BIOL 261: Study Guides for Exam 1 (Chs. 1-5)
BIOL 261: Study Guides for Exam 1 (Chs. 1-5) BIOL 261
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This 46 page Study Guide was uploaded by Alexis Ward on Friday September 30, 2016. The Study Guide belongs to BIOL 261 at University of Louisiana at Lafayette taught by Professor P. Antley in Fall 2016. Since its upload, it has received 7 views. For similar materials see General Microbiology in Microbiology at University of Louisiana at Lafayette.
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Study Guide for Chapter 1 – Biol 261 Vocabulary – have a working knowledge of the following words. You can use your book to define them or the flash card in the study area of mastering microbiology. • Cell wall- A rigid layer present outside the cytoplasmic membrane that confers structural strength on the cell and protection from osmotic lysis. • Chemolithotrophy- An organism that obtains its energy from the oxidation of inorganic compounds (the gain of energy for cell biosynthesis and maintenance from the oxidation of inorganic compounds (= electron donors), in the absence of light) • Culture- A particular strain or kind of organism growing in a laboratory medium. • Cytoplasmic membrane- A semipermeable barrier that separates the cell interior (cytoplasm) from the environment. • Differentiation- The modification of a cell in terms of structure and/or function occurring during the course of development. • Domain- (1) The highest level of biological classification. The three domains of organisms are the Bacteria, the Archaea, and the Eukarya. (2) A region of a protein having a defined structure and function. • Enrichment culture technique- The use of selective culture media and incubation conditions to isolate specific microorganisms from natural samples. • Enzyme- A catalyst, usually composed of protein, that promotes specific reactions or groups of reactions. • Eukaryote- A cell or organism having a unit membrane-enclosed nucleus and usually other organelles; a member of the Eukarya. • Evolution- Descent with modification; DNA sequence variation and the inheritance of that variation. • Extremophiles- An organism that grows optimally under one or more chemical or physical extremes, such as high or low temperature or pH. • Genome- The total complement of genetic information of a cell or a virus. • Genomics- The discipline that maps, sequences, analyzes, and compares genomes. • Genus- A taxonomic group of related species. • Growth- In microbiology, an increase in cell number. • Heterocyst- A differentiated cyanobacterial cell that carries out nitrogen fixation. • Koch’s postulates- A set of criteria for proving that a given microorganism causes a given disease. • Metabolism- All biochemical reactions in a cell, both anabolic and catabolic. • Microorganism- A microscopic organism consisting of a single cell or cell cluster, also including the viruses, which are not cellular. • Motility- The property of movement of a cell under its own power. • Nodule- A tumor-like growth on the roots of certain plants containing symbiotic nitrogen- fixing bacteria. • Nucleoid- The aggregated mass of DNA that makes up the chromosome of prokaryotic cells. • Nucleus- A membrane-enclosed structure in eukaryotes containing the genetic material (DNA) organized in chromosomes. • Organelles- A bilayer membrane-enclosed structure such as the mitochondrion found in eukaryotic cells. • Pathogen- A disease-causing microorganism. • Prokaryote- A cell or organism lacking a nucleus and other membrane- enclosed organelles and usually having its DNA in a single circular molecule. Members of the Bacteria and the Archaea. • Pure culture- A culture containing a single kind of microorganism. • Ribosomes- A structure composed of RNAs and proteins upon which new proteins are made. • Species- Defined in microbiology as a collection of strains that all share the same major properties and differ in one or more significant properties from other collections of strains; defined phylogenetically as a monophyletic, exclusive group based on DNA sequence. • Spontaneous generation- The hypothesis that living organisms can originate from nonliving matter. • Sterile- Free of all living organisms and viruses. Review Questions – Answer these questions as you work with the material in chapter one. 1) Do microorganisms typically live in pure culture? How can a person get a pure culture of a bacteria? What type of media is needed to get a pure culture? - No, microorganisms do not typically live in a pure culture. - A person can get a pure culture of a bacteria by using a solid surface/media (such as a transparent double-sided Petri dish with agar) , doing a streak for isolation, and incubating it. Koch originally began with potato slices, but eventually devised a uniform and reproducible nutrient solutions solidified with gelatin and agar (an algal polysaccharide with excellent properties for this purpose.) 2) Compare and contrast prokaryotic cells to eukaryotic cells. Give examples of each. - Prokaryotes: include Bacteria & Archaea No membrane-enclosed organelles, no nucleus Cells are generally smaller than eukaryotic cells - Eukaryotes: include algae, protozoa & other protists, fungi, and cells of plants & animals Contain membrane-enclosed organelles DNA enclosed in a membrane-bound nucleus Cells are generally larger and more complex than prokaryotic cells 3) How old is the Earth? - Earth is 4.6 billion years old (with microbial cells first appearing around 3.8/3.9 b.y.a.) 4) What are cyanobacteria and why were they important to the evolution of man? - Cyanobacteria- Prokaryotic oxygenic (oxygen-evolving) phototrophs containing chlorophyll a and phycobilins; evolved from anoxygenic (non-oxygen-evolving) phototrophs nearly a billion years after them & began the slow process of oxygenating Earth’s atmosphere. - Triggered by the increase in O2 in the atmosphere (from the cyanobacteria), multicellular life forms eventually evolved and continued to increase in complexity, culminating in the plants and animals we have today (having only existed about ½ a billion years). 5) What is unique about cyanobacteria? Name two genera of cyanobacteria. - Cyanobacteria can go through photosynthesis (Exs: anabaena, ocillatoria) & undergo nitrogen fixation (which takes place in the heterocyst). - Two genera of cyanobacteria are: Anabaena, Aphanizomenon, and Microcystis - sometimes referred to as Annie, Fannie, and Mike (account for the vast majority of algal blooms worldwide). Ocillatoria, also. 6) Describe the progression of the types of organisms and changes in the environment of the Earth since the beginning of time. - ~4.6 bya Origin of Earth ~4-3.9 bya Origin of cellular life ~3.6 bya Anoxygenic phototrophic bacteria ~3-2.7 bya Origin of cyanobacteria ~2-1.4 bya Modern eukaryotes ~1.4 bya Algal diversity ~0.5 bya Shelly invertebrates ~0.4 bya Vascular plants ~0.2 bya Mammals ~Present Humans - Notice that the bacteria are the oldest followed by eukaryotes, then algae, invertebrates, plants, mammals, and then humans. 7) What important functions do the following play in a cell…Cytoplasmic membrane, ribosomes, cell wall? - Cytoplasmic membrane- A semipermeable barrier that separates the cell interior (cytoplasm) from the environment; Barrier that separates the inside of the cell from the outside environment - Ribosomes- A structure composed of RNAs and proteins upon which new proteins are made. - Cell Wall- A rigid layer present outside the cytoplasmic membrane that confers structural strength on the cell and protection from osmotic lysis. 8) What type of cells have a nucleus? Nucleoid? What is a cell’s genome and why is it important? - Prokaryotic cells have a Nuceloid while Eukaryotic cells have a Nucleus. - Genome- the total complement of genetic information of a cell or a virus in which the life processes of a cell are controlled by; the living blueprint of an organism (the characteristics, activities, and very survival are governed by the genome.) 9) What do the terms “growth” and “motility” mean in microbiology? - Growth- In microbiology, an increase in cell number. - Motility- The property of movement of a cell under its own power. 10)What are the three domains and how are they related? - Bacteria, Archaea, & Eukaryotes *Archaea and Bacteria are NOT closely related *Archaea are more closely related to Eukarya than Bacteria - The 3 domains are related, because natural selection has filled every suitable environment on Earth with microorganisms whose ancestry can be traced back to one of these three domains. The domains also descended from a common ancestral cell the last universal common ancestor (LUCA). 11)What is phylogeny? - Phylogeny- The evolutionary (natural) history of organisms. Phylogenetic tree- A diagram that depicts the evolutionary history of an organism; consists of nodes and branches. 12)Where are most of the microorganisms found in the environment? - Most microorganisms are found underground in the oceanic and terrestrial sub- surfaces at depths up to about 10 km. 13)How has the leading causes of death changed between 1900 and today? - In 1900, the top 3 leading causes of death were: Influenza & pneumonia, Tuberculosis, and Gastroenteritis (infectious diseases.) Today, the top 3 leading causes of death are: Heart disease, Cancer, and Stroke (non- microbial diseases.) - Control of infectious disease has come from a combination of advances including our increased understanding of disease processes, improved sanitary and public health practices, active vaccine campaigns, and the widespread use of antimicrobial agents (antibiotics). 14)What are biofuels? Give examples. - Biofuels- A fuel made by microorganisms from the fermentation of carbon-rich feedstocks. - Exs: ethanol (often made from corn in the United States and sugarcane in Brazil), biodiesel (vegetable oils and liquid animal fats), green diesel (derived from algae and other plant sources) and biogas (methane derived from animal manure and other digested organic material.)) 15)What is bioremediation? - Bioremediation- The use of microorganisms to remove or detoxify toxic or unwanted chemicals in an environment. 16)What contribution to microbiology did the following people make? Robert Hooke, Anton van Leeuwenhoek, Ferdinand Cohn, Louis Pasteur, Robert Koch, Sergei Winogradsky, Joseph Lister and Martinus Berijerinck? (Microbiology began with the microscope) - Robert Hooke (1635–1703): the first to describe microbes. Illustrated the fruiting structures of molds. - Antoni van Leeuwenhoek (1632–1723): the first to describe bacteria. Further progress required development of more powerful microscopes. - Ferdinand Cohn (1828–1898): founded the field of bacterial classification and discovered bacterial endospores. - Louis Pasteur (1822–1895): discovered that living organisms discriminate between optical isomers & alcoholic fermentation was a biologically mediated process (originally thought to be purely chemical). Disproved theory of spontaneous generation (something from nothing; swan-necked flask experiment where m icroorganisms grew only in the flask exposed to the air) which led to the development of methods for controlling the growth of microorganisms (aseptic technique) & developed vaccines for anthrax, fowl cholera, and rabies. - Robert Koch (1843–1910): demonstrated the link between microbes and infectious diseases & identified causative agents of anthrax and tuberculosis. Koch's postulates- developed techniques (developed solid media ((agar)) and put it in dishes which enabled them to get the bacteria into pure culture by doing a streak for isolation) for obtaining pure cultures of microbes, some still in existence today. The whole purpose for these postulates is to prove that a specific organism causes a specific disease. Koch work with Bacillus anthracis which is the cause or etiological agent of anthrax. He also worked with Mycobacterium tuberculosis which is the etiological agent of tuberculosis… He was awarded the Nobel Prize for Physiology and Medicine in 1905. - Sergei Winogradsky (1856–1953): demonstrated that specific bacteria are linked to specific biogeochemical transformations (Ex: S and N cycles) & proposed concept of chemolithotrophy (oxidation of inorganic compounds is linked to energy conservation.) - Joseph Lister (1867): developed methods for preventing infections during surgeries. - Martinus Beijerinck (1851–1931): developed enrichment culture technique. Microbes can be isolated from natural samples in a highly selective fashion by manipulating nutrient and incubation conditions. (Ex: nitrogen-fixing bacteria). 17)What is spontaneous generation? How was it disproved? Why would people believe in it? - Spontaneous generation- The hypothesis that living organisms can originate from nonliving matter. - It was disproved by Louis Pasteur (1822-1895) through a famous experiment in which he compared the growth of microorganisms in one swan-necked flask containing sterile broth that was exposed to the air (neck tipped where sterile liquid touched the dust) and another containing sterile broth that was not exposed to the air (dust microorganisms were trapped in bent neck and liquid remained sterile). - Microorganisms grew only in the flask exposed to the air, thereby refuting the idea that cells can arise spontaneously from nonliving matter. 18)What is the purpose of Koch’s postulates? When would it not be possible to use them? - The whole purpose for these postulates is to prove that a specific organism causes a specific disease. - It would not be possible to use them when: not always possible to satisfy all postulates for every infectious disease-- animal models not always available (Exs: cholera, rickettsias, chlamydias) 19)What are some of the major sub disciplines of microbiology? - Medical microbiology: infectious diseases Immunology: immune system Agricultural microbiology: microbes associated with soil Industrial microbiology: production of antibiotics, alcohols, and other chemicals Aquatic microbiology: water, wastewater, and drinking water Biotechnology: products of genetically engineered microorganisms 20)What is microbiology? What type of organisms do microbiologist study? - Microbiology- is the study of microscopic organisms - Exs: bacteria, viruses, archaea, fungi, and protozoa. 21)List the scientific names of at least three microorganisms. How are these organisms helpful or detrimental to society? - They can be divided into six major types: bacteria, archaea, fungi, protozoa, algae, and viruses. - Bacteria: exist in four major shapes-- bacillus (rod shape), coccus (spherical shape), spirilla (spiral shape), and vibrio (curved shape). Most bacteria have a peptidoglycan cell wall; they divide by binary fission; and they may possess flagella for motility & can be classified as either Gram-positive or Gram-negative when using the Gram staining. (Exs: gram-positive cocci is Staphylococcus aureus, the bacteria associated with staph infections; gram-negative bacteria is Escherichia coli, the cause of many urinary tract infections.) - Archaea: can be divided into the following groups-- methanogens (methane- producing organisms), halophiles (archaeans that live in salty environments), thermophiles (archaeans that live at extremely hot temperatures), and psychrophiles (cold-temperature Archaeans) & use different energy sources like hydrogen gas, carbon dioxide, and sulphur. Some of them use sunlight to make energy, but not the same way plants do. They absorb sunlight using their membrane pigment, bacteriorhodopsin. This reacts with light, leading to the formation of the energy molecule adenosine triphosphate (ATP). - Fungi: eukaryotic cells (with a true nucleus). Most are multicellular and their cell wall is composed of chitin. They obtain nutrients by absorbing organic material from their environment (decomposers), through symbiotic relationships with plants (symbionts), or harmful relationships with a host (parasites). They form characteristic filamentous tubes called hyphae that help absorb material. The collection of hyphae is called mycelium. Fungi reproduce by releasing spores. - Protozoa: unicellular aerobic eukaryotes. They have a nucleus, complex organelles, and obtain nourishment by absorption or ingestion through specialized structures. They make up the largest group of organisms in the world in terms of numbers, biomass, and diversity. Their cell walls are made up of cellulose. Protozoa have been traditionally divided based on their mode of locomotion: flagellates produce their own food and use their whip-like structure to propel forward, ciliates have tiny hair that beat to produce movement, amoeboids have false feet or pseudopodia used for feeding and locomotion, and sporozoans are non-motile. They also have different means of nutrition, which groups them as autotrophs or heterotrophs. - Algae- also called cyanobacteria or blue-green algae, are unicellular or multicellular eukaryotes that obtain nourishment by photosynthesis. They live in water, damp soil, and rocks and produce oxygen and carbohydrates used by other organisms. It is believed that cyanobacteria are the origins of green land plants. - Viruses: noncellular entities that consist of a nucleic acid core (DNA or RNA) surrounded by a protein coat. Although viruses are classified as microorganisms, they are not considered living organisms. Viruses cannot reproduce outside a host cell and cannot metabolize on their own. Viruses often infest prokaryotic and eukaryotic cells causing diseases. - Multicellular Animal Parasites: eukaryotic organisms consisting of the flatworms and roundworms, which are collectively referred to as the helminths. Although they are not microorganisms by definition, since they are large enough to be easily seen with the naked eye, they live a part of their life cycle in microscopic form. - Source: Boundless. “Types of Microorganisms.” Boundless Microbiology. Boundless, 26 May. 2016. Retrieved 06 Sep. 2016 from https://www.boundless.com/microbiology/textbooks/boundless-microbiology-textbook/introduction-to-microbiology- 1/microbes-and-the-world-19/types-of-microorganisms-207-1066/ - Start collecting information about the different organisms that we will study this semester. You need to know the complete name of the organism (Capitalize the genus name and underline or put in italics the whole name.) List whether or not the organism is bacterial, viral, fungal, etc. If it is bacterial record if it is gram negative or gram positive; morphology and arrangement; anything unique about it. Is it associated with a disease? If so, which one. Learning objectives for Chapter 1 - Upon completion of studying the material in chapter one you will be able to do the following…. Define microbiology. Develop a timeline of the types of organisms found on earth from the oldest to the youngest noting especially what type of microorganisms are the oldest and which group is responsible for oxygenating the Earth. Compare and contrast prokaryotic and eukaryotic organisms giving examples of each. Give examples of the microorganisms studied by bacteriologist, mycologists, phycologists, parasitologists, and clinical microbiologists using their scientific name (genus and species -underlined or in italics). Describe at least five ways that microorganisms impact humans and whether or not that impact is beneficial or detrimental to humans. Describe the historical significance each of these individuals had in the history of microbiology. Robert Hooke, Anton van Leeuwenhoek, Jenner, Ferdinand Cohn, Louis Pasteur, and Robert Koch. Describe at least five sub disciplines of the field of microbiology and a career associated with that sub discipline. MM Qs and As: Protein catalysts involved in the acceleration of the rate of chemical reactions are called - enzymes The disease anthrax is caused by the pathogenic bacterium ________, which produces heat- resistant structures known as ________. - Bacillus anthracis / endospores Applied microbiology deals with important practical problems in - medicine, agriculture, and industry Fannie Hesse is credited with giving ________ the idea to use agar as a solidifying agent. - Robert Koch Major classes of macromolecules present in all living microorganisms include - amino acids, carbohydrates, lipids, and nucleic acids. Not only do some microorganisms tolerate extremely hot temperatures, some actually require high temperatures for optimal growth. - True Most prokaryotic cells reside - In the oceanic and terrestrial sub-surfaces Approximately two billion years ago, ________ were primarily responsible for initially oxygenating Earth. - Cyanobacteria The structure that confers structural strength on the cell is known as the - Cell wall The production of human proteins (e.g., insulin) by genetically engineered microorganisms is an example of ________, a subdiscipline of microbiology. - Biotechnology The first documented description of a microorganism was of a ________ by ________. - Mold / Robert Hooke Microbial control in wastewaters would most logically be a part of - Aquatic microbiology Transparent double-sided dishes used for growing microbes are most commonly called - Petri dishes The theory of spontaneous generation was refuted by the work of - Louis Pasteur The bubonic plague was caused by Yersinia pestis, a highly pathogenic virus. - False Archaea and Bacteria are unified as prokaryotes in lacking ________ which Eukarya contain, such as golgi. - Nuclei and membrane-enclosed organelles ________ was the first to describe microorganisms, while ________ was the first person to see bacteria. - Robert Hooke / Antoni van Leeuwenhoek The person who described the "wee animalcules" was - Antoni van Leeuwenhoek. A Pasteur flask has a(n) - swan neck to prevent particulate matter from getting into the main body of the flask. A pure culture - Is a population of identical cells A microbial cell's membrane is considered ________, because its internal constituents are maintained within the cell. However, it also imports and exports other molecules in response to its environment. - semipermeable Microbes playing a role in nitrogen fixation in plants live in ________, while those playing a role in the digestive tract of certain herbivores live in ________. - Nodules / rumens In what/which domain(s) of life is/are microorganisms represented? - Archaea, Bacteria, Eukarya The science of grouping and classifying microorganisms is known as - microbial systematics Microorganisms play key roles in the cycling of important nutrients in plant nutrition, particularly those of - Carbon, nitrogen, and sulfur The largest mass of living material on Earth comes from - Microorganisms The process whereby microorganisms are used to help clean up pollution created by human activities is known as - Bioremediation Study Guide for Chapter 2 – Biol 261 Vocabulary • Capsule- A dense, well-defined polysaccharide or protein layer closely surrounding a cell. • Chemotaxis- Movement toward or away from a chemical. • Cytoplasmic membrane- A semipermeable barrier that separates the cell interior (cytoplasm) from the environment. • Dipicolinic acid- A substance unique to endospores that confers heat resistance on these structures. • Endospore- A differentiated cell formed within the cells of certain gram-positive bacteria that is extremely resistant to heat as well as to other harmful agents. • Endosymbiosis- The engulfment of one cell type by another cell type and the subsequent and stable association of the two cells. • Flagellum- A long, thin cellular appendage that rotates (in prokaryotic cells) and is responsible for swimming motility. • Gram Stain- A differential staining technique in which cells stain either pink (gram- negative) or purple (gram-positive), depending upon their structural makeup. • Gram-positive bacteria- A major phylogenetic lineage of prokaryotic cells containing mainly peptidoglycan in their cell wall; stain purple in the Gram stain. • Gram-negative bacteria- A major phylogenetic lineage of prokaryotic cells with a cell wall containing relatively little peptidoglycan, and an outer membrane composed of lipopolysaccharide, lipoprotein, and other complex macromolecules; stain pink in the Gram stain. • Lipopolysaccharide (LPS)- Complex lipid structure containing unusual sugars and fatty acids found in most gram-negative Bacteria and constituting the chemical structure of the outer membrane. • Morphology- The shape of an organism. • Nucleus- membrane-enclosed structure in eukaryotes containing the genetic material (DNA) organized in chromosomes. • Outer membrane- A phospholipid- and polysaccharide-containing unit membrane that lies external to the peptidoglycan layer in cells of gram-negative Bacteria (relatively little peptidoglycan). • Peptidoglycan- The rigid layer of the cell walls of Bacteria, a thin sheet composed of W- acetylglucosamine, W-acetylmuramic acid, and a few amino acids. • Periplasm- The area between the cytoplasmic membrane and the outer membrane in gram-negative Bacteria (relatively little peptidoglycan). • Peritrichous flagellation- In flagellar arrangements, having flagella attached to many places on the cell surface. • Pili- A filamentous structure that extends from the surface of a cell and, depending on type, facilitates cell attachment, genetic exchange, or twitching motility. • Plasmid- An extrachromosomal genetic element that is not essential for growth and has no extracellular form. • Polar flagellation- In flagellar arrangements, having flagella attached at one end or both ends of the cell. • Resolution- In microbiology, the ability to distinguish two objects as distinct and separate under the microscope. • Teichoic acid- A phosphorylated polyalcohol found in the cell wall of some gram- positive Bacteria (mainly peptidoglycan). Review Questions… 1) What is resolution and what is the resolution of a light microscope? - Resolution- In microbiology, the ability to distinguish two objects as distinct and separate under the microscope; is determined by the wavelength of light used and numerical aperture of the lens. - The limit of resolution for a light microscope is about 0.2 µm (microns). 2) Which has greater resolution? A light or electron microscope? - The electron microscope has a greater resolution than a light microscope. 3) What are the possible total magnifications of each objective on a light microscope? - Two sets of lenses form the image-- objective lens and ocular lens Total magnification = objective magnification X ocular magnification - 4X x 10 = 40 10X x 10 = 100 40X x 10 = 400 100X x 10 = 1,000 - Maximum magnification is ~2,000x (eyepieces can range from 5X-30X) 4) What is the function of stains? - Dyes can be used to stain cells and increase their contrast so that they can be more easily seen in the bright-field microscope. (Exs: of common stains are methylene blue (blue), safranin (red), and crystal violet (purple)) 5) What is the purpose of heat-fixing a smear? - The purpose of heat-fixing a smear is: to kill bacteria stuck to the slide. 6) Explain the steps of a Gram stain and what happens to Gram negative and Gram positive cells in each step. What color are Gram positive and Gram negative cells after a completed Gram stain? - Step 1: Flood the heat-fixed smear with Crystal Violet (dye) for 1 min. Result- all cells are purple. - Step 2: Add iodine solution for 1 min. Result- all cells remain purple. - Step 3: Decolorize with alcohol, briefly (~20 secs.) Result- Gram (+) cells are purple, Gram (-) cells are colorless. - Step 4: Counterstain with Safranin (dye) for 1-2 mins. Result- Gram (+) cells are purple, Gram (-) cells are pink/red. 7) Which type of microscopy is good to look at live specimens? - Phase Contrast microscopy is best for viewing live specimens. 8) Which type of microscopy is good to look at motility? What makes bacteria motile? - Dark Field microscopy is best for viewing motility. - Bundles of flagella (flagellum) are the structures responsible for the swimming motility in bacteria. 9) What is the basic premise of fluorescent microscopy? - The basic premise of Fluorescent microscopy is: Used to visualize specimens that fluoresce; they emit light of one color when illuminated with light of another color. - Cells fluoresce naturally (autofluorescence) or after they have been stained with a fluorescent dye like DAPI (stains cells bright blue, because it complexes with the cell’s DNA.) Widely used in microbial ecology for enumerating bacteria in natural samples 10)What is the basic premise of confocal laser microscopy? - The basic premise of Confocal Laser microscopy is: uses a computerized microscope coupled with a laser source to generate a three-dimensional image. - The computer can focus the laser on single layers of the specimen & different layers can then be compiled to produce a three-dimensional image. (Resolution is 0.1 µm for CSLM) 11)How is TEM different from SEM? - Transmission Electron Microscope (TEM)- used to examine cells and internal cell structure at very high magnification and resolution (enables visualization of structures at the molecular level & the specimen must be very thin-- fixed and cut with diamond knives into very thin specimens (20–60 nm) and be stained with heavy metal dyes); electromagnets function as lenses & the system operates in a vacuum. (High magnification and resolution (0.2 nm)) - Scanning Electron microscopy (SEM)- for optimal 3D imaging of cells and used to look at the surface of cells; the specimen is coated with a thin film of heavy metal (e.g., gold), an electron beam scans the object, scattered electrons are collected by a detector, and an image is produced. Even very large specimens can be observed. (Magnification range of 15x–100,000x) 12)How are prokaryotic cells different from eukaryotic cells? Give examples of both. Which ones are smaller? - The size range for Prokaryotes cells: 0.2 µm to >700 µm in diameter. *most cultured rod-shaped bacteria are between 0.5 and 4.0 µm wide and < 15 µm long. (Exs: of very large prokaryotes Epulopiscium fishelsoni (rod-shaped, ~600 µm long & 75µm wide) Thiomargarita namibiensis (cocci-shaped, ~400-750 µm) - The size range for Eukaryotic cells: 10 to >200 µm in diameter. *most are 8 µm in diameter, but can be 2-600 µm in diameter. - Prokaryotes are smaller than Eukaryotes, typically. 13)Why are viruses not cells? - Viruses are not considered "alive" because they lack many of the properties that scientists associate with living organisms. Primarily, they lack the ability to reproduce without the aid of a host cell, and don't use the typical cell- division approach to replication. - Source: http://scienceline.ucsb.edu/getkey.php?key=3316 14)What type of microscope do you need to see viruses? Why? - Viruses can only be seen with electron microscopes, because they are usually so small (100 nm-10 nm). 15)What type of chromosome do bacteria have? What is the chromosome? - Not all bacteria have a single circular chromosome: some bacteria have multiple circular chromosomes, and many bacteria have linear chromosomes and linear plasmids. - Plasmids are the chromosome. - Source: http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/chroms-genes-prots/chromosomes.html 16)What is a plasmid? What is its function? - Plasmid- An extrachromosomal genetic element that is not essential for growth and has no extracellular form. - A plasmid is a small, circular, double-stranded DNA molecule that is distinct from a cell's chromosomal DNA. Plasmids naturally exist in bacterial cells, and they also occur in some eukaryotes. Often, the genes carried in plasmids provide bacteria with genetic advantages, such as antibiotic resistance. - Source: http://www.nature.com/scitable/definition/plasmid-plasmids-28 17)What type of chromosome do yeast have? Where are they compared to bacteria? - Yeast artificial chromosomes (YACs) are genetically engineered chromosomes derived from the DNA of the yeast, Saccharomyces cerevisiae, which is then ligated - Source: https://en.wikipedia.org/wiki/Yeast_artificial_chromosome 18)What is endosymbiosis? - Endosymbiosis- The engulfment of one cell type by another cell type and the subsequent and stable association of the two cells. 19)What are the basic morphologies found in bacteria? - Basic morphologies: Coccus (pl. cocci; spherical or ovoid), Rod (cylindrical shape), & Spirillum (spiral shape). - Cells with unusual shapes: Spirochetes, appendaged bacteria, and filamentous bacteria. - (Exs:) Gram (+) cocci in clusters: Staphylococcus (gram + purple) Gram (+) cocci in chains: Streptococcus (gram + purple) Gram (+) cocci in tetrads: Micrococcus (4 circles in shape of square) (gram + purple) Gram (+) rods with spores: Bacillus (oval with circle in it)/Clostridium (gram + purple) Gram (+) rods without spores: Lactobacillus (oval) (in yogurt) (gram + purple) Gram (-) cocci in pairs: Neisseria (gram -, two circles) (gram – red) Gram (-) rods: E. Coli (oval) (1x3 microns) (gram – red) Gram (-) curved rods: Vibrio (gram – red) Gram (-) spiral shaped cells: Treponema (gram – red) 20)What units are bacteria measured in? viruses? What size is E. coli and Staphylococcus? - Bacteria are measured in microns (µm). - Viruses are measured in nanometers (nm), because they are smaller. - E. coli is: 1.3 microns Staphylococcus is: 1 micron 21)Describe a cytoplasmic membrane. What is it’s function? - Cytoplasmic membrane- A thin semipermeable barrier that separates the cell interior (cytoplasm) from the environment; enables concentration of specific metabolites and excretion of waste products. - The function of the cytoplasmic membrane is: to control what enters the cell. 22)Compare and contrast the cell wall of gram negative and gram positive bacteria. What is unique to each? - Gram-negative (-) cell wall: two layers-- LPS and peptidoglycan (thin) - Gram-positive (+) cell wall: one layer—peptidoglycan (thick) 23)What is peptidoglycan? How is it arranged and cross-linked? - Peptidoglycan- The rigid layer of the cell walls of Bacteria that provide strength, a thin sheet composed of N-acetylglucosamine, N-acetylmuramic acid, and a few amino acids (lysine or diaminopimelic acid (DAP)). - Cross-linked differently in gram-negative bacteria and gram-positive bacteria: DAP is an amino acid that is unique to Gram negative (-) bacteria like E. coli. The repeating glycine interbridges linked to the lysine are unique to Gram positive (+) bacteria like Staphylococcus aureus. Gram positive cell walls have multiple layers of the glycan backbone. 24)What type of bacteria lack cell walls and what disease are they associated with? - Prokaryotes that lack cell walls: Mycoplasmas (group of pathogenic bacteria) & Thermoplasma (species of Archaea). - Mycoplasma are bacteria that are associated with walking pneumonia. Thermoplasa is an Archaean cell that does not have a cell wall. 25)What is endotoxin? - Endotoxin- The lipopolysaccharide portion of the cell envelope of certain Gram- negative (-) Bacteria, which is a toxin when solubilized. Compare with exotoxin. 26)How are archaeal cell walls and cell membranes different from true bacteria? - Archael cell walls & membranes are different from bacteria (and can survive in extreme environments) in that their cell walls have a different sugar (N- acetylalasaminuronic acid) and thus do not contain peptidoglycan. Their cell walls are composed of pseudomurein or pseudopeptidoglycan. Murein in an old term for peptidoglycan. It is smilar to PG but contains a different sugar. They also do not have outer membranes. 27)What does lysozyme do? Why doesn’t it kill archaeal cells? - Lysozyme is a special enzyme found in tears, saliva, sweat, and other body fluids. Other mucosal linings, such as the nasal cavity, also contain lysozyme. It destroys bacteria that attempt to enter our body through these passageways. - Lysozyme is capable of breaking the chemical bonds in the outer cell wall of the bacteria. Bacterial cell walls contain a layer of peptidoglycan, which is the specific site that lysozyme targets. The peptidoglycan layer contains alternating molecules called N-acetylglucosamine and N-acetylmuramic acid. These molecules form a strong glycan chain that act as the backbone for the cell wall. The link between the N- acetylglucosamine and N-acetylmuramic acid is cleaved by lysozyme. Once this chain is broken by lysozyme, it results in bacterial death. - It doesn’t kill archaeal cells, because archaeal cell walls and outer membranes are different and do not contain PG which lysozymes attack at. - Source: http://study.com/academy/lesson/lysozyme-definition-function-structure.html 28)What function do capsules serve and what are they made of? Where are they located on the cell? - Capsule- A dense, well-defined polysaccharide or protein layer closely surrounding a cell. - The layer is organized in a tight matrix and can be visible with light microscopy is India Ink is used. 29)How are fimbriae and pili similar and different? - Fimbriae- Short, filamentous structure on a bacterial cell; although flagella-like in structure, it is generally present in many copies and not involved in motility. Plays a role in adherence to surfaces and in the formation of pellicles. See also pilus. - Pili- A longer filamentous structure that extends from the surface of a cell and, depending on type, facilitates cell attachment, genetic exchange (conjugation), or twitching motility. 30)What are some possible cell inclusions found in bacteria? - Possible cell inclusions in bacteria: Carbon storage polymers Poly-β-hydroxybutyric acid (PHB): lipid Glycogen: glucose polymer Polyphosphates: accumulations of inorganic phosphate Sulfur globules: composed of elemental sulfur Carbonate minerals: composed of barium, strontium, and magnesium Magnetosomes: magnetic storage inclusions 31)What is the function of endospores? What two genera make endospores? How are they alike and different? - Endospores- A highly differentiated cell formed within the cells of certain gram- positive bacteria that is extremely resistant to heat as well as to other harmful agents; “dormant” stage of bacterial cell cycle; Ideal for dispersal via wind, water, or animal gut, is present only in some Gram-positive (+) bacteria, & colorless on Gram stain. - 2 Genera make endospores: Clostridium (anaerobe); Bacillus (aerobe); both are commonly found in the soil. 32)What chemical is unique to endospores? - Dipicolinic acid is unique to endospores. Also enriched in Ca2+ and the core contains small acid-soluble spore proteins (SASP) 33)What makes bacteria motile? - Flagellar structure of Bacteria: consists of several components-- filament composed of flagellin & move by rotation. - Flagellar structure of Archaea: half the diameter of bacterial flagella, composed of several different proteins, & move by rotation. 34)What is positive and negative chemotaxis? - The cell has chemoreceptors that senses the chemical and results in the cell moving & is best studied in E. coli. + toward - away Chapter 2 – Learning Objectives Define resolution and total magnification. Identify a use for phase contrast, dark-field, and fluorescence microscopy and compare each with bright-field illumination. Explain the principle of basic, acidic, simple and differential stains and give examples of each. List the steps and function of each step in a Gram stain including what happens to Gram negative and Gram positive cells during each step and why. Give examples of Gram negative and Gram positive bacteria. Explain how electron microscopy differs from light microscopy. Compare and contrast SEM to TEM. Compare and contrast prokaryotic and eukaryotic cells. Give examples of each. Diagram a typical gram positive and gram negative cell including all possible parts and know their function. Explain the theory of endosymbiosis. MM Qs & As: What is the role of lenses in microscopy? - Lenses focus either light or electrons to create a magnified image of a specimen. Figure 2.11 (cell morphologies) Figure 2.15 (structure of the cytoplasmic membrane) Figure 2.27c (structure of the gram-positive bacterial cell) Figure 2.29a (the gram-negative cell wall) Bacterial cell wall: - Gram positive cell wall includes: Teichoic & Lipoteichoic acids and a thick layer of Peptidoglycan which is made up of Peptide Cross-Links and Glycan chains which are long polymers of N-acetylglucosamine & N-acetylmuramic acid. - Gram negative cell wall includes:Athin layer of Peptidoglycan which is made up of Peptide Cross-Links and Glycan chains which are long polymers of N- acetylglucosamine & N-acetylmuramic acid, and Periplasm and an Outer Membrane which consists of Phospholipids Lipopolysaccharide (LPS) which contains LipidA also known as Endotoxin and Porins which function as Transport Channels. PartA: Which of the following molecules is shared by both Gram-positive and Gram- negative organisms? - N-acetylmuramic acid Part B:Amoxicillin is an antibiotic that inhibits the formation of peptide cross-links. Amoxicillin, therefore, would most likely inhibit the growth of __________. - Both Gram-positive and Gram-negative organisms. Part C: Porins are present in ______________bacteria because, in these organisms, molecules entering the cell must pass through an extra layer of ___________. - Gram-negative / membrane Gram Stain includes four steps: - 1: Crystal Violet (CV) which is the Primary Stain 2: Iodine which is the Mordant 3: Ethanol &Acetone which is the Decolorizer 4: Safranin which is the Counterstain Gram stain differentiates bacteria into two groups : - Gram-positive bacteria: will stain Purple and cell wall has a Thick Peptidoglycan Layer. - Gram-negative bacteria: will stain Pink and cell wall has a Thin Peptidoglycan Layer & an Outer Membrane. PartA: While staining a mixed culture of Gram-positive and Gram-negative bacteria, switching the order of steps 2 and 3 would result in ______________________. - All bacteria appearing pink Part B: Which structural feature of Gram-positive bacteria enhances their ability to retain the crystal violet dye? - Athick peptidoglycan layer Part C: What would you anticipate seeing if you accidentally switched crystal violet and safranin while performing a Gram stain? - All bacteria would appear purple Part D: What would you expect to see if you forgot to perform step 2 of the Gram stain procedure? - All bacteria would appear pink Bacteria stain as gram-positive or gram-negative because of differences in the cell - Wall You are given an electron micrograph of a bacterial cell. In the micrograph you can clearly see three thin layers of different densities surrounding the cell. Based on the micrograph, you can infer that this cell is ________ and would appear ________ after application of the Gram stain procedure. - Gram-negative / pink In gram-positive Bacteria, the cell walls are composed mainly of thick ________ layers. - Peptidoglycan The rigid layer that is present in the cell walls of Bacteria that is primarily responsible for the strength of the wall is known as - Peptidoglycan Teichoic acids are commonly found in gram-negative cell walls. - False Lysozyme is an enzyme that can ultimately lyse and kill eukaryotic cells by breaking β- 1,4-glycosidic bonds in peptidoglycan. - False Figure 2.4a (the gram stain) Electron microscopy has greater ________ than light microscopy, because the wavelengths of visible light are much larger than the wavelengths of electrons. - Resolution An organism of the genus Staphylococcus is ________, while an organism of the genus Spirochaeta is ________. - Spherical / coiled Aquaporins are - Water transport proteins The cytoplasmic membrane could best be described as - Ahighly selective permeability layer The lipopolysaccharide (LPS) layer is found ONLY in the cell walls of - Gram-negative bacteria An endotoxin is - The toxin portion of the LPS Amajor function of prokaryotic gas vesicles is to - confer buoyancy on cells by decreasing their density. What is the biological function of endospores? - They enable organisms to endure extremes of temperature, drying, and nutrient depletion. The terms "run" and "tumble" are generally associated with - Chemotaxis Mitochondria and chloroplasts have their own DNAand ribosomes, which supports the endosymbiosis hypothesis. - True Which of the following types of microscopy can be used with live cells? - Phase Contrast Which of the following types of microscopy could be used to visualize the layers of the cell membrane and the cell wall? - Transmission electron microscopy Electron microscopes have less resolving power than light microscopes. - False The use of the Gram stain in microbiology is important because it differentiates - Bacterial cells with different types of cell walls The lipids in the cytoplasmic membrane of Bacteria and ________ contain ester linkages, while the cytoplasmic membrane of ________ contain ether linkages. - Eukarya / Archaea Which is/are a function(s) of the cytoplasmic membrane in prokaryotes? - It serves as a permeability barrier, a docking station for proteins involved in bioenergetics reactions and transport, and a site for energy conservation (all of the above) Some membrane proteins are involved in bioenergetic reactions, while others are involved in membrane transport. - True Both hydrophilic and charged molecules readily diffuse through the cytoplasmic membrane. - False Although the inner leaflet of the gram-negative outer membrane is composed mainly of phospholipids, the outer leaflet of the outer membrane contains - Lipopolysaccharides (LPS) Cellular inclusions in prokaryotic cells serve to - store energy rich compounds and position cells in the appropriate environment for survival. Chapter 3 – Study Guide – Biol 261 Vocabulary • Activation energy- The energy needed to make substrate molecules more reactive; enzymes function by lowering activation energy. • Adenosine triphosphate (ATP)- Anucleotide that is the primary form in which chemical energy is conserved and utilized in cells. • Anabolic reactions (anabolism)- The biochemical processes involved in the synthesis of cell constituents from simpler molecules, usually requiring energy. • Anaerobic respiration- Use of an electron acceptor other than O2 in an electron transport- based oxidation leading to a proton motive force. • Aseptic technique- The manipulation of sterile instruments or culture media in such a way as to maintain sterility. • Autotroph- An organism able to grow with CO2 as its sole source of carbon. • Catabolic reactions (catabolism)- The biochemical processes involved in the breakdown of organic or inorganic compounds, usually leading to the production of energy. • Catalyst- Asubstance that promotes a chemical reaction without itself being changed in the end. • Chemolithotroph- An organism that obtains its energy from the oxidation of inorganic compounds. • Chemoorganotroph- An organism that obtains its energy from the oxidation of organic compounds. • Citric acid cycle- Acyclical series of reactions resulting in the conversion of acetate to CO2 and NADH.Also called the tricarboxylic acid cycle or the Krebs cycle. • Coenzyme- A low-molecular-weight molecule that participates in an enzymatic reaction by accepting and donating electrons or functional groups. Examples: NAD+, FAD. • Complex medium- Any culture medium whose precise chemical composition is unknown. Also called undefined media. • Culture medium- An aqueous solution of various nutrients suitable for the growth of microorganisms. • Defined medium- Any culture medium whose exact chemical composition is known. Compare with complex medium. • Enzyme- A catalyst, usually composed of protein, that promotes specific reactions or groups of reactions. • Fermentation- The anaerobic catabolism of an organic compound in which the compound serves as both an electron donor and an electron acceptor and in which ATP is usually produced by substrate-level phosphorylation. • Glycolysis- Reactions of the Embden-Meyerhof-Parnas pathway in which glucose is converted to pyruvate. • Heterotroph- An organism that requires organic carbon as its carbon source; also a chemoorganotroph. • Respiration- Catabolic reactions producing ATP in which either organic or inorganic compounds are primary electron donors and organic or inorganic compounds are ultimate electron acceptors. Review Questions…. 1) How are catabolic and anabolic reactions similar and different? How are they related? - Catabolic reactions (catabolism)- The biochemical processes involved in the breakdown of organic or inorganic compounds, usually leading to the production of energy; polysaccharides, starches, lipids, proteins, nucleic acids (DNA, RNA) are the substrates/macromolecules that enzymes act on. - Anabolic reactions (anabolism)- The biochemical processes involved in the synthesis of cell constituents from simpler molecules, usually requiring energy. 2) What type of reactions produceATP and which type useATP? - Catabolism generates/producesATP whileAnabolism take up/useATP. 3) What elements are essential for all microorganisms to grow? - Macronutrients- nutrients required in large amounts. Carbon: required by ALL cells and is a major element in ALL classes of macromolecules. A typical bacterial cell is ~50% carbon (by dry weight). Heterotrophs use organic carbon while Autotrophs use carbon dioxide (CO2). Nitrogen: a typical bacterial cell is ~13% nitrogen (by dry weight). Key element in proteins, nucleic acids, and many more cell constituents. Phosphorus (P): synthesis of nucleic acids and phospholipids. Sulfur (S): sulfur-containing amino acids (cysteine and methionine) & vitamins (Exs: thiamine, biotin, lipoic acid) and coenzyme A. Potassium (K): required by enzymes for activity. Magnesium (Mg): stabilizes ribosomes, membranes, and nucleic acids & is also required for many enzymes. Calcium (Ca): helps stabilize cell walls in microbes & plays key role in heat stability of endospores. Sodium (Na): required by some microbes (e.g., marine microbes) - Micronutrients- nutrients required in trace amounts. Iron (Fe): key component of cytochromes and FeS proteins involved in electron transport. Growth factors: organic compounds required in small amounts by certain organisms (Exs: vitamins, amino acids, purines, pyrimidines) Vitamins: most commonly required growth factor & most function as coenyzmes. 4) What are the essential cations and anions for most microorganisms? - The essential Cations (+) andAnions (-) for most microorganisms are: Sodium (Na), Magnesium (Mg), Potassium (K), Calcium (Ca), and Chlorine (Cl). 5) What do heterotrophs use as a carbon source? Autotrophs? What do they do with the carbon? - Heterotrophs- An organism that requires organic carbon as its carbon source; also a chemoorganotroph. Autotrophs- An organism able to grow with CO2 as its sole source of carbon. - All cells require carbon in large amounts in order to make new cell materials. 6) Why do cells need nitrogen? Phosphorus? Sulfur? Potassium? - Cells need: Nitrogen: because it is a key element in proteins, nucleic acids, and many more cell constituents. Phosphorus: for the synthesis of nucleic acids and phospholipids. Sulfur: because there are sulfur-containing amino acids (cysteine and methionine) & vitamins (Exs: thiamine, biotin, lipoic acid) and coenzymeA. Potassium: because it is required by enzymes for activity. 7) How is a defined medium different from a complex medium? Give an example of a complex medium. Which type of media is used to grow most bacteria? - Defined medium- Any culture medium whose exact chemical composition is known. Compare with complex medium. Complex medium- Any culture medium whose precise chemical composition is unknown.Also called undefined media (Exs: yeast & meat extracts). - EMB (Eosin Methylene Blue) agar is selective for Gram negative rods because it contains the dyes eosin and methylene blue and it also contains bile salts all of which inhibit the growth of most Gram positive bacteria. It is differential because it contains lactose which bacteria may or may not ferment. E. coli is able to ferment the lactose and when it does it produces so much acid that it changes the pH and the eosin dye which is metallic dye precipitates out of solution give the appearance of a green sheen. 8) What makes a medium selective? Differential? Give examples of both including why they are differential and or selective. - Selective Media- A growth medium that enhances the growth of certain organisms while inhibiting the growth of others due to an added media component; contains compounds that selectively inhibit growth of some microbes but not others Differential Media- Growth media that allow identification of microorganisms based on phenotypic properties; contains an indicator, usually a dye, that detects particular chemical reactions occurring during growth - (Exs:) Selective: MSA is selective for Staphylococcus because it contains 7.5% NaCl which causes most bacteria to dehydrate and die. It is differential for the Staphylococci because it contains mannitol which is a fermentable sugar. Selective & Differential: mannitol salt, EMB agar, Blood agar is both enriched and differential. Blood agar is TSA (trypticase soy agar) with 5% sheep’s blood added to it. The blood enriches the media which allows most all bacteria to have the nutrients they need to grow. Some bacteria produce hemolysins which are proteins that lyse red blood cells. 9) What type of medium is EMB and what is it used for? What organism gives a green metallic sheen on EMB and why? - EMB (Eosin Methylene Blue) agar is a Selective medium for Gram negative rods, because it contains the dyes eosin and methylene blue and it also contains bile salts all of which inhibit the growth of most Gram positive bacteria. It is also Differential because it contains lactose which bacteria may or may not ferment. - E. coli is able to ferment the lactose and when it does it produces so much acid that it changes the pH and the eosin dye which is metallic dye precipitates out of solution give the appearance of a green sheen seen in the picture. 10)What is blood agar? What makes it differential? - Blood agar is both enriched and Differential. Blood agar is TSA (trypticase soy agar) with 5% sheep’s blood added to it. The blood enriches the media which allows most all bacteria to have the nutrients they need to grow. Some bacteria produce hemolysins which are proteins that lyse red blood cells. 11)What type of media is MSAand why? What would Staphylococcus epidermidis and Staphylococcus aureus look like on MSA? Why? - MSA is mannitol salt agar. MSA is selective for Staphylococcus because it contains 7.5% NaCl which causes most bacteria to dehydrate and die. It is differential for the Staphylococci because it contains mannitol which is a fermentable sugar. - Pathogenic staphylococci, like Staphylococcus aureus (right/yellow/acidic), ferments the mannitol. When it ferments the mannitol it produces acids that lower the pH and cause the pH indicator, phenol red, to turn from red (neutral) to yellow (acidic). Non-pathogenic staphylococci, like Staphylococcus epidermidis (left/red/neutral), do not ferment the mannitol and thus grow on the media put it remains red since the pH does not change. 12)What is beef extract and what does it provide in the medium? - Examples of ingredients that we don’t know the exact chemical structure for, or Complex mediums, are beef extract, yeast extract, tryptone, etc. Extract are made by taking a large macromolecule like meat and exposing it to enzymes or chemicals which breaks it into smaller subunits but not all the way to the monomers. - Beef extract, or complex mediums, may suffice and are used for culturing any microorganisms when knowledge of the exact composition of a medium is not essential. 13)What makes a medium solid? - Solid media are prepared by addition of a gelling agent (agar or gelatin). 14)How can you get a pure culture? - Pure culture- A culture containing a single kind of microorganism. - One must quadrant streak for isolation, incubate the plates, and get a single colony from that one bacteria that went through binary fission (doubled and doubled) to make a colony. Make a stock culture (pure, because its only one kind of bacteria). 15)What is aseptic technique? An autoclave? - Aseptic technique- The manipulation of sterile instruments or culture media in such a way as to maintain sterility; should be followed for sterilization of media. (Ex: Aseptic transfer-- flame the loop tool (sterilizes), remove tube cap, flame the tube tip (sterilizes), only sterilized portion of loop tool enters tube, tube is re-flamed (re-sterilizes), and cap is put back on tube.) - Autoclave- A sealed sterilizing device that destroys microorganisms with temperature and steam under pressure. 16)Why do enzymes speed up reactions? - Enzyme- A biological catalyst, usually composed of protein, that promotes specific reactions or groups of reactions. - Catalyst- A substance that promotes a chemical reaction without itself being changed in the end; a substance that lowers the activation energy of a reaction, increases the reaction rate, & is also not changed or consumed in the reaction. - Enzymes are catalyst and so they lower the activation energy and speed up reactions. This graph shows that the enzyme makes the reaction happen faster because it lowers the activation energy. 17)Typically, what are enzymes made of? What is an active site and what happens there? - Enzymes are biological catalysts; they are typically proteins (some RNAs), highly specific, generally larger than the substrate, & typically rely on weak bonds. (Exs: hydrogen bonds, van der Waals forces, hydrophobic interactions). Active site is the region of the enzyme that binds to the substrate. 18)Give examples of substrates and the enzymes that act on them. - 19)How is fermentation similar and different from respiration? - Fermentation- The anaerobic catabolism of an organic compound in which the compound serves as both an electron donor and an electron acceptor and in which ATP is usually produced by substrate-level phosphorylation. - Respiration- The catabolic reactions producing ATP in which either organic or inorganic compounds are primary electron donors and organic or inorganic compounds are ultimate electron acceptors. - Fermentation (on the right) starts with glycolysis and then the pyruvic acid is converted to various acids, gases and alcohols. Respiration (on the left) starts with glycolysis which feeds into the Krebs cycle and finally the electron transport chain which is in the membrane and is where the most ATP is produced. Oxygen is the final electron acceptor to make water so this is aerobic respiration. 20)How is aerobic and anaerobic respiration different? - Aerobic respiration- is the process of producing cellular energy involving oxygen. Cells break down food in the mitochondr
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