Microbiology Chapter 8: Microbial Metabolism

pH

A ___ above or below optimal ___ will alter enzyme structure by disrupting bonds and leading to a decreased reaction rate. Extreme changes in ___ can lead to protein denaturation. Example: Amylase, an enzyme in human saliva, is active in the mouth, but is quickly deactivated when it reaches the low ___ of the stomach. Stomach acid interferes with activity of many enzymes, which limits bacterial growth in that organ. Most pathogens prefer a neutral ___, but some bacteria have special adaptions that allow them to live in ___ extremes. Example: H. pylori can thrive in the low ___ environment of the stomach and cause stomach ulcers.

FADH2

A coenzyme that is the reduced form of FAD. Acts as an electron sponge. Help enzymes in redox reactions to extract energy from carbs, fats, and proteins.

NADH

A coenzyme that is the reduced form of NAD+. Acts as an electron sponge. Help enzymes in redox reactions to extract energy from carbs, fats, and proteins.

Oxidative Phosphorylation

A phosphorylation mechanism to recharge ADP to ATP. Involves a collection of redox reactions. Electrons are stripped from a food source (such as carbs, fats, or proteins) and are eventually handed to an electron transport chain to fuel the phosphorylation of ADP to ATP. Used in aerobic and anaerobic electron transport chains of cellular respiration. ADP is recharged to ATP using electron transport chains that are powered by nutrients. The last stage of cellular respiration and the step where most ATP is made.

Substrate-Level Phosphorylation

A phosphorylation mechanism to recharge ADP to ATP. Occurs when an enzyme transfers a phosphoryl group (PO3 2-) from a donor substrate directly to ADP to make ATP. Electron transport chain is not used. Used in glycolysis, Krebs cycle, and fermentation. What many bacteria use. Phosphoryl group donors are called high-energy intermediates.

Photophosphorylation

A phosphorylation mechanism to recharge ADP to ATP. Relies on the redox reactions of an electron transport chain. Light energy is used to activate electrons. Only photosynthetic cells can perform this. Used in light-dependent reactions of photosynthesis. ADP is recharged to ATP using electron transport chains powered by solar energy.

Anabolic Pathways

ATP provides energy for these reactions. Combine energy and molecules to build new substances. ____ reactions, also called biosynthetic reactions, involve dehydration synthesis reactions and tend to be endergonic. "Ana" is Greek for "up". Example: Amino acids build proteins, nucleotides build nucleic acids, and simple sugars build polysaccharides. Often coupled with catabolic reactions. Use energy from catabolic reactions to build molecules. Include the building of large macromolecules from building-block precursors. Reuses energy released from catabolic reactions to build new, more complex molecules.

ATP-ADP Cycle

Adding and removing of the terminal phosphate group. The terminal phosphate group can be removed from ATP via dephosphorylation to form ADP and releases energy for anabolism. Energy from catabolism "recharges" ADP to add a phosphate group via phosphorylation to make ATP.

Holoenzyme

An enzyme with its cofactor (active form).

Apoenzyme

An enzyme without its cofactor (inactive form).

Cellular Respiration

Collection of reactions that extract energy from foods using redox reactions and then transfer that energy into the bonds of ATP. How cells primarily extract energy from carbs. Can be aerobic or anaerobic. Occurs through combined efforts of glycolysis, an intermediate step, Krebs cycle, and electron transport chain.

Purines and Pyrimidines

Collectively called nitrogenous bases because they are weakly basic, nitrogen-containing compounds. Can be built as completely new molecules from scratch (de novo synthesis) or they can be recycled. Essential ingredients in nucleic acids (DNA and RNA) and in energy-carrying molecules like ATP. Purines are A and G which are used to make DNA and RNA. Other naturally occurring purines such as caffeine and uric acid, which is found in kidney stones. Pyrimidines are structurally and functionally related to purines and include molecules such as U, T, and C.

ADP

Contains 2 phosphate groups. Released by removing the terminal phosphate group from ATP via dephosphorylation. When a cell needs more ATP, it can add back a phosphate group to ____ via phosphorylation.

Phosphatases

Enzymes that use dephosphorylation reactions to remove phosphate groups from their targets.

Kinases

Enzymes that use phosphorylation reactions to add phosphate groups to their targets.

Lithotrophs

Get reducing power from inorganic sources to fuel anabolic processes. Example: Inorganic sources of electrons for reducing power are metals, H2S, and elemental hydrogen.

Organotrophs

Get reducing power from organic sources to fuel anabolic processes. Example: Most common organic course of reducing power is glucose. All animals, all fungi, and most pathogenic bacteria are ___.

Cofactors

Help enzymes function. Bind to enzyme and gives it a confirmation that makes the substrate fit better. Nonprotein components to help enzymes perform a function. Some enzymes require ___ to carry out a reaction. Do not necessarily affect whether a substrate can bind to the enzyme, but are often require for the actual chemical reaction to occur. Example: Iron, zinc, magnesium, and calcium are inorganic ___ that may help catalyze a reaction by forming a bridge between the enzyme and the substrate. Many trace elements also act as inorganic ___. Organic ____ are called coenzymes.

Polysaccharide Biosynthesis

Important process for peptidoglycan (made by F6P) synthesis for bacterial cell walls.

Noncompetitive Inhibitors

Inhibitors that decrease enzyme activity by binding to the enzyme at a site other than the active site. Can bind reversibly or irreversibly. Sometimes they deform the enzyme's structure so substrates cannot interact with the active site. In most cases, ____ and the substrate can simultaneously bind to the enzyme, but the enzyme's activity is decreases since the ____ distorts the enzyme's normal structure. Example: lead can build up to a point that it impacts enough host enzymes to cause lead poisoning.

Competitive Inhibitors

Inhibitors that slow reactions by competing with a substrate for the target enzyme's active site. The affected enzyme cannot carry out the reaction until the ____ leaves the active site and the substrate can enter. The ____ can be overcome if the concentration of the substrate is greater than the concentration of the ____. Example: The antibiotic sulfanilamide. Because PABA (the normal substrate) and sulfanilamide have similar structures, they compete with each other for the active site of an enzyme important in folic acid production. When the sulfanilamide enters the enzyme instead of PABA, folic acid production decreases. The affected bacterial cell soon suffers from a lack of folic acid, stops growing, and eventually dies. Since we get folic acid from our diet and human cells cannot make it, sulfanilamide selectively affects bacterial cells without causing harm to human cells.

Entner-Duodoroff Pathway

Pathway found primarily in Gram-negative bacteria that require oxygen to grow (obligate aerobes). Also found in certain facultative anaerobes, select Gram-positive bacteria, and some eukaryotic microbes. Catabolizes glucose. Less efficient than glycolysis because it only produces 1 ATP per glucose molecule. Makes NADPH (unlike NADH made in glycolysis), which is used in anabolic reactions. E. coli requires this pathway to successfully colonize the intestines of mammals. Not found in human cells.

Amphibolic Pathways

Pathways that have a dual role, and can be used for both breaking down and building substances. Simultaneously function in anabolism and catabolism.

Catalase Test

Test that detects if an organism has the enzyme catalase, which protects organisms from toxic oxygen radicals. Performed by adding H2O2 to the test specimen. If catalase is present, it will break the H2O2 down into water and gaseous oxygen. The oxygen is released as bubbles and is easily seen in the puddle of H2O2 on the sample smear. If bubbles are made, the organism is catalase positive. An organism that is catalase negative will be unable to break the H2O2 down into oxygen and water and will not generate bubbles. Most aerobes and facultative anaerobes are catalase positive. Most anaerobes are catalase negative.

Amino Acid Catabolism Tests

Tests that detect catabolism of a specific amino acid. They look for specific enzymes, such as deaminases and decarboxylases, that some cells use to catabolize a defined amino acid that is included in the test medium. Helpful in identifying certain enteric bacteria based on their amino acid catabolism profiles. Example: Sulfur reduction test. Salmonella species are differentiated from E. coli based on their ability to make H2S by catabolizing amino acids that contain sulfur. In media used to detect the production of H2S, the H2S combines with iron to form a black precipitate. Examples: Phenylalanine deaminase test, and the ornithine decarboxylase test.

Intermediate Step

The 2 pyruvates made in glycolysis are made in 2 acetyl-CoAs (2-C molecules), and releases CO2. Occurs in the cytoplasm of prokaryotic cells and the mitochondrial matrix of eukaryotic cells. This is the transitory step between gylcolysis and the Krebs cycle. This represents the first time carons are lost (as CO2) in cellular respiration.

Gluconeogenesis

The chemical process of building glucose from non-sugar starting materials. Once glucose molecules are built, cells can assembly them into polysaccharides such as glycogen and starch.

Glycogenesis

The production of glycogen (branched polymer of glucose) from glucose. Bacteria make glycogen by chemically modifying G6P.

Allosteric Site

The site where an allosteric inhibitor or allosteric activator binds on an enzyme. A site on the enzyme other than the active site.

Oxidase Test

This test detects if the electron carrier called cytochrome c oxidase is present. Used to identify bacteria. Example: Neisseria gonorrhoeae cause the STI gonorrhea, has the cytochrome c oxidase and is said to be "oxidase positive". Example: Salmonella species cause foodborne illnesses, do not have cyctochrome c oxidase and are "oxidase negative". Organisms that have cytochromce c oxidase can use oxygen as a final electron acceptor.

Aerobic Respiratory Chains

Used in aerobic cellular respiration, and require oxygen as a final electron acceptor. Depend on membrane-associated electron carrier molecules to carry out redox reactions. Electrons are passing from higher to lower energy states. Theoretically make a maximum of 38 ATP from one molecule of glucose. Oxygen that is central to ______ is eventually reduced to water.

Anaerobic Respiratory Chains

Used in anaerobic cellular respiration, and use an inorganic substance (nitrite or nitrate) other than oxygen as the final electron acceptor. Depend on membrane-associated electron carrier molecules to carry out redox reactions. Electrons are passing from higher to lower energy states. Diverse species in a number of biological niches here oxygen is limited use ____. These environments range from intestinal tract to the organic sludge at the bottom of marshes and ponds.

Pentose Phosphate Pathway

Uses a carbon-shuffling process to convert pentoses (5-C sugars) into trioses (3-C sugars) and hexoses (6-C sugars) that can be directly funneled into glycolysis. Produces NADPH coenzyme, which is used in anabolic pathways. Can shift G6P away from glycolysis, repurposing it to make pentoses (building blocks for amino acids and nucleotides). Used by many bacteria including Bacillus subtilis and E. coli. Also used by some eukaryotes including human red blood cells.

Reduction

When an atom or molecule gains an electron. Sugars and fats are highly ___ because they contain abundant hydrocarbon bonds and will thus make more ATP. Proteins are less ____, and will make less ATP. Therefore, your body prefers sugars and fats first, and then goes to proteins for energy.

Oxidation

When an atom or molecule loses an electron. Cells harvest energy from nutrients by ____ them.

Enzyme Activity

Cofactors, temp, pH, amount of substrate present, phosphorylation state, and the presence of inhibitors can all affect ____.

Electron Transport Chain

As electrons are passed from carrier to carrier, energy is released. The released energy is used to pump protons across the membrane that houses the carrier molecules. Uses many different electron carriers. The organization of the ___ can differ between prokaryotic and eukaryotic cells, and even one bacterial cell could have several types of ____. This diversity in ____ carrier molecules is sometimes used to identify bacteria. Where NADH and FADH2 harvest protons that are used to make a proton motive force. It is ATP synthase that phosphorylates ADP back to ATP. Made 34 ATPs. When oxygen is the final electron acceptor, water is made. Occurs in the plasma membrane of prokaryotic cells and the inner mitochondrial membrane of eukaryotic cells. Carry out coordinated redox reactions that transfer electrons from donor molecules to acceptor molecules. Drives oxidative phosphorylation and photophosphorlyation.

Heterotrophs

Cannot fix carbon. Require an external source of organic carbon in order to live and grow. Multicellular animals, such as humans, are ____. The storage molecule of glucose in humans is glycogen.

Metabolism

Chemical reactions that organisms use to break down substances to release energy as well as reactions that use the released energy to build new substances.

Fermentation Tests

Biochemical test commonly used to identify an unknown species. Involve inoculating a pure culture of bacteria into the fermentation test media and then observing the medium after the specimen has had time to grow. Can be used to distinguish pathogens from harmless bacteria. Example: Commensal E. coli ferment the carb sorbitol and the pathogenic E. coli O157:H7 strain does nor ferment sorbitol. Media contains protein, a single carb, pH indicator (used to detect drop in pH), and sometimes an inverted Durham tube that captures gas. Fermentation pathways tend to produce acids. Accumulation of acidic end products with decrease the pH of the medium and change the color. Some organisms make gas and acid when they ferment carbs; in such a case, the gas formed would be captured in the inverted Durham tube and a bubble would be seen.

Catabolic Pathways

Break down substances and release energy. Makes ATP. _____ reactions are generally hydrolytic and exergonic. "Cata" is Greek for "down". Example: A cell breaking down sugars into CO2 and H2O. Often coupled with anabolic reactions. Splits bigger molecules into smaller components, releasing energy in the process.

ATP

Key molecules for energy supply for catabolic and anabolic reactions. All cells require __ to do cellular work. If a cell loses its ability to make ___, it will die. ___ is made by catabolic reactions and provides the energy for anabolic reactions. Most widely nucleoside triphosphate used by cells. Certain enzymes make it possible for cells to readily phoshporylate ____, making it an excellent molecule to fuel a cell's work. The higher the energy of a starting molecule, the more ___ will be made when that molecule is cashed in through metabolic pathways. Example: fats contain more chemical energy in their bonds than do carbs, so catabolizing one lipid molecule would produce more ___ for a cell than catabolizing one glucose molecule. ____ is made on demand because cells use so much that they could never effectively store enough. In humans, an average adult burns through 132 lbs of ____ per day. Cells store energy in fats, proteins, and polysaccharides, and cash in these more complex molecules to create __ as needed. The cash that cells get when they break down nutrients. Made of adenine, ribose, and 3 phosphate groups. Removing the terminal phosphate group from ___ by dephosphorylation releases energy and ADP. ___ is like metabolic money.

Temperature

Lower ____, enzyme activity decreases, and cells grow slower. This is why keeping food at cold ___ usually slows food spoilage. Warmer __, enzyme activity increases. ___ above an enzymes optimal ____ (the ___ where an enzyme's activity is highest) significantly reduces enzyme activity. High ___ can cause enzymes and other proteins to become denatured, or lose their 3D structure and become non-functional. All proteins have a ___ at which they denature. For most pathogenic bacteria and human cells, ___ above 41 C (105.8 F) can lead to protein denaturation. This is partially why a high fever can be dangerous.

Ribozymes

Made of the nucleic acid RNA and they have a more limited range of substrates. Man-made ___ hold promise as drug therapies, especially in genetic disorders and as antiviral therapies. Specialized catalytic RNA molecules. Only been show to act on other RNA molecules.

Glycolysis

Means of splitting sugar. Extracts energy from complex carbs such as starches, from disaccharides like sucrose and lactose, and from simple sugars such as mannose, fructose, and glucose. Starts with glucose (6-C sugar) and invests 2 ATPs. Ends with 2 pyruvates and 4 ATPS. Net gain of 2 ATPs, so 2 molecules of ATP are made for each molecule of glucose that is oxidized in ____. NAD+ is reduced to NADH, which contains the energy that will be harvested later using the electron transport chain. Uses substrate-level phosphorylation to make ATP. Does not require oxygen. Occurs in the cytoplasm of eukaryotic and prokaryotic cells. Requires glucose, and an initial investment of energy (2 ATPs) to get reaction going.

Saprobes

Most fungi that feed on dead organic material to survive.

Coenzymes

Organic cofactors. Nonprotein factors that range from free molecules that can move about to factors that are anchored to the enzyme they assist. Often vitamins or are made from vitamins. In cells, often collect electrons from one reaction and shuttle them to other reactions in the cell. Can pick up and drop off electrons over and over again. If the electron carrier ______ is occupied (has electron passengers), it must drop off those electrons before it can pick up more. NAD+ and NADP+ exist as free molecules in a cell. FMN and FAD are anchored to enzymes and are sometimes called prosthetic groups. Many of the B vitamins are ____ and are needed for electron transfer in cellular metabolisms.

Anaerobic Organism

Organisms that do not require oxygen as their final electron acceptor. Example: Use nitrate, carbonate, and sulfate. May be unable to grow in presence of oxygen because they are not well equipped to deal with toxic oxygen intermediates such as oxygen radicals. Microbes that carry out anaerobic respiration are centrally important to our carbon, nitrogen, and sulfur cycles that sustain our planet. Anaerobic respiration makes less ATP than aerobic respiration.

Enzymes

Protein catalysts that help chemical reactions occur under cellular conditions. Tools that cells use to hold reactants in their proper orientation and lower the energy required for starting the reaction. Help chemical reactions occur under physiological conditions and within a time frame conductive to life. Facilitate the ATP-ADP cycle and guarantees that nutrients are not needlessly funneled into catabolic pathways to make ATP when the cell would be better served by storing them for later use as carbs, fats, or proteins. Can denature through contact with strong acids, bases, detergents, alcohol, radiation, and heavy metals such as ions of lead, arsenic, or mercury. Do not get used up, specific to substrates, need little amounts. If we did not have ___, would take 2 weeks to break down a meal. Not all ___ are proteins. Some require cofactors to be active. Function is closely linked to structure, and even small structural changes can affect function. Cells can change the structure of certain ___ by adding or removing phosphate groups.

Alcohol Fermentation

Pyruvate from glycolysis is converted to ethanol and CO2. CO2 produced by yeast such as S. cerevisia causes bread to rise. The ethanol that yeast cells make is central to beer and wine production (causes beer to have a foam). Carried out by some bacteria, fungi, and certain plant cells. Human cells cannot carry out ____.

Homolactic Fermentation

Pyruvate made in glycolysis is reduced to lactate. Our muscle cells use this when oxygen is limited, as during anaerobic exercise. Human cells that carry out fermentation can only survive for brief periods using this process. Gain of 2 ATPs made in glycolysis. Used by yogurt bacteria, sauerkraut bacteria, and human muscle cells.

Redox Reactions

Reactions that transfer electrons and carry protons. Composed of oxidation and reduction reactions. When an atom or molecule loses an electron, another entity absorbs that electron and is reduced.

Heterolactic Fermentation

Results in the production of equal quantities of lactate, ethanol, and CO2, with minor amounts of acid end products, such as acetate and formate. Gain of 1 ATP (less efficient than homolactic fermentation). Example: Used by a variety of bacteria and fungi such as Lactobacillus, Leuconostoc, and Weissella.

Exoenzymes

Secreted by bacteria into their local environments to break down large macromolecules into smaller molecules that can be transported across the cell's plasma membrane into the cell. Example: The carb starch is broken down by ___ into glucose subunits before it can enter the catabolic pathways. Cells can then funnel the smaller molecules into intracellular catabolic pathways to harvest energy from them (or recycle certain nutrients). Different bacterial species can make different ____, therefore detecting the presence of certain ___ can be helpful in identifying an unknown organism. Example: Lipases dismantle lipids into glycerol and fatty acids. Example: Proteases and peptidase dismantle proteins into smaller peptides and eventually amino acids. Example: Nucleases help cells break down nucleic acids into nucleotides.

Autotrophs

Self feeders because they are able to make their own organic molecules from inorganic start materials using a process called carbon fixation. All plants are ____ that can "fix" inorganic carbon by incorporating it into sugars. The storage molecule of glucose in plants is starch.

Krebs Cycle

Series of redox and decarboxylation reactions in which CO2 is removed. Begins with the formation of citric acid from oxaloacetate and acetyl-CoA. Produces 2 ATP and a lot of reduced cofactors NADH and FADH2. Runs twice for each glucose molecule that entered glycolysis because 2 pyruvates where made from one glucose molecule in glycolysis. By the end, every carbon in glucose is converted to CO2. The main energy benefit of the ____ is the mass production of reduced cofactors NADH (pass electrons that were in glucose to the electron transport chain) and FADH2. Occurs in the cytoplasm of prokaryotic cells and the mitochondrial matrix of eukaryotic cells.

Phosphorylation

Some enzymes are more active when they are attached to phosphate groups, while others are less active. Example: E. coli use ___ to regulate the production of LPS, a toxin in Gram-negative bacteria that can accumulate in an infected person and cause septic shock. Example: In humans, a key enzyme used in making cholesterol, HMG-CoA reductase, is inactivated by ____ and activated by dephosphorylation.