Microbiology Sample Exam - First Exam, With Solutions PDF

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Microbiology Exam #1 History of Microbiology 1. What is the difference between inductive and deductive reasoning? Who was an early advocate for using scientific methods based on inductive reasoning? a. Deductive reasoning: If one or more general statements (called premises) are true, then a conclusion reached by sound logical reasoning is necessarily true i. Eg. All cellular organisms have DNA as their genetic material; all bacteria are cellular organisms; all bacteria have DNA as their genetic material b. Inductive reasoning: conclusion is probably true. Constructs or evaluates general propositions that are derived from specific… *science* i. Eg. All bacteria “probably” have DNA as their genetic material c. Francis Bacon was an early advocate for using scientific methods based on inductive reasoning. 2. Who championed the idea that scientific theories must meet the criterion of empirical falsifiability? What does this idea mean? a. Karl Popper: Favored testing a scientific theory by the criterion of empirical falsifiability- a theory in the empirical sciences can never be proven, but it can be falsified, meaning that it can & should be scrutinized by critical tests 3. What historical factors nurtured the extraordinary intellectual achievements in the Netherlands in the 1600s? a. The discovery of microorganisms was in the Netherlands in the 1600s during the Dutch Golden age i. Became crossroads for international trade. ii. Had large merchant fleet iii. Won independence from Spain and wealthy middle class wanted to be pioneers to new discoveries. 4. What contributions did Robert Hooke and Antonie van Leeuwenhoek make in the history of microbiology? a. Robert Hooke— published micrographia, gave the 1st description of cells. Looked at plant tissues that were divided by “square things” and coined the term “cells” b. Antonie van Leeuwenhoek— discovered unicellular microorganisms using a simple(single lens) microscope 5. What is the difference between a simple and compound microscope? a. Simple microscope: one lens b. Compound microscope: two lens, the ocular eyepiece: to see through and the objective lens: magnify and show the real and virtual image. 6. What important conclusion did Robert Koch reach from his studies of anthrax? a. Demonstrated that a specific bacterium causes a specific disease in mammals i. Koch took infected animal blood, researched and developed new techniques 7. What are the four steps of Koch’s postulates and how do they relate to the isolation of pure cultures? a. The microbe must be present in every case of the disease (but absent from healthy individuals) b. The microbe must be isolated from the diseased host and grown in pure culture

c. The pure culture must be inoculated into a healthy host and this host must come down with the same disease (experimental infection) d. The microbe must be re-isolated in pure culture from the experimentally infected host Microscopy 1. What three factors determine the quality of an optical image? a. Magnification: makes image larger b. Resolution: makes image clearer c. Contrast: to make the bacteria stand out from the background 2. What is Snell’s law and what is it used to determine? (Know the equation) a. The analysis of light bending/refraction i.

Equation:

sinθi sinθr

=

n2 n1

1. Subscript i stands for incidence 2. Subscript r stands for refraction ii. n= index of refraction 1. Vacuum: n=1 2. Air: n=1.0003 3. Water: n=1.33 4. Glass: n≈1.5 3. What is the index of refraction (also called the refractive index) of a substance refer to? a. A measure of how much the speed of light slows down when it goes through a medium. 4. What is the difference between a convex and a concave lens a. Convex: The rays of light from the person are converged by the convex lens forming an image on the film or charged couple device b. Concave: Thinner in the middle. A concave lens is a diverging lens. When parallel rays of light pass through a concave lens the refracted rays diverge so that they appear to come from one point called the principal focus. 5. What do the axis, focal length(s), and focal point(s) of a lens describe? a. Axis:a line normal to the lens at its center b. Focal length: the point at which the light rays cross c. Focal point: the distance from the center of the lens to its focal point

6. What is a real image? What is a virtual image? How do they differ? a. Real image: i. Physically exists. It is created by converging light rays from a lens or mirror ii. Is formed when the object is outside the focal length of the lens iii. Is upside down with respect to the object that forms it b. Virtual image: i. Only appears to exist. It is created by the brain when diverging light rays from a lens (or mirror) enter the eye ii. Is formed when the object is inside the focal length iii. Is right side up with respect to the object 7. What are the lens system in a modern compound microscope called? How do they work together to create the image of a specimen that you view through the microscope? a. Ocular lens: to see through b. Objective lens: magnifies image; shows real and virtual image i. Visual Perception (real image): In the human eye the lens projects a real image (upside down) on to the photoreceptor cells of the retina ii. Visual Perception (virtual image): The optic nerve transmits the visual info to the brain, where the neural pathways of the visual cortex process the image and interpret it as inverted (rightside up). What the observer “sees” is a virtual image of the object 8. What is the difference between magnification and resolution? What are some practical ways of improving resolution? a. Magnification: the ability to make small objects seem larger, such as making a microscopic organism visible. b. Resolution: the ability to distinguish two objects from each other ( i.e. make things clearer) c. Practical ways of improving resolution: i. We can increase resolution by increasing the index of refraction ii. Immersion oil changes the index of refraction increasing resolution but only on 100x objective. 9. What is the Abbe equation and what is it used to calculate? (know the equation) a. Abbe equation: shows how good our resolution can get. i. Formula: d=λ/2*i*𝝰 (i= index of refraction) 10. Why do we stain microorganisms? What is the difference between direct staining and indirect (negative) staining? (You learned this one in lab). a. We stain small bacteria to increase contrast and make it easier to see them i. Direct staining: Requires heat fixing while indirect does not require it. Next is the part that gets stained. In direct stain it stains directly on the bacteria since the stain is positive charge and bacteria has negative charge cells. ii. Indirect (negative) staining: stains the surrounding of the bacteria and leaves the bacteria colorless. It does not stain the bacteria since indirect staining is a acidic dye which does not combine with the negative cells of the bacteria

Cultivation of Microorganisms 1. What is the definition of a pure culture? How can we isolate a pure culture in the laboratory? Pure culture is a population of cells grown from one or a few identical parent cells. We can isolate a pure culture by doing a streak plate and obtaining single colonies considered a pure culture. 2. What important conclusion did Louis Pasteur reach from his studies of wine fermentation? Observations: -Yeast cells are always present when beet sugar is converted into alcohol. -Small spherical and rod-shaped bacteria are always present when beet sugar is converted to lactic acid (rooted). -The same microorganisms (MOs) always reappear when trace inoculations are made into fresh sugar solutions. Conclusion: Specific MOs are the active agents in specific fermentations. 3. What are aseptic techniques and what purpose are they used for in the cultivation of microorganisms? Aseptic Techniques are a set of procedures designed to keep MOs contained as they are grown and transferred to prevent contamination. 4. What is agar and who first used it in microbiological culture media? What properties does it have that make it ideal for this purpose? Agar is a polysaccharide derived from algae that are a commonly used solidifying in a culture media. Walther and Angelica Fannie Hesse introduced its use in microbiological culture media. Biological Molecules 1. By definition, what is a carbohydrate? What is the chemical formula of a pentose monosaccharide? A hexose monosaccharide? a. Carbohydrate (CH 2O)n : the sugars, starches and fibers found in fruits, grains, vegetables and milk products. i. Hexose (C6 H12C6) 1. Glucose (blood sugar) 2. Fructose (fruit sugar) ii. Pentose (C 5H10O5 ) 1. Xylose (sugar found in wood) 2. Ribose (sugar found in RNA) 2. Give several examples of polysaccharides and identify their biological functions. a. Polysaccharides: carbon and energy storage forms, structural (e.g. cell wall), Composed of more than 10 monosaccharides i. Glucose polymers: starch, cellulose, and glycogen ii. Galactose polymers: agar iii. Branched vs Unbranched polymers (more branches=more complex)

3. In general, what is the molecular structure of a fatty acid? How are fatty acid molecules incorporated into the structure of a phospholipid? What other components are found in the phospholipid molecule?

Hydrophobic, long fatty acid chain Phospholipid: amphipathic, a hydrophilic head and hydrophobic tail(prevents microbes from crossing the barrier) Also have a phosphate group and ester linkages 4. How do the chemical properties of phospholipids explain the barrier function of the cell membrane? a. The head is hydrophilic, and tail is hydrophobic, so they are able to form a bilayer to protect the inside mechanisms of the cell b. They can also form a Micelle(the spherical structure of the cell, to help transport nutrients throughout the body, or excrete toxins 5. œIn general, what is the molecular structure of an amino acid? ----------> 6. In what way are two amino acids linked together, and what is the resulting chemical bond between them called? a. Dehydration reactions link two amino acids by a peptide bond 7. What type of structural information is represented at each level of protein structure? a. Primary Structure: the amino acid sequence b. Secondary Structure: bending and folding over short stretches of the polypeptide c. Tertiary Structure: bending and folding over long stretches of the polypeptide (i.e. the secondary structure folds can themselves be folded) d. Quaternary Structure: arrangement of 2 or more subunits 8. What is the biological importance of protein structure? What happens to a protein when it becomes denatured? a. Biological Importance i. The biological activity of protein depends entirely on its 3 dimensional folded structure (conformation) it determines the function of it. ii. The conformation of a protein is specified by its amino acid sequence b. Disruption of a protein structure (such as by chemicals or heat) causes loss of function: Denaturation

9. What is a nucleotide, and what three chemical compounds make up its structure? a. A compound consisting of a nucleoside linked to a phosphate group. Nucleotides form the basic structural unit of nucleic acids such as DNA. i. Made up of: 1. Nitrogenous Bases: Purine or Pyrimidines 2. Pentose Sugar: In DNA, the sugar is 2'-deoxyribose. In RNA, the sugar is ribose. 3. Phosphate Group: A single phosphate group is PO 4 3- (backbone) 10. What are the two chemical differences between the nucleic acids RNA and DNA? a. DNA: the sugar is 2'-deoxyribose (one less hydroxyl than RNA) b. RNA: the sugar is ribose (one extra hydroxyl than DNA) 11. In what way are two nucleotides linked together, and what is the resulting chemical bond between them called? a. Links a phosphate group and a hydroxyl group b. Phosphodiester bonds: links adjacent nucleotides into a sequence of polypeptides

Microbial Cell Structure 1. What is the most widely used approach to classify living organisms today? What is this approach based on? a. By Nucleic acid sequences: i. Bacteria ii. Archaea iii. Eukarya 1. Woese 1977 2. What are the most common bacterial cell shapes? a. Coccus b. Bacillus c. Spirillum d. Spirochete (lyme disease, syphilis) e. Vibrio (cholera) f. Filamentous

3. As a cell becomes larger, what happens to the surface-to-volume ratio? a. As the cell gets larger, volume doubles as surface area increases. 4. What are some of the special cell arrangements that can occur? a. Diplococci (2 cells) eg.streptococcus pneumonia b. Streptococci (long chains) c. Tetras (4 cells) d. Cubic packets (8 cells) e. Staphylococci (grape-like clusters) 5. What is a capsule and what functions does it have? What does glycocalyx refer to? a. Capsule= thick mucosal material, made of polysaccharide fibers i. Bacterial capsule 1. Function a. Protects bacterial cells from phagocytosis b. Helps bacteria adhere to surfaces (eg. Dental plaque) 2. Structure a. Glycocalyx: a mat of polysaccharide fibers extending from the cell surface i. Genus of anthrax has a protein capsule instead of a polysaccharide capsule 6. What are 3 structural components of a bacterial flagellum? In what way does a flagellum confer motility? How can flagella be arranged on the cell surface? a. Monotrichous: single polar b. Amphitrichous: single flagellum at both ends c. Lophotrichous: tuft of flagella at one or both ends (plume of heads) d. Peritrichous (lateral flagella): flagella all over the cell surface (peri=around)

7. What are pili (fimbriae) and what function does it have? a. Function: Help the cells attach to surfaces i. Liquid-solid and liquid-gas interfaces ii. Other bacterial cells (to promote gene transfer) iii. Can help pathogenic bacteria attach to the surface of the host cell iv. Help clotting factors attach

8. What is the basic structure of Peptidoglycan? How does the cell wall protect the cell from osmotic damage? a. The cell wall protects the cell from osmotic pressure- acts as chain mail, if the cell is in a hypotonic environment it prevents the cell from breaking. PYN makes bacteria swell up and pop to make them have a faulty cell wall i. Peptidoglycan, otherwise known as the murein layer

9. What are the major differences between Gram-negative & Gram-Positive bacterial cell walls? What major antigens (molecules that induce an immune response) found in association with the cell wall are unique to gram-negative or gram-positive bacterial cells? a. Positive: thick Peptidoglycan layer (10x thicker) i. Teichoic Acid- associated w/ gram + some stick above & are exposed to the environment. b. Negative: thinner Peptidoglycan layer i. Lipopolysaccharide (LPS)= only in gram (—) a. Sugar tail sticks pit and a particularly immunogenic & lets body know that it is not supposed to be there. 10. What is the structure of the bacterial cell membrane? What major functions do proteins embedded in the cell membrane have? a. Structure: i. Bilayer or unit membrane: consist of two layers (leaflets) of phospholipid molecules. b. Functions of Proteins in the cell membrane: i. Transporters: nutrient uptake and waste disposal ii. Cell wall synthesis iii. Flagellar “motor” proteins iv. Some of the cellular components for energy generation v. Chromosome replication and segregation. c. Bacteria do NOT have a membrane-enclosed nucleus, they instead have a nucleus

11. What different types of inclusions are found in the cytoplasm of bacterial cells and what are their functions? a. Storage granules- starch, glycogen, polyphosphate, sulfur, or polyhydroxybutyrate i. When nutrients are lacking they store these to survive. b. Gas vesicles- provide buoyancy in some aquatic bacteria c. Magnetosomes- membrane-enclosed, iron-containing particles found in magnetotactic bacteria. d. Carboxysomes- protein shells that enzymes for CO2 fixation in some bacteria. Enzymes 1. What is the difference between exergonic and endergonic chemical reaction? a. Exergonic= energy releasing b. Endergonic= requires energy 2. By definition, under what thermodynamic conditions is the energy of a chemical reaction described by ΔG? What does it mean when ΔG has a positive vs. negative value? a. ΔG= under conditions of constant pressure and temperature b. + requires energy to go forward c. - will release energy 3. What is it called when two (or more) microorganisms cooperate to (usually anaerobically) degrade a substance that neither can degrade alone? a. Syntrophic relationships with ΔG, the organisms have to obey the laws of thermodynamics, but they can work together to allow processes to work together b. Transformation of H gas from one organism to another 4. What is activation energy? How does this relate to the transition state in a chemical reaction? a. The minimum energy that is needed to break certain bonds of the

reactants so as to turn them into products. b. TS- state where certain bonds of the reactants break. 5. What are the properties of a catalyst? How does an enzyme act as a catalyst? a. A catalyst alters the kinetic properties (path) of the reaction but not its thermodynamic properties. i. in a chemical reaction ii. Increases the rate of the reaction by lowering the activation energy iii. Is unchanged (not used up) at the end of the reaction 6. What is the difference between an enzyme and a ribozyme? a. Catalytic protein is an Enzyme b. Ribozyme- Catalytic RNA molecule c. Enzyme- Catalytic protein 7. What are the 2 different categories of cofactors? How are they related to vitamins? a. Cofactors are nonprotein components of some enzymes. i. Inorganic cofactors such as metal ions (eg. Mg, Zn) and Fe-S clusters ii. Organic cofactors (coenzymes) 1. Tightly bound organic cofactors (usually cannot be removed without denaturing the protein) are sometimes called prosthetic groups (eg. heme) 2. Usually derived from vitamins in your diet.

8. How is an apoenzyme different from a holoenzyme? a. Apoenzyme(inactive protein) + cofactor = holoenzyme(active protein) 9. What is an active site of an enzyme? What is an allosteric site? a. Active site- the region of an enzyme where substrate molecules bind and undergo a chemical reaction. b. Allosteric site- the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site. 10. What distinguishes competitive and non-competitive inhibition? a. Competitive- when a structurally similar molecule (structural analog) usually competes with the substrate for binding to the same enzyme active site. b. Non-competitive- when a molecule (either different than substrate, similar to the substrate, or the substrate itself) binds to a regulatory site (allosteric site) different from the active site. 11. What is end-product (feedback) inhibition? a. A type of noncompetitive inhibition in which the end product of an enzyme pathway “feeds back” to allosterically inhibit the activity of the first enzyme in the pathway. Microbial Metabolism, Part 1 1. What characteristics distinguish catabolism from biosynthesis (anabolism)? a. Catabolism- breakdown reactions produce energy b. Biosynthesis- Build-up reactions consume energy 2. What is the most abundant high-energy carrier molecule found in cells? How is its molecular structure suited for this purpose? a. ATP i. 3. How does the proton gradient store energy? a. By building up the concentration ions & electrical i. Protons flow across membrane and create “electricity”

Francis Bacon

Advocate for using scientific methods based on inductive reasoning

Karl Popper

Criterion of empirical falsifiability

Robert Hooke

1st description of cells and coined name”cells”

Antonie van Leeuwenhoek

Discovered unicellular MOs

Robert Koch

A specific MOs cause a specific disease Koch’s Postulates: 1. Must be present in every case 2. Must be isolated in a pure culture 3. Healthy host when infected has same disease 4. Must be reisolated and infect experimental host again

Louis Parker

Specific MOs are the active agents in specific fermentations

Walter & Angelica Fannie Hesse

Introduced agar into micr...