BIOL 2604 F04 STUDY GUIDE for EXAM 1 Thought questions for some of the key topics covered:

History: Do you know the names of key scientists, their major discoveries and an approximate timeline for when these discoveries were made? Robert Hooke (late 1600s) was probably the first person to observe microorganisms, coined the term cell Antoni Van Leeuwenhock (late 1600s) o was father of microbiology o made a single lens microsope ~300X to see if artisans were cheating him o first person to see movement, liked to look at endothelial cells Francesco Redi (mid 1600s) o challenged idea of spontaneous generation with the maggot experiment John Needham (late 1700s) and Felix Pouchet (late 1800s) o Advocated the idea of spontaneous generation o Experiment had endospores Lousis Jablot (late 1600s) and Spallanzani (late 1700s) o Believed that microbes arose from other microbes o Experiments did not have endospores Louis Pasteur (mid 1800s) o first practical use of microscope in wine industry o pasteurization decreases the number of contaminating organisms but does not completely remove them 1) flash method-heat to 71.6 C for 15s 2) batch method-heat to 63-66 C for 30min then rapid cooling is used o vaccines for fowl cholera and rabies o concept of Attenuation-isolate organism, grow for long time, and organism loses its ability to infect with great force Robert Koch (1800s) o Germ Theory of Disease o Kochs Postulates 1) The organism should be constantly present in animals suffering from the disease and should not be present in healthy individuals 2) The organism must me cultivated in a pure culture away from the animal body 3) Such a culture, when inoculated into susceptible animals, should initiate the characteristic disease symptoms 4) The organism should be re-isolated from these experimental animals and cultured again in the laboratory, after which it should still be the same as the original organism Tyndall (late 1800s) o Tyndallization-repetitive heating procedure Cohn (late 1800s) o father of bacteriology

o process of sporulation Edward Jenner (late 1700s) o vaccination for small pox from cow pox Ignaz Semmelweis and Oliver Wendell Holmes (mid 1800s) o Separately developed ideas of cleanliness in hospitals Joseph Lister (mid 1800s) o Concept of disinfection in surgical rooms ~phenol was sprayed on the patient and around the lab to disinfect Fannie and Walter Hesse o Discovered greatness of agar which is made from seaweed o Better than gelatin which melts at temps >28 C Martinus Beijernick and Sergei Winowgradsky (late 1800s/early 1900s) o Pioneers in microbiology o Isolated microorganisms from environmental samples and discovered that not all bacteria cause infection and not all bacteria can be grown in pure culture

Do you under stand the idea of spontaneous generation? The idea that living organisms formed spontaneously from natural elements o vital force ~ life present in all things dead -the Germ Theory of Disease? Microorganisms cause disease Microscopy: Do you understand the concepts of magnification and resolution? Magnification-the extent to which the image of an object is larger than itself (product of objective and ocular lens) Resolution or resolving power-the degree to which details are retained in a magnified image; the ability to distinguish between two points What impacts the resolution of a microscope? The smaller the value of R the more you can see, or the better the resolution What are the advantages/disadvantages of using the different types of microscopes? 1) Light microscope-most common, light transmitted through specimen, contrast generated by absorption or scattering of light, staining generally required which the process kills cells, (but live cells can be viewed if are big enough) 2) Darkfield microsope-light reaches specimen from side only and enters objective lens if scattered by specimen, unstained cells bright against dark background, better resolution than brightfield, see smaller cells or structures and SURFACE APPENDAGES, but cant see color, and distorts size

3) Phase Contrast microscope-enhances difference between diffracted ray and direct ray, converts phase difference in rays to difference in light intensity, no staining required and VIEW LIVE CELLS 4) Fluorescence microscope-light source at one causes specimen to fluoresce at different , autofluorescence or special dyes, environmental applications 5) Electron microscope: R is 0.0002, ALL DEAD AND STAINED CELLS a. Transmission-one-dimensional, thin sections of fixed samples, special stains, internal contents CAN be viewed b. Scanning-3-D, coat cells with heavy metal, internal contents CANT be viewed 6) Confocal laser microscope-3-D in complex structure/layers containing LIVE CELLS, fluorescent labels/dyes often used What is the difference between a simple and differential stain? Simple stains-only one dye used, mostly aromatic compounds with conjugated double bonds, generally charged, cell surface carries a negative charge therefore basic stains most commonly used Differential stains-greater than one dye used o Gram stain-gram +/gram - gram positive is purple b/c of thick peptidoglycan wall not allowing secondary stain to penetrate, gram negative is pink b/c of thin peptidoglycan wall allowing secondary stain to penetrate o Acid fast stain-mycobacteria (red) vs. other bacteria (blue) o Endospore stain-spore (green) within mother cell (red) How can live cells be viewed? Phase contrast and Confocal laser microscopes allow viewing of living cells The hanging drop method-large, eukaryotic cells Wet mount method-small, compact cells Phylogenetic Tree of Life: What characteristics do all living cells share? 1) DNA 2) Membranes 3) Metabolism What are the typical sizes of eukaryotic vs. prokaryotic cells and how do they differ in their subcellular organization? Eukaryotes are typically larger, but not always Subcellular organization o prokaryotes are haploid and contain circular plasmids o eukaryotes are diploid and contain linear chromosomes What are the appropriate terms used to describe the morphology of prokaryotes? Coccus, Rod, Spirillum, Spirochete, Filamentous, *vibrio(bent shape)

Do you know the different forms of metabolic diversity? 1) Chemoorganotrophs-organic material to get E 2) Chemolitho(auto)trophs-inorganic material to get E 3) Phototrophs-photons of light to get E a. Heterotrophs-consume other organisms for food b. Autotrophs-make their own food What were some of the early attempts at developing phylogenetic trees? 1) Linnaeus (1753) NO MICROSCOPES 2 kingdoms: animalia, and plantae, NO PROKARYOTES 2) Haeckel (1865) 3 kingdoms: animalia, plantae, protista 3) Whittaker (1969) 5 kingdom classification system: monera, protista, animalia, fungi, plantae 4) Carl Woese (1970s) Molecular-based approach to phylogeny CENTRAL DOGMA: DNARNAPOLYPEPTIDE 1) DNARNA by transcription and the use of RNA polymerase 2) RNAPOLYPEPTIDE by translation and the use of ribosomes How and why did Carl Woese use rRNA to develop the current phylogenetic tree? 16S rRNA in prokaryotes and 18S rRNA in eukaryotes o ancient molecule that all cells have o changed very slowly over evolutionary time o sequenced easily What are the three branches of life and the major characteristics of each? 1. Bacteria-no nucleus, has peptidoglycan, ester-linked, 70 S 2. Archaea-no nucleus, no peptidoglycan, ether-linked, 70 S 3. Eukarya-has nucleus, no peptidoglycan, ester-linked, 80 S Biochemistry: List the three types of bonds used to generate macromolecules and the functional groups that are needed to create these bonds. 1. Phosphodiester /---nucleic acids---/ -OH (hydroxyl) and PO3- (phosphate) 2. Peptide /---amino acids---/ -COOH (carboxyl) and +NH3- (amino) 3. Glycosidic /---carbohydrates---/ -OH and OH Linear 1,4 and 1.4 bonds Branched 1,6 bonds ***Sulfhydryl (-SH) How are polypeptides / proteins able to function as enzymes?

They are able to form H-bonds with other proteins and lower the activation E Look over lock and key and induced-fit models

What are the 6 classes of enzymes and the types of reactions they carry out? 1. Oxidoreductases-redox reactions 2. Transferases-transfer a group 3. Hydrolases-catalyze a hydrolytic cleavage reaction b/w C-O, C-N, C-C 4. Lyases-cleave C-O, C-N, C-C bonds by elimination, leave double bonds or rings 5. Isomerases-catalyze the rearrangement of bonds within a single molecule 6. Ligases-join together two molecules, couple to ATP hydrolysis Are you able to recognize the different types of C-containing/organic molecules discussed in class? ***LOOK OVER DIAGRAMS FOR NUCLEIC ACIDS, CARBOHYDRATES, AMINO ACIDS, AND FATTY ACIDS*** Why is water essential to life? H2O is polar and promotes cohesiveness Enables the hydrophobic/hydrophilic interactions as solvent and doesnt alter solute H-bonding in double-stranded DNA, nucleic acids, and amino acids Not only in water Water serves as a coolant for every cell What is the difference between a prosthetic group and a coenzyme? Prosthetic group-covalently bound to enzyme and is critical to the functionality of the enzyme (i.e. heme, Fe-S cluster) o ***INORGANIC*** Coenzyme-move between enzymes, recycled o I.E. NAD+, FAD, and coenzyme A (coA) What is the difference between an oxidized/reduced molecule? ***OIL RIG oxidation is loss (of electrons)reduction is gain (of electrons) LEO GER*** lose electrons oxidizedgain electrons reduced OR Less energy oxidizedgreater energy reduced OR Less electrons oxidizedgreater electrons reduced How can difference in electrode potential get converted into energy? Greater the distance between the most reduced and the most oxidized creates more energy

Metabolism: What is Gibbs free energy? E available to do work Gproduct of enthalpy and entropy o enthalpy-heat released or absorbed during the reaction o entropy-degree of disorder produced by a reaction What is a high energy bond? Chemical energy released in redox reactions are conserved in these bonds o Normally in phosphate bonds such as ATP o Some are sulfur bonds What does the cell gain from glycolysis? glucose (6C) + 2 ATP + 4 (ADP + 2 Pi) + 2 NAD+ 2 pyruvate (3C) + 2 ADP + 4 ATP + 2 NADH ***net 2 ATP via substrate-level phosphorylation Not a lot of E produced b/c it does not completely hydrolyze the glucose*** fermentations? Net yield of 2 ATP via substrate-level phosphorylation Recycles NAD+/NADH What is the difference between substrate level phosphorylation, or SLP, and oxidative phosphorylation? Oxidative phosphorylation requires the electron transport chain What does the cell gain from the TCA cycle? 2 pyruvate (3C) + 8 NAD+ + 2 FAD + 2 (GDP + 2 Pi) 6 CO2 (1C) + 8 NADH + 2 FADH + 2 GTP (ATP) (formed by SLP) ***CoA is recycled*** What are the major components of an electron transport chain? Dehydrogenases: (flavoproteins and Fe-S protein) Quinone (lipids) Cytochrome e- acceptor How does ATP synthase work? Takes H+ from outside the cell and uses it to add a phosphate group to ADP, NAD+, and FAD to ATP, NADH and FADH respectively You get 2 ATP for every FADH and 3 ATP for every NADH

What is the difference between catabolism and anabolism? Catabolism is exergonic Anabolism is endergonic