Final Exam Study Outline PDF

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What will be on the final exam - study guide...

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Chapter 1    

Theory of Spontaneous Generation: belief that live arises spontaneously from nonliving material. Debated for a long time. Theory of Biogenesis: living things come from other living things Germ Theory: pathogens…Henle proposed that many diseases are likely caused by microorganisms (germs) Louis Pasteur’s role: disputed against spontaneous generation. Showed that air is full of microorganisms by filtering air through cotton plug. Used swan neck flask to prove that microorganisms did not arrive from nothing. This form of flask showed that nothing could get in, so broth stayed sterile.

Chapter 3 

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Prokaryotes vs. Eukaryotes Prokaryotes: all bacteria and archaea. Unicellular. Lack membrane bound nucleus and organelles. Have cell envelope, cytoplasmic membrane (phospholipid bilayer), cell wall. They are selectively permeable, use osmosis for example. Eukaryotes: animals, plants, fungi. Larger than prokaryotes, have membrane bound organelles and nucleus which stores DNA, lack cell wall, can be single or multicellular. Some eukaryotes DO have cell wall (plant cells) which are made of cellulose. (chitin in fungis) Microorganisms vs. Microbes Microbe – general term encompassing microorganisms and acellular infectious agents such as viruses Microorganism – organisms too small to be seen with the naked eye Structure & Permeability of cytoplasmic membrane Structure: phospholipid bilayer. Hydrophobic tails and hydrophilic heads. o Simple Diffusion: goes straight through lipid bilayer. Naturally flow from high concentrations to low concentrations. (passive transport) o Osmosis: water. Solute concentration. Water moves from hypotonic to hypertonic. From Low concentration to High concentration. (Hypotonic solution: high water concentration, not a lot of molecules. Move across membrane into cell with high number of molecules to reach equilibrium.) (Hypertonic solution outside of cell: lots of molecules. Water moves across membrane to outside of cell to reach equilibrium.) o Facilitated Diffusion: Use proteins embedded in membrane to move though lipid bilayer. (passive diffusion, high concentration to low concentration) o Active Transport: Need protein embedded in membrane, also need ATP. Active transport takes places and needs this ATP when going from low concentration to high concentration. Cell Wall Structure of bacterial cells o Gram positive vs. Gram negative o Gram positive and gram negative contain peptidoglycan in their cell wall. There is a larger amount in gram + cells. In bacterial cell walls only. o Gram +: Purple. From staining thick layer of peptidoglycan, Teichoic acids extend above peptidoglycan layer, Gel like material below peptidoglycan. All this above the cytoplasmic membrane. Not as antibiotic resistant as Gram –. o Gram –: Pink. harder cell for antibiotics to fight, more complex cell wall (antibiotic resistance). Lipopolysaccharide at top layer that contains lipid A and lipoprotein. There is a thin outer membrane layer under this. Then there is a thin layer of peptidoglycan above the cytoplasmic membrane. Also contain porins – a secretion system to move things out of bacterial cell. Penicillin and Lysozyme function Penicillin: fungal product. Body does not make it. Inhibits the linkage of peptidoglycan. Generally, more effective against Gram + bacteria. Constant remodeling.

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Lysozyme: you make it. Hydrolyze the NAM-NAG linkages (in peptidoglycan). Generally, more effective against Gram +. 1st line of defense. Flagella – Chemotaxis: major form of propulsion for most prokaryotes. Anchored into cytoplasm and cell wall. Pathogenic bacteria can have powerful flagella. Use to penetrate host mucus. Driven by proton gradient. Components: basal body, hook, filament. Chemotaxis: movement induced by the sensing of certain chemicals or nutrients (run, tumble, run). Endospore formation: (sporulation) leave the dormant state (germinate) and enter active state (vegetative). Cells can be dormant for 100 years. Deprivation of C and N triggers sporulation, lack of nutrients triggers formation. Germination: heat, nutrients, water-absorb-crack. Bacillus, Clostridium can both from endospores. They do not reproduce; the bacteria divide within its cell wall to multiply. Endosymbiotic theory: states that some of the organelles in eukaryotic cells were once prokaryotic microbes. Mitochondria and chloroplasts are the same size as prokaryotic cells and divide by binary fission

Chapter 4 

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Binary fission: prokaryotic growth using binary fission. Faster than mitosis. Not sexual reproduction (meiosis). Complete doubling. Exponential growth. HOW: chromosome duplicates and cell continues to grow. The cell divides into two. Now have two cells and the same exact prokaryotic chromosome. Biofilm formation: Bacteria are optimized for life in a biofilm (slime layer and capsule). It is a polymer encased community. (Dental plaque) Biofilms provide protections from immune system of host and medications. Bacteria move to surface and adhere. Bacteria multiply and produce extracellular polymeric substances where other bacteria can attach still. Cells communicate. Create channels so that nutrients and waste products pass along. This biofilm continues to grow. Eventually cells detach and move to other surfaces to create additional biofilms. Growth curve

Lag phase: enzyme synthesis Log: exponential growth. Primary target of drugs. Stationary: exhaustion of nutrients. Take nutrients from dead cells. Death: exponential (slower than growth) Prolonged decline: adaptation to adversity. Oxygen requirements of bacteria Obligate aerobe: Requires O2 Microaerophile: 2-10% O2, but above that then O2 is toxic Facultative anaerobe: best with O2, but don’t need it Obligate anaerobes: O2 is TOXIS Aerotolerant anaerobes: Don’t utilize O2. Can grow in presence of it, just don’t use it. Significance of nitrogen fixation and carbon fixation Nitrogen fixation: (and only bacteria. Prokaryotes.) take nitrogen from the air and convert it to a form that can be used in our body for metabolism. N2 gas converted into ammonia NH3 which is then incorporated into cellular material (amino acid, protein). Carbon fixation: important because a lot of bacteria can do that. But plant can do that as well. Take carbon and can convert it through the Calvin cycle into a form that can be used by plants during photosynthesis.

Chapter 6 

Catabolism: breaking down of compounds for energy. Energy converted to ATP and anabolism uses.

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Anabolism: chemical reactions a cell uses to synthesize macromolecules that make up cell structures. Enzymes – function & regulation. Enzymes needed for the reactions of metabolism. Organic catalysts. Rapid acting. Regulate all cell activities. Highly selection. Lower energy barrier. A substrate binds to enzyme at active site. Central Metabolic Pathways o Glycolysis Oxidizes glucose into pyruvate. (1 molecule of glycose yields two pyruvates.) 2 ATP used to phosphorylate glucose and fructose. Generates 4 ATP and 2 NADH. (Net yield: 2 ATP and 2 NADH) o Transition step The two pyruvates at end of glycolysis (or PPP) release CO2 and yield two Acetyl-CoA that go into TCA cycle. Also forms 2 NADH. o TCA cycle (Tricarboxylic Acid) From glycolysis, the two pyruvates turn into Acetyl-CoA and enter cycle ^^^. (For every 1 glucose, there are two turns of the TCA cycle). Generates 2 ATP, 6 NADH + 6H, 2 FADH2, precursor metabolites. (Lots of reducing power) o Pentose Phosphate pathway Anabolic pathway also used to break down glucose. Creates G3P and F6P that can feed into glycolysis. Alternative to glycolysis. Only generator of NADPH reducing power. Two phases: 1. Oxidative (generate 2 NADPH) and Non-oxidative (generate 5C sugar used for nucleotide synthesis). Can work “backwards” to provide G3P and F6P for use in glycolysis and TCA. Electron Transport Chain and Proton Motive Force Electron transport chain: energy release is used to pump protons out. ETC pumps protons from one side of membrane to other creating a proton gradient that drives the ETC. There are multiple complexes (serve as proton pumps) that reducing agents (NADH and FADH) go through that send H out. The H then come back in using the proton motive force. ATP synthase turns ADP into ATP. (For anaerobic: harvest less energy.) Proton motive force: proton pumps move protons outside the cell membrane. Turns membrane into a battery. Protons get used by other cellular transport mechanisms. Makes electrochemical gradient that forms potential energy. Oxidative phosphorylation vs. substrate level phosphorylation Substrate level phosphorylation: (when phosphate group is added directly to ADP to make ATP and create energy source.) What happens with JUST glycolysis. Where ATP are formed without the process of the transfer of electrons. Organs without ETC that don’t have electron carriers that have to use fermentation (not krebs cycle) can just go through glycolysis and create ATP. NADH converted back into NAD during fermentation and can keep going through cycle. Oxidative Phosphorylation: refers to two processes: ETC and ATP synthesis. Happens with proton motive force in ETC that drives ATP. Makes more ATP. Oxidized NADH and FADH. Occurs in aerobic and anaerobic respiration (in cytoplasmic membrane for prokaryotes and in mitochondria matrix in eukaryotes) Fermentation – significance and some end products Not all prokaryotes have an ETC! Fermentation: metabolic process that stops short of oxidizing glucose or other organic compounds completely (use organic intermediates as terminal electron acceptors.) ATP comes from glycolysis, reducing power from glycolysis (NADH), electrons still go to terminal acceptor (pyruvate). Used by organisms that cannot go through cellular respiration. Lack of terminal electron acceptors (so pyruvate acts as one). Do not have ETC. Some microbes switch between cellular respiration and fermentation. Oxidize NADH to regenerate NAD – needed for the continuation of glycolysis. End produce: lactic acid, ethanol, acetone. Anabolic pathways Prokaryotes remarkably similar in biosynthesis processes. Synthesize subunits using precursor metabolites formed in the central metabolic pathways. If enzymes are lacking, end product must be supplied. (PPP, glycolysis, TCA) Photosynthesis

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Photophosphorylation: using captured radiant energy to fuel ATP synthesis. Generate reducing power NADPH and NADH that is needed for carbon fixation. Significant by-products and end products 6CO2 + 12H2X  C6H12O6 + 12X + 6H2O

Chapter 7 

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DNA and RNA structure DNA: double stranded. base pairing. A:T, G:C. Two complimentary strands. Antiparallel. 5’-3’ and 3’-5’. RNA: use DNA as template. Single stranded. Three types: mRNA, rRNA, mRNA A:U G:C DNA Replication 1. Helicase unzips the two stands of DNA into leading stand and lagging strand. DNA polymerase adds nucleotides onto the 3’ end 2. Synthesis of leading strand continues as new template exposed. RNA primer on lagging strand from primase synthesis. Forms Okazaki fragments on the lagging strand 3. Synthesis of lagging strand must be continuously reinitiated. Every time: new RNA primer made. Discontinuous fragments form Okazaki fragments. 4. As DNA polymerase adds to 3’ end of Okazaki fragments, it encounters 5’ and of another. Different DNA primase removes RNA primer and replace with nucleotides 5. DNA ligase seals the gaps between Okazaki fragments with covalent bonds Transcription/ Translation: Prokaryotes vs. Eukaryotes o Prokaryotes: All in cytoplasm, No nucleus. Translation begins as transcription is still occurring (simultaneous). Start codon codes for (f-met). Multiple ribosomes can be translating a strand of mRNA at the same time (quick) o Eukaryotes: Completes transcript is sent out of the nucleus where it is translated by ribosomes. Start codon is for (Met). One ribosome translates a strand of mRNA before translation can begin again. Gene regulation o Induction. RNA polymerase binds to promotor. Repressor on operator. Blocking transcription. BUT if inducer binds to repressor & alters its shape it is then unable to bind to operator. DNA open for transcription. o Repression: protein that blocks transcription. Binds to the operator downstream of the promoter. Repressor alone can’t bind to operator. When corepressor bind to repressor it is then able to bind to operator and block transcription. o Activation: facilitates transcription. Protein binds to an activator binding site that helps RNA polymerase bind to the promotor. Activator cannot bind to activator binding site so the RNA polymerase cannot bind to the promoter to start transcription. BUT if inducer binds to activator, it can then bind to activator binding site. And RNA polymerase can bind to promotor and transcribe. o Types of enzymes regulated Lac operon – for lactose metabolism. No lactose in cell: repressor binds to operator and the RNA polymerase, bound to the promotor, is unable to start transcription (blocked). Lactose present in cell: some of it converted to allolactose. This binds to the repressor and alters its shape, so it can no longer bind to the operator. SO, transcription occurs. Only when glucose is not present. (Allolactose is inducer)

Chapter 8 

Definitions of Genotype and Phenotype

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Change in an organism’s DNA alters genotype. Change in genotype often changes observable characteristics, phenotype. Spontaneous Mutations: genetic changes that result from normal processes. Occur randomly at infrequent characteristic rates. Occasionally change back to original: reversion. o Types Base substitutions most common. Incorrect nucleotide incorporated during DNA synthesis. (Point mutation is change of a single base pair) 1. Silent (synonymous) mutation: there is a change in the base pair, but yield same result as wild type amino acid 2. Missense mutation: different amino acid formed. Resulting in PRO often does not function normally 3. Nonsense mutation: specifies stop codon. Yields shorter, often non-functional PRO Deletion or addition of nucleotides (one or two pairs) can yield frameshift mutation. Different set of codons translated, often results in premature stop codon, shortened nonfunctional protein Transposons: jumping genes – pieces of DNA that can move from one location to another in a cell’s genome; process of transposition. Insertional inactivation: gene into which transposon jumps is inactivated Induced Mutations: result from outside influence. Agent that induces change is mutagen. Geneticists may use mutagens to increase mutation rate. There are Chemical agent and radiation. Chemical Mutagens: Chemicals that modify nucleobases – change base-pairing properties of nucleobases. Increase chance of incorrect nucleotide. Nucleotide substitution. Base analogs – base-pairing properties differ from those of nucleobases normally found in DNA. Resemble nucleobases, but have different hydrogen bonding properties. Nucleotide substitution. Intercalating agents – randomly insert into DNA. Increase frameshift mutations. Addition or subtraction of nucleotides. Radiation: usually UV light (cause thymine dimers to form and errors during repair occur) and X rays (cause single and double DNA strands to break and result in deletions) Horizontal Gene Transfer o Transformation – segments enter new bacterial cell and integrate into DNA. Transformation involves uptake of short fragments of naked DNA by naturally transformable bacteria. [ a single strand of DNA enters. It integrates into recipient chromosome by homologous recombination.) o Transduction – transfer of DNA from one bacterium into another with bacteriophages involved. Phage attaches to and infects bacterial cell by injecting nucleic acid. Phage enzymes cut bacterial DNA into small pieces. Bacterial cell enzymes produce phage nucleic acid and a phage coat – components of a new phage particles. Phage particles are released from bacterial cell. (Generalized and specialized) The lytic and lysogenic. Generalized transduction: results when a fragment of bacterial DNA enters the phage protein coat. Lytic – nucleic acid enters and begins to replicate and assemble new phage particle, cell then lyses and releases new virons. Generalized: when this is happening, there is an error. Some of the bacterial DNA is put in that virus DNA and goes into cell. Specialized: when you have a phage that is able to have a lysogenic cycle. Go in and recombine homogenously and be dormant in cell. Can then go into lytic cycle later to assemble new viron particles. (bacterial DNA gets in instead of viral.) •Lytic infection (Productive) virus replicates and cell lyses •Lysogenic infection (hidden) virus incorporates into host DNA and is replicated along with the host DNA, referred to as a “prophage”, can become lytic later o

Conjugation – transfer of genetic information (DNA) from one to another by sexual pilus and requires cell to cell contact. (f plasmid) Contacts another cell and transfers plasmid to other cell.

DNA transfer between bacterial cells. Requires contact between cells. Conjugative plasmids direct their own transfer. F plasmid (fertility), encodes F pilus connects two cells. A single stand of F plasmid transferred to recipient cell. At end of transfer both donor and recipient are F+ and synthesis of F pilus. Chapter 10 

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Classification – rRNA Sequencing ribosomal RNAs (rRNA) or the DNA that encodes them is used in identification. Sequences relatively stable. 16S rRNA most useful because of moderate size (1500 nucleotides). Sequences compared with extensive databases and use that to identify organisms that cannot be grown in culture Identification methods (phenotypic) Microscopy: size and shape. Gram stain. Morphology (colony shape). Protein profile (MALDI-TOF). Metabolic capabilities. Identification methods (genotypic) Identify by detecting specific nucleotide sequences: nucleic acid probes and nucleic acid amplification tests can be used to identify. Sequencing rRNA genes: requires amplifying and then sequencing rRNA genes, but it can be used to identify organism not yet grown in culture. Probe: separate DNA of known organism. Probe on each end, labeled. Unknown organism DNA denatured and placed. If probe binds to DNA, then unknown organism is beginning organism. (If doesn’t attach, not it.)

Chapter 13 

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Virus structure Icosahedral, helical, complex: icosahedral head and helical tail with fibers. Nucleocapsids: nucleic acid and capsid (protein coat). Can be enveloped by having lipid bilayer obtained from a host cell. Types of Bacteriophages Lytic (lyse the host cells and then end of infection). Bacteriophage attaches to call and phage DNA injected into bacterial cell. Phage genome transcribed and proteins synthesized. Phage DNA replicated, other virion components are made. Phage components are assembled into mature virions. Bacterial cell lyses and many new infections virions released. Temperate (lytic or lysogenic) – injected linear phage DNA circularizes and enters lytic or lysogenic cycle. Can go straight to lytic cycle. OR can go to lysogenic infection. Lysogenic: integrated DNA (prophage integrated into bacterial chromosome), cell divides, excision of phage DNA, then enters Lytic infection. Filamentous (rod shaped) requires F-pilus. Phage attaches to the F pilus of a bacterial cell and injects its singlestranded DNA. Phage DNA replicates; phage capsomeres are synthesized and embedded in the host cell membrane. Phage nucleic acid gains its capsid as it excrudes through the membrane. Bacteria do not lyse. Generalized vs. Specialized Transduction – horizontal gene transfer. Specialized transduction: excision mistake during transition from lysogenic to lytic cycle of temperate phage. Short piece of bacteria...