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UNIT 1 TICKET TO CLASS Chapter 1 The Microbial World and You

1-1 List several ways in which microbes affect our lives. Describe some of the destructive and beneficial actions of microbes. A) The majority of microbes help maintain the balance of living organisms and chemicals in the environment. Their uses vary including forming the basis of the food chain in oceans, lakes, and rivers to soil microbes that help break down wastes and incorporate nitrogen gas from the air into organic compounds, thereby recycling chemical elements between soil, water, life, and air. There are microbes that help with photosynthesis, which is critical to the food/oxygen process on Earth. Both humans and animals depend upon certain microbes in our intestines to produce certain vitamins (vitamin K and some B) and aid in digestion. Using microbes in the production of acetone for making cordite was important in WWI. Certain microbes have been manipulated to help create insulin, indigo dyes, and even some types of cloth. The development of vaccines and antibiotics are through using microbes to help fight infections. A minority of microbes are disease producing which the aged and infirm are more susceptible to being harmed by, although there have been a number of epidemics throughout history which of course are caused by microbes.

1-2 Recognize the system of scientific nomenclature that uses two names: a genus and a specific epithet. Distinguish a genus from a specific epithet. A) Genus is capitalized and quite often describes the appearance of the cell, honors the researcher, or describes where it was found; ex Salmonella enterica Salmonella is the genus. enterica is the specific epithet, which is not capitalized and generally describes the where it is found (skin, intestines etc.), what it forms, or what its color is, there are times the specific epithet will honor the researcher as well.

1-3 Differentiate the major characteristics of each group of microorganisms. Which groups of microbes are prokaryotes? Which are eukaryotes? A) Prokaryotes mean pre-nucleus includes bacteria which generally appear in one of many shapes bacillus (rod-like), coccus (spherical/ovoid), spiral (corkscrewed or curved, star-shaped, and square they can form clusters, chains, or formations which are enclosed in cell walls that are composed largely of peptidoglycan (carbohydrate and protein complex); and Archaea which do have cell walls that lack peptidoglycan and are found in extreme environments (methanogens produce methane, extreme halophiles like extremely salty environs, and extreme thermophiles love hot watery places). Eukaryotes have distinct nucleuses that contain the cells genetic material and a nuclear membrane. Eukaryotes consist of fungi (both unicellular and multicellular, asexual and sexual reproduction), protozoa (unicellular) asexual and sexual reproduction, that move by flagella or cilia; live as either free entities or parasites, Algae (asexual and sexual reproduction, photosynthesis is common, wide variety of shapes and sizes and abundant).

1-4 List the three domains. What are the three domains? Bacteria, Archaea, Eukarya

1-5 Explain the importance of observations made by Hooke and van Leeuwenhoek. 1665 Hooke was able to see individual large cells with his improved compound microscope. Van Leeuwenhoek was probably the first to see live microorganisms (bacteria and protozoa) What is the cell theory? Cell theory All living things are composed of cells. 1-6 Compare spontaneous generation and biogenesis. What evidence supported spontaneous generation? During studies John Needham boiled solutions that were found to be teeming with microorganisms. Later Lavoisier was able to showed that without oxygen life could not exist which seemed to support the spontaneous generation argument How was spontaneous generation disproved? Louis Pasteur was able to demonstrate that microbes are present in nonliving matter by putting beef broth in a long necked flask (microbes were present) he then heated the neck and

bent the flask in a s shape followed by heating the broth for several minutes thereby killing the microbes. After long periods of time the microbes did not appear even with the flask being open to receive the vital force

1-7 Identify the contributions to microbiology made by Needham, Spallanzani, Virchow, and Pasteur. Needham showed that even after heating nutrients and killing microbes the cooled solutions were soon full of microbes again, Spallanzani suggested that microbes were found in the air and had entered the solutions after they were boiled. When he then experimented by boiling the nutrients and sealing them in jars and there was no growth. Needham then stated that there was no vital force able to get in which was necessary for life. Virchow challenged spontaneous generation with the concept of biogenesis (claiming that living cells can only arise from preexisting living cells. Pasteur resolved the argument by proving that microbes are in the air and can contaminate sterile solutions but the air doesnt create microorganisms 1-8 Explain how Pasteurs work influenced Lister and Koch. Summarize in your own words the germ theory of disease. Pasteurs work with microbes/yeasts causing fermentation led to pasteurization to reduce spoilage and kill harmful organisms. At the time the prevailing belief was that air changed sugars in food and beverages but Pasteur was able to prove that bacteria / yeasts was the cause. Other scientists used these findings to expand and find a tie between microbes causing diseases in plants, and animals. Lister took these theories and applied them to medical procedures using a phenol solution (which kills bacteria) to treat wounds, which reduced infection. Koch was the first to prove that actually cause disease by discovering rod shaped bacteria in the blood of cows stricken by a disease. He infected healthy animals with the cultures he created from the bacteria in the sick animals blood and was able to see the same bacteria in the once healthy animals. Koch established Kochs postulates (sequence of experimental steps for directly relating a specific microbe with a specific disease. Germ Theory of Disease disease in plants, animals, and humans are caused by microorganisms, which could be passed from person to person or carried on clothes and not spirits or bad karma. 1-9 Identify the importance of Kochs postulates. Directly relates a specific microbe to a specific disease. What is the importance of Kochs postulates? Kochs postulates have helped to prove that specifics microorganisms cause many diseases.

1-10 Identify the importance of Jenners work. Jenner was the first in Western culture to experiment with using a living viral agent to produce immunity. What is the significance of Jenners discovery? Jenners discovery led to Pasteurs discovery of why vaccinations work.

1-11 Identify the contributions to microbiology made by Ehrlich and Fleming. Ehrlich found salvarsan (arsenic derivative) in 1910, which was effective in treating syphilis. Leading the way for other scientists to find more medicines over the next 20 years. Fleming discovered penicillin, the first antibiotic by accident which has since led the way to discovering many other antibiotics. What was Ehrlichs magic bullet? Ehrlichs magic bullet is something that could hunt down a pathogen and destroy it without harming the host 1-12 Define bacteriology, mycology, parasitology, immunology, and virology. Bacteriology is the study of bacteria. Mycology is the study of fungi. Parasitology is the study of parasites and protozoa. Immunology is the study of immunity. Virology is the study of viruses. 1-13 Explain the importance of microbial genetics and molecular biology. Microbial genetics and molecular biology have helped us understand how genes determine specific traits since bacteria are less complex than plants or animals and the life cycles of many bacteria last less than an hour allowing the cultivation of large numbers in a small amount of time. Differentiate microbial genetics from molecular biology. Microbial genetics studies the way microorganisms inherit traits. Molecular biology specifically studies how genetic information is carried in molecules of DNA and how the DNA directs the synthesis of proteins.

1-14 List at least four beneficial activities of microorganisms. Produce methane and ethanol for use as alternative fuels; naturally convert atmospheric nitrogen to a form available to plants and animals; used to naturally control some pests; bioremediation- using bacteria to clean up toxins and waste; biotechnology using microorganisms to produce common foods and chemicals

1-15 Name two examples of biotechnology that use recombinant DNA technology and two examples that do not. Do: Gene therapy inserting a missing gene or replacing a defective one in human cells also genetically altering bacteria to control insects or protect fruit from frost. Dont: using indigenous bacteria to make detergents to clean spots or unclog pipes 1-16 Define normal microbiota and resistance. Normal microbiota: a variety of flora/microorganisms that we carry naturally on the skin or in our bodies; Resistance: the ability to ward off diseases. Differentiate biotechnology from recombinant DNA technology. Biotechnology: uses microorganisms to produce some common foods and chemicals for practical uses. Recombinant DNA technology: microorganisms are genetically modified by inserting recombinant DNA into bacteria or other microbes to produce large amounts of desired proteins. Differentiate normal microbiota and infectious disease. We carry normal microbiota naturally and they do not harm us and in some cases can help us by producing certain vitamins. Infectious disease is when a pathogen invades a susceptible host and causes illness. 1-17 Define biofilm. Biofilm: A complex aggregation of microbes; microorganisms attaching themselves to each other and /or some other usually solid surface. Why are biofilms important? Biofilms can protect us by forming a barrier or also can be an important food in lakes for fish and other animals.

1-18 Define emerging infectious disease. What factors contribute to the emergence of an infectious disease? New or changing diseases that are increasing or have the potential to increase in incidence in the near future.

CHAPTER 2 Chemical Principles 2-1 Describe the structure of an atom and its relation to the physical properties of elements. Protons and neutrons are in the nucleus, electrons move around the nucleus. A proton, electron, neutron Proton are positively charged, Electrons are negatively charged, and neutrons are uncharged particles. The atomic weight & number? Atomic number equals the number of protons the atom contains; the atomic weight is the total of protons and neutrons in an atom 2-2 Define ionic bond, covalent bond, hydrogen bond. Ionic bond: the attraction between ions of opposite charge. Covalent bond: forms when two atoms share one or more pairs of electrons. Hydrogen bond: forms when a hydrogen atom is covalently bonded to an Oxygen or Nitrogen atom that is attracted to another N or O atom in another molecule. 2-3 Diagram three basic types of chemical reactions. Synthesis reaction: A+B -combinesAB (new molecule) Decomposition reaction: AB-breaks down A+B Exchange reaction: AB + CD- recombine to formAD+BC

2-4 List several properties of water that are important to living systems. Growth, repair, maintenance, and reproduction, nutrients dissolve in water, which makes it easier for them to pass through cell membranes, water makes up between 5-95% of every cell. Why is the polarity of a water molecule important? Hi heat capacity, universal solvent

2-5 Define acid, base, salt, and pH. Acid: can be defined as a substance that dissociates into one or more hydrogen ions and one or more negative ions can also be defined as a proton donor. Base: dissociates into one or more positive ions plus one or more negatively charges hydroxide ions that can accept or combine with protons. Salt: a substance that dissociates in water into cations (positive ions) and anions (negative ions) neither of which is H+ or OH-. pH: a logarithm to track hydrogen concentration or a measure of the relative acidity or alkalinity of a solution.

2-6 Distinguish organic and inorganic compounds. Organic compound contains both carbon and hydrogen atoms able to combine in a numbers of ways and capable of complex biological functions. Inorganic compound: relatively simple component, whose molecules only have a few atoms, cannot be used by cells to perform complex biological functions. 2-7 Identify the building blocks of carbohydrates. Give an example of a monosaccharide, a disaccharide, and a polysaccharide. The building blocks of carbohydrates are carbon, oxygen, and hydrogen. Monosaccharide: glucose Disaccharide: milk Polysaccharide: Starch

2-8 Differentiate simple lipids, complex lipids, and steroids. How do simple lipids differ from complex lipids? Simple lipids: contains glycerol, and fatty acids. Has 3 carbon atoms attached to 3 hydroxyl atoms. Complex lipids: Contains phosphorous, nitrogen, and sulfur in addition to carbon and hydroxyl. Called phospholipids Steroids : the most important lipid

2-9 Identify the building blocks and structure of proteins. What two functional groups are in all amino acids? Amino acids are the building blocks of proteins. The generalized amino acid contains at least one carboxyl group in the center and one amino group attached to the same carbon atom and across is a carboxyl group. The two functional groups in all amino acids are amino and carboxyl. 2-10 Identify the building blocks of nucleic acids. Nucleotides are the building blocks of nucleic acids. How do DNA and RNA differ? RNA is usually single stranded instead of a double helix. DNA has deoxyribose instead of ribose RNA has uracil not thymine.

2-13 Describe the role of ATP in cellular activities. ATP is the principal energy-carrying molecule off all cells, stores the chemical energy released by some chemical reactions, provides the energy for the reactions that require energy. Which can provide more energy for a cell and why: ATP or ADP? ATP, it has an extra phosphate bond that has more energy.

Chapter 4 Functional Anatomy of Prokaryotic and Eukaryotic Cells 4-1 Compare and contrast the overall cell structure of prokaryotes and eukaryotes The DNA of the prokaryote is not within a membrane, DNA not associated with histones, lack membrane enclosed organelles; cell walls almost always contain complex polysaccharide peptidoglycan, and usually divide by binary fission. The eukaryote divides by mitosis, has membrane enclosed organelles and their DNA is found in the cell nucleus, cell walls are chemically simple, DNA associated with histones and non-histones. . What is the main feature that distinguishes prokaryotes from eukaryotes? The cell wall structure and lack of organelles.

4-2 Identify the three basic shapes of bacteria. Cocci berries, bacillus rod shaped, spiral .

4-3 Describe the structure and function of the glycocalyx. Glycocalyx means a sugar coat, a gelatinous polysaccharide and/or polypeptide covering (capsule, slime layer, or extracellular polysaccharide. Why are bacterial capsules medically important? Capsules often protect pathogenic bacteria from phagocytosis by the cells host.

4-4 Differentiate flagella, axial filaments, fimbriae, and pili. Flagella: long filamentous appendages that propel bacteria. Axial filaments: bundles of fibril that arise at the end of a cell beneath the outer sheath and spiral around the spirochete. Fimbriae: occur at the poles of the bacterial cell or evenly distributed over the entire surface; they are involved in forming biofilms and other aggregations on the surface of liquids, rocks, and glass. Pili: usually longer than fimbriae and one or tow to the cell, they are involved in motility and DNA transfer. How do bacteria move? Flagella, axial filaments, fimbriae, and pili propel the bacteria via movements like swimming gliding and twitching.

4-5 Compare and contrast the cell walls of gram-positive bacteria, gram-negative bacteria, acid-fast bacteria, archaea, and mycoplasmas. Gram-positive bacteria: the cell wall consists of many layers of peptidoglycan, forming a thick rigid layer, contains teichoic acids, 2-ring basal body. Gram-negative bacteria: cell walls contain only a thin layer of peptidoglycan, and no teichoic acids peptidoglycan is bonded to lipoproteins, 4-ring basal body. Archaea: wall-less or walls of pseudomurein. Acid-fast bacteria: prevents the uptake of dyes including gram stain due to the high concentrations of hydrophobic waxy lipids. Mycoplasmas: lack cell walls; sterols in plasma membrane. Why are drugs that target cell wall synthesis useful? Stop certain pathogens with without harming other cells, allows phagocytosis by the cells host. 4-6 Compare and contrast archaea and mycoplasmas. Archaea: wall-less or walls of pseudomurein do not contain peptidoglycan. Mycoplasmas: lack cell walls; sterols in plasma membrane

4-7 Why are mycoplasmas resistant to antibiotics that interfere with cell wall synthesis? Mycoplasmas do not have cell walls

4-8 Describe the structure, chemistry, and functions of the prokaryotic plasma membrane. Lipid bilayer, selective permeability allowing some molecules to pass; peripheral proteins, integral proteins, trans-membrane proteins. Which agents can cause injury to the bacterial plasma membrane? Certain alcohols, quarternary ammonium compounds (disinfectants) 4-9 Define simple diffusion, facilitated diffusion, osmosis, active transport, and group translocation. Simple Diffusion: the net overall movement of molecules or ions from and area of high concentration to low concentration continuing until the molecules or ions are evenly distributed. Facilitated diffusion: integral membrane proteins function as channels or carriers that facilitate of ions or large molecules across the plasma membrane. Osmosis: The movement of solvent molecules across a selectively permeable membrane from an area with high concentration of solvent molecules to and are of low concentration of solvent molecules. Active transport: cells use energy in the form of ATP to transport substances across the plasma membrane. Group translocation: a special form of active transport that occurs exclusively in prokaryotes a substance in chemically altered during transport across the membrane. Once the substance s altered and inside the cell the plasma membrane remains impermeable to it so it stays inside the cell. How are simple diffusion and facilitated diffusion similar? They are similar in that the cell doesnt expend energy; the movement of molecules is from high to low concentration. How are they different? Simple transfusion moves solute directly through the bilayer whereas facilitated transport uses ATP to transport the proteins.

4-10 Identify the functions of the nucleoid and ribosomes. Nucleoid functions: contains the genetic material (DNA), Ribosomes: the site of protein synthesis Where is the DNA located in a prokaryotic cell? In the nucleoid.

4-11 Identify the functions of four inclusions. Metachromatic granules: contain a reserve of phosphate that can be used in the synthesis of ATP (diagnostic significance) Polysaccharide granules: store glycogen and starch very important source of substrate in carbohydrate metabolism during starvation conditions in these bacteria. Sulfur globules: derive energy by oxidizing sulfur serves as energy reserve. Carboxysomes: contain the enzyme ribulose 1,5-diphosphate carboxylase. What is the general function of inclusions? Cells accumulate certain nutrients when they are plentiful and use the when the environment is deficient.

4-12 Describe the functions of endospores, sporulation, and endospore germination. Endospores are highly durable dehydrated cells with thick walls and additional layers. Sporulation: the process of endospore formation within a vegetative cell. Endospore germination: when an endospore returns to its vegetative state, triggered by physical or chemical damage to the endospores coat. Under what conditions do endospores form? Endospores are resting cells for when essential nutrients are depleted.

4-13 Differentiate prokaryotic and eukaryotic flagella. Eukaryotic flagella: Complex consist of multiple microtubes; Prokaryotic flagella: consist of two protein building blocks Identify at least one significant difference between eukaryotic and prokaryotic flagella Eukaryotic flagella: move in a wavelike manner; prokaryotic flagella rotate 4-14 Compare and contrast prokaryotic and eukaryotic cell walls and glycocalyxes. Eukaryotic cell walls: when present, chemically simple may be chitin or cellulose; Eukaryotic glycocalyxes: present in some cells that lack a cell wall. Prokaryotic cell walls: usually present, chemically complex (typical bacterial cell wall includes peptidoglycan; Prokaryotic glycocayxes: present as a capsule or slime layer. 4-15 Compare and contrast prokaryotic and eukaryotic plasma membranes. Prokaryotic plasma membrane: no carbs and generally lacks sterols; Eukaryotic plasma membrane: sterols and carbs that serve as receptors

4-16 Compare and contrast prokaryotic and eukaryotic cytoplasms. Prokaryotic cytoplasm: no cytoskeleton or cytoplasmic streaming. Eukaryotic cytoplasm: cytoskeleton; cytoplasmic streaming 4-17 Compare the structure and function of eukaryotic and prokaryotic ribosomes. The antibiotic erythromycin binds with the 50S portion of a ribosome. What effect does this have on a prokaryotic cell? On a eukaryotic cell? Eukaryotic: smaller size 70s; prokaryotic larger size 80s smaller size 70s in organelles 4-18 Define organelle. Structures with specific shapes and specialized functions, characteristic of eukaryotic cells 4-19 Describe the functions of the nucleus, endoplasmic reticulum, Golgi complex, lysosomes, vacuoles, mitochondria, chloroplasts, peroxisomes, and centrosomes. How do rough and smooth ER compare structurally and functionally? Which three organelles are not associated with the Golgi complex? What does this suggest about their origin? Nucleus function: Contains chromosomes; Endoplasmic reticulum: Transport mechanism; Golgi complex: membrane formation and secretion; Lysosomes: Digestive enzymes; Vacuoles: Brings food into cells and provides support; Mitochondria: Cellular respiration; Chloroplast: Photosynthesis; Peroxisomes: Oxidation of fatty acids; destroys H2O2; Centrosomes: Consists of protein fibers and centrioles. Rough ER: Synthesis of protein, rough outer wall due to ribosomes attached Smooth ER: Storage organelle, smooth outer wall; 3 organelles not associated w/the Golgi Complex: Chloroplasts, mitochondria, eukaryotic flagella suggesting that they were not present in ancestral eukaryotic cells

4-20 Discuss evidence that supports the endosymbiotic theory of eukaryotic evolution. Both mitochondria & chloroplasts resemble bacteria, have circular DNA like prokaryotes can reproduce independently of host its protein synthesis mechanism is similar to bacteria

CHAPTER 5 Microbial Metabolism 5-1 Define metabolism, and describe the fundamental differences between anabolism and catabolism. Metabolism refers to the sum of all chemical reactions within a living organism. Catabolism is the breakdown of complex organic compounds into simpler ones. Anabolism is the building of complex organic molecules from simpler ones. What is the purpose of metabolic pathways? A metabolic pathway is a sequence of enzymatically catalyzed chemical reactions in a cell. Metabolic pathways are determined by enzymes, which are in turn determined by the cells genetic makeup. 5-2 Identify the role of ATP as an intermediate between catabolism and anabolism. Distinguish catabolism from anabolism. Catabolism is exergonic meaning that they make more energy then they use. Anabolism on the other hand is endergonic meaning that they use more energy than they make. ATP stores energy derived from catabolic reactions and releases it later to drive anabolic reactions and perform other cellular work.

5-3 Describe the mechanism of enzymatic action. Why is enzyme specificity important? Enzymes are the biological catalysts. As catalysts, each enzyme is specific. Each acts on a specific substrate and each catalyzes only one reaction. For example, sucrose is the substrate of the enzyme sucrose, which catalyzes the hydrolysis of sucrose to glucose and fructose. Enzyme specificity is important because their structures. They have unique configurations, which enables it to find the correct substrate from all of the diverse molecules that are in the cell. Mechanism of enzymatic reaction: Enzymes lower the activation energy of chemical reactions. 1- The surface of he substrate contracts a specific region of the surface of the enzyme molecule, this is called the active site. 2- A temporary intermediate compound forms, called and enzyme-substrate complex. 3- The substrate molecule is transformed by the rearrangement of existing atoms, the breakdown of the substrate molecule, or in combination with another substrate molecule. 4- The transformed substrate molecules- the products of the reaction- are released from the enzyme molecule because they no longer fit in the active site of the enzyme. 5- The unchanged enzyme is now free to react with other substrate molecules. 5-4 List the factors that influence enzymatic activity. - Temperature: most chemical reactions increase as the temperature is increased. Molecules move slower at lower temperatures. If the temperature is too high, the rate of reaction decreases drastically. - pH- most enzymes have an optimal pH at which their activity is characterized as maximal. When the H+ concentration is changed drastically, the structure of the protein is changed. Extreme pH can also denature the protein. - Substrate concentration There is a maximum rate at which a certain amount of enzyme can catalyze a specific reaction. Only when the concentration of substrate is high can the maximum rate be achieved. When the high concentration of substrate occurs, the enzyme is said to be in saturation. This means that the active site is always occupied by a substrate or a product molecule. - Inhibitors- A way to control the growth of a bacteria is to control their enzymes. You can introduce a poison like cyanide, arsenic or mercury to stop the enzymatic reactions which in turn kills off the cell because they cant function properly without the presence of enzymes. 5-7 Distinguish competitive and noncompetitive inhibition. Competitive inhibition- these fill the active site of an enzyme and compete with the normal substrate for the active site. They are able to do this because they have similar size and shape of the normal substrate. But, unlike the substrate the competitive inhibitor doesnt have any functions when they bind to the active site and they dont form a product. Some competitive inhibitors bind once and never leave the active site and others are reversible. They adhere, and then leave at times. This slows down enzymatic activity. Noncompetitive inhibitors- these inhibitors do not compete with normal substrates for the enzymatic active sites. Instead they bind to another part of the enzyme. This is called an allosteric inhibition because they bind to another

site other than the active site. When an inhibitor binds to another part of the enzyme, the enzyme changes shape, which makes the enzyme nonfunctional. This in turn slows down enzymatic reactions. This can either be reversible or irreversible. What happens to an enzyme below its optimal temperature? Enzymes below their optimal temperature move a lot slower and in turn they do not have enough energy to complete an enzymatic reaction. Above its optimal temperature? The rate of most chemical reactions increases as the temperature rises. The rate of reaction declines beyond the optimal temperature because of the enzymes denaturization. This is the loss of the characteristic threedimensional structure. Denaturization of a protein involves the breakage of hydrogen bonds and other noncovalent bonds. Why is feedback inhibition noncompetitive inhibition? In many anabolic pathways, the final product can allosterically inhibit the activity of one of the enzymes earlier in the pathway. This phenomenon is called feedback inhibition. This is a sort of biochemical control. The control mechanism, feedback inhibition, stops the cell from making more of the substrate than it needs and there by wasting chemical resources. 5-8 Explain the term oxidation-reduction. Oxidation is the removal of electrons and a reduction is when there is a gain of electrons. Obviously you can see that these two will always be paired together. The pairing of theses reactions are called oxidation-reduction reactions. 5-9 List and provide examples of three types of phosphorylation reactions that generate ATP. Outline the three ways that ATP is generated. Substrate level phosphorylation- ATP is usually generated when a high-level phosphate group is directly transferred from a phosphorylated compound to ADP. Generally the phosphate group has required energy during an earlier reaction in which the substrate itself was oxidized. Oxidized phosphorylation- electrons are transferred from organic compounds to one group of electron carriers. Then, the electrons are passed through a series of different electron carriers to molecules of oxygen or other oxidized inorganic and organic molecules. This process occurs in the plasma membrane of prokaryotes and in the inner mitochondrial membrane of eukaryotes. The sequence of electron carriers used in oxidative phosphorylation is called an electron transport chain system. Photophosphorylation- this occurs in the photosynthetic cells, which contain light-trapping pigments such as chlorophylls. In photosynthesis, organic molecules, especially sugars, are synthesized with the energy of light from the energy-poor building blocks carbon dioxide and water. Photophosphorylation starts this process by converting light energy to the chemical energy of ATP and NADPH, which, in turn, are used to synthesize organic molecules. Similar to oxidative phosphorylation, an electron transport chain is involved. 5-10 Explain the overall function of metabolic pathways. Organisms release and store energy from organic molecules by a series of controlled reaction rather than in a single burst. If that energy were released all at once, as a large amount of heat, It could not be readily used to drive chemical reactions and would, in fact, damage the cell. To extract energy from organic coumpounds and store it in chemical form, organisms pass electrons from one compound to another through a series of oxidation-reduction reactions. 5-11 Describe the chemical reactions of glycolysis. Glycolysis is the oxidation of glucose into pyruvic acid and it is usually the first stage of carbohydrate catabolism. Most organisms use this pathway. The term glycolysis means the splitting of sugar and this is exactly what it does. The enzymes of glycolysis catalyze the splitting of 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 NAD, and there is a net production of 2 ATP molecules by substrate-level phosphorylation. Glycolysis can occur whether oxygen is present or not.

5-12 Identify the functions of the pentose phosphate and Entner-Doudoroff pathways. The pentose phosphate pathway operates stimultaneously with glycolysis and provides a means for the breakdown of five-carbon sugars, pentoses,

as well as glucose. A key feature of this pathway is that it produces important intermediate pentoses ised in the synthesis of nucleic acids, glucose from carbon dioxide in photosynthesis, and certain amino acids. The EntnerDoudoroff pathway produces two molecules of NADPH and one molecule of ATP for use in cellular biosynthetic reaction. The bacteria that have the enzymes for the Entner- Doudoroff pathway can metabolize glucose without either glycolysis or the pentose phosphate pathway. The pathway is normally found in gram negative bacteria and generally not found in gram positive bacteria.What is the value of the pentose phosphate and Entner-Doudoroff pathways if they produce only one ATP molecule? Because they help in the formation of nucleotides. The pentose phosphate pathway helps E.coli and Bacillus. The Entner-Doudoroff pathway can metabolize glucose. 5-13 Explain the products of the Krebs cycle. The krebs cycle is the oxidation of acetyl CoA to carbon dioxide, with the production of some ATP, energycontaining NADH, and another reduced electron carrier, FADH2. What are the principal products of the Krebs cycle? CO2, NAD+, NADH, acetyl CoA, FADH2 and ATP 5-14 Describe the chemiosmotic model for ATP generation. Chemiosmotic model for ATP generation is the movement of ions across a selectively permeable membrane down their electrochemical gradient. Remember that substances diffuse passively across membranes from areas of high concentration to areas of low concentration. In chemiosmosis, the energy released when a substance moves along a gradient is used to synthesize ATP. The substance is refered to as protons. In respiration, chemiosmosis is responsible for most of the ATP that is generated. How do carrier molecules function in the electron transport chain? There are three classes of carrier molecules in the electron transport chains. There are flavoproteins which contain flavin, a coenzyme derived from riboflavin, and are capable of performing alternating oxidations and reductions. The second class of carrier molecules are cytochromes, proteins with an iron-containing group, heme, capable of existing alternately as a reduced form and an oxidized form. The third group is known as uniquinones or coenzyme Q. These are small nonprotein carriers. 5-15 Compare and contrast aerobic and anaerobic respiration. In aerobic respiration the final electron acceptor is O2. In anaerobic respiration the final electron acceptor is an inorganic molecule other than O2 or rarely, an organic molecule. Compare the energy yield (ATP) of aerobic and anaerobic respiration The total ATP yield is less than in aerobic respiration because only part of the Krebs cycle operates under anaerobic condition. Aerobic requires O2 therefor requiring more ATP and more energy then anaerobic respiration, which does not require O2.

CHPTER 6 6-1 Classify microbes into five groups on the basis of preferred temperature range. Why are hyperthermophiles that grow at temperatures above 100C seemingly limited to oceanic depths? Psychrophiles -10C-20C , Pschrotrophs-0C-30C, Mesophiles 10C-50C, Thermophiles 40C-75C, Hyperthermophiles 65C-110C. 6-2 Identify how and why the pH of culture media is controlled. At the deep-ocean floor, photosynthesis is not possible, however, the primary producers at the ocean floor are chemotrophic bacteria, where an environment is created that supports higher life forms. 6-3 Explain the importance of osmotic pressure to microbial growth. Why might primitive civilizations have used Mirccrorganisms obtain almost all of their nutrients in solution from the surrounding water and they require water for growth. Primitive civiliztions may have used food preservation techniques that rely on osmotic pressure because for example adding salts to fish, increased the osmotic pressure, drawing water out of the cells, hence not allowing microorganisms to grow.

6-4 Name a use for each of the four elements (carbon, nitrogen, sulfur, and phosphorus) needed in large amounts for microbial growth. If bacterial cells were given a sulfur source containing radioactive sulfur (35S) in their culture media, in what molecules would the S be found in the cells? Half of the bacterial weight is carbon, nitrogen is used in protein synthesis, the synthesis of DNA and RNA as well as ATP also needs nitrogen, as well as phosphorus. Nitrogen makes up about 14% of the dry weight of bacterial cell, and sulfur and phosphorus together constitute about another 4%. 6-5 Explain how microbes are classified on the basis of oxygen requirements. Obligate aerobes are organisms that need oxygen to survive and facultative anaerobes are organisms that can survive with or without oxygen, but their efficiency in producing energy is strained in the absence of oxygen. 6-6 Describe the formation of biofilms and their potential for causing infection. Biofilms are communities of microorganisms that live together. Their potential for causing infection increases because they are probably 1000 times more resistant to microbicides. 6-7 Distinguish chemically defined and complex media. Chemically defined media is one whose exact chemical composition is known and complex media is usually made up of nutrients such as yeasts, meat, or plants, or digests of proteins from these and other sources. 6-8 Justify the use of each of the following: anaerobic techniques, living host cells, candle jars, selective and differential media, enrichment medium. Anaerobic techniques such as reducing media must be used to deplete the oxygen in the culture medium. Living Host CellsCandle Jars- generates carbon dioxide atmospheres in containers. Selective Media- designed to suppress the growth of unwanted bacteria and encourage the growth of the desired microbes. Differential media- makes it easier to distinguish colonies of the desired organism from other colonies growing on the same plate. Enrichment Media- Provides nutrients and environmental conditions that favor the growth of a particular microbe. 6-10 Define colony. Can you think of any reason why a colony does not grow to an infinite size, or at least fill the confines of the Petri plate? Colony arises from a single spore or vegetative cell or from a group of the same microorganisms attached to one another in clumps or chains. A colony does not grow to an infinite size because its growth is done by selective enrichment. 6-11 Compare the phases of microbial growth, and describe their relation to generation time. Lag Phase- Little or no cell division, can last one hour to several days. Log Phase- Cells begin to divide and enter a period of growth. Cellular reproduction is most active. Stationary Phase- The number of microbial deaths balances the number of new cells and the population stabilizes. Death Phase- The number of deaths eventually exceeds the number of new cells formed.

CHAPTER 7 The Control of Microbial Growth 7-1 Define the following key terms related to microbial control: sterilization, disinfection, antisepsis, degerming, sanitization, biocide, germicide, bacteriostasis, and asepsis. Sterilization- removal of all microbial life. Disinfection- Removing pathogens. Antisepsis- Removing pathogens from living tissues. Degerming- Remving microbe from a limited area. Sanitization- Lowering microbial counts on eating utensils. Biocide- Kills microbes. Germicide- Kills microbes.

Bacteriostasis- Inhibiting, not killing, microbes. Asepsis- Is the absence of significant contamination. 7-2 Describe the patterns of microbial death caused by treatments with microbial control agents. Several factors influence the effectiveness of antimicrobial treatments, including the number of microbes, environmental influences, time of exposure, and microbial characteristic. Microbial death rate is constant and for every minute of treatment, approximately 90% of microbes die. 7-3 Describe the effects of microbial control agents on cellular structures. Some microbial control agents damage cellular proteins by breaking hydrogen bonds and covalent bonds. Other agents interfere with DNA and RNA and protein synthesis. 7-4 Compare the effectiveness of moist heat (boiling, autoclaving, pasteurization) and dry heat. Moist heat kills microbes by denaturing enzymes, where dry heat kills by oxidation. Autoclaing is the most effective method of moist heat sterilization. It takes longer to sterilize in a dry heat, than by moist heat. 7-5 Describe how filtration, low temperatures, high pressure, desiccation, and osmotic pressure suppress microbial growth. Osmotic Pressure causes plasmolysis. Low temperature inhibits microbial growth. High pressure denatures proteins. Desiccation prevents metabolism. Filtration- passage of a liquid or gas through a filter with pores small enough to retain microbes. 7-6 Explain how radiation kills cells. What is the connection between the killing effect of radiation and hydroxyl radical forms of oxygen? The effects of radiation depend on its wavelength, intensity, and duration. Ionizing radiation has a high degree of penetration and exerts its effect primarily by ionizing water and forming highly reactive hydroxyl radicals. 7-7 List the factors related to effective disinfection. Factors related to effective disinfection include concentration of disinfectant, organic matter, pH, and time. 7-8 Identify the methods of action and preferred uses of chemical disinfectants. Chemical agents are used on living tissue (as antispetics) and aon inanimate objects (as disinfectants). 7-9 Differentiate halogens used as antiseptics from halogens used as disinfectants. If you wanted to disinfect a surface contaminated by vomit and a surface contaminated by a sneeze, why would your choice of disinfectant make a difference? Halogens such as iodine and chlorine are extremely effective antimicrobial agenbts. Iodine is an effective antiseptic and chlorine is a widely used disinfectant. 7-10 Identify the appropriate uses for surface-active agents. Soap is used for degerming, Acid-anionic detergents is used for sanitizing, and quaternary ammonium compounds is used for bactericidal, to denature proteins, and to disrupt plasma membrane. 7-11 List the advantages of glutaraldehyde over other chemical disinfectants. It is a chemical relative of formaldehyde, but is less irritating and more effective. It is used to disinfect hospital instruments. It is one of the few chemicals that is considered a sterilizing agent. 7-12 Identify chemical sterilizers. What chemicals are used to sterilize? It is used to substitute for physical sterilization processes and requires a closed chamber similar to a team autoclave. Chemicals such as ethylene oxide,, which kills all microbes and endospores, but requires a lengthy exposure time. Another chemical is chlorine dioxide and is used to fumigate buildings contaminated with endospores of anthrax. 7-15 Explain how the type of microbe affects the control of microbial growth.

Not all microbes react the same way to control methods. For example, many biocides are more effective against gram-positive bacteria, than gram-negative bacteria, because of the gram negatives external lipopolysaccharide layer. The resistance of viruses from biocides largely depends on the presence or absence of an envelope.

CHAPTER 8 Microbial Genetics 8-1 Define genetics, genome, chromosome, gene, genetic code, genotype, phenotype, and genomics. Genetics the science of heredity. Genome the genetic information in a cell. Chromosome structures containing DNA that physically carry hereditary information; the chromosomes contain the genes. Gene segments of DNA (except in some viruses, in which they are made of RNA) that code for functional products. Genetic code the set of rules that determines how a nucleotide sequence is converted into the amino acid sequence of a protein. Genotype is the genetic makeup of an organism, the information that codes for all the particular characteristics of the organism. Phenotype refer to actual, expressed properties, such as the organisms ability to perform a particular chemical reaction. It is the manifestation of genotype. Genomics the sequencing and molecular characterization of genomes.

8-2 Describe how DNA serves as genetic information. The DNA of a cell replicates before cell division so that each offspring cell receives a chromosome identical to the parents. Within each metabolizing cell, the genetic information contained in DNA also flows in another way: it is transcribed into mRNA and them translated into protein. 8-3 Describe the process of DNA replication. In DNA replication, one parental double-stranded DNA molecule is converted to two identical daughter molecules. Because the bases along the two strands of double-helical DNA are complementary, one strand can act as a template for the production of the other strand. 8-4 Describe protein synthesis, including transcription, RNA processing, and translation. What is the role of the promoter, terminator, and mRNA in transcription? In the process of transcription, genetic information in DNA is copied, or transcribed, into a complementary base sequence of RNA. The cell then uses the information encoded in this RNA to synthesize specific proteins through the process of translation. Transcription is the synthesis of a complementary strand of RNA from a DNA template. Protein synthesis is called translation because it involves decoding the language of nucleic acids and converting that information into the language of proteins. The promoter is the site where transcription begins when RNA polymerase binds to the DNA. The terminator is the site on the DNA where RNA synthesis continues until RNA polymerase reaches. During transcription, a strand of mRNA is synthesized using a specific portion of the cells DNA as a template. 8-5 Compare protein synthesis in prokaryotes and eukaryotes. Protein synthesis in prokaryotes is ribosomal RNA forms an integral part of ribosomes, the cellular machinery for protein synthesis. Messenger RNA carries the coded information for making specific proteins from DNA to ribosomes, where proteins are synthesized. Protein synthesis in eukaryotes transcription takes place in the nucleus. The mRNA must be completely synthesized and moved through the nuclear membrane to the cytoplasm before translation can begin. The RNA undergoes processing before it leaves the nucleus. The regions of genes that code from proteins are often interrupted by noncoding DNA. 8-6 Define operon. A set of operator and promoter sites and the structural genes they control. 8-7 Explain pre-transcriptional regulation of gene expression in bacteria. Two genetic control mechanisms known as repression and induction regulate the transcription of mRNA and consequently the synthesis of enzymes from. These mechanisms control the formation and amounts of enzymes in the cell, mot the activities of the enzymes. 8-8 Explain post-transcriptional regulation of gene expression. Some regulatory mechanisms stop protein synthesis after transcription has occurred. Single-stranded RNA molecules of approximately 22 nucleotides, called mircoRNAs, inhibit protein production in eukaryotic cells.

8-9 Classify mutations by type. How can a mutation be beneficial? Base substitution is the most common type involving single base pairs and is when a single base at one point in the DNA sequence is replaced with a different base. If the base substitution results in an amino acid substitution in the synthesized protein, the change in the DNA is known as a missense mutation. A base substitution resulting in a nonsense codon is a nonsense mutation. Besides base-pair mutations, there are also changes in DNA called frameshift mutation, in which one or a few nucleotide pairs are deleted or inserted in the DNA. Spontaneous mutations occur in the absence of any mutation-causing agents because of a occasional mistakes made during DNA replication. A mutation can be beneficial if the altered enzyme encoded by the mutant gene has a new or enhanced activity that benefits the cell. 8-10 Describe two ways mutations can be repaired. How can mutations be repaired? Photolyases, also known as light-repair enzymes, use visible light energy to separate the dimer back to the original two thymines. Nucleotide excision repair is not restricted to UV-induced damage; it can repair mutations from other causes as well. Enzymes cu tout the incorrect base and fill in the gap with newly synthesized DNA that is complementary to the correct strand. 8-11 Differentiate horizontal and vertical 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. 8-12 Compare the mechanisms of genetic recombination in bacteria. In nature, some bacteria, perhaps after death and cell lysis, release their DNA into the environment. Other bacteria can the encounter the DNA and, depending on the particular species and growth conditions, take up fragments of DNA and integrate them into their own chromosomes by recombination. A protein called RecA binds to the cells DNA and then to donor DNA causing the exchange of strands. A recipient cell with this new combination of genes is a kind of hybrid, or recombinant cell will be identical to it. Transformation occurs naturally among very few genera of bacteria including Bacillus, Haemophilus, Neisseria, Acinetobacter, and certain strains of the genera Streptococcus and Staphylococcus. 8-13 Describe the functions of plasmids. The plasmids are self-replicating, gene-containing circular pieces of DNA about 1-5% the size of bacterial chromosomes. The F factor is a conjugative plasmid that carries genes for sex pili and for the transfer of the plasmid to another cell. Plasmids can be crucial to the survival and growth of the cell. Dissimilation plasmids code for enzymes that trigger the catabolism of certain unusual sugars and hydrocarbons. Other plasmids code for proteins that enhance the pathogenicity of a bacterium.

CHAPTER 9 Biotechnology and DNA Technology

9-1 Compare and contrast biotechnology, genetic modification, and recombinant DNA technology. Biotechnology is the use of microorganisms, cells, or cell components to make a product. Now, microorganisms as well as entire plants are being used as factories to produce chemicals that the organisms dont naturally make. The latter is made possible by inserting genes into cells by recombinant DNA (rDNA) technology, which is sometimes called genetic engineering. 9-2 Identify the roles of a clone and a vector in making recombinant DNA. The gene of interest is inserted into the vector DNA in vitro. The DNA molecule chosen as a vector must be a self-respecting type, such as a plasmid or a viral genome. This recombinant vector DNA is taken up by a cell such as a bacterium, where it can multiply. The cell containing the recombinant vector is then grown in culture to form a clone of many genetically identical cells, each of which carries copies of the vector. This cell clone therefore contains many copies of the gene of interest. This is why DNA vectors are often called gene-cloning vectors, or simply cloning vectors. The final step varies according to whether the gene itself or the product of the gene is of interest. From the cell clone, the researcher may isolate large quantities of the gene of interest, which may then be used for a variety of purposes. The gene may even be inserted into another vector for introduction into another kind of cell. Alternatively, if the gene of interest is expressed in the cell clone, its protein product can be harvested and used for a variety of purposes. 9-3 Compare selection and mutation. How are selection and mutation used in biotechnology? Natural selection is in nature, organisms with characteristics that enhance survival are more likely to survive and reproduce than are variants that lack the desirable traits. Artificial selection is used to select desirable breeds of animals or strains of plants to

cultivate. Mutation is responsible for much of the diversity of life. A bacterium with a mutation that confers resistance to an antibiotic will survive and reproduce in the presence of that antibiotic. Both are used to create antibiotics on some level. 9-4 List the four properties of vectors. What criteria must a vector meet? The four properties of vectors are: selfreplication, need to be of a size that allows them to be manipulated outside the cell during recombinant DNA procedures, preservation, and common selectable marker genes. The vector must be capable of replicating, the size has to be small enough to manipulate, must be protected to prevent destruction by the recipient of the vector, and the gene markers can be helpful in selecting more easily. 9-5 Describe the use of plasmid and viral vectors. Plasmids are one of the primary vectors in use, particularly variants of R factor plasmids. Some plasmids are capable of existing in several different species called shuttle vectors and can be used to move cloned DNA sequences. Viral vectors can usually accept much larger pieces of foreign DNA than plasmids can. 9-6 Outline the steps in PCR, and provide an example of its use. Each strand of the target DNA will serve as a template for DNA synthesis. To this DNA is added a supply of the four nucleotides (for assembly into new DNA) and the enzyme for catalyzing the synthesis, DNA polymerase. Short pieces of nucleic acid called primers are also added to help start the reaction. The primers are complementary to the ends of the target DNA and will hybridize to the fragments to be amplified. Then, the polymerase synthesizes new complementary strands. After each cycle of synthesis, the DNA is heated to convert all the new DNA into single strands. Each newly synthesized DNA strand serves in turn as a template for more new DNA. 9-7 Describe five ways of getting DNA into a cell. 1. In nature, plasmids usually transfer between closely related microbes by cell-to-cell contact such as in conjugation. To modify a cell, a plasmid must be inserted into a cell by transformation, a procedure during which cells can take up DNA from the surrounding environment. 2. Mixing competent cells with the clones DNA and given a mild heat shock after the cells are either treated with a simple chemical or by being soaked in a solution of calcium chloride for a brief period. 3. A process called electroporation uses an electrical current to form microscopic pores in the membranes of cells; the DNA then enters the cells through the pores. 4. The process of protoplast fusion also takes advantage of the properties of protoplasts. Protoplasts in solution fuse at a low but significant rate; the addition of polyethylene glycol increases the frequency of fusion. 5. DNA can be introduced directly into an animal cell by microinjection as well. 9-8 Describe how a genomic library is made. Researchers interested in genes from a particular organism start by extracting the organisms DNA, which can be obtained from cells of any organism, whether plant, animal, or microbe, by lysing the cells and participating the DNA. This process results in a DNA mass that includes the organisms entire genome. After the DNA is digested by restriction enzymes, the restriction fragments are then spliced into plasmid or phage vectors, and the recombinant vectors are introduced into bacterial cells. The goal is to make a collection of clones large enough to ensure that at least one clone exists for every gene in the organism. This collection of clones containing different DNA fragments is called a genome library; each book is a bacterial or phage strain that contains a fragment of the genome. 9-9 List one advantage of modifying each of the following: E. coli, Saccharomyces cerevisiae, mammalian cells, plant cells. The synthesis of great amounts of the cloned gene product can then be directed by the addition of an inducer. Such a method has been used to produce gamma interferon in E. coli. Saccharomyces cerevisiae is also used as a vehicle for expressing rDNA. Mammalian cells are can be genetically modified to produce various products such as making protein products for medical use because the cells secrete their products and there is a low risk of toxins or allergens. Plant cells can also be grown in culture, altered by recombinant DNA techniques, and then used to generate genetically modified plants. 9-10 List at least five applications of DNA technology. Subunit vaccines, gene therapy, gene silencing, small interfering RNAs (siRNAs), RNA-induced silencing complex (RISC), and RNA interference (RNAi).