Microbiology Exam 2
Microbiology Exam 2 MICR 3050
Popular in General Microbiology
verified elite notetaker
Popular in Microbiology
This 26 page Study Guide was uploaded by Toni Franken on Sunday February 28, 2016. The Study Guide belongs to MICR 3050 at Clemson University taught by Dr. Whitehead in Spring 2016. Since its upload, it has received 260 views. For similar materials see General Microbiology in Microbiology at Clemson University.
Reviews for Microbiology Exam 2
Report this Material
What is Karma?
Karma is the currency of StudySoup.
You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!
Date Created: 02/28/16
MICR 3050 – Exam 2 Study Guide Dr. Whitehead, Clemson University Exam 2: Chapters 3, 11, 10, and 7 Modeled around Dr. Whitehead’s recommended subjects to study – color coded/organized by power point chapters. Chapter 3: Bacterial Cell Structure and Function 1. Compare and contrast the structure, composition, and functions of the cell walls of grampositive and gramnegative bacteria. Be able to label them. Cell Walls of Bacteria: The difference between gram positive and gram negative cell walls: o Gram +: Contain a plasma membrane and a very thick wall of peptidoglycan, which makes up to 90% of the cell wall. May contain cell wall polymers (only found in grampositive cells, never gram negative). They are negatively charged, and give the bacteria an overall negative charge. Believed to help maintain structure of the cell wall, and may protect the cell from various compounds due to their negative charge. It is also hypothesized that teichoic acids help pathogenic cells attach to host cells.: Teichoic acids attached to the peptidoglycan of the cell wall. Lipoteichoic acids attached to the plasma membrane (phospholipids in the plasma membrane). Their negative charge gives the bacteria a negative surface charge. We don’t fully understand their functions – some evidence that they help maintain the structure of the cell wall. Evidence that they may protect the cell from various compounds because of the negative charge. May repel some types of antibiotics and/or toxins. Some gram positive bacteria also have a layer of proteins on the surface of the peptidoglycan. The composition and role of protein varies from bacteria to bacteria. It is believed that these proteins have to do with interactions between cell and external surroundings. Periplasmic Space: Have a thin periplasmic space (space between plasma membrane and cell wall) that might contain a few proteins here and there, but most stuff is able to escape from this space into the environment through the one membrane and wall. Also contains exoenzymes (enzymes that function externally from the cell – will be sent into the environment to break down large carbs to be brought into the cell). o Gram : Contain the internal plasma membrane, a thin wall of peptidoglycan, and then an outer membrane. Both membranes are phospholipid bilayers. The two membranes sandwich the cell wall, of which peptidoglycan only makes up about 5 – 10%. Periplasmic Space: Everything in between the two membranes is in the periplasmic space, including the cell wall. This space constitutes 20 – 40% of the cell volume. Many proteins get trapped within the periplasmic space, and they’re used to allow the organism to acquire nutrients from the environment. They are also involved in metabolism, and making the peptidoglycan layer. Some can be involved in defense, and others have the function to break down toxic compounds. Braun’s lipoproteins: Connect the outer membrane to the peptidoglycan, and keeps the cell together. In the outer membrane (a phospholipid bilayer), there will be some lipoproteins, and lipopolysaccharides (LPS) that are only found in gramnegative cells. No teichoic or lipoteichoic acids are present. Lipopolysaccharides (LPS): LPS are instrumental in gramnegative cells’ abilities to cause illness. They are antigens, or the substance your immune system is going form antibodies against. They also provide the negative charge to gramnegative bacteria. LPS create a permeability barrier that protects the cell against bile and other toxic compounds. Purified LPS are considered a very deadly toxin. There are three parts to LPS: o Lipid A (part of the LPS that is embedded in the membrane): Helps to stabilize the outer membrane structure. Can act as an endotoxin during infection, which can cause septic shock if they enter the blood stream (a very deadly complication from a bacterial infection). o Core Polysaccharide (main purpose is to connect lipid A to the O portion): Extends out from the cell, and is the largest contributor to the negative charge of the bacteria. o O side chain (O antigen – what the immune system is responding to in order to make antibodies): Extends out from the cell. E. coli O 157H7 – O part of name is telling information about the O part of the antigen. May contribute to attachment to surfaces and biofilm formation. The O antigen plays a role in stimulating the immune response of a host, but some cells have the capability of changing their O antigen during the course of infection, which means that the bacteria can hide from the immune system for a period of time. Some pathogens can do this multiple times. Outer membrane permeability: It is harder for things to breach the double membrane of gramnegative cells than grampositive, but there are proteins called porin proteins (as well as transporter proteins) in the outer membrane. They tend to cluster together in groups of three (forming trimers), and span the entire outer membrane. They’re basically waterfilled channels that let hydrophilic items through the membrane. They tend to allow things of a certain size through – pore size restricts how large of an item can pass through. o It is believed that gramstaining works because the thicker layer of peptidoglycan in gram positive bacteria prevents the crystal violet from being washed away by ethanol (unless you degrade the cell wall too much). In addition, the thinner layer of peptidoglycan of gram negative bacteria is more porous, and allows the crystal violet to escape when washed. 2. Describe the effects of lysozyme and penicillin on a bacterial cell wall. Reminder: Hypotonic solutions are those that have a lower solute concentration than the cell does, causing water to rush into the cell. Hypertonic solutions are those that have a higher solute concentration than the cell, forcing water to rush out of the cell. Isotonic means the cell and its environment have about the same solute concentration. Evidence of protective nature of the cell wall: We use an enzyme called lysozyme (found in saliva/tears/egg whites) to break the bond between NAG and NAM – the Beta 14 linkage. Once you break that, you can see that the cell is more susceptible to a hypotonic solution without the protection of the cell wall. Penicillin inhibits peptidoglycan synthesis due to the transpeptidase. This damage the cell wall, you take away some of the osmotic resistance of the bacteria, allowing them to lyse more readily. 3. Explain how bacteria may survive without a cell wall. Mycoplasma (NOT TO BE CONFUSED WITH MYCOBACTERIUM) are an exception, and they lack a cell wall. You would assume, then, they would be very susceptible to osmotic stress. However, they get some protection from their plasma membrane, which is more resistant to osmotic pressure than other plasma membranes. They are more susceptible than other bacteria, though. 4. Describe capsules and slime layers and their functions. Capsules: A thick slimy layer around a bacterial cell. They tend to be very well organized and not easily removed from the cell – adhere very well to the organism. They’re main role is thought to be protection – help to resist various types of stresses such as phagocytosis (engulfment by other cells), desiccation (being dried out due to hydrophilic nature of capsule – water filled), and keep viruses and detergents from entering the cell. o Capsules are not required for growth – we can make a mutant bacterium of a strain that normally produces a capsule, and the mutant will grow without it just fine. o If you take the capsulemaking ability away from some pathogens, they can no longer cause disease – Example of this is Streptococcus pneumoniae. It is incredibly dangerous, but if you take away the capsulemaking ability, it’s much less virulent. Slime layer: Similar to capsules in the fact that they are a slimy layer around the cell. However, they are diffuse, unorganized, and easily removed from the bacterium. May aid in motility, but other functions are unknown. 5. Describe the following bacterial structures and their functions: cytoskeleton and cell inclusions Cytoskeleton: Bacteria have a cytoskeleton, which plays an important role in determining cell shape, cell division, protein localization, and general organization. o Homologues between eukaryotic and prokaryotic cytoskeletons. FtsZ – type of tubulin homologue in the cytoskeleton – where septim forms to allow for cell division during binary fission. MreB/Mbl – helps to determine cell shape – responsible for making sure that machinery for peptidoglycan creation is in the correct place. CreS – gene involved in production of the curved shape of most cells. Inclusions: Accumulations/aggregations of certain substances. Can be a wide range of material – inorganic, organic, or others. The cell can save large quantities of material in these inclusions during times of healthy, good conditions. Then, they have something to use when times get tough. May be crystalshaped, circular, or other wide varieties. There are some that are enclosed by a singlelayer membrane, but most do not have membranes. o Storage inclusions: Storage of nutrients, metabolic end products, energy, building blocks. Carbons (glycogen, polyBhydroxybutyrate (PHB)) – saves this in carbon inclusions in case it gets to a carbondeficient environment. Polyphosphate granules Sulfur globules Nitrogen – cyanophycin granules o Other types of inclusions not used for storage – used for movement/positioning: Gas vacuoles: provide buoyancy – one type where you would probably find some type of membrane. You’ll have a structure where the outside is permeable to gasses, but not to water and other material. Much like a tiny balloon. Typically found in aquatic organisms. Cells would ideally be able to move up or down depending on environmental conditions – let gas out, or let more in. Ex: photosynthetic organism that has to get a particular area with a necessary wavelength of light. Oxygen content also tends to be closer to surface, and nutrients can be different concentrations. Magnetosomes: Magnetite particles for orientation in Earth’s magnetic field. Rare feature – most bacteria don’t have this. Use it to adjust their placement within the environment. These tend to be held in folds of the plasma membrane. Chapter 3: Second half PowerPoint and lectures: 1. Describe the following bacterial structures and their functions: fimbriae, pili, flagella, and endospores. External Structures that extend beyond the cell envelope in bacteria and archaea – General functions include protection, attachment to surfaces (to other cells or environmental features), horizontal gene transfer, and cell movement. NOTE: Bacteria DO NOT have cilia!!! Cilia are only inn eukaryotic cells, not prokaryotic. Flagella: Long, threadlike appendage that goes all the way through the plasma membrane and the cell wall. Used mainly for motility and swarming behavior. Not all bacteria have them. Can play a role in attachment of bacteria to host cells or surfaces, and may be virulence factors (vital factors to allowing a bacteria to cause infection). o H. pylori is an example of a bacterium that uses flagella as a virulence factor. As soon as it gets into your stomach, it quickly swims over to the lining of the stomach, and embeds in the mucous lining to cause an infection. Pili: Can be used interchangeably with fimbriae, but not always. Short, thin, hairlike appendages that are very numerous on the cell. They are usually made from proteins (proteinaceous). They often mediate attachment to surfaces (bacteria that attach to the urinary tract to resist flushing out by urination), and some are required for motility or DNA uptake (type IV pili). o Plasmids: Smaller, circular pieces of DNA separate from the single, circular chromosome. Not all bacteria have them. Don’t tend to have information on them that are required for life, and therefore can lose or gain them without death. Tend to give the cell an advantage o Sex pili: Similar to fimbriae except longer, thicker, and less numerous (1 – 10 per cell). Sex pili genes for formation often found on plasmids. They are required for conjugation (a form of horizontal gene transfer) where a bacterial cell (called a donor) has a plasmid that has genetic info for a sex pilus, which allows for it to form a pilus between it and another cell to send some genetic information from the donor to the recipient. Recipient does not have to have the gene info for a sex pilus. The recipient will also gain the ability to create a sex pilus. NOTE: Unless an exam question says sex pilus, pili and fimbriae can be used interchangeably. Fimbriae: Can be used interchangeably with pili, but not always. Short, thin, hairlike appendages, usually made from proteins (proteinaceous) that are very numerous on the cell. They often mediate attachment to surfaces (bacteria that attach to the urinary tract to resist flushing out by urination), and some are required for motility or DNA uptake (type IV pili). 2. Describe flagellar structure, arrangement on cells, and movement. Parts of a flagellum: o Filament: The part of the flagellum that extends out from the cell – longest, most obvious piece. It is, for the most part, a hollow structure, and has a cap that helps prevent degradation. Usually made up of protein subunits, the most common of which is flagellin. o Hook: The linker between the filament (external part of the flagellum) and the basal body (embedded in cell envelope). It is sort of curved, and helps in the orientation of the flagella, how it’s pointing, how it’s turning. o Basal Body: Very complex motor portion of the flagellum. This is where you get the energy that allows the flagellum to move. It is embedded in the cell wall. This is the case in both gram positives and gram negatives, but they are different between the two. It is structured like an actual motor made of 2 parts: Stator: Stationary section of Basal Body. Rotor: Moving part of Basal Body. The energy source here involves a hydrogen gradient – generates energy from movement of hydrogen ions (difference in charge and pH created across the plasma membrane, which creates a tremendous amount of potential energy). Gram positives: Basal body tends to be less complex than gramnegatives. Two rings. Gram negatives: Basal body tends to be more complex than grampositives due to the multiple anchoring pieces that are required for the plasma membrane, cell wall, and outer membrane. Tend to have multiple “rings” – about 4. NOTE: Don’t need to know the rings involved in each. Synthesis of flagellum: The process of building a flagellum tends to be very complicated – many (20 – 30) genes are used to build them. However, we still don’t know everything about the regulation of flagellum. We know that the flagellin components are produced inside the cell, then must be transported outside to actually build the flagellum outside the cell. The flagellin subunits are added to the top of the flagellum, away from the cell. Growing from the top down, not the base up. Patterns of Flagella Distirbution: o Peritrichous: Bacteria just look hairy, evenly distributed over the entire surface. Ex: P. vulgaris o Monotrichous: A single flagellum, and are usually polar (at one end of the cell or the other. – ex: Pseudomonas) o Polar Flagellum: Flagella located at one end or the other o Amphitrichous: One flagella located at both poles. o Lophotrichous: Clusters of flagellum – may be polar lophotrichous (Spirillum), or may be lophotrichous at both ends. Flagellar movement: Flagellum rotates like a propeller – up to 1100 rev/sec. o Bacterium move in a series of runs and tumbles. Run: Uniform, straight movement. Counterclockwise flagella rotation usually results in a “run” due to the uniform direction of flagella rotation and hook placement. Tumble: Bacteria pauses for a brief second, and then changes directions. It’s more of a directional change than anything else. A clockwise rotation throws the flagellum out in a less organized formation, and usually results in a “tumble.” This is true for cells with single or multiple flagella. 3. Define chemotaxis and describe how bacteria move toward an attractant (or away from a repellent). Chemotaxis: Main way of bacterial movement. Bacteria response to chemical gradients. Cells will move towards chemicals that are attractive such as food, or move away from detrimental materials such as toxins. o Phototaxis – bacteria move based on wavelengths of light. Based on chemoreceptors on the surface of the cell that are incredibly sensitive to even low concentrations of attractants or repellants in the environment (chemoattractants and chemorepellants). Complex, but rapid. Responses occur in less than 20 milliseconds. Bacteria can then move from 2 to 60 cell lengths/sec. Positive/Negative Chemotaxis: If you have no chemical gradient that cells are responding to, their movement is completely random. They’ll continue that until they sense some type of attractant or repellent. o If they sense a chemical attractant, they want to move towards – caused by lowering the frequency of tumbles, and increase the length of runs. Still somewhat random, still tumbles and random changes in direction, but it is biased. It’s got some form of direction to it. Runs in direction of attractant, with intermittent tumbles. General direction is towards the attractant. o The same thing happens if there is a repellent, it’s just biased random movement AWAY from the repellent. 4. Describe other types of motility (spirochete, twitching, and gliding). Spriochete Motility: Many spirochetes have flagella, and some have single polar flagellum. However, they have a unique type of flagella that wraps around the corkscrew shape of the cell. They extend through the plasma membrane, but not to the outside environment. It stays in the periplasmic space – flagella come out of both ends of the cell, but remain in the periplasmic space of either gramnegative or grampositive spirochetes. This results in an axial fibril that wraps around the cell. It causes a flexation or bending of the entire cell, which allows the cell to move. The entire cell is being moved through movements of the axial fibril. They tend to call this a creeping or crawling motion. Based on contractions and expansions. Twitching: Can involve pili or fimbriae, but it’s usually pili functioning at each end of the cell. Believe they extend and retract alternately, pulling the cell along. It’s a very jerky movement that happens in short bursts. So, results in a twitching motility pattern. In order for twitching to work, the cell has to be in contact with something else so the pili have something to grab onto. May be gripping other bacteria, host cells, or surfaces. Gliding: Often involves the extrusion of slime. Smooth movements – not well understood (believed that there are multiple mechanisms by which cells can glide). No flagella are involved, and doesn’t appear to be using pili for movement, either. Slime is often made of polysaccharides. As bacteria extrudes slime, the slime pushes the bacteria along. You usually need a surface in order for the bacteria to move. Typically relatively slow. Some bacteria, as they’re gliding, they twist. They appear to extrude some type of slime, but we aren’t sure why they twist. There may be some sort of internal structure (kind of like a track) where there are particular structures that stay in a single location relative to the surface that bacteria is on that the bacteria twists around. There are bacteria that can switch between types of movement. Myxococcus – “hunt” in packs. When it is alone, the cells can move by themselves, and they glide. Called the adventurous state. When out hunting and working as a group, they use pili dependent movement. They excrete enzymes to break down another bacteria to break down to usable nutrients. 5. Understand the structure and functions of bacterial endospores, the basics of sporulation and germination, and endospore resistance. Bacterial Endospore: Extremely stress resistant structures that some bacterial cells form – often think of Clostridial and Bacillus species. They are complex, dormant structures that can be located in various locations in the cell. Can survive boiling for an hour or more, which is why we have to use autoclaves to truly sterilize things. Can survive radiation, incredibly cold temperatures, and nonspore specific disinfectants, etc. The location of the endospore in the mother cell can give us good information on the type of cell we’re looking at. o On the outside of the spore, there is a thin coat called the exosporium, which allows for germination into an actively growing cell. o Below that you have a spore coat that is thicker and made of proteins that is more stress resistant. o Then there is a cortex that can make up to half the volume of the spore – made of peptidoglycan. o There is a core wall inside the cortex. o Then the innermost portion is the core itself (where the vital parts of the cell needed to end up with a healthy, active new cell – ribosomes and DNA – are located) in the very center. There is very little water inside the core. SASPs: Within the core are small, acidsoluble, DNAbinding proteins that provide most of the protection for the DNA. The core also has a slightly lower pH, calcium dipicolinate (also called dipiconic acid?), and very low water content. o Exosporium and spore coat provide a small amount of protection (mostly spore coat – thick, hardy layer of protein to keep molecules out). NOTE: A vegetative cell is metabolically active, and an endospore is not. There is difficulty staining endospores due to the resistance of stresses – only stainable by certain methods. o Vegetative cell, metabolically active cell, reacts to starvation, dehydration, or other stressors from the environment, and begins to develop an endospore. The mother cell ruptures (save yourself kind of mechanism – active cell will die), and releases the endospore into the environment. This endospore can last weeks, months, years, and sometimes thousands of years. Remains dormant until conditions are once again favorable. Sporulation (spore formation): We know it happens, but don’t know all of the mechanisms and the why’s. o DNA condenses into an axial filament – want to form the nucleic material away from the rest of the cell. o Cell membrane folds in to isolate where the endospore begins to form. Sometimes called the foreseptum). o The membrane completely engulfs the forming spore (the condensed DNA) o Cortex forms inside the engulfed forming spore. Begin to accumulate calcium and depicolinic acid (which vegetative cells do not have.) o Formation of endospore coat (made of proteins). o End up with a mature endospore – There are some other changes that we won’t go into for this class. o There are lytic enzymes that will cause lysis of mother cell, and therefore release into the environment. Reactivation of Endospore to an Active Cell: Note, germination is only 1 step of formation of the vegetative cell. o Activation: Spore somehow receives a signal that conditions are good. Location, environmental conditions, maybe heat o Spore begins to prepare for germination. o Germination: Environmental nutrients are detected – spore swells and ruptures the spore coat. There is increased metabolic activity. o Outgrowth: emergence of vegetative cell. Chapter 11: Catabolism – Energy Release and Conservation 6. Compare and contrast aerobic respiration, anaerobic respiration, and fermentation in bacteria. Aerobic Respiration: Energy production that uses Oxygen as the terminal electron receptors from the Electron Transport Chain. Oxygen is an exogenous electron receptor, or an electron receptor that comes from outside of the cell. o Obligate (strict) Aerobes: Microorganisms that absolutely require oxygen to produce energy. Grow best in environments of 20% oxygen or greater. Anaerobic Respiration: Energy production that uses anything other than Oxygen as the terminal electron receptors from the Electron Transport Chain. Requires exogenous electron receptors, or electron receptors from outside the cell. 2 o Examples of Electron Receptors: NO , S3 , C4 , and2fumarate. o generally yields less energy than aerobic respiration becaus0 E of electron acceptor is less positive than 0 of2O Fermentation: energy production that does not use the Electron Transport chain, but derives energy from pyruvate or pyruvate derivatives. This is the only process that we will study that uses endogenous electron receptors, or electron receptors that come from inside of the cell. We usually think of substrate level phosphorylation in fermentation. o Often produces fermentation byproducts, such as alcohol. o Can also produce end products to be used in biosynthesis. 7. Compare and contrast substratelevel phosphorylation and oxidative phosphorylation. Substrate Level Phosphorylation: Does not involved the Electron Transport Chain – produces a much smaller amount of ATP. Usually used in fermentation. Produces about 4 net ATP. Oxidative Phosphorylation: Involves the process of passing electron through the Electron Transport Chain to the final electron acceptor. This creates a proton motive force, which pushes Hydrogen ions to the outside of the membrane as electrons are transferred from NADH and FADH th2 ugh the membrane. A large quantity of ATP will be produced from this process. Produces about 28 net ATP. 8. Describe aerobic catabolism (overview). Stage 1: During the first part of aerobic catabolism, the cell uses exoenzymes. These enzymes are created within the cell, and then sent into the environment to break down large molecules to be brought into the cell for break down to capture energy. These nutrients may be proteins, polysaccharides, or lipids. o Exoenzymes are Inducible: This means that the cell only produces them in the presence of nutrient molecules. Stage 2: During the second part of aerobic catabolism, the cell uses endoenzymes. These enzymes are created and used within the cell during the processes of substratelevel phosphorylation. This stage has some portions that are amphibolic, or both catabolic and anabolic. o Endoenzymes are Constitutive: this means that these enzymes are produced almost constantly. They are an integral part to energy production in the cell. o Produces a small amount of ATP, but also produces NADH and FADH that 2an be used later in oxidative phosphorylation. Stage 3: Involves the citric acid cycle and the electron transport chain. The citric acid cycle produces a small amount of ATP, and also produces NADH and FADH that c2n be used to produce greater amounts of ATP during in the electron transport chain. This cycle is considered amphibolic, or both catabolic and anabolic. o Following the Citric Acid Cycle (Krebs cycle), NADH and FADH are 2ent to the ETC to create greater amounts of ATP. 9. Describe the organization and functions of the electron transport chain in aerobic respiration including its role in ATP production. As electrons pass through the ETC to the final electron acceptor, a proton motive force (PMF) is generated and used to synthesize ATP (oxidative phosphorylation). The electron transport chain is a series of complexes within the plasma membrane that pass electrons along to a terminal receptor. As this happens, a proton motive force is created, pushing hydrogen ions to one side of the membrane. As the electrons are transported, energy is gradually released (represented by the hydrogen ions), and can be used to make ATP through oxidative phosphorylation. o The released energy, in the form of hydrogen ions, causes ATP synthase to rotate, exposing the active site that allows for the combination of ADP and Pi (phosphorous) to create ATP. 10. Understand the Chemiosmotic Hypothesis. Proposed by Peter Mitchell in 1961. The theory is based on the idea that ATP is synthesized within a cell, eukaryotic or prokaryotic, through the release of energy by transferring electrons from carriers to acceptors by passing these electrons across an electrochemical gradient. o In most cases, this refers to the use of electron carriers NADH and FADH 2(produced from breaking down glucose) to pass electrons through a membrane via carrier proteins to a terminal electron acceptor (such as oxygen). Chemiosmosis is defined as the movement of ions across a selectively permeable membrane, down their electrochemical gradient. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane during cellular respiration or photosynthesis. 11. Explain the function of ATP synthase. Enzyme located in the plasma membrane of bacterial cells. Used to produce ATP from combining ADP and inorganic Phosphate (Pi). Has 2 portions – Fo and F1 o F – embedded in the membrane, where hydrogen ions cross. Hydrogen ions are the o energy that results from the proton motive force created by passing of electrons through the ETC. The passage of these Hydrogen ions causes the Fo portion to rotate to expose active sites on 1 . o F1 – Portion of ATP synthase that is contained within the cell. As the Fo portion rotates, the site on1F where ADP and Pi can be combined with energy to synthesize ATP becomes exposed. This can ONLY happen if energy is produced from the ETC by the oxidation of NADH and FADH . 2 12. Know the functions of proton motive force and how it is established. The proton motive force is an electrochemical gradient that is formed when electrons are passed along the ETC in the plasma membrane, which releases energy. This pumps hydrogen ions to the periplasmic space, or the outside of the plasma membrane. These hydrogen ions can then be accessed by ATP synthase, and used to create ATP. 13. For aerobic respiration, explain where in the pathway ATP is produced (glycolysis, TCA cycle, and ETC), the methods of ATP production used for each ATP generated, the electron carriers used, and the number of ATPs produced (during the process and the final net yield). Process that can completely catabolize an organic energy source to CO u2ing the following processes. The total maximum ATP yield is 32. During this process, these ATP are produced, and electron carriers are recycled. If the electron carriers weren’t recycled, the process would halt. o Glycolytic pathway: The breakdown of a carbon source (typically glucose) into pyruvate, then to Acetyl CoA, which can be sent to the citric acid (TCA) cycle. 4 total ATP are produced during this process, but 2 get used immediately, giving a net ATP yield of 2. 2 NADH are also produced, and can later be used in the ETC. o TCA cycle: Acetyl CoA gets sent to the Citric Acid Cycle, and sent through an entire pathway that produces a small amount of ATP (only 2) itself, but produces a large amount of NADH (8) and FADH (2). Th2 e two molecules can be used in the ETC to produce larger quantities of ATP. o ETC with O2 as the final e acceptor: A net total of 28 ATP molecules are made when NADH and FADH are o2 dized in ETC (oxidative phosphorylation) Electrons are taken from NADH and FADH2 and transferred to oxygen, the terminal electron receptor. As this occurs, energy is released in gradual increments as electrons are passed down the ETC. This energy is turned into ATP through oxidative phosphorylation. 14. Describe the process of fermentation, its functions, and its products. Fermentation Process: Fermentation takes place in the absence of an exogenous electron acceptor, unlike either aerobic or anaerobic respiration. It DOES NOT need oxygen. Instead, it uses pyruvate, or a pyruvate derivative as an endogenous electron receptor. o Glucose begins to be broken down through glycolysis, producing ATP in the process, as well as NADH. The glycolytic pathway continues as normal until pyruvate (or pyruvate derivatives) are produced. o Unlike in respiration pathways, pyruvate is then reduced by oxidizing NADH back to NAD . This can then be recycled in the earlier portions of the chain so that fermentation can continue. If NADH was not oxidized through reducing pyruvate, the cycle could not continue. This makes for a continues recycling of electron carriers o ATP is formed via substratelevel phosphorylation o Besides ATP, fermentation also produces various fermentation end products that may be beneficial to the cell (products to be used in biosynthesis, , or that humans can gain from. Various Fermentation Byproducts: o Ethanol (alcohol): Used to make breads, wine, and beer. o Lactic Acid: Homolactic (only produce lactic acid): cheeses, sour cream, yogurt Heterolactic (produce lactic acid, but can also produce other products): Used to make sauerkraut, pickles, buttermilk, and involved in food spoilage o Mixed acid: Allows us to distinguish between types of bacteria. o 2,3Butanediol: Allows us to distinguish between types of bacteria. o Propionic acid: Used to make swiss cheese 15. Know why bacteria produce fermentation products and how these products are useful to humans. Many fermentation products are completely accidental byproducts of substratelevel phosphorylation. In fact, fermentation byproducts, if they build up too much, can even be toxic to the cell (such as alcohol at high concentrations). See number 14 for benefits to humans. 16. Distinguish between homolactic and heterolactic acid fermentation. Homolactic Acid Fermentation: Fermentation that produces a single type of acid – this is lactic acid, and this process is used to make cheeses, sour cream, and yogurt. Heterolactic Acid Fermentation: Fermentation that can produce more than one type of acid – lactic acid, and possibly some other acid such as ethanol. This is used in many pickling processes. Sauerkraut, buttermilk, and pickles are made using this type of fermentation. Heterolactic fermentation is also heavily involved in the process of food spoilage. 17. Distinguish between mixed acid and butanediol fermentation. MixedAcid: A bacterial may produce a mixture of lactic acid, acetic acid, formic acid, succinate and ethanol, with the possibility of gas formation (C2 and H2). The Durham tube in the medium allows for visualization of gas production, while a the pH indicator Methyl Red allows for visualization of presence of mixedacids. 2,3 Butanediol Fermentation: Produces mixedacid and gases, but also reduces the production of acid through the production of neutral 2,3 Butanediol. The test itself is looking for the presence of an intermediate, acetoin. 18. Explain the purpose of the MRVP test and know how it works Used to distinguish between members of Enterobacteriaceae. Determines if the organism produces mixed stable acids with a pH of less than 5, or determines if acetoin, an intermediate product during 2,3 – Butanediol Fermentation, is present. o MR: The MR portion of the test is used to determine if the bacteria produces a stable acid that creates a pH of less than 5. The medium (originally a yellow/clear color) is inoculated with the bacteria, allowed to incubate for 3 – 5 days (at 37° C), and then has Methyl Red indicator added to it. This is a pH indicator, and if the pH is greater than 5, the liquid will remain clear/yellow, which is a negative result. If the pH is less than 5 (indicating MixedAcid production), the positive test will turn the fluid red. Note: The incubation time is very important, because some bacteria will produce acids at first, but then break them down again after. This creates a temporary drop in pH, but SHOULD NOT produce a positive test if incubated for the proper amount of time due to the denaturing of the acid. o VP: The VP portion of the test is carried out in a separate tube of medium. Again, the medium starts out yellow/clear, and is inoculated with bacteria, and incubated for 3 – 5 days at 37°C. After the incubation time is complete, 18 drops EACH of Barrit’s Reagent A and Barrit’s Reagent B are added to the tube. It is then allowed to sit for 30 minutes. If the tube turns red/pink, the test is positive for acetoin. Acetoin is ONLY present as an intermediate of 2,3 – Butandiol Fermentation, creating a positive test. If the test is negative, the fluid will remain a clear/yellow color with some dark discoloration from the Barrit’s reagents. Chapter 11 and 10.1 – 10.4: 1. Know the requirements for microbial survival and growth and their sources. Microorganisms need 3 basic things to survive, but can get them from various places: o Source of Energy: Needed for a cell to continue its normal metabolic functions – needed for cellular work. Organic or Inorganic Chemical Compounds: Energy is obtained by oxidizing (removing electrons from) a compound Chemotrophs get energy from chemical compounds. Sunlight: Phototrophs = organisms that get energy from sunlight. o Source of Electrons: Needed to produce energy, and used to reduce CO 2to form organic molecules Organic or Inorganic Chemical Compounds: Lithotrophs: Microorganisms get electrons from inorganic sources Organotrophs: Microorganisms get electrons from organic sources o Nutrients: The basic three nutrients microbes need are carbon, hydrogen, and oxygen, and they are needed to synthesize organic building blocks used for cell maintenance and growth. Naming is based on carbon source: Heterotrophs use external organic molecules as carbon sources (which often serve as energy and electron source as well) Autotrophs use Carbondioxide as their sole or principal carbon source, and are able to fix it – typically thinking of photosynthetic cells. o must obtain energy and electrons from other sources o “primary producers” – make their own food. 2. Define and recognize the major nutritional types of microorganisms based on their energy source, electron source, and carbon source. See above for basic break down Make sure to be able to tell from a name what an organism uses: o Chemolithoautotroph – Uses CO2 as its carbon source (auto), uses inorganic chemicals as its energy source (chemo), and has inorganic electron donors (litho). o Chemolithoheterotroph – Uses outside sources of organic carbon (hetero), uses inorganic chemicals as its energy source (chemo), and uses inorganic electron donors (litho). o Photoorganoheterotroph – Uses outside organic carbon sources (hetero), uses organic chemicals as an electron source (organo), and uses light for energy (photo). 3. Define metabolism, catabolism, and anabolism. Metabolism: The total of all chemical reactions occurring in the cell – since we don’t have mitochondria, it will be a slightly different process. o Cellular respiration: MUST UNDERSTAND IT – but don’t have to know specific steps or process. o The main thing that cells will get from energy sources is ATP – used to drive work. Carbon sources use to get macromolecules (building blocks of the cell – fats, proteins, etc.). Need electron sources for reducing power. Catabolism: Reactions used to capture energy from one source and using it for something else. Fueling/energy conserving reactions. Where we can get some electrons, and generate precursors for biosynthesis. (destruction of molecules to get energy – think Catastrophy). Anabolism: The synthesis of complex organic molecules from simpler ones – requires energy from fueling reactions. We won’t talk about this too in depth. 4. Understand the concepts of free energy (G) and standard free energy change (deltaG). Energy: The capacity to do work or to cause particular changes (in cells different types of work – transport/mechanical/etc.). o G value: the amount of free energy, or the amount of energy that is available to do useful work. o ∆G: The change in energy that can occur in chemical reactions. Some reactions require energy in order to work – have to put energy in. Other reactions release energy. 5. Distinguish between exergonic and endergonic chemical reactions and their relationship to ∆G° Exergonic reactions release energy: A + B results in C + D + energy. (can think of it as energy exiting the reaction). Basics of thermodynamics – don’t create or destroy energy. Energy is leaving the system. Therefore ∆G standard is negative (reaction proceeds spontaneously). End up with higher energy level in reactants, and a lower level of energy in the products due to release of energy. o Let’s say there is level 2 of energy in the products, and a level 5 energy in reactants. 25 = 3. Don’t usually need any energy input to proceed. o Often will produce ATP – can capture energy and put it into ATP for cell use. Endergonic reactions require energy: Have to put energy into the process. As you go from reactants to products, if you actually want it to proceed, you have to feed energy into the system. A + B + energy gives you C + D. Products have a higher level of energy than reactants, resulting in a positive ∆G. Reaction will not proceed spontaneously. It is often times going to use ATP to drive these reactions. 6. Explain the importance of ATP. ATP is the currency of all cells, including prokaryotic. It is basically the storage of free energy that the cell can use in metabolic processes, and to run various pathways. ATP is the currency of both eukaryotic and prokaryotic cells. ATP is used for Mechanical, Chemical, and transport work. 7. Be aware of other important energyrich compounds. Acetyl CoA ADP (used to make ATP) Phosphoenolpyruvate Glucose 6phosphate Acetyl Phosphate AMP 8. Understand redox reactions including the standard reduction potential (E ) of hal0 reactions, the electron tower, and their relationship to ∆G. Standard reduction potential: The tendency of a compound to get rid of an electron (donate an electron). Redox reactions involved the reduction of one compound (addition of electrons) and the oxidation of another (removal of electrons). For example, during the process of oxidative phosphorylation, NADH may be oxidized, and Oxygen may be reduced, for electrons are + transferred from NADH (oxidizing it to NAD ) to Oxygen. o Half Reactions: A half reactions is simply one half of a redox reaction, so either the oxidation portion, or the reduction portion. This is where the oxidative state change of each compound involved in the reaction is considered separately. H 22e + 2H = The Electron Donating halfreaction of formation of water. (oxidation). 2 ½ O 2 2e O = The Electron Accepting halfreaction of formation of water. (reduction). 2H + O H O 2 2 H + ½ O 2 H O2= The net reaction, according to each half reaction. The Electron Tower: The electron tower is organized by standard reduction potential, and ranges from more negative values at the top, to more positive values at the bottom. The higher on the tower a compound is (more negative), the better of an electron DONOR it is. The lower on the tower a compound is (more positive), the better of an electron RECIEVER it is. If two compounds are very far apart from each other on the tower, there is a greater amount of energy that can be released between the two if an electron exchange takes place (more energy release = more negative ∆G). o NADH and Oxygen are very far from each other on the tower, giving an enormous amount of ∆G available for release when they exchange electrons during aerobic respiration. o Anaerobic respiration often does not yield as much energy because the electron donor (NADH/FADH2) and the terminal electron receptor (compound other than oxygen) are closer together on the tower. They have less free energy to release. o The net change in the energy of a reaction results from the difference in reduction potential between the primary electron donor and the terminal electron receptor. 9. Describe the location, organization, and functions of the Electron Transport Chains in bacteria. The Electron Transport Chain (ETC): Located in the Plasma membrane of prokaryotic cells (mitochondria or chloroplasts in eukaryotic). + The ETC is used to oxidize (remove electrons from) NADH and FADH to NAD2 and FADH. The electrons are then passed through the ETC in the membrane from one complex to the next (details of which we do not need to know). Each carrier is reduced as the electrons are passed along, releasing energy with each step. This energy release creates the proton motive force. The Proton Motive Force causes the pumping of hydrogen ions across the gradient to one side of the membrane (the periplasmic side), and continues until the electrons settle at a terminal electron receptor, which may be oxygen (aerobic) or another compound (anaerobic). In the meantime, the hydrogen ions (representing the released energy) are used by ATP synthase within the ETC to produce ATP from ADP and inorganic Phosphate. The gradual step by step reduction process of the ETC allows for the maximum energy to be captured from a substance. If all of the energy was released at one point in time, much of it would be wasted and unable to be used. 10. Define the two classes of electron carriers. Coenzymes: Prosthetic groups of enzymes. A substance that works with an enzyme to initiate or aid the function of the enzyme. It is usually an organic substance, and is involved in the active site of enzymes. NAD may be considered a coenzyme in redox reactions. o Coenzymes cannot function on their own and require the presence of an enzyme. Prosthetic groups: A nonamino acid group that is strongly bound to a protein and is necessary for it to function properly within an enzyme. May be organic (lipids/sugars) or inorganic (metals). They can ac
Are you sure you want to buy this material for
You're already Subscribed!
Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'