 grams. This property simplifies many chemical computations.
If you have 1.25 grams of a molecule with molecular weight of 134.1 g/mol, how many moles of that molecule do you have?
1.25g×1 mole134.1g=0.0093 moles.1.25g×1 mole134.1g=0.0093 moles.
The Mole, Avogadro: This video introduces counting by mass, the mole, and how it relates to atomic mass units (AMU) and Avogadro’s number. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.02%3A_Chemical_Bonds/2.2.04%3A_Avogadro%27s_Number_and_the_Mole.txt |
The average atomic mass of an element is the sum of the masses of its isotopes, each multiplied by its natural abundance.
Learning Objectives
• Calculate the average atomic mass of an element given its isotopes and their natural abundance
Key Points
• An element can have differing numbers of neutrons in its nucleus, but it always has the same number of protons. The versions of an element with different neutrons have different masses and are called isotopes.
• The average atomic mass for an element is calculated by summing the masses of the element’s isotopes, each multiplied by its natural abundance on Earth.
• When doing any mass calculations involving elements or compounds, always use average atomic mass, which can be found on the periodic table.
Key Terms
• mass number: The total number of protons and neutrons in an atomic nucleus.
• natural abundance: The abundance of a particular isotope naturally found on the planet.
• average atomic mass: The mass calculated by summing the masses of an element’s isotopes, each multiplied by its natural abundance on Earth.
The atomic number of an element defines the element’s identity and signifies the number of protons in the nucleus of one atom. For example, the element hydrogen (the lightest element) will always have one proton in its nucleus. The element helium will always have two protons in its nucleus.
Isotopes
Atoms of the same element can, however, have differing numbers of neutrons in their nucleus. For example, stable helium atoms exist that contain either one or two neutrons, but both atoms have two protons. These different types of helium atoms have different masses (3 or 4 atomic mass units ), and they are called isotopes. For any given isotope, the sum of the numbers of protons and neutrons in the nucleus is called the mass number. This is because each proton and each neutron weigh one atomic mass unit (amu). By adding together the number of protons and neutrons and multiplying by 1 amu, you can calculate the mass of the atom. All elements exist as a collection of isotopes. The word ‘isotope’ comes from the Greek ‘isos’ (meaning ‘same’) and ‘topes’ (meaning ‘place’) because the elements can occupy the same place on the periodic table while being different in subatomic construction.
Calculating Average Atomic Mass
The average atomic mass of an element is the sum of the masses of its isotopes, each multiplied by its natural abundance (the decimal associated with percent of atoms of that element that are of a given isotope).
Average atomic mass = f1M1 + f2M2 +… + fnMnwhere f is the fraction representing the natural abundance of the isotope and M is the mass number (weight) of the isotope.
The average atomic mass of an element can be found on the periodic table, typically under the elemental symbol. When data are available regarding the natural abundance of various isotopes of an element, it is simple to calculate the average atomic mass.
• For helium, there is approximately one isotope of Helium-3 for every million isotopes of Helium-4; therefore, the average atomic mass is very close to 4 amu (4.002602 amu).
• Chlorine consists of two major isotopes, one with 18 neutrons (75.77 percent of natural chlorine atoms) and one with 20 neutrons (24.23 percent of natural chlorine atoms). The atomic number of chlorine is 17 (it has 17 protons in its nucleus).
To calculate the average mass, first convert the percentages into fractions (divide them by 100). Then, calculate the mass numbers. The chlorine isotope with 18 neutrons has an abundance of 0.7577 and a mass number of 35 amu. To calculate the average atomic mass, multiply the fraction by the mass number for each isotope, then add them together.
Average atomic mass of chlorine = (0.7577 ⋅⋅ 35 amu) + (0.2423 ⋅⋅ 37 amu) = 35.48 amu
Another example is to calculate the atomic mass of boron (B), which has two isotopes: B-10 with 19.9% natural abundance, and B-11 with 80.1% abundance. Therefore,
Average atomic mass of boron = (0.199⋅⋅10 amu) + (0.801⋅⋅11 amu) = 10.80 amu
Whenever we do mass calculations involving elements or compounds (combinations of elements), we always use average atomic masses.
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• Mole (unit). Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Mole_(unit). License: CC BY-SA: Attribution-ShareAlike
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Carbon is the most important element to living things because it can form many different kinds of bonds and form essential compounds.
Learning Objectives
• Explain the properties of carbon that allow it to serve as a building block for biomolecules
Key Points
• All living things contain carbon in some form.
• Carbon is the primary component of macromolecules, including proteins, lipids, nucleic acids, and carbohydrates.
• Carbon’s molecular structure allows it to bond in many different ways and with many different elements.
• The carbon cycle shows how carbon moves through the living and non-living parts of the environment.
Key Terms
• octet rule: A rule stating that atoms lose, gain, or share electrons in order to have a full valence shell of 8 electrons (has some exceptions).
• carbon cycle: the physical cycle of carbon through the earth’s biosphere, geosphere, hydrosphere, and atmosphere; includes such processes as photosynthesis, decomposition, respiration and carbonification
• macromolecule: a very large molecule, especially used in reference to large biological polymers (e.g., nucleic acids and proteins)
Carbon is the fourth most abundant element in the universe and is the building block of life on earth. On earth, carbon circulates through the land, ocean, and atmosphere, creating what is known as the Carbon Cycle. This global carbon cycle can be divided further into two separate cycles: the geological carbon cycles takes place over millions of years, whereas the biological or physical carbon cycle takes place from days to thousands of years. In a nonliving environment, carbon can exist as carbon dioxide (CO2), carbonate rocks, coal, petroleum, natural gas, and dead organic matter. Plants and algae convert carbon dioxide to organic matter through the process of photosynthesis, the energy of light.
Carbon is Important to Life
In its metabolism of food and respiration, an animal consumes glucose (C6H12O6), which combines with oxygen (O2) to produce carbon dioxide (CO2), water (H2O), and energy, which is given off as heat. The animal has no need for the carbon dioxide and releases it into the atmosphere. A plant, on the other hand, uses the opposite reaction of an animal through photosynthesis. It intakes carbon dioxide, water, and energy from sunlight to make its own glucose and oxygen gas. The glucose is used for chemical energy, which the plant metabolizes in a similar way to an animal. The plant then emits the remaining oxygen into the environment.
Cells are made of many complex molecules called macromolecules, which include proteins, nucleic acids (RNA and DNA), carbohydrates, and lipids. The macromolecules are a subset of organic molecules (any carbon-containing liquid, solid, or gas) that are especially important for life. The fundamental component for all of these macromolecules is carbon. The carbon atom has unique properties that allow it to form covalent bonds to as many as four different atoms, making this versatile element ideal to serve as the basic structural component, or “backbone,” of the macromolecules.
Structure of Carbon
Individual carbon atoms have an incomplete outermost electron shell. With an atomic number of 6 (six electrons and six protons), the first two electrons fill the inner shell, leaving four in the second shell. Therefore, carbon atoms can form four covalent bonds with other atoms to satisfy the octet rule. The methane molecule provides an example: it has the chemical formula CH4. Each of its four hydrogen atoms forms a single covalent bond with the carbon atom by sharing a pair of electrons. This results in a filled outermost shell. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.03%3A_Chemical_Reactions/2.3.01%3A_The_Chemical_Basis_of_Life.txt |
Chemical reactions often produce changes in energy.
Learning Objectives
• Describe the types of energy changes that can occur in chemical reactions
Key Points
• Chemical reactions often involve changes in energy due to the breaking and formation of bonds.
• Reactions in which energy is released are exothermic reactions, while those that take in heat energy are endothermic.
Key Terms
• endothermic: A description of a chemical reaction that absorbs heat energy from its surroundings.
• enthalpy: In thermodynamics, a measure of the heat content of a chemical or physical system. The change in enthalpy of a chemical reaction is symbolized as ΔH.
• exothermic: A description of a chemical reaction that releases heat energy to its surroundings.
Due to the absorption of energy when chemical bonds are broken, and the release of energy when chemical bonds are formed, chemical reactions almost always involve a change in energy between products and reactants. By the Law of Conservation of Energy, however, we know that the total energy of a system must remain unchanged, and that oftentimes a chemical reaction will absorb or release energy in the form of heat, light, or both. The energy change in a chemical reaction is due to the difference in the amounts of stored chemical energy between the products and the reactants. This stored chemical energy, or heat content, of the system is known as its enthalpy.
Exothermic Reactions
Exothermic reactions release heat and light into their surroundings. For example, combustion reactions are usually exothermic. In exothermic reactions, the products have less enthalpy than the reactants, and as a result, an exothermic reaction is said to have a negative enthalpy of reaction. This means that the energy required to break the bonds in the reactants is less than the energy released when new bonds form in the products. Excess energy from the reaction is released as heat and light.
Endothermic Reactions
Endothermic reactions, on the other hand, absorb heat and/or light from their surroundings. For example, decomposition reactions are usually endothermic. In endothermic reactions, the products have more enthalpy than the reactants. Thus, an endothermic reaction is said to have a positive enthalpy of reaction. This means that the energy required to break the bonds in the reactants is more than the energy released when new bonds form in the products; in other words, the reaction requires energy to proceed.
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• octet rule. Provided by: Wiktionary. Located at: en.wiktionary.org/wiki/octet_rule. License: CC BY-SA: Attribution-ShareAlike
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The orientation of hydrogen bonds as water changes states dictates the properties of water in its gaseous, liquid, and solid forms.
Learning Objectives
• Explain the biological significance of ice’s ability to float on water
Key Points
• As water is boiled, kinetic energy causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor).
• When water freezes, water molecules form a crystalline structure maintained by hydrogen bonding.
• Solid water, or ice, is less dense than liquid water.
• Ice is less dense than water because the orientation of hydrogen bonds causes molecules to push farther apart, which lowers the density.
• For other liquids, solidification when the temperature drops includes the lowering of kinetic energy, which allows molecules to pack more tightly and makes the solid denser than its liquid form.
• Because ice is less dense than water, it is able to float at the surface of water.
Key Terms
• density: A measure of the amount of matter contained by a given volume.
Water’s States: Gas, Liquid, and Solid
The formation of hydrogen bonds is an important quality of liquid water that is crucial to life as we know it. As water molecules make hydrogen bonds with each other, water takes on some unique chemical characteristics compared to other liquids, and since living things have a high water content, understanding these chemical features is key to understanding life. In liquid water, hydrogen bonds are constantly formed and broken as the water molecules slide past each other. The breaking of these bonds is caused by the motion (kinetic energy) of the water molecules due to the heat contained in the system. When the heat is raised as water is boiled, the higher kinetic energy of the water molecules causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas (steam or water vapor). On the other hand, when the temperature of water is reduced and water freezes, the water molecules form a crystalline structure maintained by hydrogen bonding (there is not enough energy to break the hydrogen bonds). This makes ice less dense than liquid water, a phenomenon not seen in the solidification of other liquids.
Phases of matter: See what happens to intermolecular bonds during phase changes in this interactive.
Water’s lower density in its solid form is due to the way hydrogen bonds are oriented as it freezes: the water molecules are pushed farther apart compared to liquid water. With most other liquids, solidification when the temperature drops includes the lowering of kinetic energy between molecules, allowing them to pack even more tightly than in liquid form and giving the solid a greater density than the liquid.
The low density of ice, an anomaly, causes it to float at the surface of liquid water, such as an iceberg or the ice cubes in a glass of water. In lakes and ponds, ice forms on the surface of the water creating an insulating barrier that protects the animals and plant life in the pond from freezing. Without this layer of insulating ice, plants and animals living in the pond would freeze in the solid block of ice and could not survive. The detrimental effect of freezing on living organisms is caused by the expansion of ice relative to liquid water. The ice crystals that form upon freezing rupture the delicate membranes essential for the function of living cells, irreversibly damaging them. Cells can only survive freezing if the water in them is temporarily replaced by another liquid like glycerol. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.04%3A_Inorganic_Compounds/2.4.01%3A_Water%27s_State-_Gas_Liquid_and_Solid.txt |
Acids dissociate into H+ and lower pH, while bases dissociate into OH and raise pH; buffers can absorb these excess ions to maintain pH.
Learning Objectives
• Explain the composition of buffer solutions and how they maintain a steady pH
Key Points
• A basic solution will have a pH above 7.0, while an acidic solution will have a pH below 7.0.
• Buffers are solutions that contain a weak acid and its a conjugate base; as such, they can absorb excess H+ ions or OH ions, thereby maintaining an overall steady pH in the solution.
• pH is equal to the negative logarithm of the concentration of H+ ions in solution: pH = – log[H+].
Key Terms
• alkaline: having a pH greater than 7; basic
• acidic: having a pH less than 7
• buffer: a solution composed of a weak acid and its conjugate base that can be used to stabilize the pH of a solution
Self-Ionization of Water
Hydrogen ions are spontaneously generated in pure water by the dissociation (ionization) of a small percentage of water molecules into equal numbers of hydrogen (H+) ions and hydroxide (OH) ions. The hydroxide ions remain in solution because of their hydrogen bonds with other water molecules; the hydrogen ions, consisting of naked protons, are immediately attracted to un-ionized water molecules and form hydronium ions (H30+). By convention, scientists refer to hydrogen ions and their concentration as if they were free in this state in liquid water.
2H2O⇋H3O++OH−2H2O⇋H3O++OH−
The concentration of hydrogen ions dissociating from pure water is 1 × 10-7moles H+ ions per liter of water. The pH is calculated as the negative of the base 10 logarithm of this concentration:
pH = -log[H+]
The negative log of 1 × 10-7 is equal to 7.0, which is also known as neutral pH. Human cells and blood each maintain near-neutral pH.
pH Scale
The pH of a solution indicates its acidity or basicity (alkalinity). The pH scale is an inverse logarithm that ranges from 0 to 14: anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is basic (or alkaline ). Extremes in pH in either direction from 7.0 are usually considered inhospitable to life. The pH in cells (6.8) and the blood (7.4) are both very close to neutral, whereas the environment in the stomach is highly acidic, with a pH of 1 to 2.
Non-neutral pH readings result from dissolving acids or bases in water. Using the negative logarithm to generate positive integers, high concentrations of hydrogen ions yield a low pH, and low concentrations a high pH.
An acid is a substance that increases the concentration of hydrogen ions (H+) in a solution, usually by dissociating one of its hydrogen atoms. A base provides either hydroxide ions (OH) or other negatively-charged ions that react with hydrogen ions in solution, thereby reducing the concentration of H+ and raising the pH.
Strong Acids and Strong Bases
The stronger the acid, the more readily it donates H+. For example, hydrochloric acid (HCl) is highly acidic and completely dissociates into hydrogen and chloride ions, whereas the acids in tomato juice or vinegar do not completely dissociate and are considered weak acids; conversely, strong bases readily donate OH and/or react with hydrogen ions. Sodium hydroxide (NaOH) and many household cleaners are highly basic and give up OH rapidly when placed in water; the OHions react with H+ in solution, creating new water molecules and lowering the amount of free H+ in the system, thereby raising the overall pH. An example of a weak basic solution is seawater, which has a pH near 8.0, close enough to neutral that well-adapted marine organisms thrive in this alkaline environment.
Buffers
How can organisms whose bodies require a near-neutral pH ingest acidic and basic substances (a human drinking orange juice, for example) and survive? Buffers are the key. Buffers usually consist of a weak acid and its conjugate base; this enables them to readily absorb excess H+ or OH, keeping the system’s pH within a narrow range.
Maintaining a constant blood pH is critical to a person’s well-being. The buffer that maintains the pH of human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3), and carbon dioxide (CO2). When bicarbonate ions combine with free hydrogen ions and become carbonic acid, hydrogen ions are removed, moderating pH changes. Similarly, excess carbonic acid can be converted into carbon dioxide gas and exhaled through the lungs; this prevents too many free hydrogen ions from building up in the blood and dangerously reducing its pH; likewise, if too much OH is introduced into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH. Without this buffer system, the body’s pH would fluctuate enough to jeopardize survival.
Antacids, which combat excess stomach acid, are another example of buffers. Many over-the-counter medications work similarly to blood buffers, often with at least one ion (usually carbonate) capable of absorbing hydrogen and moderating pH, bringing relief to those that suffer “heartburn” from stomach acid after eating. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.04%3A_Inorganic_Compounds/2.4.02%3A_pH_Buffers_Acids_and_Bases.txt |
Some salts, such as ammonium bicarbonate (NH4HCO3), contain cations and anions that can both undergo hydrolysis.
Learning Objectives
• Predict the pH of a solution of a salt containing cations and anions, both of which participate in hydrolysis.
Key Points
• Basic salts result from the neutralization of a strong base with a weak acid.
• Acid salts result from the neutralization of a strong acid with a weak base.
• For salts in which both cation and anion are capable of hydrolysis, compare Ka and Kb values to determine the solution ‘s resulting pH.
Key Terms
• neutralization reaction: a reaction between an acid and a base in which water and a salt are formed
• hydrolysis: a reaction with water in which chemical bonds break
• salt: in acid-base chemistry, one of the products in a neutralization reaction
Summary of Acidic and Basic Salts
As we have discussed, salts can form acidic or basic solutions if their cations and/or anions are hydrolyzable (able to react in water). Basic salts form from the neutralization of a strong base and a weak acid; for instance, the reaction of sodium hydroxide (a strong base) with acetic acid (a weak acid) will yield water and sodium acetate. Sodium acetate is a basic salt; the acetate ion is capable of deprotonating water, thereby raising the solution’s pH.
Acid salts are the converse of basic salts; they are formed in the neutralization reaction between a strong acid and a weak base. The conjugate acid of the weak base makes the salt acidic. For instance, in the reaction of hydrochloric acid (a strong acid) with ammonia (a weak base), water is formed, along with ammonium chloride. The ammonium ion contains a hydrolyzable proton, which makes it an acid salt.
Salts in Which Both Ions Hydrolyze
The following is a more complicated scenario in which a salt contains a cation and an anion, both of which are capable of participating in hydrolysis. A good example of such a salt is ammonium bicarbonate, NH4HCO3; like all ammonium salts, it is highly soluble, and its dissociation reaction in water is as follows:
NH4CO3(s)→NH+4(aq)+HCO−3(aq)NH4CO3(s)→NH4+(aq)+HCO3−(aq)
However, as we have already discussed, the ammonium ion acts as a weak acid in solution, while the bicarbonate ion acts as a weak base. The reactions are as follows:
NH+4(aq)+H2O(l)⇌H3O+(aq)+NH3(aq)Ka=5.6×10−10NH4+(aq)+H2O(l)⇌H3O+(aq)+NH3(aq)Ka=5.6×10−10
HCO−3(aq)+H2O(l)⇌H2CO3(aq)+OH−(aq)Kb=2.4×10−8HCO3−(aq)+H2O(l)⇌H2CO3(aq)+OH−(aq)Kb=2.4×10−8
Because both ions can hydrolyze, will a solution of ammonium bicarbonate be acidic or basic? We can determine the answer by comparing Ka and Kb values for each ion. In this case, the value of Kb for bicarbonate is greater than the value of Ka for ammonium. Therefore, bicarbonate is a slightly more alkaline than ammonium is acidic, and a solution of ammonium bicarbonate in pure water will be slightly basic (pH > 7.0). In summary, when a salt contains two ions that hydrolyze, compare their Ka and Kb values:
• If Ka > Kb, the solution will be slightly acidic.
• If Kb > Ka, the solution will be slightly basic.
Hydrolysis of salts: This video examines the hydrolysis of an acid salt, a basic salt, and a salt in which both ions hydrolyze.
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Carbohydrates are essential macromolecules that are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.
Learning Objectives
• Describe the structure of mono-, di-, and poly-saccharides
Key Points
• Monosaccharides are simple sugars made up of three to seven carbons, and they can exist as a linear chain or as ring-shaped molecules.
• Glucose, galactose, and fructose are monosaccharide isomers, which means they all have the same chemical formula but differ structurally and chemically.
• Disaccharides form when two monosaccharides undergo a dehydration reaction (a condensation reaction); they are held together by a covalent bond.
• Sucrose (table sugar) is the most common disaccharide, which is composed of the monomers glucose and fructose.
• A polysaccharide is a long chain of monosaccharides linked by glycosidic bonds; the chain may be branched or unbranched and can contain many types of monosaccharides.
Key Terms
• isomer: Any of two or more compounds with the same molecular formula but with different structure.
• dehydration reaction: A chemical reaction in which two molecules are covalently linked in a reaction that generates H2O as a second product.
• biopolymer: Any macromolecule of a living organism that is formed from the polymerization of smaller entities; a polymer that occurs in a living organism or results from life.
Carbohydrates can be represented by the stoichiometric formula (CH2O)n, where n is the number of carbons in the molecule. Therefore, the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. The origin of the term “carbohydrate” is based on its components: carbon (“carbo”) and water (“hydrate”). Carbohydrates are classified into three subtypes: monosaccharides, disaccharides, and polysaccharides.
Monosaccharides
Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars. In monosaccharides, the number of carbons usually ranges from three to seven. If the sugar has an aldehyde group (the functional group with the structure R-CHO), it is known as an aldose, and if it has a ketone group (the functional group with the structure RC(=O)R’), it is known as a ketose. Depending on the number of carbons in the sugar, they also may be known as trioses (three carbons), pentoses (five carbons), and or hexoses (six carbons). Monosaccharides can exist as a linear chain or as ring-shaped molecules; in aqueous solutions they are usually found in ring forms.
Common Monosaccharides
Glucose (C6H12O6) is a common monosaccharide and an important source of energy. During cellular respiration, energy is released from glucose and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize glucose using carbon dioxide and water, and glucose, in turn, is used for energy requirements for the plant.
Galactose (a milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose, galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and stereochemically. This makes them different molecules despite sharing the same atoms in the same proportions, and they are all isomers of one another, or isomeric monosaccharides. Glucose and galactose are aldoses, and fructose is a ketose.
Disaccharides
Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (also known as a condensation reaction or dehydration synthesis). During this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another monosaccharide, releasing a molecule of water and forming a covalent bond. A covalent bond formed between a carbohydrate molecule and another molecule (in this case, between two monosaccharides) is known as a glycosidic bond. Glycosidic bonds (also called glycosidic linkages) can be of the alpha or the beta type.
Common Disaccharides
Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed by a dehydration reaction between two glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and fructose.
Polysaccharides
A long chain of monosaccharides linked by glycosidic bonds is known as a polysaccharide (poly- = “many”). The chain may be branched or unbranched, and it may contain different types of monosaccharides. Starch, glycogen, cellulose, and chitin are primary examples of polysaccharides.
Plants are able to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. Starch is the stored form of sugars in plants and is made up of glucose monomers that are joined by α1-4 or 1-6 glycosidic bonds. The starch in the seeds provides food for the embryo as it germinates while the starch that is consumed by humans is broken down by enzymes into smaller molecules, such as maltose and glucose. The cells can then absorb the glucose.
Common Polysaccharides
Glycogen is the storage form of glucose in humans and other vertebrates. It is made up of monomers of glucose. Glycogen is the animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen is broken down to release glucose in a process known as glycogenolysis.
Cellulose is the most abundant natural biopolymer. The cell wall of plants is mostly made of cellulose and provides structural support to the cell. Cellulose is made up of glucose monomers that are linked by β 1-4 glycosidic bonds. Every other glucose monomer in cellulose is flipped over, and the monomers are packed tightly as extended long chains. This gives cellulose its rigidity and high tensile strength—which is so important to plant cells.
Carbohydrate Function
Carbohydrates serve various functions in different animals. Arthropods have an outer skeleton, the exoskeleton, which protects their internal body parts. This exoskeleton is made of chitin, which is a polysaccharide-containing nitrogen. It is made of repeating units of N-acetyl-β-d-glucosamine, a modified sugar. Chitin is also a major component of fungal cell walls | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.05%3A_Organic_Compounds/2.5.01%3A_Carbohydrate_Molecules.txt |
Fats and oils, which may be saturated or unsaturated, can be unhealthy but also serve important functions for plants and animals.
Learning Objectives
• Differentiate between saturated and unsaturated fatty acids
Key Points
• Fats provide energy, insulation, and storage of fatty acids for many organisms.
• Fats may be saturated (having single bonds) or unsaturated (having double bonds).
• Unsaturated fats may be cis (hydrogens in same plane) or trans (hydrogens in two different planes).
• Olive oil, a monounsaturated fat, has a single double bond whereas canola oil, a polyunsaturated fat, has more than one double bond.
• Omega-3 fatty acid and omega-6 fatty acid are essential for human biological processes, but they must be ingested in the diet because they cannot be synthesized.
Key Terms
• hydrogenation: The chemical reaction of hydrogen with another substance, especially with an unsaturated organic compound, and usually under the influence of temperature, pressure and catalysts.
• ester: Compound most often formed by the condensation of an alcohol and an acid, by removing water. It contains the functional group carbon-oxygen double bond joined via carbon to another oxygen atom.
• carboxyl: A univalent functional group consisting of a carbonyl and a hydroxyl functional group (-CO.OH); characteristic of carboxylic acids.
Fats have important functions, and many vitamins are fat soluble. Fats serve as a long-term storage form of fatty acids and act as a source of energy. They also provide insulation for the body.
Glycerol and Fatty Acids
A fat molecule consists of two main components: glycerol and fatty acids. Glycerol is an alcohol with three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons with a carboxyl group attached and may have 4-36 carbons; however, most of them have 12-18. In a fat molecule, the fatty acids are attached to each of the three carbons of the glycerol molecule with an ester bond through the oxygen atom. During the ester bond formation, three molecules are released. Since fats consist of three fatty acids and a glycerol, they are also called triacylglycerols or triglycerides.
Saturated vs. Unsaturated Fatty Acids
Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the hydrocarbon chain, the fatty acid is said to be saturated. Saturated fatty acids are saturated with hydrogen since single bonds increase the number of hydrogens on each carbon. Stearic acid and palmitic acid, which are commonly found in meat, are examples of saturated fats.
When the hydrocarbon chain contains a double bond, the fatty acid is said to be unsaturated. Oleic acid is an example of an unsaturated fatty acid. Most unsaturated fats are liquid at room temperature and are called oils. If there is only one double bond in the molecule, then it is known as a monounsaturated fat; e.g. olive oil. If there is more than one double bond, then it is known as a polyunsaturated fat; e.g. canola oil. Unsaturated fats help to lower blood cholesterol levels whereas saturated fats contribute to plaque formation in the arteries.
Unsaturated fats or oils are usually of plant origin and contain cis unsaturated fatty acids. Cis and trans indicate the configuration of the molecule around the double bond. If hydrogens are present in the same plane, it is referred to as a cis fat; if the hydrogen atoms are on two different planes, it is referred to as a trans fat. The cis double bond causes a bend or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at room temperature.
Trans Fats
In the food industry, oils are artificially hydrogenated to make them semi-solid and of a consistency desirable for many processed food products. During this hydrogenation process, gas is bubbled through oils to solidify them, and the double bonds of the cis-conformation in the hydrocarbon chain may be converted to double bonds in the trans-conformation.
Margarine, some types of peanut butter, and shortening are examples of artificially-hydrogenated trans fats. Recent studies have shown that an increase in trans fats in the human diet may lead to an increase in levels of low-density lipoproteins (LDL), or “bad” cholesterol, which in turn may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have recently banned the use of trans fats, and food labels are required to display the trans fat content.
Essential Fatty Acids
Essential fatty acids are fatty acids required for biological processes, but not synthesized by the human body. Consequently, they have to be supplemented through ingestion via the diet and are nutritionally very important. Omega-3 fatty acid, or alpha-linoleic acid (ALA), falls into this category and is one of only two fatty acids known to be essential for humans (the other being omega-6 fatty acid, or linoleic acid). These polyunsaturated fatty acids are called omega-3 because the third carbon from the end of the hydrocarbon chain is connected to its neighboring carbon by a double bond. Salmon, trout, and tuna are good sources of omega-3 fatty acids.
Research indicates that omega-3 fatty acids reduce the risk of sudden death from heart attacks, reduce triglycerides in the blood, lower blood pressure, and prevent thrombosis by inhibiting blood clotting. They also reduce inflammation and may help reduce the risk of some cancers in animals. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.05%3A_Organic_Compounds/2.5.02%3A_Lipid_Molecules.txt |
DNA and RNA are nucleic acids that carry out cellular processes, especially the regulation and expression of genes.
Learning Objectives
• Describe the structure of nucleic acids and the types of molecules that contain them
Key Points
• The two main types of nucleic acids are DNA and RNA.
• Both DNA and RNA are made from nucleotides, each containing a five-carbon sugar backbone, a phosphate group, and a nitrogen base.
• DNA provides the code for the cell ‘s activities, while RNA converts that code into proteins to carry out cellular functions.
• The sequence of nitrogen bases (A, T, C, G) in DNA is what forms an organism’s traits.
• The nitrogen bases A and T (or U in RNA) always go together and C and G always go together, forming the 5′-3′ phosphodiester linkage found in the nucleic acid molecules.
Key Terms
• nucleotide: the monomer comprising DNA or RNA molecules; consists of a nitrogenous heterocyclic base that can be a purine or pyrimidine, a five-carbon pentose sugar, and a phosphate group
• genome: the cell’s complete genetic information packaged as a double-stranded DNA molecule
• monomer: A relatively small molecule which can be covalently bonded to other monomers to form a polymer.
Types of Nucleic Acids
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is found in the nucleus of eukaryotes and in the chloroplasts and mitochondria. In prokaryotes, the DNA is not enclosed in a membranous envelope, but rather free-floating within the cytoplasm.
The entire genetic content of a cell is known as its genome and the study of genomes is genomics. In eukaryotic cells, but not in prokaryotes, DNA forms a complex with histone proteins to form chromatin, the substance of eukaryotic chromosomes. A chromosome may contain tens of thousands of genes. Many genes contain the information to make protein products; other genes code for RNA products. DNA controls all of the cellular activities by turning the genes “on” or “off. ”
The other type of nucleic acid, RNA, is mostly involved in protein synthesis. In eukaryotes, the DNA molecules never leave the nucleus but instead use an intermediary to communicate with the rest of the cell. This intermediary is the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA, and microRNA—are involved in protein synthesis and its regulation.
Nucleotides
DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a polynucleotide: DNA or RNA. Each nucleotide is made up of three components:
1. a nitrogenous base
2. a pentose (five-carbon) sugar
3. a phosphate group
Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to one or more phosphate groups.
Nitrogenous Base
The nitrogenous bases are organic molecules and are so named because they contain carbon and nitrogen. They are bases because they contain an amino group that has the potential of binding an extra hydrogen, and thus, decreasing the hydrogen ion concentration in its environment, making it more basic. Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T).
Adenine and guanine are classified as purines. The primary structure of a purine consists of two carbon-nitrogen rings. Cytosine, thymine, and uracil are classified as pyrimidines which have a single carbon-nitrogen ring as their primary structure. Each of these basic carbon-nitrogen rings has different functional groups attached to it. In molecular biology shorthand, the nitrogenous bases are simply known by their symbols A, T, G, C, and U. DNA contains A, T, G, and C whereas RNA contains A, U, G, and C.
Five-Carbon Sugar
The pentose sugar in DNA is deoxyribose and in RNA it is ribose. The difference between the sugars is the presence of the hydroxyl group on the second carbon of the ribose and hydrogen on the second carbon of the deoxyribose. The carbon atoms of the sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as “one prime”).
Phosphate Group
The phosphate residue is attached to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms a 5′3′ phosphodiester linkage. The phosphodiester linkage is not formed by simple dehydration reaction like the other linkages connecting monomers in macromolecules: its formation involves the removal of two phosphate groups. A polynucleotide may have thousands of such phosphodiester linkages. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.05%3A_Organic_Compounds/2.5.03%3A_DNA_and_RNA.txt |
An amino acid contains an amino group, a carboxyl group, and an R group, and it combines with other amino acids to form polypeptide chains.
Learning Objectives
• Describe the structure of an amino acid and the features that confer its specific properties
Key Points
• Each amino acid contains a central C atom, an amino group (NH2), a carboxyl group (COOH), and a specific R group.
• The R group determines the characteristics (size, polarity, and pH) for each type of amino acid.
• Peptide bonds form between the carboxyl group of one amino acid and the amino group of another through dehydration synthesis.
• A chain of amino acids is a polypeptide.
Key Terms
• amino acid: Any of 20 naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
• R group: The R group is a side chain specific to each amino acid that confers particular chemical properties to that amino acid.
• polypeptide: Any polymer of (same or different) amino acids joined via peptide bonds.
Structure of an Amino Acid
Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. In the aqueous environment of the cell, the both the amino group and the carboxyl group are ionized under physiological conditions, and so have the structures -NH3+ and -COO, respectively. Every amino acid also has another atom or group of atoms bonded to the central atom known as the R group. This R group, or side chain, gives each amino acid proteins specific characteristics, including size, polarity, and pH.
Types of Amino Acids
The name “amino acid” is derived from the amino group and carboxyl-acid-group in their basic structure. There are 21 amino acids present in proteins, each with a specific R group or side chain. Ten of these are considered essential amino acids in humans because the human body cannot produce them and they must be obtained from the diet. All organisms have different essential amino acids based on their physiology.
Characteristics of Amino Acids
Which categories of amino acid would you expect to find on the surface of a soluble protein, and which would you expect to find in the interior? What distribution of amino acids would you expect to find in a protein embedded in a lipid bilayer?
The chemical composition of the side chain determines the characteristics of the amino acid. Amino acids such as valine, methionine, and alanine are nonpolar (hydrophobic), while amino acids such as serine, threonine, and cysteine are polar (hydrophilic). The side chains of lysine and arginine are positively charged so these amino acids are also known as basic (high pH) amino acids. Proline is an exception to the standard structure of an amino acid because its R group is linked to the amino group, forming a ring-like structure.
Amino acids are represented by a single upper case letter or a three-letter abbreviation. For example, valine is known by the letter V or the three-letter symbol val.
Peptide Bonds
The sequence and the number of amino acids ultimately determine the protein’s shape, size, and function. Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond. When two amino acids are covalently attached by a peptide bond, the carboxyl group of one amino acid and the amino group of the incoming amino acid combine and release a molecule of water. Any reaction that combines two monomers in a reaction that generates H2O as one of the products is known as a dehydration reaction, so peptide bond formation is an example of a dehydration reaction.
Polypeptide Chains
The resulting chain of amino acids is called a polypeptide chain. Each polypeptide has a free amino group at one end. This end is called the N terminal, or the amino terminal, and the other end has a free carboxyl group, also known as the C or carboxyl terminal. When reading or reporting the amino acid sequence of a protein or polypeptide, the convention is to use the N-to-C direction. That is, the first amino acid in the sequence is assumed to the be one at the N terminal and the last amino acid is assumed to be the one at the C terminal.
Although the terms polypeptide and protein are sometimes used interchangeably, a polypeptide is technically any polymer of amino acids, whereas the term protein is used for a polypeptide or polypeptides that have folded properly, combined with any additional components needed for proper functioning, and is now functional. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.05%3A_Organic_Compounds/2.5.04%3A_Amino_Acids.txt |
Proteins perform many essential physiological functions, including catalyzing biochemical reactions.
Learning Objectives
• Differentiate among the types and functions of proteins
Key Points
• Proteins are essential for the main physiological processes of life and perform functions in every system of the human body.
• A protein’s shape determines its function.
• Proteins are composed of amino acid subunits that form polypeptide chains.
• Enzymes catalyze biochemical reactions by speeding up chemical reactions, and can either break down their substrate or build larger molecules from their substrate.
• The shape of an enzyme’s active site matches the shape of the substrate.
• Hormones are a type of protein used for cell signaling and communication.
Key Terms
• amino acid: Any of 20 naturally occurring α-amino acids (having the amino, and carboxylic acid groups on the same carbon atom), and a variety of side chains, that combine, via peptide bonds, to form proteins.
• polypeptide: Any polymer of (same or different) amino acids joined via peptide bonds.
• catalyze: To accelerate a process.
Types and Functions of Proteins
Proteins perform essential functions throughout the systems of the human body. These long chains of amino acids are critically important for:
• catalyzing chemical reactions
• synthesizing and repairing DNA
• transporting materials across the cell
• receiving and sending chemical signals
• responding to stimuli
• providing structural support
Proteins (a polymer) are macromolecules composed of amino acid subunits (the monomers ). These amino acids are covalently attached to one another to form long linear chains called polypeptides, which then fold into a specific three-dimensional shape. Sometimes these folded polypeptide chains are functional by themselves. Other times they combine with additional polypeptide chains to form the final protein structure. Sometimes non-polypeptide groups are also required in the final protein. For instance, the blood protein hemogobin is made up of four polypeptide chains, each of which also contains a heme molecule, which is ring structure with an iron atom in its center.
Proteins have different shapes and molecular weights, depending on the amino acid sequence. For example, hemoglobin is a globular protein, which means it folds into a compact globe-like structure, but collagen, found in our skin, is a fibrous protein, which means it folds into a long extended fiber-like chain. You probably look similar to your family members because you share similar proteins, but you look different from strangers because the proteins in your eyes, hair, and the rest of your body are different.
Because form determines function, any slight change to a protein’s shape may cause the protein to become dysfunctional. Small changes in the amino acid sequence of a protein can cause devastating genetic diseases such as Huntington’s disease or sickle cell anemia.
Enzymes
Enzymes are proteins that catalyze biochemical reactions, which otherwise would not take place. These enzymes are essential for chemical processes like digestion and cellular metabolism. Without enzymes, most physiological processes would proceed so slowly (or not at all) that life could not exist.
Because form determines function, each enzyme is specific to its substrates. The substrates are the reactants that undergo the chemical reaction catalyzed by the enzyme. The location where substrates bind to or interact with the enzyme is known as the active site, because that is the site where the chemistry occurs. When the substrate binds to its active site at the enzyme, the enzyme may help in its breakdown, rearrangement, or synthesis. By placing the substrate into a specific shape and microenvironment in the active site, the enzyme encourages the chemical reaction to occur. There are two basic classes of enzymes:
• Catabolic enzymes: enzymes that break down their substrate
• Anabolic enzymes: enzymes that build more complex molecules from their substrates
Enzymes are essential for digestion: the process of breaking larger food molecules down into subunits small enough to diffuse through a cell membrane and to be used by the cell. These enzymes include amylase, which catalyzes the digestion carbohydrates in the mouth and small intestine; pepsin, which catalyzes the digestion of proteins in the stomach; lipase, which catalyzes reactions need to emulsify fats in the small intestine; and trypsin, which catalyzes the further digestion of proteins in the small intestine.
Enzymes are also essential for biosynthesis: the process of making new, complex molecules from the smaller subunits that are provided to or generated by the cell. These biosynthetic enzymes include DNA Polymerase, which catalyzes the synthesis of new strands of the genetic material before cell division; fatty acid synthetase, which the synthesis of new fatty acids for fat or membrane lipid formation; and components of the ribosome, which catalyzes the formation of new polypeptides from amino acid monomers.
Hormones
Some proteins function as chemical-signaling molecules called hormones. These proteins are secreted by endocrine cells that act to control or regulate specific physiological processes, which include growth, development, metabolism, and reproduction. For example, insulin is a protein hormone that helps to regulate blood glucose levels. Other proteins act as receptors to detect the concentrations of chemicals and send signals to respond. Some types of hormones, such as estrogen and testosterone, are lipid steroids, not proteins.
Other Protein Functions
Proteins perform essential functions throughout the systems of the human body. In the respiratory system, hemoglobin (composed of four protein subunits) transports oxygen for use in cellular metabolism. Additional proteins in the blood plasma and lymph carry nutrients and metabolic waste products throughout the body. The proteins actin and tubulin form cellular structures, while keratin forms the structural support for the dead cells that become fingernails and hair. Antibodies, also called immunoglobins, help recognize and destroy foreign pathogens in the immune system. Actin and myosin allow muscles to contract, while albumin nourishes the early development of an embryo or a seedling. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.05%3A_Organic_Compounds/2.5.05%3A_Types_and_Functions_of_Protiens.txt |
Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions to harness the energy within the bonds of ATP.
Learning Objectives
• Explain the role of ATP as the currency of cellular energy
Key Points
• Adenosine triphosphate is composed of the nitrogenous base adenine, the five-carbon sugar ribose, and three phosphate groups.
• ATP is hydrolyzed to ADP in the reaction ATP+H2O→ADP+Pi+ free energy; the calculated ∆G for the hydrolysis of 1 mole of ATP is -57 kJ/mol.
• ADP is combined with a phosphate to form ATP in the reaction ADP+Pi+free energy→ATP+H2O.
• The energy released from the hydrolysis of ATP into ADP is used to perform cellular work, usually by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions.
• Sodium-potassium pumps use the energy derived from exergonic ATP hydrolysis to pump sodium and potassium ions across the cell membrane while phosphorylation drives the endergonic reaction.
Key Terms
• energy coupling: Energy coupling occurs when the energy produced by one reaction or system is used to drive another reaction or system.
• endergonic: Describing a reaction that absorbs (heat) energy from its environment.
• exergonic: Describing a reaction that releases energy (heat) into its environment.
• free energy: Gibbs free energy is a thermodynamic potential that measures the useful or process-initiating work obtainable from a thermodynamic system at a constant temperature and pressure (isothermal, isobaric).
• hydrolysis: A chemical process of decomposition involving the splitting of a bond by the addition of water.
ATP: Adenosine Triphosphate
Adenosine triphosphate (ATP) is the energy currency for cellular processes. ATP provides the energy for both energy-consuming endergonic reactions and energy-releasing exergonic reactions, which require a small input of activation energy. When the chemical bonds within ATP are broken, energy is released and can be harnessed for cellular work. The more bonds in a molecule, the more potential energy it contains. Because the bond in ATP is so easily broken and reformed, ATP is like a rechargeable battery that powers cellular process ranging from DNA replication to protein synthesis.
Molecular Structure
Adenosine triphosphate (ATP) is comprised of the molecule adenosine bound to three phosphate groups. Adenosine is a nucleoside consisting of the nitrogenous base adenine and the five-carbon sugar ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. The two bonds between the phosphates are equal high-energy bonds (phosphoanhydride bonds) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. The bond between the beta and gamma phosphate is considered “high-energy” because when the bond breaks, the products [adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)] have a lower free energy than the reactants (ATP and a water molecule). ATP breakdown into ADP and Pi is called hydrolysis because it consumes a water molecule (hydro-, meaning “water”, and lysis, meaning “separation”).
ATP Hydrolysis and Synthesis
ATP is hydrolyzed into ADP in the following reaction:
ATP+H2O→ADP+Pi+free energy
Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction combines ADP + Pi to regenerate ATP from ADP. Since ATP hydrolysis releases energy, ATP synthesis must require an input of free energy.
ADP is combined with a phosphate to form ATP in the following reaction:
ADP+Pi+free energy→ATP+H2O
ATP and Energy Coupling
Exactly how much free energy (∆G) is released with the hydrolysis of ATP, and how is that free energy used to do cellular work? The calculated ∆G for the hydrolysis of one mole of ATP into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). However, this is only true under standard conditions, and the ∆G for the hydrolysis of one mole of ATP in a living cell is almost double the value at standard conditions: 14 kcal/mol (−57 kJ/mol).
ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. To harness the energy within the bonds of ATP, cells use a strategy called energy coupling.
Energy Coupling in Sodium-Potassium Pumps
Cells couple the exergonic reaction of ATP hydrolysis with the endergonic reactions of cellular processes. For example, transmembrane ion pumps in nerve cells use the energy from ATP to pump ions across the cell membrane and generate an action potential. The sodium-potassium pump (Na+/K+ pump) drives sodium out of the cell and potassium into the cell. When ATP is hydrolyzed, it transfers its gamma phosphate to the pump protein in a process called phosphorylation. The Na+/K+ pump gains the free energy and undergoes a conformational change, allowing it to release three Na+ to the outside of the cell. Two extracellular K+ ions bind to the protein, causing the protein to change shape again and discharge the phosphate. By donating free energy to the Na+/K+ pump, phosphorylation drives the endergonic reaction.
Energy Coupling in Metabolism
During cellular metabolic reactions, or the synthesis and breakdown of nutrients, certain molecules must be altered slightly in their conformation to become substrates for the next step in the reaction series. In the very first steps of cellular respiration, glucose is broken down through the process of glycolysis. ATP is required for the phosphorylation of glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction causes a conformational change that allows enzymes to convert the phosphorylated glucose molecule to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. In this example, the exergonic reaction of ATP hydrolysis is coupled with the endergonic reaction of converting glucose for use in the metabolic pathway.
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Learning Objectives
• Analyze the importance of carbohydrate metabolism to energy production
Metabolism of Carbohydrates
Carbohydrates are one of the major forms of energy for animals and plants. Plants build carbohydrates using light energy from the sun (during the process of photosynthesis), while animals eat plants or other animals to obtain carbohydrates. Plants store carbohydrates in long polysaccharides chains called starch, while animals store carbohydrates as the molecule glycogen. These large polysaccharides contain many chemical bonds and therefore store a lot of chemical energy. When these molecules are broken down during metabolism, the energy in the chemical bonds is released and can be harnessed for cellular processes.
Energy Production from Carbohydrates (Cellular Respiration )
The metabolism of any monosaccharide (simple sugar) can produce energy for the cell to use. Excess carbohydrates are stored as starch in plants and as glycogen in animals, ready for metabolism if the energy demands of the organism suddenly increase. When those energy demands increase, carbohydrates are broken down into constituent monosaccharides, which are then distributed to all the living cells of an organism. Glucose (C6H12O6) is a common example of the monosaccharides used for energy production.
Inside the cell, each sugar molecule is broken down through a complex series of chemical reactions. As chemical energy is released from the bonds in the monosaccharide, it is harnessed to synthesize high-energy adenosine triphosphate (ATP) molecules. ATP is the primary energy currency of all cells. Just as the dollar is used as currency to buy goods, cells use molecules of ATP to perform immediate work and power chemical reactions.
The breakdown of glucose during metabolism is call cellular respiration can be described by the equation:
$\ce{C6H12O6 + 6O2 → 6CO2 + 6H2O + energy}$
Producing Carbohydrates (Photosynthesis)
Plants and some other types of organisms produce carbohydrates through the process called photosynthesis. During photosynthesis, plants convert light energy into chemical energy by building carbon dioxide gas molecules (CO2) into sugar molecules like glucose. Because this process involves building bonds to synthesize a large molecule, it requires an input of energy (light) to proceed. The synthesis of glucose by photosynthesis is described by this equation (notice that it is the reverse of the previous equation):
$\ce{6CO2 + 6H2O + energy → C6H12O6 + 6O2}$
As part of plants’ chemical processes, glucose molecules can be combined with and converted into other types of sugars. In plants, glucose is stored in the form of starch, which can be broken down back into glucose via cellular respiration in order to supply ATP.
Key Points
• The breakdown of glucose living organisms utilize to produce energy is described by the equation: $\ce{C6H12O6 + 6O2 → 6CO2 + 6H2O + energy} \nonumber$
• The photosynthetic process plants utilize to synthesize glucose is described by the equation: $\ce{6CO2 + 6H2O + energy → C6H12O6 + 6O2} \nonumber$
• Glucose that is consumed is used to make energy in the form of ATP, which is used to perform work and power chemical reactions in the cell.
• During photosynthesis, plants convert light energy into chemical energy that is used to build molecules of glucose.
Key Terms
• adenosine triphosphate: a multifunctional nucleoside triphosphate used in cells as a coenzyme, often called the “molecular unit of energy currency” in intracellular energy transfer
• glucose: a simple monosaccharide (sugar) with a molecular formula of C6H12O6C6H12O6C6H12O6; it is a principal source of energy for cellular metabolism | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.06%3A_Energy/2.6.01%3A_Metabolism_of_Carbohydrates.txt |
ΔG determines the direction and extent of chemical change.
Learning Objectives
• Recall the possible free energy changes for chemical reactions.
Key Points
• If the free energy of the reactants is greater than that of the products, the entropy of the world will increase when the reaction takes place as written, and so the reaction will tend to take place spontaneously.
• If the free energy of the products exceeds that of the reactants, then the reaction will not take place.
• An important consequence of the one-way downward path of the free energy is that once it reaches its minimum possible value, net change comes to a halt.
• In a spontaneous change, Gibbs energy always decreases and never increases.
Key Terms
• spontaneous change: A spontaneous process is the time-evolution of a system in which it releases free energy (usually as heat) and moves to a lower, more thermodynamically stable energy state.
The Direction and Extent of Chemical Change
ΔG determines the direction and extent of chemical change. Remember that ΔG is meaningful only for changes in which the temperature and pressure remain constant. These are the conditions under which most reactions are carried out in the laboratory. The system is usually open to the atmosphere (constant pressure) and the process is started and ended at room temperature (after any heat that has been added or which was liberated by the reaction has dissipated.)
The importance of the Gibbs function can hardly be over-stated: it determines whether a given chemical change is thermodynamically possible. Thus, if the free energy of the reactants is greater than that of the products, the entropy of the world will increase and the reaction takes place spontaneously. Conversely, if the free energy of the products exceeds that of the reactants, the reaction will not take place.
In a spontaneous change, Gibbs energy always decreases and never increases. This of course reflects the fact that the entropy of the world behaves in the exact opposite way (owing to the negative sign in the TΔS term). Here is an example:
H2O(liquid)→H2O(ice)H2O(liquid)→H2O(ice)
Water below zero degrees Celsius undergoes a decrease in its entropy, but the heat released into the surroundings more than compensates for this so the entropy of the world increases, the free energy of the H2O diminishes, and the process proceeds spontaneously.
An important consequence of the one-way downward path of the free energy is that once it reaches its minimum possible value, net change comes to a halt. This, of course, represents the state of chemical equilibrium. These relations are summarized as follows:
• ΔG<0ΔG<0: The reaction will occur spontaneously to the right.
• ΔG>0ΔG>0: The reaction will occur spontaneously to the left.
• ΔG=0ΔG=0: The reaction is at equilibrium and will not proceed in either direction.
Conditions for Spontaneous Change
Recall the condition for spontaneous change:
ΔG = ΔH – TΔS < 0
where ΔG = change in Gibbs free energy, ΔH = change in enthalpy, T = absolute temperature, and ΔS = change in entropy
It is apparent that the temperature dependence of ΔG depends almost entirely on the entropy change associated with the process. (it is appropriate to say “almost” because the values of ΔH and ΔS are themselves slightly temperature dependent; both gradually increase with temperature). In particular, notice that in the above equation the sign of the entropy change determines whether the reaction becomes more or less spontaneous as the temperature is raised.
For any given reaction, the sign of ΔH can also be positive or negative. This means that there are four possibilities for the influence that temperature can have on the spontaneity of a process:
Case 1: ΔH < 0 and ΔS > 0
Under these conditions, both the ΔH and TΔS terms will be negative, so ΔG will be negative regardless of the temperature. An exothermic reaction whose entropy increases will be spontaneous at all temperatures.
Case 2: ΔH < 0 and ΔS < 0
If the reaction is sufficiently exothermic it can force ΔG to be negative only at temperatures below which |TΔS| < |ΔH|. This means that there is a temperature defined by T=ΔHΔST=ΔHΔS at which the reaction is at equilibrium; the reaction will only proceed spontaneously below this temperature. The freezing of a liquid or the condensation of a gas are the most common examples of this condition.
Case 3: ΔH > 0 and ΔS > 0
This is the reverse of the previous case; the entropy increase must overcome the handicap of an endothermic process so that TΔS > ΔH. Since the effect of the temperature is to “magnify” the influence of a positive ΔS, the process will be spontaneous at temperatures above T=ΔHΔST=ΔHΔS. (Think of melting and boiling. )
Case 4: ΔH > 0 and ΔS < 0
With both ΔH and ΔS working against it, this kind of process will not proceed spontaneously at any temperature. Substance A always has a greater number of accessible energy states, and is therefore always the preferred form. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.06%3A_Energy/2.6.02%3A_Free_Energy_Changes_in_Chemical_Reactions.txt |
The enthalpy of reaction measures the heat released/absorbed by a reaction that occurs at constant pressure.
Learning Objectives
• Review enthalpy of reaction
Key Points
• At constant volume, the heat of reaction is equal to the change in the internal energy of the system.
• At constant pressure, the heat of reaction is equal to the enthalpy change of the system.
• Most chemical reactions occur at constant pressure, so enthalpy is more often used to measure heats of reaction than internal energy.
Key Terms
• enthalpy: In thermodynamics, a measure of the heat content of a chemical or physical system.
• internal energy: A property characteristic of the state of a thermodynamic system, the change in which is equal to the heat absorbed minus the work done by the system.
• first law of thermodynamics: Heat and work are forms of energy transfer; the internal energy of a closed system changes as heat and work are transferred into or out of it.
In thermodynamics, work (W) is defined as the process of an energy transfer from one system to another. The first law of thermodynamics states that the energy of a closed system is equal to the amount of heat supplied to the system minus the amount of work done by the system on its surroundings. The amount of energy for a closed system is written as follows:
ΔU=Q−WΔU=Q−W
In this equation, U is the total energy of the system, Q is heat, and W is work. In chemical systems, the most common type of work is pressure-volume (PV) work, in which the volume of a gas changes. Substituting this in for work in the above equation, we can define the change in internal energy for a chemical system:
ΔU=Q−PΔVΔU=Q−PΔV
Internal Energy Change at Constant Volume
Let’s examine the internal energy change, ΔUΔU, at constant volume. At constant volume, ΔV=0ΔV=0, the equation for the change in internal energy reduces to the following:
ΔU=QVΔU=QV
The subscript V is added to Q to indicate that this is the heat transfer associated with a chemical process at constant volume. This internal energy is often very difficult to calculate in real life settings, though, because chemists tend to run their reactions in open flasks and beakers that allow gases to escape to the atmosphere. Therefore, volume is not held constant, and calculating ΔUΔU becomes problematic. To correct for this, we introduce the concept of enthalpy, which is much more commonly used by chemists.
Standard Enthalpy of Reaction
The enthalpy of reaction is defined as the internal energy of the reaction system, plus the product of pressure and volume. It is given by:
H=U+PVH=U+PV
By adding the PV term, it becomes possible to measure a change in energy within a chemical system, even when that system does work on its surroundings. Most often, we are interested in the change in enthalpy of a given reaction, which can be expressed as follows:
ΔH=ΔU+PΔVΔH=ΔU+PΔV
When you run a chemical reaction in a laboratory, the reaction occurs at constant pressure, because the atmospheric pressure around us is relatively constant. We will examine the change in enthalpy for a reaction at constant pressure, in order to see why enthalpy is such a useful concept for chemists.
Enthalpy of Reaction at Constant Pressure
Let’s look once again at the change in enthalpy for a given chemical process. It is given as follows:
ΔH=ΔU+PΔVΔH=ΔU+PΔV
However, we also know that:
ΔU=Q−W=Q−PΔVΔU=Q−W=Q−PΔV
Substituting to combine these two equations, we have:
ΔH=Q−PΔV+PΔV=QPΔH=Q−PΔV+PΔV=QP
Thus, at constant pressure, the change in enthalpy is simply equal to the heat released/absorbed by the reaction. Due to this relation, the change in enthalpy is often referred to simply as the “heat of reaction.”
Enthalpy: An explanation of why enthalpy can be viewed as “heat content” in a constant pressure system.
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• NADPH. Provided by: Wiktionary. Located at: http://en.wiktionary.org/wiki/NADPH. License: CC BY-SA: Attribution-ShareAlike
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Learning Objectives
• Explain the effect of an enzyme on chemical equilibrium
Control of Metabolism Through Enzyme Regulation
Cellular needs and conditions vary from cell to cell and change within individual cells over time. For example, a stomach cell requires a different amount of energy than a skin cell, fat storage cell, blood cell, or nerve cell. The same stomach cell may also need more energy immediately after a meal and less energy between meals.
A cell’s function is encapsulated by the chemical reactions it can carry out. Enzymes lower the activation energies of chemical reactions; in cells, they promote those reactions that are specific to the cell’s function. Because enzymes ultimately determine which chemical reactions a cell can carry out and the rate at which they can proceed, they are key to cell functionality.
Competitive and Noncompetitive Inhibition
The cell uses specific molecules to regulate enzymes in order to promote or inhibit certain chemical reactions. Sometimes it is necessary to inhibit an enzyme to reduce a reaction rate, and there is more than one way for this inhibition to occur. In competitive inhibition, an inhibitor molecule is similar enough to a substrate that it can bind to the enzyme’s active site to stop it from binding to the substrate. It “competes” with the substrate to bind to the enzyme.
In noncompetitive inhibition, an inhibitor molecule binds to the enzyme at a location other than the active site (an allosteric site). The substrate can still bind to the enzyme, but the inhibitor changes the shape of the enzyme so it is no longer in optimal position to catalyze the reaction.
Allosteric Inhibition and Activation
In noncompetitive allosteric inhibition, inhibitor molecules bind to an enzyme at the allosteric site. Their binding induces a conformational change that reduces the affinity of the enzyme’s active site for its substrate. The binding of this allosteric inhibitor changes the conformation of the enzyme and its active site, so the substrate is not able to bind. This prevents the enzyme from lowering the activation energy of the reaction, and the reaction rate is reduced.
However, allosteric inhibitors are not the only molecules that bind to allosteric sites. Allosteric activators can increase reaction rates. They bind to an allosteric site which induces a conformational change that increases the affinity of the enzyme’s active site for its substrate. This increases the reaction rate.
Cofactors and Coenzymes
Many enzymes only work if bound to non-protein helper molecules called cofactors and coenzymes. Binding to these molecules promotes optimal conformation and function for their respective enzymes. These molecules bind temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds.
Cofactors are inorganic ions such as iron (Fe2+) and magnesium (Mg2+). For example, DNA polymerase requires a zinc ion (Zn2+) to build DNA molecules. Coenzymes are organic helper molecules with a basic atomic structure made up of carbon and hydrogen. The most common coenzymes are dietary vitamins. Vitamin C is a coenzyme for multiple enzymes that take part in building collagen, an important component of connective tissue. Pyruvate dehydrogenase is a complex of several enzymes that requires one cofactor and five different organic coenzymes to catalyze its chemical reaction. The availability of various cofactors and coenzymes regulates enzyme function.
Enzyme Compartmentalization
In eukaryotic cells, molecules such as enzymes are usually compartmentalized into different organelles. This organization contributes to enzyme regulation because certain cellular processes are contained in separate organelles. For example, the enzymes involved in the later stages of cellular respiration carry out reactions exclusively in the mitochondria. The enzymes involved in the digestion of cellular debris and foreign materials are located within lysosomes.
Feedback Inhibition in Metabolic Pathways
Feedback inhibition is when a reaction product is used to regulate its own further production. Cells have evolved to use feedback inhibition to regulate enzyme activity in metabolism, by using the products of the enzymatic reactions to inhibit further enzyme activity. Metabolic reactions, such as anabolic and catabolic processes, must proceed according to the demands of the cell. In order to maintain chemical equilibrium and meet the needs of the cell, some metabolic products inhibit the enzymes in the chemical pathway while some reactants activate them.
The production of both amino acids and nucleotides is controlled through feedback inhibition. For an example of feedback inhibition, consider ATP. It is the product of the catabolic metabolism of sugar (cellular respiration), but it also acts as an allosteric regulator for the same enzymes that produced it. ATP is an unstable molecule that can spontaneously dissociate into ADP; if too much ATP were present, most of it would go to waste. This feedback inhibition prevents the production of additional ATP if it is already abundant. However, while ATP is an inhibitor, ADP is an allosteric activator. When levels of ADP are high compared to ATP levels, ADP triggers the catabolism of sugar to produce more ATP.
Key Points
• In competitive inhibition, an inhibitor molecule competes with a substrate by binding to the enzyme ‘s active site so the substrate is blocked.
• In noncompetitive inhibition (also known as allosteric inhibition), an inhibitor binds to an allosteric site; the substrate can still bind to the enzyme, but the enzyme is no longer in optimal position to catalyze the reaction.
• Allosteric inhibitors induce a conformational change that changes the shape of the active site and reduces the affinity of the enzyme’s active site for its substrate.
• Allosteric activators induce a conformational change that changes the shape of the active site and increases the affinity of the enzyme’s active site for its substrate.
• Feedback inhibition involves the use of a reaction product to regulate its own further production.
• Inorganic cofactors and organic coenzymes promote optimal enzyme orientation and function.
• Vitamins act as coenzymes (or precursors to coenzymes) and are necessary for enzymes to function.
Key Terms
• coenzyme: An organic molecule that is necessary for an enzyme to function.
• allosteric site: A site other than the active site on an enzyme.
• cofactor: An inorganic molecule that is necessary for an enzyme to function. | textbooks/bio/Microbiology/Microbiology_(Boundless)/02%3A_Chemistry/2.07%3A_Enzymes/2.7.01%3A_Control_of_Metabolism_Through_Enzyme_Regulation.txt |
Enzymes catalyze chemical reactions by lowering activation energy barriers and converting substrate molecules to products.
Learning Objectives
• Describe models of substrate binding to an enzyme’s active site.
Key Points
• The enzyme ‘s active site binds to the substrate.
• Increasing the temperature generally increases the rate of a reaction, but dramatic changes in temperature and pH can denature an enzyme, thereby abolishing its action as a catalyst.
• The induced fit model states an substrate binds to an active site and both change shape slightly, creating an ideal fit for catalysis.
• When an enzyme binds its substrate it forms an enzyme-substrate complex.
• Enzymes promote chemical reactions by bringing substrates together in an optimal orientation, thus creating an ideal chemical environment for the reaction to occur.
• The enzyme will always return to its original state at the completion of the reaction.
Key Terms
• substrate: A reactant in a chemical reaction is called a substrate when acted upon by an enzyme.
• induced fit: Proposes that the initial interaction between enzyme and substrate is relatively weak, but that these weak interactions rapidly induce conformational changes in the enzyme that strengthen binding.
• active site: The active site is the part of an enzyme to which substrates bind and where a reaction is catalyzed.
Enzyme Active Site and Substrate Specificity
Enzymes bind with chemical reactants called substrates. There may be one or more substrates for each type of enzyme, depending on the particular chemical reaction. In some reactions, a single-reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products.
The enzyme’s active site binds to the substrate. Since enzymes are proteins, this site is composed of a unique combination of amino acid residues (side chains or R groups). Each amino acid residue can be large or small; weakly acidic or basic; hydrophilic or hydrophobic; and positively-charged, negatively-charged, or neutral. The positions, sequences, structures, and properties of these residues create a very specific chemical environment within the active site. A specific chemical substrate matches this site like a jigsaw puzzle piece and makes the enzyme specific to its substrate.
Active Sites and Environmental Conditions
Environmental conditions can affect an enzyme’s active site and, therefore, the rate at which a chemical reaction can proceed. Increasing the environmental temperature generally increases reaction rates because the molecules are moving more quickly and are more likely to come into contact with each other.
However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the enzyme and change its shape. If the enzyme changes shape, the active site may no longer bind to the appropriate substrate and the rate of reaction will decrease. Dramatic changes to the temperature and pH will eventually cause enzymes to denature.
Induced Fit and Enzyme Function
For many years, scientists thought that enzyme-substrate binding took place in a simple “lock-and-key” fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view called induced fit. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the substrate. This dynamic binding maximizes the enzyme’s ability to catalyze its reaction.
Enzyme-Substrate Complex
When an enzyme binds its substrate, it forms an enzyme-substrate complex. This complex lowers the activation energy of the reaction and promotes its rapid progression by providing certain ions or chemical groups that actually form covalent bonds with molecules as a necessary step of the reaction process. Enzymes also promote chemical reactions by bringing substrates together in an optimal orientation, lining up the atoms and bonds of one molecule with the atoms and bonds of the other molecule. This can contort the substrate molecules and facilitate bond-breaking. The active site of an enzyme also creates an ideal environment, such as a slightly acidic or non-polar environment, for the reaction to occur. The enzyme will always return to its original state at the completion of the reaction. One of the important properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme is done catalyzing a reaction, it releases its products (substrates).
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Thumbnail: A compound microscope in a Biology lab. (CC -BY-SA 4.0; Acagastya).
03: Microscopy
Microbes are often very small, even in comparison to microscopic cells from animals.
Learning Objectives
• Recall the size of microbes in comparison to human cells and viruses
Key Points
• Microbes are generally described as being microscopic in size. Therefore, they are smaller than a human eye can see.
• The size of microbes can be hard to imagine because they are so small. In comparison to animal cells, microbes tend to be smaller. They are about 1/10th the size of a typical human cell.
• Microbes are generally measured in the scale of one millionth of a meter, which is known as a micrometer.
Key Terms
• protozoan: Any of the diverse group of eukaryotes, of the phylum Protozoa, that are primarily unicellular, existing singly or aggregating into colonies, are usually nonphotosynthetic, and are often classified further into phyla according to their capacity for and means of motility, as by pseudopods, flagella, or cilia.
• macroscopic: Visible to the unassisted eye.
Microbiology is the study of microbes. The name of the field is driven by the tool that largely determines if something is a microbe. Basically, microbiology is the study of organisms that one needs to use a microscope to visualize. Of course, there are exceptions. There are types of microscopes that visualize to the atomic level, which is significantly smaller than microbes. Alternatively, there are single cell organisms, such as some types of green algae and some protozoans that are generally studied by microbiologists. These are macroscopic or view-able without a microscope.
The size of microbes can be hard to imagine because they are so small in comparison to what most people see day to day. Even in comparison to animal cells, microbes tend to be smaller. They are about 1/10th the size of a typical human cell. So, a microbe such as a bacteria cell would be the size of a cat or small dog in comparison to a human-sized animal-cell. Viruses are about 1/10th the size of other microbes such as bacteria. Therefore, if a bacteria is the size of cat, then a virus would be about the size of a mouse.
To put a numerical value on microbial size, most measurements of microbes are done with the unit of measure of micrometer, which is one millionth of a meter (one 2,500th of an inch). In relation to something more tangible a period or “. ” is about 0.5 millimeters or 0.5/1,000th of a meter. A typical microbe would be about 1/500th of a period.
Of course there are exceptions. Some unicellular organisms studied by microbiologists are macroscopic. This includes Valonia ventricosa, which can be up to 5 cm in length. It is a member of the Chlorophyta phylum which are a sub-group of green algae. Many types of green algae are not microscopic, but they are often studied by microbiologists.
3.1B: Units of Measurement for Microbes
Measuring microbes presents challenges because they are very small, requiring indirect measures of microbes to understand them better.
Learning Objectives
• Recognize the methods used to measure microbial growth
Key Points
• Understanding microbiological life means quantifying it. Since microbes are so small, this is a challenge.
• The size of a microbe is usually measured in micrometers, or one millionth of a meter.
• There are many aspects of microbes that can be measured in addition to size, including metric like genome size and growth rates.
Key Terms
• flow cytometry: A technique used to sort and classify cells by using fluorescent markers on their surface.
• genome: The complete genetic information (either DNA or, in some viruses, RNA) of an organism, typically expressed in the number of basepairs.
Microbes are broadly defined as organisms that are microscopic. As a result, measuring them can be very difficult. The units used to describe objects on a microscopic length scale are most commonly the Micrometer (oi) – one millionth of 1 meter and smaller units. Most microbes are around 1 micrometer in size. Viruses are typically 1/10th that size. Animal cells are typically around 10 micrometers in size. However, length is not the only measurement that pertains to microbes. Microbes have genomes and these are typically smaller than the genomes of macroscopic organisms such as humans. DNA is measured in base pairs of DNA. For example, the human genome is about 3.4 billion base pairs while the common intestinal bacteria Escherichia coli is 4.6 million base pairs. Additionally, microbes are usually not weighed individually, but can be as an aggregate for various experiments. An estimate of the weight of an individual microbe can be made by estimating the number of microbes. This is especially important for biomass studies where the units of measurement are in units like picog, 10-12 of a kilogram (Kg), nanogram 10-9 of a Kg, and microgram, 10-6 of a Kg (a kilogram is a little over 2 pounds).
Microbial growth is an important measure in understanding microbes. Microbial growth is the division of one microbe into two daughter cells in a process called binary fission. As a result, “local doubling” of the microbial population occurs. Both daughter cells from the division do not necessarily survive. However, if the number surviving exceeds unity on average, the microbial population undergoes exponential growth. The measurement of an exponential microbial growth curve in batch culture was traditionally a part of the training of all microbiologists; The basic means requires bacterial enumeration (cell counting) by direct and individual (microscopic, flow cytometry), direct and bulk (biomass), indirect and individual (colony counting), or indirect and bulk (most probable number, turbidity, nutrient uptake) methods. Since there are limits on space, food, and other factors, actual growth never matches actual measured growth.
3.1C: Refraction and Magnification
Learning Objectives
• Describe refraction and distinguish between convex and concave lenses
The underlying principle of a microscope is that lenses refract light which allows for magnification. Refraction occurs when light travels through an area of space that has a changing index of refraction. The simplest case of refraction occurs when there is an interface between a uniform medium with an index of refraction and another medium with an index of refraction.
Some media have an index of refraction that varies gradually with position. Therefore, light rays curve through the medium rather than traveling in straight lines. This effect is what is responsible for mirages seen on hot days where the changing index of refraction of the air causes the light rays to bend creating the appearance of specular reflections in the distance (as if on the surface of a pool of water).
Taking advantage of the principle of refraction, devices can be built that can focus light. A device that produces converging or diverging light rays due to refraction is known as a lens. In general, two types of lenses exist: convex lenses, which cause parallel light rays to converge, and concave lenses, which cause parallel light rays to diverge. The former property of convex lenses is of special interest to microbiologists. In essence, a convex lens allows magnification. Light reflecting off an object is focused to a point. The simplest example of this that most people know is a magnifying glass. A magnifying glass is one convex lens, and this by itself allows the magnification of objects.
A microscope is basically a series of lenses that take advantage of the nature of refraction. Due to the nature of light, and the maximum amount of refraction that can be possible by a material, there are limits to the amount of magnification that can be done by a light microscope.
Summary
• Convex lenses allow light to converge.
• Concave lenses spread light that travels through it.
• There are limits to the amount of refraction that can be done by a material, and therefore, limits to the amount a microscope can magnify a sample.
Key Terms
• concave: Curved like the inner surface of a sphere or bowl.
• convex: Curved or bowed outward like the outside of a bowl or sphere or circle.
• specular: Pertaining to mirrors; mirror-like, reflective. | textbooks/bio/Microbiology/Microbiology_(Boundless)/03%3A_Microscopy/3.01%3A_Looking_at_Microbes/3.1A%3A_Microbe_Size.txt |
Magnification is the enlargement of an image; resolution is the ability to tell two objects apart.
Learning Objectives
• Define magnification and resolution
Key Points
• Magnification is the ability to make small objects seem larger, such as making a microscopic organism visible.
• Resolution is the ability to distinguish two objects from each other.
• Light microscopy has limits to both its resolution and its magnification.
Key Terms
• airy disks: In optics, the Airy disk (or Airy disc) and Airy pattern are descriptions of the best-focused spot of light that a perfect lens with a circular aperture can make, limited by the diffraction of light.
• diffraction: the breaking up of an electromagnetic wave as it passes a geometric structure (e.g., a slit), followed by reconstruction of the wave by interference
Magnification is the process of enlarging something only in appearance, not in physical size. This enlargement is quantified by a calculated number also called “magnification. ” The term magnification is often confused with the term “resolution,” which describes the ability of an imaging system to show detail in the object that is being imaged. While high magnification without high resolution may make very small microbes visible, it will not allow the observer to distinguishbetween microbes or sub-cellular parts of a microbe. In reality, therefore, microbiologists depend more on resolution, as they want to be able to determine differences between microbes or parts of microbes. However, to be able to distinguish between two objects under a microscope, a viewer must first magnify to a point at which resolution becomes relevant.
Resolution depends on the distance between two distinguishable radiating points. A microscopic imaging system may have many individual components, including a lens and recording and display components. Each of these contributes to the optical resolution of the system, as will the environment in which the imaging is performed. Real optical systems are complex, and practical difficulties often increase the distance between distinguishable point sources.
At very high magnifications with transmitted light, point objects are seen as fuzzy discs surrounded by diffraction rings. These are called Airy disks. The resolving power of a microscope is taken as the ability to distinguish between two closely spaced Airy disks (or, in other words, the ability of the microscope to distinctly reveal adjacent structural detail). It is this effect of diffraction that limits a microscope’s ability to resolve fine details. The extent and magnitude of the diffraction patterns are affected by the wavelength of light (λ), the refractive materials used to manufacture the objective lens, and the numerical aperture (NA) of the objective lens. There is therefore a finite limit beyond which it is impossible to resolve separate points in the objective field. This is known as the diffraction limit.
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Learning Objectives
• Compare and contrast light and electron microscopy.
Cells vary in size. With few exceptions, individual cells cannot be seen with the naked eye, so scientists use microscopes (micro- = “small”; -scope = “to look at”) to study them. A microscope is an instrument that magnifies an object. Most photographs of cells are taken with a microscope; these images can also be called micrographs.
The optics of a microscope’s lenses change the orientation of the image that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when viewed through a microscope, and vice versa. Similarly, if the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Because of the manner by which light travels through the lenses, this system of two lenses produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but they include an additional magnification system that makes the final image appear to be upright).
Light Microscopes
To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter; the head of a pin of is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on the head of a pin.
Most student microscopes are classified as light microscopes. Visible light passes and is bent through the lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells.
Light microscopes, commonly used in undergraduate college laboratories, magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the ability of a microscope to distinguish two adjacent structures as separate: the higher the resolution, the better the clarity and detail of the image. When oil immersion lenses are used for the study of small objects, magnification is usually increased to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes.
Electron Microscopes
In contrast to light microscopes, electron microscopes use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail, it also provides higher resolving power. The method used to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so living cells cannot be viewed with an electron microscope.
In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes.
Key Points
• Light microscopes allow for magnification of an object approximately up to 400-1000 times depending on whether the high power or oil immersion objective is used.
• Light microscopes use visible light which passes and bends through the lens system.
• Electron microscopes use a beam of electrons, opposed to visible light, for magnification.
• Electron microscopes allow for higher magnification in comparison to a light microscope thus, allowing for visualization of cell internal structures.
Key Terms
• resolution: The degree of fineness with which an image can be recorded or produced, often expressed as the number of pixels per unit of length (typically an inch).
• electron: The subatomic particle having a negative charge and orbiting the nucleus; the flow of electrons in a conductor constitutes electricity. | textbooks/bio/Microbiology/Microbiology_(Boundless)/03%3A_Microscopy/3.02%3A_Other_Types_of_Microscopy/3.2A%3A_Microscopy.txt |
Learning Objectives
• Compare and contrast in vitro and in vivo staining
Staining is a technique used in microscopy to enhance contrast in a microscopic image. Stains and dyes are frequently used to highlight structures in microbes for viewing, often with the aid of different microscopes. Stains may be used to define and examine different types of microbes, various stages of cellular life (e.g., the mitotic cycle), and even organelles within individual cells (e.g., mitochondria or chloroplasts).
In-vivo staining is the process of dyeing living tissue — in vivo means “in life” (as contrasted to in-vitro staining). When a certain cell or structure takes on contrasting color(s), its form (morphology) or position within a cell or tissue can be readily seen and studied. The usual purpose is to reveal cytological details that might otherwise not be apparent; however, staining can also reveal where certain chemicals or specific chemical reactions are taking place within cells. In-vitro staining involves coloring cells or structures that have been removed from their biological context. Certain stains are often combined to reveal more details and features than a single stain could reveal alone, and a counterstain is a stain that increases visibility of cells or structures when the principal stain is not sufficient. Scientists and physicians can combine staining with specific protocols for fixation and sample preparation and can use these standard techniques as consistent, repeatable diagnostic tools.
There are an incredible number of stains that can be used in a variety of different methods. What follows here are some common aspects of the process of preparing for in-vitro staining.
• Fixation: This can itself consist of several steps. Fixation aims to preserve the shape of the cells (in this case, microbes) as much as possible. Sometimes heat fixation is used to kill, adhere, and alter the cells so they will accept stains. Most chemical fixatives generate chemical bonds between proteins and other substances within the sample, increasing their rigidity. Common fixatives include formaldehyde, ethanol, methanol, and picric acid.
• Permeabilization: This involves treatment of the cells with (usually) a mild surfactant. This treatment dissolves cell membranes, allowing larger dye molecules to enter the cell’s interior.
• Mounting: This step usually involves attaching the samples to a glass microscope slide for observation and analysis. In some cases, cells may be grown directly on a slide. For samples of loose cells the sample can be directly applied to a slide.
At its simplest, the actual staining process may involve immersing the sample (before or after fixation and mounting) in dye solution, followed by rinsing and observation. Many dyes, however, require the use of a mordant — a chemical compound that reacts with the stain to form an insoluble colored precipitate. When the excess dye solution is washed away, the mordanted stain remains. There is an incredible array of stains that can be used at this step, from those that stain specific microbial types (see the figure below) to those that highlight sub-compartments or organelles of a cell, such as the nucleus or endoplasmic reticulum. Alternatively, negative staining can be employed. This is a simple staining method for bacteria, performed by smearing the cells onto the slide and then applying nigrosin (a black synthetic dye) or Indian ink (an aqueous suspension of carbon particles). After drying, the microorganisms may be viewed in bright field microscopy as lighter inclusions contrast well against the dark environment surrounding them
Live, in-vivo staining microscopy shares many of these steps, with the exception of fixation, which invariably kills the microbe to be examined.
Key Points
• In-vivo staining, which visualizes cells that are alive, and in-vitro staining, which visualizes fixed cells, both have important uses.
• There is a vast array of stains that can be used on microbes that can highlight almost any characteristic of a cell, even organelles within a cell.
• Staining protocols can be complex, but they share some basic steps: preparation, fixation, staining, and mounting.
Key Terms
• surfactant: a surface active agent, or wetting agent, capable of reducing the surface tension of a liquid; typically organic compounds having a hydrophilic “head” and a hydrophobic “tail”
• organelle: a specialized structure found inside cells that carries out a specific life process (e.g., ribosomes, vacuoles)
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• Chlamydia Geimsa Stain CDC. Provided by: Wikimedia. Located at: commons.wikimedia.org/wiki/Fi..._Stain_CDC.jpg. License: Public Domain: No Known Copyright | textbooks/bio/Microbiology/Microbiology_(Boundless)/03%3A_Microscopy/3.02%3A_Other_Types_of_Microscopy/3.2B%3A_General_Staining_Methods.txt |
Learning Objectives
• Generalize the process of dark-field microscopy
Radiance Against a Dark Background
Dark-field microscopy is ideally used to illuminate unstained samples causing them to appear brightly lit against a dark background. This type of microscope contains a special condenser that scatters light and causes it to reflect off the specimen at an angle. Rather than illuminating the sample with a filled cone of light, the condenser is designed to form a hollow cone of light. The light at the apex of the cone is focused at the plane of the specimen; as this light moves past the specimen plane it spreads again into a hollow cone. The objective lens sits in the dark hollow of this cone; although the light travels around and past the objective lens, no rays enter it.
The entire field appears dark when there is no sample on the microscope stage; thus the name dark-field microscopy. When a sample is on the stage, the light at the apex of the cone strikes it. The rays scattered by the sample and captured in the objective lens thus make the image.
Samples observed under dark-field microscopy should be carefully prepared since dust and other particles also scatter the light and are easily detected. Glass slides need to be thoroughly cleaned of extraneous dust and dirt. It may be necessary to filter sample media (agar, water, saline) to exclude confusing contaminants. Sample materials need to be spread thinly; too much material on the slide creates many overlapping layers and edges, making it difficult to interpret structures.
Dark-field microscopy has many applications in microbiology. It allows the visualization of live bacteria, and distinguishes some structure (rods, curved rods, spirals, or cocci) and movement.
Key Points
• In dark-field microscopy, the light reaches the specimen from an angle with the help of an opaque disk.
• The specimen appears lit up agains a dark background.
• Dark-field microscopy is most useful for extremely small living organisms that are invisible in the light microscope.
Key Terms
• condenser: A lens (or combination of lenses) designed to gather light and focus it onto a specimen or part of a mechanism.
3.3B: Phase-Contrast Microscopy
Phase-contrast microscopy visualizes differences in the refractive indexes of different parts of a specimen relative to unaltered light.
Learning Objectives
• Describe the mechanics, advantages, and disadvantages of phase-contrast microscopy
Key Points
• A phase-contrast microscope splits a beam of light into 2 types of light, direct and refracted (reflected) and brings them together to form an image of the specimen.
• Where the lights are “in-phase” the image is brighter, where the lights are “out of phase” the image is darker, and by amplifying these differences in the light, it enhances contrast.
• Phase-contrast microscopy allows for the detailed observation of living organisms, especially the internal structures.
Key Terms
• refractive index: the ratio of the speed of light in air or vacuum to that in another medium.
Phase-contrast microscopy is a method of manipulating light paths through the use of strategically placed rings in order to illuminate transparent objects. Dutch physicist Fritz Zernike developed the technique in the 1930s; for his efforts he was awarded the Nobel Prize in 1953.
In phase-contrast microscopy, parallel beams of light are passed through objects of different densities. The microscope contains special condensers that throw light “out of phase” causing it to pass through the object at different speeds. Internal details and organelles of live, unstained organisms (e.g. mitochondria, lysosomes, and the Golgi body) can be seen clearly with this microscope.
A phase ring in condenser allows a cylinder of light to pass through it while still in phase. Unaltered light hits the phase ring in the lens and is excluded. Light that is slightly altered by passing through a different refractive index is allowed to pass through. Light passing through cellular structures, such as chromosomes or mitochondria is retarded because they have a higher refractive index than the surrounding medium. Elements of lower refractive index advance the wave. Much of the background light is removed and light that constructively or destructively interfered is let through with enhanced contrast.
Phase-contrast microscopy allows the visualization of living cells in their natural state with high contrast and high resolution. This tool works best with a thin specimen and is not ideal for a thick specimen. Phase-contrast images have a characteristic grey background with light and dark features found across the sample. One disadvantage of phase-contrast microscopy is halo formation called halo-light ring. | textbooks/bio/Microbiology/Microbiology_(Boundless)/03%3A_Microscopy/3.03%3A_Other_Types_of_Microscopy/3.3A%3A_Dark-Field_Microscopy.txt |
LEARNING OBJECTIVES
• Describe the principles and different types of interference microscopy
Stereo Light Source
Interference microscopy uses a prism to split light into two slightly diverging beams that then pass through the specimen. It is thus based on measuring the differences in refractive index upon recombining the two beams. Interference occurs when a light beam is retarded or advanced relative to the other.
There are three types of interference microscopy: classical, differential contrast, and fluorescence contrast. Since its introduction in the late 1960s differential interference contrast microscopy (DIC) has been popular in biomedical research because it produces high-resolution images of fine structures by enhancing the contrasted interfaces. The image produced is of a thin optical section and appears three-dimensional, with a shadow around it. This creates a contrast across the specimen that is bright on one side and darker on the other.
The Interference Microscope
The microscope is a bright field light microscope with the addition of the following elements: a polarizer between the light source and the condenser, a DIC beam-splitting prism, a DIC beam-combining prism, and an analyzer. Manipulating the prism changes the beam separation, which alters the contrast of the image. When the two beams pass through the same material across the specimen they produce no interference. When the two beams pass through different material across the specimen such as on the edges, they produce alteration when combined.
Fluorescence differential interference contrast (FLIC) microscopy was developed by combining fluorescence microscopy with DIC to minimize the effects of photobleaching on fluorochromes bound to the stained specimen. The same microscope is equipped to simulataneously image a specimen using DIC and fluorescence illumination.
Key Points
• Interference microscopy is superior to phase-contrast microscopy in its ability to eliminate halos and extra light.
• In differential interference contrast microscopy (DIC), the optical path difference is determined by the product of the refractive index difference (between the specimen and its surrounding medium) and the thickness traversed by a light beam between two points on the optical path.
• Images produced by DIC have a distinctive shadow-cast appearance.
Key Terms
• photobleaching: The destruction of a photochemical fluorescence by high-intensity light
• fluorochrome: Any of various fluorescent dyes used to stain biological material before microscopic examination
3.3D: Fluorescence Microscopy
Learning Objectives
• Describe the techniques, advantages, and disadvantages of fluorescence microscopy
The fluorescent microscope uses a high-pressure mercury, halogen, or xenon vapor lamp that emits a shorter wavelength than that emitted by traditional brightfield microscopy. These light sources produce ultraviolet light. When ultraviolet light hits an object, it excites the electrons of the object, and they give off light in various shades of color. Since ultraviolet light is used a larger amount of information can be gathered; thus, the resolution of the object increases.
Fluorescent-Antibody Technique and Dyes
This laboratory technique employs fluorescent dyes chemically linked to antibodies to help identify unknown microorganisms. This method uses the specificity of an antibody to its antigen to deliver a fluorescent dye to a target molecule. A filter is used to block the heat generated from the lamp and to match the fluorescent dye labeling the specimen. An additional barrier filter between the objective and the detector can filter out the remaining excitation light from fluorescent light.
Fluorescent dyes—molecules that absorb light of one wavelength and then re-emit it at a longer visible wavelength—can be used alone or in combination to gain specificity of the stained structure being visualized. The light emitted from the fluorophore is magnified through traditional objectives and ocular lenses. Staining organisms with these special dyes reduces the non-specific autofluorescence that some organisms can emit. Cells or organisms stained with fluorochromes appear colored against a dark background when fixed on a glass slide. Fluorescence microscopy does not allow examination of live microorganisms as it requires them to be fixed and permeabilized for the antibody to penetrate inside the cells.
Key Points
• In fluorescence microscopy, specimens are first stained with fluorochromes and then viewed through a compound microscope by using an ultraviolet (or near-ultraviolet) light source.
• Microorganisms appear as bright objects against a dark background.
• Fluorescence microscopy is used primarily in a procedure called fluorescent- antibody (FA) technique, or immunofluorescence.
Key Terms
• autofluorescence: Self-induced fluorescence
• halogen: any element of group 7, i.e. fluorine, chlorine, bromine, iodine and astatine, which form a salt by direct union with a metal
3.3E: Confocal Micropscopy
Learning Objectives
• Compare and contrast confocal and fluorescence microscopy
Confocal microscopy is a non-invasive fluorescent imaging technique that uses lasers of various colors to scan across a specimen with the aid of scanning mirrors. The point of illumination is brought to focus in the specimen by the objective lens. The scanning process uses a device that is under computer control. The sequences of points of light from the specimen are detected by a photomultiplier tube through a pinhole. The output is built into an image and transferred onto a digital computer screen for further analysis. The technique employs optical sectioning to take serial slices of the image. The slices are then stacked (Z-stack) to reconstruct the three-dimensional image of the biological sample. Optical sectioning is useful in determining cellular localization of targets. The biological sample to be studied is stained with antibodies chemically bound to fluorescent dyes similar to the method employed in fluorescence microscopy. Unlike in conventional fluorescence microscopy where the fluorescence is emitted along the entire illuminated cone creating a hazy image, in confocal microscopy the pinhole is added to allow passing of light that comes from a specific focal point on the sample and not the other. The light detected creates an image that is in focus with the original sample. Confocal microscopy has multiple applications in microbiology such as the study of biofilms and antibiotic-resistant strains of bacteria. Development of modern confocal microscopes has been accelerated by new advances in computer and storage technology, laser systems, detectors, interference filters, and fluorophores for highly specific targets.
Key Points
• Confocal microscopy requires immunoflurescence staining of biological samples.
• Confocal microscopy serves to control depth of field, eliminate background, and collect optical sections.
• The use of confocal microscopy has expanded to study both fixed and live cells with the ability to quantify targets.
Key Terms
• photomultiplier tube: A vacuum tube that detects ultraviolet, visible, and near infrared light and multiplies it 100 million times. | textbooks/bio/Microbiology/Microbiology_(Boundless)/03%3A_Microscopy/3.03%3A_Other_Types_of_Microscopy/3.3C%3A_Interference_Microscopy.txt |
Learning Objectives
• Describe the technique employed for electron microscopy, distinguishing between different types
Electron microscopy uses a beam of electrons as an energy source. An electron beam has an exceptionally short wavelength and can hit most objects in its path, increasing the resolution of the final image captured. The electron beam is designed to travel in a vacuum to limit interference by air molecules. Magnets are used to focus the electrons on the object viewed.
There are two types of electron microscopes. The more traditional form is the transmission electron microscope (TEM). To use this instrument, ultra-thin slices of microorganisms or viruses are placed on a wire grid and then stained with gold or palladium before viewing, to create contrast. The densely coated parts of the specimen deflect the electron beam and both dark and light areas show up on the image. TEM can project images in a much higher resolution—up to the atomic level of thinner objects.
The second and most contemporary form is the scanning electron microscope (SEM). It allows the visualization of microorganisms in three dimensions as the electrons are reflected when passed over the specimen. The same gold or palladium staining is employed.
Electron microscopy has multiple applications. It is ideal to:
• explore the in vivo molecular mechanisms of disease;
• visualize the three dimensional architecture of tissues and cells;
• determine the conformation of flexible protein structures and complexes;
• observe individual viruses and macromolecular complexes in their natural biological context.
Sample preparation can be critical to generate a successful image because the choice of reagents and methods used to process a sample largely depends on the nature of the sample and the analysis required.
Key Points
• A beam of electrons, instead of light, is used with an electron microscope.
• Electron microscopes have a greater magnification because the wavelengths of electrons are much smaller than those of visible light (0.005nm as opposed to 500nm respectively–one hundred thousand times smaller).
• There are two types of electron microscopes, scanning and transmission.
• The best compound light microscopes can magnify 2000x, electron microscopes can magnify up to 100,000x.
Key Terms
• electron beam: a stream of electrons observed in vacuum tubes.
3.3G: Scanned-Probe Microscopy
Learning Objectives
• Describe the different types of scanning probe techniques and their advantages over other types of microscopy
3-D Images
Scanned-probe microscopy (SPM) produces highly magnified and three-dimensional-shaped images of specimens in real time. SPM employs a delicate probe to scan the surface of the specimen, eliminating the limitations that are found in electron and light microscopy. SPM covers several related technologies for imaging and measuring surfaces on a fine scale, down to the level of molecules and groups of atoms.
A scan may cover a distance of over 100 micrometers in the x and y directions and 4 micrometers in the z direction. SPM technologies share the concept of scanning a sharp probe tip with a small radius of curvature across the object surface. The tip is mounted on a flexible cantilever, allowing the tip to follow the surface profile. When the tip moves in proximity to the investigated object, forces of interaction between the tip and the surface influence the movement of the cantilever. Selective sensors detect these movements. Various interactions can be studied depending on the mechanics of the probe.
There are three common scanning probe techniques: atomic force microscopy (AFM) measures the interaction force between the tip and surface. The tip may be dragged across the surface, or may vibrate as it moves. The interaction force will depend on the nature of the sample, the probe tip and the distance between them. Scanning tunneling microscopy (STM) measures a weak electrical current flowing between tip and sample as they are held apart. Near-field scanning optical microscopy (NSOM) scans a very small light source very close to the sample. Detection of this light energy forms the image.
Key Points
• Scanned-probe microscopy has enabled researchers to create images of surfaces at the nanometer scale with a probe.
• The probe has an extremely sharp tip that interacts with the surface of the specimen.
• There are several variations of scanned-probe microscopy of which atomic force microscopy, scanning tunneling microscopy, and near-field scanning optical microscopy are most commonly used.
Key Terms
• micrometer: An SI/MKS unit of measure, the length of one one-millionth of a meter. Symbols: µm, um, rm | textbooks/bio/Microbiology/Microbiology_(Boundless)/03%3A_Microscopy/3.03%3A_Other_Types_of_Microscopy/3.3F%3A_Electron_Microscopy.txt |
Learning Objectives
• Summarize the methods used for x-ray diffraction analysis and the contributions they have made to science
X-ray diffraction (XRD) is a tool for characterizing the arrangement of atoms in crystals and the distances between crystal faces. The technique reveals detailed information about the chemical composition, crystallography, and microstructure of all types of natural and manufactured materials, which is key in understanding the properties of the material being studied.
Since many materials can form crystals—such as salts, metals, minerals, semiconductors, as well as various inorganic, organic, and biological molecules —X-ray crystallography has been fundamental in the development of many scientific fields. The method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences among various materials, especially minerals and alloys. The method also revealed the structure and function of many biological molecules, including vitamins, drugs, proteins, and nucleic acids such as DNA.
Samples are commonly analyzed in a crystal form. X-ray diffraction is caused by constructive interference of x-ray waves that reflect off internal crystal planes. A thin film or layer of powder is fixed in the path of monochromatic x-rays. A detector measures x-rays from the sample over a range of angles. The powder consists of tiny crystals randomly oriented. At certain angles of the sensor, populations of crystals have the correct angle so that Bragg’s equation is satisfied for one of the crystal planes, resulting in a spike in X-rays.
The output graph displays x-ray intensity over 2 theta, the angle of the detector. The data generated with this technique requires extensive mathematical analysis that is now made easier by available computer algorithms. The analysis consists of indexing, merging, and phasing variations in electron density. It begins with the identification of molecules using the international center for diffraction database (ICDD). This is an organization dedicated to collecting, editing, publishing, and distributing powder diffraction data for the identification of crystalline materials. Further analysis involves structure refinement and quantitative phase using the general structure analysis system (GSAS), which ultimately leads to the identification of the amorphous or crystalline phase of a matter and helps construct its three dimensional atomic model.
Key Points
• X-ray diffraction utilizes x-ray beams targeted to hit crystallized matter and generates a diffraction pattern.
• Data collected using this method undergo a systematic analytical process that employes mathematical models and computer algorithms to obtain the final 3D atom model of a matter.
• X-ray diffraction analysis identifies composition and chemical bonds between atoms of crystal, liquid, powder, or amorphous samples.
Key Terms
• Bragg’s equation: Gives the angles for coherent and incoherent scattering from a crystal lattice.
• crystallography: The experimental science of determining the arrangement of atoms in solids.
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04: Cell Structure of Bacteria Archaea and Eukaryotes
A prokaryote is a simple, unicellular organism that lacks an organized nucleus or other membrane-bound organelle.
Learning Objectives
• Describe the structure of prokaryotic cells
Key Points
• Prokaryotes lack an organized nucleus and other membrane-bound organelles.
• Prokaryotic DNA is found in a central part of the cell called the nucleoid.
• The cell wall of a prokaryote acts as an extra layer of protection, helps maintain cell shape, and prevents dehydration.
• Prokaryotic cell size ranges from 0.1 to 5.0 μm in diameter.
• The small size of prokaryotes allows quick entry and diffusion of ions and molecules to other parts of the cell while also allowing fast removal of waste products out of the cell.
Key Terms
• eukaryotic: Having complex cells in which the genetic material is organized into membrane-bound nuclei.
• prokaryotic: Of cells, lacking a nucleus.
• nucleoid: the irregularly-shaped region within a prokaryote cell where the genetic material is localized
Components of Prokaryotic Cells
All cells share four common components:
1. a plasma membrane: an outer covering that separates the cell’s interior from its surrounding environment.
2. cytoplasm: a jelly-like cytosol within the cell in which other cellular components are found
3. DNA: the genetic material of the cell
4. ribosomes: where protein synthesis occurs
However, prokaryotes differ from eukaryotic cells in several ways.
A prokaryote is a simple, single-celled (unicellular) organism that lacks an organized nucleus or any other membrane-bound organelle. We will shortly come to see that this is significantly different in eukaryotes. Prokaryotic DNA is found in a central part of the cell: the nucleoid.
Most prokaryotes have a peptidoglycan cell wall and many have a polysaccharide capsule. The cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. The capsule enables the cell to attach to surfaces in its environment. Some prokaryotes have flagella, pili, or fimbriae. Flagella are used for locomotion. Pili are used to exchange genetic material during a type of reproduction called conjugation. Fimbriae are used by bacteria to attach to a host cell.
Cell Size
At 0.1 to 5.0 μm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10 to 100 μm. The small size of prokaryotes allows ions and organic molecules that enter them to quickly diffuse to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly diffuse out. This is not the case in eukaryotic cells, which have developed different structural adaptations to enhance intracellular transport.
Small size, in general, is necessary for all cells, whether prokaryotic or eukaryotic. Let’s examine why that is so. First, we’ll consider the area and volume of a typical cell. Not all cells are spherical in shape, but most tend to approximate a sphere. You may remember from your high school geometry course that the formula for the surface area of a sphere is 4πr2, while the formula for its volume is 4/3πr3. Thus, as the radius of a cell increases, its surface area increases as the square of its radius, but its volume increases as the cube of its radius (much more rapidly). Therefore, as a cell increases in size, its surface area-to-volume ratio decreases. This same principle would apply if the cell had the shape of a cube. If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. In other words, as a cell grows, it becomes less efficient. One way to become more efficient is to divide; another way is to develop organelles that perform specific tasks. These adaptations led to the development of more sophisticated cells called eukaryotic cells. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.01%3A_Overview_of_Prokaryotic_and_Eukaryotic_Cells/4.1A%3A_Characteristics_of_Prokaryotic_Cells.txt |
The plasma membrane protects the cell from its external environment, mediates cellular transport, and transmits cellular signals.
Learning Objectives
• Describe the function and components of the plasma membrane
Key Points
• The principal components of the plasma membrane are lipids ( phospholipids and cholesterol), proteins, and carbohydrates.
• The plasma membrane protects intracellular components from the extracellular environment.
• The plasma membrane mediates cellular processes by regulating the materials that enter and exit the cell.
• The plasma membrane carries markers that allow cells to recognize one another and can transmit signals to other cells via receptors.
Key Terms
• plasma membrane: The semipermeable barrier that surrounds the cytoplasm of a cell.
• receptor: A protein on a cell wall that binds with specific molecules so that they can be absorbed into the cell.
Structure of Plasma Membranes
The plasma membrane (also known as the cell membrane or cytoplasmic membrane) is a biological membrane that separates the interior of a cell from its outside environment.
The primary function of the plasma membrane is to protect the cell from its surroundings. Composed of a phospholipid bilayer with embedded proteins, the plasma membrane is selectively permeable to ions and organic molecules and regulates the movement of substances in and out of cells. Plasma membranes must be very flexible in order to allow certain cells, such as red blood cells and white blood cells, to change shape as they pass through narrow capillaries.
The plasma membrane also plays a role in anchoring the cytoskeleton to provide shape to the cell, and in attaching to the extracellular matrix and other cells to help group cells together to form tissues. The membrane also maintains the cell potential.
In short, if the cell is represented by a castle, the plasma membrane is the wall that provides structure for the buildings inside the wall, regulates which people leave and enter the castle, and conveys messages to and from neighboring castles. Just as a hole in the wall can be a disaster for the castle, a rupture in the plasma membrane causes the cell to lyse and die.
The Plasma Membrane and Cellular Transport
The movement of a substance across the selectively permeable plasma membrane can be either “passive”—i.e., occurring without the input of cellular energy —or “active”—i.e., its transport requires the cell to expend energy.
The cell employs a number of transport mechanisms that involve biological membranes:
1. Passive osmosis and diffusion: transports gases (such as O2 and CO2)and other small molecules and ions
2. Transmembrane protein channels and transporters: transports small organic molecules such as sugars or amino acids
3. Endocytosis: transports large molecules (or even whole cells) by engulfing them
4. Exocytosis: removes or secretes substances such as hormones or enzymes
The Plasma Membrane and Cellular Signaling
Among the most sophisticated functions of the plasma membrane is its ability to transmit signals via complex proteins. These proteins can be receptors, which work as receivers of extracellular inputs and as activators of intracellular processes, or markers, which allow cells to recognize each other.
Membrane receptors provide extracellular attachment sites for effectors like hormones and growth factors, which then trigger intracellular responses. Some viruses, such as Human Immunodeficiency Virus (HIV), can hijack these receptors to gain entry into the cells, causing infections.
Membrane markers allow cells to recognize one another, which is vital for cellular signaling processes that influence tissue and organ formation during early development. This marking function also plays a later role in the “self”-versus-“non-self” distinction of the immune response. Marker proteins on human red blood cells, for example, determine blood type (A, B, AB, or O).
LICENSES AND ATTRIBUTIONS | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.02%3A_The_Cytoplasmic_Membrane_of_Prokaryotic_and_Eukaryotic_Cells/4.2A%3A_Components_of_Plasma_Membranes.txt |
Learning Objectives
• Explain why and how passive transport occurs
Facilitated transport is a type of passive transport. Unlike simple diffusion where materials pass through a membrane without the help of proteins, in facilitated transport, also called facilitated diffusion, materials diffuse across the plasma membrane with the help of membrane proteins. A concentration gradient exists that would allow these materials to diffuse into the cell without expending cellular energy. However, these materials are ions or polar molecules that are repelled by the hydrophobic parts of the cell membrane. Facilitated transport proteins shield these materials from the repulsive force of the membrane, allowing them to diffuse into the cell.
The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are then passed to specific integral proteins that facilitate their passage. Some of these integral proteins are collections of beta-pleated sheets that form a channel through the phospholipid bilayer. Others are carrier proteins which bind with the substance and aid its diffusion through the membrane.
Channels
The integral proteins involved in facilitated transport are collectively referred to as transport proteins; they function as either channels for the material or carriers. In both cases, they are transmembrane proteins. Channels are specific for the substance that is being transported. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids; they additionally have a hydrophilic channel through their core that provides a hydrated opening through the membrane layers. Passage through the channel allows polar compounds to avoid the nonpolar central layer of the plasma membrane that would otherwise slow or prevent their entry into the cell. Aquaporins are channel proteins that allow water to pass through the membrane at a very high rate.
Channel proteins are either open at all times or they are “gated,” which controls the opening of the channel. The attachment of a particular ion to the channel protein may control the opening or other mechanisms or substances may be involved. In some tissues, sodium and chloride ions pass freely through open channels, whereas in other tissues, a gate must be opened to allow passage. An example of this occurs in the kidney, where both forms of channels are found in different parts of the renal tubules. Cells involved in the transmission of electrical impulses, such as nerve and muscle cells, have gated channels for sodium, potassium, and calcium in their membranes. Opening and closing of these channels changes the relative concentrations on opposing sides of the membrane of these ions, resulting in the facilitation of electrical transmission along membranes (in the case of nerve cells) or in muscle contraction (in the case of muscle cells).
Carrier Proteins
Another type of protein embedded in the plasma membrane is a carrier protein. This protein binds a substance and, in doing so, triggers a change of its own shape, moving the bound molecule from the outside of the cell to its interior; depending on the gradient, the material may move in the opposite direction. Carrier proteins are typically specific for a single substance. This adds to the overall selectivity of the plasma membrane. The exact mechanism for the change of shape is poorly understood. Proteins can change shape when their hydrogen bonds are affected, but this may not fully explain this mechanism. Each carrier protein is specific to one substance, and there are a finite number of these proteins in any membrane. This can cause problems in transporting enough of the material for the cell to function properly.
An example of this process occurs in the kidney. Glucose, water, salts, ions, and amino acids needed by the body are filtered in one part of the kidney. This filtrate, which includes glucose, is then reabsorbed in another part of the kidney. Because there are only a finite number of carrier proteins for glucose, if more glucose is present than the proteins can handle, the excess is not transported; it is excreted from the body in the urine. In a diabetic individual, this is described as “spilling glucose into the urine.” A different group of carrier proteins called glucose transport proteins, or GLUTs, are involved in transporting glucose and other hexose sugars through plasma membranes within the body.
Channel and carrier proteins transport material at different rates. Channel proteins transport much more quickly than do carrier proteins. Channel proteins facilitate diffusion at a rate of tens of millions of molecules per second, whereas carrier proteins work at a rate of a thousand to a million molecules per second.
Key Points
• A concentration gradient exists that would allow ions and polar molecules to diffuse into the cell, but these materials are repelled by the hydrophobic parts of the cell membrane.
• Facilitated diffusion uses integral membrane proteins to move polar or charged substances across the hydrophobic regions of the membrane.
• Channel proteins can aid in the facilitated diffusion of substances by forming a hydrophilic passage through the plasma membrane through which polar and charged substances can pass.
• Channel proteins can be open at all times, constantly allowing a particular substance into or out of the cell, depending on the concentration gradient; or they can be gated and can only be opened by a particular biological signal.
• Carrier proteins aid in facilitated diffusion by binding a particular substance, then altering their shape to bring that substance into or out of the cell.
Key Terms
• facilitated diffusion: The spontaneous passage of molecules or ions across a biological membrane passing through specific transmembrane integral proteins.
• membrane protein: Proteins that are attached to, or associated with the membrane of a cell or an organelle. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.03%3A_Transport_Across_the_Cell_Membrane/4.3A%3A_Facilitated_Transport.txt |
Learning Objectives
Describe how a cell moves sodium and potassium out of and into the cell against its electrochemical gradient
The sodium-potassium pump maintains the electrochemical gradient of living cells by moving sodium in and potassium out of the cell. The primary active transport that functions with the active transport of sodium and potassium allows secondary active transport to occur. The secondary transport method is still considered active because it depends on the use of energy as does primary transport.
One of the most important pumps in animals cells is the sodium-potassium pump ( Na+-K+ ATPase ), which maintains the electrochemical gradient (and the correct concentrations of Na+ and K+) in living cells. The sodium-potassium pump moves two K+ into the cell while moving three Na+ out of the cell. The Na+-K+ ATPase exists in two forms, depending on its orientation to the interior or exterior of the cell and its affinity for either sodium or potassium ions. The process consists of the following six steps:
• With the enzyme oriented towards the interior of the cell, the carrier has a high affinity for sodium ions. Three sodium ions bind to the protein.
• ATP is hydrolyzed by the protein carrier, and a low-energy phosphate group attaches to it.
• As a result, the carrier changes shape and re-orients itself towards the exterior of the membrane. The protein’s affinity for sodium decreases, and the three sodium ions leave the carrier.
• The shape change increases the carrier’s affinity for potassium ions, and two such ions attach to the protein. Subsequently, the low-energy phosphate group detaches from the carrier.
• With the phosphate group removed and potassium ions attached, the carrier protein repositions itself towards the interior of the cell.
• The carrier protein, in its new configuration, has a decreased affinity for potassium, and the two ions are released into the cytoplasm. The protein now has a higher affinity for sodium ions, and the process starts again.
Several things have happened as a result of this process. At this point, there are more sodium ions outside of the cell than inside and more potassium ions inside than out. For every three ions of sodium that move out, two ions of potassium move in. This results in the interior being slightly more negative relative to the exterior. This difference in charge is important in creating the conditions necessary for the secondary process. The sodium-potassium pump is, therefore, an electrogenic pump (a pump that creates a charge imbalance), creating an electrical imbalance across the membrane and contributing to the membrane potential.
Key Points
• The sodium-potassium pump moves K+ into the cell while moving Na+ at a ratio of three Na+ for every two K+ ions.
• When the sodium-potassium- ATPase enzyme points into the cell, it has a high affinity for sodium ions and binds three of them, hydrolyzing ATP and changing shape.
• As the enzyme changes shape, it reorients itself towards the outside of the cell, and the three sodium ions are released.
• The enzyme’s new shape allows two potassium to bind and the phosphate group to detach, and the carrier protein repositions itself towards the interior of the cell.
• The enzyme changes shape again, releasing the potassium ions into the cell.
• After potassium is released into the cell, the enzyme binds three sodium ions, which starts the process over again.
Key Terms
• electrogenic pump: An ion pump that generates a net charge flow as a result of its activity.
• Na+-K+ ATPase: An enzyme located in the plasma membrane of all animal cells that pumps sodium out of cells while pumping potassium into cells.
4.3C: ABC Transporters
Learning Objectives
• Summarize the function of the three major ABC transporter categories: in prokaryotes, in gram-negative bacteria and the subgroup of ABC proteins
ATP-binding cassette transporters (ABC-transporters) are members of a protein superfamily that is one of the largest and most ancient families with representatives in all extant phyla from prokaryotes to humans. ABC transporters are transmembrane proteins that utilize the energy of adenosine triphosphate (ATP) hydrolysis to carry out certain biological processes including translocation of various substrates across membranes and non-transport-related processes such as translation of RNA and DNA repair. They transport a wide variety of substrates across extra- and intracellular membranes, including metabolic products, lipids and sterols, and drugs. Proteins are classified as ABC transporters based on the sequence and organization of their ATP-binding cassette (ABC) domain(s).
ABC transporters are involved in tumor resistance, cystic fibrosis and a range of other inherited human diseases along with both bacterial (prokaryotic) and eukaryotic (including human) development of resistance to multiple drugs. Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity.
ABC transporters are divided into three main functional categories. In prokaryotes, importers mediate the uptake of nutrients into the cell. The substrates that can be transported include ions, amino acids, peptides, sugars, and other molecules that are mostly hydrophilic. The membrane-spanning region of the ABC transporter protects hydrophilic substrates from the lipids of the membrane bilayer thus providing a pathway across the cell membrane. In gram-negative bacteria, exporters transport lipids and some polysaccharides from the cytoplasm to the periplasm. Eukaryotes do not possess any importers. Exporters or effluxers, which are both present in prokaryotes and eukaryotes, function as pumps that extrude toxins and drugs out of the cell. The third subgroup of ABC proteins do not function as transporters, but rather are involved in translation and DNA repair processes.
In bacterial efflux systems, certain substances that need to be extruded from the cell include surface components of the bacterial cell (e.g. capsular polysaccharides, lipopolysaccharides, and teichoic acid), proteins involved in bacterial pathogenesis (e.g. hemolysis, heme-binding protein, and alkaline protease), heme, hydrolytic enzymes, S-layer proteins, competence factors, toxins, antibiotics, bacteriocins, peptide antibiotics, drugs and siderophores. They also play important roles in biosynthetic pathways, including extracellular polysaccharide biosynthesis and cytochrome biogenesis.
Key Points
• ABC transporters use the energy of ATP hydrolysis to transport substrates across cell membranes.
• Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity.
• The substrates that can be transported include ions, amino acids, peptides, sugars, and other molecules that are mostly hydrophilic.
Key Terms
• membrane: A flexible enclosing or separating tissue forming a plane or film and separating two environments (usually in a plant or animal).
• hydrolysis: A chemical process of decomposition involving the splitting of a bond and the addition of the hydrogen cation and the hydroxide anion of water.
• ATP-binding cassette (ABC) domain: The ATP-binding cassette (ABC) family is a group of proteins which bind and hydrolyse ATP in order to transport substances across cellular membranes. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.03%3A_Transport_Across_the_Cell_Membrane/4.3B%3A_Primary_Active_Transport.txt |
Learning Objectives
• Describe the function and variety of siderophores
Iron is essential for almost all living organisms as it is involved in a wide variety of important metabolic processes. However, iron is not always readily available; therefore, microorganisms use various iron uptake systems to secure sufficient supplies from their surroundings. There is considerable variation in the range of iron transporters and iron sources utilized by different microbial species. Pathogens, in particular, require efficient iron acquisition mechanisms to enable them to compete successfully for iron in the highly iron-restricted environment of the host’s tissues and body fluids.
Siderophores are small, high-affinity iron chelating compounds secreted by microorganisms such as bacteria, fungi, and grasses. Siderophores are amongst the strongest soluble Fe3+ binding agents known. Iron is essential for almost all life, because of its vital role in processes like respiration and DNA synthesis. However, despite being one of the most abundant elements in the Earth’s crust, the bioavailability of iron in many environments such as the soil or sea is limited by the very low solubility of the Fe3+ ion. This ion state is the predominant one of iron in aqueous, non-acidic, oxygenated environments, and accumulates in common mineral phases such as iron oxides and hydroxides (the minerals that are responsible for red and yellow soil colours). Hence, it cannot be readily utilized by organisms. Microbes release siderophores to scavenge iron from these mineral phases by formation of soluble Fe3+complexes that can be taken up by active transport mechanisms. Many siderophores are nonribosomal peptides, although several are biosynthesised independently.
Siderophores are amongst the strongest binders to Fe3+ known, with enterobactin being one of the strongest of these. Because of this property, they have attracted interest from medical science in metal chelation therapy, with the siderophore desferrioxamine B gaining widespread use in treatments for iron poisoning and thalassemia.
Iron is tightly bound to proteins such as hemoglobin, transferrin, lactoferrin, and ferritin. There are great evolutionary pressures put on pathogenic bacteria to obtain this metal. For example, the anthrax pathogen Bacillus anthracisreleases two siderophores, bacillibactin and petrobactin, to scavenge ferric iron from iron proteins. While bacillibactin has been shown to bind to the immune system protein siderocalin, petrobactin is assumed to evade the immune system and has been shown to be important for virulence in mice.
Besides siderophores, some pathogenic bacteria produce hemophores ( heme binding scavenging proteins) or have receptors that bind directly to iron/heme proteins. In eukaryotes, other strategies to enhance iron solubility and uptake are the acidification of the surrounding (e.g. used by plant roots) or the extracellular reduction of Fe3+ into the more soluble Fe2+ ions.
Siderophores usually form a stable, hexadentate, octahedral complex with Fe3+preferentially compared to other naturally occurring abundant metal ions, although if there are less than six donor atoms water can also coordinate. The most effective siderophores are those that have three bidentate ligands per molecule, forming a hexadentate complex and causing a smaller entropic change than that caused by chelating a single ferric ion with separate ligands.
Siderophores are usually classified by the ligands used to chelate the ferric iron. The majors groups of siderophores include the catecholates (phenolates), hydroxamates and carboxylates (e.g. derivatives of citric acid). Citric acid can also act as a siderophore. The wide variety of siderophores may be due to evolutionary pressures placed on microbes to produce structurally different siderophores, which cannot be transported by other microbes’ specific active transport systems, or in the case of pathogens deactivated by the host organism.
Key Points
• Siderophores are important for some pathogenic bacteria for their acquisition of iron. Many siderophores are nonribosomal peptides, although several are biosynthesised independently.
• The wide variety of siderophores may be due to evolutionary pressures placed on microbes to produce structurally different siderophores which cannot be transported by other microbes’ specific active transport systems, or in the case of pathogens deactivated by the host organism.
• Microbes release siderophores to scavenge iron from these mineral phases by formation of soluble Fe3+ complexes that can be taken up by active transport mechanisms.
Key Terms
• siderophores: Sidereophores are small, high-affinity iron chelating compounds secreted by microorganisms such as bacteria and fungi, and also grasses. Siderophores are amongst the strongest soluble Fe3+ binding agents known. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.03%3A_Transport_Across_the_Cell_Membrane/4.3D%3A_Siderophores.txt |
Group translocation is a protein export or secretion pathway found in plants, bacteria, and archaea.
Learning Objectives
• Recall the following types of transport systems: PEP group translocation and the TAT pathway
Key Points
• PEP is known as a multi-component system that always involves enzymes of the plasma membrane and those in the cytoplasm. An example of this transport is found in E. coli cells.
• The Tat pathway is a protein export, or secretion pathway, that serves to actively translocate folded proteins across a lipid membrane bilayer.
• Systems for secreting proteins across the bacterial outer membrane may be quite complex and play key roles in pathogenesis.
Key Terms
• phosphotransferase system: A distinct method used by bacteria for sugar uptake where the source of energy is from phosphoenolpyruvate (PEP).
• Tat pathway: A protein export or secretion pathway found in plants, bacteria, and archaea.
With some exceptions, bacteria lack membrane-bound organelles as found in eukaryotes, but they may assemble proteins onto various types of inclusions such as gas vesicles and storage granules. Bacteria may have a single plasma membrane (Gram-positive bacteria) or an inner membrane plus an outer membrane separated by the periplasm ( Gram-negative bacteria). Proteins may be incorporated into the plasma membrane. They can also be trapped in either the periplasm or secreted into the environment, according to whether or not there is an outer membrane. The basic mechanism at the plasma membrane is similar to the eukaryotic one. In addition, bacteria may target proteins into or across the outer membrane. Systems for secreting proteins across the bacterial outer membrane may be quite complex. The systems play key roles in pathogenesis. These systems may be described as type I secretion, type II secretion, etc. In most Gram-positive bacteria, certain proteins are targeted for export across the plasma membrane and subsequent covalent attachment to the bacterial cell wall.
A specialized enzyme, sortase, cleaves the target protein at a characteristic recognition site near the protein C-terminus, such as an LPXTG motif (where X can be any amino acid), then transfers the protein onto the cell wall. Several analogous systems are found that also feature a signature motif on the extracytoplasmic face, a C-terminal transmembrane domain, and cluster of basic residues on the cytosolic face at the protein’s extreme C-terminus. The PEP-CTERM/exosortase system, found in many Gram-negative bacteria, seems to be related to extracellular polymeric substance production. The PGF-CTERM/archaeosortase A system in archaea is related to S-layer production. The GlyGly-CTERM/rhombosortase system, found in the Shewanella, Vibrio, and a few other genera, seems involved in the release of proteases, nucleases, and other enzymes.
PEP group translocation, also known as the phosphotransferase system or PTS, is a distinct method used by bacteria for sugar uptake where the source of energy is from phosphoenolpyruvate (PEP). It is known as a multi-component system that always involves enzymes of the plasma membrane and those in the cytoplasm. An example of this transport is found in E. coli cells. The system was discovered by Saul Roseman in 1964.
The twin-arginine translocation pathway (Tat pathway) is a protein export or secretion pathway found in plants, bacteria, and archaea. In contrast to the Sec pathway which transports proteins in an unfolded manner, the Tat pathway serves to actively translocate folded proteins across a lipid membrane bilayer. In bacteria, the Tat translocase is found in the cytoplasmic membrane and serves to export proteins to the cell envelope or to the extracellular space. In Gram-negative bacteria the Tat translocase is composed of three essential membrane proteins: TatA, TatB, and TatC. In the most widely studied Tat pathway, that of the Gram-negative bacterium Escherichia coli, these three proteins are expressed from an operon with a fourth Tat protein, TatD, which is not required for Tat function. A fifth Tat protein TatE that is homologous to the TatA protein is present at a much lower level in the cell than TatA. It is not believed to play any significant role in Tat function.
The Tat pathways of Gram-positive bacteria differ in that they do not have a TatB component. In these bacteria the Tat system is made up from a single TatA and TatC component, with the TatA protein being bifunctional and fulfilling the roles of both E. coli TatA and TatB. Not all bacteria carry the tatABC genes in their genome. However, of those that do, there seems to be no discrimination between pathogens and nonpathogens. Despite that fact, some pathogenic bacteria such as Pseudomonas aeruginosa, Legionella pneumophila, Yersinia pseudotuberculosis, and E. coli O157:H7 rely on a functioning Tat pathway for full virulence in infection models. In addition, a number of exported virulence factors have been shown to rely on the Tat pathway. One such category of virulence factors are the phospholipase C enzymes, which have been shown to be Tat-exported in Pseudomonas aeruginosa and thought to be Tat-exported in Mycobacterium tuberculosis.
LICENSES AND ATTRIBUTIONS
CC LICENSED CONTENT, SPECIFIC ATTRIBUTION | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.03%3A_Transport_Across_the_Cell_Membrane/4.3E%3A_Group_Translocation.txt |
Learning Objectives
• Recall the characteristics of a bacterial cell wall
Bacterial cells lack a membrane bound nucleus. Their genetic material is naked within the cytoplasm. Ribosomes are their only type of organelle. The term “nucleoid” refers to the region of the cytoplasm where chromosomal DNA is located, usually a singular, circular chromosome. Bacteria are usually single-celled, except when they exist in colonies. These ancestral cells reproduce by means of binary fission, duplicating their genetic material and then essentially splitting to form two daughter cells identical to the parent. A wall located outside the cell membrane provides the cell support, and protection against mechanical stress or damage from osmotic rupture and lysis.
The major component of the bacterial cell wall is peptidoglycan or murein. This rigid structure of peptidoglycan, specific only to prokaryotes, gives the cell shape and surrounds the cytoplasmic membrane. Peptidoglycan is a huge polymer of disaccharides (glycan) cross-linked by short chains of identical amino acids (peptides) monomers. The backbone of the peptidoglycan molecule is composed of two derivatives of glucose: N-acetylglucosamine (NAG) and N-acetlymuramic acid (NAM) with a pentapeptide coming off NAM and varying slightly among bacteria. The NAG and NAM strands are synthesized in the cytosol of the bacteria. They are connected by inter-peptide bridges. They are transported across the cytoplasmic membrane by a carrier molecule called bactoprenol. From the peptidoglycan inwards all bacterial cells are very similar. Going further out, the bacterial world divides into two major classes: Gram positive (Gram +) and Gram negative (Gram -). The cell wall provides important ligands for adherence and receptor sites for viruses or antibiotics.
Key Points
• A cell wall is a layer located outside the cell membrane found in plants, fungi, bacteria, algae, and archaea.
• A peptidoglycan cell wall composed of disaccharides and amino acids gives bacteria structural support.
• The bacterial cell wall is often a target for antibiotic treatment.
Key Terms
• binary fission: The process whereby a cell divides asexually to produce two daughter cells.
4.4B: Gram-Negative Outer Membrane
Learning Objectives
• Recognize the characteristics of a gram-negative bacteria
The Gram-negative cell wall is composed of an outer membrane, a peptidoglygan layer, and a periplasm.
In the Gram-negative Bacteria the cell wall is composed of a single layer of peptidoglycan surrounded by a membranous structure called the outer membrane. The gram-negative bacteria do not retain crystal violet but are able to retain a counterstain, commonly safranin, which is added after the crystal violet. The safranin is responsible for the red or pink color seen with a gram-negative bacteria. The Gram-negative’s cell wall is thinner (10 nanometers thick) and less compact than that of Gram-positive bacteria, but remains strong, tough, and elastic to give them shape and protect them against extreme environmental conditions. The outer membrane of Gram-negative bacteria invariably contains a unique component, lipopolysaccharide (LPS) in addition to proteins and phospholipids. The LPS molecule is toxic and is classified as an endotoxin that elicits a strong immune response when the bacteria infect animals.
In Gram-negative bacteria the outer membrane is usually thought of as part of the outer leaflet of the membrane structure and is relatively permeable. It contains structures that help bacteria adhere to animal cells and cause disease. The peptidoglycan layer is non-covalently anchored to lipoprotein molecules called Braun’s lipoproteins through their hydrophobic head. Sandwiched between the outer membrane and the plasma membrane, a concentrated gel-like matrix (the periplasm) is found in the periplasmic space. It is in fact an integral compartment of the gram-negative cell wall and contains binding proteins for amino acids, sugars, vitamins, iron, and enzymes essential for bacterial nutrition. The periplasm space can act as reservoir for virulence factors and a dynamic flux of macromolecules representing the cell’s metabolic status and its response to environmental factors. Together, the plasma membrane and the cell wall (outer membrane, peptidoglycan layer, and periplasm) constitute the gram-negative envelope.
Key Points
• The outer membrane of Gram-negative bacteria contains lipopolysaccharides, proteins, and phospholipids.
• The lipopolysaccharide component acts as a virulence factor and causes disease in animals.
• More virulence factors are harbored in the periplasmic space between the outer membrane and the plasma membrane.
Key Terms
• lipopolysaccharide: any of a large class of lipids conjugated with polysaccharides
• endotoxin: Any toxin secreted by a microorganism and released into the surrounding environment only when it dies.
4.4C: Gram-Positive Cell Envelope
Gram-positive bacteria have cell envelopes made of a thick layer of peptidoglycans.
Learning Objectives
• Compare and contrast a gram-positive and negative stain
Key Points
• Gram-positive bacteria stain violet by Gram staining due the presence of peptidoglycan in their cell wall.
• Peptidoglycans are attached to negatively-charged lipoteichoic acid monomers important for cell direction and adherence.
• Lipoteichoic acids are covalently linked to lipids within the cytoplasmic membrane, thus connecting the peptidoglycans to the cell cytoplasm.
Key Terms
• Gram stain: A method of differentiating bacterial species into two large groups (Gram-positive and Gram-negative).
Gram-positive bacteria are stained dark blue or violet by Gram staining. While Gram staining is a valuable diagnostic tool in both clinical and research settings, not all bacteria can be definitively classified by this technique, thus forming Gram-variable and Gram-indeterminate groups as well.
It is based on the chemical and physical properties of their cell walls. Primarily, it detects peptidoglycan, which is present in a thick layer in Gram-positive bacteria. A Gram-positive results in a purple/blue color while a Gram-negative results in a pink/red color. The Gram stain is almost always the first step in the identification of a bacterial organism, and is the default stain performed by laboratories over a sample when no specific culture is referred.
In Gram-positive bacteria, the cell wall is thick (15-80 nanometers), and consists of several layers of peptidoglycan. They lack the outer membrane envelope found in Gram-negative bacteria. Running perpendicular to the peptidoglycan sheets is a group of molecules called teichoic acids, which are unique to the Gram-positive cell wall. Teichoic acids are linear polymers of polyglycerol or polyribitol substituted with phosphates and a few amino acids and sugars.
The teichoic acid polymers are occasionally anchored to the plasma membrane (called lipoteichoic acid, LTA), and apparently directed outward at right angles to the layers of peptidoglycan. Teichoic acids give the Gram-positive cell wall an overall negative charge due to the presence of phosphodiester bonds between teichoic acid monomers. The functions of teichoic acid are not fully known but it is believed to serve as a chelating agent and means of adherence for the bacteria. These are essential to the viability of Gram-positive bacteria in the environment and provide chemical and physical protection.
One idea is that they provide a channel of regularly-oriented, negative charges for threading positively-charged substances through the complicated peptidoglycan network. Another theory is that teichoic acids are in some way involved in the regulation and assembly of muramic acid sub-units on the outside of the plasma membrane.
There are instances, particularly in the streptococci, wherein teichoic acids have been implicated in the adherence of the bacteria to tissue surfaces and are thought to contribute to the pathogenicity of Gram-positive bacteria. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.04%3A_Cell_Walls_of_Prokaryotes/4.4A%3A_The_Cell_Wall_of_Bacteria.txt |
Some bacteria lack a cell wall but retain their ability to survive by living inside another host cell.
Learning Objectives
• Distinguish between bacteria with and without cell walls
Key Points
• Examples of bacteria that lack a cell wall are Mycoplasma and L-form bacteria.
• Mycoplasma is an important cause of disease in animals and is not affected by antibiotic treatments that target cell wall synthesis.
• Mycoplasma acquire cholesterol from the environment and form sterols to build their cytoplasmic membrane.
Key Terms
• osmotic environment: environment with controlled net movement of molecules from a region of high solvent concentration to a region of low solvent concentration through a permeable membrane.
For most bacterial cells, the cell wall is critical to cell survival, yet there are some bacteria that do not have cell walls. Mycoplasma species are widespread examples and some can be intracellular pathogens that grow inside their hosts. This bacterial lifestyle is called parasitic or saprophytic. Cell walls are unnecessary here because the cells only live in the controlled osmotic environment of other cells. It is likely they had the ability to form a cell wall at some point in the past, but as their lifestyle became one of existence inside other cells, they lost the ability to form walls.
Consistent with this very limited lifestyle within other cells, these microbes also have very small genomes. They have no need for the genes for all sorts of biosynthetic enzymes, as they can steal the final components of these pathways from the host. Similarly, they have no need for genes encoding many different pathways for various carbon, nitrogen and energy sources, since their intracellular environment is completely predictable. Because of the absence of cell walls, Mycoplasma have a spherical shape and are quickly killed if placed in an environment with very high or very low salt concentrations. However, Mycoplasma do have unusually tough membranes that are more resistant to rupture than other bacteria since this cellular membrane has to contend with the host cell factors. The presence of sterols in the membrane contributes to their durability by helping to increase the forces that hold the membrane together. Other bacterial species occasionally mutate or respond to extreme nutritional conditions by forming cells lacking walls, termed L-forms. This phenomenon is observed in both gram-positive and gram-negative species. L-forms have varied shapes and are sensitive to osmotic shock.
4.4E: Cell Walls of Archaea
Archaeal cell walls differ from bacterial cell walls in their chemical composition and lack of peptidoglycans.
Learning Objectives
• State the similarities between the cell walls of archaea and bacteria
Key Points
• Archaea are single-celled microorganisms that lack a cell nucleus and membrane -bound organelles.
• Like other living organisms, archaea have a semi-rigid cell wall that protects them from the environment.
• The cell wall of archaea is composed of S-layers and lack peptidoglycan molecules with the exception of methanobacteria who have pseudopeptidoglycan in their cell wall.
Key Terms
• cellulose: A complex carbohydrate that forms the main constituent of the cell wall in most plants and is important in the manufacture of numerous products, such as paper, textiles, pharmaceuticals, and explosives.
• chitin: A complex polysaccharide, a polymer of N-acetylglucosamine, found in the exoskeletons of arthropods and in the cell walls of fungi; thought to be responsible for some forms of asthma in humans.
• cytoplasm: The contents of a cell except for the nucleus. It includes cytosol, organelles, vesicles, and the cytoskeleton.
As with other living organisms, archaeal cells have an outer cell membrane that serves as a protective barrier between the cell and its environment. Within the membrane is the cytoplasm, where the living functions of the archeon take place and where the DNA is located. Around the outside of nearly all archaeal cells is a cell wall, a semi-rigid layer that helps the cell maintain its shape and chemical equilibrium. All three of these regions may be distinguished in the cells of bacteria and most other living organisms.
A closer look at each region reveals structural similarities but major differences in chemical composition between bacterial and archaeal cell wall. Archaea builds the same structures as other organisms, but they build them from different chemical components. For instance, the cell walls of all bacteria contain the chemical peptidoglycan. Archaeal cell walls do not contain this compound, though some species contain a similar one. It is assembled from surface-layer proteins called S-layers. Likewise, archaea do not produce walls of cellulose (as do plants) or chitin (as do fungi). The cell wall of archaeans is chemically distinct. Methanogens are the only exception and possess pseudopeptidoglycan chains in their cell wall that lacks amino acids and N-acetylmuramic acid in their chemical composition. The most striking chemical differences between Archaea and other living things lie in their cell membrane. There are four fundamental differences between the archaeal membrane and those of all other cells: (1) chirality of glycerol, (2) ether linkage, (3) isoprenoid chains, and (4) branching of side chains. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.04%3A_Cell_Walls_of_Prokaryotes/4.4D%3A_Mycoplasmas_and_Other_Cell-Wall-Deficient_Bacteria.txt |
The cell wall is responsible for bacterial cell survival and protection against environmental factors and antimicrobial stress.
Learning Objectives
• Discuss the effects that damage to the cell wall has on the bacterial cell
Key Points
• Gram-positive and Gram-negative bacteria are protected by an external cell wall composed of varying layers of peptidoglycan.
• Damage to bacterial cell wall compromises its integrity and creates imbalance of electrolytes that trigger cell death.
• Some antibiotic classes act by inhibiting the synthesis of cell wall building blocks leading to cell lysis and death.
Key Terms
• hydrolase: An enzyme that catalyzes the hydrolysis of a substrate.
• transpeptidase: Any enzyme that catalyzes the transfer of an amino or peptide group from one molecule to another
The cell wall is the principal stress-bearing and shape-maintaining element in bacteria. Its integrity is thus of critical importance to the viability of a particular cell. In both gram-positive and gram-negative bacteria, the scaffold of the cell wall consists of a cross-linked polymer peptidoglycan. The cell wall of gram-negative bacteria is thin (approximately only 10 nanometers in thickness), and is typically comprised of only two to five layers of peptidoglycan, depending on the growth stage. In gram-positive bacteria, the cell wall is much thicker (20 to 40 nanometers thick).
While the peptidoglycan provides the structural framework of the cell wall, teichoic acids, which make up roughly 50% of the cell wall material, are thought to control the overall surface charge of the wall. This affects murein hydrolase activity, resistance to antibacterial peptides, and adherence to surfaces. Although both of these molecules are polymerized on the surface of the cytoplasmic membrane, their precursors are assembled in the cytoplasm. Any event that interferes with the assembling of the peptidoglycan precursor, and the transport of that object across the cell membrane, where it will integrate into the cell wall, would compromise the integrity of the wall. Damage to the cell wall disturbs the state of cell electrolytes, which can activate death pathways (apoptosis or programmed cell death). Regulated cell death and lysis in bacteria plays an important role in certain developmental processes, such as competence and biofilm development. They also play an important role in the elimination of damaged cells, such as those irreversibly injured by environmental or antibiotic stress. An example of an antibiotic that interferes with bacterial cell wall synthesis is Penicillin. Penicillin acts by binding to transpeptidases and inhibiting the cross-linking of peptidoglycan subunits. A bacterial cell with a damaged cell wall cannot undergo binary fission and is thus certain to die.
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Learning Objectives
• Describe the function and advantage of endospore formation, as well as the methods for viewing it.
An endospore is a dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum. Endospore formation is usually triggered by lack of nutrients, and usually occurs in Gram-positive bacteria. In endospore formation, the bacterium divides within its cell wall. One side then engulfs the other. Endospores enable bacteria to lie dormant for extended periods, even centuries. When the environment becomes more favorable, the endospore can reactivate itself to the vegetative state. Examples of bacteria that can form endospores include Bacillus and Clostridium. The endospore consists of the bacterium’s DNA and part of its cytoplasm, surrounded by a very tough outer coating. Endospores can survive without nutrients. They are resistant to ultraviolet radiation, desiccation, high temperature, extreme freezing and chemical disinfectants. They are commonly found in soil and water, where they may survive for long periods of time. Bacteria produce a single endospore internally.
Viewing endospores under the light microscope can be difficult due to the impermeability of the endospore wall to dyes and stains. While the rest of a bacterial cell may stain, the endospore is left colorless. To combat this, a special stain technique called a Moeller stain is used. That allows the endospore to show up as red, while the rest of the cell stains blue. Another staining technique for endospores is the Schaeffer-Fulton stain, which stains endospores green and bacterial bodies red. There are variations in endospore morphology. Examples of bacteria having terminal endospores include Clostridium tetani, the pathogen that causes the disease tetanus. Bacteria having a centrally placed endospore include Bacillus cereus, and those having a subterminal endospore include Bacillus subtilis. Sometimes the endospore can be so large that the cell can be distended around the endospore. This is typical of Clostridium tetani.
When a bacterium detects environmental conditions are becoming unfavorable it may start the process of endosporulation, which takes about eight hours. The DNA is replicated and a membrane wall known as a spore septum begins to form between it and the rest of the cell. The plasma membrane of the cell surrounds this wall and pinches off to leave a double membrane around the DNA, and the developing structure is now known as a forespore. Calcium dipicolinate is incorporated into the forespore during this time. Next the peptidoglycan cortex forms between the two layers and the bacterium adds a spore coat to the outside of the forespore. Sporulation is now complete, and the mature endospore will be released when the surrounding vegetative cell is degraded.
While resistant to extreme heat and radiation, endospores can be destroyed by burning or by autoclaving. Endospores are able to survive boiling at 100°C for hours, although the longer the number of hours the fewer that will survive. An indirect way to destroy them is to place them in an environment that reactivates them to their vegetative state. They will germinate within a day or two with the right environmental conditions, and then the vegetative cells can be straightforwardly destroyed. This indirect method is called Tyndallization. It was the usual method for a while in the late 19th century before the advent of inexpensive autoclaves. Prolonged exposure to ionising radiation, such as x-rays and gamma rays, will also kill most endospores.
Reactivation of the endospore occurs when conditions are more favourable and involves activation, germination, and outgrowth. Even if an endospore is located in plentiful nutrients, it may fail to germinate unless activation has taken place. This may be triggered by heating the endospore. Germination involves the dormant endospore starting metabolic activity and thus breaking hibernation. It is commonly characterised by rupture or absorption of the spore coat, swelling of the endospore, an increase in metabolic activity, and loss of resistance to environmental stress.
As a simplified model for cellular differentiation, the molecular details of endospore formation have been extensively studied, specifically in the model organism Bacillus subtilis. These studies have contributed much to our understanding of the regulation of gene expression, transcription factors, and the sigma factor subunits of RNA polymerase.
Endospores of the bacterium Bacillus anthracis were used in the 2001 anthrax attacks. The powder found in contaminated postal letters was composed of extracellular anthrax endospores. Inhalation, ingestion or skin contamination of these endospores led to a number of deaths.
Geobacillus stearothermophilus endospores are used as biological indicators when an autoclave is used in sterilization procedures. Bacillus subtilis spores are useful for the expression of recombinant proteins and in particular for the surface display of peptides and proteins as a tool for fundamental and applied research in the fields of microbiology, biotechnology and vaccination.
Key Points
• Examples of bacteria that can form endospores include Bacillus and Clostridium.
• Endospores can survive without nutrients. They are resistant to ultraviolet radiation, desiccation, high temperature, extreme freezing and chemical disinfectants.
• While resistant to extreme heat and radiation, endospores can be destroyed by burning or by autoclaving.
Key Terms
• endospore: A dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum.
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• Cell Biology/Cell types/Bacteria. Provided by: Wikibooks. Located at: en.wikibooks.org/wiki/Cell_Bi...types/Bacteria. License: CC BY-SA: Attribution-ShareAlike
• Endospores. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/Endospores. License: CC BY-SA: Attribution-ShareAlike
• endospore. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/endospore. License: CC BY-SA: Attribution-ShareAlike
• Bacillus subtilis Spore. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Ba...ilis_Spore.jpg. License: CC BY-SA: Attribution-ShareAlike
• Bakterien%20Sporen. Provided by: Wikipedia. Located at: en.Wikipedia.org/wiki/File:Ba...ien_Sporen.png. License: Public Domain: No Known Copyright | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.05%3A_Specialized_External_Structures_of_Prokaryotes/4.5A%3A_Endospores.txt |
Learning Objectives
• Compare and contrast ribosome structure and function in prokaryotes and eukaryotes
Ribosomes are tiny spherical organelles that make proteins by joining amino acids together. Many ribosomes are found free in the cytosol, while others are attached to the rough endoplasmic reticulum. The purpose of the ribosome is to translate messenger RNA (mRNA) to proteins with the aid of tRNA. In eukaryotes, ribosomes can commonly be found in the cytosol of a cell, the endoplasmic reticulum or mRNA, as well as the matrix of the mitochondria. Proteins synthesized in each of these locations serve a different role in the cell. In prokaryotes, ribosomes can be found in the cytosol as well. This protein-synthesizing organelle is the only organelle found in both prokaryotes and eukaryotes, asserting the fact that the ribosome is a trait that evolved early on, most likely present in the common ancestor of eukaryotes and prokaryotes. Ribosomes are not membrane bound.
Ribosomes are composed of two subunits, one large and one small, that only bind together during protein synthesis. The purpose of the ribosome is to take the actual message and the charged aminoacyl-tRNA complex to generate the protein. To do so, they have three binding sites. One is for the mRNA; the other two are for the tRNA. The binding sites for tRNA are the A site, which holds the aminoacyl-tRNA complex, and the P site, which binds to the tRNA attached to the growing polypeptide chain.
In most bacteria, the most numerous intracellular structure is the ribosome which is the site of protein synthesis in all living organisms. All prokaryotes have 70S (where S=Svedberg units) ribosomes while eukaryotes contain larger 80S ribosomes in their cytosol. The 70S ribosome is made up of a 50S and 30S subunits. The 50S subunit contains the 23S and 5S rRNA while the 30S subunit contains the 16S rRNA. These rRNA molecules differ in size in eukaryotes and are complexed with a large number of ribosomal proteins, the number and type of which can vary slightly between organisms. The ribosome is the most commonly observed intracellular multiprotein complex in bacteria.
Ribosome assembly consists of transcription, translation, the folding of rRNA and ribosomal proteins, the binding of ribosomal proteins, and the binding and release of the assembly components to make the ribosome. In vivo assembly of the 30S subunit has two intermediates (p130S and p230S) and the 50S subunit has three intermediates (p150S, p250S, and p350S). However, the reconstitution intermediates are not the same as in vitro. The intermediates of the 30S subunit yield 21S and 30S particles while the intermediates of the 50S subunit yield 32S, 43S, and 50S particles. The intermediates in the in vivo assembly are precursor rRNA which is different from in vitro which uses matured rRNA. To complete the mechanism of ribosome assembly, these precursor rRNA gets transformed in the polysomes.
Key Points
• All prokaryotes have 70S (where S=Svedberg units) ribosomes while eukaryotes contain larger 80S ribosomes in their cytosol. The 70S ribosome is made up of a 50S and 30S subunits.
• Ribosomes play a key role in the catalysis of two important and crucial biological processes. peptidyl transfer and peptidyl hydrolysis.
• Ribosomes are tiny spherical organelles that make proteins by joining amino acids together. Many ribosomes are found free in the cytosol, while others are attached to the rough endoplasmic reticulum.
Key Terms
• ribosome: Small organelles found in all cells; involved in the production of proteins by translating messenger RNA.
• translation: A process occurring in the ribosome, in which a strand of messenger RNA (mRNA) guides assembly of a sequence of amino acids to make a protein.
• Svedberg: The Svedberg unit (S) offers a measure of particle size based on its rate of travel in a tube subjected to high g-force. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.06%3A_Specialized_Internal_Structures_of_Prokaryotes/4.6A%3A_Ribosomes.txt |
Bacteria have different methods of nutrient storage that are employed in times of plenty, for use in times of want.
Learning Objectives
• Explain the hypothesis regarding the formation of inclusion bodies and the importance of storage granules
Key Points
• Sulfur granules are especially common in bacteria that use hydrogen sulfide as an electron source.
• When genes from one organism are expressed in another, the resulting protein sometimes forms inclusion bodies.
• Many bacteria store excess carbon in the form of polyhydroxyalkanoates or glycogen.
Key Terms
• Inclusion bodies: Inclusion bodies are nuclear or cytoplasmic aggregates of stainable substances, usually proteins.
Cell Inclusions and Storage Granules
Bacteria, despite their simplicity, contain a well-developed cell structure responsible for many unique biological properties not found among archaea or eukaryotes. Because of the simplicity of bacteria relative to larger organisms, and the ease with which they can be manipulated experimentally, the cell structure of bacteria has been well studied, revealing many biochemical principles that have been subsequently applied to other organisms.
Most bacteria do not live in environments that contain large amounts of nutrients at all times. To accommodate these transient levels of nutrients, bacteria contain several different methods of nutrient storage that are employed in times of plenty, for use in times of want. For example, many bacteria store excess carbon in the form of polyhydroxyalkanoates or glycogen. Some microbes store soluble nutrients, such as nitrate in vacuoles. Sulfur is most often stored as elemental (S0) granules which can be deposited either intra- or extracellularly. Sulfur granules are especially common in bacteria that use hydrogen sulfide as an electron source. Most of the above mentioned examples can be viewed using a microscope, and are surrounded by a thin non-unit membrane to separate them from the cytoplasm.
Inclusion bodies are nuclear or cytoplasmic aggregates of stainable substances, usually proteins. They typically represent sites of viral multiplication in a bacterium or a eukaryotic cell, and usually consist of viral capsid proteins. Inclusion bodies have a non-unit lipid membrane. Protein inclusion bodies are classically thought to contain misfolded protein. However, this has recently been contested, as green fluorescent protein will sometimes fluoresce in inclusion bodies, which indicates some resemblance of the native structure and researchers have recovered folded protein from inclusion bodies.
When genes from one organism are expressed in another the resulting protein sometimes forms inclusion bodies. This is often true when large evolutionary distances are crossed; for example, a cDNA isolated from Eukarya and expressed as a recombinant gene in a prokaryote, risks the formation of the inactive aggregates of protein known as inclusion bodies. While the cDNA may properly code for a translatable mRNA, the protein that results will emerge in a foreign microenvironment. This often has fatal effects, especially if the intent of cloning is to produce a biologically active protein. For example, eukaryotic systems for carbohydrate modification and membrane transport are not found in prokaryotes.
The internal microenvironment of a prokaryotic cell (pH, osmolarity) may differ from that of the original source of the gene. Mechanisms for folding a protein may also be absent, and hydrophobic residues that normally would remain buried may be exposed and available for interaction with similar exposed sites on other ectopic proteins. Processing systems for the cleavage and removal of internal peptides would also be absent in bacteria. The initial attempts to clone insulin in a bacterium suffered all of these deficits. In addition, the fine controls that may keep the concentration of a protein low will also be missing in a prokaryotic cell, and overexpression can result in filling a cell with ectopic protein that, even if it were properly folded, would precipitate by saturating its environment. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.06%3A_Specialized_Internal_Structures_of_Prokaryotes/4.6B%3A_Cell_Inclusions_and_Storage_Granules.txt |
Learning Objectives
• Generalize the function of carboxysomes in autotrophic bacteria
Carboxysomes are intracellular structures found in many autotrophic bacteria, including Cyanobacteria, Knallgasbacteria, Nitroso- and Nitrobacteria. They are proteinaceous structures resembling phage heads in their morphology; they contain the enzymes of carbon dioxide fixation in these organisms. It is thought that the high local concentration of the enzymes, along with the fast conversion of bicarbonate to carbon dioxide by carbonic anhydrase, allows faster and more efficient carbon dioxide fixation than is possible inside the cytoplasm. Similar structures are known to harbor the B12-containing coenzyme glycerol dehydratase, the key enzyme of glycerol fermentation to 1,3-propanediol, in some Enterobacteriaceae, such as Salmonella.
Carboxysomes are bacterial microcompartments that contain enzymes involved in carbon fixation. Carboxysomes are made of polyhedral protein shells about 80 to 140 nanometres in diameter. These compartments are thought to concentrate carbon dioxide to overcome the inefficiency of RuBisCo (ribulose bisphosphate carboxylase/oxygenase) – the predominant enzyme in carbon fixation and the rate limiting enzyme in the Calvin cycle. These organelles are found in all cyanobacteria and many chemotrophic bacteria that fix carbon dioxide.
Carboxysomes are an example of a wider group of protein micro-compartments that have dissimilar functions but similar structures, based on homology of the two shell protein families. Using electron microscopy the first carboxysomes were seen in 1956, in the cyanobacterium Phormidium uncinatum. In the early 1960s, similar polyhedral objects were observed in other cyanobacteria. These structures were named polyhedral bodies in 1961; over the next few years they were also discovered in some chemotrophic bacteria that fixed carbon dioxide. Among these are Halothiobacillus, Acidithiobacillus, Nitrobacter and Nitrococcus.
Carboxysomes were first purified from Thiobacillus neapolitanus in 1973, and were shown to contain RuBisCo held within a rigid outer covering.
Key Points
• Carboxysomes are proteinaceous structures resembling phage heads in their morphology and contain the enzymes of carbon dioxide fixation in these organisms.
• Carboxysomes are made of polyhedral protein shells about 80 to 140 nanometres in diameter.
• These organelles are found in all cyanobacteria and many chemotrophic bacteria that fix carbon dioxide.
Key Terms
• carboxysome: A bacterial organelle that contains enzymes involved in carbon fixation.
4.6D: Magnetosomes
Learning Objectives
• Illustrate the structure of magnetosomes and the advantages that they provide to magentotactic bacteria
Magnetosomes are intracellular organelles found in magnetotactic bacteria that allow them to sense and align themselves along a magnetic field (magnetotaxis). They contain 15 to 20 magnetite crystals that together act like a compass needle to orient magnetotactic bacteria in geomagnetic fields, thereby simplifying their search for their preferred microaerophilic environments. Each magnetite crystal within a magnetosome is surrounded by a lipid bilayer. Specific soluble and transmembrane proteins are sorted to the membrane. Recent research has shown that magnetosomes are invaginations of the inner membrane and not freestanding vesicles. Magnetite-bearing magnetosomes have also been found in eukaryotic magnetotactic algae, with each cell containing several thousand crystals.
Magnetotactic bacteria usually mineralize either iron oxide magnetosomes, which contain crystals of magnetite (Fe3O4), or iron sulfide magnetosomes, which contain crystals of greigite (Fe3S4). Several other iron sulfide minerals have also been identified in iron sulfide magnetosomes — including mackinawite (tetragonal FeS) and a cubic FeS — which are thought to be precursors of Fe3S4. One type of magnetotactic bacterium present at the oxic-anoxic transition zone (OATZ) of the southern basin of the Pettaquamscutt River Estuary, Narragansett, Rhode Island is known to produce both iron oxide and iron sulfide magnetosomes.
The particle morphology of magnetosome crystals varies, but is consistent within cells of a single magnetotactic bacterial species or strain. Three general crystal morphologies have been reported in magnetotactic bacteria on the basis: roughly cuboidal, elongated prismatic (roughly rectangular), and tooth-, bullet-, or arrowhead-shaped. Magnetosome crystals are typically 35–120 nm long, which makes them single- domain. Single-domain crystals have the maximum possible magnetic moment per unit volume for a given composition. Smaller crystals are superparamagnetic–that is, not permanently magnetic at ambient temperature, and domain walls would form in larger crystals. In most magnetotactic bacteria, the magnetosomes are arranged in one or more chains.
Magnetic interactions between the magnetosome crystals in a chain cause their magnetic dipole moments to orientate parallel to each other along the length of the chain. The magnetic dipole moment of the cell is usually large enough so that its interaction with Earth’s magnetic field overcomes thermal forces that tend to randomize the orientation of the cell in its aqueous surroundings. Magnetotactic bacteria also use aerotaxis, a response to changes in oxygen concentration that favors swimming toward a zone of optimal oxygen concentration. In lakes or oceans the oxygen concentration is commonly dependent on depth. As long as the Earth’s magnetic field has a significant downward slant, the orientation along field lines aids the search for the optimal concentration. This process is called magneto-aerotaxis.
Key Points
• Magnetosomes contain 15 to 20 magnetite crystals that together act like a compass needle to orient magnetotactic bacteria in geomagnetic fields, thereby simplifying their search for their preferred microaerophilic environments.
• The particle morphology of magnetosome crystals varies, but is consistent within cells of a single magnetotactic bacterial species or strain.
• Each magnetite crystal within a magnetosome is surrounded by a lipid bilayer. Specific soluble and transmembrane proteins are sorted to the membrane.
Key Terms
• magnetotaxis: The supposed ability to sense a magnetic field and coordinate movement in response, later discovered to be natural magnetism: such creatures orient themselves magnetically even after death.
• magnetosome: A membranous prokaryotic organelle, containing mineral crystals, present in magnetotactic bacteria.
4.6E: Gas Vesicles
Learning Objectives
• Discuss the role of a gas vesicle in regards to survival.
Gas vesicles are spindle-shaped structures found in some planktonic bacteria that provides buoyancy to these cells by decreasing their overall cell density. Positive buoyancy is needed to keep the cells in the upper reaches of the water column, so that they can continue to perform photosynthesis. They are made up of a shell of protein that has a highly hydrophobic inner surface, making it impermeable to water (and stopping water vapor from condensing inside), but permeable to most gases. Because the gas vesicle is a hollow cylinder, it is liable to collapse when the surrounding pressure becomes too great.
Natural selection has fine-tuned the structure of the gas vesicle to maximize its resistance to buckling by including an external strengthening protein, GvpC, rather like the green thread in a braided hosepipe. There is a simple relationship between the diameter of the gas vesicle and pressure at which it will collapse – the wider the gas vesicle the weaker it becomes. However, wider gas vesicles are more efficient. They provide more buoyancy per unit of protein than narrow gas vesicles. Different species produce gas vesicles of different diameters, allowing them to colonize different depths of the water column (fast growing, highly competitive species with wide gas vesicles in the top most layers; slow growing, dark-adapted, species with strong narrow gas vesicles in the deeper layers). The diameter of the gas vesicle will also help determine which species survive in different bodies of water. Deep lakes that experience winter mixing will expose the cells to the hydrostatic pressure generated by the full water column. This will select for species with narrower, stronger gas vesicles.
Key Points
• They are made up of a shell of protein that has a highly hydrophobic inner surface, making it impermeable to water (and stopping water vapour from condensing inside), but permeable to most gases.
• Natural selection has fine tuned the structure of the gas vesicle to maximize its resistance to buckling, including an external strengthening protein, GvpC, rather like the green thread in a braided hosepipe.
• The diameter of the gas vesicle will also help determine which species survive in different bodies of water.
Key Terms
• gas vesicle: Gas vesicles are spindle-shaped structures found in some planktonic bacteria that provide buoyancy to these cells by decreasing their overall cell density.
• gas gangrene: a bacterial infection that produces gas in tissues in necrotizing or rotting tissues
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Found within eukaryotic cells, the nucleus contains the genetic material that determines the entire structure and function of that cell.
Learning Objectives
• Explain the purpose of the nucleus in eukaryotic cells
Key Points
• The nucleus contains the cell ‘s DNA and directs the synthesis of ribosomes and proteins.
• Found within the nucleoplasm, the nucleolus is a condensed region of chromatin where ribosome synthesis occurs.
• Chromatin consists of DNA wrapped around histone proteins and is stored within the nucleoplasm.
• Ribosomes are large complexes of protein and ribonucleic acid (RNA) responsible for protein synthesis when DNA from the nucleus is transcribed.
Key Terms
• histone: any of various simple water-soluble proteins that are rich in the basic amino acids lysine and arginine and are complexed with DNA in the nucleosomes of eukaryotic chromatin
• nucleolus: a conspicuous, rounded, non-membrane bound body within the nucleus of a cell
• chromatin: a complex of DNA, RNA, and proteins within the cell nucleus out of which chromosomes condense during cell division
The Nucleus
One of the main differences between prokaryotic and eukaryotic cells is the nucleus. As previously discussed, prokaryotic cells lack an organized nucleus while eukaryotic cells contain membrane-bound nuclei (and organelles ) that house the cell’s DNA and direct the synthesis of ribosomes and proteins.
The nucleus stores chromatin (DNA plus proteins) in a gel-like substance called the nucleoplasm. To understand chromatin, it is helpful to first consider chromosomes. Chromatin describes the material that makes up chromosomes, which are structures within the nucleus that are made up of DNA, the hereditary material. You may remember that in prokaryotes, DNA is organized into a single circular chromosome. In eukaryotes, chromosomes are linear structures. Every eukaryotic species has a specific number of chromosomes in the nuclei of its body’s cells. For example, in humans, the chromosome number is 46, while in fruit flies, it is eight. Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. In order to organize the large amount of DNA within the nucleus, proteins called histones are attached to chromosomes; the DNA is wrapped around these histones to form a structure resembling beads on a string. These protein-chromosome complexes are called chromatin.
The nucleoplasm is also where we find the nucleolus. The nucleolus is a condensed region of chromatin where ribosome synthesis occurs. Ribosomes, large complexes of protein and ribonucleic acid (RNA), are the cellular organelles responsible for protein synthesis. They receive their “orders” for protein synthesis from the nucleus where the DNA is transcribed into messenger RNA (mRNA). This mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein.
Lastly, the boundary of the nucleus is called the nuclear envelope. It consists of two phospholipid bilayers: an outer membrane and an inner membrane. The nuclear membrane is continuous with the endoplasmic reticulum, while nuclear pores allow substances to enter and exit the nucleus.
4.7B: Mitochondria
Learning Objectives
• Explain the role of the mitochondria.
One of the major features distinguishing prokaryotes from eukaryotes is the presence of mitochondria. Mitochondria are double-membraned organelles that contain their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy consumption. Each mitochondrion measures 1 to 10 micrometers (or greater) in length and exists in the cell as an organelle that can be ovoid to worm-shaped to intricately branched.
Mitochondria Structure
Most mitochondria are surrounded by two membranes, which would result when one membrane-bound organism was engulfed into a vacuole by another membrane-bound organism. The mitochondrial inner membrane is extensive and involves substantial infoldings called cristae that resemble the textured, outer surface of alpha-proteobacteria. The matrix and inner membrane are rich with the enzymes necessary for aerobic respiration.
Mitochondria have their own (usually) circular DNA chromosome that is stabilized by attachments to the inner membrane and carries genes similar to genes expressed by alpha-proteobacteria. Mitochondria also have special ribosomes and transfer RNAs that resemble these components in prokaryotes. These features all support the hypothesis that mitochondria were once free-living prokaryotes.
Mitochondria Function
Mitochondria are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. ATP represents the short-term stored energy of the cell. Cellular respiration is the process of making ATP using the chemical energy found in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product. In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a by-product.
It is important to point out that muscle cells have a very high concentration of mitochondria that produce ATP. Your muscle cells need a lot of energy to keep your body moving. When your cells don’t get enough oxygen, they do not make a lot of ATP. Instead, the small amount of ATP they make in the absence of oxygen is accompanied by the production of lactic acid. In addition to the aerobic generation of ATP, mitochondria have several other metabolic functions. One of these functions is to generate clusters of iron and sulfur that are important cofactors of many enzymes. Such functions are often associated with the reduced mitochondrion-derived organelles of anaerobic eukaryotes.
Origins of Mitochondria
There are two hypotheses about the origin of mitochondria: endosymbiotic and autogenous, but the most accredited theory at present is endosymbiosis. The endosymbiotic hypothesis suggests mitochondria were originally prokaryotic cells, capable of implementing oxidative mechanisms. These prokaryotic cells may have been engulfed by a eukaryote and became endosymbionts living inside the eukaryote.
Key Points
• Mitochondria contain their own ribosomes and DNA; combined with their double membrane, these features suggest that they might have once been free-living prokaryotes that were engulfed by a larger cell.
• Mitochondria have an important role in cellular respiration through the production of ATP, using chemical energy found in glucose and other nutrients.
• Mitochondria are also responsible for generating clusters of iron and sulfur, which are important cofactors of many enzymes.
Key Terms
• alpha-proteobacteria: A taxonomic class within the phylum Proteobacteria — the phototropic proteobacteria.
• adenosine triphosphate: a multifunctional nucleoside triphosphate used in cells as a coenzyme, often called the “molecular unit of energy currency” in intracellular energy transfer
• cofactor: an inorganic molecule that is necessary for an enzyme to function | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.07%3A_Internal_Structures_of_Eukaryotic_Cells/4.7A%3A_The_Nucleus_and_Ribosomes.txt |
Although they are both eukaryotic cells, there are unique structural differences between animal and plant cells.
Learning Objectives
• Differentiate between the structures found in animal and plant cells
Key Points
• Centrosomes and lysosomes are found in animal cells, but do not exist within plant cells.
• The lysosomes are the animal cell’s “garbage disposal”, while in plant cells the same function takes place in vacuoles.
• Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole, which are not found within animal cells.
• The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell.
• The chloroplasts, found in plant cells, contain a green pigment called chlorophyll, which captures the light energy that drives the reactions of plant photosynthesis.
• The central vacuole plays a key role in regulating a plant cell’s concentration of water in changing environmental conditions.
Key Terms
• protist: Any of the eukaryotic unicellular organisms including protozoans, slime molds and some algae; historically grouped into the kingdom Protoctista.
• autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy
• heterotroph: an organism that requires an external supply of energy in the form of food, as it cannot synthesize its own
Animal Cells versus Plant Cells
Each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, vacuoles; however, there are some striking differences between animal and plant cells. While both animal and plant cells have microtubule organizing centers (MTOCs), animal cells also have centrioles associated with the MTOC: a complex called the centrosome. Animal cells each have a centrosome and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole, whereas animal cells do not.
The Centrosome
The centrosome is a microtubule-organizing center found near the nuclei of animal cells. It contains a pair of centrioles, two structures that lie perpendicular to each other. Each centriole is a cylinder of nine triplets of microtubules. The centrosome (the organelle where all microtubules originate) replicates itself before a cell divides, and the centrioles appear to have some role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the exact function of the centrioles in cell division isn’t clear, because cells that have had the centrosome removed can still divide; and plant cells, which lack centrosomes, are capable of cell division.
The Centrosome Structure: The centrosome consists of two centrioles that lie at right angles to each other. Each centriole is a cylinder made up of nine triplets of microtubules. Nontubulin proteins (indicated by the green lines) hold the microtubule triplets together.
Lysosomes
Animal cells have another set of organelles not found in plant cells: lysosomes. The lysosomes are the cell’s “garbage disposal.” In plant cells, the digestive processes take place in vacuoles. Enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. These enzymes are active at a much lower pH than that of the cytoplasm. Therefore, the pH within lysosomes is more acidic than the pH of the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, so the advantage of compartmentalizing the eukaryotic cell into organelles is apparent.
The Cell Wall
The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protistan cells also have cell walls. While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose, a polysaccharide comprised of glucose units. When you bite into a raw vegetable, like celery, it crunches. That’s because you are tearing the rigid cell walls of the celery cells with your teeth.
Chloroplasts
Like mitochondria, chloroplasts have their own DNA and ribosomes, but chloroplasts have an entirely different function. Chloroplasts are plant cell organelles that carry out photosynthesis. Photosynthesis is the series of reactions that use carbon dioxide, water, and light energy to make glucose and oxygen. This is a major difference between plants and animals; plants (autotrophs) are able to make their own food, like sugars, while animals (heterotrophs) must ingest their food.
Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked fluid-filled membrane sacs called thylakoids. Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane that surrounds the grana is called the stroma.
The chloroplasts contain a green pigment called chlorophyll, which captures the light energy that drives the reactions of photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria perform photosynthesis, but their chlorophyll is not relegated to an organelle.
The Central Vacuole
The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. When you forget to water a plant for a few days, it wilts. That’s because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of plant cells results in the wilted appearance of the plant. The central vacuole also supports the expansion of the cell. When the central vacuole holds more water, the cell gets larger without having to invest a lot of energy in synthesizing new cytoplasm. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.07%3A_Internal_Structures_of_Eukaryotic_Cells/4.7C%3A_Comparing_Plant_and_Animal_Cells.txt |
The endoplasmic reticulum is an organelle that is responsible for the synthesis of lipids and the modification of proteins.
Learning Objectives
• Describe the structure of the endoplasmic reticulum and its role in synthesis and metabolism
Key Points
• If the endoplasmic reticulum (ER) has ribosomes attached to it, it is called rough ER; if it does not, then it is called smooth ER.
• The proteins made by the rough endoplasmic reticulum are for use outside of the cell.
• Functions of the smooth endoplasmic reticulum include synthesis of carbohydrates, lipids, and steroid hormones; detoxification of medications and poisons; and storage of calcium ions.
Key Terms
• lumen: The cavity or channel within a tube or tubular organ.
• reticulum: A network
The Endoplasmic Reticulum
The endoplasmic reticulum (ER) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. However, these two functions are performed in separate areas of the ER: the rough ER and the smooth ER. The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope.
Rough ER
The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope. Ribosomes transfer their newly synthesized proteins into the lumen of the RER where they undergo structural modifications, such as folding or the acquisition of side chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles —or secreted from the cell (such as protein hormones, enzymes ). The RER also makes phospholipids for cellular membranes. If the phospholipids or modified proteins are not destined to stay in the RER, they will reach their destinations via transport vesicles that bud from the RER’s membrane. Since the RER is engaged in modifying proteins (such as enzymes, for example) that will be secreted from the cell, the RER is abundant in cells that secrete proteins. This is the case with cells of the liver, for example.
Smooth ER
The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface. Functions of the SER include synthesis of carbohydrates, lipids, and steroid hormones; detoxification of medications and poisons; and storage of calcium ions. In muscle cells, a specialized SER called the sarcoplasmic reticulum is responsible for storage of the calcium ions that are needed to trigger the coordinated contractions of the muscle cells.
4.7E: The Golgi Apparatus
Learning Objectives
• Describe the structure of the Golgi apparatus and its role in protein modification and secretion
We have already mentioned that vesicles can bud from the ER and transport their contents elsewhere, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles still need to be sorted, packaged, and tagged so that they wind up in the right place. Sorting, tagging, packaging, and distribution of lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranes.
The receiving side of the Golgi apparatus is called the cis face. The opposite side is called the trans face. The transport vesicles that formed from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. The most frequent modification is the addition of short chains of sugar molecules. These newly-modified proteins and lipids are then tagged with phosphate groups or other small molecules so that they can be routed to their proper destinations.
Finally, the modified and tagged proteins are packaged into secretory vesicles that bud from the trans face of the Golgi. While some of these vesicles deposit their contents into other parts of the cell where they will be used, other secretory vesicles fuse with the plasma membrane and release their contents outside the cell.
In another example of form following function, cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundance of Golgi. In plant cells, the Golgi apparatus has the additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell.
Key Points
• The Golgi apparatus is a series of flattened sacs that sort and package cellular materials.
• The Golgi apparatus has a cis face on the ER side and a trans face opposite of the ER.
• The trans face secretes the materials into vesicles, which then fuse with the cell membrane for release from the cell.
Key Terms
• vesicle: A membrane-bound compartment found in a cell.
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Learning Objectives
• Name the various functions that peroxisomes perform inside the cell
A type of organelle found in both animal cells and plant cells, a peroxisome is a membrane-bound cellular organelle that contains mostly enzymes. Peroxisomes perform important functions, including lipid metabolism and chemical detoxification. They also carry out oxidation reactions that break down fatty acids and amino acids.
In contrast to the digestive enzymes found in lysosomes, the enzymes within peroxisomes serve to transfer hydrogen atoms from various molecules to oxygen, producing hydrogen peroxide (H2O2). In this way, peroxisomes neutralize poisons, such as alcohol, that enter the body. In order to appreciate the importance of peroxisomes, it is necessary to understand the concept of reactive oxygen species.
Reactive oxygen species (ROS), such as peroxides and free radicals, are the highly-reactive products of many normal cellular processes, including the mitochondrial reactions that produce ATP and oxygen metabolism. Examples of ROS include the hydroxyl radical OH, H2O2, and superoxide (O−2). Some ROS are important for certain cellular functions, such as cell signaling processes and immune responses against foreign substances. Many ROS, however, are harmful to the body. Free radicals are reactive because they contain free unpaired electrons; they can easily oxidize other molecules throughout the cell, causing cellular damage and even cell death. Free radicals are thought to play a role in many destructive processes in the body, from cancer to coronary artery disease.
Peroxisomes oversee reactions that neutralize free radicals. They produce large amounts of the toxic H2O2 in the process, but contain enzymes that convert H2O2into water and oxygen. These by-products are then safely released into the cytoplasm. Like miniature sewage treatment plants, peroxisomes neutralize harmful toxins so that they do not cause damage in the cells. The liver is the organ primarily responsible for detoxifying the blood before it travels throughout the body; liver cells contain an exceptionally high number of peroxisomes.
Key Points
• Lipid metabolism and chemical detoxification are important functions of peroxisomes.
• Peroxisomes are responsible for oxidation reactions that break down fatty acids and amino acids.
• Peroxisomes oversee reactions that neutralize free radicals, which cause cellular damage and cell death.
• Peroxisomes chemically neutralize poisons through a process that produces large amounts of toxic H2O2, which is then converted into water and oxygen.
• The liver is the organ primarily responsible for detoxifying the blood before it travels throughout the body; as a result, liver cells contain large amounts of peroxisomes.
Key Terms
• enzyme: a globular protein that catalyses a biological chemical reaction
• free radical: Any molecule, ion or atom that has one or more unpaired electrons; they are generally highly reactive and often only occur as transient species.
4.8B: Lysosomes
Learning Objectives
• Describe how lysosomes function as the cell’s waste disposal system
Lysosomes are organelles that digest macromolecules, repair cell membranes, and respond to foreign substances entering the cell.
Lysosomes
A lysosome has three main functions: the breakdown/digestion of macromolecules (carbohydrates, lipids, proteins, and nucleic acids), cell membrane repairs, and responses against foreign substances such as bacteria, viruses and other antigens. When food is eaten or absorbed by the cell, the lysosome releases its enzymes to break down complex molecules including sugars and proteins into usable energy needed by the cell to survive. If no food is provided, the lysosome’s enzymes digest other organelles within the cell in order to obtain the necessary nutrients.
In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are considered to be parts of the endomembrane system. Lysosomes also use their hydrolytic enzymes to destroy pathogens (disease-causing organisms) that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis or endocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen.
A lysosome is composed of lipids, which make up the membrane, and proteins, which make up the enzymes within the membrane. Usually, lysosomes are between 0.1 to 1.2μm, but the size varies based on the cell type. The general structure of a lysosome consists of a collection of enzymes surrounded by a single-layer membrane. The membrane is a crucial aspect of its structure because without it the enzymes within the lysosome that are used to breakdown foreign substances would leak out and digest the entire cell, causing it to die.
Lysosomes are found in nearly every animal-like eukaryotic cell. They are so common in animal cells because, when animal cells take in or absorb food, they need the enzymes found in lysosomes in order to digest and use the food for energy. On the other hand, lysosomes are not commonly-found in plant cells. Lysosomes are not needed in plant cells because they have cell walls that are tough enough to keep the large/foreign substances that lysosomes would usually digest out of the cell.
Key Points
• Lysosomes breakdown/digest macromolecules (carbohydrates, lipids, proteins, and nucleic acids), repair cell membranes, and respond against foreign substances such as bacteria, viruses and other antigens.
• Lysosomes contain enzymes that break down the macromolecules and foreign invaders.
• Lysosomes are composed of lipids and proteins, with a single membrane covering the internal enzymes to prevent the lysosome from digesting the cell itself.
• Lysosomes are found in all animal cells, but are rarely found within plant cells due to the tough cell wall surrounding a plant cell that keeps out foreign substances.
Key Terms
• enzyme: a globular protein that catalyses a biological chemical reaction
• lysosome: An organelle found in all types of animal cells which contains a large range of digestive enzymes capable of splitting most biological macromolecules. | textbooks/bio/Microbiology/Microbiology_(Boundless)/04%3A_Cell_Structure_of_Bacteria_Archaea_and_Eukaryotes/4.08%3A_Other_Eukaryotic_Components/4.8A%3A_Peroxisomes.txt |
Microtubules are part of the cell’s cytoskeleton, helping the cell resist compression, move vesicles, and separate chromosomes at mitosis.
Learning Objectives
• Describe the roles of microtubules as part of the cell’s cytoskeleton
Key Points
• Microtubules help the cell resist compression, provide a track along which vesicles can move throughout the cell, and are the components of cilia and flagella.
• Cilia and flagella are hair-like structures that assist with locomotion in some cells, as well as line various structures to trap particles.
• The structures of cilia and flagella are a “9+2 array,” meaning that a ring of nine microtubules is surrounded by two more microtubules.
• Microtubules attach to replicated chromosomes during cell division and pull them apart to opposite ends of the pole, allowing the cell to divide with a complete set of chromosomes in each daughter cell.
Key Terms
• microtubule: Small tubes made of protein and found in cells; part of the cytoskeleton
• flagellum: a flagellum is a lash-like appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells
• cytoskeleton: A cellular structure like a skeleton, contained within the cytoplasm.
Microtubules
As their name implies, microtubules are small hollow tubes. Microtubules, along with microfilaments and intermediate filaments, come under the class of organelles known as the cytoskeleton. The cytoskeleton is the framework of the cell which forms the structural supporting component. Microtubules are the largest element of the cytoskeleton. The walls of the microtubule are made of polymerized dimers of α-tubulin and β-tubulin, two globular proteins. With a diameter of about 25 nm, microtubules are the widest components of the cytoskeleton. They help the cell resist compression, provide a track along which vesicles move through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. Like microfilaments, microtubules can dissolve and reform quickly.
Microtubules are also the structural elements of flagella, cilia, and centrioles (the latter are the two perpendicular bodies of the centrosome ). In animal cells, the centrosome is the microtubule-organizing center. In eukaryotic cells, flagella and cilia are quite different structurally from their counterparts in prokaryotes.
Intermediate Filaments
Intermediate filaments (IFs) are cytoskeletal components found in animal cells. They are composed of a family of related proteins sharing common structural and sequence features. Intermediate filaments have an average diameter of 10 nanometers, which is between that of 7 nm actin (microfilaments), and that of 25 nm microtubules, although they were initially designated ‘intermediate’ because their average diameter is between those of narrower microfilaments (actin) and wider myosin filaments found in muscle cells. Intermediate filaments contribute to cellular structural elements and are often crucial in holding together tissues like skin.
Flagella and Cilia
Flagella (singular = flagellum ) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, many of them extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecia) or substances along the outer surface of the cell (for example, the cilia of cells lining the Fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that trap particulate matter and move it toward your nostrils).
Despite their differences in length and number, flagella and cilia share a common structural arrangement of microtubules called a “9 + 2 array.” This is an appropriate name because a single flagellum or cilium is made of a ring of nine microtubule doublets surrounding a single microtubule doublet in the center.
4.8D: Extracellular Matrix of Animal Cells
The extracellular matrix of animal cells holds cells together to form a tissue and allow tissues to communicate with each other.
LEARNING OBJECTIVES
Explain the role of the extracellular matrix in animal cells
Key Points
• The extracellular matrix of animal cells is made up of proteins and carbohydrates.
• Cell communication within tissue and tissue formation are main functions of the extracellular matrix of animal cells.
• Tissue communication is kick-started when a molecule within the matrix binds a receptor; the end results are conformational changes that induce chemical signals that ultimately change activities within the cell.
Key Terms
• collagen: Any of more than 28 types of glycoprotein that forms elongated fibers, usually found in the extracellular matrix of connective tissue.
• proteoglycan: Any of many glycoproteins that have heteropolysaccharide side chains
• extracellular matrix: All the connective tissues and fibres that are not part of a cell, but rather provide support.
Extracellular Matrix of Animal Cells
Most animal cells release materials into the extracellular space. The primary components of these materials are proteins. Collagen is the most abundant of the proteins. Its fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. Collectively, these materials are called the extracellular matrix. Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other.
How does this cell communication occur? Cells have protein receptors on the extracellular surfaces of their plasma membranes. When a molecule within the matrix binds to the receptor, it changes the molecular structure of the receptor. The receptor, in turn, changes the conformation of the microfilaments positioned just inside the plasma membrane. These conformational changes induce chemical signals inside the cell that reach the nucleus and turn “on” or “off” the transcription of specific sections of DNA. This affects the production of associated proteins, thus changing the activities within the cell.
An example of the role of the extracellular matrix in cell communication can be seen in blood clotting. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When a tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel and stimulates the adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel). Subsequently, a series of steps are initiated which then prompt the platelets to produce clotting factors.
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Learning Objectives
• Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis.
Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different variations of endocytosis, but all share a common characteristic: the plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly-created intracellular vesicle formed from the plasma membrane.
Phagocytosis
Phagocytosis (the condition of “cell eating”) is the process by which large particles, such as cells or relatively large particles, are taken in by a cell. For example, when microorganisms invade the human body, a type of white blood cell called a neutrophil will remove the invaders through this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil.
In preparation for phagocytosis, a portion of the inward-facing surface of the plasma membrane becomes coated with a protein called clathrin, which stabilizes this section of the membrane. The coated portion of the membrane then extends from the body of the cell and surrounds the particle, eventually enclosing it. Once the vesicle containing the particle is enclosed within the cell, the clathrin disengages from the membrane and the vesicle merges with a lysosome for the breakdown of the material in the newly-formed compartment ( endosome ). When accessible nutrients from the degradation of the vesicular contents have been extracted, the newly-formed endosome merges with the plasma membrane and releases its contents into the extracellular fluid. The endosomal membrane again becomes part of the plasma membrane.
Pinocytosis
A variation of endocytosis is called pinocytosis. This literally means “cell drinking” and was named at a time when the assumption was that the cell was purposefully taking in extracellular fluid. In reality, this is a process that takes in molecules, including water, which the cell needs from the extracellular fluid. Pinocytosis results in a much smaller vesicle than does phagocytosis, and the vesicle does not need to merge with a lysosome.
Potocytosis, a variant of pinocytosis, is a process that uses a coating protein, called caveolin, on the cytoplasmic side of the plasma membrane, which performs a similar function to clathrin. The cavities in the plasma membrane that form the vacuoles have membrane receptors and lipid rafts in addition to caveolin. The vacuoles or vesicles formed in caveolae (singular caveola) are smaller than those in pinocytosis. Potocytosis is used to bring small molecules into the cell and to transport these molecules through the cell for their release on the other side of the cell, a process called transcytosis.
Receptor-mediated Endocytosis
A targeted variation of endocytosis, known as receptor-mediated endocytosis, employs receptor proteins in the plasma membrane that have a specific binding affinity for certain substances. In receptor-mediated endocytosis, as in phagocytosis, clathrin is attached to the cytoplasmic side of the plasma membrane. If uptake of a compound is dependent on receptor-mediated endocytosis and the process is ineffective, the material will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. Some human diseases are caused by the failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also referred to as “bad” cholesterol) is removed from the blood by receptor-mediated endocytosis. In the human genetic disease familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening levels of cholesterol in their blood, because their cells cannot clear LDL particles from their blood.
Although receptor-mediated endocytosis is designed to bring specific substances that are normally found in the extracellular fluid into the cell, other substances may gain entry into the cell at the same site. Flu viruses, diphtheria, and cholera toxin all have sites that cross-react with normal receptor-binding sites and gain entry into cells.
Key Points
• Endocytosis consists of phagocytosis, pinocytosis, and receptor -mediated endocytosis.
• Endocytosis takes particles into the cell that are too large to passively cross the cell membrane.
• Phagocytosis is the taking in of large food particles, while pinocytosis takes in liquid particles.
• Receptor-mediated endocytosis uses special receptor proteins to help carry large particles across the cell membrane.
Key Terms
• endosome: An endocytic vacuole through which molecules internalized during endocytosis pass en route to lysosomes
• neutrophil: A cell, especially a white blood cell that consumes foreign invaders in the blood.
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Thumbnail: The Krebs cycle, also known as the citric acid cycle, is summarized here. Note incoming two-carbon acetyl results in the main outputs per turn of two CO2, three NADH, one FADH2, and one ATP (or GTP) molecules made by substrate-level phosphorylation. Two turns of the Krebs cycle are required to process all of the carbon from one glucose molecule.
05: Microbial Metabolism
Learning Objectives
• Differentiate photoautotrophs from photoheterotrophs
Phototrophs are organisms that use light as their source of energy to produce ATP and carry out various cellular processes. Not all phototrophs are photosynthetic but they all constitute a food source for heterotrophic organisms. All phototrophs either use electron transport chain or direct proton pumping to establish an electro-chemical gradient utilized by ATP synthase to provide molecular energy for the cell. Phototrophs can be of two types based on their metabolism.
Photoautotrophs
An autotroph is an organism able to make its own food. Photoautotrophs are organisms that carry out photosynthesis. Using energy from sunlight, carbon dioxide and water are converted into organic materials to be used in cellular functions such as biosynthesis and respiration. In an ecological context, they provide nutrition for all other forms of life (besides other autotrophs such as chemotrophs ). In terrestrial environments plants are the predominant variety, while aquatic environments include a range of phototrophic organisms such as algae, protists, and bacteria. In photosynthetic bacteria and cyanobacteria that build up carbon dioxide and water into organic cell materials using energy from sunlight, starch is produced as final product. This process is an essential storage form of carbon, which can be used when light conditions are too poor to satisfy the immediate needs of the organism.
Photoheterotrophs
A heterotroph is an organism that depends on organic matter already produced by other organisms for its nourishment. Photoheterotrophs obtain their energy from sunlight and carbon from organic material and not carbon dioxide. Most of the well-recognized phototrophs are autotrophs, also known as photoautotrophs, and can fix carbon. They can be contrasted with chemotrophs that obtain their energy by the oxidation of electron donors in their environments. Photoheterotrophs produce ATP through photophosphorylation but use environmentally obtained organic compounds to build structures and other bio-molecules. Photoautotrophic organisms are sometimes referred to as holophytic.
Key Points
• Phototrophs are organisms that carry out photon capture to acquire energy.
• Photoautotrophs convert inorganic materials into organic materials for use in cellular functions such as biosynthesis and respiration and provide nutrition for many other forms of life.
• Photoheterotrophs depend on light for their source of energy and mostly organic compounds from the environment for their source of carbon.
Key Terms
• ATP synthase: an important enzyme that catalyzes the conversion of adenosine diphosphate into adenosine triphosphate.
• photosynthesis: The process by which plants and other photoautotrophs generate carbohydrates and oxygen from carbon dioxide, water, and light energy in chloroplasts.
5.1B: Chemoautotrophs and Chemohetrotrophs
Learning Objectives
• Compare chemoautotrophs and chemoheterotrophs
Chemotrophs are a class of organisms that obtain their energy through the oxidation of inorganic molecules, such as iron and magnesium. The most common type of chemotrophic organisms are prokaryotic and include both bacteria and fungi. All of these organisms require carbon to survive and reproduce. The ability of chemotrophs to produce their own organic or carbon-containing molecules differentiates these organisms into two different classifications–chemoautotrophs and chemoheterotrophs.
Chemoautotrophs
Chemoautotrophs are able to synthesize their own organic molecules from the fixation of carbon dioxide. These organisms are able to produce their own source of food, or energy. The energy required for this process comes from the oxidation of inorganic molecules such as iron, sulfur or magnesium. Chemoautotrophs are able to thrive in very harsh environments, such as deep sea vents, due to their lack of dependence on outside sources of carbon other than carbon dioxide. Chemoautotrophs include nitrogen fixing bacteria located in the soil, iron oxidizing bacteria located in the lava beds, and sulfur oxidizing bacteria located in deep sea thermal vents.
Chemoheterotrophs
Chemoheterotrophs, unlike chemoautotrophs, are unable to synthesize their own organic molecules. Instead, these organisms must ingest preformed carbon molecules, such as carbohydrates and lipids, synthesized by other organisms. They do, however, still obtain energy from the oxidation of inorganic molecules like the chemoautotrophs. Chemoheterotrophs are only able to thrive in environments that are capable of sustaining other forms of life due to their dependence on these organisms for carbon sources. Chemoheterotrophs are the most abundant type of chemotrophic organisms and include most bacteria, fungi and protozoa.
Key Points
• Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environment.
• Chemoautotrophs use inorganic energy sources to synthesize organic compounds from carbon dioxide.
• Chemoheterotrophs are unable to utilize carbon dioxide to form their own organic compounds. Their carbon source is rather derived from sulfur, carbohydrates, lipids, and proteins.
Key Terms
• inorganic molecule: lacks carbon and hydrogen atoms.
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Learning Objectives
• Explain how catabolic pathways are controlled
Enzymes, proteins, electron carriers, and pumps that play roles in glycolysis, the citric acid cycle, and the electron transport chain tend to catalyze non-reversible reactions. In other words, if the initial reaction takes place, the pathway is committed to proceeding with the remaining reactions. Whether a particular enzyme activity is released depends upon the energy needs of the cell (as reflected by the levels of ATP, ADP, and AMP).
Glycolysis
The control of glycolysis begins with the first enzyme in the pathway, hexokinase. This enzyme catalyzes the phosphorylation of glucose, which helps to prepare the compound for cleavage in a later step. The presence of the negatively-charged phosphate in the molecule also prevents the sugar from leaving the cell. When hexokinase is inhibited, glucose diffuses out of the cell and does not become a substrate for the respiration pathways in that tissue. The product of the hexokinase reaction is glucose-6-phosphate, which accumulates when a later enzyme, phosphofructokinase, is inhibited.
Phosphofructokinase is the main enzyme controlled in glycolysis. High levels of ATP, citrate, or a lower, more acidic pH decrease the enzyme’s activity. An increase in citrate concentration can occur because of a blockage in the citric acid cycle. Fermentation, with its production of organic acids like lactic acid, frequently accounts for the increased acidity in a cell; however, the products of fermentation do not typically accumulate in cells.
The last step in glycolysis is catalyzed by pyruvate kinase. The pyruvate produced can proceed to be catabolized or converted into the amino acid alanine. If no more energy is needed and alanine is in adequate supply, the enzyme is inhibited. The enzyme’s activity is increased when fructose-1,6-bisphosphate levels increase. (Recall that fructose-1,6-bisphosphate is an intermediate in the first half of glycolysis. ) The regulation of pyruvate kinase involves phosphorylation, resulting in a less-active enzyme. Dephosphorylation by a phosphatase reactivates it. Pyruvate kinase is also regulated by ATP (a negative allosteric effect).
If more energy is needed, more pyruvate will be converted into acetyl CoA through the action of pyruvate dehydrogenase. If either acetyl groups or NADH accumulate, there is less need for the reaction and the rate decreases. Pyruvate dehydrogenase is also regulated by phosphorylation: a kinase phosphorylates it to form an inactive enzyme, and a phosphatase reactivates it. The kinase and the phosphatase are also regulated.
Citric Acid Cycle
The citric acid cycle is controlled through the enzymes that catalyze the reactions that make the first two molecules of NADH. These enzymes are isocitrate dehydrogenase and α-ketoglutarate dehydrogenase. When adequate ATP and NADH levels are available, the rates of these reactions decrease. When more ATP is needed, as reflected in rising ADP levels, the rate increases. α-Ketoglutarate dehydrogenase will also be affected by the levels of succinyl CoA, a subsequent intermediate in the cycle, causing a decrease in activity. A decrease in the rate of operation of the pathway at this point is not necessarily negative as the increased levels of the α-ketoglutarate not used by the citric acid cycle can be used by the cell for amino acid (glutamate) synthesis.
Electron Transport Chain
Specific enzymes of the electron transport chain are unaffected by feedback inhibition, but the rate of electron transport through the pathway is affected by the levels of ADP and ATP. Greater ATP consumption by a cell is indicated by a buildup of ADP. As ATP usage decreases, the concentration of ADP decreases: ATP begins to build up in the cell. This change in the relative concentration of ADP to ATP triggers the cell to slow down the electron transport chain.
Key Points
• Glycolysis, the citric acid cycle, and the electron transport chain are catabolic pathways that bring forth non-reversible reactions.
• Glycolysis control begins with hexokinase, which catalyzes the phosphorylation of glucose; its product is glucose-6- phosphate, which accumulates when phosphofructokinase is inhibited.
• The citric acid cycle is controlled through the enzymes that break down the reactions that make the first two molecules of NADH.
• The rate of electron transport through the electron transport chain is affected by the levels of ADP and ATP, whereas specific enzymes of the electron transport chain are unaffected by feedback inhibition.
Key Terms
• phosphofructokinase: any of a group of kinase enzymes that convert fructose phosphates to biphosphate
• glycolysis: the cellular metabolic pathway of the simple sugar glucose to yield pyruvic acid and ATP as an energy source
• kinase: any of a group of enzymes that transfers phosphate groups from high-energy donor molecules, such as ATP, to specific target molecules (substrates); the process is termed phosphorylation
5.2B: Transforming Chemical Energy
Learning Objectives
• Discuss the importance of cellular respiration
Introduction: Cellular Respiration
An electrical energy plant converts energy from one form to another form that can be more easily used. For example, geothermal energy plants start with underground thermal energy (heat) and transform it into electrical energy that will be transported to homes and factories.
Like a generating plant, living organisms must take in energy from their environment and convert it into to a form their cells can use. Organisms ingest large molecules, like carbohydrates, proteins, and fats, and convert them into smaller molecules like carbon dioxide and water. This process is called cellular respiration, a form of catabolism, and makes energy available for the cell to use. The energy released by cellular respiration is temporarily captured by the formation of adenosine triphosphate (ATP) within the cell. ATP is the principle form of stored energy used for cellular functions and is frequently referred to as the energy currency of the cell.
The nutrients broken down through cellular respiration lose electrons throughout the process and are said to be oxidized. When oxygen is used to help drive the oxidation of nutrients the process is called aerobic respiration. Aerobic respiration is common among the eukaryotes, including humans, and takes place mostly within the mitochondria. Respiration occurs within the cytoplasm of prokaryotes. Several prokaryotes and a few eukaryotes use an inorganic molecule other than oxygen to drive the oxidation of their nutrients in a process called anaerobic respiration. Electron acceptors for anaerobic respiration include nitrate, sulfate, carbon dioxide, and several metal ions.
The energy released during cellular respiration is then used in other biological processes. These processes build larger molecules that are essential to an organism’s survival, such as amino acids, DNA, and proteins. Because they synthesize new molecules, these processes are examples of anabolism.
Key Points
• Organisms ingest organic molecules like the carbohydrate glucose to obtain the energy needed for cellular functions.
• The energy in glucose can be extracted in a series of chemical reactions known as cellular respiration.
• Cellular respiration produces energy in the form of ATP, which is the universal energy currency for cells.
Key Terms
• aerobic respiration: the process of converting the biochemical energy in nutrients to ATP in the presence of oxygen
• adenosine triphosphate: a multifunctional nucleoside triphosphate used in cells as a coenzyme, often called the “molecular unit of energy currency” in intracellular energy transfer
• cellular respiration: the set of the metabolic reactions and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP)
• catabolism: the breakdown of large molecules into smaller ones usually accompanied by the release of energy | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.02%3A_Energy_Production/5.2A%3A_Control_of_Catabolic_Pathways.txt |
Learning Objectives
• Identify the types of sugars involved in glucose metabolism
You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than glucose for food. How does a turkey sandwich end up as ATP in your cells? This happens because all of the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways.
Metabolic pathways should be thought of as porous; that is, substances enter from other pathways, and intermediates leave for other pathways. These pathways are not closed systems. Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways. Like sugars and amino acids, the catabolic pathways of lipids are also connected to the glucose catabolism pathways.
Glycogen, a polymer of glucose, is an energy-storage molecule in animals. When there is adequate ATP present, excess glucose is shunted into glycogen for storage. Glycogen is made and stored in both the liver and muscles. The glycogen is hydrolyzed into the glucose monomer, glucose-1-phosphate (G-1-P), if blood sugar levels drop. The presence of glycogen as a source of glucose allows ATP to be produced for a longer period of time during exercise. Glycogen is broken down into G-1-P and converted into glucose-6-phosphate (G-6-P) in both muscle and liver cells; this product enters the glycolytic pathway.
Galactose is the sugar in milk. Infants have an enzyme in the small intestine that metabolizes lactose to galactose and glucose. In areas where milk products are regularly consumed, adults have also evolved this enzyme. Galactose is converted in the liver to G-6-P and can thus enter the glycolytic pathway.
Fructose is one of the three dietary monosaccharides (along with glucose and galactose) which are absorbed directly into the bloodstream during digestion. Fructose is absorbed from the small intestine and then passes to the liver to be metabolized, primarily to glycogen. The catabolism of both fructose and galactose produces the same number of ATP molecules as glucose.
Sucrose is a disaccharide with a molecule of glucose and a molecule of fructose bonded together with a glycosidic linkage. The catabolism of sucrose breaks it down to monomers of glucose and fructose. The glucose can directly enter the glycolytic pathway while fructose must first be converted to glycogen, which can be broken down to G-1-P and enter the glycolytic pathway as described above.
Key Points
• When blood sugar levels drop, glycogen is broken down into glucose -1-phosphate, which is then converted to glucose-6-phosphate and enters glycolysis for ATP production.
• In the liver, galactose is converted to glucose-6-phosphate in order to enter the glycolytic pathway.
• Fructose is converted into glycogen in the liver and then follows the same pathway as glycogen to enter glycolysis.
• Sucrose is broken down into glucose and fructose; glucose enters the pathway directly while fructose is converted to glycogen.
Key Terms
• disaccharide: A sugar, such as sucrose, maltose, or lactose, consisting of two monosaccharides combined together.
• glycogen: A polysaccharide that is the main form of carbohydrate storage in animals; converted to glucose as needed.
• monosaccharide: A simple sugar such as glucose, fructose, or deoxyribose that has a single ring.
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Learning Objectives
• Summarize various types of catabolism included in metabolism (catabolism of carbohydrates, proteins and fats)
Catabolism is the set of metabolic processes that break down large molecules. These include breaking down and oxidizing food molecules. The purpose of catabolic reactions is to provide the energy and components needed by anabolic reactions. The exact nature of these catabolic reactions differ from organism to organism; organisms can be classified based on their sources of energy and carbon, their primary nutritional groups. Organic molecules are used as a source of energy by organotrophs, while lithotrophs use inorganic substrates and phototrophs capture sunlight as chemical energy.
All these different forms of metabolism depend on redox reactions that involve the transfer of electrons from reduced donor molecules such as organic molecules, water, ammonia, hydrogen sulfide or ferrous ions to acceptor molecules such as oxygen, nitrate or sulfate. In animals these reactions involve complex organic molecules being broken down to simpler molecules, such as carbon dioxide and water. In photosynthetic organisms such as plants and cyanobacteria, these electron-transfer reactions do not release energy, but are used as a way of storing energy absorbed from sunlight.
The most common set of catabolic reactions in animals can be separated into three main stages. In the first, large organic molecules such as proteins, polysaccharides, or lipids are digested into their smaller components outside cells. Next, these smaller molecules are taken up by cells and converted to yet smaller molecules, usually the acetyl coenzyme A (acetyl-CoA), which releases some energy. Finally, the acetyl group on the CoA is oxidized to water and carbon dioxide in the citric acid cycle and electron transport chain, releasing the energy that is stored by reducing the coenzyme nicotinamide adenine dinucleotide (NAD+) into NADH.
Macromolecules such as starch, cellulose or proteins cannot be rapidly taken up by cells and must be broken into their smaller units before they can be used in cell metabolism. Several common classes of enzymes digest these polymers. These digestive enzymes include proteases that digest proteins into amino acids, as well as glycoside hydrolases that digest polysaccharides into monosaccharides. Microbes secrete digestive enzymes into their surroundings, while animals only secrete these enzymes from specialized cells in their guts. The amino acids or sugars released by these extracellular enzymes are then pumped into cells by specific active transport proteins. A simplified schematic of the catabolism of carbohydrates, proteins and fats is shown in.
Carbohydrate Catabolism
Carbohydrate catabolism is the breakdown of carbohydrates into smaller units. Carbohydrates are usually taken into cells once they have been digested into monosaccharides. Once inside, the major route of breakdown is glycolysis, where sugars such as glucose and fructose are converted into pyruvate and some ATP is generated. Pyruvate is an intermediate in several metabolic pathways, but the majority is converted to acetyl-CoA and fed into the citric acid cycle. Although some more ATP is generated in the citric acid cycle, the most important product is NADH, which is made from NAD+ as the acetyl-CoA is oxidized. This oxidation releases carbon dioxide as a waste product. In anaerobic conditions, glycolysis produces lactate, through the enzyme lactate dehydrogenase re-oxidizing NADH to NAD+ for re-use in glycolysis.
The Pentose Phosphate Pathway
An alternative route for glucose breakdown is the pentose phosphate pathway, which reduces the coenzyme NADPH and produces pentose sugars such as ribose, the sugar component of nucleic acids. Fats are catabolised by hydrolysis to free fatty acids and glycerol. The glycerol initiates glycolysis and the fatty acids are broken down by beta oxidation to release acetyl-CoA, which then is fed into the citric acid cycle. Fatty acids release more energy upon oxidation than carbohydrates because carbohydrates contain more oxygen in their structures.
Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy. The oxidation pathway starts with the removal of the amino group by a transaminase. The amino group is fed into the urea cycle, leaving a deaminated carbon skeleton in the form of a keto acid. Several of these keto acids are intermediates in the citric acid cycle, for example the deamination of glutamate forms α-ketoglutarate. The glucogenic amino acids can also be converted into glucose, through gluconeogenesis.
Key Points
• The purpose of the catabolic reactions is to provide the energy and components needed by anabolic reactions.
• Microbes simply secrete digestive enzymes into their surroundings, while animals only secrete these enzymes from specialized cells in their guts.
• Fats are catabolised by hydrolysis to free fatty acids and glycerol.
• Amino acids are either used to synthesize proteins and other biomolecules, or oxidized to urea and carbon dioxide as a source of energy.
• Carbohydrates are usually taken into cells once they have been digested into monosaccharides and then processed inside the cell via glycolysis.
Key Terms
• polymer: A long or larger molecule consisting of a chain or network of many repeating units, formed by chemically bonding together many identical or similar small molecules called monomers. A polymer is formed by polymerization, the joining of many monomer molecules.
• acetyl CoA: Acetyl coenzyme A or acetyl-CoA is an important molecule in metabolism, used in many biochemical reactions. 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.
• catabolism: Destructive metabolism, usually includes the release of energy and breakdown of materials. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.03%3A_Catabolism/5.3A%3A_Types_of_Catabolism.txt |
Learning Objectives
• Outline the metabolic processes that involve pyruvate
Pyruvic acid (CH3COCOOH; is an organic acid, a ketone, and the simplest of the alpha-keto acids. The carboxylate (COO) anion of pyruvic acid. The Brønsted–Lowry conjugate base, CH3COCOO, is known as pyruvate, and is a key intersection in several metabolic pathways.
Pyruvic acid can be made from glucose through glycolysis, converted back to carbohydrates (such as glucose) via gluconeogenesis, or to fatty acids through acetyl-CoA. It can also be used to construct the amino acid alanine, and it can be converted into ethanol.
Pyruvic acid supplies energy to living cells through the citric acid cycle (also known as the Krebs cycle) when oxygen is present (aerobic respiration); when oxygen is lacking, it ferments to produce lactic acid. Pyruvate is an important chemical compound in biochemistry. It is the output of the anaerobic metabolism of glucose known as glycolysis. One molecule of glucose breaks down into two molecules of pyruvate, which are then used to provide further energy in one of two ways. Pyruvate is converted into acetyl- coenzyme A, which is the main input for a series of reactions known as the Krebs cycle. Pyruvate is also converted to oxaloacetate by an anaplerotic reaction, which replenishes Krebs cycle intermediates; also, oxaloacetate is used for gluconeogenesis. These reactions are named after Hans Adolf Krebs, the biochemist awarded the 1953 Nobel Prize for physiology, jointly with Fritz Lipmann, for research into metabolic processes. The cycle is also known as the citric acid cycle or tri-carboxylic acid cycle, because citric acid is one of the intermediate compounds formed during the reactions.
If insufficient oxygen is available, the acid is broken down anaerobically, creating lactate in animals and ethanol in plants and microorganisms. Pyruvate from glycolysis is converted by fermentation to lactate using the enzyme lactate dehydrogenase and the coenzyme NADH in lactate fermentation. Alternatively it is converted to acetaldehyde and then to ethanol in alcoholic fermentation.
Pyruvate is a key intersection in the network of metabolic pathways. Pyruvate can be converted into carbohydrates via gluconeogenesis, to fatty acids or energy through acetyl-CoA, to the amino acid alanine, and to ethanol. Therefore, it unites several key metabolic processes.
Key Points
• Pyruvic acid can be made from glucose through glycolysis, converted back to carbohydrates (such as glucose) via gluconeogenesis, or to fatty acids through acetyl-CoA.
• Pyruvic acid supplies energy to living cells through the citric acid cycle (also known as the Krebs cycle ) when oxygen is present (aerobic respiration); it ferments to produce lactic acid when oxygen is lacking ( fermentation ).
• Pyruvate is the output of the anaerobic metabolism of glucose known as glycolysis.
• Pyruvate can be converted into carbohydrates via gluconeogenesis, to fatty acids or energy through acetyl-CoA, to the amino acid alanine, and to ethanol.
Key Terms
• pyruvic acid: A colourless liquid; an important intermediate in the metabolism of proteins and carbohydrates, and in fermentation.
• conjugate base: Any compound, of general formula Xn+, which can be transformed into a conjugate acid HX(n+1)+ by the gain of a proton.
• Krebs cycle: A series of enzymatic reactions that occurs in all aerobic organisms; it involves the oxidative metabolism of acetyl units and serves as the main source of cellular energy.
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Learning Objectives
• Explain the importance of glycolysis to cells
Nearly all of the energy used by living cells comes to them from the energy in the bonds of the sugar glucose. Glucose enters heterotrophic cells in two ways. One method is through secondary active transport in which the transport takes place against the glucose concentration gradient. The other mechanism uses a group of integral proteins called GLUT proteins, also known as glucose transporter proteins. These transporters assist in the facilitated diffusion of glucose. Glycolysis is the first pathway used in the breakdown of glucose to extract energy. It takes place in the cytoplasm of both prokaryotic and eukaryotic cells. It was probably one of the earliest metabolic pathways to evolve since it is used by nearly all of the organisms on earth. The process does not use oxygen and is, therefore, anaerobic.
Glycolysis is the first of the main metabolic pathways of cellular respiration to produce energy in the form of ATP. Through two distinct phases, the six-carbon ring of glucose is cleaved into two three-carbon sugars of pyruvate through a series of enzymatic reactions. The first phase of glycolysis requires energy, while the second phase completes the conversion to pyruvate and produces ATP and NADH for the cell to use for energy. Overall, the process of glycolysis produces a net gain of two pyruvate molecules, two ATP molecules, and two NADH molecules for the cell to use for energy. Following the conversion of glucose to pyruvate, the glycolytic pathway is linked to the Krebs Cycle, where further ATP will be produced for the cell’s energy needs.
Key Points
• Glycolysis is present in nearly all living organisms.
• Glucose is the source of almost all energy used by cells.
• Overall, glycolysis produces two pyruvate molecules, a net gain of two ATP molecules, and two NADH molecules.
Key Terms
• glycolysis: the cellular metabolic pathway of the simple sugar glucose to yield pyruvic acid and ATP as an energy source
• heterotroph: an organism that requires an external supply of energy in the form of food, as it cannot synthesize its own
5.4B: Electron Donors and Acceptors
Learning Objectives
• Recognize the various types of electron donors and acceptors
In prokaryotes (bacteria and archaea) there are several different electron donors and several different electron acceptors. Note that electrons can enter the chain at three levels: at the level of a dehydrogenase, at the level of the quinone pool, or at the level of a mobile cytochrome electron carrier. These levels correspond to successively more positive redox potentials, or to successively decreased potential differences relative to the terminal electron acceptor. In other words, they correspond to successively smaller Gibbs free energy changes for the overall redox reaction Donor → Acceptor.
Individual bacteria use multiple electron transport chains, often simultaneously. Bacteria can use a number of different electron donors, a number of different dehydrogenases, a number of different oxidases and reductases, and a number of different electron acceptors. For example, E. coli (when growing aerobically using glucose as an energy source) uses two different NADH dehydrogenases and two different quinol oxidases, for a total of four different electron transport chains operating simultaneously.
A common feature of all electron transport chains is the presence of a proton pump to create a transmembrane proton gradient. Bacterial electron transport chains may contain as many as three proton pumps, like mitochondria, or they may contain only one or two. They always contain at least one proton pump.
In the present day biosphere, the most common electron donors are organic molecules. Organisms that use organic molecules as an energy source are called organotrophs. Organotrophs (animals, fungi, protists) and phototrophs (plants and algae) constitute the vast majority of all familiar life forms.
Some prokaryotes can use inorganic matter as an energy source. Such organisms are called lithotrophs (“rock-eaters”). Inorganic electron donors include hydrogen, carbon monoxide, ammonia, nitrite, sulfur, sulfide, and ferrous iron. Lithotrophs have been found growing in rock formations thousands of meters below the surface of Earth. Because of their volume of distribution, lithotrophs may actually out number organotrophs and phototrophs in our biosphere.
The use of inorganic electron donors as an energy source is of particular interest in the study of evolution. This type of metabolism must logically have preceded the use of organic molecules as an energy source.
Just as there are a number of different electron donors (organic matter in organotrophs, inorganic matter in lithotrophs), there are a number of different electron acceptors, both organic and inorganic. If oxygen is available, it is invariably used as the terminal electron acceptor, because it generates the greatest Gibbs free energy change and produces the most energy.
In anaerobic environments, different electron acceptors are used, including nitrate, nitrite, ferric iron, sulfate, carbon dioxide, and small organic molecules such as fumarate.
Since electron transport chains are redox processes, they can be described as the sum of two redox pairs. For example, the mitochondrial electron transport chain can be described as the sum of the NAD+/NADH redox pair and the O2/H2O redox pair. NADH is the electron donor and O2 is the electron acceptor.
Not every donor-acceptor combination is thermodynamically possible. The redox potential of the acceptor must be more positive than the redox potential of the donor. Furthermore, actual environmental conditions may be far different from standard conditions (1 molar concentrations, 1 atm partial pressures, pH = 7), which apply to standard redox potentials. For example, hydrogen-evolving bacteria grow at an ambient partial pressure of hydrogen gas of 10-4 atm. The associated redox reaction, which is thermodynamically favorable in nature, is thermodynamically impossible under “standard” conditions.
Bacterial electron transport pathways are, in general, inducible. Depending on their environment, bacteria can synthesize different transmembrane complexes and produce different electron transport chains in their cell membranes. Bacteria select their electron transport chains from a DNA library containing multiple possible dehydrogenases, terminal oxidases and terminal reductases. The situation is often summarized by saying that electron transport chains in bacteria are branched, modular, and inducible.
Key Points
• Bacterial electron transport chains may contain as many as three proton pumps.
• The most common electron donors are organic molecules.
• There are a number of different electron acceptors, both organic and inorganic. If oxygen is available, it is invariably used as the terminal electron acceptor.
Key Terms
• organotroph: An organism that obtains its energy from organic compounds.
• lithotroph: An organism that obtains its energy from inorganic compounds (such as ammonia) via electron transfer. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.04%3A_Glycolysis/5.4A%3A_Importance_of_Glycolysis.txt |
The amount of energy (as ATP) gained from glucose catabolism varies across species and depends on other related cellular processes.
Learning Objectives
• Describe the origins of variability in the amount of ATP that is produced per molecule of glucose consumed
Key Points
• While glucose catabolism always produces energy, the amount of energy (in terms of ATP equivalents) produced can vary, especially across different species.
• The number of hydrogen ions the electron transport chain complexes can pump through the membrane varies between species.
• NAD+ provides more ATP than FAD+ in the electron transport chain and can lead to variance in ATP production.
• The use of intermediates from glucose catabolism in other biosynthetic pathways, such as amino acid synthesis, can lower the yield of ATP.
Key Terms
• catabolism: Destructive metabolism, usually including the release of energy and breakdown of materials.
ATP Yield
In a eukaryotic cell, the process of cellular respiration can metabolize one molecule of glucose into 30 to 32 ATP. The process of glycolysis only produces two ATP, while all the rest are produced during the electron transport chain. Clearly, the electron transport chain is vastly more efficient, but it can only be carried out in the presence of oxygen.
The number of ATP molecules generated via the catabolism of glucose can vary substantially. For example, the number of hydrogen ions the electron transport chain complexes can pump through the membrane varies between species. Another source of variance occurs during the shuttle of electrons across the membranes of the mitochondria. The NADH generated from glycolysis cannot easily enter mitochondria. Thus, electrons are picked up on the inside of mitochondria by either NAD+ or FAD+. These FAD+ molecules can transport fewer ions; consequently, fewer ATP molecules are generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver, and FAD+ acts in the brain.
Another factor that affects the yield of ATP molecules generated from glucose is the fact that intermediate compounds in these pathways are used for other purposes. Glucose catabolism connects with the pathways that build or break down all other biochemical compounds in cells, but the result is not always ideal. For example, sugars other than glucose are fed into the glycolytic pathway for energy extraction. Moreover, the five-carbon sugars that form nucleic acids are made from intermediates in glycolysis. Certain nonessential amino acids can be made from intermediates of both glycolysis and the citric acid cycle. Lipids, such as cholesterol and triglycerides, are also made from intermediates in these pathways, and both amino acids and triglycerides are broken down for energy through these pathways. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose.
5.4D: Respiration and Proton Motive Force
Respiration is one of the key ways a cell gains useful energy to fuel cellular activity.
Learning Objectives
• Describe the role of the proton motive force in respiration
Key Points
• The reactions involved in respiration are catabolic reactions, which break large molecules into smaller ones, releasing energy in the process as they break high-energy bonds.
• Aerobic respiration requires oxygen in order to generate energy ( ATP ).
• Aerobic metabolism is up to 15 times more efficient than anaerobic metabolism (which yields two molecules ATP per one molecule glucose).
• With the help of the solar-driven enzyme bacteriorhodopsin, some bacteria make proton gradients by pumping in protons from the environment.
Key Terms
• exothermic: releasing energy in the form of heat
• redox: a reversible process in which one reaction is an oxidation and the reverse is a reduction
Cellular Respiration
Cellular respiration is a set of metabolic reactions and processes that take place within the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP). The reactions involved in this respiration are considered to be catabolic reactions that release energy as larger molecules are broken down into smaller ones and high-energy bonds are broken. Respiration is one of the key ways a cell gains useful energy to fuel cellular activity.
Chemically, cellular respiration is considered an exothermic redox reaction. The overall reaction is broken into many smaller ones when it occurs in the body. Most of these smaller reactions are redox reactions themselves. Although technically, cellular respiration is a combustion reaction, it does not resemble one when it occurs in a living cell. This is because it occurs in many separate steps. While the overall reaction is a combustion reaction, no single reaction that comprises it is a combustion reaction.
Aerobic and Anaerobic Reactions
Aerobic reactions require oxygen for ATP generation. Although carbohydrates, fats and proteins can be used as reactants, the preferred method is the process of glycolysis. During glycolysis, pyruvate is formed from glucose metabolism. During aerobic conditions, the pyruvate enters the mitochondrion to be fully oxidized by the Krebs cycle. The products of the Krebs cycle include energy in the form of ATP (via substrate level phosphorylation ), NADH, and FADH2.
The simplified reaction is as follows:
C6H12O6 (s) + 6 O2 (g) → 6 CO2 (g) + 6 H2O (l) + heat
ΔG = -2880 kJ per mole of C6H12O6
A negative ΔG indicates that the reaction can occur spontaneously.
Aerobic metabolism is up to 15 times more efficient than anaerobic metabolism, which yields two molecules ATP per one molecule glucose. Both types of metabolism share the initial pathway of glycolysis, but aerobic metabolism continues with the Krebs cycle and oxidative phosphorylation. In eukaryotic cells, the post-glycolytic reactions take place in the mitochondria, while in prokaryotic cells, these reactions take place in the cytoplasm.
Glycolysis
Glycolysis takes place in the cytosol, does not require oxygen, and can therefore function under anaerobic conditions. The process converts one molecule of glucose into two molecules of pyruvate, generating energy in the form of two net molecules of ATP. Four molecules of ATP per glucose are actually produced, but two of these are consumed as part of the preparatory phase. The initial phosphorylation of glucose is required to destabilize the molecule for cleavage into two pyruvate. During the pay-off phase of glycolysis, four phosphate groups are transferred to ADP by substrate-level phosphorylation to make four ATP, and two NADH are produced when the pyruvate are oxidized. The overall reaction can be expressed this way:
Glucose + 2 NAD+ + 2 Pi + 2 ADP → 2 pyruvate + 2 NADH + 2 ATP + 2 H+ + 2 H2O + heat
Starting with glucose, one ATP is used to donate a phosphate to glucose to produce glucose 6-phosphate. With the help of glycogen phosphorylase, glycogen can change into glucose 6-phosphate as well. During energy metabolism, glucose 6-phosphate turns into fructose 6-phosphate. With the help of phosphofructokinase, an additional ATP can be used to turn phosphorylate fructose 6-phosphate into fructose 1, 6-diphosphate. Fructose 1, 6-diphosphate then splits into two phosphorylated molecules with three carbon chains that later degrades into pyruvate.
Making Proton Gradients
Some archaea, the most notable ones being halobacteria, make proton gradients by pumping in protons from the environment. They are able to do this with the help of the solar-driven enzyme bacteriorhodopsin, which is used to drive the molecular motor enzyme ATP synthase to make the necessary conformational changes required to synthesize ATP. By running ATP synthase in reverse, proton gradients are also made by bacteria and are used to drive flagella. The F1FO ATP synthase is a reversible enzyme. Large enough quantities of ATP cause it to create a transmembrane proton gradient. This is used by fermenting bacteria, which lack an electron transport chain, and which hydrolyze ATP to make a proton gradient. Bacteria use these gradients for flagella and for the transportation of nutrients into the cell. In respiring bacteria under physiological conditions, ATP synthase, in general, runs in the opposite direction. This creates ATP while using the proton motive force created by the electron transport chain as a source of energy. The overall process of creating energy in this fashion is termed oxidative phosphorylation.
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A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein’s biological activity.
Learning Objectives
• Recognize the various types of cofactors involved in biochemical reactions
Key Points
• Cofactors are commonly enzymes, and cofactors can be considered “helper molecules ” that assist in biochemical transformations.
• Some enzymes or enzyme complexes require several cofactors.
• Each class of group-transfer reaction is carried out by a particular cofactor, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it.
Key Terms
• cofactor: A substance, especially a coenzyme or a metal, that must be present for an enzyme to function.
• enzymes: Enzymes are large biological molecules responsible for the thousands of chemical interconversions that sustain life. They are highly selective catalysts, greatly accelerating both the rate and specificity of metabolic reactions, from the digestion of food to the synthesis of DNA.
• reaction: A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. Classically, chemical reactions encompass changes that strictly involve the motion of electrons in the forming and breaking of chemical bonds between atoms, and can often be described by a chemical equation.
• apoenzyme: an inactive haloenzyme lacking a cofactor
A cofactor is a non- protein chemical compound that is bound to a protein and is required for the protein’s biological activity. These proteins are commonly enzymes. Cofactors can be considered “helper molecules” that assist in biochemical transformations.
Cofactors are either organic or inorganic. They can also be classified depending on how tightly they bind to an enzyme, with loosely-bound cofactors termed coenzymes and tightly-bound cofactors termed prosthetic groups. Some sources also limit the use of the term “cofactor” to inorganic substances. An inactive enzyme without the cofactor is called an apoenzyme, while the complete enzyme with cofactor is the holoenzyme.
Some enzymes or enzyme complexes require several cofactors. For example, the multienzyme complex pyruvate dehydrogenase at the junction of glycolysis and the citric acid cycle requires five organic cofactors and one metal ion: loosely bound thiamine pyrophosphate (TPP), covalently bound lipoamide and flavin adenine dinucleotide (FAD), and the cosubstrates nicotinamide adenine dinucleotide (NAD+) and coenzyme A (CoA), and a metal ion (Mg2+).
Organic cofactors are often vitamins or are made from vitamins. Many contain the nucleotide adenosine monophosphate (AMP) as part of their structures, such as ATP, coenzyme A, FAD, and NAD+. This common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the AMP part of the molecule can be considered a kind of “handle” by which the enzyme can “grasp” the coenzyme to switch it between different catalytic centers.
Cofactors can be divided into two broad groups: organic cofactors, such as flavin or heme, and inorganic cofactors, such as the metal ions Mg2+, Cu+, Mn2+, or iron-sulfur clusters.
Vitamins can serve as precursors to many organic cofactors (e.g., vitamins B1, B2, B6, B12, niacin, folic acid) or as coenzymes themselves (e.g., vitamin C). However, vitamins do have other functions in the body. Many organic cofactors also contain a nucleotide, such as the electron carriers NAD and FAD, and coenzyme A, which carries acyl groups. Most of these cofactors are found in a huge variety of species, and some are universal to all forms of life. An exception to this wide distribution is a group of unique cofactors that evolved in methanogens, which are restricted to this group of archaea.
Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are the loosely-bound organic cofactors, often called coenzymes.
Each class of group-transfer reaction is carried out by a particular cofactor, which is the substrate for a set of enzymes that produce it and a set of enzymes that consume it. An example of this is the dehydrogenases that use nicotinamide adenine dinucleotide (NAD+) as a cofactor. Here, hundreds of separate types of enzymes remove electrons from their substrates and reduce NAD+ to NADH. This reduced cofactor is then a substrate for any of the reductases in the cell that require electrons to reduce their substrates.
Therefore, these cofactors are continuously recycled as part of metabolism. As an example, the total quantity of ATP in the human body is about 0.1 mole. This ATP is constantly being broken down into ADP, and then converted back into ATP. Therefore, at any given time, the total amount of ATP + ADP remains fairly constant. The energy used by human cells requires the hydrolysis of 100 to 150 moles of ATP daily, which is around 50 to 75 kg. In typical situations, humans use up their body weight of ATP over the course of the day. This means that each ATP molecule is recycled 1,000 to 1,500 times daily.
The term is used in other areas of biology to refer more broadly to non-protein (or even protein) molecules that either activate, inhibit, or are required for the protein to function. For example, ligands such as hormones that bind to and activate receptor proteins are termed cofactors or coactivators, whereas molecules that inhibit receptor proteins are termed corepressors. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.05%3A_Respiratory_ETS_and_ATP_Synthase/5.5A%3A_Cofactors_and_Energy_Transitions.txt |
In biochemistry, an oxidoreductase is an enzyme that catalyzes the transfer of electrons from one molecule to another.
Learning Objectives
• Recognize the function of oxidoreductase protein complexes
Key Points
• The reductant is the electron donor.
• The oxidant is the electron acceptor.
• This group of enzymes usually utilizes NADP or NAD+ as cofactors.
Key Terms
• oxidoreductase: Any enzyme that catalyzes an oxidation-reduction (redox) reaction.
• enzyme: A globular protein that catalyses a biological chemical reaction.
• catalyzes: Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself.
In biochemistry, an oxidoreductase is an enzyme that catalyzes the transfer of electrons from one molecule, the reductant, also called the electron donor, to another the oxidant, also called the electron acceptor. This group of enzymes usually utilizes NADP or NAD+ as cofactors.
For example, an enzyme that catalyzed this reaction would be an oxidoreductase: A– + B → A + B–. In this example, A is the reductant (electron donor) and B is the oxidant (electron acceptor).
In biochemical reactions, the redox reactions are sometimes more difficult to see, such as this reaction from glycolysis: Pi + glyceraldehyde-3-phosphate + NAD+ → NADH + H+ + 1,3-bisphosphoglycerate. In this reaction, NAD+ is the oxidant (electron acceptor) and glyceraldehyde-3-phosphate is the reductant (electron donor).
Oxidoreductases are classified as EC 1 in the EC number classification of enzymes. Oxidoreductases can be further classified into 22 subclasses:
• EC 1.1 includes oxidoreductases that act on the CH-OH group of donors (alcohol oxidoreductases);
• EC 1.2 includes oxidoreductases that act on the aldehyde or oxo group of donors;
• EC 1.3 includes oxidoreductases that act on the CH-CH group of donors (CH-CH oxidoreductases);
• EC 1.4 includes oxidoreductases that act on the CH-NH2 group of donors (Amino acid oxidoreductases, Monoamine oxidase);
• EC 1.5 includes oxidoreductases that act on CH-NH group of donors;
• EC 1.6 includes oxidoreductases that act on NADH or NADPH;
• EC 1.7 includes oxidoreductases that act on other nitrogenous compounds as donors;
• EC 1.8 includes oxidoreductases that act on a sulfur group of donors;
• EC 1.9 includes oxidoreductases that act on a heme group of donors;
• EC 1.10 includes oxidoreductases that act on diphenols and related substances as donors;
• EC 1.11 includes oxidoreductases that act on peroxide as an acceptor (peroxidases);
• EC 1.12 includes oxidoreductases that act on hydrogen as donors;
• EC 1.13 includes oxidoreductases that act on single donors with incorporation of molecular oxygen (oxygenases);
• EC 1.14 includes oxidoreductases that act on paired donors with incorporation of molecular oxygen;
• EC 1.15 includes oxidoreductases that act on superoxide radicals as acceptors;
• EC 1.16 includes oxidoreductases that oxidize metal ions; EC 1.17 includes oxidoreductases that act on CH or CH2 groups;
• EC 1.18 includes oxidoreductases that act on iron-sulfur proteins as donors;
• EC 1.19 includes oxidoreductases that act on reduced flavodoxin as a donor;
• EC 1.20 includes oxidoreductases that act on phosphorus or arsenic in donors;
• EC 1.21 includes oxidoreductases that act on X-H and Y-H to form an X-Y bond; and EC 1.97 includes other oxidoreductases. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.05%3A_Respiratory_ETS_and_ATP_Synthase/5.5B%3A_Oxidoreductase_Protein_Complexes.txt |
ATP synthase is an important enzyme that provides energy for the cell to use through the synthesis of adenosine triphosphate.
Learning Objectives
• Discuss the structure and function of ATP synthase, including the F1 and FO components
Key Points
• Energy is often released in the form of protium or H+, moving down an electrochemical gradient.
• ATP synthase consists of 2 regions: the FO portion is within the membrane and the F1 portion of the ATP synthase is above the membrane, inside the matrix of the mitochondria.
• E. coli ATP synthase is the simplest known form of ATP synthase, with 8 different subunit types.
Key Terms
• synthase: Any enzyme that catalyzes the synthesis of a biological compound but, unlike synthetases, does not make use of ATP as a source of energy
• adenosine triphosphate: Adenosine-5′-triphosphate (ATP) is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the “molecular unit of currency” of intracellular energy transfer.
• enzyme: A globular protein that catalyses a biological chemical reaction.
ATP synthase is an important enzyme that provides energy for the cell to use through the synthesis of adenosine triphosphate (ATP). ATP is the most commonly used “energy currency” of cells from most organisms. It is formed from adenosine diphosphate (ADP) and inorganic phosphate (Pi), and needs energy.
The overall reaction sequence is: ATP synthase + ADP + Pi → ATP Synthase + ATP
Energy is often released in the form of protium or H+, moving down an electrochemical gradient, such as from the lumen into the stroma of chloroplasts or from the inter-membrane space into the matrix in mitochondria.
Located within the mitochondria, ATP synthase consists of 2 regions: the FO portion is within the membrane and the F1 portion of the ATP synthase is above the membrane, inside the matrix of the mitochondria.
The nomenclature of the enzyme suffers from a long history. The F1 fraction derives its name from the term “Fraction 1” and FO (written as a subscript letter “o”, not “zero”) derives its name from being the oligomycin binding fraction. Oligomycin, an antibiotic, is able to inhibit the FO unit of ATP synthase.
F1- ATP Synthase structure: The F1 particle is large and can be seen in the transmission electron microscope by negative staining. These are particles of 9 nm diameter that pepper the inner mitochondrial membrane. They were originally called elementary particles and were thought to contain the entire respiratory apparatus of the mitochondrion, but, through a long series of experiments, Ephraim Racker and his colleagues (who first isolated the F1 particle in 1961) were able to show that this particle is correlated with ATPase activity in uncoupled mitochondria and with the ATPase activity in submitochondrial particles created by exposing mitochondria to ultrasound. This ATPase activity was further associated with the creation of ATP by a long series of experiments in many laboratories.
The FO region of ATP synthase is a proton pore that is embedded in the mitochondrial membrane. It consists of three main subunits A, B, and C, and (in humans) six additional subunits, d, e, f, g, F6, and 8 (or A6L).
E. coli ATP synthase is the simplest known form of ATP synthase, with 8 different subunit types. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.05%3A_Respiratory_ETS_and_ATP_Synthase/5.5C%3A_F10_ATP_Synthase.txt |
Most bacteria rely on proton motive force as a source of energy for a variety of cellular processes.
Learning Objectives
• Describe the mechanisms of sodium pumps and its role as an alternative proton pump
Key Points
• The Na+/K+-ATPase helps maintain resting potential, avail transport and regulate cellular volume.
• The pump, while binding ATP, binds 3 intracellular Na+ ions. ATP is hydrolyzed, leading to phosphorylation of the pump at a highly conserved aspartate residue and subsequent release of ADP.
• Some extremophilic bacteria can use Na+ as a coupling ion in an Na+ cycle instead of, or in addition to, the H+ cycle.
• Na+-based membrane energetics provide an additional means of ATP synthesis, motility and solute uptake for pathogenic microbes.
• Because Na+ concentrations in most natural environments are almost 106-fold higher than H+ concentrations, sodium motive force levels are unlikely to change as rapidly as proton motive force levels, making sodium motive force a much more reliable source of energy.
Key Terms
• antiporter: A cell protein that acts within an antiport to transport different molecules or ions across the membrane in opposite directions
• resting potential: The nearly latent membrane potential of inactive cells.
• hydrolyzed: Hydrolysis usually means the cleavage of chemical bonds by the addition of water.
What Are Sodium Pumps?
Na+/K+-ATPase (Sodium-potassium adenosine triphosphatase, also known as Na+/K+ pump, sodium-potassium pump, or sodium pump) is an antiporter enzyme (EC 3.6.3.9) (an electrogenic transmembrane ATPase) located in the plasma membrane of all animal cells.
Active transport is responsible for cells containing relatively high concentrations of potassium ions but low concentrations of sodium ions. The mechanism responsible for this is the sodium-potassium pump, which moves these two ions in opposite directions across the plasma membrane. This was investigated by following the passage of radioactively labeled ions across the plasma membrane of certain cells. It was found that the concentrations of sodium and potassium ions on the two sides of the membrane are interdependent, suggesting that the same carrier transports both ions. It is now known that the carrier is an ATP-ase and that it pumps three sodium ions out of the cell for every two potassium ions pumped in.
Discovery and Significance
The sodium-potassium pump was discovered in the 1950s by Danish scientist Jens Christian Skou. It marked an important step in our understanding of how ions get into and out of cells, and has a particular significance for excitable cells like nervous cells, which depend on this pump for responding to stimuli and transmitting impulses.
The Na+/K+-ATPase helps maintain resting potential, avail transport and regulate cellular volume. It also functions as signal transducer/integrator to regulate MAPK pathway, ROS, as well as intracellular calcium. In most animal cells, the Na+/K+-ATPase is responsible for about 1/5 of the cell’s energy expenditure. For neurons, the Na+/K+-ATPase can be responsible for up to 2/3 of the cell’s energy expenditure.
Functions
Functions include resting potential, transport, controlling cell volume and acting as a signal transducer. The pump, while binding ATP, binds 3 intracellular Na+ ions. ATP is hydrolyzed, leading to phosphorylation of the pump at a highly conserved aspartate residue and subsequent release of ADP. A conformational change in the pump exposes the Na+ ions to the outside. The phosphorylated form of the pump has a low affinity for Na+ ions, so they are released.The pump binds 2 extracellular K+ ions. This causes the dephosphorylation of the pump, reverting it to its previous conformational state, transporting the K+ ions into the cell.The unphosphorylated form of the pump has a higher affinity for Na+ ions than K+ ions, so the two bound K+ ions are released. ATP binds, and the process starts again.
Proton Motive Force
Most bacteria rely on proton motive force as a source of energy for a variety of cellular processes. Usually, an H+ cycle includes generation of the transmembrane electrochemical gradient of H+ (proton motive force) by primary transport systems (H+ pumps) and its use for ATP synthesis, solute transport, motility and reverse electron transport. A substantial body of evidence indicates, however, that certain extremophilic bacteria can use Na+ as a coupling ion in an Na+ cycle instead of, or in addition to, the H+ cycle. As in the H+ cycle, a fully operational Na+ cycle would include a primary Na+ pump that directly couples Na+ translocation to a chemical reaction, an Na+-transporting membrane ATP synthetase, a number of Na+-dependent membrane transporters, and an Na+-dependent flagellar motor. While certain Na+-dependent functions, like Na+-dependent uptake of melibiose, proline, and glutamate, have been observed in many bacteria, the ion gradients that served as energy sources for these transports have been generated by primary H+ pumps and converted to Na+ gradients by Na+/H+ antiporters.
One could think of several possible explanations for the widespread distribution of the elements of the Na+ cycle among pathogenic bacteria. First, Na+-based membrane energetics could improve the versatility of a pathogen by providing it with additional means of ATP synthesis, motility and solute uptake. This would improve its chances for colonization of the host cells and survival in the host organisms where defense mechanisms, including generation of superoxide radicals, impair the integrity of the bacterial membrane and decrease the levels of the proton motive force. Second, because Na+ concentrations in most natural environments are almost 106-fold higher than H+ concentrations, sodium motive force levels are unlikely to change as rapidly as proton motive force levels, making sodium motive force a much more reliable source of energy.
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Learning Objectives
• List the steps of the Krebs (or citric acid) cycle
Like the conversion of pyruvate to acetyl CoA, the citric acid cycle takes place in the matrix of the mitochondria. Almost all of the enzymes of the citric acid cycle are soluble, with the single exception of the enzyme succinate dehydrogenase, which is embedded in the inner membrane of the mitochondrion. Unlike glycolysis, the citric acid cycle is a closed loop: the last part of the pathway regenerates the compound used in the first step. The eight steps of the cycle are a series of redox, dehydration, hydration, and decarboxylation reactions that produce two carbon dioxide molecules, one GTP/ATP, and reduced forms of NADH and FADH2. This is considered an aerobic pathway because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. If this transfer does not occur, the oxidation steps of the citric acid cycle also do not occur. Note that the citric acid cycle produces very little ATP directly and does not directly consume oxygen.
Steps in the Citric Acid Cycle
Step 1. The first step is a condensation step, combining the two-carbon acetyl group (from acetyl CoA) with a four-carbon oxaloacetate molecule to form a six-carbon molecule of citrate. CoA is bound to a sulfhydryl group (-SH) and diffuses away to eventually combine with another acetyl group. This step is irreversible because it is highly exergonic. The rate of this reaction is controlled by negative feedback and the amount of ATP available. If ATP levels increase, the rate of this reaction decreases. If ATP is in short supply, the rate increases.
Step 2. Citrate loses one water molecule and gains another as citrate is converted into its isomer, isocitrate.
Steps 3 and 4. In step three, isocitrate is oxidized, producing a five-carbon molecule, α-ketoglutarate, together with a molecule of CO2 and two electrons, which reduce NAD+ to NADH. This step is also regulated by negative feedback from ATP and NADH and by a positive effect of ADP. Steps three and four are both oxidation and decarboxylation steps, which release electrons that reduce NAD+ to NADH and release carboxyl groups that form CO2 molecules. α-Ketoglutarate is the product of step three, and a succinyl group is the product of step four. CoA binds the succinyl group to form succinyl CoA. The enzyme that catalyzes step four is regulated by feedback inhibition of ATP, succinyl CoA, and NADH.
Step 5. A phosphate group is substituted for coenzyme A, and a high- energy bond is formed. This energy is used in substrate-level phosphorylation (during the conversion of the succinyl group to succinate) to form either guanine triphosphate (GTP) or ATP. There are two forms of the enzyme, called isoenzymes, for this step, depending upon the type of animal tissue in which they are found. One form is found in tissues that use large amounts of ATP, such as heart and skeletal muscle. This form produces ATP. The second form of the enzyme is found in tissues that have a high number of anabolic pathways, such as liver. This form produces GTP. GTP is energetically equivalent to ATP; however, its use is more restricted. In particular, protein synthesis primarily uses GTP.
Step 6. Step six is a dehydration process that converts succinate into fumarate. Two hydrogen atoms are transferred to FAD, producing FADH2. The energy contained in the electrons of these atoms is insufficient to reduce NAD+ but adequate to reduce FAD. Unlike NADH, this carrier remains attached to the enzyme and transfers the electrons to the electron transport chain directly. This process is made possible by the localization of the enzyme catalyzing this step inside the inner membrane of the mitochondrion.
Step 7. Water is added to fumarate during step seven, and malate is produced. The last step in the citric acid cycle regenerates oxaloacetate by oxidizing malate. Another molecule of NADH is produced.
Products of the Citric Acid Cycle
Two carbon atoms come into the citric acid cycle from each acetyl group, representing four out of the six carbons of one glucose molecule. Two carbon dioxide molecules are released on each turn of the cycle; however, these do not necessarily contain the most recently-added carbon atoms. The two acetyl carbon atoms will eventually be released on later turns of the cycle; thus, all six carbon atoms from the original glucose molecule are eventually incorporated into carbon dioxide. Each turn of the cycle forms three NADH molecules and one FADH2 molecule. These carriers will connect with the last portion of aerobic respiration to produce ATP molecules. One GTP or ATP is also made in each cycle. Several of the intermediate compounds in the citric acid cycle can be used in synthesizing non-essential amino acids; therefore, the cycle is amphibolic (both catabolic and anabolic).
Key Points
• The four-carbon molecule, oxaloacetate, that began the cycle is regenerated after the eight steps of the citric acid cycle.
• The eight steps of the citric acid cycle are a series of redox, dehydration, hydration, and decarboxylation reactions.
• Each turn of the cycle forms one GTP or ATP as well as three NADH molecules and one FADH2 molecule, which will be used in further steps of cellular respiration to produce ATP for the cell.
Key Terms
• citric acid cycle: a series of chemical reactions used by all aerobic organisms to generate energy through the oxidization of acetate derived from carbohydrates, fats, and proteins into carbon dioxide
• Krebs cycle: a series of enzymatic reactions that occurs in all aerobic organisms; it involves the oxidative metabolism of acetyl units and serves as the main source of cellular energy
• mitochondria: in cell biology, a mitochondrion (plural mitochondria) is a membrane-enclosed organelle, often described as “cellular power plants” because they generate most of the ATP | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.06%3A_The_Citric_Acid_%28Krebs%29_Cycle/5.6A%3A_Citric_Acid_Cycle.txt |
Learning Objectives
• Explain why cells break down pyruvate
In order for pyruvate, the product of glycolysis, to enter the next pathway, it must undergo several changes to become acetyl Coenzyme A (acetyl CoA). Acetyl CoA is a molecule that is further converted to oxaloacetate, which enters the citric acid cycle (Krebs cycle). The conversion of pyruvate to acetyl CoA is a three-step process.
Step 1. A carboxyl group is removed from pyruvate, releasing a molecule of carbon dioxide into the surrounding medium. (Note: carbon dioxide is one carbon attached to two oxygen atoms and is one of the major end products of cellular respiration. ) The result of this step is a two-carbon hydroxyethyl group bound to the enzyme pyruvate dehydrogenase; the lost carbon dioxide is the first of the six carbons from the original glucose molecule to be removed. This step proceeds twice for every molecule of glucose metabolized (remember: there are two pyruvate molecules produced at the end of glycolysis); thus, two of the six carbons will have been removed at the end of both of these steps.
Step 2. The hydroxyethyl group is oxidized to an acetyl group, and the electrons are picked up by NAD+, forming NADH (the reduced form of NAD+). The high- energy electrons from NADH will be used later by the cell to generate ATP for energy.
Step 3. The enzyme-bound acetyl group is transferred to CoA, producing a molecule of acetyl CoA. This molecule of acetyl CoA is then further converted to be used in the next pathway of metabolism, the citric acid cycle.
Key Points
• In the conversion of pyruvate to acetyl CoA, each pyruvate molecule loses one carbon atom with the release of carbon dioxide.
• During the breakdown of pyruvate, electrons are transferred to NAD+ to produce NADH, which will be used by the cell to produce ATP.
• In the final step of the breakdown of pyruvate, an acetyl group is transferred to Coenzyme A to produce acetyl CoA.
Key Terms
• acetyl CoA: a molecule that conveys the carbon atoms from glycolysis (pyruvate) to the citric acid cycle to be oxidized for energy production
5.6C: Acetyl CoA and the Citric Acid Cycle
Learning Objectives
• Recall the citric acid cycle
The citric acid cycle, shown in —also known as the tricarboxylic acid cycle (TCA cycle) or the Krebs cycle—is a series of chemical reactions used by all aerobic organisms to generate energy through the oxidation of acetate—derived from carbohydrates, fats, and proteins—into carbon dioxide. The cycle provides precursors including certain amino acids as well as the reducing agent NADH that is used in numerous biochemical reactions. Its central importance to many biochemical pathways suggests that it was one of the earliest established components of cellular metabolism; it may have originated abiogenically.
The name of this metabolic pathway is derived from citric acid, a type of tricarboxylic acid that is first consumed and then regenerated by this sequence of reactions to complete the cycle. The cycle consumes acetate (in the form of acetyl-CoA) and water, reduces NAD+ to NADH, and produces carbon dioxide. The NADH generated by the TCA cycle is fed into the oxidative phosphorylation pathway. The net result of these two closely linked pathways is the oxidation of nutrients to produce usable energy in the form of ATP.
Components of the TCA cycle were derived from anaerobic bacteria, and the TCA cycle itself may have evolved more than once. Theoretically there are several alternatives to the TCA cycle, however the TCA cycle appears to be the most efficient. If several alternatives independently evolved, they all rapidly converged to the TCA cycle.
The citric acid cycle is a key component of the metabolic pathway by which all aerobic organisms generate energy. Through the catabolism of sugars, fats, and proteins, a two carbon organic product acetate in the form of acetyl-CoA is produced. Acetyl-CoA along with two equivalents of water (H2O) are consumed by the citric acid cycle, producing two equivalents of carbon dioxide (CO2) and one equivalent of HS-CoA. In addition, one complete turn of the cycle converts three equivalents of nicotinamide adenine dinucleotide (NAD+) into three equivalents of reduced NAD+ (NADH), one equivalent of ubiquinone (Q) into one equivalent of reduced ubiquinone (QH2), and one equivalent each of guanosine diphosphate (GDP) and inorganic phosphate (Pi) into one equivalent of guanosine triphosphate (GTP). The NADH and QH2 that is generated by the citric acid cycle is used by the oxidative phosphorylation pathway to generate energy-rich adenosine triphosphate (ATP).
One of the primary sources of acetyl-CoA is sugars that are broken down by glycolysis to produce pyruvate that, in turn, is decarboxylated by the enzyme pyruvate dehydrogenase. This generates acetyl-CoA according to the following reaction scheme:
CH3C(=O)C(=O)O(pyruvate) + HSCoA + NAD+ → CH3C(=O)SCoA (acetyl-CoA) + NADH + H+ + CO2
The product of this reaction, acetyl-CoA, is the starting point for the citric acid cycle.
Key Points
• The Krebs cycle is a series of chemical reactions used by all aerobic organisms to generate energy through the oxidization of acetate—derived from carbohydrates, fats, and proteins —into carbon dioxide.
• Theoretically there are several alternatives to the TCA cycle, but the TCA cycle appears to be the most efficient.
• The citric acid cycle consumes acetate (in the form of acetyl-CoA) and water, reduces NAD+ to NADH, and produces carbon dioxide.
Key Terms
• acetyl CoA: Acetyl coenzyme A or acetyl-CoA is an important molecule in metabolism, used in many biochemical reactions. 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.
• citric acid cycle: An alternative name for the Krebs cycle.
• glycolysis: The cellular degradation of the simple sugar glucose to yield pyruvic acid and ATP as an energy source.
LICENSES AND ATTRIBUTIONS
CC LICENSED CONTENT, SPECIFIC ATTRIBUTION | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.06%3A_The_Citric_Acid_%28Krebs%29_Cycle/5.6B%3A_Breakdown_of_Pyruvate.txt |
Learning Objectives
• Distinguish between the Entner-Doudoroff pathway and glycolysis
The Entner–Doudoroff pathway describes an alternate series of reactions that catabolize glucose to pyruvate using a set of enzymes different from those used in either glycolysis or the pentose phosphate pathway. Glycolysis (from glycose, an older term for glucose + -lysis degradation) is the metabolic pathway that converts glucose \(\ce{C6H12O6}\), into pyruvate, \(\ce{CH3COCOO^{−} }\). The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide). Most bacteria use glycolysis and the pentose phosphate pathway. This pathway was first reported in 1952 by Michael Doudoroff and Nathan Entner.
Distinct features of the Entner–Doudoroff pathway are that it occurs only in prokaryotes and it uses 6-phosphogluconate dehydratase and 2-keto-3-deoxyphosphogluconate aldolase to create pyruvate from glucose. The Entner–Doudoroff pathway has a net yield of 1 ATP for every glucose molecule processed, as well as 1 NADH and 1 NADPH. By comparison, glycolysis has a net yield of 2 ATP and 2 NADH for every one glucose molecule processed.
There are a few bacteria that substitute classic glycolysis with the Entner-Doudoroff pathway. They may lack enzymes essential for glycolysis, such as phosphofructokinase-1. This pathway is generally found in Pseudomonas, Rhizobium, Azotobacter, Agrobacterium, and a few other Gram-negative genera. Very few Gram-positive bacteria have this pathway, with Enterococcus faecalis being a rare exception. Most organisms that use the pathway are aerobes due to the low ATP yield per glucose such as Pseudomonas, a genus of Gram-negative bacteria, and Azotobacter, a genus of Gram-negative bacteria.
Key Points
• Glycolysis is the metabolic pathway that converts glucose into pyruvate and hydrogen ions.
• The Entner-Doudoroff pathway was first reported in 1952 by Michael Doudoroff and Nathan Entner.
• There are a few bacteria that substitute classic glycolysis with the Entner-Doudoroff pathway.
Key Terms
• glycolysis: The metabolic pathway that converts glucose into pyruvate and hydrogen ions.
• ATP: Adenosine-5′-triphosphate (ATP) is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the “molecular unit of currency” of intracellular energy transfer. ATP transports chemical energy within cells for metabolism.
5.7B: Aerobic Hydrocarbon Oxidation
Learning Objectives
• Discuss the advantages of organisms that can undergo aerobic hydrocarbon oxidation
Microbes can utilize hydrocarbons via oxidation as an energy source.
Microbes can use many different carbon sources for energy. The best known and perhaps most common example is glucose. Microbes can utilize hydrocarbons via a stepwise oxidation of a hydrocarbon by oxygen produces water and, successively, an alcohol, an aldehyde or a ketone, a carboxylic acid, and then a peroxide. Note the presence of oxygen, thus defining this as aerobic hydrocarbon oxidation. There are examples of anaerobic hydrocarbon oxidation, which will not be discussed here. This is of special interest as many of the environment pollutants released by human industry are often hydrocarbon based. One of the best examples is oil spills. Understanding how microbes digest hydrocarbons has started the field of microbial biodegradation, a type of bioremediation. The goal of this is to find ways of using microbes to degrade hydrocarbon spills or waste into less dangerous byproducts such as alcohol.
Hydrocarbon utilizing microorganisms, mostly Cladosporium resinae and Pseudomonas aeruginosa, colloquially known as “HUM bugs,” are commonly present in jet fuel. They live in the water-fuel interface of the water droplets, form dark black/brown/green, gel-like mats, and cause microbial corrosion to plastic and rubber parts of the aircraft fuel system by consuming them, and to the metal parts by the means of their acidic metabolic products. They are also incorrectly called algae due to their appearance. FSII, which is added to the fuel, acts as a growth retardant for them. There are about 250 kinds of bacteria that can live in jet fuel, but fewer than a dozen are meaningfully harmful.
Biosurfactants are surface-active substances synthesized by living cells. Interest in microbial surfactants has been steadily increasing in recent years due to their diversity, environmentally friendly nature, possibility of large-scale production, selectivity, performance under extreme conditions, and potential applications in environmental protection. Biosurfactants enhance the emulsification of hydrocarbons, have the potential to solubilize hydrocarbon contaminants, and increase their availability for microbial degradation. The use of chemicals for the treatment of a hydrocarbon polluted site may contaminate the environment with their by-products, whereas biological treatment may efficiently destroy pollutants, while being biodegradable themselves. Therefore, biosurfactant-producing microorganisms may play an important role in the accelerated bioremediation of hydrocarbon-contaminated sites. These compounds can also be used in enhanced oil recovery and may be considered for other potential applications in environmental protection. Other applications include herbicides and pesticides formulations, detergents, healthcare and cosmetics, pulp and paper, coal, textiles, ceramic processing and food industries, uranium ore-processing, and mechanical dewatering of peat. Several microorganisms are known to synthesize surface-active agents; most of them are bacteria and yeasts. When grown on hydrocarbon substrate as the carbon source, these microorganisms synthesize a wide range of chemicals with surface activity, such as glycolipid, phospholipid, and others. These chemicals are synthesized to emulsify the hydrocarbon substrate and facilitate its transport into the cells. In some bacterial species such as Pseudomonas aeruginosa, biosurfactants are also involved in a group motility behavior called swarming motility.
Key Points
• Microbes in aerobic conditions can use hydrocarbons via oxidation of the hydrocarbon. This leads to byproducts such as water, alcohol, and peroxide.
• Many hydrocarbons are environmentally damaging, thus the break down of hydrocarbons by microbes is of special interest.
• HUM bugs can function as biosurfactants to facilitate the emulsification of hydrocarbons.
Key Terms
• hydrocarbon: A compound consisting only of carbon and hydrogen atoms.
• biosurfactant: Surface-active substances synthesized by living cells.
• bioremediation: The use of biological organisms, usually microorganisms, to remove contaminants, especially from polluted water. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.07%3A_Alternatives_to_Glycolysis/5.7A%3A_The_Entner-Doudoroff_Pathway.txt |
Learning Objectives
• Outline the two major phases of the pentose phosphate shunt: oxidative and non-oxidative phases
The pentose phosphate pathway (PPP; also called the phosphogluconate pathway and the hexose monophosphate shunt) is a process that breaks down glucose-6-phosphate into NADPH and pentoses (5-carbon sugars) for use in downstream biological processes. There are two distinct phases in the pathway: the oxidative phase and the non-oxidative phase. The first is the oxidative phase in which glucose-6-phosphate is converted to ribulose-5-phosphate. During this process two molecules of NADP+are reduced to NADPH. The overall reaction for this process is:
Glucose 6-phosphate + 2 NADP++ H2O → ribulose-5-phosphate + 2 NADPH + 2 H+ + CO2
The second phase of this pathway is the non-oxidative synthesis of 5-carbon sugars. Depending on the body’s state, ribulose-5-phosphate can reversibly isomerize to ribose-5-phosphate. Ribulose-5-phosphate can alternatively undergo a series of isomerizations as well as transaldolations and transketolations that result in the production of other pentose phosphates including fructose-6-phosphate, erythrose-4-phosphate, and glyceraldehyde-3-phosphate (both intermediates in glycolysis). These compounds are used in a variety of different biological processes including production of nucleotides and nucleic acids (ribose-5-phosphate), as well as synthesis of aromatic amino acids (erythrose-4-phosphate).
Glucose-6-phosphate dehydrogenase is the rate-controlling enzyme in this pathway. It is allosterically stimulated by NADP+. NADPH-utilizing pathways, such as fatty acid synthesis, generate NADP+, which stimulates glucose-6-phosphate dehydrogenase to produce more NADPH. In mammals, the PPP occurs exclusively in the cytoplasm; it is found to be most active in the liver, mammary gland, and adrenal cortex. The ratio of NADPH:NADP+ is normally about 100:1 in liver cytosol, making the cytosol a highly-reducing environment.
The PPP is one of the three main ways the body creates molecules with reducing power, accounting for approximately 60% of NADPH production in humans. While the PPP does involve oxidation of glucose, its primary role is anabolic rather than catabolic, using the energy stored in NADPH to synthesize large, complex molecules from small precursors.
Additionally, NADPH can be used by cells to prevent oxidative stress. NADPH reduces glutathione via glutathione reductase, which converts reactive H2O2 into H2O by glutathione peroxidase. For example, erythrocytes generate a large amount of NADPH through the pentose phosphate pathway to use in the reduction of glutathione.
Key Points
• There are two distinct phases in the pathway: the oxidative phase and the non-oxidative phase.
• In the oxidative phase, two molecules of NADP+ are reduced to NADPH, utilizing the energy from the conversion of glucose-6-phosphate into ribulose-5-phosphate. These NADPH molecules can then be used as an energy source in elsewhere in the cell.
• The non-oxidative phase generates 5-carbon sugars, which can be used in the synthesis of nucleotides, nucleic acids, and amino acids.
• The pentose phosphate pathway is an alternative to glycolysis.
Key Terms
• glycolysis: The cellular degradation of the simple sugar glucose to yield pyruvic acid and ATP as an energy source.
• NADPH: Nicotinamide adenine dinucleotide phosphate (NADP) carrying electrons and bonded with a hydrogen (H) ion; the reduced form of NADP+.
• oxidative stress: Damage caused to cells or tissue by reactive oxygen species. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.07%3A_Alternatives_to_Glycolysis/5.7C%3A_The_Pentose_Phosphate_Shunt.txt |
Microbes can harness energy and carbon derived from organic acids by using a variety of dedicated metabolic enzymes.
LEARNING OBJECTIVES
Give examples of types of organic acid metabolism that are used by microorganisms for a sole source of energy
Key Points
• Some microbes are capable of utilizing organic acids such as fatty acids, amino acids, or straight-chain unsaturated acids (e.g., lactate) as a sole source of energy.
• Metabolism of the organic acid formate is important in methylotrophic organisms. It is vital in the catabolism of C1 compounds (such as methanol).
• Many bacteria are capable of utilizing fatty acids as sole energy and carbon sources through the cyclic β-oxidation pathway, which ultimately yields acetyl-CoA.
Key Terms
• fatty acid: Any of a class of aliphatic carboxylic acids, of general formula CnH2n+1COOH, that occur combined with glycerol as animal or vegetable oils and fats. Only those with an even number of carbon atoms are normally found in natural fats.
• acyl: Any of class of organic radicals, RCO-, formed by the removal of a hydroxyl group from a carboxylic acid.
• acetyl CoA: Acetyl coenzyme A or acetyl-CoA is an important molecule in metabolism, used in many biochemical reactions. 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.
Organic Acid Metabolism
A great many organisms generate organic acids (such as lactate) as a byproduct of fermentation. Some microbes are capable of utilizing such compounds as a sole source of energy.
The most commonly metabolized organic acids are the carboxylic acids, which are organic acids containing at least one carboxyl (-COOH) group. The general formula of a carboxylic acid is R-COOH, where R is a monovalent functional group. Many types of carboxylic acids can be metabolized by microbes, including:
• Fatty acids (carboxylic acids with long acyl tails)
• Amino acids (the building blocks of proteins)
• Straight-chained, saturated acids (e.g., formate, acetate, and palmitate)
FORMATE METABOLISM
Formate metabolism is important in methylotrophic organisms. It is vital in the catabolism of C1 compounds such as methanol (see the “Methylotrophy and Methanotrophy” atom for more information on C1 compound utilization). Methylotrophic microbes convert single-carbon compounds to formaldehyde, which is oxidized to formate by formaldehyde dehydrogenase. Degradation of formate is then catalyzed by formate dehydrogenase (FDH), which oxidizes formate to ultimately yield CO2. It permits the donation of electrons to a second substrate (such as NAD+) in the process. This is a critical late step in the hydrocarbon utilization pathway. The ability to metabolize formate is also critical in bacterial anaerobic metabolism, in which case formate is also oxidized by an FDH enzyme but the electrons are donated to cytochromes (proteins involved in electron transport).
FATTY ACID METABOLISM
Many bacteria are capable of utilizing fatty acids of various tail lengths as sole energy and carbon sources. This process requires the β-oxidation pathway, a cyclic process that catalyzes the sequential shortening of fatty acid acyl chains to the final product, acetyl-CoA. The step-by-step process occurs as follows:
1. Fatty acid chains are converted to enoyl-CoA (catalyzed by acyl-CoA dehydrogenase).
2. Enoyl-CoA is converted to 3-hydroxyacyl-CoA (catalyzed by enoyl-CoA hydratase).
3. 3-hydroxyacyl-CoA is converted to 3-ketoacyl-CoA (catalyzed by 3-hydroxyacyl-CoA dehydrogenase).
4. 3-ketoacyl-CoA is thiolated (by 3-ketoacyl-CoA thiolase) to yield one molecule of acetyl-CoA and a derivative of the original input fatty acid that is now shorter by two carbons.
The fatty acid chain that is left over after the thiolation step can then reenter the β-oxidation pathway, which can cycle until the fatty acid has been completely reduced to acetyl-CoA. Acertyl-CoA is the entry molecule for the TCA cycle. The TCA cycle is the process used by all aerobic organisms to generate energy. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.07%3A_Alternatives_to_Glycolysis/5.7D%3A_Organic_Acid_Metabolism.txt |
Biological lipids, which are broken down and utilized though β-oxidation, represent a potent energy source.
Learning Objectives
• Outline the process of lipid metabolism, specifically beta-oxidation
Key Points
• In addition to their role as the primary component of cell membranes, lipids can be metabolized for use as a primary energy source.
• Lipid metabolism involves the degradation of fatty acids, which are fundamental biological molecules and the building blocks of more structurally complex lipids.
• In order to be metabolized by the cell, lipids are hydrolyzed to yield free fatty acids that then converted to acetyl-CoA through the β- oxidation pathway.
• One major feature of anaerobic digestion is the production of biogas (with the most useful component being methane), which can be used in generators for electricity production and/or in boilers for heating purposes.
Key Terms
• carboxylic acid: Any of a class of organic compounds containing a carboxyl functional group.
• coenzyme A: A coenzyme, formed from pantothenic acid and adenosine triphosphate, that is necessary for fatty acid synthesis and metabolism.
Lipid Metabolism
Lipids are universal biological molecules. Not only does this broad class of compounds represent the primary structural component of biological membranes in all organisms, they also serve a number of vital roles in microorganisms. Among these, lipids can be metabolized by microbes for use as a primary energy source. Although not stated explicitly, the “Organic Acid Metabolism” atom in this module introduces the concept of lipid metabolism by describing the process of fatty acid metabolism through β-oxidation. This atom will expand on the metabolic pathway that enables degradation and utilization of lipids. Fatty acids are the building blocks of lipids. They are made of a hydrocarbon chain of variable length that terminates with a carboxylic acid group (-COOH). The fatty acid structure (see below) is one of the most fundamental categories of biological lipids. It is commonly used as a building block of more structurally complex lipids (such as phospholipids and triglycerides). When metabolized, fatty acids yield large quantities of ATP, which is why these molecules are important energy sources. Lipids are an energy and carbon source. Before complex lipids can be used to produce energy, they must first be hydrolyzed. This requires the activity of hydrolytic enzymes called lipases, which release fatty acids from derivatives such as phospholipids. These fatty acids can then enter a dedicated pathway that promotes step-wise lipid processing that ultimately yields acetyl-CoA, a critical metabolite that conveys carbon atoms to the TCA cycle (aka Krebs cycle or citric acid cycle) to be oxidized for energy production.
β-oxidation
The metabolic process by which fatty acids and their lipidic derivatives are broken down is called β-oxidation. This process bears significant similarity to the mechanism by which fatty acids are synthesized, except in reverse. In brief, the oxidation of lipids proceeds as follows: two-carbon fragments are removed sequentially from the carboxyl end of the fatty acid after dehydrogenation, hydration, and oxidation to form a keto acid, which is then cleaved by thiolysis. The acetyl-CoA molecule liberated by this process is eventually converted into ATP through the TCA cycle.
β-oxidation can be broken down into a series of discrete steps:
1. Activation: Before fatty acids can be metabolized, they must be “activated. ” This activation step involves the addition of a coenzyme A (CoA) molecule to the end of a long-chain fatty acid, after which the activated fatty acid (fatty acyl -CoA) enters the β-oxidation pathway.
2. Oxidation: The initial step of β-oxidation is catalyzed by acyl-CoA dehydrogenase, which oxidizes the fatty acyl-CoA molecule to yield enoyl-CoA. As a result of this process, a trans double bond is introduced into the acyl chain.
3. Hydration: In the second step, enoyl-CoA hydratase hydrates the double bond introduced in the previous step, yielding an alcohol (-C-OH).
4. Oxidation: Hydroxyacyl-CoA dehydrogenase oxidizes the alcohol formed in the previous step to a carbonyl (-C=O).
5. Cleavage: A thiolase then cleaves off acetyl-CoA from the oxidized molecule, which also yields an acyl-CoA that is two carbons shorter than the original molecule that entered the β-oxidation pathway.
This cycle repeats until the fatty acid has been completely reduced to acetyl-CoA, which is fed through the TCA cycle to ultimately yield cellular energy in the form of ATP. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.07%3A_Alternatives_to_Glycolysis/5.7E%3A_Lipid_Metabolism.txt |
Excess amino acids are converted into molecules that can enter the pathways of glucose catabolism.
Learning Objectives
• Describe the role played by proteins in glucose metabolism
Key Points
• Amino acids must be deaminated before entering any of the pathways of glucose catabolism: the amino group is converted to ammonia, which is used by the liver in the synthesis of urea.
• Deaminated amino acids can be converted into pyruvate, acetyl CoA, or some components of the citric acid cycle to enter the pathways of glucose catabolism.
• Several amino acids can enter the glucose catabolism pathways at multiple locations.
Key Terms
• catabolism: Destructive metabolism, usually including the release of energy and breakdown of materials.
• keto acid: Any carboxylic acid that also contains a ketone group.
• deamination: The removal of an amino group from a compound.
Metabolic pathways should be thought of as porous; that is, substances enter from other pathways and intermediates leave for other pathways. These pathways are not closed systems. Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways. Proteins are a good example of this phenomenon. They can be broken down into their constituent amino acids and used at various steps of the pathway of glucose catabolism.
Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time, the amino acids are recycled into the synthesis of new proteins or are used as precursors in the synthesis of other important biological molecules, such as hormones, nucleotides, or neurotransmitters. However, if there are excess amino acids, or if the body is in a state of starvation, some amino acids will be shunted into the pathways of glucose catabolism.
Each amino acid must have its amino group removed (deamination) prior to the carbon chain’s entry into these pathways. When the amino group is removed from an amino acid, it is converted into ammonia through the urea cycle. The remaining atoms of the amino acid result in a keto acid: a carbon chain with one ketone and one carboxylic acid group. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals produced from the nitrogen originating in amino acids; it leaves the body in urine. The keto acid can then enter the citric acid cycle.
When deaminated, amino acids can enter the pathways of glucose metabolism as pyruvate, acetyl CoA, or several components of the citric acid cycle. For example, deaminated asparagine and aspartate are converted into oxaloacetate and enter glucose catabolism in the citric acid cycle. Deaminated amino acids can also be converted into another intermediate molecule before entering the pathways. Several amino acids can enter glucose catabolism at multiple locations.
5.7G: Methylotrophy and Methanotrophy
Methylotrophs and methanotrophs are a diverse group of microorganisms that can derive energy from the metabolism of single-carbon compounds.
Learning Objectives
• Distinguish between methylotrophs and methanotrophs and their energy sources
Key Points
• Microbes with the ability to utilize single-carbon (C1) compounds (or multi-carbon compounds lacking carbon bonds) as the sole energy source for their growth are known as methylotrophs.
• Methanotrophs, a specific type of methylotroph, are able to metabolize methane as their only source of carbon and energy.
• Methylotrophs aerobically utilize C1 compounds by oxidizing them to yield formaldehyde, which in turn can either be used for energy or assimilated into biomass.
Key Terms
• methylotroph: Any organism that utilizes simple methyl compounds (such as methane or methanol) as a source of carbon and of energy.
• monooxygenase: Any oxygenase enzyme that catalyzes the incorporation of a single atom of molecular oxygen into a substrate, the other atom being reduced to water; active in the metabolism of many foreign compounds.
• methanogenesis: The generation of methane by anaerobic bacteria.
Methylotrophs
Multiple diverse microorganisms have evolved the intriguing ability to utilize single-carbon (C1) compounds (e.g. methanol or methane) or multi-carbon compounds lacking carbon bonds (e.g. dimethyl ether and dimethylamine) as the sole energy source for their growth. Microbes with this capability are known as methylotrophs.
Methylotrophs, in general, aerobically utilize C1 compounds by oxidizing them to yield formaldehyde. Formaldehyde, in turn, can either be “burned” for energy (by dissimilation to CO2) or assimilated into biomass, allowing the cell to grow using molecules like methanol as a sole carbon source. Because methanol is more abundant, more easily purified, and cheaper than sugar carbon sources (e.g. glucose), methylotrophs are particularly useful in biotechnology for the production of amino acids, vitamins, recombinant proteins, single-cell proteins, co- enzymes, and cytochromes.
Here are examples of methylotrophs:
• Methanosarcina, which can both utilize and produce methane;
• Methylococcus capsulatus, which requires methane to survive; and
• Pichia pastoris, a biotechnologically important model organism that can use methanol as a carbon and energy source.
Methanotrophs
Some methylotrophs can degrade the greenhouse gas methane. Organisms of this type are referred to as methanotrophs. Methanotrophs are able to metabolize methane as their only source of carbon and energy. Most known methanotrophs are bacteria that strictly require methane for growth (“obligate methanotrophs”). The fact that some methylotrophs can also make use of multi-carbon compounds distinguishes them from methanotrophs, which are usually fastidious methane and methanol oxidizers.
Methanotrophs occur mostly in soils. They are especially common near environments where methane is produced, such as:
• oceans
• mud
• marshes
• underground environments
• soils
• rice paddies
• landfills
Methanotrophs are of special interest to researchers studying global warming because they prevent a potential greenhouse gas (methane), far more potent than carbon dioxide, from being released into the atmosphere. Methanophilic (“methane-loving”) bacteria, therefore, are significant in the global methane budget.
Methane Utilization
Methanotrophs oxidize methane by first initiating reduction of oxygen (O2) to water (H2O) and oxidation of methane (CH4) to a more active species, methanol (CH3OH), using oxidoreductase enzymes called methane monooxygenases (MMOs). Two types of MMO have been isolated from methanotrophs:
• soluble methane monooxygenase (sMMO), which is found in the cell cytoplasm.
• particulate methane monooxygenase (pMMO), which is found in the cell membrane.
Cells containing pMMO demonstrate higher growth capabilities and higher affinity for methane than cells that contain sMMO. Because pMMO is a membrane protein, cells that use it for methane metabolism characteristically have a system of internal membranes within which methane oxidation occurs.
As in the general case described above for methylotrophs, methanotrophs ultimately oxidize the methanol produced by MMOs to yield formaldehyde. The method of formaldehyde fixation differs between various methanotrophic organisms. This difference (along with variability in membrane structure) divides methanotrophs into several subgroups, such as the Methylococcaceae, Methylocystaceae, and Verrucomicrobiae. Although the mechanism by which it occurs is not entirely clear, it is also apparent that certain bacteria can utilize methane anaerobically by essentially running the methanogenesis pathway (normally used by methanogenic bacteria to produce methane) in reverse. This typically occurs in microbes dwelling in marine sediments where oxygen is scarce or altogether absent.
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Learning Objectives
• Describe the process of anaerobic cellular respiration.
Anaerobic Cellular Respiration
The production of energy requires oxygen. The electron transport chain, where the majority of ATP is formed, requires a large input of oxygen. However, many organisms have developed strategies to carry out metabolism without oxygen, or can switch from aerobic to anaerobic cell respiration when oxygen is scarce.
During cellular respiration, some living systems use an organic molecule as the final electron acceptor. Processes that use an organic molecule to regenerate NAD+ from NADH are collectively referred to as fermentation. In contrast, some living systems use an inorganic molecule as a final electron acceptor. Both methods are called anaerobic cellular respiration, where organisms convert energy for their use in the absence of oxygen.
Certain prokaryotes, including some species of bacteria and archaea, use anaerobic respiration. For example, the group of archaea called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria and archaea, most of which are anaerobic, reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.
Eukaryotes can also undergo anaerobic respiration. Some examples include alcohol fermentation in yeast and lactic acid fermentation in mammals.
Lactic Acid Fermentation
The fermentation method used by animals and certain bacteria (like those in yogurt) is called lactic acid fermentation. This type of fermentation is used routinely in mammalian red blood cells and in skeletal muscle that has an insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). The excess amount of lactate in those muscles is what causes the burning sensation in your legs while running. This pain is a signal to rest the overworked muscles so they can recover. In these muscles, lactic acid accumulation must be removed by the blood circulation and the lactate brought to the liver for further metabolism. The chemical reactions of lactic acid fermentation are the following:
Pyruvic acid + NADH ↔ lactic acid + NAD+
The enzyme used in this reaction is lactate dehydrogenase (LDH). The reaction can proceed in either direction, but the reaction from left to right is inhibited by acidic conditions. Such lactic acid accumulation was once believed to cause muscle stiffness, fatigue, and soreness, although more recent research disputes this hypothesis. Once the lactic acid has been removed from the muscle and circulated to the liver, it can be reconverted into pyruvic acid and further catabolized for energy.
Alcohol Fermentation
Another familiar fermentation process is alcohol fermentation, which produces ethanol, an alcohol. The use of alcohol fermentation can be traced back in history for thousands of years. The chemical reactions of alcoholic fermentation are the following (Note: CO2 does not participate in the second reaction):
Pyruvic acid → CO2 + acetaldehyde + NADH → ethanol + NAD+
The first reaction is catalyzed by pyruvate decarboxylase, a cytoplasmic enzyme, with a coenzyme of thiamine pyrophosphate (TPP, derived from vitamin B1 and also called thiamine). A carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the size of the molecule by one carbon, making acetaldehyde. The second reaction is catalyzed by alcohol dehydrogenase to oxidize NADH to NAD+ and reduce acetaldehyde to ethanol.
The fermentation of pyruvic acid by yeast produces the ethanol found in alcoholic beverages. Ethanol tolerance of yeast is variable, ranging from about 5 percent to 21 percent, depending on the yeast strain and environmental conditions.
Other Types of Fermentation
Various methods of fermentation are used by assorted organisms to ensure an adequate supply of NAD+ for the sixth step in glycolysis. Without these pathways, that step would not occur and no ATP would be harvested from the breakdown of glucose.Other fermentation methods also occur in bacteria. Many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of oxygen. Certain prokaryotes, like Clostridia, are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these microorganisms, killing them on exposure.
It should be noted that all forms of fermentation, except lactic acid fermentation, produce gas. The production of particular types of gas is used as an indicator of the fermentation of specific carbohydrates, which plays a role in the laboratory identification of the bacteria.
Key Points
• Anaerobic respiration is a type of respiration where oxygen is not used; instead, organic or inorganic molecules are used as final electron acceptors.
• Fermentation includes processes that use an organic molecule to regenerate NAD+ from NADH.
• Types of fermentation include lactic acid fermentation and alcohol fermentation, in which ethanol is produced.
• All forms of fermentation except lactic acid fermentation produce gas, which plays a role in the laboratory identification of bacteria.
• Some types of prokaryotes are facultatively anaerobic, which means that they can switch between aerobic respiration and fermentation, depending on the availability of oxygen.
Key Terms
• archaea: A group of single-celled microorganisms. They have no cell nucleus or any other membrane-bound organelles within their cells.
• anaerobic respiration: A form of respiration using electron acceptors other than oxygen.
• fermentation: An anaerobic biochemical reaction. When this reaction occurs in yeast, enzymes catalyze the conversion of sugars to alcohol or acetic acid with the evolution of carbon dioxide. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.08%3A_Fermentation/5.8A%3A_Anaerobic_Cellular_Respiration.txt |
Learning Objectives
• Discuss the process of acidogenesis and the production of propionate
Four Stages of Anaerobic Digestion
Acidogenesis is the second stage in the four stages of anaerobic digestion: hydrolysis, acidogenesis, acetogenesis, and methanogenesis. Hydrolysis is a chemical reaction wherein particulates are solubilized and large polymers are converted into simpler monomers. Acidogenesis is a biological reaction wherein simple monomers are converted into volatile fatty acids. Acetogenes is a biological reaction wherein volatile fatty acids are converted into acetic acid, carbon dioxide, and hydrogen. Finally, methanogenesis is a biological reaction wherein acetates are converted into methane and carbon dioxide, and hydrogen is consumed.
Anaerobic digestion is a complex biochemical process of mediated reactions undertaken by a consortium of microorganisms to convert organic compounds into methane and carbon dioxide. It is a stabilization process, reducing odor, pathogens, and mass reduction. Hydrolytic bacteria form a variety of reduced end-products from the fermentation of a given substrate.
One fundamental question in anaerobic digestion concerns the metabolic features that control carbon and electron flow. This flow is directed toward a reduced end-product during pure culture and mixed methanogenic cultures of hydrolytic bacteria. Thermoanaerobium brockii is a representative thermophilic, hydrolytic bacterium, which ferments glucose, via the Embden–Meyerhof Parnas Pathway.
Acidogenisis
Acidogenic activity was found in the early 20th century, but it was not until mid-1960s that the engineering of phases separation was assumed in order to improve the stability and waste digester treatment. In this phase, complex molecules (carbohydrates, lipids, and proteins) are depolymerized into soluble compounds by hydrolytic enzymes (cellulases, hemicellulases, amylases, lipases and proteases). The hydrolyzed compounds are fermented into volatile fatty acids (acetate, propionate, butyrate, and lactate), neutral compounds (ethanol, methanol), ammonia, hydrogen and carbon dioxide. Acetogenesis is one of the main reactions of this stage. In this reaction, the intermediary metabolites produced are metabolized to acetate, hydrogen, and carbonic gas by the three main groups of bacteria—homoacetogens, syntrophes, and sulphoreductors. For the acetic acid production are considered three kind of bacteria: Clostridium aceticum, Acetobacter woodii, and Clostridium termoautotrophicum.
In 1979, Winter and Wolfe demonstrated that A. wodii in syntrophic association with Methanosarcina produce methane and carbon dioxide from fructose, instead of three molecules of acetate. C. thermoaceticum and C. formiaceticum are able to reduce the carbonic gas to acetate, but they do not have hydrogenases to inhabilite the hydrogen use, so they can produce three molecules of acetate from fructose. Acetic acid is equally a co-metabolite of the organic substrates’ fermentation (sugars, glycerol, lactic acid, etc.) by diverse groups of microorganisms, which produce different acids:
• propionic bacteria (propionate + acetate)
• Clostridium (butyrate + acetate)
• Enterobacteria (acetate + lactate)
• Hetero-fermentative bacteria (acetate, propionate, butyrate, valerate, etc.)
Key Points
• Acetogenesis is the third stage in the four stages of anaerobic digestion.
• Acetogenesis end products are acetate, hydrogen, and carbonic gas.
• Acetogenesis occurs in three main groups of bacteria: homoacetogens, syntrophes, and sulphoreductors.
Key Terms
• acetogenesis: The anaerobic production of acetic acid or acetate by bacteria.
• metabolite: Any substance produced by, or taking part in, a metabolic reaction.
5.8C: Fermentation Without Substrate-Level Phosphorylation
Learning Objectives
• Give examples of various types of fermentation: homolactic, heterolactic and alcoholic
Fermentation is the process of extracting energy from the oxidation of organic compounds, such as carbohydrates, using an endogenous electron acceptor, which is usually an organic compound. In contrast, respiration is where electrons are donated to an exogenous electron acceptor, such as oxygen, via an electron transport chain. Fermentation is important in anaerobic conditions when there is no oxidative phosphorylation to maintain the production of ATP (adenosine triphosphate) by glycolysis.
During fermentation, pyruvate is metabolised to various compounds. Homolactic fermentation is the production of lactic acid from pyruvate; alcoholic fermentation is the conversion of pyruvate into ethanol and carbon dioxide; and heterolactic fermentation is the production of lactic acid as well as other acids and alcohols. Fermentation does not necessarily have to be carried out in an anaerobic environment. For example, even in the presence of abundant oxygen, yeast cells greatly prefer fermentation to oxidative phosphorylation, as long as sugars are readily available for consumption (a phenomenon known as the Crabtree effect). The antibiotic activity of Hops also inhibits aerobic metabolism in Yeast.
Sugars are the most common substrate of fermentation, and typical examples of fermentation products are ethanol, lactic acid, lactose, and hydrogen. However, more exotic compounds can be produced by fermentation, such as butyric acid and acetone. Yeast carries out fermentation in the production of ethanol in beers, wines, and other alcoholic drinks, along with the production of large quantities of carbon dioxide. Fermentation occurs in mammalian muscle during periods of intense exercise where oxygen supply becomes limited, resulting in the creation of lactic acid.
Key Points
• Fermentation without substrate level phosphorylation uses an endogenous electron acceptor, which is usually an organic compound.
• Fermentation is important in anaerobic conditions when there is no oxidative phosphorylation to maintain the production of ATP (adenosine triphosphate) by glycolysis.
• During fermentation, pyruvate is metabolised to various compounds such as lactic acid, ethanol and carbon dioxide or other acids.
Key Terms
• fermentation: Any of many anaerobic biochemical reactions in which an enzyme (or several enzymes produced by a microorganism) catalyses the conversion of one substance into another; especially the conversion (using yeast) of sugars to alcohol or acetic acid with the evolution of carbon dioxide.
• substrate: a surface on which an organism grows or to which it is attached
• oxidative phosphorylation: Oxidative phosphorylation (or OXPHOS in short) is a metabolic pathway that uses energy released by the oxidation of nutrients to produce adenosine triphosphate (ATP).
• electron acceptor: An electron acceptor is a chemical entity that accepts electrons transferred to it from another compound. It is an oxidizing agent that, by virtue of its accepting electrons, is itself reduced in the process. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.08%3A_Fermentation/5.8B%3A_Clostridial_and_Propionic_Acid_Fermentation.txt |
Learning Objectives
• Give examples of syntrophy in microbial metabolism
Syntrophy, or symbiosis, is the phenomenon involving one species living off the products of another species. For example, house dust mites live off human skin flakes. A healthy human being produces about 1 gram of skin flakes per day. These mites can also produce chemicals that stimulate the production of skin flakes. People can become allergic to these compounds. Another example are the many organisms that feast on feces or dung. A cow eats a lot of grass, the cellulose of which is transformed into lipids by micro-organisms in the cow’s large intestine.
These microorganisms cannot use the lipids because of a lack of dioxygen in the intestine, so the cow does not take up all the lipids produced. When the processed grass leaves the intestine as dung and comes into open air, many organisms, such as the dung beetle, feast on it. Yet another example is the community of micro-organisms in soil that live off leaf litter. Leaves typically last one year and are then replaced by new ones. These microorganisms mineralize the discarded leaves and release nutrients that are taken up by the plant. Such relationships are called reciprocal syntrophy because the plant lives off the products of micro-organisms. Many symbiotic relationships are based on syntrophy. Finally, anaerobic fermentation/methanogenesis is an example of a syntrophic relationship between different groups of microorganisms. Although fermentative bacteria are not strictly dependent on syntrophyic relationships, they still gain profit from the activities of the hydrogen-scavenging organisms. The fermentative bacteria gain maximum energy yield when protons are used as electron acceptor with concurrent H2 production.
Fermentation is a specific type of heterotrophic metabolism that uses organic carbon instead of oxygen as a terminal electron acceptor. This means that these organisms do not use an electron transport chain to oxidize NADH to NAD+ and therefore must have an alternative method of using this reducing power and maintaining a supply of NAD+ for the proper functioning of normal metabolic pathways (e.g. glycolysis ). As oxygen is not required, fermentative organisms are anaerobic. Many organisms can use fermentation under anaerobic conditions and aerobic respiration when oxygen is present. These organisms are facultative anaerobes. To avoid the overproduction of NADH, obligately fermentative organisms usually do not have a complete citric acid cycle. Instead of using an ATP synthase as in respiration, ATP in fermentative organisms is produced by substrate-level phosphorylation where a phosphate group is transferred from a high-energy organic compound to ADP to form ATP. As a result of the need to produce high energy phosphate-containing organic compounds (generally in the form of CoA-esters) fermentative organisms use NADH and other cofactors to produce many different reduced metabolic by-products, often including hydrogen gas (H2). These reduced organic compounds are generally small organic acids and alcohols derived from pyruvate, the end product of glycolysis. Examples include ethanol, acetate, lactate, and butyrate. Fermentative organisms are very important industrially and are used to make many different types of food products. The different metabolic end products produced by each specific bacterial species are responsible for the different tastes and properties of each food.
The best studied example of syntrophy in microbial metabolism is the oxidation of fermentative end products (such as acetate, ethanol and butyrate) by organisms such as Syntrophomonas. Alone, the oxidation of butyrate to acetate and hydrogen gas is energetically unfavorable. However, when a hydrogenotrophic (hydrogen-using) methanogen is present the use of the hydrogen gas will significantly lower the concentration of hydrogen (down to 10−5 atm) and thereby shift the equilibrium of the butyrate oxidation reaction under standard conditions (ΔGº) to non-standard conditions (ΔG’). Because the concentration of one product is lowered, the reaction is “pulled” towards the products and shifted towards net energetically favorable conditions (for butyrate oxidation: ΔGº= +48.2 kJ/mol, but ΔG’ = -8.9 kJ/mol at 10−5 atm hydrogen and even lower if also the initially produced acetate is further metabolized by methanogens). Conversely, the available free energy from methanogenesis is lowered from ΔGº= -131 kJ/mol under standard conditions to ΔG’ = -17 kJ/mol at 10−5 atm hydrogen. This is an example of intraspecies hydrogen transfer. In this way, low energy-yielding carbon sources can be used by a consortium of organisms to achieve further degradation and eventual mineralization of these compounds. These reactions help prevent the excess sequestration of carbon over geologic time scales, releasing it back to the biosphere in usable forms such as methane and CO2.
Key Points
• Anaerobic fermentation / methanogenesis is an example of a syntrophic relationship between different groups of microorganisms.
• Fermentation is a specific type of heterotrophic metabolism that uses organic carbon instead of oxygen as a terminal electron acceptor.
• The best studied example of syntrophy in microbial metabolism is the oxidation of fermentative end products (such as acetate, ethanol and butyrate) by organisms such as Syntrophomonas.
Key Terms
• syntrophy: The relationship between the individuals of different species (especially of bacteria) in which one or both benefit nutritionally from the presence of the other.
• symbiosis: A close, prolonged association between two or more organisms of different species, regardless of benefit to the members.
• fermentation: Any of many anaerobic biochemical reactions in which an enzyme (or several enzymes produced by a microorganism) catalyses the conversion of one substance into another; especially the conversion (using yeast) of sugars to alcohol or acetic acid with the evolution of carbon dioxide.
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In anaerobic respiration, a molecule other than oxygen is used as the terminal electron acceptor in the electron transport chain.
Learning Objectives
• Describe various types of electron acceptors and donors including: nitrate, sulfate, hydrgoen, carbon dioxide and ferric iron
Key Points
• Both inorganic and organic compounds may be used as electron acceptors in anaerobic respiration. Inorganic compounds include sulfate (SO42-), nitrate (NO3), and ferric iron (Fe3+). Organic compounds include DMSO.
• These molecules have a lower reduction potential than oxygen. Therefore, less energy is formed per molecule of glucose in anaerobic versus aerobic conditions.
• The reduction of certain inorganic compounds by anaerobic microbes is often ecologically significant.
Key Terms
• anaerobic: Without oxygen; especially of an environment or organism.
• reduction: A reaction in which electrons are gained and valence is reduced; often by the removal of oxygen or the addition of hydrogen.
• anaerobic respiration: metabolic reactions and processes that take place in the cells of organisms that use electron acceptors other than oxygen
Anaerobic respiration is the formation of ATP without oxygen. This method still incorporates the respiratory electron transport chain, but without using oxygen as the terminal electron acceptor. Instead, molecules such as sulfate (SO42-), nitrate (NO3), or sulfur (S) are used as electron acceptors. These molecules have a lower reduction potential than oxygen; thus, less energy is formed per molecule of glucose in anaerobic versus aerobic conditions.
Many different types of electron acceptors may be used for anaerobic respiration. Denitrification is the utilization of nitrate (NO3) as the terminal electron acceptor. Nitrate, like oxygen, has a high reduction potential. This process is widespread, and used by many members of Proteobacteria. Many denitrifying bacteria can also use ferric iron (Fe3+) and different organic electron acceptors.
Sulfate reduction uses sulfate (SO2−4) as the electron acceptor, producing hydrogen sulfide (H2S) as a metabolic end product. Sulfate reduction is a relatively energetically poor process, and is used by many Gram negative bacteria found within the δ-Proteobacteria. It is also used in Gram-positive organisms related to Desulfotomaculum or the archaeon Archaeoglobus.
Sulfate reduction requires the use of electron donors, such as the carbon compounds lactate and pyruvate (organotrophic reducers), or hydrogen gas (lithotrophic reducers). Some unusual autotrophic sulfate-reducing bacteria, such as Desulfotignum phosphitoxidans, can use phosphite (HPO3) as an electron donor. Others, such as certain Desulfovibrio species, are capable of sulfur disproportionation (splitting one compound into an electron donor and an electron acceptor) using elemental sulfur (S0), sulfite (SO3−2), and thiosulfate (S2O32-) to produce both hydrogen sulfide (H2S) and sulfate (SO2−).
Acetogenesis is a type of microbial metabolism that uses hydrogen (H2) as an electron donor and carbon dioxide (CO2) as an electron acceptor to produce acetate, the same electron donors and acceptors used in methanogenesis.
Ferric iron (Fe3+) is a widespread anaerobic terminal electron acceptor used by both autotrophic and heterotrophic organisms. Electron flow in these organisms is similar to those in electron transport, ending in oxygen or nitrate, except that in ferric iron-reducing organisms the final enzyme in this system is a ferric iron reductase. Since some ferric iron-reducing bacteria (e.g.G. metallireducens) can use toxic hydrocarbons (e.g. toluene) as a carbon source, there is significant interest in using these organisms as bioremediation agents in ferric iron contaminated aquifers.
Other inorganic electron acceptors include the reduction of Manganic ion (Mn4+) to manganous (Mn2+), Selenate (SeO42−) to selenite (SeO32−) to selenium (Se), Arsenate (AsO43−) to arsenite (AsO33-), and Uranyl (UO22+) to uranium dioxide (UO2)
Organic compounds may also be used as electron acceptors in anaerobic respiration. These include the reduction of fumarate to succinate, Trimethylamine N-oxide (TMAO) to trimethylamine (TMA), and Dimethyl sulfoxide (DMSO) to Dimethyl sulfide (DMS). | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.09%3A_Anaerobic_Respiration/5.9A%3A_Electron_Donors_and_Acceptors_in_Anaerobic_Respiration.txt |
Denitrification is a type of anaerobic respiration that uses nitrate as an electron acceptor.
Learning Objectives
• Outline the processes of nitrate reduction and denitrification and the organisms that utilize it
Key Points
• Denitrification generally proceeds through a stepwise reduction of some combination of the following intermediate forms: NO3 → NO2→ NO + N2O → N2.
• Generally, several species of bacteria are involved in the complete reduction of nitrate to molecular nitrogen, and more than one enzymatic pathway has been identified in the reduction process.
• Complete denitrification is an environmentally significant process as some intermediates of denitrification (nitric oxide and nitrous oxide) are significant greenhouse gases that react with sunlight and ozone to produce nitric acid, a component of acid rain.
Key Terms
• electron acceptor: An electron acceptor is a chemical entity that accepts electrons transferred to it from another compound. It is an oxidizing agent that, by virtue of its accepting electrons, is itself reduced in the process.
• eutrophication: The process of becoming eutrophic.
• facultative: Not obligate; optional, discretionary or elective
In anaerobic respiration, denitrification utilizes nitrate (NO3) as a terminal electron acceptor in the respiratory electron transport chain. Denitrification is a widely used process; many facultative anaerobes use denitrification because nitrate, like oxygen, has a high reduction potential
Denitrification is a microbially facilitated process involving the stepwise reduction of nitrate to nitrite (NO2) nitric oxide (NO), nitrous oxide (N2O), and, eventually, to dinitrogen (N2) by the enzymes nitrate reductase, nitrite reductase, nitric oxide reductase, and nitrous oxide reductase. The complete denitrification process can be expressed as a redox reaction: 2 NO3− + 10 e + 12 H+ → N2 + 6 H2O.
Protons are transported across the membrane by the initial NADH reductase, quinones and nitrous oxide reductase to produce the electrochemical gradient critical for respiration. Some organisms (e.g. E. coli) only produce nitrate reductase and therefore can accomplish only the first reduction leading to the accumulation of nitrite. Others (e.g. Paracoccus denitrificans or Pseudomonas stutzeri) reduce nitrate completely. Complete denitrification is an environmentally significant process because some intermediates of denitrification (nitric oxide and nitrous oxide) are significant greenhouse gases that react with sunlight and ozone to produce nitric acid, a component of acid rain. Denitrification is also important in biological wastewater treatment, where it can be used to reduce the amount of nitrogen released into the environment, thereby reducing eutrophication.
Denitrification takes place under special conditions in both terrestrial and marine ecosystems. In general, it occurs where oxygen is depleted and bacteria respire nitrate as a substitute terminal electron acceptor. Due to the high concentration of oxygen in our atmosphere, denitrification only takes place in anaerobic environments where oxygen consumption exceeds the oxygen supply and where sufficient quantities of nitrate are present. These environments may include certain soils and groundwater, wetlands, oil reservoirs, poorly ventilated corners of the ocean, and in sea floor sediments.
Denitrification is performed primarily by heterotrophic bacteria (e.g. Paracoccus denitrificans), although autotrophic denitrifiers have also been identified (e.g., Thiobacillus denitrificans). Generally, several species of bacteria are involved in the complete reduction of nitrate to molecular nitrogen, and more than one enzymatic pathway have been identified in the reduction process.
Rhizobia are soil bacteria with the unique ability to establish a N2-fixing symbiosis on legume roots. When faced with a shortage of oxygen, some rhizobia species are able to switch from O2-respiration to using nitrates to support respiration.
The direct reduction of nitrate to ammonium (dissimilatory nitrate reduction) can be performed by organisms with the nrf- gene. This is a less common method of nitrate reduction than denitrification in most ecosystems. Other genes involved in denitrification include nir (nitrite reductase) and nos (nitrous oxide reductase), which are possessed by such organisms as Alcaligenes faecalis, Alcaligenes xylosoxidans, Pseudomonas spp, Bradyrhizobium japonicum, and Blastobacter denitrificans. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.09%3A_Anaerobic_Respiration/5.9B%3A_Nitrate_Reduction_and_Denitrification.txt |
Sulfate reduction is a type of anaerobic respiration that utilizes sulfate as a terminal electron acceptor in the electron transport chain.
Learning Objectives
• Outline the process of sulfate and sulfur reduction including its various purposes
Key Points
• Sulfate reduction is a vital mechanism for bacteria and archaea living in oxygen-depleted, sulfate-rich environments.
• Sulfate reducers may be organotrophic, using carbon compounds, such as lactate and pyruvate as electron donors, or lithotrophic, and use hydrogen gas (H2) as an electron donor.
• Before sulfate can be used as an electron acceptor, it must be activated by ATP -sulfurylase, which uses ATP and sulfate to create adenosine 5′-phosphosulfate (APS).
• Sulfate-reducing bacteria can be traced back to 3.5 billion years ago and are considered to be among the oldest forms of microorganisms, having contributed to the sulfur cycle soon after life emerged on Earth.
• Toxic hydrogen sulfide is one waste product of sulfate-reducing bactera, and is the source of the rotten egg odor.
• Sulfate-reducing bacteria may be utilized for cleaning up contaminated soils.
Key Terms
• lithotrophic: Obtains electrons for respiration from inorganic substrates.
• organotrophic: Obtains electrons for respiration from organic substrates.
Sulfate reduction is a type of anaerobic respiration that utilizes sulfate as a terminal electron acceptor in the electron transport chain. Compared to aerobic respiration, sulfate reduction is a relatively energetically poor process, though it is a vital mechanism for bacteria and archaea living in oxygen-depleted, sulfate-rich environments.
Many sulfate reducers are organotrophic, using carbon compounds, such as lactate and pyruvate (among many others) as electron donors, while others are lithotrophic, and use hydrogen gas (H2) as an electron donor. Some unusual autotrophic sulfate-reducing bacteria (e.g., Desulfotignum phosphitoxidans) can use phosphite (HPO3-) as an electron donor, whereas others (e.g., Desulfovibrio sulfodismutans, Desulfocapsa thiozymogenes, and Desulfocapsa sulfoexigens) are capable of sulfur disproportionation (splitting one compound into two different compounds, in this case an electron donor and an electron acceptor) using elemental sulfur (S0), sulfite (SO32−), and thiosulfate (S2O32−) to produce both hydrogen sulfide (H2S) and sulfate (SO42−).
Before sulfate can be used as an electron acceptor, it must be activated. This is done by the enzyme ATP-sulfurylase, which uses ATP and sulfate to create adenosine 5′-phosphosulfate (APS). APS is subsequently reduced to sulfite and AMP. Sulfite is then further reduced to sulfide, while AMP is turned into ADP using another molecule of ATP. The overall process, thus, involves an investment of two molecules of the energy carrier ATP, which must to be regained from the reduction.
All sulfate-reducing organisms are strict anaerobes. Because sulfate is energetically stable, it must be activated by adenylation to form APS (adenosine 5′-phosphosulfate) to form APS before it can be metabolized, thereby consuming ATP. The APS is then reduced by the enzyme APS reductase to form sulfite (SO32−) and AMP. In organisms that use carbon compounds as electron donors, the ATP consumed is accounted for by fermentation of the carbon substrate. The hydrogen produced during fermentation is actually what drives respiration during sulfate reduction.
Sulfate-reducing bacteria can be traced back to 3.5 billion years ago and are considered to be among the oldest forms of microorganisms, having contributed to the sulfur cycle soon after life emerged on Earth. Sulfate-reducing bacteria are common in anaerobic environments (such as seawater, sediment, and water rich in decaying organic material) where they aid in the degradation of organic materials. In these anaerobic environments, fermenting bacteria extract energy from large organic molecules; the resulting smaller compounds (such as organic acids and alcohols) are further oxidized by acetogens, methanogens, and the competing sulfate-reducing bacteria.
Many bacteria reduce small amounts of sulfates in order to synthesize sulfur-containing cell components; this is known as assimilatory sulfate reduction. By contrast, sulfate-reducing bacteria reduce sulfate in large amounts to obtain energy and expel the resulting sulfide as waste; this is known as “dissimilatory sulfate reduction. ” Most sulfate-reducing bacteria can also reduce other oxidized inorganic sulfur compounds, such as sulfite, thiosulfate, or elemental sulfur (which is reduced to sulfide as hydrogen sulfide).
Toxic hydrogen sulfide is one waste product of sulfate-reducing bacteria; its rotten egg odor is often a marker for the presence of sulfate-reducing bacteria in nature. Sulfate-reducing bacteria are responsible for the sulfurous odors of salt marshes and mud flats. Much of the hydrogen sulfide will react with metal ions in the water to produce metal sulfides. These metal sulfides, such as ferrous sulfide (FeS), are insoluble and often black or brown, leading to the dark color of sludge. Thus, the black color of sludge on a pond is due to metal sulfides that result from the action of sulfate-reducing bacteria.
Some sulfate-reducing bacteria play a role in the anaerobic oxidation of methane (CH4+ SO42- → HCO3– + HS– + H2O). An important fraction of the methane formed by methanogens below the seabed is oxidized by sulfate-reducing bacteria in the transition zone separating the methanogenesis from the sulfate reduction activity in the sediments.This process is also considered a major sink for sulfate in marine sediments. In hydrofracturing fluids used to frack shale formations to recover methane (shale gas), biocide compounds are often added to water to inhibit the microbial activity of sulfate-reducing bacteria in order to avoid anaerobic methane oxidation and to minimize potential production loss.
Sulfate-reducing bacteria often create problems when metal structures are exposed to sulfate-containing water. The interaction of water and metal creates a layer of molecular hydrogen on the metal surface. Sulfate-reducing bacteria oxidize this hydrogen, creating hydrogen sulfide, which contributes to corrosion. Hydrogen sulfide from sulfate-reducing bacteria also plays a role in the biogenic sulfide corrosion of concrete, and sours crude oil.
Sulfate-reducing bacteria may be utilized for cleaning up contaminated soils; some species are able to reduce hydrocarbons, such as benzene, toluene, ethylbenzene, and xylene. Sulfate-reducing bacteria may also be a way to deal with acid mine waters. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.09%3A_Anaerobic_Respiration/5.9C%3A_Sulfate_and_Sulfur_Reduction.txt |
Methanogenesis is a form of anaerobic respiration that uses carbon as a electron acceptor and results in the production of methane.
Learning Objectives
• Recognize the characteristics associated with methanogenesis
Key Points
• Carbon dioxide or acetic acid are the most commonly used electron acceptor in methanogenesis.
• Microbes capable of producing methane are called methanogens. They have been identified only from the domain Archaea – a group that is phylogenetically distinct from eukaryotes and bacteria.
• The production of methane is an important and widespread form of microbial metabolism. In most environments, it is the final step in the decomposition of biomass.
• Methane is a major greenhouse gas. The average cow emits around 250 liters of methane a day as a result of the breakdown of cellulose by methanogens. Therefore, the large scale raising of cattle for meat is a considerable contributor to global warming.
Key Terms
• methanethiol: A colourless gas, a thiol with a smell like rotten cabbage, found naturally in plants and animals.
• cofactor: A substance, especially a coenzyme or a metal, that must be present for an enzyme to function.
• fermentation: Any of many anaerobic biochemical reactions in which an enzyme (or several enzymes produced by a microorganism) catalyses the conversion of one substance into another; especially the conversion (using yeast) of sugars to alcohol or acetic acid with the evolution of carbon dioxide.
Methanogenesis, or biomethanation, is a form of anaerobic respiration that uses carbon as the terminal electron acceptor, resulting in the production of methane. The carbon is sourced from a small number of low molecular weight organic compounds, such as carbon dioxide, acetic acid, formic acid (formate), methanol, methylamines, dimethyl sulfide, and methanethiol. The two best described pathways of methanogenesis use carbon dioxide or acetic acid as the terminal electron acceptor:
CO2 + 4 H2 → CH4 + 2H2O
CH3COOH → CH4+ CO2
The biochemistry of methanogenesis is relatively complex. It involves the coenzymes and cofactors F420, coenzyme B, coenzyme M, methanofuran, and methanopterin.
Microbes capable of producing methane are called methanogens. They have been identified only from the domain Archaea – a group that is phylogenetically distinct from eukaryotes and bacteria – though many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism, and in most environments, it is the final step in the decomposition of biomass.
During the decay process, electron acceptors (such as oxygen, ferric iron, sulfate, and nitrate) become depleted, while hydrogen (H2), carbon dioxide, and light organics produced by fermentation accumulate. During advanced stages of organic decay, all electron acceptors become depleted except carbon dioxide, which is a product of most catabolic processes. It is not depleted like other potential electron acceptors.
Only methanogenesis and fermentation can occur in the absence of electron acceptors other than carbon. Fermentation only allows the breakdown of larger organic compounds, and produces small organic compounds. Methanogenesis effectively removes the semi-final products of decay: hydrogen, small organics, and carbon dioxide. Without methanogenesis, a great deal of carbon (in the form of fermentation products) would accumulate in anaerobic environments.
Methanogenesis also occurs in the guts of humans and other animals, especially ruminants. In the rumen, anaerobic organisms, including methanogens, digest cellulose into forms usable by the animal. Without these microorganisms, animals such as cattle would not be able to consume grass. The useful products of methanogenesis are absorbed by the gut. Methane is released from the animal mainly by belching (eructation). The average cow emits around 250 liters of methane per day. Some, but not all, humans emit methane in their flatus!
Some experiments even suggest that leaf tissues of living plants emit methane, although other research indicates that the plants themselves do not actually generate methane; they are just absorbing methane from the soil and then emitting it through their leaf tissues. There may still be some unknown mechanism by which plants produce methane, but that is by no means certain.
Methane is one of the earth’s most important greenhouse gases, with a global warming potential 25 times greater than carbon dioxide (averaged over 100 years). Therefore, the methane produced by methanogenesis in livestock is a considerable contributor to global warming.
Methanogenesis can also be beneficially exploited. It is the primary pathway that breaks down organic matter in landfills (which can release large volumes of methane into the atmosphere if left uncontrolled), and can be used to treat organic waste and to produce useful compounds. Biogenic methane can be collected and used as a sustainable alternative to fossil fuels. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.09%3A_Anaerobic_Respiration/5.9D%3A_Methanogenesis.txt |
Anaerobic respiration utilizes highly reduced species – such as a proton gradient – to establish electrochemical membrane gradients.
Learning Objectives
• Outline the role of the proton motive force in metabolism
Key Points
• In denitrification, protons are transported across the membrane by the initial NADH reductase, quinones, and nitrous oxide reductase to produce the electrochemical gradient critical for respiration.
• An electrochemical gradient represents one of the many interchangeable forms of potential energy through which energy may be conserved. In biological processes, the direction an ion moves by diffusion or active transport across a membrane is determined by the electrochemical gradient.
• In mitochondria and chloroplasts, proton gradients are used to generate a chemiosmotic potential that is also known as a proton motive force.
Key Terms
• phosphorylation: The process of transferring a phosphate group from a donor to an acceptor; often catalysed by enzymes
Proton Gradients in Reductive Metabolism
Biological energy is frequently stored and released by means of redox reactions, or the transfer of electrons. Reduction occurs when an oxidant gains an electron. Photosynthesis involves the reduction of carbon dioxide into sugars and the oxidation of water into molecular oxygen. The reverse reaction, respiration, oxidizes sugars (loses an electron) to produce carbon dioxide and water. As intermediate steps, the reduced carbon compounds are used to reduce nicotinamide adenine dinucleotide (NAD+), which then contributes to the creation of a proton gradient. This then drives the synthesis of adenosine triphosphate ( ATP ) and is maintained by the reduction of oxygen, or alternative receptors for anaerobic respiration. In animal cells, the mitochondria performs similar functions.
An electrochemical gradient represents one of the many interchangeable forms of potential energy through which energy may be conserved. In biological processes, the direction an ion moves by diffusion or active transport across a membrane is determined by the electrochemical gradient. In the mitochondria and chloroplasts, proton gradients are used to generate a chemiosmotic potential that is also known as a proton motive force. This potential energy is used for the synthesis of ATP by phosphorylation. An electrochemical gradient has two components. First, the electrical component is caused by a charge difference across the lipid membrane. Second, a chemical component is caused by a differential concentration of ions across the membrane. The combination of these two factors determines the thermodynamically favorable direction for an ion’s movement across a membrane. The electrochemical potential difference between the two sides of the membrane in mitochondria, chloroplasts, bacteria, and other membranous compartments that engage in active transport involving proton pumps, is at times called a chemiosmotic potential or proton motive force.
In respiring bacteria under physiological conditions, ATP synthase, in general, runs in the opposite direction, creating ATP while using the proton motive force created by the electron transport chain as a source of energy. The overall process of creating energy in this fashion is termed oxidative phosphorylation. The same process takes place in the mitochondria, where ATP synthase is located in the inner mitochondrial membrane, so that F1 part sticks into the mitochondrial matrix where ATP synthesis takes place.
Cellular respiration (both aerobic and anaerobic) utilizes highly reduced species such as NADH and FADH2 to establish an electrochemical gradient (often a proton gradient) across a membrane, resulting in an electrical potential or ion concentration difference across the membrane. The reduced species are oxidized by a series of respiratory integral membrane proteins with sequentially increasing reduction potentials, the final electron acceptor being oxygen (in aerobic respiration) or another species (in anaerobic respiration). The membrane in question is the inner mitochondrial membrane in eukaryotes and the cell membrane in prokaryotes. A proton motive force or pmf drives protons down the gradient (across the membrane) through the proton channel of ATP synthase. The resulting current drives ATP synthesis from ADP and inorganic phosphate.
Proton reduction is important for setting up electrochemical gradients for anaerobic respiration. For example, in denitrification, protons are transported across the membrane by the initial NADH reductase, quinones, and nitrous oxide reductase to produce the electrochemical gradient critical for respiration. In organisms that use hydrogen as an energy source, hydrogen is oxidized by a membrane-bound hydrogenase causing proton pumping via electron transfer to various quinones and cytochromes. Sulfur oxidation is a two step process that occurs because energetically sulfide is a better electron donor than inorganic sulfur or thiosulfate, allowing for a greater number of protons to be translocated across the membrane.
In contrast, fermentation does not utilize an electrochemical gradient. Instead, it only uses substrate-level phosphorylation to produce ATP. The electron acceptor NAD+ is regenerated from NADH formed in oxidative steps of the fermentation pathway by the reduction of oxidized compounds. These oxidized compounds are often formed during the fermentation pathway itself, but may also be external. For example, in homofermentative lactic acid bacteria, NADH formed during the oxidation of glyceraldehyde-3-phosphate is oxidized back to NAD+ by the reduction of pyruvate to lactic acid at a later stage in the pathway. In yeast, acetaldehyde is reduced to ethanol.
5.9F: Anoxic Hydrocarbon Oxidation
Anoxic hydrocarbon oxidation can be used to degrade toxic hydrocarbons, such as crude oil, in anaerobic environments.
Learning Objectives
• Describe the process of anoxic hydrocarbon oxidation in regards to marine environments
Key Points
• Hydrocarbons are organic compounds consisting entirely of hydrogen and carbon.
• The majority of hydrocarbons occur naturally in crude oil, where decomposed organic matter provides an abundance of carbon and hydrogen. The combustion of hydrocarbons is the primary energy source for current civilizations.
• Anaerobic oxidation of methane (AOM) is a microbial process that occurs in anoxic marine sediments. AOM is considered to be a very important process, reducing the emission of methane (a greenhouse gas) from the ocean into the atmosphere by up to 90%.
Key Terms
• methanotrophic: The ability to metabolize methane as an only source of carbon and energy.
• syntrophic: When one species lives off the products of another species.
• anoxic: Lacking oxygen.
Hydrocarbons are organic compounds consisting entirely of hydrogen and carbon. The majority of hydrocarbons occur naturally in crude oil, where decomposed organic matter provides an abundance of carbon and hydrogen. The combustion of hydrocarbons is the primary energy source for current civilizations.
Crude oil contains aromatic compounds that are toxic to most forms of life. Their release into the environment by human spills and natural seepages can have detrimental effects. Marine environments are especially vulnerable. Despite its toxicity, a considerable fraction of crude oil entering marine systems is eliminated by the hydrocarbon-degrading activities of microbial communities. Although it was once thought that hydrocarbon compounds could only be degraded in the presence of oxygen, the discovery of anaerobic hydrocarbon-degrading bacteria and pathways show that the anaerobic degradation of hydrocarbons occurs naturally.
The facultative denitrifying proteobacteria Aromatoleum aromaticum strain EbN1 was the first to be determined as an anaerobic hydrocarbon degrader, using toluene or ethylbenzene as substrates. Some sulfate-reducing bacteria can reduce hydrocarbons such as benzene, toluene, ethylbenzene, and xylene, and have been used to clean up contaminated soils. The genome of the iron-reducing and hydrocarbon degrading species Geobacter metallireducens was recently determined.
Anaerobic oxidation of methane (AOM) is a microbial process that occurs in anoxic marine sediments. During this process, the hydrocarbon methane is oxidized with sulfate as the terminal electron acceptor: CH4 + SO42- → HCO3- + HS + H2O. It is believed that AOM is mediated by a syntrophic aggregation of methanotrophic archaea and sulfate-reducing bacteria, although the exact mechanisms of this syntrophic relationship are still poorly understood. AOM is considered to be a very important process in reducing the emission of methane (a greenhouse gas) from the ocean into the atmosphere. It is estimated that almost 90% of all the methane that arises from marine sediments is oxidized anaerobically by this process. Recent investigations have shown that some syntrophic pairings are able to oxidize methane with nitrate instead of sulfate.
LICENSES AND ATTRIBUTIONS
CC LICENSED CONTENT, SPECIFIC ATTRIBUTION | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.09%3A_Anaerobic_Respiration/5.9E%3A_Proton_Reduction.txt |
Learning Objectives
• Outline the characteristics associated with chemolithotrophs
A lithotroph is an organism that uses an inorganic substrate (usually of mineral origin) to obtain reducing equivalents for use in biosynthesis (e.g., carbon dioxide fixation) or energy conservation via aerobic or anaerobic respiration. Known chemolithotrophs are exclusively microbes; no known macrofauna possesses the ability to utilize inorganic compounds as energy sources. Macrofauna and lithotrophs can form symbiotic relationships, in which case the lithotrophs are called “prokaryotic symbionts”. An example of this is chemolithotrophic bacteria in deep sea worms or plastids, which are organelles within plant cells that may have evolved from photolithotrophic cyanobacteria-like organisms.
Chemotrophs are organisms that obtain energy through the oxidation of electron donors in their environments. These molecules can be organic (chemoorganotrophs) or inorganic (chemolithotrophs). The chemotroph designation is in contrast to phototrophs, which utilize solar energy. Chemotrophs can be either autotrophic or heterotrophic. Chemoautotrophs generally fall into several groups: methanogens, halophiles, sulfur oxidizers and reducers, nitrifiers, anammox bacteria, and thermoacidophiles. Chemolithotrophic growth could be dramatically fast, such as Thiomicrospira crunogena with a doubling time around one hour.
In chemolithotrophs, the compounds – the electron donors – are oxidized in the cell, and the electrons are channeled into respiratory chains, ultimately producing ATP. The electron acceptor can be oxygen (in aerobic bacteria), but a variety of other electron acceptors, organic and inorganic, are also used by various species. Unlike water, the hydrogen compounds used in chemosynthesis are high in energy. Other lithotrophs are able to directly utilize inorganic substances, e.g., iron, hydrogen sulfide, elemental sulfur, or thiosulfate, for some or all of their energy needs.
Key Points
• Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environments. These molecules can be organic (chemoorganotrophs) or inorganic ( chemolithotrophs ).
• In chemolithotrophs, the compounds – the electron donors – are oxidized in the cell, and the electrons are channeled into respiratory chains, ultimately producing ATP.
• The electron acceptor can be oxygen (in aerobic bacteria ), but a variety of other electron acceptors, organic and inorganic, are also used by various species.
Key Terms
• chemolithotroph: chemoautotroph
• symbiont: An organism that lives in a symbiotic relationship; a symbiote.
• chemotroph: an organism that obtains energy by the oxidation of electron-donating molecules in the environment
• lithotroph: An organism that obtains its energy from inorganic compounds (such as ammonia) via electron transfer.
5.10B: Hydrogen Oxidation
Learning Objectives
• Discuss the process of hydrogen oxidation in organisms that use hydrogen aerobically
Chemolithotrophy is a type of metabolism where energy is obtained from the oxidation of inorganic compounds. Most chemolithotrophic organisms are also autotrophic. There are two major objectives to chemolithotrophy: the generation of energy (via ATP) and the generation of reducing power (via NADH). Hydrogen oxidizing bacteria (sometimes called Knallgas-bacteria) are bacteria that oxidize hydrogen. These bacteria include Hydrogenobacter thermophilus, Hydrogenovibrio marinus, and Helicobacter pylori. There are both Gram positive and Gram negative knallgas bacteria.
Most grow best under microaerophilic conditions. They do this because the hydrogenase enzyme used in hydrogen oxidation is inhibited by the presence of oxygen, but oxygen is still needed as a terminal electron acceptor.
Many organisms are capable of using hydrogen (H2) as a source of energy. While there are several mechanisms of anaerobic hydrogen oxidation (e.g. sulfate reducing- and acetogenic bacteria), hydrogen can also be used as an energy source aerobically. In these organisms, hydrogen is oxidized by a membrane-bound hydrogenase causing proton pumping via electron transfer to various quinones and cytochromes. In many organisms, a second cytoplasmic hydrogenase is used to generate reducing power in the form of NADH, which is subsequently used to fix carbon dioxide via the Calvin cycle. Hydrogen-oxidizing organisms, such as Cupriavidus necator (formerly Ralstonia eutropha), often inhabit oxic-anoxic interfaces in nature to take advantage of the hydrogen produced by anaerobic fermentative organisms while still maintaining a supply of oxygen.
Helicobacter pylori (H. pylori), previously named Campylobacter pyloridis, is a Gram-negative, microaerophilic bacterium found in the stomach. It was identified in 1982 by Barry Marshall and Robin Warren. They found that it was present in patients with chronic gastritis and gastric ulcers, conditions that were not previously believed to have a microbial cause. It is also linked to the development of duodenal ulcers and stomach cancer. However, over 80 percent of individuals infected with the bacterium are asymptomatic. It has been postulated that it may play an important role in the natural stomach ecology. More than 50% of the world’s population harbor H. pylori in their upper gastrointestinal tract. Infection is more prevalent in developing countries and incidence is decreasing in Western countries. H. pylori’s helix shape (from which the generic name is derived) is thought to have evolved to penetrate the mucoid lining of the stomach.
Key Points
• In some organisms, hydrogen is oxidized by a membrane-bound hydrogenase causing proton pumping via electron transfer to various quinones and cytochromes.
• Hydrogen-oxidizing organisms, such as Cupriavidus necator (formerly Ralstonia eutropha), often inhabit oxic-anoxic interfaces in nature to take advantage of the hydrogen produced by anaerobic fermentative organisms while still maintaining a supply of oxygen.
• Helicobacter pylori is a Gram-negative, microaerophilic bacterium found in the stomach. It has been postulated that it may play an important role in the natural stomach ecology.
Key Terms
• Knallgas-bacteria: Bacteria which oxidize hydrogen.
• calvin cycle: A series of biochemical reactions that take place in the stroma of chloroplasts in photosynthetic organisms. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.10%3A_Chemolithotrophy/5.10A%3A_The_Energetics_of_Chemolithotrophy.txt |
Sulfur oxidation involves the oxidation of reduced sulfur compounds, inorganic sulfur, and thiosulfate to form sulfuric acid.
Learning Objectives
• Describe the process of sulfur oxidation
Key Points
• The oxidation of sulfide occurs in stages, with inorganic sulfur being stored either inside or outside of the cell until needed.
• This two step process occurs because sulfide is a better electron donor than inorganic sulfur or thiosulfate; this allows a greater number of protons to be translocated across the membrane.
• Sulfur-oxidizing organisms generate reducing power for carbon dioxide fixation via the Calvin cycle using reverse electron flow—an energy-requiring process that pushes the electrons against their thermodynamic gradient to produce NADH.
Key Terms
• calvin cycle: A series of biochemical reactions that take place in the stroma of chloroplasts in photosynthetic organisms.
• thiosulfate: Any salt or ester of thiosulfuric acid.
• chemolithoautotrophic: The characteristic of a microorganism that obtains energy from the oxidation of inorganic compounds and carbon from the fixation of carbon dioxide.
Sulfur is an essential element for all life, and it is widely used in biochemical processes. In metabolic reactions, sulfur compounds serve as both fuels and respiratory (oxygen-alternative) materials for simple organisms. Sulfur is an important part of many enzymes and antioxidant molecules such as glutathione and thioredoxin.
Sulfur Oxidation
Sulfur oxidation involves the oxidation of reduced sulfur compounds such as sulfide (H2S), inorganic sulfur (S0), and thiosulfate (S2O2−3) to form sulfuric acid (H2SO4). An example of a sulfur-oxidizing bacterium is Paracoccus.
Generally, the oxidation of sulfide occurs in stages, with inorganic sulfur being stored either inside or outside of the cell until needed. The two step process occurs because sulfide is a better electron donor than inorganic sulfur or thiosulfate; this allows a greater number of protons to be translocated across the membrane. Sulfur-oxidizing organisms generate reducing power for carbon dioxide fixation via the Calvin cycle using reverse electron flow—an energy-requiring process that pushes the electrons against their thermodynamic gradient to produce NADH. Biochemically, reduced sulfur compounds are converted to sulfite (SO2−3) and, subsequently, sulfate (SO2−4) by the enzyme sulfite oxidase. Some organisms, however, accomplish the same oxidation using a reversal of the APS reductase system used by sulfate-reducing bacteria (see above). In all cases the energy liberated is transferred to the electron transport chain for ATP and NADH production. In addition to aerobic sulfur oxidation, some organisms (e.g. Thiobacillus denitrificans) use nitrate (NO−3) as a terminal electron acceptor and therefore grow anaerobically.
Beggiatoa
A classic example of a sulfur-oxidizing bacterium is Beggiatoa, a microbe originally described by Sergei Winogradsky, one of the founders of environmental microbiology. Beggiatoa can be found in marine or freshwater environments. They can usually be found in habitats that have high levels of hydrogen sulfide. These environments include cold seeps, sulfur springs, sewage contaminated water, mud layers of lakes, and near deep hydrothermal vents. Beggiatoa can also be found in the rhizosphere of swamp plants. During his research in Anton de Bary’s laboratory of botany in 1887, Russian botanist Winogradsky found that Beggiatoa oxidized hydrogen sulfide (H2S) as an energy source, forming intracellular sulfur droplets. Winogradsky referred to this form of metabolism as inorgoxidation (oxidation of inorganic compounds). The finding represented the first discovery of lithotrophy.
Beggiatoa can grow chemoorgano-heterotrophically by oxidizing organic compounds to carbon dioxide in the presence of oxygen, though high concentrations of oxygen can be a limiting factor. Organic compounds are also the carbon source for biosynthesis. Some species may oxidize hydrogen sulfide to elemental sulfur as a supplemental source of energy (facultatively litho-heterotroph). This sulfur is stored intracellularly. Some species have the ability of chemolithoautotrophic growth, using sulfide oxidation for energy and carbon dioxide as a source of carbon for biosynthesis. In this metabolic process, internal stored nitrate is the electron acceptor and reduced to ammonia.
Sulfide oxidation: 2H2S + O2 → 2S + 2H2O
Marine autotrophic Beggiatoa species are able to oxidize intracellular sulfur to sulfate. The reduction of elemental sulfur frequently occurs when oxygen is lacking. Sulfur is reduced to sulfide at the cost of stored carbon or by added hydrogen gas. This may be a survival strategy to bridge periods without oxygen | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.10%3A_Chemolithotrophy/5.10C%3A_Oxidation_of_Reduced_Sulfur_Compounds.txt |
Learning Objectives
• Outline the purpose of iron oxidation and the three types of ferrous iron-oxidizing microbes (acidophiles, microaerophiles and anaerobic photosynthetic bacteria)
Ferric iron (Fe3+) is a widespread anaerobic terminal electron acceptor both for autotrophic and heterotrophic organisms. Electron flow in these organisms is similar to those in electron transport, ending in oxygen or nitrate, except that in ferric iron-reducing organisms the final enzyme in this system is a ferric iron reductase. Model organisms include Shewanella putrefaciens and Geobacter metallireducens. Since some ferric iron-reducing bacteria (e.g. G. metallireducens) can use toxic hydrocarbons such as toluene as a carbon source, there is significant interest in using these organisms as bioremediation agents in ferric iron-rich contaminated aquifers.
Ferrous iron is a soluble form of iron that is stable at extremely low pHs or under anaerobic conditions. Under aerobic, moderate pH conditions ferrous iron is oxidized spontaneously to the ferric (Fe3+) form and is hydrolyzed abiotically to insoluble ferric hydroxide (Fe(OH)3). There are three distinct types of ferrous iron-oxidizing microbes. The first are acidophiles, such as the bacteria Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, as well as the archaeon Ferroplasma. These microbes oxidize iron in environments that have a very low pH and are important in acid mine drainage. The second type of microbes oxidizes ferrous iron at cirum-neutral pH. These micro-organisms (for example Gallionella ferruginea or Leptothrix ochracea) live at the oxic-anoxic interfaces and are microaerophiles. The third type of iron-oxidizing microbes is anaerobic photosynthetic bacteria such as Rhodopseudomonas, which use ferrous iron to produce NADH for autotrophic carbon dioxide fixation. Biochemically, aerobic iron oxidation is a very energetically poor process which therefore requires large amounts of iron to be oxidized by the enzyme rusticyanin to facilitate the formation of proton motive force. Like sulfur oxidation, reverse electron flow must be used to form the NADH used for carbon dioxide fixation via the Calvin cycle.
Although ferric iron is the most prevalent inorganic electron acceptor, a number of organisms (including the iron-reducing bacteria mentioned above) can use other inorganic ions in anaerobic respiration. While these processes may often be less significant ecologically, they are of considerable interest for bioremediation, especially when heavy metals or radionuclides are used as electron acceptors. Examples include:
• Manganic ion (Mn4+) reduction to manganous ion]] (Mn2+)
• Selenate (SeO2−4) reduction to selenite (SeO2−3) and selenite reduction to inorganic selenium (Se0)
• Arsenate (AsO3−4) reduction to arsenite (AsO3−3)
• Uranyl ion ion (UO2+2) reduction to uranium dioxide (UO2)
Key Points
• Ferrous iron is a soluble form of iron that is stable at extremely low pHs or under anaerobic conditions. Under aerobic, moderate pH conditions ferrous iron is oxidized spontaneously to the ferric (Fe3+) form and is hydrolyzed abiotically to insoluble ferric hydroxide (Fe(OH)3).
• Three distinct types of ferrous iron-oxidizing microbes: acidophiles, microaerophiles that oxidize ferrous iron at cirum-neutral pH, anaerobic photosynthetic bacteria which use ferrous iron to produce NADH for autotrophic carbon dioxide fixation.
• Although ferric iron is the most prevalent inorganic electron acceptor, a number of organisms can use other inorganic ions in anaerobic respiration.
Key Terms
• autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.
• heterotroph: An organism that requires an external supply of energy in the form of food as it cannot synthesize its own. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.10%3A_Chemolithotrophy/5.10D%3A__Iron_Oxidation.txt |
Learning Objectives
• Describe the process of nitrification and its importance
Nitrification is the process by which ammonia (NH3) or ammonium (NH4+) is converted to nitrate (NO3). Nitrification is the net result of two distinct processes: oxidation of ammonium to nitrite (NO2) by nitrosifying or ammonia-oxidizing bacteria and oxidation of nitrite (NO2) to nitrate (NO3) by the nitrite-oxidizing bacteria. Nitrification is an important step in the nitrogen cycle in soil. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.
Chemistry of Nitrogen Compound Oxidation
Nitrification is a process of nitrogen compound oxidation (effectively, loss of electrons from the nitrogen atom to the oxygen atoms):
1. 2 NH4+ + 3 O2 → 2 NO2 + 2 H2O + 4 H+ (Nitrosomonas)
2. 2 NO2 + O2 → 2 NO3 (Nitrobacter, Nitrospina)
3. NH3 + O2 → NO2 + 3H+ + 2e
4. NO2 + H2O → NO3 + 2H+ + 2e
Both of these processes are extremely energetically poor, which leads to very slow growth rates for both types of organisms.
Ammonium Oxidation
The transformation of ammonia to nitrite is usually the rate limiting step of nitrification. Biochemically, ammonium oxidation occurs by the stepwise oxidation of ammonium to hydroxylamine (NH2OH) by the enzyme ammonium monooxygenase in the cytoplasm, followed by the oxidation of hydroxylamine to nitrite by the enzyme hydroxylamine oxidoreductase in the periplasm. Electron and proton cycling are very complex, but as a net result only one proton is translocated across the membrane per molecule of ammonium oxidized.
Nitrite Reduction
Nitrite reduction is much simpler, with nitrite being oxidized by the enzyme nitrite oxidoreductase coupled to proton translocation by a very short electron transport chain, again leading to very low growth rates for these organisms. Oxygen is required in ammonium and nitrite oxidation, meaning that both nitrosifying and nitrite-oxidizing bacteria are aerobes. As in sulfur and iron oxidation, NADH for carbon dioxide fixation using the Calvin cycle is generated by reverse electron flow, thereby placing a further metabolic burden on an already energy-poor process.
Human Applications of Nitrification
Nitrification is important in agricultural systems, where fertilizer is often applied as ammonia. Nitrification also plays an important role in the removal of nitrogen from municipal wastewater. The conventional removal is nitrification, followed by denitrification.
Key Points
• Nitrification is actually the net result of two distinct processes: the oxidation of ammonia (NH3) or ammonium (NH4+) to nitrite (NO2) by ammonia-oxidizing bacteria (e.g. Nitrosomonas) and the oxidation of nitrite (NO2) to nitrate (NO3) by the nitrite-oxidizing bacteria (e.g. Nitrobacter).
• Nitrification is extremely energetically poor leading to very slow growth rates for both types of organisms.
• Oxygen is required in ammonium and nitrite oxidation; ammonia-oxidizing and nitrite-oxidizing bacteria are aerobes.
Key Terms
• chemolithotrophy: A type of metabolism where energy is obtained from the oxidation of inorganic compounds.
• nitrification: The biological oxidation of ammonia or ammonium with oxygen into nitrite followed by the oxidation of these nitrites into nitrates.
5.10F: Anammox
Anammox, an abbreviation for ANaerobic AMMonium OXidation, is a globally significant microbial process of the nitrogen cycle.
Learning Objectives
• Describe the overall process of ANaerobic AMMonium OXidation (Anammox) and its purpose
Key Points
• The bacteria mediating this process were identified in 1999, and at the time were a great surprise for the scientific community.
• This form of metabolism occurs in members of the Planctomycetes (e.g. Candidatus Brocadia anammoxidans) and involves the coupling of ammonia oxidation to nitrite reduction.
• To deal with the high toxicity of hydrazine, anammox bacteria contain a hydrazine-containing intracellular organelle called the anammoxasome, surrounded by highly compact ladderane lipid membrane. These lipids are unique in nature, as is the use of hydrazine as a metabolic intermediate.
Key Terms
• Anammox: An abbreviation for ANaerobic AMMonium OXidation, a globally significant microbial process of the nitrogen cycle.
• anaerobes: Organisms that do not require oxygen for growth.
• ladderane: Any of a class of polycyclic hydrocarbons, consisting of repeating cyclobutane moieties, that resemble ladders
Anammox, an abbreviation for ANaerobic AMMonium OXidation, is a globally significant microbial process of the nitrogen cycle. The bacteria mediating this process were identified in 1999, and at the time were a great surprise to the scientific community. Anammox takes place in many natural environments, contributing up to 50% of the dinitrogen gas produced in the oceans. In this biological process, nitrite and ammonium are converted directly into dinitrogen gas. The overall catabolic reaction is:
NH4+ + NO2 → N2 + 2H2O.
This form of metabolism involves the coupling of ammonia oxidation to nitrite reduction. Since oxygen is not required for the process, these organisms are strict anaerobes. Amazingly, hydrazine (N2H4 — rocket fuel) is produced as an intermediate during anammox metabolism. To deal with the high toxicity of hydrazine, anammox bacteria have a hydrazine-containing intracellular organelle called the anammoxasome (a compartment inside the cytoplasm which is the locus of anammox catabolism), which is surrounded by an unusual and highly compact ladderane lipid membrane. Further, the membranes of these bacteria mainly consist of ladderane lipids so far unique in biology. Of special interest is the conversion to hydrazine (normally used as a high-energy rocket fuel, and poisonous to most living organisms) as an intermediate. A final striking feature of the organism is the extremely slow growth rate. The doubling time is nearly two weeks. The anammox process was originally found to occur only from 20°C to 43°C but more recently, anammox has been observed at temperatures from 36°C to 52°C in hot springs and 60°C to 85°C at hydrothermal vents located along the Mid-Atlantic Ridge.
Anammox organisms are autotrophs although the mechanism for carbon dioxide fixation is still unclear. Because of this property, these organisms could be used industrially to remove nitrogen in wastewater treatment processes. The bacteria that perform the anammox process belong to the bacterial phylum Planctomycetes (e.g. Candidatus Brocadia anammoxidans), of which Planctomyces and Pirellula are the best known genera. Currently five genera of anammox bacteria have been (provisionally) defined: Brocadia, Kuenenia, Anammoxoglobus, Jettenia (all fresh water species), and Scalindua (marine species). | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.10%3A_Chemolithotrophy/5.10E%3A_Nitrification.txt |
Rhodobacter sphaeroides is able to produce hydrogen from a wide range of organic compounds (chiefly organic acids) and light.
Learning Objectives
• List a function of Rhodococcus in the scientific community
Key Points
• In the absence of water-splitting, photosynthesis is anoxygenic. Therefore, hydrogen production is sustained without inhibition from generated oxygen.
• Strains of Rhodococcus are applicably important owing to their ability to catabolize a wide range of compounds and produce bioactive steroids, acrylamide, and acrylic acid, and their involvement in fossil fuel biodesulfurization.
• The use of Rhodococcus is borne out of its ability to metabolize harmful environmental pollutants, such as toluene, naphthalene, herbicides, and PCBs.
Key Terms
• catabolism: Destructive metabolism, usually includes the release of energy and breakdown of materials.
• Rhodococcus: a genus of aerobic, nonsporulating, nonmotile Gram-positive bacteria closely related to Mycobacteria and Corynebacteria.
• benzoate: Any salt or ester of benzoic acid.
Benzoate catabolism is a series of chemical reactions resulting in the breakdown of benzoate. The purple non-sulphur (PNS) bacteria Rhodobacter sphaeroides is able to produce hydrogen from a wide range of organic compounds (chiefly organic acids) and light. The photo-system required for hydrogen production in Rhodobacter (PS-I) differ from its oxygenic photosystem (PS-II) due to the requirement of organic acids and the inability to oxidize water. In the absence of water-splitting, photosynthesis is anoxygenic. Therefore, hydrogen production is sustained without inhibition from generated oxygen. In PNS bacteria, hydrogen production is due to catalysis by nitrogenase. Hydrogenases are also present but the production of hydrogen by [FeFe]-hydrogenase is less than ten times the hydrogen uptake by [NiFe]-hydrogenase. Only under nitrogen-deficient conditions is nitrogenase activity sufficient to overcome uptake hydrogenase activity, resulting in net generation of hydrogen.
Rhodococcus is a genus of aerobic, nonsporulating, nonmotile Gram-positive bacteria closely related to Mycobacteria and Corynebacteria. While a few species are pathogenic, most are benign and have been found to thrive in a broad range of environments, including soil, water, and eukaryotic cells. Fully sequenced in October 2006, the genome is known to be 9.7 megabasepairs long and 67% G/C. Strains of Rhodococcus are applicably important owing to their ability to catabolize a wide range of compounds and produce bioactive steroids, acrylamide, and acrylic acid, and their involvement in fossil fuel biodesulfurization. This genetic and catabolic diversity is not only due to the large bacterial chromosome, but also to the presence of three large linear plasmids. Rhodococcus is also an experimentally advantageous system owing to a relatively fast growth rate and simple developmental cycle. However, as it stands now, Rhodococcus is not well characterized. Another important application of Rhodococcus comes from bioconversion, using biological systems to convert cheap starting material into more valuable compounds. This use of Rhodococcus is borne out of its ability to metabolize harmful environmental pollutants, such as toluene, naphthalene, herbicides, and PCBs. Rhodococci typically metabolize aromatic substrates by first oxygenating the aromatic ring to form a diol (two alcohol groups). Then, the ring is cleaved with intra/extradiol mechanisms, opening the ring and exposing the substrate to further metabolism. Since the chemistry here is very stereospecific, the diols are created with predictable chirality. While controlling the chirality of chemical reaction presents a significant challenge for synthetic chemists, biological processes can be used instead to faithfully produce chiral molecules in cases where direct chemical synthesis is infeasible or inefficient. An example of this is the use of Rhodococcus to produce indene, a precursor to the AIDS drug CrixivanTM, a protease inhibitor, and containing two of the five chiral centers needed in the complex. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.10%3A_Chemolithotrophy/5.10G%3A_Benzoate_Catabolism.txt |
Polycyclic aromatic hydrocarbons are potent atmospheric pollutants that consist of fused aromatic rings and do not contain heteroatoms.
Learning Objectives
• Recognize various sources of polycyclic aromatic hydrocarbons and means of removal (bio-, phy
Key Points
• Polycyclic aromatic hydrocarbons (PAHs) occur in oil, coal, and tar deposits, and they are produced as byproducts of fuel burning (whether fossil fuel or biomass ).
• Bioremediation is the use of microorganism metabolism to remove pollutants. These technologies can be generally classified as in situ or ex situ.
• Mycoremediation is a form of bioremediation that uses fungi to degrade or sequester contaminants in the environment. Stimulating microbial and enzyme activity, mycelium reduces toxins in situ.
Key Terms
• Polycyclic aromatic hydrocarbons: also known as poly-aromatic hydrocarbons or polynuclear aromatic hydrocarbons, are potent atmospheric pollutants that consist of fused aromatic rings and do not contain heteroatoms or carry substituents.
• carcinogenic: Causing or tending to cause cancer.
• mutagenic: Capable of causing mutation.
PAHs
Polycyclic aromatic hydrocarbons (PAHs), also known as poly-aromatic hydrocarbons or polynuclear aromatic hydrocarbons, are seen in. PAHs are potent atmospheric pollutants that consist of fused aromatic rings and do not contain heteroatoms or carry substituents. Naphthalene is the simplest example of a PAH. PAHs occur in oil, coal, and tar deposits, and are produced as byproducts of fuel burning (whether fossil fuel or biomass). As a pollutant, they are of concern because some compounds have been identified as carcinogenic, mutagenic, and teratogenic. PAHs are also found in cooked foods—studies have found PAHs in meat cooked at high temperatures such as grilling or barbecuing, and in smoked fish. They are also found in the interstellar medium, comets, and meteorites. PAHs are a candidate for the molecule acted as a basis for the earliest forms of life. In graphene the PAH motif is extended to large 2D sheets.
Natural crude oil and coal deposits contain significant amounts of PAHs from chemical conversion of natural product molecules, such as steroids, to aromatic hydrocarbons. They are also found in processed fossil fuels, tar, and various edible oils.
PLFA Analysis
Phospholipid -derived fatty acids (PLFA) are widely used in microbial ecology as chemotaxonomic markers of bacteria and other organisms. Phospholipids are the primary lipids composing cellular membranes. They can be esterified to many types of fatty acids. Once the phospholipids of an unknown sample are esterfied, the composition of the resulting PLFA can be compared to the PLFA of known organisms to determine the identity of the sample organism. PLFA analysis may be combined with stable isotope probing to determine which microbes are metabolically active in a sample.
The basic premise for PLFA analysis is that as individual organisms (especially bacteria and fungi) die, phospholipids are rapidly degraded and the remaining phospholipid content of the sample is assumed to be from living organisms. As the phospholipids of different groups of bacteria and fungi contain a variety of somewhat unique fatty acids, they can serve as useful biomarkers for such groups. PLFA profiles and composition can be determined by purifying the phospholipids and then cleaving the fatty acids for further analysis.
Bioremediation
Bioremediation is the use of micro-organism metabolism to remove pollutants. Technologies can be generally classified as in situ or ex situ. In situbioremediation involves treating the contaminated material at the site, while ex situ involves the removal of the contaminated material to be treated elsewhere. Some examples of bioremediation related technologies are phytoremediation, bioventing, bioleaching, landfarming, bioreactor, composting, bioaugmentation, rhizofiltration, and biostimulation.
Bioremediation can occur on its own (natural attenuation or intrinsic bioremediation) or can be spurred on via the addition of fertilizers to increase the bioavailability within the medium (biostimulation). Recent advancements have found success by adding matched microbe strains to the medium to enhance the resident microbe population ‘s ability to break down contaminants. Microorganisms used to perform the function of bioremediation are known as bioremediators. Not all contaminants, however, are easily treated by bioremediation using microorganisms. For example, heavy metals such as cadmium and lead are not readily absorbed or captured by microorganisms. The assimilation of metals such as mercury into the food chain may worsen matters.
Phytoremediation
Phytoremediation is useful in these circumstances because natural plants or transgenic plants are able to bioaccumulate these toxins in their above-ground parts, which are then harvested for removal. The heavy metals in the harvested biomass may be further concentrated by incineration or recycled for industrial use. The elimination of a wide range of pollutants and wastes from the environment requires increasing our understanding of the relative importance of different pathways and regulatory networks to carbon flux in particular environments and for particular compounds, and they will certainly accelerate the development of bioremediation technologies and biotransformation processes.
Mycoremediation
Mycoremediation, is a form of bioremediation, the process of using fungi to degrade or sequester contaminants in the environment. Stimulating microbial and enzyme activity, mycelium reduces toxins in situ. Some fungi are hyperaccumulators, capable of absorbing and concentrating heavy metals in the mushroom fruit bodies. One of the primary roles of fungi in the ecosystem is decomposition, which is performed by the mycelium. The mycelium secretes extracellular enzymes and acids that break down lignin and cellulose, the two main building blocks of plant fiber. These organic compounds are composed of long chains of carbon and hydrogen, structurally similar to many organic pollutants. The key to mycoremediation is determining the right fungal species to target a specific pollutant.
Gallaecimonas is a recently described genus of bacteria. It is a Gram-negative, rod-shaped, halotolerant bacterium in the class Gammaproteobacteria. It can degrade high molecular mass polycyclic aromatic hydrocarbons of 4 and 5 rings. The 16S rRNA gene sequences of the type strain CEE_131(T) proved to be distantly related to those of Rheinheimera and Serratia.
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The process of photosynthesis converts light energy to chemical energy, which can be used by organisms for different metabolic processes.
Learning Objectives
• Describe the process of photosynthesis
Key Points
• Photosynthesis evolved as a way to store the energy in solar radiation as high-energy electrons in carbohydrate molecules.
• Plants, algae, and cyanobacteria, known as photoautotrophs, are the only organisms capable of performing photosynthesis.
• Heterotrophs, unable to produce their own food, rely on the carbohydrates produced by photosynthetic organisms for their energy needs.
Key Terms
• photosynthesis: the process by which plants and other photoautotrophs generate carbohydrates and oxygen from carbon dioxide, water, and light energy in chloroplasts
• photoautotroph: an organism that can synthesize its own food by using light as a source of energy
• chemoautotroph: a simple organism, such as a protozoan, that derives its energy from chemical processes rather than photosynthesis
The Importance of Photosynthesis
The processes of all organisms—from bacteria to humans—require energy. To get this energy, many organisms access stored energy by eating food. Carnivores eat other animals and herbivores eat plants. But where does the stored energy in food originate? All of this energy can be traced back to the process of photosynthesis and light energy from the sun.
Photosynthesis is essential to all life on earth. It is the only biological process that captures energy from outer space (sunlight) and converts it into chemical energy in the form of G3P (
Glyceraldehyde 3-phosphate) which in turn can be made into sugars and other molecular compounds. Plants use these compounds in all of their metabolic processes; plants do not need to consume other organisms for food because they build all the molecules they need. Unlike plants, animals need to consume other organisms to consume the molecules they need for their metabolic processes.
The Process of Photosynthesis
During photosynthesis, molecules in leaves capture sunlight and energize electrons, which are then stored in the covalent bonds of carbohydrate molecules. That energy within those covalent bonds will be released when they are broken during cell respiration. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis almost 200 million years ago.
Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis. Because they use light to manufacture their own food, they are called photoautotrophs (“self-feeders using light”). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs (“other feeders”) because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlight’s energy, but by extracting energy from inorganic chemical compounds; hence, they are referred to as chemoautotrophs.
The importance of photosynthesis is not just that it can capture sunlight’s energy. A lizard sunning itself on a cold day can use the sun’s energy to warm up. Photosynthesis is vital because it evolved as a way to store the energy in solar radiation (the “photo-” part) as high-energy electrons in the carbon-carbon bonds of carbohydrate molecules (the “-synthesis” part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via respiration. Therefore, photosynthesis powers 99 percent of Earth’s ecosystems. When a top predator, such as a wolf, preys on a deer, the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to light, to photosynthesis, to vegetation, to deer, and finally to wolf. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.11%3A_Phototrophy/5.11A%3A_The_Purpose_and_Process_of_Photosynthesis.txt |
In multicellular autotrophs, the main cellular structures that allow photosynthesis to take place include chloroplasts, thylakoids, and chlorophyll.
Learning Objectives
• Describe the main structures involved in photosynthesis and recall the chemical equation that summarizes the process of photosynthesis
Key Points
• The chemical equation for photosynthesis is 6CO2+6H2O→C6H12O6+6O2.6CO2+6H2O→C6H12O6+6O2.
• In plants, the process of photosynthesis takes place in the mesophyll of the leaves, inside the chloroplasts.
• Chloroplasts contain disc-shaped structures called thylakoids, which contain the pigment chlorophyll.
• Chlorophyll absorbs certain portions of the visible spectrum and captures energy from sunlight.
Key Terms
• chloroplast: An organelle found in the cells of green plants and photosynthetic algae where photosynthesis takes place.
• mesophyll: A layer of cells that comprises most of the interior of the leaf between the upper and lower layers of epidermis.
• stoma: A pore in the leaf and stem epidermis that is used for gaseous exchange.
Overview of Photosynthesis
Photosynthesis is a multi-step process that requires sunlight, carbon dioxide, and water as substrates. It produces oxygen and glyceraldehyde-3-phosphate (G3P or GA3P), simple carbohydrate molecules that are high in energy and can subsequently be converted into glucose, sucrose, or other sugar molecules. These sugar molecules contain covalent bonds that store energy. Organisms break down these molecules to release energy for use in cellular work.
The energy from sunlight drives the reaction of carbon dioxide and water molecules to produce sugar and oxygen, as seen in the chemical equation for photosynthesis. Though the equation looks simple, it is carried out through many complex steps. Before learning the details of how photoautotrophs convert light energy into chemical energy, it is important to become familiar with the structures involved.
Photosynthesis and the Leaf
In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll. The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma ), which also play a role in the plant’s regulation of water balance. The stomata are typically located on the underside of the leaf, which minimizes water loss. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes.
Photosynthesis within the Chloroplast
In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast. For plants, chloroplast-containing cells exist in the mesophyll. Chloroplasts have a double membrane envelope composed of an outer membrane and an inner membrane. Within the double membrane are stacked, disc-shaped structures called thylakoids.
Embedded in the thylakoid membrane is chlorophyll, a pigment that absorbs certain portions of the visible spectrum and captures energy from sunlight. Chlorophyll gives plants their green color and is responsible for the initial interaction between light and plant material, as well as numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen. A stack of thylakoids is called a granum, and the liquid-filled space surrounding the granum is the stroma or “bed.”
5.11C: The Two Parts of Photosynthesis
Light-dependent and light-independent reactions are two successive reactions that occur during photosynthesis.
Learning Objectives
• Distinguish between the two parts of photosynthesis
Key Points
• In light-dependent reactions, the energy from sunlight is absorbed by chlorophyll and converted into chemical energy in the form of electron carrier molecules like ATP and NADPH.
• Light energy is harnessed in Photosystems I and II, both of which are present in the thylakoid membranes of chloroplasts.
• In light-independent reactions (the Calvin cycle), carbohydrate molecules are assembled from carbon dioxide using the chemical energy harvested during the light-dependent reactions.
Key Terms
• photosystem: Either of two biochemical systems active in chloroplasts that are part of photosynthesis.
Photosynthesis takes place in two sequential stages:
1. The light-dependent reactions;
2. The light-independent reactions, or Calvin Cycle.
Light-Dependent Reactions
Just as the name implies, light-dependent reactions require sunlight. In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and converted into stored chemical energy, in the form of the electron carrier molecule NADPH (nicotinamide adenine dinucleotide phosphate) and the energy currency molecule ATP (adenosine triphosphate). The light-dependent reactions take place in the thylakoid membranes in the granum (stack of thylakoids), within the chloroplast.
Photosystems
The process that converts light energy into chemical energy takes place in a multi-protein complex called a photosystem. Two types of photosystems are embedded in the thylakoid membrane: photosystem II ( PSII) and photosystem I (PSI). Each photosystem plays a key role in capturing the energy from sunlight by exciting electrons. These energized electrons are transported by “energy carrier” molecules, which power the light-independent reactions.
Photosystems consist of a light-harvesting complex and a reaction center. Pigments in the light-harvesting complex pass light energy to two special chlorophyll a molecules in the reaction center. The light excites an electron from the chlorophyll a pair, which passes to the primary electron acceptor. The excited electron must then be replaced. In photosystem II, the electron comes from the splitting of water, which releases oxygen as a waste product. In photosystem I, the electron comes from the chloroplast electron transport chain.
The two photosystems oxidize different sources of the low-energy electron supply, deliver their energized electrons to different places, and respond to different wavelengths of light.
Light-Independent Reactions
In the light-independent reactions or Calvin cycle, the energized electrons from the light-dependent reactions provide the energy to form carbohydrates from carbon dioxide molecules. The light-independent reactions are sometimes called the Calvin cycle because of the cyclical nature of the process.
Although the light-independent reactions do not use light as a reactant (and as a result can take place at day or night), they require the products of the light-dependent reactions to function. The light-independent molecules depend on the energy carrier molecules, ATP and NADPH, to drive the construction of new carbohydrate molecules. After the energy is transferred, the energy carrier molecules return to the light-dependent reactions to obtain more energized electrons. In addition, several enzymes of the light-independent reactions are activated by light. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.11%3A_Phototrophy/5.11B%3A_Main_Structures_and_Summary_of_Photosynthesis.txt |
Bacteriorhodopsin acts a proton pump, generating cellular energy in a manner independent of chlorophyll.
Learning Objectives
• Discuss the function of bacteriorhodopsin
Key Points
• Bacteriorhodopsin is a proton pump found in Archaea, it takes light energy and coverts it into chemical energy, ATP, that can be used by the cell for cellular functions.
• Bacteriorhodopsin forms chains, which contain retinal molecule within, it is the retinal molecule that absorbs a photon from light, it then changes the confirmation of the nearby Bacteriorhodopsin protein, allowing it to act as a proton pump.
• While chlorophyll based ATP generation depends on a protein gradient, like bacteriorhodopsin, but with striking differences, suggesting that phototrophy evolved in bacteria and archaea independently of each other.
Key Terms
• isomerized: converted from one isomer to another
• retinal: One of several yellow or red carotenoid pigments formed from rhodopsin by the action of light; retinene
• phototrophy: The synthesis of an organism’s food from inorganic material using light as a source of energy
Bacteriorhodopsin is a protein used by Archaea, the most notable one being Halobacteria. It acts as a proton pump; that is, it captures light energy and uses it to move protons across the membrane out of the cell. The resulting proton gradient is subsequently converted into chemical energy. The resulting proton gradient is subsequently converted into chemical energy.
Bacteriorhodopsin is an integral membrane protein usually found in two-dimensional crystalline patches known as “purple membrane”, which can occupy up to nearly 50% of the surface area of the archaeal cell. The bacteriorhodopsin forms repeating elements that are arranged in chains. Each chain has seven transmembrane alpha helices and contains one molecule of retinal buried deep within, the typical structure for retinylidene proteins. It is the retinal molecule that changes its conformation when absorbing a photon, resulting in a conformational change of the surrounding protein and the proton pumping action. This releases a proton from a “holding site” into the extracellular side (EC) of the membrane. Reprotonation of the retinal molecule by restores its original isomerized form. This results in a second proton being released to the EC side. The releases the proton from its “holding site,” where a new cycle may begin.
The bacteriorhodopsin molecule is purple and is most efficient at absorbing green light (wavelength 500-650 nm, with the absorption maximum at 568 nm). Bacteriorhodopsin belongs to a family of bacterial proteins related to vertebrate rhodopsins, the pigments that sense light in the retina. Many molecules have homology to bacteriorhodopsin, including the light-driven chloride pump halorhodopsin, and some directly light-activated channels like channelrhodopsin. All other phototrophic systems in bacteria, algae, and plants use chlorophylls or bacteriochlorophylls rather than bacteriorhodopsin. These also produce a proton gradient, but in a quite different and more indirect way involving an electron transfer chain consisting of several other proteins. Furthermore, chlorophylls are aided in capturing light energy by other pigments known as “antennas”; these are not present in bacteriorhodopsin-based systems. Last, chlorophyll-based phototrophy is coupled to carbon fixation (the incorporation of carbon dioxide into larger organic molecules) and for that reason is photosynthesis, which is not true for bacteriorhodopsin-based system. Thus, it is likely that phototrophy independently evolved at least twice, once in bacteria and once in archaea.
5.11E: Carotenoids and Phycobilins
To aid chlorophylls in the absorption of light not many photosynthetic organisms use carotenoids and phycobilins.
Learning Objectives
• Distinguish between carotenoids and phycobilins
Key Points
• Chlorophylls absorb light most efficiently at the ultraviolet end of the spectrum, however not all light that an organism gets is at that wavelength. Thus many photosynthetic organisms rely on accessory compounds to get light from different spectrums.
• Caretenoids aid in the absorption of light in the blue-range spectrum, while at the same time help with the oxidative stress due to the photosynthetic process.
• Phycobilins aid in the absorption of light in the red, orange, yellow, and green light, wavelengths.
Key Terms
• isoprene: An unsaturated hydrocarbon, C5H8, that is readily polymerized; natural rubber (caoutchouc) is cis-1,4-polyisoprene, and trans-1,4-polyisoprene is present in gutta-percha and balata; it is the structural basis for the terpenes.
• photosynthesis: The process by which plants and other photoautotrophs generate carbohydrates and oxygen from carbon dioxide, water, and light energy in chloroplasts.
Photosynthesis in many plants and algae depend on chlorophylls which absorb light closer to the ultraviolet side of the spectrum, and emit light in the green end of the spectrum. However during certain times of the year or in various location most of the light may be shifted to other wavelengths away from the ultraviolet spectrum. To deal with these problems, organisms dependent on photosynthesis express various compounds that allow them to absorb different spectrum of light. Notably are carotenoids and phycobilins.
Chromoplasts of plants and some other photosynthetic organisms like algae, some bacteria, and some fungi. Carotenoids can be produced from fats and other basic organic metabolic building blocks by all these organisms. Carotenoids generally cannot be manufactured by species in the animal kingdom so animals obtain carotenoids in their diets, and may employ them in various ways in metabolism.There are over 600 known carotenoids; they are split into two classes, xanthophylls (which contain oxygen) and carotenes (which are purely hydrocarbons, and contain no oxygen). All carotenoids are tetraterpenoids, meaning that they are produced from 8 isoprene molecules and contain 40 carbon atoms. Carotenoids in general absorb blue light. They serve two key roles in plants and algae: they absorb light energy for use in photosynthesis, and they protect chlorophyll from photodamage.
Phycobilins (from Greek: φ (phykos) meaning “alga”, and from Latin: bilis meaning “bile”) are chromophores (light-capturing molecules) found in cyanobacteria and in the chloroplasts of red algae, glaucophytes and some cryptomonads (though not in green algae and higher plants). They are unique among the photosynthetic pigments in that they are bonded to certain water-soluble proteins, known as phycobiliproteins. Phycobiliproteins then pass the light energy to chlorophylls for photosynthesis.The phycobilins are especially efficient at absorbing red, orange, yellow, and green light, wavelengths that are not well absorbed by chlorophyll a. Organisms growing in shallow waters tend to contain phycobilins that can capture yellow/red light, while those at greater depth often contain more of the phycobilins that can capture green light, which is relatively more abundant there. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.11%3A_Phototrophy/5.11D%3A_Bacteriorhodopsin.txt |
A facultative phototroph can rely on photosynthesis and alternative energy sources to survive and grow.
Learning Objectives
• Recognize the traits associated with the classification of facultative phototrophy
Key Points
• Phototrophs can obtain cellular energy from light as well as using light to fix carbon to make complex macromolecules on which to survive.
• Chlamydomonas reinhardtii is an organism that can rely on photosynthetic and chemical energy sources, depending on conditions.
• Facultative means optional, in terms of biology it refers to an organism that can switch energy sources for survival.
Key Terms
• autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.
• pyrenoid: any of several transparent structures found in the chloroplast of certain algae etc.; they are responsible for the fixation of carbon dioxide and the formation of starch
An autotroph or “producer”, is an organism that produces complex organic compounds (such as carbohydrates, fats, and proteins) from simple substances present in its surroundings, generally using energy from light ( photosynthesis ) or inorganic chemical reactions (chemosynthesis). They are the producers in a food chain, such as plants on land or algae in water. They are able to make their own food, and do not need a living energy or carbon source. Autotrophs can reduce carbon dioxide to make organic compounds, creating a store of chemical energy. Phototrophs, a type of autotroph, convert physical energy from sunlight (in case of green plants) into chemical energy in the form of reduced carbon.
In terms of biology facultative means “optional” or “discretionary” the antonym of which is obligate meaning “by necessity”. Thus facultative phototrophy means an organism that can switch between phototrophy to make organix compounds and other means of getting cellular energy. Probably the best studied example of a facultative phototrophy is Chlamydomonas reinhardtii.
Chlamydomonas reinhardtii is a single celled green alga about 10 micrometres in diameter that swims with two flagella. It has a cell wall made of hydroxyproline-rich glycoproteins, a large cup-shaped chloroplast, a large pyrenoid, and an “eyespot” that senses light. Although widely distributed worldwide in soil and fresh water, C. reinhardtii is primarily used as a model organism in biology in a wide range of subfields. When illuminated, C. reinhardtii can grow in media lacking organic carbon and chemical energy sources, and can also grow in the dark when supplied with these. C. reinhardtii is also of interest in the biofuel field, as a source of hydrogen. As one can imagine switching energy sources under varying conditions allows facultative microbes to live in different conditions, in the case of a facultative phototroph it can rely of light other energy sources.
5.11G: Oxygenic Photosynthesis
Oxygenic photosynthesis, provides energy to organism and allows for carbon fixation, all the while producing oxygen as a byproduct.
Learning Objectives
• Describe oxygenic photosynthesis
Key Points
• Plants, algae and cyanobacteria release oxygen during photosynthesis.
• Photosynthesis is also needed for carbon fixation.
• While different organisms may have differences during oxygenic photosynthesis, they all follow the general equation of, carbon dioxide + water + light energy → carbohydrate + oxygen.
Key Terms
• cyanobacteria: Cyanobacteria, also known as blue-green bacteria, blue-green algae, and Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis.
• oxygenic: of, relating to, containing or producing oxygen
In plants, algae and cyanobacteria, photosynthesis releases oxygen. This is called oxygenic photosynthesis. Although there are some differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. Photosynthesis is not only needed by photosynthetic organism for energy but also for carbon fixation.
Carbon dioxide is converted into sugars in a process called carbon fixation. Carbon fixation is a redox reaction, so photosynthesis needs to supply both a source of energy to drive this process, and the electrons needed to convert carbon dioxide into a carbohydrate, which is a reduction reaction. In general outline, photosynthesis is the opposite of cellular respiration, where glucose and other compounds are oxidized to produce carbon dioxide, water, and release chemical energy. However, the two processes take place through a different sequence of chemical reactions and in different cellular compartments. The general equation for photosynthesis is therefore:
2n CO2 + 2n DH2 + photons → 2(CH2O)n + 2n DO
Carbon dioxide + electron donor + light energy → carbohydrate + oxidized electron donor.
In oxygenic photosynthesis water is the electron donor and, since its hydrolysis releases oxygen, the equation for this process is:
2n CO2 + 4n H2O + photons → 2(CH2O)n + 2n O2 + 2n H2O
carbon dioxide + water + light energy → carbohydrate + oxygen + water
Often 2n water molecules are cancelled on both sides, yielding:
2n CO2 + 2n H2O + photons → 2(CH2O)n + 2n O2
carbon dioxide + water + light energy → carbohydrate + oxygen
In plants, algae and cyanobacteria, photosynthesis releases oxygen. This is called oxygenic photosynthesis. Although there are some differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.11%3A_Phototrophy/5.11F%3A_Facultative_Phototrophy.txt |
Photosynthetic reactions can be anoxygenic, thus they do not produce oxygen.
Learning Objectives
• Discuss the characteristics that classify a specific type of chlorophototrophy as anoxygenic photosynthesis
Key Points
• Anoxygenic photosynthesis produces cellular energy ( ATP ), without oxygen as a by-product.
• As opposed to eukaryotic organisms, which rely on chlorophylls for photosynthesis, anoxygenic organisms rely on bacteriochlorophylls.
• The electron transport chain of anoxygenic phototrophs is cyclic, meaning the electrons used during photosynthesis are fed back into the system, therefore no electrons are left over to oxidize water into oxygen.
Key Terms
• electron transport chain: An electron transport chain (ETC) couples electron transfer between an electron donor (such as NADH) and an electron acceptor (such as O2) with the transfer of H+ ions (protons) across a membrane. The resulting electrochemical proton gradient is used to generate chemical energy in the form of adenosine triphosphate (ATP). Electron transport chains are the cellular mechanisms used for extracting energy from sunlight in photosynthesis and also from redox reactions, such as the oxidation of sugars (respiration).
• electron donor: An electron donor is a chemical entity that donates electrons to another compound. It is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process.
• anoxygenic: That does not involve the production of oxygen
Phototrophy is the process by which organisms trap light energy (photons) and store it as chemical energy in the form of ATP and/or reducing power in NADPH. There are two major types of phototrophy: chlorophyll-based chlorophototrophy and rhodopsin-based retinalophototrophy. Chlorophototrophy can further be divided into oxygenic photosynthesis and anoxygenic phototrophy. Oxygenic and anoxygenic photosynthesizing organisms undergo different reactions either in the presence of light or with no direct contribution of light to the chemical reaction (colloquially called “light reactions” and “dark reactions”, respectively).
Anoxygenic photosynthesis is the phototrophic process where light energy is captured and converted to ATP, without the production of oxygen. Water is therefore not used as an electron donor. There are several groups of bacteria that undergo anoxygenic photosynthesis: Green sulfur bacteria, green and red filamentous anoxygenic phototrophs (FAPs), phototrophic purple bacteria, phototrophic Acidobacteria, and phototrophic heliobacteria. Anoxygenic phototrophs have photosynthetic pigments called bacteriochlorophylls (similar to chlorophyll found in eukaryotes). Bacteriochlorophyll a and b have wavelengths of maximum absorption at 775 nm and 790 nm, respectively in ether. In vivo however, due to shared extended resonance structures, these pigments were found to maximally absorb wavelengths out further into the near-infrared. Bacteriochlorophylls c-g have the corresponding “peak” absorbance at more blue wavelengths when dissolved in an organic solvent, but are similarly red-shifted within their natural environment (with the exception of bacteriochlorophyll f, which has not been naturally observed).Unlike oxygenic phototrophs, anoxygenic photosynthesis only functions using (by phylum) either one of two possible types of photosystem. This restricts them to cyclic electron flow and are therefore unable to produce O2 from the oxidization of H2O.
The cyclic nature of the electron flow is typified in purple non-sulfur bacteria. The electron transport chain of purple non-sulfur bacteria begins when the reaction centre bacteriochlorophyll pair, P870, becomes excited from the absorption of light. Excited P870 will then donate an electron to Bacteriopheophytin, which then passes it on to a series of electron carriers down the electron chain. In the process, it will generate a proton motor force (PMF) which can then be used to synthesize ATP by oxidative phosphorylation. The electron returns to P870 at the end of the chain so it can be used again once light excites the reaction-center. Therefore electrons are not left over to oxidize H2O into O2.
LICENSES AND ATTRIBUTIONS
CC LICENSED CONTENT, SPECIFIC ATTRIBUTION | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.11%3A_Phototrophy/5.11H%3A_Anoxygenic_Photosynthesis.txt |
Major metabolic pathways require substrates to be acted upon for the formation of larger, more complex products.
Learning Objectives
• Describe the importance of substrates for biosynthesis
Key Points
• Biogenesis or anabolism, requires substrates to be acted upon that result in the formation of larger more complex molecules.
• A central metabolic pathway that produces precursors and substrates used in biosynthetic processes is the TCA cycle.
• A central metabolic pathway that produces precursors and substrates used in biosynthetic processes is glycolysis.
Key Terms
• reducing agent: A substance that functions in reducing or donating electrons to another substance until that specific substance becomes oxidized.
• oxidation: A reaction in which the atoms of an element lose electrons and the valence of the element increases.
Microorganisms have numerous pathways and processes in place to ensure both energy and nutrient production. These pathways are necessary for survival and cellular function. The major metabolic pathways require substrates to be acted upon for the formation of larger, more complex products. Biosynthetic processes are defined by the production of more complex products that are required for growth and maintenance of life. These processes require pathways that are often multi-step. There are various components deemed necessary for biosynthetic processes to occur, including: precursor compounds, chemical energy, and carious catalytic enzymes.
TCA Cycle
The citric acid cycle, commonly referred to as the Krebs cycle, is characterized by the production of energy through the oxidation of acetate derived from carbohydrates, fats, and proteins into carbon dioxide. The cycle is one of the major metabolic processes utilized to generate energy. The citric acid cycle, comprised of a series of chemical reactions, provides precursors for additional biochemical pathways. These precursors are used as substrates for the biogenesis of large complex products. The precursors include amino acids and reducing agents such as NADH. Additional pathways that require precursors formed by the TCA include amino acid and nucleotide synthesis.
Glycolysis
An additional central metabolic pathway includes glycolysis. Glycolysis is characterized by a series of reactions that results in the conversion of glucose into pyruvate. This process is characterized by the production of various intermediates and molecules that function as substrates in additional pathways. Additional pathways that require substrates or metabolites produced by the glycolytic pathway include: gluconeogenesis, lipid metabolism, the pentose phosphate pathway, and the TCA.
5.12B: Biosynthesis and Energy
Biosynthetic processes ensure the production of complex products necessary for cellular and metabolic processes.
Learning Objectives
• Discuss the principles of biosynthesis and provide examples
Key Points
• Anabolism is the form of metabolism responsible for building large complexes from precursors.
• The three categories of carbon fixation pathways are the Calvin cycle, the reverse TCA, and acetyl-CoA pathways.
• One example of a biosynthetic process is gluconeogenesis, which is responsible for the production of glucose from noncarbohydrate precursors.
Key Terms
• anabolism: Anabolism is the set of metabolic pathways that construct molecules from smaller units.
• biosynthesis: Biosynthesis is an enzyme-catalyzed process in cells of living organisms by which substrates are converted to more complex products.
• metabolic: Of or pertaining to metabolism; as, metabolic activity; metabolic force.
Biosynthesis and Energy
Biosynthesis in living organisms is a process in which substrates are converted to more complex products. The products which are produced as a result of biosynthesis are necessary for cellular and metabolic processes deemed essential for survival. Biosynthesis is often referred to as the anabolism branch of metabolism that results in complex proteins such as vitamins.
A majority of the organic compounds required by microorganisms are produced via biosynthetic pathways. The components which are utilized by biosynthetic pathways to promote the production of large molecules include chemical energy and catalytic enzymes. Biosynthetic building blocks utilized by organisms include amino acids, purines, pyrimidines, lipids, sugars, and enzyme cofactors. There are numerous mechanisms in place to ensure biosynthetic pathways are properly controlled so a cell will produce a specific amount of a compound. Biosynthetic metabolism (also known as anabolism) involves the synthesis of macromolecules from specific building blocks. A majority of these processes are considered to be multi-step or multi-enzymatic processes.
Carbon Dioxide Fixation
Carbon dioxide fixation is necessary to ensure carbon dioxide can be converted into organic carbon. The major pathways utilized to ensure fixation of carbon dioxide include: the Calvin cycle, the reductive TCA cycle, and the acetyl-CoA pathway. The Calvin cycle involves utilizing carbon dioxide and water to form organic compounds. The reductive TCA cycle, commonly referred to as the reverse Krebs cycle, also produces carbon compounds from carbon dioxide and water. In the acetyl-CoA pathway, carbon dioxide is reduced to carbon monoxide and then acetyl-CoA.
Glucose and Fructose Synthesis
An additional biosynthetic pathway utilized by microorganisms includes the synthesis of sugars and polysaccharides. The ability to synthesize sugars and polysaccharides from noncarbohydrate precursors is key to survival in numerous microorganisms. The process of gluconeogenesis, characterized by the production of glucose or fructose from noncarbohydrate precursors, is an ubiquitous process. This process utilizes precursors such as pyruvate, lactate, or glycerol. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.12%3A_Biosynthesis/5.12A%3A_Substrates_for_Biosysnthesis.txt |
The Calvin cycle is organized into three basic stages: fixation, reduction, and regeneration.
Learning Objectives
• Describe the Calvin Cycle
Key Points
• The Calvin cycle refers to the light-independent reactions in photosynthesis that take place in three key steps.
• Although the Calvin Cycle is not directly dependent on light, it is indirectly dependent on light since the necessary energy carriers (ATP and NADPH) are products of light-dependent reactions.
• In fixation, the first stage of the Calvin cycle, light-independent reactions are initiated; CO2 is fixed from an inorganic to an organic molecule.
• In the second stage, ATP and NADPH are used to reduce 3-PGA into G3P; then ATP and NADPH are converted to ADP and NADP+, respectively.
• In the last stage of the Calvin Cycle, RuBP is regenerated, which enables the system to prepare for more CO2 to be fixed.
Key Terms
• light-independent reaction: chemical reactions during photosynthesis that convert carbon dioxide and other compounds into glucose, taking place in the stroma
• rubisco: (ribulose bisphosphate carboxylase) a plant enzyme which catalyzes the fixing of atmospheric carbon dioxide during photosynthesis by catalyzing the reaction between carbon dioxide and RuBP
• ribulose bisphosphate: an organic substance that is involved in photosynthesis, reacts with carbon dioxide to form 3-PGA
The Calvin Cycle
In plants, carbon dioxide (CO2) enters the leaves through stomata, where it diffuses over short distances through intercellular spaces until it reaches the mesophyll cells. Once in the mesophyll cells, CO2 diffuses into the stroma of the chloroplast, the site of light-independent reactions of photosynthesis. These reactions actually have several names associated with them. Other names for light-independent reactions include the Calvin cycle, the Calvin-Benson cycle, and dark reactions. The most outdated name is dark reactions, which can be misleading because it implies incorrectly that the reaction only occurs at night or is independent of light, which is why most scientists and instructors no longer use it.
The light-independent reactions of the Calvin cycle can be organized into three basic stages: fixation, reduction, and regeneration.
Stage 1: Fixation
In the stroma, in addition to CO2,two other components are present to initiate the light-independent reactions: an enzyme called ribulose bisphosphate carboxylase (RuBisCO) and three molecules of ribulose bisphosphate (RuBP). RuBP has five atoms of carbon, flanked by two phosphates. RuBisCO catalyzes a reaction between CO2 and RuBP. For each CO2 molecule that reacts with one RuBP, two molecules of 3-phosphoglyceric acid (3-PGA) form. 3-PGA has three carbons and one phosphate. Each turn of the cycle involves only one RuBP and one carbon dioxide and forms two molecules of 3-PGA. The number of carbon atoms remains the same, as the atoms move to form new bonds during the reactions (3 atoms from 3CO2 + 15 atoms from 3RuBP = 18 atoms in 3 atoms of 3-PGA). This process is called carbon fixation because CO2 is “fixed” from an inorganic form into organic molecules.
Stage 2: Reduction
ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called glyceraldehyde 3-phosphate (G3P). This is a reduction reaction because it involves the gain of electrons by 3-PGA. Recall that a reduction is the gain of an electron by an atom or molecule. Six molecules of both ATP and NADPH are used. For ATP, energy is released with the loss of the terminal phosphate atom, converting it to ADP; for NADPH, both energy and a hydrogen atom are lost, converting it into NADP+. Both of these molecules return to the nearby light-dependent reactions to be reused and reenergized.
Stage 3: Regeneration
At this point, only one of the G3P molecules leaves the Calvin cycle and is sent to the cytoplasm to contribute to the formation of other compounds needed by the plant. Because the G3P exported from the chloroplast has three carbon atoms, it takes three “turns” of the Calvin cycle to fix enough net carbon to export one G3P. But each turn makes two G3Ps, thus three turns make six G3Ps. One is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which enables the system to prepare for more CO2 to be fixed. Three more molecules of ATP are used in these regeneration reactions. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.12%3A_Biosynthesis/5.12C%3A_The_Calvin_Cycle.txt |
The Calvin Cycle involves the process of carbon fixation to produce organic compounds necessary for metabolic processes.
Learning Objectives
• Outline the function of the intermediates produced in the major phases of the Calvin Cycle
Key Points
• The Calvin Cycle can be divided into three major phases: Phase 1: carbon fixation; Phase 2: reduction; Phase 3: regeneration.
• The intermediates of the Calvin Cycle include ADP, NADP+, inorganic phosphate, and 3-phosphoglycerate.
• Many of the intermediates or products of the Calvin Cycle are regenerated back into earlier stages of the process.
Key Terms
• autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.
• coenzyme: Any small molecule that is necessary for the functioning of an enzyme.
• phosphorylation: The process of transferring a phosphate group from a donor to an acceptor; often catalysed by enzymes
The Calvin Cycle is characterized as a carbon fixation pathway. The Calvin Cycle is also referred to as the reductive pentose phosphate cycle or the Calvin-Benson-Bassham cycle. The process of carbon fixation involves the reduction of carbon dioxide to organic compounds by living organisms. The Calvin cycle is most often associated with carbon fixation in autotrophic organisms, such as plants, and is recognized as a dark reaction. In organisms that require carbon fixation, the Calvin cycle is a means to obtain energy and necessary components for growth. Some examples of microorganisms that utilize the Calvin cycle include cyanobacteria, purple bacteria, and nitrifying bacteria. Specifically, the Calvin cycle involves reducing carbon dioxide to the sugar triose phosphate, most commonly known as glyceraldehyde 3-phosphate (GAP). Throughout the Calvin Cycle, there are numerous intermediate molecules made which are consistently withdrawn and utilized to create cellular material and participate in cellular processes. The Calvin cycle can be divided into three major phases which include: Phase 1: carbon fixation; Phase 2: reduction; and Phase 3: regeneration of ribulose. The following is a brief overview of the intermediates created during the Calvin cycle.
Phase 1: Carbon Fixation Intermediates
During phase 1 of this cycle, the CO2 molecule is incorporated into one of two 3-phosphoglycerate molecules (3-PGA). This process requires the enzyme RuBisCO and both ATP and NADPH. Once 3-PGA is formed, one of two molecules formed continues into the reduction phase (phase 2). The additional 3-PGA is utilized in additional metabolic pathways such as glycolysis and gluconeogenesis. The structure of 3-PGA allows it to be combined and rearranged to form sugars which can be transported to additional cells or stored for energy.
Phase 2: Reduction
During phase 2 of this cycle, the newly formed 3-PGA undergoes phosphorylation by the enzyme phosphoglycerate kinase which utilizes ATP. The result of this phosphorylation is the production of 1,3-bisphosphoglycerates and ADP products. The ADP product that is produced via the breakdown of ATP will be utilized in additional pathways and be converted back into ATP. The inter conversions of ATP to ADP and ADP to ATP is a key process in supplying energy in numerous processes. This energy is necessary for cellular growth and metabolic processes.
Once the bisphosphoglycerate molecules are formed, they must be converted and further reduced to GAP by NADPH. The intermediate of this product is the conversion of NADPH to NADP+ and an inorganic phosphate ion. NADP+ is a coenzyme which is necessary for the function of NADPH. The functions that require NADP+ include anabolic reactions such as lipid and nucleic acid synthesis. The inorganic phosphate ion is often a result of regulatory metabolic processes. The phosphate ions are used in processes such as buffering cells, conversions of AMP/ADP to ATP and production of materials involved in structure such as bone and teeth. It is important to note that these intermediates or products (inorganic phosphate, NADP+ and ADP) processed by phase 2 are often regenerated back into the cycle.
Phase 3: Regeneration of Ribulose
The GAP molecules at this point are the end product of the Calvin cycle, which is responsible for reducing carbon to a sugar form. However, additional GAP molecules that are formed will be converted to ribulose-1,5-bisphosphate (RuBP), which is responsible for the conversion of CO2 to 3-PGA in phase 1, via numerous steps. The G3P, which is destined to exit the cycle, will be used for carbohydrate synthesis and additional pathways. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.12%3A_Biosynthesis/5.12D%3A_Intermediates_Produced_During_the_Calvin_Cycle.txt |
Learning Objectives
• Outline the three major phases of the Calvin cycle: carbon fixation, reduction, and regeneration of ribulose
The Calvin cycle is a process utilized to ensure carbon dioxide fixation. In this process, carbon dioxide and water are converted into organic compounds that are necessary for metabolic and cellular processes. There are various organisms that utilize the Calvin cycle for production of organic compounds including cyanobacteria and purple and green bacteria. The Calvin cycle requires various enzymes to ensure proper regulation occurs and can be divided into three major phases:
1. carbon fixation,
2. reduction, and
3. regeneration of ribulose.
Each of these phases are tightly regulated and require unique and specific enzymes.
During the first phase of the Calvin cycle, carbon fixation occurs. The carbon dioxide is combined with ribulose 1,5-bisphosphate to form two 3-phosphoglycerate molecules (3-PG). The enzyme that catalyzes this specific reaction is ribulose bisphosphate carboxylase (RuBisCO). RuBisCO is identified as the most abundant enzyme on earth, to date. RuBisCO is the first enzyme utilized in the process of carbon fixation and its enzymatic activity is highly regulated. RuBisCO is only active during the day as its substrate, ribulose 1,5-bisphosphate, is not generated in the dark. RuBisCO enzymatic activity is regulated by numerous factors including: ions, RuBisCO activase, ATP /ADP and reduction/oxidation states, phosphate and carbon dioxide. The various factors influencing RuBisCO activity directly affect phase 1 of the Calvin cycle.
During the second phase of the Calvin cycle, reduction occurs. The 3-PG molecules synthesized in phase 1 are reduced to glyceraldehyde-3-phosphate (G3P). This reducing process is mediated by both ATP and NADPH. One of the two G3P molecules formed are further converted to dihydroxyacetone phosphate (DHAP) and the enzyme aldolase is used to combine G3P and DHAP to form fructose-1,6-bisphosphate. The enzyme aldolase is typically characterized as a glycolytic enzyme with the ability to split fructose 1,6-bisphosphate into DHAP and G3P. However, in this specific phase of the Calvin cycle, it is used in reverse. Therefore, aldolase is said to regulate a reverse reaction in the Calvin cycle. Additionally, aldolase can be utilized to promote a reverse reaction in gluconeogenesis as well. The fructose-1,6-bisphosphate formed in phase 2 is then converted into fructose-6-phosphate.
During the third phase of the Calvin cycle, regeneration of RuBisCO occurs. This specific phase involves a series of reactions in which there are a variety of enzymes required to ensure proper regulation. This phase is characterized by the conversion of G3P, which was produced in earlier phase, back to ribulose 1,5-bisphosphate. This process requires ATP and specific enzymes. The enzymes involved in this process include: triose phosphate isomerase, aldolase, fructose-1,6-bisphosphatase, transketolase, sedoheptulase-1,7-bisphosphatase, phosphopentose isomerase, phosphopentose epimerase, and phosphoribulokinase. The following is a brief summary of each enzyme and its role in the regeneration of ribulose 1,5-bisphosphate in the order it appears in this specific phase.
1. Triose phosphate isomerase: converts all G3P molecules into DHAP
2. Aldolase and fructose-1,6-bisphosphatase: converts G3P and DHAP into fructose 6-phosphate
3. Transketolase: removes two carbon molecules in fructose 6-phosphate to produce erythrose 4-phosphate (E4P); the two removed carbons are added to G3P to produce xylulose-5-phosphate (Xu5P)
4. Aldolase: converts E4P and a DHAP to sedoheptulose-1,7-bisphosphate
5. Sedoheptulase-1,7-bisphosphatase: cleaves the sedohetpulose-1,7-bisphosphate into sedoheptulase-7-phosphate (S7P)
6. Transketolase: removes two carbons from S7P and two carbons are transferred to one of the G3P molecules producing ribose-5-phosphate (R5P)and another Xu5P
7. Phosphopentose isomerase: converts the R5P into ribulose-5-phosphate (Ru5P)
8. Phosphopentose epimerase: converts the Xu5P into Ru5P
9. Phosphoribulokinase: phosphorylates Ru5P into ribulose-1,5-bisphosphate
After this final enzyme performs this conversion, the Calvin cycle is considered complete. The regulation of the Calvin cycle requires many key enzymes to ensure proper carbon fixation.
Key Points
• In this process, carbon dioxide and water are converted into organic compounds that are necessary for metabolic and cellular processes.
• The three phases of the Calvin cycle, fixation, reduction, and regeneration require specific enzymes to ensure proper regulation.
• The last phase of the Calvin cycle, regeneration, is considered the most complex and regulated phase of the cycle.
Key Terms
• calvin cycle: A series of biochemical reactions that take place in the stroma of chloroplasts in photosynthetic organisms.
• gluconeogenesis: A metabolic process which glucose is formed from non-carbohydrate precursors.
• ribulose: A ketopentose whose phosphate derivatives participate in photosynthesis. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.12%3A_Biosynthesis/5.12E%3A_Regulation_of_the_Calvin_Cycle.txt |
The reverse TCA cycle utilizes carbon dioxide and water to form carbon compounds.
Learning Objectives
• List the enzymes and function that are unique to the reverse TCA cycle (ATP citrate lyase; 2-oxoglutarate:ferredoxin oxidoreductase; pyruvate:ferredoxin oxidoreductase)
Key Points
• The TCA cycle utilizes complex carbon molecules and oxidizes them to carbon dioxide and water.
• The reverse TCA utilizes carbon dioxide and water to produce carbon molecules.
• There are three major enzymes that are unique to reverse TCA including ATP citrate lyase which converts citrate into oxaloacetate and acetyl CoA.
Key Terms
• Krebs cycle: A series of enzymatic reactions that occurs in all aerobic organisms; it involves the oxidative metabolism of acetyl units and serves as the main source of cellular energy.
• ATP citrate lyase: ATP citrate lyase is an enzyme that represents an important step in fatty acid biosynthesis. This step in fatty acid biosynthesis occurs because ATP citrate lyase is the link between the metabolism of carbohydrates (which causes energy) and the production of fatty acids.
• carboxylation: A reaction that introduces a carboxylic acid into a molecule.
The citric acid cycle (TCA) or Krebs cycle, is a process utilized by numerous organisms to generate energy via the oxidation of acetate derived from carbohydrates, fats, and proteins into carbon dioxide. The cycle plays a critical role in the maintenance of numerous central metabolic processes. However, there are numerous organisms that undergo reverse TCA or reverse Krebs cycles. This process is characterized by the production of carbon compounds from carbon dioxide and water. The chemical reactions that occur are the reverse of what is seen in the TCA cycle. There are numerous anaerobic organisms that utilize a cyclic reverse TCA cycle and an example includes organisms classified as Thermoproteus. The following is a brief overview of the reverse TCA cycle.
Reverse TCA Summary
The reverse TCA cycle is a series of chemical reactions by which organisms produce carbon compounds from carbon dioxide and water. The reverse TCA cycle requires electron donors and often times, bacteria will use hydrogen, sulfide or thiosulfate for this purpose. The reverse TCA is considered to be an alternative to photosynthesis which produces organic molecules as well. Reverse TCA, a form of carbon fixation, utilizes numerous ATP molecules, hydrogen and carbon dioxide to generate an acetyl CoA. This process requires a number of reduction reactions using various carbon compounds. The enzymes, unique to reverse TCA, that function in catalyzing these reactions include: ATP citrate lyase, 2-oxoglutarate:ferredoxin oxidoreductase, and pyruvate:ferredoxin oxidoreductase. ATP citrate lyase is one of the key enzymes that function in reverse TCA. ATP citrate lyase is the enzyme responsible for cleaving citrate into oxaloacetate and acetyl CoA. These enzymes are unique to reverse TCA and are necessary for the reductive carboxylation to occur.
In reverse TCA, the following occurs in a cyclic manner:
1) oxaloacetate is converted to malate (NADH/H+ is utilized and NAD+ is produced)
2) malate is converted to fumarate (H20 molecule is produced)
3) fumarate is converted to succinate via a fumarate-reductase enzyme (FADH2 is converted to FAD)
4) succinate is converted to succinyl-CoA (ATP is hydrolyzed to ADP+Pi)
5) succincyl CoA is converted to alpha-ketoglutarate via an alpha-ketoglutarate synthase (reduction of carbon dioxide occurs and oxidation of coenzyme A)
6) alpha-ketoglutarate is converted to isocitrate (NAD(P)H/H+ and CO2 is broken down to NAD(P+)
7) isocitrate is converted to citrate
8) ATP citrate lyase is then used to convert citrate to oxaloacetate and acetyl CoA (ATP is hydrolyzed to ADP and Pi).
9) Pathway is cyclic and continues cycle from step 1
An example of a microorganism that utilizes reverse TCA includes Thermoproteus. Thermoproteusis type of prokaryotic that is characterized as a hydrogen-sulfur autotroph. The organisms classified as Thermoproteus utilizes sulfur reduction for metabolic processes. As previously mentioned, organisms that use reverse TCA may use sulfur as an electron donor to carry out this metabolic process. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.12%3A_Biosynthesis/5.12F%3A_The_Reverse_TCA_Cycle.txt |
The acetyl-CoA pathway utilizes carbon dioxide as a carbon source and often times, hydrogen as an electron donor to produce acetyl-CoA.
Learning Objectives
• Describe the role of the carbon monoxide dehydrogenase and acetyl-CoA synthetase in the acetyl-CoA pathway
Key Points
• The acetyl-CoA pathway utilizes two major enzymes in the production of acetyl-CoA: carbon monoxide dehydrogenase and acetyl-CoA synthase.
• Carbon monoxide dehydrogenase functions in the reduction of carbon dioxide to a methyl group.
• Acetyl-CoA synthase functions in combining carbon monoxide and a methyl group to produce acetyl-CoA.
Key Terms
• acetogenesis: The anaerobic production of acetic acid or acetate by bacteria.
The acetyl coenzyme A (CoA) pathway, commonly referred to as the Wood-Ljungdahl pathway or the reductive acetyl-CoA pathway, is one of the major metabolic pathways utilized by bacteria. This specific pathway is characterized by the use of hydrogen as an electron donor and carbon dioxide as an electron acceptor to produce acetyl-CoA as the final product. Acetyl-CoA is a major component in numerous metabolic processes as it plays a key role in the citric acid cycle. The main function of acetyl-CoA in the citric cycle is to transport carbon atoms. In regards to molecular structure, acetyl-CoA functions as the thioester between conezyme A and acetic acid. Specific types of organisms that utilize this pathway include archaea classified as methanogens and acetate-producing bacteria as well. The following is a brief overview of the acetyl-CoA pathway..
The acetyl-CoA pathway begins with the reduction of a carbon dioxide to carbon monoxide. The other carbon dioxide is reduced to a carbonyl group. The two major enzymes involved in these processes are carbon monoxide dehydrogenase and acetyl CoA synthase complex. The carbon dioxide that is reduced to a carbonyl group, via the carbon monoxide dehydrogenase, is combined with the methyl group to form acetyl-CoA. The acetyl-CoA synthase complex is responsible for this reaction.
Carbon Monoxide Dehydrogenase
Carbon monoxide dehydrogenase, the enzyme responsible for the reduction of a carbon dioxide to a carbonyl group, functions in numerous biochemical processes. These processes include metabolism of methanogens, acetogenic and sulfate-reducing bacteria. Specifically, the acetyl-CoA pathway is utilized by bacteria that are classified as methanogens and acetate-producing organisms. The carbon monoxide dehydrogenase allows organisms to use carbon dioxide as a source of carbon and carbon monoxide as a source of energy.The carbon monoxide dehydrogenase can also form a complex with the acetyl-CoA synthase complex which is key in the acetyl-CoA pathway.
Acetyl-CoA Synthetase
Acetyl-CoA synthetase is a class of enzymes that is key to the acetyl-CoA pathway. The acetyl-CoA synthetase functions in combining the carbon monoxide and a methyl group to produce acetyl-CoA..
Microorganisms and the Acetyl-CoA Pathway
The ability to utilize the acetyl-CoA pathway is advantageous due to the ability to utilize both hydrogen and carbon dioxide to produce acetyl-CoA. Specific types of bacteria which utilize the acetyl-CoA pathway include methanogens and acetate-producing bacteria.
Methanogens
Methanogens are types of organisms, classified as archaea, that exhibit the ability to produce methane as a metabolic byproduct. Methanogens, which are found in numerous environments including wetlands, marine sediments, hot springs and hydrothermal vents, are able to use carbon dioxide as a source of carbon for growth. In addition, the carbon dioxide is used as an electron acceptor in the production of methane. Methanogens are able to utilize the acetyl-CoA pathway to fix carbon dioxide.
Acetogens
Acetate producing bacteria, or acetogens, are a class of microorganisms that are able to generate acetate as a product of anaerobic respiration. This process, known as acetogenesis, will occur in organisms that are typically found in anaerobic environments. Acetogens are able to use carbon dioxide as a source of carbon and hydrogen as a source of energy.
5.12H: The 3-Hydroxypropionate Cycle
Learning Objectives
• Recall the two major phases and known steps in the 3-hydroxypropionate cycle
Carbon fixation is a key pathway in numerous microorganisms, resulting in the formation of organic compounds deemed necessary for cellular processes. One of the pathways that is utilized for carbon fixation is the 3-hydroxypropionate cycle. Specifically, in this cycle, the carbon dioxide is fixed by acetyl-CoA and propionyl-CoA carboxylases. This process results in the formation of malyl-CoA which is further split into acetyl-CoA and glyoxylate. Propionyl-CoA carboxylase is an enzyme that functions in the carboxylation of propionyl CoA. This enzyme functions in the mitochondrial matrix and is biotin dependent. The acetyl-CoA carboxylase utilized in this cycle is biotin-dependent as well and catalyzes the carboxylation of acetyl-CoA to malonyl-CoA.
This pathway produces pyruvate via conversion of bicarbonate and also results in the production of intermediates such as acetyl-CoA, gloxylate and succinyl-CoA. To date, this pathway has been identified in organisms classified as green non sulfur bacteria, specifically Chloroflexus aurantiacus () and in chemotrophic archaea. The green non sulfur bacteria uses reduced sulfur compounds, such as hydrogen sulfide or thiosulfate as an electron donor for metabolism. The ability of Chloroflexus aurantiacus to utilize this pathway is unique. The 3-hydroxypropionate cycle is a newly discovered pathway, thus, the exact details involving this process in regards to enzymes and intracellular components are still currently under investigation. However, the cycle can be broken down into two major phases, carbon dioxide fixation and glyoxylate assimilation. Glyoxylate, the conjugate base of glyoxylic acid, is the form that exists at a neutral pH. The importance of glyoxylate within microorganisms is in its ability to convert fatty acids into carbohydrates. Numerous types of organisms including bacteria, fungi and plants can utilize glyoxylate for these processes.
Key Points
• The 3-hydroxypropionate cycle is a newly identified pathway and many of the exact details which occur are currently under investigation.
• This pathway is utilized in green non sulfur bacteria such as Chloroflexus aurantiacus.
• The pathway can be divided into major phases which includes carbon dioxide fixation and gloxylate assimilation.
Key Terms
• glyoxylate: a salt or ester of glyoxylic acid
• carboxylation: A reaction that introduces a carboxylic acid into a molecule.
LICENSES AND ATTRIBUTIONS
CC LICENSED CONTENT, SPECIFIC ATTRIBUTION | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.12%3A_Biosynthesis/5.12G%3A_The_Acetyl-CoA_Pathway.txt |
Polysaccharides are synthesized from two forms of activated glucose molecules: UDP-glucose and ADP-glucose.
Learning Objectives
• Describe the mechanism of polysaccharide biosynthesis and its importance in bacteria
Key Points
• Uridine diphosphate glucose (UDP-glucose) is a nucleotide sugar. UDP-glucose consists of the pyrophosphate group, the pentose sugar ribose, glucose, and the nucleobase uracil. It is used as a substrate for enzymes called glucosyltransferases.
• UDP-glucose can also be used as a precursor of lipopolysaccharides, and peptidoglycan. ADP-glucose is usually the precursor for glycogen production in bacteria.
• When the cells are grown on a carbon source different than glucose, gluconeogenesis (abbreviated GNG) is the metabolic pathway used to produce glucose from non- carbohydrate carbon substrates such as phosphoenolpyruvate (PEP).
• Pathogenic bacteria can produce a thick, mucous-like, layer of polysaccharide. This “capsule” cloaks antigenic proteins on the bacterial surface. Bacteria and other microbes, secrete polysaccharides as an evolutionary adaptation to help them adhere to surfaces and to prevent them from drying out.
Key Terms
• Polysaccharides: Polysaccharides are long, carbohydrate molecules of repeated monomer units joined together by glycosidic bonds. They range in structure from linear to highly branched. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit.
• gluconeogenesis: Gluconeogenesis (abbreviated GNG) is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as pyruvate, lactate, glycerol, and glucogenic amino acids.
• glucosyltransferases: Glucosyltransferases are a type of glycosyltransferase that enable the transfer of glucose such as glycogen synthesis.
Polysaccharides are long carbohydrate molecules of repeated monomer units joined together by glycosidic bonds. They range in structure from linear to highly branched. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure, these macromolecules can have distinct properties from their monosaccharide building blocks. They may be amorphous or even insoluble in water.
One of the most common building block of polysaccharides is glucose. However, glucose has to be in its activated forms. There are two forms of activated glucose: UDP-glucose and ADP-glucose.
Uridine diphosphate glucose (uracil-diphosphate glucose, UDP-glucose) is a nucleotide sugar. Components UDP-glucose consists of the pyrophosphate group, the pentose sugar ribose, glucose, and the nucleobase uracil. It is used in nucleotide sugars metabolism as an activated form of glucose as a substrate for enzymes called glucosyltransferases. UDP-glucose can also be used as a precursor of lipopolysaccharides, and peptidoglycan. ADP-glucose is usually the precursor for glycogen production in bacteria.
When the cells are grown on a carbon source different than glucose, then polysaccharides are synthesized using a different pathway. Gluconeogenesis (abbreviated GNG) is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as phosphoenolpyruvate (PEP). PEP is formed from the decarboxylation of oxaloacetate and hydrolysis of one guanosine triphosphate molecule. This reaction is a rate-limiting step in gluconeogenesis.
Pathogenic bacteria commonly produce a thick, mucous-like, layer of polysaccharide. This “capsule” cloaks antigenic proteins on the bacterial surface that would otherwise provoke an immune response and thereby lead to the destruction of the bacteria. Bacteria and many other microbes, including fungi and algae, often secrete polysaccharides as an evolutionary adaptation to help them adhere to surfaces and to prevent them from drying out. Humans have developed some of these polysaccharides into useful products including xanthan gum, dextran, welan gum, gellan gum, diutan gum, and pullulan. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.13%3A_Anabolism/5.13A%3A_Polysaccharide_Biosynthesis.txt |
Many of the immune activating abilities of lipopolysaccharide can be attributed to the lipid A unit.
Learning Objectives
• Outline the characteristics and processes of lipid biosynthesis, including:; lipogenesis and fatty acid biosynthesis
Key Points
• Lipid A is a lipid component of an endotoxin held responsible for toxicity of Gram-negative bacteria.
• The synthesis of unsaturated fatty acids involves a desaturation reaction, whereby a double bond is introduced into the fatty acyl chain.
• In archaea, the mevalonate pathway produces reactive precursors isopentenyl pyrophosphate and dimethylallyl pyrophosphate from acetyl-CoA, while in plants and bacteria the non-mevalonate pathway uses pyruvate and glyceraldehyde 3-phosphate as substrates.
Key Terms
• lipid A: Lipid A is a lipid component of an endotoxin held responsible for toxicity of Gram-negative bacteria. It is the innermost of the three regions of the lipopolysaccharide (LPS, also called endotoxin) molecule, and its hydrophobic nature allows it to anchor the LPS to the outer membrane.
• endotoxin: Any toxin secreted by a microorganism and released into the surrounding environment only when it dies.
• lipogenesis: The biochemical production of fat, especially the conversion of carbohydrate into fat so that it may be stored as a long-term source of energy when food is scarce.
Lipids constitute a broad group of naturally occurring molecules that include fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides, phospholipids, and others. The main biological functions of lipids include energy storage, as structural components of cell membranes, and as important signaling molecules.
Lipids may be broadly defined as hydrophobic or amphiphilic small molecules. The amphiphilic nature of some lipids allows them to form structures such as vesicles, liposomes, or membranes in an aqueous environment. Biological lipids originate entirely or in part from two distinct types of biochemical subunits or “building-blocks”: ketoacyl and isoprene groups. Using this approach, lipids may be divided into eight categories: fatty acids, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids, and polyketides (derived from condensation of ketoacyl subunits); and sterol lipids and prenol lipids (derived from condensation of isoprene subunits).
Although humans and other mammals use various biosynthetic pathways to both break down and synthesize lipids, some essential lipids cannot be made this way and must be obtained from the diet.
In animals, when there is an oversupply of dietary carbohydrate, the excess carbohydrate is converted to triglycerides. This involves the synthesis of fatty acids from acetyl-CoA and the esterification of fatty acids in the production of triglycerides, a process called lipogenesis. Fatty acids are made by fatty acid synthases that polymerize and then reduce acetyl-CoA units. The acyl chains in the fatty acids are extended by a cycle of reactions that add the acetyl group, reduce it to an alcohol, dehydrate it to an alkene group and then reduce it again to an alkane group.
The enzymes of fatty acid biosynthesis are divided into two groups, in animals and fungi all these fatty acid synthase reactions are carried out by a single multifunctional protein, while in plant plastids and bacteria separate enzymes perform each step in the pathway. The fatty acids may be subsequently converted to triglycerides that are packaged in lipoproteins and secreted from the liver.
One important reaction that uses these activated isoprene donors is steroid biosynthesis. Here, the isoprene units are joined together to make squalene and then folded up and formed into a set of rings to make lanosterol. Lanosterol can then be converted into other steroids such as cholesterol and ergosterol. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.13%3A_Anabolism/5.13B%3A_Lipid_Biosynthesis.txt |
Attenuation is a regulatory feature found throughout Archaea and Bacteria domains which causes premature termination of transcription.
Learning Objectives
• Discuss how attenuation can regulate expression of biosynthetic enzymes
Key Points
• Attenuators may be classified according to the type of molecule that induces the change in RNA structure.
• Attenuator is a nucleotide sequence in DNA that can lead to premature termination of transcription.
• An example of attenuation is the trp gene in bacteria.
Key Terms
• transcription: The synthesis of RNA under the direction of DNA.
• termination: The process of terminating or the state of being terminated.
• Attenuation: Attenuation (in genetics) is a proposed mechanism of control in some bacterial operons that results in premature termination of transcription. It is based on the fact that, in bacteria, transcription and translation can and do proceed simultaneously.
Attenuation (in genetics) is a proposed mechanism of control in some bacterial operons that results in premature termination of transcription. It is based on the fact that, in bacteria, transcription and translation can and do proceed simultaneously. Attenuation involves a provisional stop signal (attenuator), located in the DNA segment that corresponds to the leader sequence of mRNA. During attenuation, the ribosome becomes stalled (delayed) in the attenuator region in the mRNA leader. Depending on the metabolic conditions, the attenuator either stops transcription at that point or allows read-through to the structural gene part of the mRNA and synthesis of the appropriate protein.
Attenuation is a regulatory feature found throughout Archaea and Bacteria causing premature termination of transcription. Attenuators are 5′-cis acting regulatory regions that fold into one of two alternative RNA structures that determine the success of transcription. The folding is modulated by a sensing mechanism producing either a Rho-independent terminator, resulting in interrupted transcription and a non-functional RNA product; or an anti-terminator structure, resulting in a functional RNA transcript. There are now many equivalent examples where the translation, not transcription, is terminated by sequestering the Shine-Dalgarno sequence (ribosomal binding site) in a hairpin-loop structure. While not meeting the previous definition of (transcriptional) attenuation, these are now considered to be variants of the same phenomena and are included in this article. Attenuation is an ancient regulatory system, prevalent in many bacterial species providing fast and sensitive regulation of gene operons and is commonly used to repress genes in the presence of their own product (or a downstream metabolite). What is an attenuator? Attenuator is a nucleotide sequence in DNA that can lead to premature termination of transcription.
Attenuators may be classified according to the type of molecule which induces the change in RNA structure. It is likely that transcription-attenuation mechanisms developed early, perhaps prior to the archaea/bacteria separation and have since evolved to use a number of different sensing molecules (the tryptophan biosynthetic operon has been found to use three different mechanisms in different organisms.)
An example is the trp gene in bacteria. When there is a high level of tryptophan in the region, it is inefficient for the bacterium to synthesize more. When the RNA polymerase binds and transcribes the trp gene, the ribosome will start translating. (This differs from eukaryotic cells, where RNA must exit the nucleus before translation starts.) The attenuator sequence, which is located between the mRNA leader sequence (5′ UTR) and trp operon gene sequence, contains four domains, where domain 3 can pair with domain 2 or domain 4.
The attenuator sequence at domain 1 contains instruction for peptide synthesis that requires tryptophans. A high level of tryptophan will permit ribosomes to translate the attenuator sequence domains 1 and 2, allowing domains 3 and 4 to form a hairpin structure, which results in termination of transcription of the trp operon. Since the protein coding genes are not transcribed due to rho independent termination, no tryptophan is synthesized.
In contrast, a low level of tryptophan means that the ribosome will stall at domain 1, causing the domains 2 and 3 to form a different hairpin structure that does not signal termination of transcription. Therefore, the rest of the operon will be transcribed and translated, so that tryptophan can be produced. Thus, domain 4 is an attenuator. Without domain 4, translation can continue regardless of the level of tryptophan. The attenuator sequence has its codons translated into a leader peptide, but is not part of the trp operon gene sequence. The attenuator allows more time for the attenuator sequence domains to form loop structures, but does not produce a protein that is used in later tryptophan synthesis. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.13%3A_Anabolism/5.13C%3A_Regulation_by_Biosynthetic_Enzymes.txt |
Polyhydroxyalkanoates or PHAs are linear polyesters produced in nature by bacterial fermentation of sugar or lipids.
Learning Objectives
• Summarize the process of PHA production and its applications
Key Points
• To produce PHA, a culture of a micro- organism such as Alcaligenes eutrophus is placed in a suitable medium and fed appropriate nutrients so that it multiplies rapidly.
• PHA synthases are the key enzymes of PHA biosynthesis.
• There are potential applications for PHA produced by micro-organisms within the medical and pharmaceutical industries, primarily due to their biodegradability.
Key Terms
• Polyhydroxyalkanoates: Polyhydroxyalkanoates or PHAs are linear polyesters produced in nature by bacterial fermentation of sugar or lipids.
• fermentation: Any of many anaerobic biochemical reactions in which an enzyme (or several enzymes produced by a microorganism) catalyses the conversion of one substance into another; especially the conversion (using yeast) of sugars to alcohol or acetic acid with the evolution of carbon dioxide.
• biodegradability: The capacity of a material to decompose over time as a result of biological activity, especially to be broken down by microorganisms
Polyhydroxyalkanoates, or PHAs, are linear polyesters produced in nature by bacterial fermentation of sugar or lipids. They are produced by the bacteria to store carbon and energy. More than 150 different monomers can be combined within this family to give materials extremely diverse properties. These plastics are biodegradeable and are used in the production of bioplastics. They can be either thermoplastic or elastomeric materials, with melting points ranging from 40 to 180°C.
The mechanical qualities and biocompatibility of PHA can also be changed by blending, modifying the surface or combining PHA with other polymers, enzymes and inorganic materials, making it possible for a wider range of applications.
PROCESS OF PHA PRODUCTION
To produce PHA, a culture of a micro-organism such as Alcaligenes eutrophus is placed in a suitable medium and fed appropriate nutrients so that it multiplies rapidly. The biosynthesis of PHA is usually caused by certain deficiency conditions (e.g. lack of macro elements such as phosphorus, nitrogen, trace elements, or lack of oxygen) and the excess supply of carbon sources. Recombinants Bacillus subtilis str. pBE2C1 and Bacillus subtilis str. pBE2C1AB were used in production of polyhydroxyalkanoates (PHA) and it was shown that they could use malt waste as carbon source for lower cost of PHA production. As raw material for the fermentation, carbohydrates such as glucose and sucrose can be used, but also vegetable oil or glycerine from biodiesel production. Researchers in the industry are working on methods with which transgenic crops will be developed that express PHA synthesis routes from bacteria and so produce PHA as energy storage in their tissues. Another group of researchers at Micromidas is working to develop methods of producing PHA from municipal waste water. Another even larger scale synthesis can be done with the help of soil organisms. For lack of nitrogen and phosphorus they produce a kilogram of PHA from three kilograms of sugar.
Polyesters are deposited in the form of highly refractive granules in the cells. Depending upon the microorganism and the cultivation conditions, homo- or copolyesters with different hydroxyalkanic acids are generated. PHAs granules are then recovered by disrupting the cells. In the industrial production of PHA, the polyester is extracted and purified from the bacteria by optimizing the conditions of microbial fermentation of sugar or glucose. Once the population has reached a substantial level, the nutrient composition is changed to force the micro-organism to synthesize PHA. The yield of PHA obtained from the intracellular inclusions can be as high as 80% of the organism’s dry weight.
PHA SYNTHASES
PHA synthases are the key enzymes of PHA biosynthesis. They use the coenzyme A – thioester of (r)-hydroxy fatty acids as substrates. The two classes of PHA synthases differ in the specific use of hydroxyfattyacids of short or medium chain length. The resulting PHA is of the two types: Poly (HA SCL) from hydroxy fatty acids with short chain lengths including three to five carbon atoms are synthesized by numerous bacteria, including Ralstonia eutropha and Alcaligenes latus (PHB). Poly (HA MCL) from hydroxy fatty acids with middle chain lengths including six to 14 carbon atoms, can be made for example, by Pseudomonas putida. A few bacteria, including Aeromonas hydrophila and Thiococcus pfennigii, synthesize copolyester from the above two types of hydroxy fatty acids. The simplest and most commonly occurring form of PHA is the fermentative production of poly-beta-hydroxybutyrate) (poly-3-hydroxybutyrate, P3HB), which consists of 1000 to 30000 hydroxy fatty acid monomers.
PHA APPLICATIONS
PHAs are processed mainly via injection molding, extrusion and extrusion bubbles into films and hollow bodies. A PHA copolymer called PHBV (poly(3-hydroxybutyrate-co-3-hydroxyvalerate)) is less stiff and tougher, and it may be used as packaging material. There are also applications for PHA produced by micro-organisms within the medical and pharmaceutical industries, primarily due to their biodegradability. Some of the fixation and orthopaedic applications that have been devised for these polymers include:
• sutures and suture fasteners
• meniscus repair and regeneration devices
• rivets, tacks, staples, and screws
• bone plates and bone plating systems
• surgical mesh, repair patches, and cardiovascular patches
• vein valves, bone marrow scaffolds
• ligament and tendon grafts
• ocular cell implants
• skin substitutes, bone graft substitutes, and wound dressings | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.13%3A_Anabolism/5.13D%3A_Bacterial_Polyesters.txt |
Polyketides are secondary metabolites produced from bacteria, fungi, plants, and animals.
Learning Objectives
• Describe the characteristics associated with polyketides, including: type I, II and III polyketides
Key Points
• Secondary metabolites are organic compounds that are not directly involved in the normal growth, development, or reproduction of an organism.
• Polyketides are usually biosynthesized through the decarboxylative condensation of malonyl-CoA derived extender units in a similar process to fatty acid biosynthesis.
• Polyketides are structurally a very diverse family of natural products with diverse biological activities and pharmacological properties.
Key Terms
• Polyketides: Polyketides are secondary metabolites from bacteria, fungi, plants, and animals. Polyketides are usually biosynthesized through the decarboxylative condensation of malonyl-CoA derived extender units in a similar process to fatty acid synthesis (a Claisen condensation).
• metabolites: Metabolites are the intermediates and products of metabolism. The term metabolite is usually restricted to small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones).
• biosynthesized: Biosynthesis (also called biogenesis or “anabolism”) is an enzyme-catalyzed process in cells of living organisms by which substrates are converted to more complex products. The biosynthesis process often consists of several enzymatic steps in which the product of one step is used as substrate in the following step.
Polyketides are secondary metabolites produced from bacteria, fungi, plants, and animals.
Secondary metabolites are organic compounds that are not directly involved in the normal growth, development, or reproduction of an organism. Unlike primary metabolites, the absence of secondary metabolites does not result in immediate death, but rather in long-term impairment of the organism’s survivability, fecundity, or aesthetics, or perhaps in no significant change at all. Secondary metabolites are often restricted to a narrow set of species within a phylogenetic group. Secondary metabolites often play an important role in plant defense against herbivory and other interspecies defenses. Humans use secondary metabolites as medicines, flavorings, and recreational drugs.
Polyketides are usually biosynthesized through the decarboxylative condensation of malonyl-CoA derived extender units in a similar process to fatty acid biosynthesis (a Claisen condensation). The polyketide chains produced by a minimal polyketide synthase are often further derivitized and modified into bioactive natural products.
Polyketides are structurally a very diverse family of natural products with diverse biological activities and pharmacological properties. They are broadly divided into three classes: type I polyketides (often macrolides produced by multimodular megasynthases), type II polyketides (often aromatic molecules produced by the iterative action of dissociated enzymes ), and type III polyketides (often small aromatic molecules produced by fungal species). Polyketide antibiotics, antifungals, cytostatics, anticholesteremic, antiparasitics, coccidiostats, animal growth promoters, and natural insecticides are in commercial use.
Examples of polyketides include: Macrolides; Pikromycin, the first isolated macrolide; the antibiotics erythromycin A; clarithromycin, and azithromycin; the immunosuppressant tacrolimus; Radicicol and Pochonin family (HSP90 inhibitor); Polyene antibiotics; Amphotericin; Tetracyclines and the tetracycline family of antibiotics.
Polyketides are synthesized by one or more specialized and highly complex polyketide synthase (PKS) enzymes.
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Learning Objectives
• Recognize the factors involved in amino acid synthesis
Amino acids are the structural units that make up proteins. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These polymers are linear and unbranched, with each amino acid within the chain attached to two neighboring amino acids. The process of making proteins is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome. The order in which the amino acids are added is read through the genetic code from an mRNA template, which is a RNA copy of one of the organism ‘s genes.
Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids. Of these, 20 are encoded by the universal genetic code. The remaining two, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode selenocysteine instead of a stop codon. Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded with the codon UAG, which is normally a stop codon in other organisms. Pyrrolysine (abbreviated as Pyl or O) is a naturally occurring amino acid similar to lysine, but with an added pyrroline ring linked to the end of the lysine side chain. Produced by a specific tRNA and aminoacyl tRNA synthetase, it forms part of an unusual genetic code in these organisms. It is considered the 22nd proteinogenic amino acid. This UAG codon is followed by a PYLIS downstream sequence.
Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all 20. Some simple parasites, such as the bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly from their hosts. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid. Amino acids are made into proteins by being joined together in a chain by peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an ester bond.
Aside from the 22 standard amino acids, there are many other amino acids that are called non-proteinogenic or non-standard. Those either are not found in proteins (for example carnitine, GABA) or are not produced directly and in isolation by standard cellular machinery (for example, hydroxyproline and selenomethionine). Non-standard amino acids that are found in proteins are formed by post-translational modification, which is modification after translation during protein synthesis. These modifications are often essential for the function or regulation of a protein. For example, the carboxylation of glutamate allows for better binding of calcium cations. The hydroxylation of proline is critical for maintaining connective tissues. Another example is the formation of hypusine in the translation initiation factor EIF5A, through modification of a lysine residue. Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane. Some nonstandard amino acids are not found in proteins. Examples include lanthionine, 2-aminoisobutyric acid, dehydroalanine, and the neurotransmitter gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids — for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism.
Key Points
• All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway.
• Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.
• Of the 22 amino acids naturally incorporated into proteins, 20 are encoded by the universal genetic code and the remaining two, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms.
Key Terms
• pyrrolysine: An amino acid found in methanogenic bacteria.
• selenocysteine: A naturally-occurring amino acid, present in several enzymes, whose structure is that of cysteine but with the sulfur atom replaced by one of selenium.
• genetic code: The set of rules by which the sequence of bases in DNA are translated into the amino acid sequence of proteins | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.14%3A_Amino_Acids_and_Nucleotide_Biosynthesis/5.14A%3A_Amino_Acid_Synthesis.txt |
Organisms vary in their ability to synthesize the 20 common amino acids, but most bacteria and plants can synthesize all 20.
Learning Objectives
• Recognize the factors involved in amino acid synthesis
Key Points
• All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway.
• Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid.
• Of the 22 amino acids naturally incorporated into proteins, 20 are encoded by the universal genetic code and the remaining two, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms.
Key Terms
• pyrrolysine: An amino acid found in methanogenic bacteria.
• selenocysteine: A naturally-occurring amino acid, present in several enzymes, whose structure is that of cysteine but with the sulfur atom replaced by one of selenium.
• genetic code: The set of rules by which the sequence of bases in DNA are translated into the amino acid sequence of proteins
Amino acids are the structural units that make up proteins. They join together to form short polymer chains called peptides or longer chains called either polypeptides or proteins. These polymers are linear and unbranched, with each amino acid within the chain attached to two neighboring amino acids. The process of making proteins is called translation and involves the step-by-step addition of amino acids to a growing protein chain by a ribozyme that is called a ribosome. The order in which the amino acids are added is read through the genetic code from an mRNA template, which is a RNA copy of one of the organism ‘s genes.
Twenty-two amino acids are naturally incorporated into polypeptides and are called proteinogenic or natural amino acids. Of these, 20 are encoded by the universal genetic code. The remaining two, selenocysteine and pyrrolysine, are incorporated into proteins by unique synthetic mechanisms. Selenocysteine is incorporated when the mRNA being translated includes a SECIS element, which causes the UGA codon to encode selenocysteine instead of a stop codon. Pyrrolysine is used by some methanogenic archaea in enzymes that they use to produce methane. It is coded with the codon UAG, which is normally a stop codon in other organisms. Pyrrolysine (abbreviated as Pyl or O) is a naturally occurring amino acid similar to lysine, but with an added pyrroline ring linked to the end of the lysine side chain. Produced by a specific tRNA and aminoacyl tRNA synthetase, it forms part of an unusual genetic code in these organisms. It is considered the 22nd proteinogenic amino acid. This UAG codon is followed by a PYLIS downstream sequence.
Structure of Pyrrolysine: Pyrrolysine (abbreviated as Pyl or O) is a naturally occurring, genetically coded amino acid used by some methanogenic archaea and one known bacterium in enzymes that are part of their methane-producing metabolism.
Organisms vary in their ability to synthesize the 20 common amino acids. Most bacteria and plants can synthesize all 20. Some simple parasites, such as the bacteria Mycoplasma pneumoniae, lack all amino acid synthesis and take their amino acids directly from their hosts. All amino acids are synthesized from intermediates in glycolysis, the citric acid cycle, or the pentose phosphate pathway. Nitrogen is provided by glutamate and glutamine. Amino acid synthesis depends on the formation of the appropriate alpha-keto acid, which is then transaminated to form an amino acid. Amino acids are made into proteins by being joined together in a chain by peptide bonds. Each different protein has a unique sequence of amino acid residues: this is its primary structure. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a huge variety of proteins. Proteins are made from amino acids that have been activated by attachment to a transfer RNA molecule through an ester bond.
Aside from the 22 standard amino acids, there are many other amino acids that are called non-proteinogenic or non-standard. Those either are not found in proteins (for example carnitine, GABA) or are not produced directly and in isolation by standard cellular machinery (for example, hydroxyproline and selenomethionine). Non-standard amino acids that are found in proteins are formed by post-translational modification, which is modification after translation during protein synthesis. These modifications are often essential for the function or regulation of a protein. For example, the carboxylation of glutamate allows for better binding of calcium cations. The hydroxylation of proline is critical for maintaining connective tissues. Another example is the formation of hypusine in the translation initiation factor EIF5A, through modification of a lysine residue. Such modifications can also determine the localization of the protein, e.g., the addition of long hydrophobic groups can cause a protein to bind to a phospholipid membrane. Some nonstandard amino acids are not found in proteins. Examples include lanthionine, 2-aminoisobutyric acid, dehydroalanine, and the neurotransmitter gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the metabolic pathways for standard amino acids — for example, ornithine and citrulline occur in the urea cycle, part of amino acid catabolism. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.14%3A_Amino_Acids_and_Nucleotide_Biosynthesis/5.14B%3A_Purine_and_Pyrimidine_Synthesis.txt |
Nonribosomal peptides (NRP) are a class of peptide secondary metabolites which can function as antibiotics.
Learning Objectives
• Outline the characteristics associated with nonribosomal peptides and the production of antibiotics
Key Points
• Nonribosomal peptides are produced by microorganisms like bacteria and fungi but are also found in higher organisms such as nudibranchs where they are thought to be made by bacteria inside these organisms.
• Nonribosomal peptides are synthesized by nonribosomal peptide synthetases, which, unlike the ribosomes, are independent of messenger RNA.
• The biosynthesis of nonribosomal peptides shares characteristics with the polyketide and fatty acid biosynthesis.
Key Terms
• peptide: A class of organic compounds consisting of various numbers of amino acids, in which the amine of one is reacted with the carboxylic acid of the next to form an amide bond.
• metabolite: Any substance produced by, or taking part in, a metabolic reaction.
• siderophores: Sidereophores are small, high-affinity iron chelating compounds secreted by microorganisms such as bacteria and fungi, and also grasses. Siderophores are amongst the strongest soluble Fe3+ binding agents known.
Nonribosomal peptides (NRP) are a class of peptide secondary metabolites, usually produced by microorganisms like bacteria and fungi. Nonribosomal peptides are also found in higher organisms (such as nudibranchs) but are thought to be made by bacteria inside these organisms. While there exists a wide range of peptides that are not synthesized by ribosomes, the term nonribosomal peptide typically refers to a very specific set of these as discussed in this article.
Nonribosomal peptides are synthesized by nonribosomal peptide synthetases, which, unlike the ribosomes, are independent of messenger RNA. Each nonribosomal peptide synthetase can synthesize only one type of peptide. Nonribosomal peptides often have a cyclic and/or branched structures, can contain non-proteinogenic amino acids including D-amino acids, carry modifications like N-methyl and N-formyl groups, or are glycosylated, acylated, halogenated, or hydroxylated. Cyclization of amino acids against the peptide “backbone” is often performed, resulting in oxazolines and thiazolines; these can be further oxidized or reduced. On occasion, dehydration is performed on serines, resulting in dehydroalanine. This is just a sampling of the various manipulations and variations that nonribosomal peptides can perform. Nonribosomal peptides are often dimers or trimers of identical sequences chained together or cyclized, or even branched.
Actinomycin D: Actinomycin D (also known generically as Actinomycin or Dactinomycin), is the most significant member of actinomycines, which are a class of polypeptide antibiotics isolated from soil bacteria of the genus Streptomyces. As one of the older chemotherapy drugs, it has been used for many years.
Nonribosomal peptides are a very diverse family of natural products with an extremely broad range of biological activities and pharmacological properties. They are often toxins, siderophores, or pigments. Nonribosomal peptide antibiotics (for example, actinomycin D ), cytostatics, and immunosuppressants are used commercially.
Nonribosomal peptides are synthesized by one or more specialized nonribosomal peptide-synthetase (NRPS) enzymes. The NRPS genes for a certain peptide are usually organized in one operon in bacteria and in gene clusters in eukaryotes. However the first fungal NRP to be found was ciclosporin. It is synthesized by a single 1.6MDa NRPS. The enzymes are organized in modules that are responsible for the introduction of one additional amino acid. Each module consists of several domains with defined functions, separated by short spacer regions of about 15 amino acids.
The biosynthesis of nonribosomal peptides shares characteristics with the polyketide and fatty acid biosynthesis. Due to these structural and mechanistic similarities, some nonribosomal peptide synthetases contain polyketide synthase modules for the insertion of acetate or propionate-derived subunits into the peptide chain. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.14%3A_Amino_Acids_and_Nucleotide_Biosynthesis/5.14C%3A_Nonribosomal_Peptide_Antibiotics.txt |
Porphyrins are the conjugate acids of ligands that bind metals to form complexes.
Learning Objectives
• Recall the process of tetrapyrrole biosynthesis
Key Points
• Porphyrins are a group of organic compounds, many naturally occurring, such as heme.
• Porphyrins are aromatic, obeying Hückel’s rule for aromaticity, possessing 4n+2 π electrons (n=4 for the shortest cyclic path) delocalized over the macrocycle.
• Porphyrin macrocycles are highly conjugated systems and typically have very intense absorption bands in the visible region, and may be deeply colored.
Key Terms
• heterocyclic: Having one or more atoms other than carbon in at least one of its rings.
• porphyrin: Any of a class of heterocyclic compounds containing four pyrrole rings arranged in a square; they are important in biochemistry in a form with a metal atom in the central cavity (hemoglobin with iron, chlorophyll with magnesium, etc.).
• aromatic: Having a closed ring of alternate single and double bonds with delocalized electrons.
Porphyrins are a group of organic compounds, many naturally occurring. One of the best-known porphyrins is heme, the pigment in red blood cells. Heme is a cofactor of the protein hemoglobin. The main “application” of porphyrins is their role in supporting aerobic life. For example, complexes of meso-tetraphenylporphyrin, e.g., the iron(III) chloride complex (TPPFeCl), catalyze a variety of reactions of potential interest in organic synthesis.
Porphyrins are heterocyclic macrocycles composed of four modified pyrrole subunits interconnected at their α carbon atoms via methine bridges (=CH-). Porphyrins are aromatic, obeying Hückel’s rule for aromaticity, possessing 4n+2 π electrons (n=4 for the shortest cyclic path) delocalized over the macrocycle. Thus, porphyrin macrocycles are highly conjugated systems. As a consequence, they typically have very intense absorption bands in the visible region and may be deeply colored. (The name porphyrin comes from a Greek word for purple. ) The macrocycle has 26 pi electrons in total. The parent porphyrin is porphine, and substituted porphines are called porphyrins.
Porphyrins are the conjugate acids of ligands that bind metals to form complexes. The metal ion usually has a charge of 2+ or 3+. A schematic equation for these syntheses is:
H2porphyrin + [MLn]2+ → M(porphyrinate)Ln-4 + 4 L + 2 H+
where M=metal ion and L=a ligand
A porphyrin without a metal ion in its cavity is a free base. Some iron-containing porphyrins are called hemes. Heme-containing proteins, or hemoproteins, are found extensively in nature. Hemoglobin and myoglobin are two O2-binding proteins that contain iron porphyrins. Various cytochromes are also hemoproteins. Several other heterocycles are related to porphyrins. These include corrins, chlorins, bacteriochlorophylls and corphins. Chlorins (2,3-dihydroporphyrin) are more reduced, contain more hydrogen than porphyrins, and feature a pyrroline subunit. This structure occurs in a chlorophyll molecule. Replacement of two of the four pyrrolic subunits with pyrrolinic subunits results in either a bacteriochlorin (as found in some photosynthetic bacteria) or an isobacteriochlorin, depending on the relative positions of the reduced rings. Some porphyrin derivatives follow Hückel’s rule, but most do not.
The “committed step” for porphyrin biosynthesis is the formation of δ-aminolevulinic acid (δ-ALA, 5-ALA or dALA) by the reaction of the amino acid glycine with succinyl-CoA from the citric acid cycle. Two molecules of dALA combine to give porphobilinogen (PBG), which contains a pyrrole ring. Four PBGs are then combined through deamination into hydroxymethyl bilane (HMB), which is hydrolysed to form the circular tetrapyrrole uroporphyrinogen III. This molecule undergoes a number of further modifications. Intermediates are used in different species to form particular substances, but, in humans, the main end-product protoporphyrin IX is combined with iron to form heme. Bile pigments are the breakdown products of heme.
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Learning Objectives
• Describe the importance of nitrogen fixation
Nitrogen fixation also refers to other biological conversions of nitrogen, such as its conversion to nitrogen dioxide. Nitrogen fixation is a process by which nitrogen (N2) in the atmosphere is converted into ammonia (NH3). Atmospheric nitrogen or elemental nitrogen (N2) is relatively inert: it does not easily react with other chemicals to form new compounds. Dinitrogen is quite inert because of the strength of its N≡N triple bond. To break one nitrogen atom away from another requires breaking all three of these chemical bonds. Fixation processes free up the nitrogen atoms from their diatomic form (N2) to be used in other ways. Nitrogen fixation, natural and synthetic, is essential for all forms of life because nitrogen is required to biosynthesize basic building blocks of plants, animals, and other life forms, e.g., nucleotides for DNA and RNA and amino acids for proteins. Therefore, nitrogen fixation is essential for agriculture and the manufacture of fertilizer. Microorganisms that fix nitrogen are bacteria called diazotrophs.
Some higher plants, and some animals (termites), have formed associations (symbioses) with diazotrophs. Diazotrophs are microbes. They are intensively studied by microbiologists. Biological nitrogen fixation was discovered by the German agronomist Hermann Hellriegel and Dutch microbiologist Martinus Beijerinck. Biological nitrogen fixation (BNF) occurs when atmospheric nitrogen is converted to ammonia by an enzyme called nitrogenase. Nitrogenases are enzymes used by some organisms to fix atmospheric nitrogen gas (N2). There is only one known family of enzymes that accomplishes this process. All nitrogenases have an iron – and sulfur-containing cofactor that includes a heterometal complex in the active site (e.g., FeMoCo). In most species, this heterometal complex has a central molybdenum atom. However, in some species it is replaced by a vanadium or iron atom. Enzymes responsible for nitrogenase action are very susceptible to destruction by oxygen. Many bacteria cease production of the enzyme in the presence of oxygen. Many nitrogen-fixing organisms exist only in anaerobic conditions, respiring to draw down oxygen levels, or binding the oxygen with proteins.
Key Points
• Nitrogen fixation takes elemental nitrogen (N2) and converts it into a ammonia, a format usable by biological organism.
• The fixed form of nitrogen (NH3) is needed as an essential component of DNA and proteins. Therefore, it is needed for all life on earth.
• Nitrogen fixation is carried out by the enzyme nitrogenase, which are found in microbes.
Key Terms
• fixation: The act of uniting chemically with a solid substance or in a solid form; reduction to a non-volatile condition; — said of gaseous elements.
• cofactor: A substance, especially a coenzyme or a metal, that must be present for an enzyme to function.
• heterometal: Describing a complex containing two (or more) different metals
• nitrogen fixation: the conversion of atmospheric nitrogen into ammonia and organic derivatives, by natural means, especially such conversion, by microorganisms in the soil, into a form that can be assimilated by plants
5.15B: Early Discoveries in Nitrogen Fixation
Learning Objectives
• Outline the early discoveries of nitrogen fixation
For thousands of years farmers were aware that plants belonging to the legume family, such as peas and soy beans, promoted crop growth when planted with other non-legumes such as wheat. Growing a legume crop in a field could also result in the next year’s crop of non-legume plants giving a far greater yield. This led to the practice of crop rotation, a practice which can be traced back to techniques recorded in Roman literature.
While the ancient Romans were aware of the improved results gained through crop rotation, they did not know that these benefits were brought about through the replenishment of nitrogen in the soil. Later people knew legumes did replenish nitrogen in the soil, but did not know how atmospheric (N2) was converted into ammonium (NH3) by legumes until research done in the 19thcentury. Hermann Hellriegel (1831-1895), a noted German agricultural chemist, discovered that leguminous plants took atmospheric nitrogen and replenished the ammonium in the soil through the process now known as nitrogen fixation. He found that the nodules on the roots of legumes are the location where nitrogen fixation takes place.
HELLRIEGEL’S AND BEIJERINCK’S DISCOVERIES
Hellriegel did not determine what factors in the root nodules carried out nitrogen fixation. Martinus Willem Beijerinck (March 16, 1851 – January 1, 1931), a Dutch microbiologist and botanist, explored the mechanism responsible, discovering that the root nodules contained microbes. He further demonstrated that these microbes were bacteria, which he named rhizobia. These rhizobia perform the chemical processes of nitrogen fixation. In addition to having discovered this biochemical reaction vital to soil fertility and agriculture, Beijerinck is responsible for the discovery of this classic example of symbiosis between plants and bacteria. The bacteria in the root nodules are needed to provide nitrogen for legume growth, while the rhizobia are dependent on the root nodules as a environment to grow.and a source of nutrition.
Key Points
• A key benefit of crop rotation is the introduction of nitrogen into the soil. Although farmers have used this technique for millennia, it wasn’t until the 19th century scientists determined how this fertilization occurred.
• Nitrogen fixation occurs in root nodules of plants belonging to the legume family.
• The root nodules of legumes contain symbiotic bacteria which contain the enzymes needed for nitrogen fixation.
Key Terms
• legume: Any of a large family (Leguminosae syn. Fabaceae) of dicotyledonous herbs, shrubs, and trees having fruits that are legumes or loments, bearing nodules on the roots that contain nitrogen-fixing bacteria, and including important food and forage plants (as peas, beans, or clovers).
• symbiosis: A close, prolonged association between two or more organisms of different species, regardless of benefit to the members. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.15%3A_Nitrogen_Fixation/5.15A%3A_Nitrogenase_and_Nitrogen_Fixation.txt |
Learning Objectives
• Distinguish between component I and II of the nitrogenase enzyme and its role in biological nitrogen fixation
Biological nitrogen fixation (BNF) occurs when atmospheric nitrogen is converted to ammonia by an enzyme called nitrogenase. The reaction for BNF is:
\[\ce{N2 + 8 H^{+} + 8 e^{−} → 2 NH3 + H2}.\]
This type of reaction results in N2 gaining electrons (see above equation) and is thus termed a reduction reaction. The exact mechanism of catalysis is unknown due to the technical difficulties biochemists have in actually visualizing this reaction in vitro, so the exact sequence of the steps of this reaction are not completely understood. Despite this, a great deal is known of the process. While the equilibrium formation of ammonia from molecular hydrogen and nitrogen has an overall negative enthalpy of reaction (i.e. it gives off energy), the energy barrier to activation is very high without the assistance of catalysis, which is done by nitrogenases. The enzymatic reduction of N2 to ammonia therefore requires an input of chemical energy, released from ATP hydrolysis, to overcome the activation energy barrier.
Nitrogenase is made up of two soluble proteins: component I and II. Component I known as MoFe protein or nitrogenase contains 2 Mo atoms, 28 to 34 Fe atoms, and 26 to 28 acid-labile sulfides, also known as a iron-molybdenum cofactor (FeMoco). Component I is composed of two copies each of two subunits (α and β); each subunit’s stability depends on the other in vivo. Component II known as Fe protein or nitrogenase reductase is composed of two copies of a single subunit. This protein has four non-heme Fe atoms and four acid-labile sulfides (4Fe-4S). Substrate binding and reduction takes place on component I, which binds to ATP and ferredoxin or flavodoxin proteins (Fdx or Fld) (see step B).
The hydrolysis of ATP supplies the energy for the reaction while the Fdx/Fld proteins supply the electrons. Note this is a reduction reaction which means that electrons must be added to the N2 to reduce it to NH4. Thus, the role of component II is to supply electrons, one at a time to component I. ATP is not hydrolyzed to ADP until component II transfers an electron to component I (see step C and D). 21-25 ATPs are required for each N2 fixed. The association of nitrogenase component I and II and later dissociation occurs several times to allow the fixation of one N2 molecule (see step B and D).
Nitrogenase ultimately bonds each atom of nitrogen to three hydrogen atoms to form ammonia (NH3). The nitrogenase reaction additionally produces molecular hydrogen as a side product, which is of special interest for people trying to produce H2 as an alternative energy source to fossil fuels.
Key Points
• Nitrogen fixation does result in the release of energy, but the activation of this reaction takes energy in the form of ATP hydrolysis.
• Nitrogenases are metalloenzymes, which are proteins that have metalic molecules as subunits.
• While a great deal is known about how nitrogenases reduce nitrogen, some steps are unknown.
Key Terms
• sulfide: Any compound of sulfur and a metal or other electropositive element or group.
• reduction: A reaction in which electrons are gained and valence is reduced; often by the removal of oxygen or the addition of hydrogen.
• enthalpy: In thermodynamics, a measure of the heat content of a chemical or physical system. | textbooks/bio/Microbiology/Microbiology_(Boundless)/05%3A_Microbial_Metabolism/5.15%3A_Nitrogen_Fixation/5.15C%3A_Nitrogen_Fixation_Mechanism.txt |
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