Exam 1 Study Guide
Exam 1 Study Guide BIOL 201
Pacific Lutheran University
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This 18 page Study Guide was uploaded by Anela Barber on Tuesday October 4, 2016. The Study Guide belongs to BIOL 201 at Pacific Lutheran University taught by Shannon B. Seidel in Fall 2016. Since its upload, it has received 104 views. For similar materials see Introductory Microbiology in Biology at Pacific Lutheran University.
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Date Created: 10/04/16
Anela Barber September 27, 2016 Exam 1 Study Guide 1. Identify common characteristics of living things Common characteristic amongst all living things include: 1. Excrete waste 2. Take in nutrients 3. Grow 4. Move 5. Respire 6. Reproduce These characteristics identify living organisms but there are also exceptions as most things. 2. Differentiate structural and functional definitions of life A structural definition of life could include many different process that give rise to the given characteristics of life. For example, to move an organism would need a structure to move. To respire, an organism would need a respiratory system. Functional definitions of life could include the “how” for the structures of life 3. Sort biological molecules in terms of size and scale Although it may be hard to believe, mitochondria and protozoa are similar sizes! A protozoa however is slightly bigger and puts mitochondria as a close second. When thinking about the relative size of biological molecules, think about what comprises the molecules. Are other subunits comprising the molecules that can therefore be considered smaller than the molecule itself (Nucleic acids are composed of atoms so atoms are therefore smaller than nucleic acids)? What other things can a certain molecule produce (Nucleic acids comprise proteins so proteins are therefore larger than nucleic acids)? Think conceptually and it is much easier to estimate the relative size. 4. Draw a prokaryote, and eukaryote accurately including and excluding key structures. Prokaryotes: Lack a nuclear membrane and membrane bound organelles. Contains a nucleoid that houses the cells DNA. Eukaryotes: Contain membrane bound organelles and a membrane bound nucleus. Has mitochondria! 5. Explain endosymbiotic theory and its relevance to the evolution of living things The endosymbiotic theory aims to describe the evolutionary evidence of small prokaryotes that engulf other smaller prokaryotes. An example/evidence for this is seen in the mitochondria within a normal sized prokaryotic cell. 6. Distinguish between signs and symptoms Signs are observable, measurable effects that an individual experiences during an illness. An example of a sign would be one’s temperature and weather or not they have a fever or not. Symptoms are personal feelings/experiences that an individual feels during an illness. One example for symptoms could be feeling pain or clammy. 7. Describe the five basic stages of an infectious disease The five basic stages of infectious disease are: 1. Incubation Phase At this stage the microbe/disease is acclimating to it’s new environment and does not have negative effects toward the individual 2. Prodromal Phase This stage relates to the mundane, seemingly unrelated signs and symptoms related to sickenss. This would be sniffing, coughing or a scratchy throat. 3. Illness Phase This stage describes the microbe/pathogen in full swing and fully effecting the individual. It is at this stage that FEVER is present as an obvious sign! 4. Decline Phase At this stage the individual is beginning to recover from the infectious disease. A reduction in body temperature may be seen, signs and symptoms may reduce and the individual is on track to normal health. 5. Convalescence Person is recovering from their illness. Signs and symptoms are absent. 8. Identify portals of entry and exit for microbial pathogens There seems to be 5 major routes of entry and exit for pathogens: 1. Oral Introducing a pathogen through the oral cavity either by eating or drinking them. 2. Respiratory Pathogen is introduced into the lungs and absorbed through the pulmonary tissues. 3. Skin Pathogens/ Microbes can be introduced onto the skin and therefore absorbed into the body system. 9. Differentiate endemic, epidemic, and pandemic disease The difference between these three words is the difference in the amount of population/spread that the disease has effected. Endemic This is a disease that effects a community but in rather low numbers and is otherwise not alarming. An example of this would be the flu Epidemic A disease that rapidly over takes a small community and is sort of alarming. Example of this would be small pox Pandemic This is a disease that is able to spread across the world from country to country and across the globe. Almost always very alarming! An example of this would be a plague. 10. Compare and contrast features of different types of microbes. The different types of microbes covered in class were: 1. Bacteria Usually are unicellular organisms and are much smaller than eukaryotes. These microbes contain peptidoglycan within their cells walls. Can be found everywhere, including extreme environment. Asexual reproduction. 2. Archaea Just about the same characteristics of bacteria. 3. Fungi These cell walls contain chitin and glucan, something not seen in other microbes. Have positive and negative effects: mold vs. cheese. 5. Protozoa Single celled organism. Tend to have cilia or flagella to move. Can be asexual or sexual to reproduce. 6. Algae Uni or Multicellular. Can be photosynthetic! Cell walls contain cellulose, like plants. Produce >70% of earths O2. 7. Viruses Acellular! No ribosomal RNA. Contains nucleic acid, DNA or RNA. There is a protein capsid to protect the nucleic acid. Replication occurs inside a host cell . Any cell can be infected! (Prokaryotic and Eukaryotic). 11. Develop a dichotomous key to systematically differentiate and identify specific microbes based on structural features. A dichotomous key is a sort of code that is able to distinguish certain microbes from others based on physical features (phenotype) or genetic characteristics (genotype). For example, if I were to differentiate between a group of viruses and prokaryotes a great isolating question to ask is “Does this cell have a capsid?” If the answer is yes, then the microbes representing that would be viruses. If the answer is no, then the microbes would be prokaryotes. The whole objective of a dichotomous key is to isolate a particular group of microbes away from any other microbes. 12. Describe the Linnaean system of classification. The Linnaean system of classification is used to categorize different types of organisms into a clear and organized fashion. The way that the organisms are classified is with a binomial nomenclature which describes the kingdom and species of the organism. The language used for this classification is traditionally Latin. 13. Explain how the Linnaean system has changed since its development. Since the fist binomial nomenclature was developed a few changes have been implemented to the organizational system. Where there were simply a few classes to be filed into, categories such as phylum have been added to further differentiate one organism from another. 14. Describe the formation and function of a bacterial endospore. A bacterial endospore is created by a microbe/pathogen in attempts to protect its DNA information in the presence of a harsh environment. The endospore is created by the microbe by means of sporulation. Sporulation is essentially replication that is cut short. When the cell is replicated and ready to split into two separate cells one side is “sacraficed.” The genetic material in the sacrificed portion is destroyed and what remains is the membrane that would have covered it. It is this extra membrane that is able to serve as a protectant for the endospore. 15. Describe the structure and function of the bacterial cell wall and explain it's importance as a target for antibiotics. Bacterial cell walls differ from eukaryotic cell walls. This makes it easy for antibiotics to target the bacterial cells rather than our self cells. Peptidoglycan in particular is a component of bacterial cell walls that eukaryotes do not possess. It is this that signals antibiotics to target these cells. 16. Compare structural similarities and differences of gram and gram+ cell walls. Similarities Both the gram and gram + cells contain the complex protein peptidoglycan. Both of these cells also contain a cell wall/membrane. Differences The gram + cells contain a thick layer of peptidoglycan while the gram cell contains a very small layer of it. Gram cells also contain a periplasm which contains sugars and proteins while the gram + cells do not. Gram + cells have what is called an S layer in order to allow the flow of certain molecules to flow freely through the cell wall whereas the Gram cell does not have this. 17. Describe key functions of pili and how they can benefit bacterial persistence. Pili are structures that protrude from the perimeter of a cell and are able to connect to other cells. Pili are then able to connect the cytoplasm from one bacteria to another and then transfer genetic material between each other. By random selection, certain genes and traits are able to be passed from one bacterial cell to the lacking cell and is then able to produce a resistance/persistence to certain antibiotics. 18. Explain how flagella motility and chemotaxis enable bacteria to respond to environmental changes. Flagella is a whiplike structure that is able to propel a cell forward with a motor like movement. There are 3 types of flagella formations on a cell: 1. Peritrichious flagella are located alone the entire perimeter of the organism 2. Polar A single flagellum is located on one side of the organism or the other. 3. Lophotrichous A turft of flagella is located at one side of the organism or another. Chemotaxis is the ability for a cell to move, with the aid of flagella, toward a desirable environment and away from an undesirable environment. An organism is driven toward a desirable environment due to it abundance in nutrients or some other attractant present. An organism is driven away from an environment due to an over accumulate of pollutants or a lack of nutrients. These items are called repellants. 19. Be able to calculate microbial growth, cell number, and division Microbial growth can be calculated by taking colony counts on petri dishes after a certain amount of time. If one is given a certain CFU and is asked to find the original cell density/concentration that can be done by using the formula: OCD = CFU/(vol. plated)(dilution factor) 20. Use proper scientific notation Scientific notation is converting very large or very small numbers into a practical way to compare them. 21. Explain how pure cultures are obtained and why they are important in medicine (LAB) Pure cultures may be obtained in a lab setting by creating a quadrant spread plate and isolating individual colonies. If individual colonies are achieved then that colony can give rise to a single organism culture. This is important to medicine because medicines and treatments can be tested on these pure cultures and their effects may be recorded. 22. Compare and contrast methods used to measure bacterial growth (LAB) Bacterial growth can be measured in a number of different ways. 1. Counting CFU’s. This would be counting the individual colony forming units and comparing it to previous data collected. 2. Turbidity A bacteria grown within a liquid medium may produce a cloudy or opaque product within the tube and can then be measured. 23. Compare different sources of carbon and energy used by diverse microbes Microbes are very diverse in the way that they use energy sources around them to survive. 1. Organotrophy this is a microbe that is able to obtain carbon from organic molecules. 2. Phototrophy these are microbes that are able to gain nutrients via sunlight. 24. Chart microbial growth and make predictions about changes in microbial growth curves (LAB) 25. Discuss the importance of biofilms and how they develop 26. Distinguish between catabolic and anabolic reactions. A catabolic reaction is essentially taking a large molecule and reducing it down into separate parts. For example, glycolysis is a catabolic reaction because it is taking a 6 carbon chain and reducing it into 2 3 carbon chains. This process is releasing energy. An anabolic reaction is the building up or creation of molecules. An example of this would be the creation of glycogen. The building blocks to create glycogen is glucose and it is then compiled into one large molecule, glycogen. This process is storing energy within bonds. 27. Explain the relationship between catabolic and anabolic reactions in sustaining cellular life. Catabolic reactions are essential to sustaining cellular life because it is what ultimately what metabolism boils down to. By taking macromolecules and nutrients (such as glucose) the energy within the molecule must be released for the cell to harvest and utilize. Without this catabolic reaction the cells would die. Anabolic relations are essential to cellular life because they are responsible for building vital components such as proteins. Without the building of proteins a cell is unable to do anything and will likely result in death as well. 28. Describe the structure and function of ATP. ATP is adenosine triphosphate. This molecule is essentially the cell’s energy currency and is how most cells are able to move, create proteins and complete all the essential reactions needed to sustain an organism. 29. Distinguish the three types of phosphorylation. 1. Oxidative Phosphorylation this type of phosphorylation is able to take an electron carrier (NADH and FADH2) and oxidize (or lose an electron) through the process of the electron transport chain. The ETC then takes the H+ ions and synthesizes ATP through ATP synthase and creates new usable energy. 2. SubstrateLevel Phosphorylation this type of phosphorylation is the production of ATP by means of another reaction taking place. For example, when glucose undergoes glycolysis a net 2 ATP is created. This ATP result is substrate level. 3. Photophosphorylation energy from the sunlight is trapped in the chlorophyll of a plant or animal and is able to go through a series of electron acceptors. ATP is released as a result of this. 30. Describe the ATP cycle and how ATP is a “renewable” energy source for the cell. ATP is a renewable energy because of its constant loss and gain of a phosphate ion. ATP (adenosine triphosphate) is in its most energy dense form and is able to give that energy up for certain processes throughout a cell. Once this energy is given up it losses a phosphate is now considered ADP (adenosine diphosphate). For ATP to be “renewed” it simply needs to gain an additional phosphate via oxidative phosphorylation. Oxidative phosphorylation is a result of the process that the electron transport chain undergoes. The pumping of H+ ions outside the cell membrane eventually creates a gradient in which the H+ ions must flow down through ATP synthase. As the H+ flow through ATP synthase ADP is joined with another phosphate and thus ATP is synthesized. ADP + P = ADP 31. Explain why enzymes are necessary to sustain life. Enzymes are essential to sustain life for many reasons. 1. Enzymes allow certain reactions to lower their activation energy. This means that the initial energy required to begin a reaction is reduced and is thus easier to complete. 2. Enzymes are able to regulate the rate of which a reaction occurs. A greater amount of enzyme present, the quicker a reaction is able to be complete and vice versa. 3. Enzymes are responsible for the chemical arrangement of the molecules reacting. 32. List the physical factors that influence enzyme activity and describe the impact of each. Physical factors that may influence enzyme activity could be the surface area present on the organism. The greater surface area for an enzyme to come into contact with, the greater opportunity the enzyme has to impact it. Other factors that may influence enzyme activity could be temperature or pH. Temperature is able to raise and lower enzyme activity level as temp. raises and lowers. 33. Describe the key substrates, products, net energy production, and reducing power for glycolysis, the Krebs cycle, and oxidative phosphorylation. Glycolysis Key substrates produced in glycolysis would be the 2 molecules of pyruvate produced that will eventually enter the Krebs Cycle. Because an initial 2 ATP is required to begin glycolysis and 4 ATP are generated, a NET total of 2 ATP are generated via glycolysis. Krebs Cycle Substrates that are important to keep in mind during this process is Acetyl CoA. Due to pyruvate transformation via the Transition Reaction, AcetylCoA is able to enter the Krebs Cycle to further oxidize and release electron carriers. Through this process a total of 4 CO2 are produced as well as 6 NADH and 2 FADH2. These electron carriers are now able to move on to the final process of aerobic respiration: The electron transport chain. Oxidative Phosphorylation This process occurs at the final stage of aerobic respiration, the electron transport chain. Oxidative refers to the use of oxygen (O2) and phosphorylation refers to the addition of a phosphate onto a molecule. The molecule that will be gaining an additional phosphate is ADP. Once H+ pass through ATP synthase (an membrane embedded protein) ADP joins and extra phosphate, creating ATP. A fully oxidized glucose molecule will produce roughly 3438 ATP. ADP + P = ATP. 34. Explain how the energy in a molecule of glucose is transformed during aerobic respiration. Aerobic Respiration is the process of fully oxidizing glucose in order to harness all possible ATP from the molecule. This process is done in 4 major steps as mapped below: Glycolysis A 1, 6 carbon chain is transformed into 2, 3 carbon chains termed pyruvate. This is an anaerobic process meaning that it does not require oxygen. This process requires an initial 2 ATP to begin and results in 4 ATP, giving a net 2 ATP in the end. No CO2 is released at this point due to the presence of the 6 original carbons just in different forms. This process occurs within the cytosol. Transition Reaction This process takes the 2 pyruvate produced by glycolysis and further continues a catabolic reaction. The 2 pyruvate are able to generate 2 NADH, electron carriers, and 2 CO2 before entering the Krebs cycle. This end result gives rise to 2 AcetylCoA molecules that are then able to enter the Krebs Cycle. This process is also within the cytosol. Krebs Cycle The 2 AcetylCoA produced by the Transition Reaction go through this particular cycle and produce 4 CO2, 6 NADH and 2 FADH2 and 2 ATP. NADH and FADH are what is known as electron carriers that are to be transported to the electron transport chain. This process takes place within the cytosol. Electron Transport Chain This process aims to take the electron carriers, oxidize them, and then create ATP. The sum of all the NADH and FADH2 created up until this point is 10 NADH and 2 FADH respectively. At 3 ATP per NADH, 30 ATP are generated from NADH. At 2 ATP per FADH2, 4 ATP are generated from FADH2. This is a total of 34 ATP per glucose molecule. This process is performed across the cell membrane with the use of membrane bound proteins. O2 is vital to aerobic cellular respiration because it is the final electron acceptor at the end of the electron transport chain. O2 binds with the free floating H+ ions released once NADH and FADH2 has been oxidized. Once O2 binds with H+ it creates H2O as a final byproduct. O2 + H = H2O 35. Compare and contrast aerobic respiration, anaerobic respiration, and fermentation. Explain why aerobic respiration produces the most ATP. Aerobic Respiration This is the process of taking molecules (such as glucose) and converting it into reusable energy in the form of ATP. Aerobic respiration differs from other systems in that the presence of O2 is required to complete the process. O2 is required because it is the final electron acceptor towards the end of the electron transport chain producing H2O as a byproduct. A total of 3438 ATP are produced by a single molecule of glucose. Anaerobic Respiration This process takes molecules and converts their structure into energy in the form of ATP. What separates this process from others is that it does not require the presence of O2. Instead of O2 acting as the final electron acceptor at the end of the electron transport chain other molecules are substituted in. A popular molecule to replace O2 in anaerobic respiration is nitrate (NO3) and sulfate (SO42). Fermentation This process aims to create a very low amount of ATP without the presence of O2. This process is much shorter and has only 2 steps. Glycolysis begins the process with the production of a net 2 ATP per glucose molecule. After this the process of fermentation occurs, regenerating the cell’s NAD+ supply so glycolysis can continue. A total of only 2 ATP is generated in this process and is thus very energy insufficient. 36. Diagram the relationship between energy intermediates such as NADH and FADH 2 , electron transport, and ATP generation. Energy intermediates (NADH and FADH2) can also be termed electron carriers. What this means is that a electron, or H+ ion, has the ability to be released and thus oxidizing the molecule. The electron transport chain is able to take advantage of these free H+ ions. During the process of the electron transport chain the free H+ ions released via the oxidation of NADH and FADH are able to pass through various membrane bound proteins. The constant flow of H+ ions outside the cell membrane produces a high H+ concentration outside the cell membrane. With the production of a strong H+ concentration outside the cell membrane a natural gradient is produced and the H+ will flow down their gradient back into the cell. The H+ ions pass through a protein named ATP synthase that generates ATP via oxidative phosphorylation. 39. Compare and contrast aerobic respiration, anaerobic respiration, and fermentation. Explain why aerobic respiration produces the most ATP. Aerobic respiration, unlike anaerobic and fermentaion, requires the use of oxygen to fully oxidize the molecule to its most energy producing potential. Aerobic respiration produces a total of 34 ATP whereas anaerobic and fermentation only produce 2 ATP. Aerobic respiration produces the most amount of ATP because it is able to fully utilize glucose to its full potential. Where the aerobic respiration is able to separate the difference between the 2 other types of energy systems is that it utilizes energy intermediates such as NADH and FADH2. The build up of these two electron donors means that an abundance of ATP is available and can be utilized with the use of O2. 40. Diagram the relationship between energy intermediates such as NADH and FADH 2 , electron transport, and ATP generation Energy intermediates such as NADH and FADH 2 are generated from the krebs cycle in order to drive ATP production. The way that these intermediates accomplish that is by simply going through the ETC. NADH and FADH 2 are electron donors in this process in that they release a H+ while traveling back and forth through the cell’s membrane. A build up of H+ ions accumulate on the outside of the ells membrane and is forced to flow down its chemical gradient through ATP synthase. ATP synthase, powered by the H+ ions, is what creates the ATP production by joining a ADP with a free P. ADP + P = ATP. 42. Make connections between microbial metabolism and growth. Microbial metabolism is ultimately what drives its particular type of growth. For example, if a microbe runs off of photosynthesis metabolism and there is no light to generate the necessary proteins for growth, then the microbe will not grow. On the other hand, if a microbe does run off of photosynthesis and light is in abundance then it is ore likely to grow rapidly. 43. Define the major classes of energyyielding metabolism including photosynthesis, organotrophy, and lithotrophy. Photosynthesis These microbes are able to harness the energy from sunlight and generate essential proteins and building blocks to thrive and survive. The main energy produced from this process is glucose. Organotrophy These microbes are able to harness carbon from BLANK BLANK BLANK Lithography 44. Explain the relationship between the structure and function of DNA. DNA’s structure is comprised of a double helix that made up of a sugar and phosphate back bone, various bases, and hydrogen bonds that ultimately hold the structure together. Because the structure of the hydrogen bonds that bind together the various bases between the two entwining backbone are so weak, they are able to come apart and connect again. This is helpful during the process of gene transcription as well as DNA replication. 45. Compare and contrast the genomes of eukaryotes and bacteria The genomes of bacteria are able to MOSTLY code for proteins. At a value of nearly 80%, these genomes are extremely efficient I suppose you could say. The genomes of eukaryotes, on the other hand, are not as compact with protein generating information. Only a whopping 1.5% of the entire genome codes for proteins. This means that there is more “nonsense” or “junk” DNA than actual usable information. 46. Describe a plasmid and how it differs from a chromosome. A plasmid differs from a chromosome in that it is smaller than that of a chromosome. Both of these structures contain genetic information, but the plasmid is able to be shared amongst other bacterial cells. By means of a pilus, different plasmids may be shared amongst microbes in order to gain a particular advantage or perhaps build up antibiotic resistance. 47. Characterize different classes of mutation and give examples of when they occur There are many different types of mutations that can occur. It is important to remember that all mutations occur at the level of transcription and translation. Point Mutation This type of mutation simply occurs when a base pair that is suppose to go together, AT and GC, is paired with something else. (AC or GT). Insertion/Deletion A base is inserted or deleted from the sequence and subsequently effects the following bases and how they pair off into codons. Frame Shift Mutation Usually due to an inserted or deleted base, all of the bases following are effected and are compromised. 48. Complete the processes of transcription/translation Transcription this is the process of DNA providing the template in which RNA polymerase is able to generate mRNA. RNA polymerase binds to the strand of DNA at the Promotor site and begins to “scan” for the start codon. Once the start codon is identified the DNA base is then paired with its RNA complimentary base. Transcription This process takes mRNA and simply reads its bases in sets of 3 (a codon) and pairs it with it’s complimentary amino acid. Once a series of amino acids are joined together a noticeable protein is built.
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