MBIO 2815 Final: Microbiology 2815 Final Exam Review

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University of Oklahoma
MBIO 2815
Karen Meysick

18. What is glycolysis? What is generated during glycolysis? What are the end products of glycolysis? Glycolysis is the oxidation of glucose to pyruvic acid, is usually the first stage of carbohydrate catabolism (breakdown of carbohydrate molecules to produce energy) The enzymes of glycolysis catalyze the splitting of glucose (a six carbon sugar) into two three-carbon sugars. These sugars are then oxidized, releasing energy, and their atoms are rearranged to form two molecules of pyruvic acid. During glycolysis, NAD is reduced to NADH, and there is a net production of two ATP molecules by substrate-level phosphorylation. Glycolysis does not require oxygen. The end product of glycolysis is pyruvic acid, which can be used by the cell to either undergo aerobic (respiration) or anaerobic (fermentation) process. There is also a net gain of two molecules of ATP for each molecule of glucose that is oxidized and 2 NADH. Understand that there are alternative pathways to glycolysis that microorganisms may use to oxidize glucose. (Ex. proteins / fat catabolism) 20. Compare and contrast aerobic vs anaerobic cycle. Aerobic Respiration Anaerobic Respiration Uses Oxygen Respiration without Oxygen Yields 34 ATP Yields 2 ATP Final Electron Acceptor O 2 Final Electron Acceptor not O 2 21. What happens to glucose during aerobic respiration, what does it become? Aerobic respiration (start with glycolysis and ends up with 32-34 ATP) 22. What is the Citric Acid Cycle (Krebs Cycle, TCA Cycle)? What is the starting molecule for this pathway and where does it come from? What is generated from the citric acid cycle? Why is it referred to as a “cycle”? Understand that the citric acid cycle is also referred to as the ”TCA cycle” and the Krebs Cycle Acetyl CoA is starting molecule for Citric Acid Cycle Glycolysis lyses glucose (six carbon sugars) into two pyruvic acids (three carbon sugars) — can happen in the presence or absence of oxygen. Glycolysis = 2 ATP and 2 NADH produced Next step is the Krebs Cycle (TCA or Citric Acid Cycle), which takes place in the inner membrane of mitochondria. In preparation for the Krebs Cycle, pyruvic acid, the end product of glycolysis, is oxidized before it can enter the Krebs Cycle (carbons are cleaved from the pyruvate resulting in a two carbon compound = Acetyl + CoA) This also reduces NAD to NADH. So 2 NADH are produced in the preparation for Krebs Cycle. Now, the Krebs Cycle can occur. Acetyl CoA is the starting molecule for the Krebs cycle. Catalyzed by enzymes, Acetyl CoA merges with oxaloacetic acid (a four carbon molecule) and they form citrate or citric acid (a six carbon sugar) and citric acid is then oxidized (carbons are cleaved from the molecule) over a number of steps to get back to oxaloacetic acid. When citric acid is oxidized, it forms CO . 2hroughout the Krebs Cycle, NAD is constantly oxidized to NADH and FAD is oxidized to FADH .2These are important compounds because they are the molecules that enter the electron transport chain. Krebs Cycle is referred to as a cycle because the molecule you start with is the molecule you end with, Oxaloacetic Acid. Krebs Cycle End Products: For every two molecules of acetyl CoA that enter the cycle, 4 molecules of CO , 6 molecules of NADH, 2 2 molecules of FADH , a2d 2 molecules of ATP are produced. 10 NADH and 2 FADH are t2e starting molecules for the electron transport chain and they are oxidized to produce ATP. Every NADH produces 3 ATP so, 10 NADH x 3 = 30 ATP Every FADH produces 2 ATP so, 2 FADH x 2 = 4 ATP 2 2 This is 34 ATP from the electron transport chain and 4 ATP from glycolysis = total net gain of 38 ATP from glycolysis, kreb’s cycle, and electron transport chain. 23. What happens in the electron transport chain? Where do the electrons that feed into the electron transport chain come from? The electron transport chain is a sequence of carrier molecules that are capable of oxidation and reduction. After glycolysis and the Kreb’s Cycle, we are left with 10 NADH and 2 FADH molecules. These molecules are used in the electron transport 2 chain, to produce ATP. Each NADH will produce 3 ATP and each FADH 2 will produce 2 ATP. All electron transport chains achieve the same basic goal: to release energy while electrons are transferred from higher energy compounds to lower energy compounds. 24. During aerobic respiration where is the most ATP generated? How is it generated? Most of the energy is generated during the electron transport chain. 2 ATP generated in glycolysis, 2 ATP generated in Krebs Cycle, and 34 generated from the electron transport chain. 25. What is an ATP synthase? What powers the ATP synthase? ATP synthase is an enzyme that is needed for protons on one side of the membrane (with higher proton concentration) to diffuse across the membrane through special protein channels. When this flow of protons occurs, energy is released and is used by the enzyme to synthesize ATP. 26. What is fermentation? Why do organisms that grow via fermentation grow more slowly than those that respire aerobically? Fermentation is a process that releases energy from sugars or other organic molecules (amino acids, purines, pyrimidines); does not require oxygen, does not require the use of the Krebs cycle or an electron transport chain, uses an organic molecule synthesized in the cell as the final electron acceptor and produces only small amounts of ATP 29. When organisms ferment, from what process do they get their energy? Only during glycolysis do organisms who ferment get their energy. 27. If an organism is capable of growing aerobically or fermenting (facultative anaerobe) which method would it utilize if the present conditions could support either mode of metabolism? If an organism is capable of growing aerobically, it will utilize this method. Organisms who can work aerobically yield more ATP and work faster. Understand that fermentation can result in many different end products. The types of end products generated are going to be determined by the enzymatic capabilities of that particular organism. In other words if the organisms does not have the enzymes necessary to convert pyruvate  ethanol, then it will not produce ethanol as an end product of fermentation. Understand that alternative sources of energy are utilized, but they are often broken down into intermediates that can be fed into the central metabolic pathway. Understand the basic mechanism of how electrons move from the donor to the final electron acceptor. (Fig 5.27) 32. Understand that organisms are defined by their source of both carbon and energy. This allows us to categorize organisms as follows: Chemoheterotroph, chemoautotroph, photoheterotroph, photoautotroph. Understand from where each of these groups obtains their carbon and energy. Chemoheterotroph: Energy Source (Chemical) Carbon Source (Organic Compounds) Chemoautotroph: Energy Source (Chemical) Carbon Source (CO ) 2 Photoautotroph: Energy Source (Light) Carbon Source (CO ) 2 Photoheterotroph: Energy Source (Light) Carbon Source (Organic Compounds) Understand that these central metabolic pathways can generally run in reverse and can be used to generate intermediates which act as building blocks for lipids, proteins, nucleic acids and carbohydrates. Chapter 6 Chapter 6 is about microbial growth, the different physical and chemical requirements that effect microbial growth, and the different ways that we can grow microorganisms. Understand that each microorganism has certain conditions that must be satisfied in order to maintain growth. Some microorganisms can form endospores that will allow them to survive unfavorable conditions. Many organisms cannot form endospores so if the growth conditions present are not favorable then the organism will not survive. Some of the physical requirements that are going to affect growth are temperature, pH and osmotic pressure (generally we look at this as the salt concentration). Every organism has a specific temperature, pH and salt range in which they are capable of growing. If the provided conditions are outside of any of those ranges then growth will not occur. In addition to the physical requirements an organism must have their chemical requirements satisfied as well. That means they must have access to carbon, nitrogen, sulfur, phosphorous in addition to trace minerals and elements that are needed to build essential macromolecules and for the operation of cellular enzymes. 1. What is a growth factor? Do all organisms have the same growth factors? Growth factors are compounds that are required for growth that must be obtained from the environment because they cannot be synthesized directly. Some examples are vitamins, amino acids, and nucleotides. Different organisms will have different growth factors 2. What are the cardinal temperatures? Cardinal temperatures are the minimum and maximum temperatures that define limits of growth and development of an organism. 3. How does growth differ between the minimum, maximum and optimum temperature? Does the optimal growth temperature occur at the minimum or the maximum or somewhere in between? Growth differs in the way that when the organism isn’t in its optimum temperature range, its growth isn’t as rapid. The minimum is the lowest temperature at which the organism can still grow whereas the maximum is the highest temperature at which it can still grow. Therefore, the optimum is a temperature in between these two temperatures where it grows the best. 4. Why are organisms only able to grow within a certain range of temperatures? High temperatures often inactivate necessary enzymatic systems of the cell Low temperatures often decrease microbial reproduction rates 5. While you do not have to be able to give the exact range of temperatures for each classification (as this is just an estimation) you should understand the general range for each group of organisms. What is a mesophile, psychrotroph, psychrophile, thermophile, hyperthermophile? Which of these groups are more likely to include the Archaea? Mesophile: Moderate temperature loving – Temp range: 25-40 degrees C Psychrotroph: Cold loving – Temperature range: 0-25/30 degrees Celsius Psychrophile: Cold loving – Temperature range: 0, 15, 20 degrees Celsius Thermophile: Heat loving – Temperature range: 50-60 degrees Celsius Hyperthermophile: Extreme heat loving – Temp range: 80 degrees C or higher Archaea are included in the hyperthermophiles 6. Organisms that cause disease are most likely to classified in which temperature category? Organisms that cause disease are most likely to be classified as a mesophile. This is because mesophiles temperature range is most closely related to that of human beings temperature range. They have adapted to live in bodies of animals and so their optimum temperature range is close to that of their hosts (37 degrees Celsius) 7. What is a neutralophile? An acidophile? An alkaliphile? A neutralophile is an organism that thrives in the neutral pH range (pH 5-8) includes most pathogens An acidophile are bacteria that are extremely tolerant of acidity (pH 0-5) found in acid mine drainage or acidic hot springs An alkaliphile are bacteria that are extremely tolerant of alkaline conditions (pH 9-11) found in saline soda lakes 8. What happens to cells when they are exposed to a high salt environment? Cells that are exposed to a high salt environment are highly susceptible to plasmolysis (shrinkage of cell’s cytoplasm). This is because high concentration of salt outside the cell causes the water inside the cell to rush out to try to neutralize the high solute concentration thus, preventing their growth. Therefore, the addition of salts to a solution and the resulting increase in osmotic pressure, can be used to preserve foods. 9. Compare and contrast halotolerant organisms to halophilic organisms. There is a difference between tolerating and requiring Halotolerant organisms are organisms that are tolerant of high salt concentrations whereas halophilic organisms are organisms that require high salt concentrations to grow 10. Microorganisms are categorized according to how they obtain carbon from their environment. List and define the two ways in which organisms obtain carbon from their environment. Chemoautotrophs and photoautotrophs derive their carbon from carbon dioxide Chemoheterotrophs derive their carbon from organic materials such as proteins, carbohydrates, and lipids 11. What is a trace element? Why do organisms need trace elements? Trace elements are mineral elements such as iron, cooper, and zinc that microorganisms require in very small amounts for the function of certain enzymes 12. List and explain the different types of relationships that an organism may have with molecular oxygen (02): Obligate aerobe, obligate anaerobe, facultative anaerobe, aerotolerant anaerobe, microaerophile. Obligate aerobe: organisms MUST be in the presence of oxygen to grow Obligate anaerobe: organisms CANNOT be in the presence of oxygen to grow Facultative anaerobe: able to grow in the presence AND absence of oxygen Aerotolerant anaerobe: cannot grow in the presence of air but can survive Microaerophile: require oxygen but grow only in the presence of oxygen concentrations lower than those in air 14. Why is it that some organisms cannot survive in the presence of oxygen and other organisms can? Many organisms can survive in the presence of oxygen because they can create an enzyme, superoxide dismutase (SOD), which neutralizes the toxic end products of oxygen as a final electron acceptor. Many organisms do not produce this enzyme thus, having a toxic end product produced from oxygen as a final electron acceptor and no way to neutralize it, kills them. Understand that the enzymes superoxide dismutase, catalase and peroxidase are responsible for taking toxic oxygen radicals and converting them to non-toxic products, or as in the case of catalase, to other products that can then be dealt with by other enzymes. 17. Understand how organisms with different oxygen requirements will grow in a tube of solid growth medium. Understand that this medium has an oxygen gradient that affects were you would find different organisms. Obligate Aerobes would grow only at the top of the tube where oxygen was present Facultative Anaerobes growth throughout the tube but most growth at the top Obligate Anaerobes growth only at the bottom of the tube where there is no oxygen Aerotolerant Anaerobes growth occurs evenly; oxygen has no effect Microaerophiles growth occurs only where there is a low concentration of oxygen (middle of tube) 18. What are biofilms? Understand that biofilms require a large number of organisms, and that these organisms may or may not be of the same species. Biofilm formation requires communication, and the production of an extracellular polymeric substance. Biofilms are thin slimy layer encasing bacteria that adheres to a surface 19. What is the function of a biofilm, and why does the production of a biofilm become a problem for treatment of bacterial infections? The function of a biofilm is to allow attachment to a surface – provide a “community” for bacteria and allow them to share nutrients as well as shelter them from harmful factors in the environment. Productions of biofilms are a problem for treatment of bacterial infections because it makes bacteria up to 1,000 more resistant to microbicides and leads to many infections. 20. Be able to define the following: culture medium, inoculum, culture, sterile Culture medium: Nutrient material prepared for the growth of microorganisms Inoculum: Microbes that are introduced into a culture medium to initiate growth Culture: Microbes that grow and multiply in or on a culture medium Sterile: Not containing any living microorganisms 21. Compare and contrast complex and synthetic media (also commonly referred to as defined and undefined media). Complex media is undefined media meaning the exact ingredients are not known. These types of media are nutrient rich and typically contain extracts. Synthetic media is a defined media, which means the exact contents are known 22. What does it mean if media is selective? What does it mean if media is differential? Can media be both selective and differential? Does media have to be selective or differential? Selective media is a type of media that selects for a certain characteristic therefore encouraging the growth of desired microbes and suppressing the growth of undesired. Ex. media, dye, and nutrients that select for a certain type of organism such as using bile salts which would encourage the growth of gram negative bacteria but suppress gram positive Differential media is media that exposes biochemical differences between different organisms. Ex. media and dyes that show their differences such as organisms that ferment turn red and organisms that cannot ferment turn white Media can be both selective or differential, as they can be combined in a single medium to test bacteria. 23. What is an enrichment? An enrichment is providing a certain kind of environment for favorable conditions for a certain organism. Such conditions you might provide could be amount of oxygen, carbon source, temperature, salt concentration. 24. What is a colony? A colony is a group of organisms that arise from a single spore 25. How do bacteria divide? Bacteria divide via binary fission. Binary fission is a process in which one cell produces two daughter cells. 26. What is the growth rate? The growth rate is the rate of increase of population or biomass The growth rate is proportional to the population size at a given time 27. What is the generation time? Understand that organisms can differ greatly in their generation time, and that the generation time for a single organism can vary greatly depending on the growth conditions. Generation time is the amount of time it takes for a cell to divide (doubling time) 28. Why is growth limited in a closed-system? Growth is limited because nutrients begin to deplete and waste products begin to build up. 30. Understand the different phases of growth and what happens in each of the phases. Lag Phase: Phase of no growth but phase of preparation – adjustment period Log Phase: Phase of most metabolic activity – phase of greatest cell division and population increase Stationary Phase: Phase where cell death and cell production equal each other Death Phase: Nutrients are depleted, waste is accumulating, population of cells are dying, occurs slowly 31. What is a spectrophotometer used for? A spectrophotometer is used to read absorbance levels of bacteria. This is a test to try to get a count of how much bacteria is present. More bacteria, less light absorbed therefore, the readings directly correlate to the microbial population count. Chapter 7 1. What were the contributions of Ignaz Semmelweis and Joseph Lister to the effort to control microorganisms for the safety of patients? These two physicians developed some of the first microbial control practices for medical procedures. These practices included hand washing with microbe-killing chloride of lime and using the techniques of aseptic surgery to prevent microbial contamination of surgical wounds. 2. What is sepsis? Asepsis? Sepsis is a term used to describe a disease condition – this word indicates bacterial contamination Asepsis is the term that describes an object or area that is free of pathogens – absence of significant contamination – important in surgery to minimize contamination 3. What is sterilization? What is the difference between sterilization and commercial sterilization? Sterilization is the destruction or removal of all forms of microbial life, including endospores. The difference between sterilization and commercial sterilization is that commercial sterilization only applies enough heat necessary to kill C. botulinum whereas sterilization is the destruction or removal of all forms of microbial life 4. What is disinfection? Antisepsis? What is the difference between disinfection and antisepsis? Disinfection is the destruction of vegetative pathogens on inanimate objects Antisepsis is the destruction of vegetative pathogens on living tissue The difference between disinfection and antisepsis is the surfaces you use them for. Antiseptics are a gentler way of removing microorganisms as it can be used on living tissue whereas disinfectants are applied only to inanimate surfaces because they are too harsh to use on living tissue. 5. What is degerming? De-germing is the removal of microbes from a limited area, such as the skin around an injection site. Some examples are alcohol swabbing the area of skin in which someone is about to receive an injection. Results mostly in the mechanical removal more so than the killing 6. What is sanitization? Sanitation is treatment that is intended to lower microbial counts on eating and drinking utensils to safe public health levels. This is not the same as sterilization since not ALL microbial life is removed during this process of controlling microbial growth. 7. What does it mean if something is bacteriostatic? What is the difference between bacteriocidal and bacteriostatic? Bacteriostatic is the inhibiting of growth or multiplying of bacteria Bacteriocidal is the outright killing of bacteria (suffix –cide) The difference between the two is that bacteriocidal results in the death of bacteria whereas bacteriostatic is only the inhibiting of growth or replication. Once a bacteriostatic agent is removed, growth might resume and bacteria may continue to grow 8. What are the parameters that determine the effectiveness of an antimicrobial treatment? Some parameters that determine the effectiveness of an antimicrobial treatment are: - Number of Microbes (the more microbes, the longer it takes to eliminate the entire population) - Environmental Influences (most disinfectants work somewhat better in warm solutions) - Time of Exposure (chemical antimicrobials often require extended exposure to thoroughly killthe more resistant microbes and endospores) - Microbial Characteristics 9. What different parts of the microbial cell are affected by microbial control agents? Different parts of the cell that are affected by microbial control agents are: - Membrane Permeability Damages to lipids or proteins of the plasma membrane by antimicrobial agents causes cellular contents to leak into the surrounding medium and interferes with the growth of the cell. - Damage to Proteins & Nucleic Acids Functional properties of proteins are the result of their three- dimensional shape. This shape is maintained by chemical bonds that link adjoining portions of the amino acid chain as it folds back and forth upon itself. Their shape is possible by hydrogen bonds (susceptible to breakage by heat or certain chemicals which results in denaturation of the protein) and covalent bonds (stronger but still subject to attack) – damage to these nucleic acids by heat, radiation, or chemicals is frequently lethal to the cell as it can no longer replicate, nor carry out normal metabolic functions 10. Be able to identify if a particular type of treatment would be considered a physical method or a chemical method of microbial control. Physical Method Chemical Method Heat Phenols and Phenolics Pasteurization Halogens Sterilization Alcohols Filtration Heavy Metals Low Temperatures Surface Active Agents (soaps & detergents) High Pressure Sanitizers Osmotic Pressure Quats Desiccation Chemical Food Preservatives Radiation Nitrites / Nitrates Aldehydes 11. An autoclave is an example of what type of sterilization? Understand that an autoclave uses pressure to increase the overall temperature. An autoclave is an example of moist heat sterilization 12. Is boiling an effective method of sterilization? Boiling will kill most pathogens. However, it is not always a reliable sterilization procedure because some bacterial endospores can resist boiling for more than 20 hours. Boiling kills vegetative forms of bacterial pathogens, almost all viruses and fungi and their spores within about 10 minutes. 13. Which treatments are effective against endospores? Treatments that are effective against endospores are autoclaving 14. What is pasteurization? Why is it a treatment used for dairy products (why don’t we use an autoclave instead)? Understand that in pasteurization if you decrease the temperature of exposure then you may need to increase the length of time the item is exposed to that temperature. Pasteurization is the mild heating method that is used to eliminate pathogenic organisms and lower microbial numbers in milk. This method also prolongs milks good quality under refrigeration. This treatment is used for dairy because products because the high pressure would cause a liquid such as milk to bubble over and it would also damage the taste of the product. High-temperature short-time is a treatment of pasteurization (72 C at 15 seconds), method is applied as milk flows continuously past a heat exchanger. This method kills pathogens and lowers total bacterial counts. 15. Is pasteurization a method of sterilization? Pasteurization is not the same as sterilization. Its purpose is to reduce the bacterial population of a liquid (such as milk) and to destroy organisms that may cause spoilage and human disease. Spores are not affected by pasteurization therefore, total removal of microbes is not achieved with this method. 16. Sterilizing your loop using a Bunsen burner would be an example of what type of sterilization? Dry heat sterilization 17. What is filtration? What is the advantage of using a filter or why is filtration sometimes necessary? Filtration is the passage of a liquid or gas through a screen-like material with pores small enough to retain microorganisms. An advantage of using a filter is they cab be used to sterilize heat- sensitive materials such as culture media, enzymes, vaccines, and antibiotic solutions 18. Why is adding salt or sugar to foods an effective method of microbial control? Adding high concentrations of salt or sugar to foods is an effective method of microbial control because it creates a hypertonic environment, which causes water to leave the cell and plasmolysis. 19. Low temperatures have a bacteriostatic effect. 20. What is the Use-dilution tests? Understand what is happening in a use-dilution test. The use-dilution tests are the standard tests used to evaluate the effectiveness of disinfectants and antiseptics Metal or glass cans are dipped into standardized cultures of bacteria, removed, dried, then placed into a solution of the disinfectant at the concentration recommended by the manufacturer and left for 10 min. Following exposure, cans are transferred to a medium that permits growth of any surviving bacteria and effectiveness is determined by the number of cultures that grow 21. What is the disk-diffusion method? How can you tell if a disinfectant is effective using this method? Where is the disinfectant most concentrated on the plate (Figure 7.6)? The disk diffusion method is a method used in laboratories to evaluate the efficacy of a chemical agent. You can tell if a disinfectant is effective using this method if there is a zone of clearing present around the disk. The disinfectant is most concentrated near the disks on the plate. The further from the disk, the less concentrated the disinfectant is. 22. What is triclosan? Triclosan is a type of biphenols (derivatives of phenol that contain two phenolic groups connected by a bridge) that is widely used in antibacterial soaps and toothpaste. So widespread that resistant bacteria have been reported – Pseudomonas aeruginosa is a gram- negative bacterium that is very resistant to triclosan. Triclosan works by inhibiting an enzyme needed for the biosynthesis of fatty acids which mainly effects the integrity of the plasma membrane. 23. What is a tincture? A tincture is a solution in aqueous alcohol 24. What is the method of action of iodine? What is the method of action of chlorine? The method of action of iodine is that it impairs protein synthesis and alters cell membranes by forming complexes with amino acids and unsaturated fatty acids. The method of action of chlorine is caused by the hypochlorous acid that forms when chlorine is added to water – hypochlorite is a strong oxidizing agent that prevents much of the cellular enzyme system from functioning. 25. Refer to Table 7.6, what does this tell you about the relative effectiveness of different concentrations of ethanol? Ethanol is most effective at concentrations of 95-60%. The optimum concentration of ethanol is 70%. This is because the denaturation of proteins – which is ethanol’s method of action – cannot occur without water therefore, it doesn’t work at 100%. 26. Understand how you would use the information in figure 7.10 to determine the agent which is most effective in treating microorganisms in the shortest amount of time. The steeper the curve, the more effective the antiseptic is 27. What is a bacteriocin? A bacteriocin is a protein that is produced by one bacterium and inhibits another – an example is Nisin which is often added to cheeses to inhibit the growth of certain endospore forming spoilage bacteria. Chapter 8 1. What is a nucleotide? How do nucleotides come together to form a nucleic acid strand? A nucleotide is what the monomers found in DNA are made up of. Nucleotides are composed of a phosphate group, a sugar, and a nitrogenous base. 2. What are the four deoxyribonucleotides found in DNA? How do they differ from one another? What are the four ribonucleotides in RNA? - The four deoxyribonucleotides found in DNA are adenine, thymine, guanine, and cytosine. - They differ from each other in the way that purines (adenines and guanines) have two nitrogen containing rings whereas pyrimidines (cytosine, thymine, and uracil) only have a single nitrogen containing ring - The four ribonucleotides found in RNA are adenine, guanine, uracil and thymine. 3. What are the differences between DNA and RNA? How are they similar? The difference between DNA and RNA is their sugars and bases. DNA contains a dexoyribose sugar and RNA contains a ribose sugar DNA utilizes thymine as a base and RNA utilizes uracil They are similar in the way that they are both built from nucleotides DNA base pairs with RNA during the replication process… RNA takes the place of DNA to protect the single strand but DNA polymerase comes in and removes all RNA replacing it with DNA 4. What is complementary base pairing, and what are the complementary base pairs? Complementary base pairing is nucleotide bases linked by a hydrogen bond to opposite strands of DNA Adenine to Thymine (Uracil) Guanine to Cytosine 5. What are the characteristics of DNA? Characteristics of DNA include: - opposite base pairs - antiparallel - negative charge due to phosphate - double helix - complementary - covalent bonds between monomers - hydrogen bonds between bases 6. What are the differences between the eukaryotic and the prokaryotic chromosome? Eukaryotic chromosomes are linear Prokaryotic chromosomes are single / circular 7. What does it mean that the two strands of the double-helix run antiparallel to each other? It means that one strand runs 5’ to 3’ and the other strand runs 3’ to 5’. They are not the same on both sides but instead, complementary. 10. Understand the process of DNA replication, and understand the name and the function of each of the enzymes covered. DNA helicase: breaks apart hydrogen bonds separating the two strands of DNA RNA polymerase: initiates synthesis of complementary strands because DNA polymerase can’t start synthesizing on its own DNA polymerase: reads nucleotide base on template strand, brings in complementary nucleotide, gets rid of RNA DNA ligase: connects all pieces together Some questions to consider: What is the template for DNA replication? The template is the strand of DNA that acts as a blueprint for the new complementary strand of DNA to be built. Once DNA is unzipped, then each separated strand is considered a template. What is the result of DNA replication? Two daughter DNA strands – should be identical Why does replication occur? Replication occurs because existing cells divide to produce new cells and each new cell needs it’s manual to operate properly aka DNA What does it mean that DNA replication is semiconservative? DNA replication being semiconservative means that when replication occurs, each new strand gets a newly synthesized strand but also a strand from the original (old) strand of DNA What is the difference between the leading strand and the lagging strand? The leading strand is replication occurring in 5’ to 3’ end (quicker) The lagging strand is replication occurring in 3’ to 5’ end (slower) What is an Okazaki fragment? An Okazaki fragment is a short piece of single-stranded DNA that is formed on the lagging strand during DNA replication. After replication has completed is there any RNA remaining on the DNA molecule? No. After replication is complete, RNA has been replaced by DNA, as they were fillers and temporary to hold the spot for DNA In what direction does the DNA polymerase synthesize a new strand of DNA? DNA polymerase synthesizes a new strand of DNA in the 5’ to 3’ direction Understand that a DNA polymerase has a proofreading ability, which makes replication much more accurate. 10. Where is the replication fork? What does it mean that DNA replication is bidirectional? The replication fork is a very active area where DNA replication takes place. It is created when DNA helicase unwinds the double helix structure of the DNA. The replication fork looks like a fork in the road that is composed of a leading strand and a lagging strand of DNA. DNA replication being bidirectional means replication occurs and proceeds in two directions 11. What is the central dogma of molecular biology? The central dogma of molecular biology is the name of the theory that proposed the sequence of nucleotides in DNA determines the sequence of amino acids in a protein – Proposed by Francis Crick. DNA  RNA  Protein 12. Understand the process of transcription. Some questions to consider: - What is transcription? Transcription is the synthesis of a complementary strand of RNA from a DNA template – RNA polymerase uses ATP to read the DNA strand and form an mRNA strand in the nucleus - What enzyme is responsible for the process of transcription? RNA polymerase is responsible for the process of transcription & a supply of RNA nucleotides. - What is the template for transcription? The template for transcription is only one of the two DNA strands - What is the product of transcription? The end product of transcription is mRNA - Where does transcription start and stop? Transcription starts at the promoter region where RNA polymerase binds to the DNA (at a site called the promoter) Transcription ends when RNA polymerase reaches a site on the DNA called the terminator 13. What are the different types of RNA? Which of these RNA molecules will be translated into a protein? mRNA: mRNA transcribes the genetic code from DNA into a form that can be read and used to make proteins. mRNA carries genetic information from the nucleus to the cytoplasm of a cell. rRNA: located in the cytoplasm of a cell, where ribosomes are found. rRNA directs the translation of mRNA into proteins tRNA: located in the cytoplasm and is involved in protein synthesis. Transfer RNA brings or transfers amino acids to the ribosome that correspond to each three-nucleotide codons of rRNA. The amino acids then can be joined together and processed to make polypeptides and proteins mRNA is translated into a protein 14. What is a promoter composed of, and what is the function of a promoter? A promoter is composed of a specific sequence of nucleotides found on the DNA template. The function of the promoter is to mark the presence of a gene on the DNA. 15. When DNA is denatured what does this mean? The hydrogen bonds that hold the double helix together break apart, separating the DNA molecule into two single strands. 16. In what direction is an RNA molecule synthesized? 5’  3’ direction 17. Understand the process of translation. Some questions to consider: - What is translation? During the process of translation the cell is changing languages. It is taking a RNA template (nucleotides), and using it to build a polypeptide (amino acids) - What cellular components are necessary for translation? Cellular components necessary for translation are: Ribosome (rRNA and proteins), RNA template, tRNA, amino acids, and translation factors - What molecule is translated, and what is it translated into? Nucleic acids are translated into proteins - How are mRNA, tRNA, and rRNA all involved in translation? mRNA: Messenger RNA (mRNA) carries the genetic information copied from DNA in the form of a series of three-base code “words,” each of which specifies a particular amino acid. tRNA: Transfer RNA (tRNA) is the key to deciphering the code words in mRNA. Each type of amino acid has its own type of tRNA, which binds it and carries it to the growing end of a polypeptide chain if the next code word on mRNA calls for it. rRNA: Ribosomal RNA (rRNA) associates with a set of proteins to form ribosomes. These complex structures, which physically move along an mRNA molecule, catalyze the assembly of amino acids into protein chains. Ribosomes are composed of a large and small subunit, each of which contains its own rRNA molecule or molecules. - Where does translation start and stop? Translation begins at a start codon, which is signaled by AUG Translation stops at a stop codon, which is signaled by UAA, UAG, or UGA. - Where does translation occur? Translation occurs in the cytoplasm of the cell 18. What is the universal code? And what is the difference between sense and nonsense codons? What is the start codon, and what does it encode for? The genetic code is called a universal code because all known organisms use the same four nucleotide bases. The (4) nucleotide bases are: adenine, thymine, cytosine and guanine. Sense codons code for amino acids and nonsense codons do not. Nonsense codons (UAA, UAG, & UGA) signal the end of protein molecule’s synthesis The start codon, AUG, encodes for methionine and also initiates the start of protein synthesis. 19. What are the codon and the anticodon? The language of mRNA is in the form of codons, which are groups of three nucleotides – the sequence of codons on an mRNA molecule determines the sequence of amino acids that will be in the protein being synthesized. The anticodon is a sequence of three bases that is complementary to a codon. In this way, a tRNA molecule can base pair with its associated codon. 20. What does it mean to regulate gene expression? Why is it important that cells be able to regulate gene expression? Are all genes regulated in the same way? A wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products is regulating gene expression. Transcription and translation take a lot of energy / it would be a waste of energy to make all proteins in all cells so we conserve energy by regulating gene expression 21. What does it mean if a gene is constitutively expressed? Constitutive meaning their products are constantly produced at a fixed rate 22. Understand the terminology of gene expression. Operon: a series of genes that are controlled by one promoter. The genes have a related function. Induction: the process that turns on the transcription of a gene or genes. Inducer: the molecule required to initiate transcription for a regulated gene or genes. Repression: mechanism that inhibits transcription of a gene or genes. Repressor: a protein that inhibits gene expression. Operator: a region of DNA that is recognized and bound by regulatory proteins. 23. If genes X, Y and Z are in the same operon, if gene X is being transcribed what does that mean for genes Y and Z? All genes will be transcribed since they are in the same operon 25. What is a mutation? Mutation: a mutation is a permanent change in the base sequence of DNA Understand that mutations can be neutral, beneficial or harmful. 27. What is vertical gene transfer? What is horizontal gene transfer? Vertical gene transfer occurs when genes are passed from an organism to its offspring Horizontal gene transfer is when bacteria can pass their genes not only to their offspring but also laterally, to other microbes of the same generation. The transfer involves a donor cell that gives a portion of its total DNA to a recipient cell – once transferred, part of the donor’s DNA is usually incorporated into the recipient’s DNA (the combination of recipient DNA and it’s own DNA = recombinant) – not a frequent event 28. What are the three different ways that bacteria may take in foreign DNA? Compare and contrast these methods. Transformation: genes are transferred from one bacterium to another as “naked” DNA in a solution – study of this led to conclusion that DNA is the genetic material – in nature, some bacteria after death and cell lysis, release their DNA into the environment where other bacteria can then encounter the DNA and possibly take up small fragments of DNA and integrate them into their own chromosomes by recombination. All descendants of bacteria that could take up this new DNA (competent = physiological state in which a recipient cell can take up donor DNA) will be identical and posses this new DNA as well. Conjugation: facilitatedby a plasmid, circular piece of DNA that replicates independently from the cell’s chromosome – doesn’t carry genes essential for growth though they are beneficial. Requires direct cell-to-cell contact and conjugating cells must be of opposite mating type – donor cells must carry the plasmid and recipient cells usually do not. Transduction: process by which foreign DNA is introduced into a cell by a virus – new DNA is transferred from a donor cell to a recipient cell inside a virus that infects bacteria called a bacteriophage or phage. Chapter 10 and 1 1. What is a microorganism? An organism that cannot be seen with the naked eye 2. What are the three domains of life? Bacteria, Archaea, Eukarya 3. Which Domains contain microorganisms? All 3 domains contain microorganisms 4. Compare and contrast prokaryotes and eukaryotes. Prokaryotes Eukaryotes • Cells do not have Both • Cells have a nucleus nucleus • Both have DNA • Membrane bound • No membrane bound • Both have ribosomes organelles organelles • Cell walls do not • Cell wall contains contain peptidoglycan peptidoglycan • Reproduce through • Reproduce through binary fission mitosis 5. Compare and contrast bacteria and archaea. Bacteria Both Archaea • Cell wall contains • Both have ribosomes • Cell wall contains no peptidoglycan • Both are prokaryotic peptidoglycan • Composed of cells • Composed of branched straight carbon carbon chains chains • Found in extreme • Found in soil, environments water, plants and animals 6. Which domains are prokaryotic? Which are eukaryotic? Prokaryotic include archaea and bacteria Eukaryotic include plants, animals, and fungi 7. How do prokaryotes reproduce? Prokaryotes reproduce through a process called binary fission. Type of cell division that produces two daughter cells. 8. Why is a Virus considered acellular? A virus is considered acellular because they do not reproduce through cellular division 9. What is taxonomy? Phylogeny? Taxonomy is the science of the classification of organisms Phylogeny is the evolutionary history of a group of organisms; phylogenetic relationships are evolutionary relationships 10. What does a phylogentic tree represent? A phylogenetic tree represents common ancestors among organisms – what characteristics they share and what common ancestor they evolved from 11. Why is it difficult to classify microorganisms by physical appearance? It is difficult to classify microorganisms by physical appearance because they are so small and contain many of the same characteristics sometimes that they don’t have their own distinct appearance. 12. What is a molecular clock? A molecular clock is an evolutionary timeline based on nucleotide sequences in organisms. 13. What gene is used to determine phylogenetic relatedness between prokaryotes? And why was this gene chosen? Carl Woese founded that the 16s rRNA gene could be used to determine phylogenetic relatedness between prokaryotes. This was chosen because all prokaryotes contain this gene and mutations in this gene are very slow to occur over time so it is easy to compare them They are examining how different the A,T,C, and G’s are in this gene 14. What are the lines of evidence that the mitochondria, and the chloroplasts found in eukaryotic cells were prokaryotic in origin? Mitochondria and chloroplasts have similarities in structure, reproduction, biochemistry, and genetic makeup to certain prokaryotes. Own genetic information, ribosomes, DNA structured like prokaryotes – evidence they lived as free living prokaryotes 15. What is the correct way to write the genus and species name? Genus name comes first and is always capitalized. The species name comes second and is lowercase. Both names are italicized or underlined. 16. Understand the order of classification (Domain, Kingdom, Phylum, Class, Order, Family, Genus and species). 17. What was the significance of Louis Pasteur’s swan-necked flask The significance of Pasteur’s swan necked flask was that it trapped microorganisms from getting inside and infecting the fluid even though it was open. The shape of the flask and the openness without a seal proved it wasn’t the oxygen that made the difference. 18. What is the Germ Theory of Disease? The Germ Theory of Disease is the idea that microorganisms themselves might cause disease 19. Who is Robert Koch and what is he credited with? Robert Koch established experimental steps for directly linking a specific microbe to a specific disease 20. Who is Edward Jenner and what is he credited with? Edward Jenner discovered the process of immunity (vaccines) from smallpox. He exposed a healthy girl to an inoculated needle with smallpox and she became mildly sick but recovered and never again contracted either cowpox or
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